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Bioconductor has moved to GIT for contributed packages; the subversion logs are no longer active. The following are the git logs.

GIT Logs

This is a list of recent commits to git.bioconductor.org, the master(development) branch of the Bioconductor GIT repository.

This list is also available as an RSS feed (master branch), and RSS feed (release branch)

Package: Rsubread
Commit: 5cd5b24648a88b67a6fa6587135fc44ba78328cf
Author: Yang Liao <yang.liao@onjcri.org.au>
Date: 2021-06-17 08:09:57 +1000
Commit message:

 fixed a wanring.

Package: Rsubread
Commit: b7991b40dedd6075a349bd1df14284c77491add9
Author: Yang Liao <yang.liao@onjcri.org.au>
Date: 2021-06-17 08:07:28 +1000
Commit message:

 fixed a warning

Package: Rsubread
Commit: c8ac0cd16f4d9f360d1881ad10565bafa2772c4d
Author: Yang Liao <liao_y@svr2672.licr.unimelb.edu.au>
Date: 2021-06-17 08:05:13 +1000
Commit message:

 fixed the bug of multiple boolean values in "if"

Package: kebabs
Commit: e237f264f3ca238e4f4f2b15462f3b4e6d2b7945
Author: UBodenhofer <ulrich@quomatic.ai>
Date: 2021-06-16 22:25:06 +0200
Commit message:

 minor fix in C++ code; fix in kebabsDemo(); version number bumped to 1.27.1

Package: restfulSE
Commit: 4ab5d63da57ae7d7ba320ee93539cdfd667540d2
Author: Shweta Gopal <sgopal@sgopal-mbp19.local>
Date: 2021-06-16 13:52:54 -0500
Commit message:

 moving rmarkdown dependency to Suggests

Package: PhyloProfile
Commit: 78cc3b873390214573d08956660d25f07f514e34
Author: trvinh <trvinh@gmail.com>
Date: 2021-06-16 19:38:05 +0200
Commit message:

 added warning to links

Package: scRepertoire
Commit: d9e7dc8847a9301996a9d98adfe043a23d356c54
Author: Nick <nicholas-borcherding@uiowa.edu>
Date: 2021-06-16 09:36:12 -0500
Commit message:

 Update DESCRIPTION

Package: scRepertoire
Commit: bdf0e5ac669772339fd0df9a21ab0e87323e78c3
Author: Nick <nicholas-borcherding@uiowa.edu>
Date: 2021-06-16 09:35:18 -0500
Commit message:

 Merge remote-tracking branch 'upstream/master'

Package: scRepertoire
Commit: e637b42dbfb343d345a45f107fd2f87751da5945
Author: Nick <nicholas-borcherding@uiowa.edu>
Date: 2021-06-16 09:31:31 -0500
Commit message:

 Update Coding Practice

Yeah that's right, just formating based on devtools and bioccheck to commit to bioconductor, not particularly sexy

Package: scRepertoire
Commit: 9e54abcdc15cb5940fa224c3724ceeab3100dc2e
Author: Nick <nicholas-borcherding@uiowa.edu>
Date: 2021-06-04 09:57:01 -0500
Commit message:

 v1.2.1

Package: scRepertoire
Commit: 78de0b824583a96411e3fa3be0734a95a01f1eeb
Author: theHumanBorch <ncborch@gmail.com>
Date: 2021-06-03 12:07:30 -0500
Commit message:

 Update utils.R

fix lengthDF function for multichains

Package: scRepertoire
Commit: 36e0b2fd957a6c26192436f7a00eb7a5c65c3f05
Author: theHumanBorch <ncborch@gmail.com>
Date: 2021-05-26 14:55:27 -0500
Commit message:

 Update seuratFunctions.R

added labels to alluvialClonotype per many suggestions

Package: scRepertoire
Commit: 1e382785fb45dd1a488053fcc7429b89a8571098
Author: theHumanBorch <ncborch@gmail.com>
Date: 2021-05-25 12:30:47 -0500
Commit message:

 Fix grabMeta()

Added conditional assessment of colnames in meta data

Package: scRepertoire
Commit: 65dcf3ae08ed97a7bac625670c7f717083914bac
Author: theHumanBorch <ncborch@gmail.com>
Date: 2021-05-25 07:49:59 -0500
Commit message:

 Update clusterTCR.R

Add group variable, reflect new annotation

Package: scRepertoire
Commit: 4b16f0fc8018d46adddde56ce4bd2b9e6bcd7cac
Author: theHumanBorch <ncborch@gmail.com>
Date: 2021-05-20 09:35:51 -0500
Commit message:

 Update README.md

fix spelling

Package: scRepertoire
Commit: 29308b09511541c5f129141a15026e132d6f664a
Author: theHumanBorch <ncborch@gmail.com>
Date: 2021-05-20 09:31:19 -0500
Commit message:

 Update viz.R

Update vizVgene for specific chain nomenclature

Package: scRepertoire
Commit: 88f4699697509d9a579c4f61496ef8b668a06342
Author: theHumanBorch <ncborch@gmail.com>
Date: 2021-05-17 17:09:35 -0500
Commit message:

 Update README.md

Package: scRepertoire
Commit: bf381de75f7d55a812e2c4af27cddacf98e652fa
Author: theHumanBorch <ncborch@gmail.com>
Date: 2021-05-17 08:22:08 -0500
Commit message:

 Update README.md

Package: scRepertoire
Commit: 2b7020b0814d18babdac576b0a93cee6653b518f
Author: theHumanBorch <ncborch@gmail.com>
Date: 2021-05-15 13:09:46 -0500
Commit message:

 Merge branch 'dev' into master

Package: scRepertoire
Commit: c2ca90630dfbe029851f175aba415018207495e6
Author: Nick <nicholas-borcherding@uiowa.edu>
Date: 2021-05-10 07:48:34 -0500
Commit message:

 CombineTCR() fix

Fixing combineTCR() and filterMulti parameters

Package: scRepertoire
Commit: c515e7f9c62fd20dd6a20450fb4111a6b2058f9d
Author: Nick <nicholas-borcherding@uiowa.edu>
Date: 2021-05-09 07:38:47 -0500
Commit message:

 CombineTCR() issue

Issue with situation in which given two contigs of a barcode - one is assumed TCRA and the other is assumed TCRB

Package: scRepertoire
Commit: 251ef773822d8ff72e0fb21c73a4b93b18735ad0
Author: Nick <nicholas-borcherding@uiowa.edu>
Date: 2021-05-07 06:01:39 -0500
Commit message:

 adding else

combineBCR and clusterTCR add else to generate mean edit distance by length of the two cdr3 sequence lengths

Package: scRepertoire
Commit: d5965eb185e73019d5e2c88d3631fe15ca1ce4b5
Author: Nick <nicholas-borcherding@uiowa.edu>
Date: 2021-04-26 08:22:19 -0500
Commit message:

 Update utils.R

Fixed _ use in length call

Package: scRepertoire
Commit: 0b42112dca9a40c872f3414a92a2a37bc9b85c98
Author: Nick <nicholas-borcherding@uiowa.edu>
Date: 2021-04-24 06:39:21 -0500
Commit message:

 Update parseTCR

Package: scRepertoire
Commit: c4f6ad738cdd0252c226d3fe07e826b03530d971
Author: Nick <nicholas-borcherding@uiowa.edu>
Date: 2021-04-14 08:06:26 -0500
Commit message:

 Update utils.R

Refined parseBCR to ensure all light chains are properly recorded

Package: scRepertoire
Commit: 50b10c39ad88804625eeaac7133c28e13ef62b44
Author: Nick <nicholas-borcherding@uiowa.edu>
Date: 2021-04-09 12:49:26 -0500
Commit message:

 Update clusterTCR.R

Removing V genes
Fixed issue with multiple chains

Package: scRepertoire
Commit: e2d079a3dd5f2b45f9fd104d247f50989c25e798
Author: Nick <nicholas-borcherding@uiowa.edu>
Date: 2021-04-09 08:58:19 -0500
Commit message:

 Update clusterTCR.R

Removal of Vgene addition

Package: scRepertoire
Commit: 96cc073cae1fe9f816880c74533ccbf86ab62f69
Author: Nick <nicholas-borcherding@uiowa.edu>
Date: 2021-04-09 08:24:58 -0500
Commit message:

 Update clusterTCR.R

Handling of multiple chains

Package: scRepertoire
Commit: bcdad5b448519bb0aedd53f03f74092c68073a6b
Author: Nick <nicholas-borcherding@uiowa.edu>
Date: 2021-04-08 14:44:59 -0500
Commit message:

 Update vignette.Rmd

Package: scRepertoire
Commit: 410d4f10fdf468d60954618e817193283e3c4aac
Author: Nick <nicholas-borcherding@uiowa.edu>
Date: 2021-04-08 12:40:20 -0500
Commit message:

 v1.0.3 Commit

Package: scRepertoire
Commit: 5b2886bf7b5cccbddde21b0bda3cf53611a1c82f
Author: Nick <nicholas-borcherding@uiowa.edu>
Date: 2021-04-08 12:10:06 -0500
Commit message:

 Updating Diversity Downsampling

Package: scRepertoire
Commit: 2ccb76000a95fe2e9725393738dab802fbc27ccf
Author: theHumanBorch <ncborch@gmail.com>
Date: 2021-03-29 07:52:34 -0500
Commit message:

 Update DESCRIPTION

Package: scRepertoire
Commit: 4a81ebf934c248e8ff8b6de682d1795d42653872
Author: Nick <nicholas-borcherding@uiowa.edu>
Date: 2021-03-28 12:54:30 -0500
Commit message:

 Merge remote-tracking branch 'origin/RELEASE_3_12'

Trying to figure this out

Package: scRepertoire
Commit: ffed3a61c0a6ebe138fdfa48ec89a38a9bb720a4
Author: Nick <nicholas-borcherding@uiowa.edu>
Date: 2021-03-28 12:52:49 -0500
Commit message:

 Update DESCRIPTION

Package: scRepertoire
Commit: c9a6fda89db8c818991676213bee1665daf755d8
Author: theHumanBorch <ncborch@gmail.com>
Date: 2021-03-28 12:39:45 -0500
Commit message:

 Merge pull request #70 from ncborcherding/master

Sync merge for bioconductor

Package: scRepertoire
Commit: b5a1307c116b8a17bb37bd95ea7b36279bb03e72
Author: Nick <nicholas-borcherding@uiowa.edu>
Date: 2021-03-28 12:08:37 -0500
Commit message:

 Update NEWS

Package: scRepertoire
Commit: fd05156682c86c981bd8d32fe800652833c6067f
Author: Nick <nicholas-borcherding@uiowa.edu>
Date: 2021-03-28 12:07:55 -0500
Commit message:

 Update diversity.R

Add bootstraps to diversity estimates

Package: scRepertoire
Commit: e182ada440f23f5b9259481a21e689d199219428
Author: Nick <nicholas-borcherding@uiowa.edu>
Date: 2021-03-06 14:18:01 -0600
Commit message:

 update annotation

Added update to function annotation for ocupiedscRepertoire and overlay

Fix combineBCR NA_NA_NA_NA values

Package: scRepertoire
Commit: 56d6cf4b884dfa604336ab307e04cca67dc35e78
Author: Nick <nicholas-borcherding@uiowa.edu>
Date: 2021-03-06 07:14:51 -0600
Commit message:

 Update seuratFunctions.R

Fixing attributes

Package: scRepertoire
Commit: 13e987069f45037663270b52ef043b7b17f313b8
Author: Nick <nicholas-borcherding@uiowa.edu>
Date: 2021-02-27 11:28:09 -0600
Commit message:

 clonalOverlay() function

Added clonalOverlay

Package: scRepertoire
Commit: ce2b228c23fd4fbba57a890d6084e49f560c81fb
Author: Nick <nicholas-borcherding@uiowa.edu>
Date: 2021-02-26 09:05:21 -0600
Commit message:

 Update vignette

Package: scRepertoire
Commit: 96ea64bed7f8efa3298484d611ec1010c85f6963
Author: Nick <nicholas-borcherding@uiowa.edu>
Date: 2021-02-25 16:50:55 -0600
Commit message:

 Update clusterTCR.R

Package: scRepertoire
Commit: 44f3fd282fb0caf2e405ae7ccbcde787cf4594a7
Author: Nick <nicholas-borcherding@uiowa.edu>
Date: 2021-02-25 15:54:14 -0600
Commit message:

 update utils

Package: scRepertoire
Commit: 95ab0ff4b576931791e421f2741b4d4268d98057
Author: Nick <nicholas-borcherding@uiowa.edu>
Date: 2021-02-25 15:37:04 -0600
Commit message:

 Merge branch 'dev' of https://github.com/ncborcherding/scRepertoire into dev

Package: scRepertoire
Commit: 7a99c9d51724e000c3735c9e49c47ffab9464ed5
Author: theHumanBorch <ncborch@gmail.com>
Date: 2021-02-25 15:36:33 -0600
Commit message:

 Merge pull request #61 from ncborcherding/refine

Setting the Dev back

Package: scRepertoire
Commit: 415c421d389e19bc4f6e20933d93b1f2daaa5e1d
Author: Nick <nicholas-borcherding@uiowa.edu>
Date: 2021-02-25 15:34:26 -0600
Commit message:

 Merge branch 'dev' of https://github.com/ncborcherding/scRepertoire into dev

Package: scRepertoire
Commit: 07e3d4f81eb47bd70d73a0138d6947cc4dd392b7
Author: theHumanBorch <ncborch@gmail.com>
Date: 2021-02-25 15:05:54 -0600
Commit message:

 Update README.md

Package: scRepertoire
Commit: d2d190d188bb12bef1c7f729f509967aeaa33438
Author: theHumanBorch <ncborch@gmail.com>
Date: 2021-02-25 15:04:59 -0600
Commit message:

 Merge branch 'dev' into refine

Package: scRepertoire
Commit: 3b3fbadc85bb2c452e79536c8fe3da400839c814
Author: Nick <nicholas-borcherding@uiowa.edu>
Date: 2021-02-20 09:28:07 -0600
Commit message:

 Devtools::check()

Package: scRepertoire
Commit: 0007d2b2434d7d0fce1227813740d4e27c4f133a
Author: Nick <nicholas-borcherding@uiowa.edu>
Date: 2021-02-20 08:53:22 -0600
Commit message:

 Update vignette.Rmd

Package: scRepertoire
Commit: a5fe99c46a7a1e4d114182dd20469777e380dafb
Author: Nick <nicholas-borcherding@uiowa.edu>
Date: 2021-02-19 12:47:43 -0600
Commit message:

 Update clusterTCR.R

Package: scRepertoire
Commit: 8f9bcefb3925fb106b7327956b464dd5a3f2fb5f
Author: Nick <nicholas-borcherding@uiowa.edu>
Date: 2021-02-19 12:16:59 -0600
Commit message:

 Update clusterTCR.R

Update documentation

Package: scRepertoire
Commit: 7d5edb5500dfe614f36c340ba5a27a899b3c85d1
Author: Nick <nicholas-borcherding@uiowa.edu>
Date: 2021-02-19 12:08:18 -0600
Commit message:

 Create clusterTCR.R

Use to cluster TCR chains by edit distance.

Package: scRepertoire
Commit: 0b37efda63a9d49560f632c362c9525ff822599f
Author: Nick <nicholas-borcherding@uiowa.edu>
Date: 2021-02-07 14:16:37 -0600
Commit message:

 Fix LVcompare

Was not outputing the LD - clusters by edit distance for use downstream in combineBCR.

Package: scRepertoire
Commit: c65e8a8be462cc4bccf0b2184e0742e18256f154
Author: theHumanBorch <ncborch@gmail.com>
Date: 2021-02-01 08:26:17 -0600
Commit message:

 Update README.md

Package: scRepertoire
Commit: ed1331737460e9f9030903efffcdfe4f62ee28b3
Author: theHumanBorch <ncborch@gmail.com>
Date: 2021-02-01 08:21:07 -0600
Commit message:

 Update utils.R

Massimo Change to refine branch

Package: scRepertoire
Commit: b0ed66d47f8f2cf1a63e549ea7a5f4f28343e19f
Author: theHumanBorch <ncborch@gmail.com>
Date: 2021-01-30 14:25:17 -0600
Commit message:

 Fix parseBCR

Package: scRepertoire
Commit: c6c8dde955eda78965dba5cdeb7f33d8d9893408
Author: Nick <nicholas-borcherding@uiowa.edu>
Date: 2021-01-22 11:48:02 -0600
Commit message:

 Update utils.R

Package: scRepertoire
Commit: f4ad06d761ece213e9bda3670bf6389b895d8b85
Author: Nick <nicholas-borcherding@uiowa.edu>
Date: 2021-01-21 14:17:33 -0600
Commit message:

 adding da truth

10x output changed for productive chains

Package: scRepertoire
Commit: 6535b7f97e4760b3467abe324d1cc8e636b4a1ec
Author: Nick <nicholas-borcherding@uiowa.edu>
Date: 2021-01-18 10:24:37 -0600
Commit message:

 Update vignette.Rmd

Package: scRepertoire
Commit: f73fd2023b2f06c6b6f2dd963128dd95e0ca88c7
Author: Nick <nicholas-borcherding@uiowa.edu>
Date: 2021-01-18 10:14:36 -0600
Commit message:

 Update seuratFunctions.R

Package: scRepertoire
Commit: 531f470b1f3317e028662b32c22c19a2c95b2058
Author: Nick <nicholas-borcherding@uiowa.edu>
Date: 2021-01-15 10:45:38 -0600
Commit message:

 Added proportion to combineExpression

Package: scRepertoire
Commit: 4eb39e907fe9348cc6fb5337a86af99657f92953
Author: Nick <nicholas-borcherding@uiowa.edu>
Date: 2021-01-04 07:44:15 -0600
Commit message:

 Updating calling of BCR clonotypes

Modified the way BCR clonotypes are called by:
1) Caclulating normalized edit distance using Levenshtein method
2) For CDR3 nucl with <= 0.15 normalized distance, a igraph is formed where the compoenents are called to create an effective clonotype cluster by global convergence
Note) This substantially increases the amount of time for combineBCR() but is so much better approach so I am cool with it for now.

In addition updated the NEWS, DESCRIPTION and startrac.R to reflect updates or edits in examples.

Package: scRepertoire
Commit: 2a6192dcb0dadb61e520e3a4c2c996f6a72f8b6c
Author: theHumanBorch <nicholas-borcherding@uiowa.edu>
Date: 2020-09-21 06:50:20 -0500
Commit message:

 Update utils.R

Adding dplyr import

Package: scRepertoire
Commit: 9f0cf3e3fbbb570efe4bea82f9d283c0c389c3ad
Author: theHumanBorch <nicholas-borcherding@uiowa.edu>
Date: 2020-09-21 06:50:20 -0500
Commit message:

 Update utils.R

Adding dplyr import

Package: scRepertoire
Commit: d62aed5b07ccb5d93f56b296111905fbb85d8a8e
Author: theHumanBorch <nicholas-borcherding@uiowa.edu>
Date: 2020-09-21 06:46:24 -0500
Commit message:

 Merge branch 'master' into dev

Package: scRepertoire
Commit: 9462768394fddae0f7ed5bd709cefa616d7b8153
Author: theHumanBorch <nicholas-borcherding@uiowa.edu>
Date: 2020-09-21 06:46:24 -0500
Commit message:

 Merge branch 'master' into dev

Package: scRepertoire
Commit: 5f598a5a1e25a593bcd2c7fd161d3de0417348b0
Author: theHumanBorch <nicholas-borcherding@uiowa.edu>
Date: 2020-06-07 12:34:17 -0500
Commit message:

 Update DESCRIPTION

Package: scRepertoire
Commit: 4515af2669a7e4e119cb4d2245f271c270cbca17
Author: theHumanBorch <nicholas-borcherding@uiowa.edu>
Date: 2020-06-07 12:33:33 -0500
Commit message:

 Update README.md

Package: scRepertoire
Commit: 69abc542a43e7cb508dfd20f78b00e86fa912845
Author: theHumanBorch <nicholas-borcherding@uiowa.edu>
Date: 2020-06-07 06:05:54 -0500
Commit message:

 Update DESCRIPTION

Package: scRepertoire
Commit: 21642ee28f0f39d2cdaa41ca4fb5b72a318ec04b
Author: theHumanBorch <nicholas-borcherding@uiowa.edu>
Date: 2020-06-07 06:05:07 -0500
Commit message:

 Update DESCRIPTION

Package: scRepertoire
Commit: 4a35c59a652399ab9030ce46ef34d4e558470a33
Author: theHumanBorch <nicholas-borcherding@uiowa.edu>
Date: 2020-06-07 06:04:11 -0500
Commit message:

 Update DESCRIPTION

Package: scRepertoire
Commit: 33aaada5d7f418c673708999a0c427a04bb34f2e
Author: theHumanBorch <nicholas-borcherding@uiowa.edu>
Date: 2020-06-04 18:38:37 -0500
Commit message:

 Merge pull request #14 from scfurl/master

Support for Monocle3

Had to update the DESCRIPTION to include monocle3 into dependencies. Will test the contributions this week.

Package: scRepertoire
Commit: 6af25ad1a8237670f5a4f53daa04a7b549cdcc3e
Author: theHumanBorch <nicholas-borcherding@uiowa.edu>
Date: 2020-06-04 18:37:29 -0500
Commit message:

 Merge branch 'dev' into master

Package: scRepertoire
Commit: 4b862eefcaadda1463064e228327ae9d9f67c3da
Author: Nick <nicholas-borcherding@uiowa.edu>
Date: 2020-06-04 17:51:31 -0500
Commit message:

 Update DESCRIPTION

Package: scRepertoire
Commit: 79f554399e7a3e9f37aeaa6b7690aa76f0db6147
Author: scfurl <scfurl@users.noreply.github.com>
Date: 2020-06-04 13:51:16 -0700
Commit message:

 add monocle3 support (3)

Package: scRepertoire
Commit: 82d11131ae782ec228b58b72ee7a58a925525218
Author: scfurl <sfurlan@uw.edu>
Date: 2020-06-04 10:54:54 -0700
Commit message:

 add support monocle3 (2)

Package: scRepertoire
Commit: 71e89f50beab8695b2a8f6441f89cd11f8436c1f
Author: scfurl <sfurlan@uw.edu>
Date: 2020-06-04 10:24:55 -0700
Commit message:

 add support monocle3 (1)

Package: BiocStyle
Commit: 62f4772d00483ecae39d36eceb73fb10a6f011e1
Author: Mike Smith <grimbough@gmail.com>
Date: 2021-06-16 14:55:20 +0200
Commit message:

 Version bump

Package: BiocStyle
Commit: bafc88d89e59425a15dd6a8360c7141351655b66
Author: Mike Smith <grimbough@gmail.com>
Date: 2021-06-16 14:41:07 +0200
Commit message:

 Switch to fixed pattern matching to try and address #88

Package: podkat
Commit: 17c976bc91883651c34a634bdceab5ea9bc4d45c
Author: UBodenhofer <ulrich@quomatic.ai>
Date: 2021-06-16 15:03:02 +0200
Commit message:

 Adapted namespace imports to account for changes in BiocGenerics; version number bumped to 1.25.1

Package: MsBackendMgf
Commit: 91bdf29192f03ef1d51d76d0d7d0f00c81056921
Author: Johannes Rainer <5506112+jorainer@users.noreply.github.com>
Date: 2021-06-16 12:43:39 +0200
Commit message:

 Merge pull request #17 from rformassspectrometry/jomaster

Fixes CHARGE export/import and adds support to export without TITLE

Package: MsBackendMgf
Commit: c400d1fdf5b21aa58faed150a8934bb9bc69ccad
Author: jorainer <johannes.rainer@gmail.com>
Date: 2021-06-16 11:22:47 +0200
Commit message:

 fix: add .github folder to gitignore

Package: MsBackendMgf
Commit: 06b4582489f616ea955bb0cb40240b8af58d636f
Author: jorainer <johannes.rainer@gmail.com>
Date: 2021-06-16 11:19:08 +0200
Commit message:

 feat: add parameter exportTitle to the export function (issue #14)

Package: MsBackendMgf
Commit: ed0f5f066a324ecdb6f2352b8fe7114fbc124cf1
Author: jorainer <johannes.rainer@gmail.com>
Date: 2021-06-16 11:00:27 +0200
Commit message:

 feat: export/import CHARGE in correct format (issue #16)

Package: SpidermiR
Commit: 552bf6582fb73100f3cd4306491f9d0c4df6d1f7
Author: claudia.cava <claudia.cava@ibfm.cnr.it>
Date: 2021-06-16 12:19:40 +0200
Commit message:

 Update version bump

Package: SpidermiR
Commit: e5e293ff2b2df897bdb2c8ee813fcf1a744fdd56
Author: claudia.cava <claudia.cava@ibfm.cnr.it>
Date: 2021-06-16 12:15:23 +0200
Commit message:

 Update version bump

Package: tximeta
Commit: 699199b8b5aa0f933e9fbf6828306292feeb4d1a
Author: mikelove <michaelisaiahlove@gmail.com>
Date: 2021-06-16 11:36:23 +0200
Commit message:

 fix cite

Package: fishpond
Commit: 28ffbbaf973660bd08abec749f3730184856e07f
Author: mikelove <michaelisaiahlove@gmail.com>
Date: 2021-06-16 10:38:50 +0200
Commit message:

 fix iso code

Package: sitePath
Commit: 55a631127fbeb8bd4b10954f7f13f43653bf554c
Author: Chengyang Ji <chengyang.ji12@alumni.xjtlu.edu.cn>
Date: 2021-06-16 07:09:23 +0000
Commit message:

 Bump verion; Update NEWS

Package: sitePath
Commit: 92d903f6030f47f944e4370fa10f33a7a02c2646
Author: Chengyang Ji <chengyang.ji12@alumni.xjtlu.edu.cn>
Date: 2021-06-16 06:08:55 +0000
Commit message:

 'biocthis' version 1.3.1 generated GHA

Package: sitePath
Commit: badb572bd1a630aa549132a77644d27cce2bc20d
Author: Chengyang Ji <chengyang.ji12@alumni.xjtlu.edu.cn>
Date: 2021-06-16 05:11:56 +0000
Commit message:

 Amend 'test-parallelSites'

Package: sitePath
Commit: 92f3c6f0f678dd333c1e472dfd9fa924491b32de
Author: Chengyang Ji <chengyang.ji12@alumni.xjtlu.edu.cn>
Date: 2021-06-15 07:03:37 +0000
Commit message:

 Add test cases for 'plotMutSites' function; Minor code reformat

Package: sitePath
Commit: 8794877215c5724022fc7056967415d7f4bc355f
Author: Chengyang Ji <chengyang.ji12@alumni.xjtlu.edu.cn>
Date: 2021-06-11 09:31:56 +0000
Commit message:

 Wrongly skipped sites in 'parallelSites' function

Package: sitePath
Commit: 25c00222643fb3589ee309179ce36bd6019945e1
Author: Chengyang Ji <chengyang.ji12@alumni.xjtlu.edu.cn>
Date: 2021-06-10 13:10:35 +0000
Commit message:

 Enable plot functions for 'parallelSites'

Package: sitePath
Commit: a20d3696d4c85544697f5615a5c7458f98b06b9b
Author: Chengyang Ji <chengyang.ji12@alumni.xjtlu.edu.cn>
Date: 2021-06-04 03:08:00 +0000
Commit message:

 Not scaling of 'minEffectiveSize' for lineages

Package: sitePath
Commit: 25d7aa318a2d02a580078a952b78289251259bd1
Author: Chengyang Ji <chengyang.ji12@alumni.xjtlu.edu.cn>
Date: 2021-05-22 08:48:05 +0000
Commit message:

 The first 'stable' path as default 'lineagePath'

Package: sitePath
Commit: 22526524a0a6aaf778b714dec7f2930794fd4782
Author: Chengyang Ji <chengyang.ji12@alumni.xjtlu.edu.cn>
Date: 2021-05-22 06:43:02 +0000
Commit message:

 Add 'usedSites' argument to 'setSiteNumbering' function

Package: GENESIS
Commit: b47ffba769561555c565d67a26baada2c41467d0
Author: Stephanie M. Gogarten <sdmorris@uw.edu>
Date: 2021-06-15 22:30:18 -0700
Commit message:

 move checks on family to method instead of internal function

Adding the two.stage argument introduced a bug where if 'family'
was not a character string, fitNullModel would fail.
One of the family checks requires the two.stage argument, which
is not passed to the internal .fitNullModel function. Move these
checks to the data.frame method instead (in the form of another
internal function). The internal function now assumes that
'family' is in the form of a function all (e.g., 'gaussian()'),
so modify unit tests accordingly.

Package: GENESIS
Commit: 0440a7a2b30908d20fe13246f24e2c9ad113d156
Author: Stephanie M. Gogarten <sdmorris@uw.edu>
Date: 2021-06-02 11:39:07 -0700
Commit message:

 version bump

Package: GENESIS
Commit: 8c5a6a22150338f8d8382768fcc36b9df991bd43
Author: Stephanie M. Gogarten <sdmorris@uw.edu>
Date: 2021-06-02 11:34:36 -0700
Commit message:

 bug fix: allow MatrixGenotypeReader in pcrelate

GenotypeData objects created with MatrixGenotypeReader would fail
since there was no readGeno method defined. Fix this by adding a
method.

Package: metapone
Commit: 5997bd66d9eb35ada8ed0063ddaff0c223c788e6
Author: Tianwei Yu <tianwei.yu@outlook.com>
Date: 2021-06-16 12:33:31 +0800
Commit message:

 changed description

Package: metapone
Commit: 9334739afd97bf117d533fa8b645cebb69322a32
Author: Tianwei Yu <tianwei.yu@outlook.com>
Date: 2021-06-16 11:49:28 +0800
Commit message:

 change description

Package: metapone
Commit: 0ccbf348d52aeb2190f408b2875ad8c9c3400624
Author: Tianwei Yu <tianwei.yu@outlook.com>
Date: 2021-06-16 11:34:39 +0800
Commit message:

 0.99.1

Package: metapone
Commit: 7d231f9b36de4ca3d762db3f31f28dece99cd0dd
Author: Tianwei Yu <tianwei.yu@outlook.com>
Date: 2021-06-16 11:28:44 +0800
Commit message:

 Merge remote-tracking branch 'origin/main'

Package: metapone
Commit: 2010a6042a665f6fdce4cd96fcbd19b003599d6d
Author: Tianwei Yu <tianwei.yu@outlook.com>
Date: 2021-06-16 11:18:30 +0800
Commit message:

 update 0.99.1

Package: metapone
Commit: a4e34862292ed7edc671cae23fd5764998357cb3
Author: tianwei-yu <65949207+tianwei-yu@users.noreply.github.com>
Date: 2021-06-16 11:16:48 +0800
Commit message:

 Add files via upload

Package: metapone
Commit: 3919c5941730dc25403547ab0672d1013ef07054
Author: tianwei-yu <65949207+tianwei-yu@users.noreply.github.com>
Date: 2021-06-16 11:16:20 +0800
Commit message:

 Delete metapone.Rmd

Package: metapone
Commit: b93750caf4abf0f47923614b4f933dc693f12f1c
Author: tianwei-yu <65949207+tianwei-yu@users.noreply.github.com>
Date: 2021-06-16 11:15:53 +0800
Commit message:

 Add files via upload

Package: metapone
Commit: 4c8468a99ddd6fe167e7634d564cb1d71a4e7384
Author: tianwei-yu <65949207+tianwei-yu@users.noreply.github.com>
Date: 2021-06-16 11:15:27 +0800
Commit message:

 Delete DESCRIPTION

Package: metapone
Commit: 407dcf4fbe18a5ee137028deb0345647a45aa3cf
Author: tianwei-yu <65949207+tianwei-yu@users.noreply.github.com>
Date: 2021-06-16 11:10:04 +0800
Commit message:

 Add files via upload

Package: metapone
Commit: 88f806739acd65b55361cf583e725042eea0f9aa
Author: tianwei-yu <65949207+tianwei-yu@users.noreply.github.com>
Date: 2021-06-16 11:09:41 +0800
Commit message:

 Delete data directory

Package: metapone
Commit: 4b4543db43f88d0ff25cbf6bb7536ddff289a82d
Author: tianwei-yu <65949207+tianwei-yu@users.noreply.github.com>
Date: 2021-06-16 11:09:23 +0800
Commit message:

 Add files via upload

Package: metapone
Commit: b01ec5b2be8ef293fa166ea19980b17f12882c01
Author: tianwei-yu <65949207+tianwei-yu@users.noreply.github.com>
Date: 2021-06-16 11:08:36 +0800
Commit message:

 Delete man directory

Package: metapone
Commit: 97f53b65cf584e87216ec2539e0b6d45a600804d
Author: tianwei-yu <65949207+tianwei-yu@users.noreply.github.com>
Date: 2021-06-16 10:12:45 +0800
Commit message:

 Update DESCRIPTION

Package: metapone
Commit: 84bacc6876fac03c897b370005d6d0a0e892b60a
Author: tianwei-yu <65949207+tianwei-yu@users.noreply.github.com>
Date: 2021-06-16 10:03:21 +0800
Commit message:

 Update DESCRIPTION

Package: metapone
Commit: 35e690d3d682bdd8944874e227780b6396079ae9
Author: tianwei-yu <65949207+tianwei-yu@users.noreply.github.com>
Date: 2021-06-16 10:02:29 +0800
Commit message:

 Update DESCRIPTION

Package: metapone
Commit: 1ba8a7ff8a64ec23558eb54c28f218320b1adba0
Author: tianwei-yu <65949207+tianwei-yu@users.noreply.github.com>
Date: 2021-06-16 10:01:54 +0800
Commit message:

 Update DESCRIPTION

Package: metapone
Commit: 052982b08abff18eaf9017cbb252df54efeaa18b
Author: tianwei-yu <65949207+tianwei-yu@users.noreply.github.com>
Date: 2021-06-16 10:01:11 +0800
Commit message:

 Update DESCRIPTION

Package: metapone
Commit: e7808a58f88146638038ac7bf4e8c1b864cd2276
Author: tianwei-yu <65949207+tianwei-yu@users.noreply.github.com>
Date: 2021-06-16 09:56:29 +0800
Commit message:

 Update metapone.result-class.Rd

Package: metapone
Commit: 3e73e2648966637c527dadbcc266eaa9620a2306
Author: tianwei-yu <65949207+tianwei-yu@users.noreply.github.com>
Date: 2021-06-16 09:56:09 +0800
Commit message:

 Update DESCRIPTION

Package: BgeeDB
Commit: 272abd85c760749c68a8101b49e1b96b808b7cb7
Author: Julien <julien.wollbrett@gmail.com>
Date: 2021-06-16 04:46:38 +0200
Commit message:

 add markdown to descrption

Package: RCy3
Commit: 36f52f26191dc205f9fff36a153f2bfd186043a3
Author: Alexander Pico <apico@gladstone.ucsf.edu>
Date: 2021-06-15 18:29:56 -0700
Commit message:

 version bump

Package: RCy3
Commit: 7cbdb8ee30558febdd955e6973ea785ae274f52e
Author: Yihang Xin <yihang.xin@gladstone.ucsf.edu>
Date: 2021-06-15 17:42:42 -0700
Commit message:

 Fix issue #141

Package: RCy3
Commit: ad4d3375581396edf0db71c48bf5719251c0dec1
Author: Yihang Xin <yihang.xin@gladstone.ucsf.edu>
Date: 2021-06-15 17:07:27 -0700
Commit message:

 Fix issue #141

Package: RCy3
Commit: 8269b0508b31d51c71ce2c54efc46347b662eee8
Author: Yihang Xin <yihang.xin@gladstone.ucsf.edu>
Date: 2021-06-15 17:06:47 -0700
Commit message:

 Fix issue #141

Package: RCy3
Commit: f699eb673e3a441f2fea94681945d0306f48443b
Author: Yihang Xin <yihang.xin@gladstone.ucsf.edu>
Date: 2021-06-15 00:14:14 -0700
Commit message:

 Fix issue #141

Package: OmnipathR
Commit: 38757b463ab27a8b56d4b7be07c420abcb6877c4
Author: Türei Dénes <turei.denes@gmail.com>
Date: 2021-06-15 14:29:06 +0200
Commit message:

 PrePPI in readme

Package: OmnipathR
Commit: f26b765ccb633d3ce3a2b7caf5da97165c0ce817
Author: Türei Dénes <turei.denes@gmail.com>
Date: 2021-06-15 02:46:39 +0200
Commit message:

 logfile is disabled if the `omnipath.logfile` config option is `"none"`

Package: OmnipathR
Commit: e32fcf36e6747fc8fb4eb41a0beadc61027a8baa
Author: Türei Dénes <turei.denes@gmail.com>
Date: 2021-06-15 02:18:28 +0200
Commit message:

 config options can be overridden by env variables

Package: OmnipathR
Commit: 641ef68a2054c31da55d3e4fd6478dfdea04db16
Author: Türei Dénes <turei.denes@gmail.com>
Date: 2021-06-15 02:18:02 +0200
Commit message:

 misc: `as_type` - convert variable to the type of another

Package: OmnipathR
Commit: 9fab07f5e6220072add5c2184141daf52d94324b
Author: Türei Dénes <turei.denes@gmail.com>
Date: 2021-06-15 01:47:30 +0200
Commit message:

 logging: `logdir` option & disable logfile if the `logfile` option is `none`

Package: OmnipathR
Commit: 4b9b6d912aa31fbde30db4c3db809e2035985e6e
Author: Türei Dénes <turei.denes@gmail.com>
Date: 2021-06-14 02:03:42 +0200
Commit message:

 PrePPI: processing dbs and pubs columns

Package: OmnipathR
Commit: fcccd6b37005e80bcf0d2ce16e0dfdc592e78a8e
Author: Türei Dénes <turei.denes@gmail.com>
Date: 2021-06-14 00:33:01 +0200
Commit message:

 filtering PrePPI by scores

Package: OmnipathR
Commit: b0f68b262516a599e7bb4809643479b3c0c5a692
Author: Türei Dénes <turei.denes@gmail.com>
Date: 2021-06-13 22:50:23 +0200
Commit message:

 docs: PrePPI scores

Package: OmnipathR
Commit: 8aef89ec7618db65d359e11fa552bc4aa11daadd
Author: Türei Dénes <turei.denes@gmail.com>
Date: 2021-06-13 22:16:12 +0200
Commit message:

 new resource: PrePPI

Package: OmnipathR
Commit: 9a307dfa930c7e2fb7349cf9123b04917af50e13
Author: Türei Dénes <turei.denes@gmail.com>
Date: 2021-05-31 19:31:20 +0200
Commit message:

 example in kegg_pathway_annotations docs

Package: OmnipathR
Commit: 8d0cf2f6889b0d1a08a45048847b102b724fac39
Author: Türei Dénes <turei.denes@gmail.com>
Date: 2021-05-31 19:19:27 +0200
Commit message:

 kegg_pathway_annotations: protein-pathway table

Package: OmnipathR
Commit: d9cde1048e962922ee2eeb4b2ac0ab4f3035bb20
Author: Türei Dénes <turei.denes@gmail.com>
Date: 2021-05-31 18:52:04 +0200
Commit message:

 v3.1.1

Package: OmnipathR
Commit: 5c1c79a18a19079c99ac8fd1451a3cf716c32b5a
Author: Türei Dénes <turei.denes@gmail.com>
Date: 2021-05-30 01:44:09 +0200
Commit message:

 fixed issue in `ontology_db_transformations` which caused critical performance loss in ontology tree lookups

Package: OmnipathR
Commit: a8e74e177c11e9e2d234b59b904e79d5f03d6f5d
Author: Türei Dénes <turei.denes@gmail.com>
Date: 2021-05-29 22:35:10 +0200
Commit message:

 go annotations: using comment character instead of skip

Package: cBioPortalData
Commit: ffbc402b4dc4a774448b3a37b2080cb8d6a0ec2d
Author: LiNk-NY <mramos09@gmail.com>
Date: 2021-06-15 11:16:41 -0400
Commit message:

 version bump 2.5.6

Package: cBioPortalData
Commit: 3f2d7b5bc330660e5fa3a208a049fd6453b57536
Author: LiNk-NY <mramos09@gmail.com>
Date: 2021-06-15 11:09:36 -0400
Commit message:

 update API

Package: cBioPortalData
Commit: c8d2f912556f1eb027e49268c4e64a57ff1527c8
Author: LiNk-NY <mramos09@gmail.com>
Date: 2021-06-15 10:51:39 -0400
Commit message:

 version bump 2.5.5

Package: cBioPortalData
Commit: 961b7739166c3e9a45a0a0b415c37c9c279f0859
Author: LiNk-NY <mramos09@gmail.com>
Date: 2021-06-15 10:51:34 -0400
Commit message:

 encapsulate single args in lists for @Bioconductor/AnVIL#37

Package: synergyfinder
Commit: 069fa11849f8618c9b59e135358c069e90c11b7b
Author: Shuyu <shuyu.zheng@helsinki.fi>
Date: 2021-06-15 17:05:53 +0300
Commit message:

 correct version number

Package: synergyfinder
Commit: e128a6dd1d2d8946af1baf72ce497fc809c870f0
Author: Shuyu <shuyu.zheng@helsinki.fi>
Date: 2021-06-15 17:03:54 +0300
Commit message:

 Update version number to 3.0.8 to start the rebuild

Package: synergyfinder
Commit: 97dfcc39ee6487dee32dabb4d98ebbbab55b37ef
Author: Shuyu <shuyu.zheng@helsinki.fi>
Date: 2021-06-15 17:02:39 +0300
Commit message:

 If there is only one concentration combination is replicated in a block, extract whole block into the response_statistic table

Package: synergyfinder
Commit: 90867967eceb9b625ba19b288a01557b02604283
Author: Shuyu <shuyu.zheng@helsinki.fi>
Date: 2021-06-15 16:59:43 +0300
Commit message:

 Fix bug: The CalculateRI can't fit dose-response curve if all the response values are exactly same.

Package: synergyfinder
Commit: 5ae2728619b887a02ad543d184070fc6501625c9
Author: Shuyu <shuyu.zheng@helsinki.fi>
Date: 2021-06-11 19:32:21 +0300
Commit message:

 update version number to 3.0.7

Package: synergyfinder
Commit: 9bcc0106015b4e6f10374e210dc2a7e2629a5d9b
Author: Shuyu <shuyu.zheng@helsinki.fi>
Date: 2021-06-04 17:44:17 +0300
Commit message:

 update version number to 3.0.6 to initiate rebuild

Package: MSstatsConvert
Commit: e979538cfbf27b9d6f6ed4f4b02a0bb2dea1efb2
Author: mstaniak <mtst@mstaniak.pl>
Date: 2021-06-15 12:52:35 +0000
Commit message:

 updated from: Version 1.3.0 to: Version 1.3.1

Package: MSstatsConvert
Commit: bd918d2510a673d5975f62f447f21d0a3a6b70a3
Author: mstaniak <mtst@mstaniak.pl>
Date: 2021-06-15 12:51:15 +0000
Commit message:

 updated fractions

Package: MSstatsConvert
Commit: 200e0a8dbd08ea0b0fe5aa2c9726fb4a3eb7ee2e
Author: Mateusz Staniak <mtst@mstaniak.pl>
Date: 2021-06-11 21:31:08 +0200
Commit message:

 Update utils_fractions.R

Package: MSstatsConvert
Commit: 9c9113cef48f881ebee833adb5b19bb4068f6f64
Author: Mateusz Staniak <mtst@mstaniak.pl>
Date: 2021-06-11 21:28:40 +0200
Commit message:

 Update utils_fractions.R

Package: MSstatsConvert
Commit: e283b4b94d756196d841e36e2c93b88153b095b9
Author: Mateusz Staniak <mtst@mstaniak.pl>
Date: 2021-06-11 21:25:16 +0200
Commit message:

 Update utils_fractions.R

Package: MSstatsConvert
Commit: 85426d47626b3322a9ce3b0c9375c9d41725bfdf
Author: Mateusz Staniak <mtst@mstaniak.pl>
Date: 2021-06-11 21:23:36 +0200
Commit message:

 Update utils_fractions.R

Package: MSstatsConvert
Commit: b7eb7addafb39fbec8c3d72a1f757b83617246ba
Author: Mateusz Staniak <mtst@mstaniak.pl>
Date: 2021-06-11 20:49:09 +0200
Commit message:

 Update utils_fractions.R

Package: MSstatsConvert
Commit: 56f2745f1e0642ea53ae952a252e80413a9bcb2f
Author: Mateusz Staniak <mtst@mstaniak.pl>
Date: 2021-06-11 20:48:46 +0200
Commit message:

 Update utils_fractions.R

Package: MSstatsConvert
Commit: 5cb35e50197c3a3c9b229ad29c4a111749ca31a2
Author: Mateusz Staniak <mtst@mstaniak.pl>
Date: 2021-06-11 20:25:10 +0200
Commit message:

 updates column names in TMT fraction

Package: wpm
Commit: 62002a8d64da032454bf3686158c37585843b332
Author: HelBor <borges.helene.sophie@gmail.com>
Date: 2021-06-15 13:53:24 +0200
Commit message:

 bug fix: wrapperWPM without any special wells not possible

Package: wpm
Commit: ec90b7c6337aaf5254f0fc706ff7ace775e8fa3c
Author: HelBor <borges.helene.sophie@gmail.com>
Date: 2021-06-15 13:32:59 +0200
Commit message:

 add citation file

Package: TreeSummarizedExperiment
Commit: 5b29f73e0db9207dba8d04f56be69a156210fde4
Author: fionarhuang <ruizhuRH@gmail.com>
Date: 2021-06-15 12:27:12 +0200
Commit message:

 version 2.1.3

Package: TreeSummarizedExperiment
Commit: edd0ba5f29a11858c2328f8b73a6b55a07d16724
Author: fionarhuang <ruizhuRH@gmail.com>
Date: 2021-06-15 12:24:46 +0200
Commit message:

 update citation

Package: imcdatasets
Commit: 160e4ce8376097eed7f45a151b304bc41d66d0ea
Author: ndamond <nicolas.damond@gmail.com>
Date: 2021-06-15 10:24:36 +0000
Commit message:

 fixed ref name zanotelli dataset

Package: TreeSummarizedExperiment
Commit: 4969dfde5163def8612ae164224433f63443f42f
Author: fionarhuang <ruizhuRH@gmail.com>
Date: 2021-06-15 11:33:41 +0200
Commit message:

 rename a file (version 2.1.2)

Package: TreeSummarizedExperiment
Commit: 04c1387a876d8d1cff716e354ad36319773460b6
Author: fionarhuang <ruizhuRH@gmail.com>
Date: 2021-06-15 11:10:56 +0200
Commit message:

 version 2.1.1

Package: TreeSummarizedExperiment
Commit: 33072578553ac23fde0ca2e7fa375a7d3d1bf7bf
Author: fionarhuang <ruizhuRH@gmail.com>
Date: 2021-06-13 19:06:26 +0200
Commit message:

 add asPhylo

Package: MOGAMUN
Commit: 546baf1df209555b5086e4a7c857f72f15645383
Author: Elva Novoa <elvanov@hotmail.com>
Date: 2021-06-15 08:21:16 +0200
Commit message:

 Added markdown as suggested package

Package: rols
Commit: 6f3687bd98f4d48f4bbdeb1a8e2472091baf6d19
Author: Laurent Gatto <laurent.gatto@uclouvain.be>
Date: 2021-06-15 08:04:41 +0200
Commit message:

 fix failing unit test

Package: rols
Commit: 711c8d6651a92227b903e3f4e5247daf96079de9
Author: Laurent Gatto <laurent.gatto@uclouvain.be>
Date: 2021-06-15 07:53:20 +0200
Commit message:

 update news

Package: rawrr
Commit: 03c65ea9c148ef3569a8912b2da33b716f1da845
Author: Christian Panse <cp@fgcz.ethz.ch>
Date: 2021-06-15 07:08:51 +0200
Commit message:

 set 'knitr::opts_chunk(error=TRUE)' in vignette to get useful error msg; version bump to 1.1.8

Package: signatureSearch
Commit: 6c193ae73064ef865123205f53fffee823e6a841
Author: Yuzhu Duan <yduan004@ucr.edu>
Date: 2021-06-14 18:05:15 -0700
Commit message:

 deal with corrupt cache; jump to 1.7.2

Package: signatureSearch
Commit: 36a02212fafcb6c09e176da43045f61cbdc7af3c
Author: Yuzhu Duan <yduan004@ucr.edu>
Date: 2021-05-20 21:04:40 -0700
Commit message:

 update vig

Package: PDATK
Commit: 627fada322931f29c0a633439c07a34772a8a4f5
Author: Christopher Eeles <44755307+ChristopherEeles@users.noreply.github.com>
Date: 2021-06-14 16:22:13 -0400
Commit message:

 Merge pull request #5 from bhklab/development

Fix: bug in validateModel,ClinicalModel,SurvivalExperiment-method

Package: PDATK
Commit: 43a670aefb006e6b61984a991fc969dc4e1c63f8
Author: ChristopherEeles <christopher.eeles@outlook.com>
Date: 2021-06-14 16:05:11 -0400
Commit message:

 Fix: forgot to import setDF in validateModel fix

Package: PDATK
Commit: 01961c1653ebc97f8d0ca5364aef106c14e25759
Author: ChristopherEeles <christopher.eeles@outlook.com>
Date: 2021-06-14 15:22:37 -0400
Commit message:

 Merge branch 'master' into development

Package: PDATK
Commit: e4103fd210748b712cbd0b089c6f3e1ee06d6b6a
Author: ChristopherEeles <christopher.eeles@outlook.com>
Date: 2021-06-14 15:20:32 -0400
Commit message:

 Fix: version bump for BioC

Package: PDATK
Commit: f37c4838a9711daad8eb262bde09095533de50d0
Author: Christopher Eeles <44755307+ChristopherEeles@users.noreply.github.com>
Date: 2021-06-14 15:16:48 -0400
Commit message:

 Fix: Update GHA to fix PR merge conflict

Package: PDATK
Commit: f11eee7e68ee7fde72b73d21086f5aa3ba1b8707
Author: ChristopherEeles <christopher.eeles@outlook.com>
Date: 2021-06-14 15:13:45 -0400
Commit message:

 Fix: updated GHA workflow to most recent working version

Package: PDATK
Commit: a7bf307ec913e6a9cec7ecd71f7287d8b246502c
Author: ChristopherEeles <christopher.eeles@outlook.com>
Date: 2021-06-14 15:09:47 -0400
Commit message:

 Fix: deleted old GHA workflow file

Package: PDATK
Commit: 01e09ad4b480ac159758f73368caeab2be53ef22
Author: ChristopherEeles <christopher.eeles@outlook.com>
Date: 2021-06-14 14:56:19 -0400
Commit message:

 Fix: bug in validateModel for ClinicalModel class was taking log of lower and upper for concordance index and AUC
* Resulted in negative values for upper and lower and forest plots with confidence intervals where the estimate is outside the CI
* Fixed to only log the upper and lower for log D index in validateModel,ClinicalModel,SurvivalExperiment-method

Package: PDATK
Commit: fd9525f458cfeaf4fcc6637f54e5cf7728877421
Author: Christopher Eeles <44755307+ChristopherEeles@users.noreply.github.com>
Date: 2021-06-01 18:51:08 -0400
Commit message:

 Testing `biocthis` GHA workflow

Package: PDATK
Commit: aae18498976c929b8a03fae75cc262dcd027905a
Author: Christopher Eeles <44755307+ChristopherEeles@users.noreply.github.com>
Date: 2021-06-01 17:14:15 -0400
Commit message:

 Revert to GHA without BiocCheck

Package: PDATK
Commit: caa11fccde989fb3f76d3fd63b1590f7b7bca9d6
Author: Christopher Eeles <44755307+ChristopherEeles@users.noreply.github.com>
Date: 2021-06-01 16:21:33 -0400
Commit message:

 Changed R version in GHA workflow

Package: scater
Commit: e47fd46b5e527b376d9eef39d3ace7acba99d424
Author: Alan O'Callaghan <alan.ocallaghan@outlook.com>
Date: 2021-05-25 23:16:33 +0100
Commit message:

 warn if colour duplicated between rows and columns

Package: scater
Commit: 092703b2bd3dca6d97ca85b5dbe887a661388281
Author: Alan O'Callaghan <alan.ocallaghan@outlook.com>
Date: 2021-05-25 21:25:16 +0100
Commit message:

 Bugfix in row annotation code

Package: scater
Commit: d4f938422a4e0df1508d0d87e975b60c95fe4727
Author: Alan O'Callaghan <alan.ocallaghan@outlook.com>
Date: 2021-05-25 20:45:26 +0100
Commit message:

 v1.21.2, add row color arguments to plotHeatmap, #147

Package: scater
Commit: 72cc85f54cb0aefc6924336b0a1bb987bd69c74d
Author: Alan O'Callaghan <alan.ocallaghan@outlook.com>
Date: 2021-05-24 18:28:58 +0100
Commit message:

 v1.21.1; correct check for BiocParallel params #148

Package: MSstatsTMT
Commit: 63c1ec3f08bf17dd0fc32242983393a511730ca5
Author: Ting Huang <huang.tin@husky.neu.edu>
Date: 2021-06-14 15:10:42 -0400
Commit message:

 fix bug in proeinSummarization

Package: MOGAMUN
Commit: ca7984d62bb7d6c4ed10a117429f7a0b06408e10
Author: Elva Novoa <elvanov@hotmail.com>
Date: 2021-06-14 20:57:39 +0200
Commit message:

 Fixed bug in mutation that caused (in very particular cases) individuals to reach bigger sizes than allowed.

Package: FEVV
Commit: e5879abd5f9bbd1d3d7ea62a7f66b402ed7d3701
Author: Isar Nassiri <isar.nassiri@oncology.ox.ac.uk>
Date: 2021-06-14 19:47:48 +0100
Commit message:

 Fixed conflicts in version change

Package: FEVV
Commit: 6e0556f9ebd420fc552f056215a1686feb0bea11
Author: Isar Nassiri <isar.nassiri@oncology.ox.ac.uk>
Date: 2021-06-14 19:47:30 +0100
Commit message:

 Merge remote-tracking branch 'origin/main'

Package: FEVV
Commit: 3ea69f4995ed99617eec9e8cc45363c8fc40aa8c
Author: isarnassiri <isar.nassiri@oncology.ox.ac.uk>
Date: 2021-06-14 19:45:01 +0100
Commit message:

 Update DESCRIPTION

Package: FEVV
Commit: 12375e5718721b953ad422dee56c87df731bf366
Author: Isar Nassiri <isar.nassiri@oncology.ox.ac.uk>
Date: 2021-06-14 19:03:17 +0100
Commit message:

 Merge remote-tracking branch 'origin/main'

git add FEVV/R/FEVV.R
git add FEVV/man/
git commit -m "Fixed conflicts in version change"
git push upstream master

Package: FEVV
Commit: 383713b1c1f8389d8b232ed457eb8598a5533703
Author: isarnassiri <isar.nassiri@oncology.ox.ac.uk>
Date: 2021-06-14 19:02:18 +0100
Commit message:

 Update DESCRIPTION

Package: FEVV
Commit: cf6845489b8c30d7250077ee762aa78288a7e6d5
Author: Isar Nassiri <isar.nassiri@oncology.ox.ac.uk>
Date: 2021-06-14 18:17:38 +0100
Commit message:

 Merge remote-tracking branch 'origin/main'

git add FEVV/R/FEVV.R
git add FEVV/man/
git commit -m "Fixed conflicts in version change"
git push upstream mastere commit.

Package: FEVV
Commit: adb46c4083f0d0a102fbd55ffe988f5db0b93117
Author: isarnassiri <isar.nassiri@oncology.ox.ac.uk>
Date: 2021-06-14 18:12:20 +0100
Commit message:

 Add files via upload

Package: GSEABenchmarkeR
Commit: 2c66a4e6b65ba1f864ad7fd03881c4621b9f7ee6
Author: lgeistlinger <ludwig.geistlinger@gmail.com>
Date: 2021-06-14 12:09:35 -0400
Commit message:

 restore original code

Package: FEVV
Commit: b6d7538bf2a8c46b6ae47e11bb9c6127f65f0ad4
Author: Isar Nassiri <isar.nassiri@oncology.ox.ac.uk>
Date: 2021-06-14 15:43:58 +0100
Commit message:

 Fixed conflicts in version change

Package: FEVV
Commit: f298d6892a61c8f055d44e978785daf59f1fd3d4
Author: Isar Nassiri <isar.nassiri@oncology.ox.ac.uk>
Date: 2021-06-14 15:39:24 +0100
Commit message:

 Merge remote-tracking branch 'origin/main'

git add FEVV/R/FEVV.R
git commit -m "Fixed conflicts in version change"Q

Package: FEVV
Commit: 5d2596d88bac34ef9c5e7dc49df9a980d3662c28
Author: isarnassiri <isar.nassiri@oncology.ox.ac.uk>
Date: 2021-06-14 15:38:28 +0100
Commit message:

 Update DESCRIPTION

Package: FEVV
Commit: 34433c4622d0cf6d810adb7e1c95a4d0184dcc77
Author: isarnassiri <isar.nassiri@oncology.ox.ac.uk>
Date: 2021-06-14 15:24:36 +0100
Commit message:

 Update DESCRIPTION

Package: FEVV
Commit: d45042984cd6ca7b54d7ea7100327190d419d49a
Author: Isar Nassiri <isar.nassiri@oncology.ox.ac.uk>
Date: 2021-06-14 15:07:13 +0100
Commit message:

 T3:wq
Merge remote-tracking branch 'origin/main'

Package: FEVV
Commit: 4045bf022e936850b5d7da4365c6e6b34da639f9
Author: isarnassiri <isar.nassiri@oncology.ox.ac.uk>
Date: 2021-06-14 15:06:22 +0100
Commit message:

 Update DESCRIPTION

Package: BgeeDB
Commit: d884b4a486537d75c42a03f78f7a3820c164a908
Author: Julien <julien.wollbrett@gmail.com>
Date: 2021-06-14 15:48:28 +0200
Commit message:

 solve warning when updating database

Package: FEVV
Commit: 532c81cb3002caa63d74e21cf5c7169a46a5d8da
Author: Isar Nassiri <isar.nassiri@oncology.ox.ac.uk>
Date: 2021-06-14 14:41:37 +0100
Commit message:

 Revidesemote-tracking branch 'origin/main'

Package: FEVV
Commit: c634a59c4108e1c1db9a87e2b181b820274bd7ee
Author: isarnassiri <isar.nassiri@oncology.ox.ac.uk>
Date: 2021-06-14 14:41:20 +0100
Commit message:

 Update FEVV.R

Package: FEVV
Commit: 351dfc4613741844fb29ac5cdae5bb7353278b0d
Author: isarnassiri <isar.nassiri@oncology.ox.ac.uk>
Date: 2021-06-14 14:40:58 +0100
Commit message:

 Update DESCRIPTION

Package: FEVV
Commit: 8153e837279e4e8136209d278c4ca9d9b24254a5
Author: Isar Nassiri <isar.nassiri@oncology.ox.ac.uk>
Date: 2021-06-14 14:05:31 +0100
Commit message:

 test merge remote-tracking branch 'origin/main'

Package: FEVV
Commit: 1aa4904eca0f99992c594247e665639fc9eef461
Author: isarnassiri <isar.nassiri@oncology.ox.ac.uk>
Date: 2021-06-14 12:50:25 +0100
Commit message:

 Update DESCRIPTION

Package: FEVV
Commit: e91d0a3d58a53516ed4fa15e6a189412d9c7ed07
Author: isarnassiri <isar.nassiri@oncology.ox.ac.uk>
Date: 2021-06-08 09:01:51 +0100
Commit message:

 Update DESCRIPTION

Package: FEVV
Commit: c8a07646f46b61a925cea71f30728060b1bfb728
Author: isarnassiri <isar.nassiri@oncology.ox.ac.uk>
Date: 2021-06-07 21:13:23 +0100
Commit message:

 Update DESCRIPTION

Package: FEVV
Commit: 037ccbe179cdbb01916f50e5915604a50e16cc93
Author: isarnassiri <isar.nassiri@oncology.ox.ac.uk>
Date: 2021-06-07 21:12:39 +0100
Commit message:

 Update FEVV.R

Package: BgeeDB
Commit: 9c32b2520cf702867471135c2133eeaed3533102
Author: Julien <julien.wollbrett@gmail.com>
Date: 2021-06-14 14:56:24 +0200
Commit message:

 update conf to be compatible with bioconductor

Package: BgeeDB
Commit: c82da02ba6db6c5430a345039a770217233a7a4c
Author: Julien <julien.wollbrett@gmail.com>
Date: 2021-06-11 13:12:33 +0200
Commit message:

 updated vignette

Package: BgeeDB
Commit: f56336fc20c9f96e225cbaab8a9de17925a1d96c
Author: Julien <julien.wollbrett@gmail.com>
Date: 2021-06-11 13:12:09 +0200
Commit message:

 allow to filter on full length for topanat analysis

Package: BgeeDB
Commit: 49b963fcb1d239166268366b38c67378e0b4cddc
Author: Julien <julien.wollbrett@gmail.com>
Date: 2021-06-11 10:24:19 +0200
Commit message:

 update the NEWS section

Package: BgeeDB
Commit: 0c811147f634c5b4db0faa9a421e484e8586d622
Author: Julien <julien.wollbrett@gmail.com>
Date: 2021-06-11 10:23:59 +0200
Commit message:

 solve bug of filtering on sex, strain, celtype for releases before Bgee 15.0

Package: BgeeDB
Commit: 244913e88fa3b49d65243c003e333089fe4b3dd2
Author: Julien <julien.wollbrett@gmail.com>
Date: 2021-06-11 09:26:01 +0200
Commit message:

 solve bugs for release before 15.0

Package: BgeeDB
Commit: b12817ab4281b3e2ca14bf92aa72e6f221d18c73
Author: Julien <julien.wollbrett@gmail.com>
Date: 2021-06-10 19:25:51 +0200
Commit message:

 correct dbClearResult error

Package: BgeeDB
Commit: e75c6dec54c5ab5001b4bd4bf1888d1cb4e4da64
Author: Julien <julien.wollbrett@gmail.com>
Date: 2021-06-10 17:42:30 +0200
Commit message:

 WARNING: commit to revert. Only meant to test locally

Package: BgeeDB
Commit: 5ebe00ffe8c0d27f23285376191c5d2d2552f543
Author: Julien <julien.wollbrett@gmail.com>
Date: 2021-06-10 16:39:26 +0200
Commit message:

 import gunzip function

Package: BgeeDB
Commit: 9db5f2163d420754c0611422ad93aa2ae8a39788
Author: Julien <julien.wollbrett@gmail.com>
Date: 2021-06-10 16:38:44 +0200
Commit message:

 update functions retrieving data

Package: BgeeDB
Commit: aca35892eddcb480a9c3ad7fdf70a3b1f0924584
Author: Julien <julien.wollbrett@gmail.com>
Date: 2021-06-10 16:37:36 +0200
Commit message:

 update functions retrieving annotations

Package: BgeeDB
Commit: 75e1e7e46d1ac734ca36f8a6efb086f78966b508
Author: Julien <julien.wollbrett@gmail.com>
Date: 2021-06-10 16:35:45 +0200
Commit message:

 update init of Bgee object

Package: BgeeDB
Commit: 886029e13e21d033ad672fad2f262cd6f8218ce7
Author: Julien <julien.wollbrett@gmail.com>
Date: 2021-06-09 18:07:07 +0200
Commit message:

 Merge branch 'BIOC_master' into develop

Package: BgeeDB
Commit: 9808b3c986d3cb66498e9c562413b82bc8520b49
Author: Julien <julien.wollbrett@gmail.com>
Date: 2020-08-10 12:24:51 +0200
Commit message:

 add doc for makeTable

Package: BgeeDB
Commit: ce4482b64bb68790ef09ef96c5b3f654ad0f598f
Author: Julien <julien.wollbrett@gmail.com>
Date: 2020-08-10 12:22:48 +0200
Commit message:

 Merge branch 'common_3_11_and_later' into develop

Package: BgeeDB
Commit: 49874731be7aeba5c220e186a08dfb63cfd78914
Author: Julien <julien.wollbrett@gmail.com>
Date: 2020-05-19 10:16:40 +0200
Commit message:

 Merge branch 'REALEASE_3_11_and_after' into develop

Package: BgeeDB
Commit: 4aff5a4fa566f18f2cca433299f22ae530315ea4
Author: Julien <julien.wollbrett@gmail.com>
Date: 2020-05-18 11:05:15 +0200
Commit message:

 Merge branch 'REALEASE_3_11_and_after' into develop

Package: xcms
Commit: d18e2437ba9d04fae3cc8948c5f849d3f701f890
Author: Steffen Neumann <sneumann@ipb-halle.de>
Date: 2021-06-14 13:52:00 +0200
Commit message:

 Merge branch 'rickhelmus-master'

Package: xcms
Commit: f8416f922cf1ffd6f353dca6e0c041d5f3558238
Author: Steffen Neumann <sneumann@ipb-halle.de>
Date: 2021-06-14 13:46:02 +0200
Commit message:

 Bump version after merging #562

Rick informed us that: nls() now passes the trace and control arguments to getInitial(),
notably for all self-starting models, so these can also be fit in zero-noise situations via a scaleOffset.
For this reason, the initial function of a selfStart model must now have ... in its argument list.

Package: xcms
Commit: a7842d017a9940d62616567f022dd4103b410dc0
Author: Rick Helmus <r.helmus@uva.nl>
Date: 2021-06-12 11:16:34 +0200
Commit message:

 SSgauss: update for R 4.1

Package: imcdatasets
Commit: 5fa1cb34871c19628299d6538324b138809296b0
Author: ndamond <nicolas.damond@gmail.com>
Date: 2021-05-25 12:55:40 +0000
Commit message:

 print out examples in help pages

Package: imcdatasets
Commit: a1a60cc60c3cfd58c63e1bf71429b410099c20b9
Author: ndamond <nicolas.damond@gmail.com>
Date: 2021-05-25 12:55:17 +0000
Commit message:

 list datasets

Package: imcdatasets
Commit: f0a88dc3b2ddf2fda067b9868694b237146773ec
Author: ndamond <nicolas.damond@gmail.com>
Date: 2021-05-21 07:27:22 +0000
Commit message:

 fixed links in README

Package: geneplast.data
Commit: a349a772d0f4845f831b910ad8673bebad20459c
Author: Leonardo RS Campos <leofields@gmail.com>
Date: 2021-06-14 09:36:43 +0200
Commit message:

 New dataset from STRING v9.1 included

Package: cytofkit2
Commit: bccc9aeb77eed8a9642a6dfe8d42b71ddcebdc9f
Author: raman91 <ramansethi91@gmail.com>
Date: 2021-06-14 09:45:00 +0800
Commit message:

 Update DESCRIPTION

Package: ASSIGN
Commit: 2473d15dac597240f158418053a8f69cbed63061
Author: David Jenkins <dfj@bu.edu>
Date: 2021-06-13 17:09:30 -0400
Commit message:

 Bug fix outputting parameter yaml

Package: HGC
Commit: 6ad11be6a01e35189084438da9484f64d97e5921
Author: zouzh14 <zouzh14@gmail.com>
Date: 2021-06-14 00:34:45 +0800
Commit message:

 version 1.1.2

Package: CeTF
Commit: 4dabcc84f814e7e11e0ec21eceb3643eda6c86f1
Author: Carlos Biagi Jr <biagi@usp.br>
Date: 2021-06-13 12:15:19 -0300
Commit message:

 Update

Package: DOSE
Commit: a7d3701d84fe3d4b59867b6a9987945cebab8923
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2021-06-13 15:31:58 +0800
Commit message:

 bump version

Package: DOSE
Commit: ca16c1a83f272635f06b58b566c7ef622ca6ae42
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2021-06-12 17:41:53 +0800
Commit message:

 Merge pull request #49 from huerqiang/dr

add `dr` slot to `compareClusterResult`, `enrichRestul` and `gseaResult`

Package: DOSE
Commit: e913c89e99583d7520fe92b63042c16c5b2d3253
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2021-06-12 17:41:41 +0800
Commit message:

 Update NEWS.md

Package: DOSE
Commit: 8ce4ca8dc4bf21493027cab0e05e781c2ddfe23d
Author: huerqiang <13766876214@163.com>
Date: 2021-05-21 12:39:28 +0800
Commit message:

 add `dr` slot to `compareClusterResult`, `enrichRestul` and `gseaResult`

Package: DOSE
Commit: 68168487e291157cf00bf54049d59f5c7c88a065
Author: Erqiang Hu <13766876214@163.com>
Date: 2021-05-21 12:30:12 +0800
Commit message:

 Merge pull request #2 from YuLab-SMU/master

merge

Package: DOSE
Commit: 7be9e37c49c6444e1f1d72fe901a922347d162de
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2021-05-20 12:15:22 +0800
Commit message:

 new release

Package: FEVV
Commit: 20953af67982c4c70a2db6e4b3108dabd6d7219a
Author: Isar Nassiri <isar.nassiri@oncology.ox.ac.uk>
Date: 2021-06-09 04:20:13 +0100
Commit message:

 Fixed conflicts in version change

Package: HGC
Commit: c9b2a6183e8769c37b726df618c0f5666c10ce0d
Author: zouzh14 <zouzh14@gmail.com>
Date: 2021-06-12 18:24:16 +0800
Commit message:

 update gitignore

Package: RGMQL
Commit: e81e03f4b2f10985bb87bee26a79311f4d75df8e
Author: marcomass <masseroli@elet.polimi.it>
Date: 2021-06-10 23:13:51 +0200
Commit message:

 Update README.md

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Commit: 1564b4967364197c09039236d7d053ac276b4675
Author: Simone <simonepallotta@hotmail.com>
Date: 2021-06-08 11:04:48 +0200
Commit message:

 fixed import gtf, granges schema

Package: RGMQL
Commit: ef6fb462e6b94d80982f2e5d4b5ca875341cbb25
Author: Simone <simonepallotta@hotmail.com>
Date: 2021-05-26 09:14:40 +0200
Commit message:

 show_all_metadata use one rest call API

Package: Rsubread
Commit: f651e89bf0de4a3648a9900e8e2f040ddb0add78
Author: Yang Liao <liao_y@svr2672.licr.unimelb.edu.au>
Date: 2021-06-12 12:12:03 +1000
Commit message:

 fixex the     _R_CHECK_LENGTH_1_CONDITION_=verbose bug

Package: airpart
Commit: bd9339fc92d8fa93932beaba3f010d570805ea12
Author: Wancen <42752661+Wancen@users.noreply.github.com>
Date: 2021-06-11 18:09:24 -0400
Commit message:

 fix only one level problem

Package: synergyfinder
Commit: b922f12ec6687f311797b0dcd6a7832ba5621879
Author: Shuyu <shuyu.zheng@helsinki.fi>
Date: 2021-06-11 19:30:29 +0300
Commit message:

 Update version number to 3.1.5

Package: synergyfinder
Commit: de2ba2f5e61be95bb736121b4bce084c22084c86
Author: Shuyu <shuyu.zheng@helsinki.fi>
Date: 2021-06-11 19:29:55 +0300
Commit message:

 Change the name style for .Own_log and .Own_log2 functions

Package: synergyfinder
Commit: a451f794b99dd07835889bd64572cc1a0d9ae10b
Author: Shuyu <shuyu.zheng@helsinki.fi>
Date: 2021-06-11 18:53:35 +0300
Commit message:

 Change fuction name "PredictModelSpecify" to ".PredictResponseFromModel" and do not export it.

Package: synergyfinder
Commit: 129d5993ed140c472016b141805c378d0ad0264c
Author: Shuyu <shuyu.zheng@helsinki.fi>
Date: 2021-06-11 09:53:24 +0300
Commit message:

 Modify details in vignette

Package: synergyfinder
Commit: 1043a1b232b4fb57a9a95cc90f2c9157246eec07
Author: Shuyu <shuyu.zheng@helsinki.fi>
Date: 2021-06-11 09:52:12 +0300
Commit message:

 Add the explaination of Baseline correction to vignette

Package: synergyfinder
Commit: ff909591773a6d8437716be1bd33cf23cd6cb5d4
Author: Shuyu <shuyu.zheng@helsinki.fi>
Date: 2021-06-11 09:50:23 +0300
Commit message:

 Change function names: "CalculateSens -> CalculateRI" and "PlotSensitiveSynergy -> PlotSensitivitySynergy"

Package: synergyfinder
Commit: 52966d5ea155c1369b70ea1b0ad7a33d39634ca1
Author: Shuyu <shuyu.zheng@helsinki.fi>
Date: 2021-06-11 09:48:51 +0300
Commit message:

 Fix the CITATION file

Package: BiocPkgTools
Commit: 57c1069f09b392188cbbff0c8db980ed51525a68
Author: LiNk-NY <mramos09@gmail.com>
Date: 2021-06-11 10:54:04 -0400
Commit message:

 version bump 1.11.3

Package: BiocPkgTools
Commit: 567546ad78c7d4632993a1e794ca768805322802
Author: LiNk-NY <mramos09@gmail.com>
Date: 2021-06-11 10:53:18 -0400
Commit message:

 update minor changes

Package: BiocPkgTools
Commit: 45793d54a2e64dbfd65841ed643137960641dd9f
Author: LiNk-NY <mramos09@gmail.com>
Date: 2021-06-11 10:48:39 -0400
Commit message:

 Merge branch 'master' of git.bioconductor.org:packages/BiocPkgTools

Package: BiocPkgTools
Commit: c55c0ebb7cb64a539aa1a13f81ebe64ae91a62df
Author: LiNk-NY <mramos09@gmail.com>
Date: 2021-06-11 10:39:57 -0400
Commit message:

 version bump 1.9.8

Package: BiocPkgTools
Commit: 6c73c178fa1889b0332817034dfc5fb73c692a1e
Author: LiNk-NY <mramos09@gmail.com>
Date: 2021-06-11 10:39:49 -0400
Commit message:

 make bd_file conditional in biocPkgRanges

Package: BiocPkgTools
Commit: 79e7fa30f1934dbeba1061c8506e878a46ce2e41
Author: LiNk-NY <mramos09@gmail.com>
Date: 2021-06-11 10:32:28 -0400
Commit message:

 make file conditional on version

Package: BiocPkgTools
Commit: 1b3fc40635bb2248a779b916a7da32f56151c7eb
Author: LiNk-NY <marcel.ramosperez@roswellpark.org>
Date: 2021-06-11 13:44:05 +0000
Commit message:

 update from STATUS_DB to BUILD_STATUS_DB

Package: psichomics
Commit: fdd7fd9dedcee2a88cbd743104adbbfd92a37b85
Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
Date: 2021-06-11 15:42:59 +0100
Commit message:

 Squashed commit of the following:

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    Squashed commit of the following:

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        Bump version to 1.18.1

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        Merge branch 'master' into dev

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        Rename custom data tutorial

        - Minor copy-editing

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        Fix Docker install instructions

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        Use GitHub Container Registry

        - Release `latest` tag
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        Simplify dependencies install in Dockerfile

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        GitHub and Docker install instructions

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        Update README.md

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        Update docker.yml

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        Update Dockerfile

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        Include cache in docker.yml

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        Update docker.yml

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        Temporary test

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        Update docker.yml

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        Revert to working docker.yml with new registry

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        Fix spelling issues

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        Update docker.yml

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        Update docker.yml

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        Merge pull request #422 from nuno-agostinho/master

        Update dev from master

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        Update docker.yml

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    Date:   Thu May 20 18:16:45 2021 +0100

        Update check-bioc.yml

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    Date:   Thu May 20 16:58:50 2021 +0100

        Update check-bioc.yml

        Update usage of environment variable

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        Merge pull request #421 from nuno-agostinho/dev

        Dev

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        Avoid problematic unit tests in Bioconductor

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        Update NEWS.md

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        Merge branch 'master' into dev

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        Bump version to 1.18.0

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        Fix issues with R CMD build/check

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        Update documentation and resolve minor issues

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        Merge branch 'dev' of github.com:nuno-agostinho/psichomics into dev

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    Date:   Thu May 13 15:38:19 2021 +0100

        Fix `plotDistribution()` for listed groups (e.g. in the CLI tutorial)

        - Fix issues with unit tests

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    Date:   Thu May 13 14:09:56 2021 +0100

        Avoid using set-env to set environment variables

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        Only animate spinning wheel when effectively loading data

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    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu May 13 13:29:26 2021 +0100

        Improve plotting of AS events

        - Allow to use `plotSplicingEvent()` directly with a PSI table
        - Improve support diagrams for IR events
        - Fix IR diagrams in distribution plots not displaying introns
        - Fix parsing of VAST-TOOLS IR events as SE for certain annotations
        - When searching particular splicing events, fix results based on the wrong genomic coordinates
        - Fix other AS events display in Y axis for distribution plots
        - Minor copy-editing

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    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue May 11 19:28:03 2021 +0100

        Improve distribution plots

        - Allow to invert axes
        - Avoid redundant code
        - Render event diagram based on axis containing PSI distribution values

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    Date:   Tue May 11 13:01:27 2021 +0100

        Suppress snapshot date message

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    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon May 10 19:28:24 2021 +0100

        Minor improvements

        - Place distribution plots on top of event diagrams
        - Timeout GTEx data retrieval after 3 seconds without server response
        - Avoid unnecessary messages when loading Firebrowse interface
        - Avoid "Matching subjects to their samples/Matching process concluded" loop

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    Date:   Mon May 10 19:18:53 2021 +0100

        Support gene symbol conversion for any species with OrgDb

        - Remove 'org.Hs.eg.db' dependency
        - Allow to select OrgDb species to use for gene symbol conversion
        - Minor code copy-editting

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    Date:   Thu Apr 8 11:00:36 2021 +0100

        Bump version to 1.16.1

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    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Apr 8 10:59:49 2021 +0100

        Fix parsing of VAST-TOOLS intron retention events as skipped exons

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    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Feb 19 13:37:06 2021 +0000

        Improve distribution plots

        - Allow to plot violin and box plots
        - Hide rug plots with 500 or more values (by default) for performance reasons
        - Add jitter to rug plot (helps to discern multiple numerous points)
        - Display IQR per group in tooltip
        - Easily add subtitles to distribution plots
        - Avoid redundant code
        - Reorganise code

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    Date:   Mon Nov 23 12:33:22 2020 +0000

        Fix setting environment variable

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    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Nov 23 12:05:11 2020 +0000

        Avoid bioc-devel while R-devel is not available

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    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Oct 9 18:35:05 2020 +0100

        Fix comments in bash commands

    commit f159bdc8ea2800c6482e439ea8f495575b52db1c
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Oct 8 14:50:53 2020 +0100

        Fix unit test function

    commit bdc246c1708d7ed3957cf74bd830467c42ab9f23
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Oct 8 14:19:13 2020 +0100

        Move unit tests to correct folder

    commit 87344cdc4a8e92eb6a3fa3c0857cd7e559986e01
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Oct 7 15:26:06 2020 +0100

        Minor changes

        * Warn about discarded events when quantifying/loading PSI data
        * Print elapsed time of loading local files
        * Improve verbosity when quantifying or loading PSI values
        * Add dev/ dir to add files of interest to the project
        * Copy-edit CLI tutorial, code and documentation

    commit 37f209a0799b21c71faffb6c21c101f115c27ba0
    Merge: a84aeb84 13b0d736
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Sep 25 18:41:27 2020 +0100

        Update NEWS from origin

        Merge branch 'dev' of github.com:nuno-agostinho/psichomics into dev

        # Conflicts:
        #	NEWS.md

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    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Sep 25 17:39:49 2020 +0100

        Improve performance of `discardLowCoveragePSIvalues()`

        - Move reusable `progressBar()` C++ function to header file

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    Merge: 3cfc873d 13b0d736
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Sun Aug 30 12:52:54 2020 +0100

        Merge pull request #415 from nuno-agostinho/dev

        1.14.4

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    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Sun Aug 30 12:52:12 2020 +0100

        Update NEWS.md

    commit 358819f2127b3340d2624489d06c1135f5808d50
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Sat Aug 29 17:15:14 2020 +0100

        Correct spelling

    commit 230f03f3e6704626e13d60417d340a1aa3adbe60
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    Date:   Sat Aug 29 16:33:23 2020 +0100

        Improve file/directory browser dialog

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    Date:   Sat Aug 29 14:59:37 2020 +0100

        Improve file/directory browser dialog

    commit 989b5aac54dc7799b9f187349a901370b402beea
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    Date:   Fri Aug 28 18:54:44 2020 +0100

        Improve file/directory browser dialog

    commit e37c62c848e3dc0091076d7dd7894aa4f9fe62da
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Aug 27 15:13:58 2020 +0100

        Bump version to 1.14.4

    commit 1bb928810f71d63daf7ae3f840b6c59f06d79d8f
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Aug 27 09:18:27 2020 +0100

        Fix file browser dialog selection of single file in macOS

    commit cc63bdb5a69a6e0c9fbdd2cb860629a6bfec404c
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Aug 26 19:02:54 2020 +0100

        Improve data loading

        - Speed up loading of GZ and BZ2 files
        - Increase verbosity while loading files
        - Speed up loading of VAST-TOOLS' inclusion levels
        - Fix loading of VAST-TOOLS' inclusion levels sometimes returning an error regarding duplicated row names
        - Fix issues with missing values as alternative splicing event complexity in VAST-TOOLS' inclusion levels

    commit cae16fb330bf82aff77ac9b6beda26e4f5462519
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Aug 24 18:17:36 2020 +0100

        Copy-edit tutorials

    commit 3cfc873db5f20c82d408f71b0522f52d7c3bf2b4
    Merge: 0db81dd6 b766d090
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Aug 21 17:41:29 2020 +0100

        Merge pull request #414 from nuno-agostinho/dev

        Expect to contain "ensembl_havena_gene" in logic_name

    commit b766d0908894fb121a93ccb575037741e22967e8
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Aug 21 17:41:05 2020 +0100

        Expect to contain "ensembl_havena_gene" in logic_name

    commit 0db81dd670f572886d9398b38bbbea7f536e3400
    Merge: b31fc62a ed83e8a1
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Aug 21 15:21:00 2020 +0100

        Merge pull request #413 from nuno-agostinho/dev

        1.14.3

    commit ed83e8a169ccaf55867e225c4e236ccd7aa1b232
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Aug 21 15:02:32 2020 +0100

        Bump version to 1.14.3

    commit 91198ec580ae300566c318391287d7e9540f83a1
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Aug 21 11:48:36 2020 +0100

        Fix upstream changes from Ensembl API response

    commit 339e0d6f658074fb96e9996014c8d9da84271d0c
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Aug 21 11:47:32 2020 +0100

        Run R CMD check regularly

    commit c04f25193841c87d7a9df28ad37bc4c7af682f97
    Merge: 548ae1f5 b31fc62a
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Aug 21 11:30:40 2020 +0100

        Merge branch 'master' into dev

    commit 548ae1f5984a6858b777a4dadc474b482bc44ca4
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Aug 21 00:33:07 2020 +0100

        Fix undefined global variables on renderBoxplot

    commit 616f2804081e240a1cedf920164015a178dfc998
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Aug 12 16:32:08 2020 +0100

        Fix incomplete final line

    commit f7f34ccde450d5666d2253c36e7436d350580771
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Aug 12 16:13:24 2020 +0100

        Pass codecov even with 1% of differences

    commit 21864c25fb5dc270d6f4d0eee9cf84aaf5a5d3e2
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Aug 12 15:17:15 2020 +0100

        Publish Docker images based on dev branch

    commit 278f77ebe6bc1b50861df5c6cad21d8f3b279609
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Aug 12 10:05:50 2020 +0100

        Minor copy-edit

    commit b31fc62a23d4a2eeb8f993baa0cadce22d3b89b1
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Aug 12 01:29:36 2020 +0100

        Avoid publishing Docker image on master push

    commit 75706aac561c5cee7e2bccb911187e7a78940df1
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Aug 12 01:26:33 2020 +0100

        Update README.md

    commit f9d0f85e50aae13d81e4394d4c85d60c35fa60b1
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Aug 12 00:24:03 2020 +0100

        Fix pkgdown deployment

    commit 96942cc2abc3e3bd8a835c0f0807be8cd13a96f1
    Merge: 49ca4891 14364a71
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Aug 11 23:26:58 2020 +0100

        Merge pull request #412 from nuno-agostinho/dev

        1.14.2

    commit 14364a719e271169cc4198cdf66974cb06606d2c
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Aug 11 21:49:36 2020 +0100

        Fix unit tests for VAST-TOOLS' data loading

    commit 40d7f93c716a914200f456c12d4013234721975b
    Merge: 31fc5ac5 140ab018
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Aug 11 21:01:28 2020 +0100

        Merge branch 'dev' of github.com:nuno-agostinho/psichomics into dev

    commit 140ab01862eb4e021430593492a0799a0f3c6333
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Aug 11 21:00:42 2020 +0100

        Update NEWS.md

    commit 31fc5ac577e056bee88e00c3565f29f2fab52291
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Aug 11 13:29:27 2020 +0100

        Improve loading of VAST-TOOLS' inclusion levels

    commit 48cc9ee5617d5a4b08e21ba7954b3e11eb719fd2
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Aug 11 13:27:58 2020 +0100

        Fix asking multiple paths in file browser on macOS

    commit cfa5ec8e6c08baf3374545828f59470038d7a2ee
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Aug 10 10:16:59 2020 +0100

        Table with supported file formats in psichomics

        - Include more information on manually loading FireBrowse and GTEx data
        - Reorganise information

    commit a3f81cfa4816ab3bdc1b3185a025d0a8d9d6a83e
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Sat Aug 8 23:19:54 2020 +0100

        Copy-edit NEWS.md

    commit 3f2a23257ed3f8735c8ea07e3f8f892378a7f80a
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Sat Aug 8 23:12:55 2020 +0100

        Publish Docker image in GitHub Packages

    commit 88b307d9598e608666281bd135c2b09ae3a92550
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Sat Aug 8 20:51:07 2020 +0100

        Fix VAST-TOOLS data loading unit tests

    commit 1977f5fe2f9038998c81577edbe0ecf745e43a39
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Aug 7 19:27:58 2020 +0100

        Test VAST-TOOLS data loading

    commit c56b728553c133747c685f7b1112555a6aa48a6e
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Aug 7 12:11:23 2020 +0100

        Fix testing expected error

    commit e751c549cfb39d44e4ff69891b94d7f3304c005e
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Aug 7 11:46:05 2020 +0100

        Fix returning only one data column for loaded data

    commit f4e6750492448d5bdd6193ada0c342cb0bf72c35
    Merge: 1301be60 23881204
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Aug 7 11:25:04 2020 +0100

        Merge branch 'vast' into dev

    commit 2388120475c3f585440dd15cc320863b6109ed13
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Aug 7 11:24:47 2020 +0100

        Replace CI tools with GitHub Actions

    commit d78cef99c576bc6922310245055b37a544cfe375
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Aug 7 11:22:39 2020 +0100

        Avoid using deprecated boxplot function

    commit 1301be607968ea9febcec01adba5dfa5873da8f5
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Aug 7 10:28:16 2020 +0100

        Avoid running interactive example

    commit 30a9b4786c606cf013d766b6a3d20538ab2c36b0
    Merge: 8d83c327 75748c4f
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Aug 5 09:37:29 2020 +0100

        Merge branch 'vast' of github.com:nuno-agostinho/psichomics into vast

    commit 8d83c327e7e37f4e4fc69ebbf9adff3d66724b34
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Aug 5 08:05:12 2020 +0100

        Minor copy-edit

        - Allow US spelling for normaliseGeneExpression()
        - Use cRPKM (singular), not cRPKMs whenever talking about the cRPKM dataset
        - Copy-edit CLI tutorial
        - Use Gene (singular), not Genes in calculateLoadingsContribution()
        - custom_data.Rm: Show usage of both gene read counts and cRPKMs in CLI

    commit 75748c4f9610e6aa078e1034dc0a2b5488f55025
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Aug 5 08:05:12 2020 +0100

        Minor copy-edit

        - Allow US spelling for normaliseGeneExpression()
        - Use cRPKM (singular), not cRPKMs
        - Copy-edit CLI tutorial

    commit 49d76fd13e0e57205efc684d3194a9eb67b14ae7
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Aug 5 08:03:09 2020 +0100

        Raise error (instead of capturing it) when perfoming PCA/ICA

    commit 03e69817e4dfe7bfbbf03d9e714c8e65cde0ffb0
    Merge: 2f41e2dd 1804e4f3
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Aug 5 01:06:16 2020 +0100

        Merge branch 'vast' of github.com:nuno-agostinho/psichomics into vast

        # Conflicts:
        #	R/data_geNormalisationFiltering.R
        #	man/normaliseGeneExpression.Rd

    commit 2f41e2ddc9aef85bbe70dc2424b3ba9d0f72df9f
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Aug 5 01:02:48 2020 +0100

        Replace label of `plotLibrarySize()` from "Gene expression" to "log10(library size)"

    commit 26beab6c7291874fa2fadeca79940017079fcea3
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Aug 4 12:24:35 2020 +0100

        Load both VAST-TOOLS' cRPKMs and gene read counts when available

        - Allow to load multiple datasets from a single file format by returning a list of data frames (for compatibility reasons, only return the first dataset unless explicitely requested otherwise)
        - All gene expression loading elements now support loading more than one gene expression file
        - Toggle specific statistics based on gene expression values when filtering
        -
        - Allow to change object attributes to unset attributes only
        - Improve gene expression documentation
        - Copy-editing

    commit 1804e4f38074cc9fb07a2db616f7c78e78f89fed
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Aug 4 12:24:35 2020 +0100

        Load both VAST-TOOLS' cRPKMs and gene read counts when available

        - Allow to load multiple datasets from a single file format by returning a list of data frames (for compatibility reasons, only return the first dataset unless explicitely requested otherwise)
        - All gene expression loading elements now support loading more than one gene expression file
        - Allow to change object attributes to unset attributes only
        - Copy-editing

    commit 868139d711321b01d291c9e6eacb8f5daff6fad6
    Merge: 364bbe0b 49ca4891
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Aug 3 11:57:18 2020 +0100

        Update with master and fix conflict

    commit 364bbe0bd4201884f093aee244667e0925d6bcbf
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Aug 3 11:30:10 2020 +0100

        Copy-edit

        - Keep event data on PCA results
        - Copy-edit welcome screen
        - Rename exported function `getSplicingEventInformation()` to `getSplicingEventData()`
        - Rename internal function `getEventData()` to `findEventData()`
        - Put group creation table preview above other elements in the page
        - Minor copy-editing code and documentation

    commit 68770871054fbe55172a3b7ebe683e37cf782002
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Jul 30 14:08:25 2020 +0100

        Copy-edit documentation

    commit a86b1bbd7b7a934767b413f51d7dfca26e8b8ac7
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Jul 30 13:54:35 2020 +0100

        Fix cognate genes when creating groups from differential splicing results

        - Change group title depending on creating group from differential splicing or expression results

    commit 2c2cbfdc5f19a4fd403f344736c75dfd3650d418
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Jul 29 19:14:09 2020 +0100

        Minor changes to visual interface

        - Improve groups interface, including larger margin between buttons when decreasing window width
        - Copy-edit text of GTEx tissue selection context

    commit 3ca2e456984732b1d3fbcde5e68d5e0829f71033
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Jul 29 17:43:55 2020 +0100

        Toggle individual parameters when filtering PSI data

        - Fix filtering settings not being reported after quantifying PSI

    commit 769e05e499d88cde8b892b93d7f7f3a9bb09229c
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Jul 29 17:06:27 2020 +0100

        Improve interface for group preview

    commit cde100637ec21e0ef51b05540ec5f1bde2bd367f
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Jul 29 11:53:19 2020 +0100

        Copy-edit custom data tutorial

    commit 231a81728c4145517d3abc2739faff64992c0076
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Jul 28 23:06:30 2020 +0100

        Improve group creation and correlation interface

        - Show an alert when there is no data to create groups
        - When creating groups by sample index/identifiers, suggest sample names not only obtained from sample information, but also from alternative splicing quantification and gene expression datasets
        - Fix suggested attributes and index/identifiers in group creation not being cleared when changing to datasets where such data is unavailable (thus showing the attributes/index/identifiers of the previous dataset)
        - Warn when selecting genes that are not available in the selected gene expression dataset (instead of crashing the app) when performing correlation
        - Avoid creating automatic groups based on gene lists when respective genes are not available
        - Rename RBPs to make it clear they are human RBPs
        - Minor copy-editing

    commit 8b018cc96486b55f95ff3f75c00382269607cded
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Jul 28 15:44:53 2020 +0100

        Preserve eventData for results from differentialAnalyses

    commit 916e3f257bd71754b6824811fd266b335410130f
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Jul 28 15:38:05 2020 +0100

        Copy-edit

        - Improve information on loading user-provided data and include it in the custom data loading tutorial
        - Improve function documentation
        - Copy-edit tutorials

    commit b4a187d34e2db7bea482648ec1d839b3c1f3029e
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Jul 28 11:02:56 2020 +0100

        Fix warning in Roxygen regarding link to unknown function

    commit 594df5196876340607c3ce0ecd94062706328d7e
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Jul 27 23:59:21 2020 +0100

        Fix issues in R CMD BiocCheck

    commit c16c21c691dc8dd40bd651d9a570efea0621ff76
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Jul 27 21:47:21 2020 +0100

        Fix R CMD check issues

    commit 671b9de8b6be89484540f15655695a052e454432
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Jul 27 21:17:01 2020 +0100

        Fix unit test issues

        - Fix plot distribution of single values
        - Fix wrong results when calculating fast row-wise stats of vectors
        - Fix error when quantifying splicing with no genes in the annotation

    commit 2ee32f8f8b25deb90bab250ae96f4d4dc53895fd
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Jul 27 19:35:36 2020 +0100

        Minor copy-editing

        - Replace icons for consistency
        - Improve vertical distance of primary buttons when window width is small
        - Avoid permanent progress bar after loading list of GTEx tissues

    commit 4ae464c767abd9b4a8c15d7a01200fd669f10912
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Jul 27 19:18:53 2020 +0100

        Fix issues with PSI filtering

        - Fix not filtering by event type events quantified via psichomics
        - Fix error when calculating stats for a single row containing missing values
        - Fix not being able to search for event types in selectize input

    commit a897e1f734a1c60ce7620f818be513959f79c6fa
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Jul 27 17:28:26 2020 +0100

        Fix not filtering splicing event (sub)types if stat filtering is disabled

        - Improve speed of filtering VAST-TOOLS by reordering steps
        - Improve filtering settings attribute
        - Copy-edit

    commit 06fb9cacdc5f74e0268536861d084842b6f1ef14
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Sat Jul 25 10:20:50 2020 +0100

        Improvements on parsing and directing user to differential page

        - Improve speed of joining all coordinates
        - Ensure groups are NULL when going to differential page from PCA loadings
        - Ensure AS events are correctly parsed by setting the alternative splicing quantification information when setting the event
        - Load test data with unparsable events
        - Correctly identify alternative splicing events: consider a string as splicing event if data's attribute dataType is "Inclusion levels"
        - Improve tooltips of PCA and volcano plots (loading plots now show cognate gene, event subtype and event position in tooltips)
        - Show AS event identifier at all times in the selectize event input and tables below volcano plots
        - Fix crash when there's no splicing event information
        - Copy-editing

    commit 850d2f7b2f27629b2276aae18f16817b5ac2fca2
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Jul 23 16:20:18 2020 +0100

        Improve PSI filtering interface

        - Filter by min/max individual PSI values
        - Discard VAST-TOOLS values based on quality scores

    commit 0cf47d34fc134ad02ec377317733d3e8b150228d
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Jul 23 14:02:36 2020 +0100

        Copy-edit documentation

    commit 6feb0f564baeb49857528bb7f685f3a39eac1756
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Jul 23 14:00:44 2020 +0100

        Remove redundant datasets from loaded data (ignoring attributes)

    commit fb0a764d4995dd34167af81be9cb1c813ade6802
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Jul 23 13:58:48 2020 +0100

        Correclty discard events containing only missing values

    commit eeb388ee789460220b0f4c214abef95ce2635811
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Jul 23 13:58:20 2020 +0100

        Fix VAST-TOOLS' IR-S event type not being parsed

    commit 4337b2452869d07fdb5ae47db7d8d413ad1d4ef9
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Jul 23 13:56:29 2020 +0100

        Vastly improve preparation of alternative text when there are no AS event diagrams

    commit 3b7414ee228b4502fc6ce9899729637a50d10392
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Jul 22 18:40:59 2020 +0100

        Improve filtering of PSI values

        - Discard low coverage PSIs from VAST-TOOLS
        - Allow to filter by event type or subtype
        - Use faster calculation of row-wise max and min
        - Improve code for row-/col-wise stats

    commit e8a0538af6cb0e523d73f59f51e0557854ce5021
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Jul 22 18:38:51 2020 +0100

        Get splicing event types from a given dataset

    commit 0c7b1fa05e2d707ce82d2c512ec38eab34b722ff
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Jul 22 18:37:20 2020 +0100

        Improve VAST-TOOLS file support

        - Support loading output from `vast-tools tidy`
        - Use ENSEMBL gene names when gene symbols are ambiguous
        - Correctly name RI events as expected in psichomics

    commit 17e5e2c819c3a99523066ccee1a86591f342516a
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Jul 22 18:32:12 2020 +0100

        Fix eventData passing from transposed PSI for dimensionality reduction

    commit 4be272d9bc5f531d68d5056b50fad6efcea08c6c
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Jul 22 18:12:04 2020 +0100

        Add exported function getSplicingEventInformation()

    commit adfc058c6ca8f0b2ad283e290a5f4b81ea1f20d3
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Jul 21 11:53:09 2020 +0100

        Improve calculation time of row- and column-wise statistics

    commit 0589f7a51f76de753fab53ad954c50f2845a6fea
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Jul 21 10:24:35 2020 +0100

        Improve consistency of function names

    commit 1e02261a0891870725ad2749528304d2ae4e8a9a
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Jul 21 09:36:36 2020 +0100

        Improve file loading and parsing

        - Import VAST-TOOLS gene expression data
        - Check if folder exists before loading files
        - Add verbosity to file loading functions
        - Return only TRUE/FALSE when checking file formats
        - Minor copy-editing

    commit 07addf93e43abf273be6596944d176bd71ba0e51
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Jul 20 11:42:28 2020 +0100

        Copy-edit NEWS

    commit 5567fcf5a6c19ba34c4b75f2d1c71425f52c260c
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Jul 20 11:42:14 2020 +0100

        Process psichomics PSI tables the same way as any other generic PSI tables

    commit b124bb55472c429167a5f63239a5739ee4458420
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Jul 20 11:39:26 2020 +0100

        Fix misc issues

        - Correctly parse AS events (major issue)
        - Try to put tooltip always on top of every element (still problematic...)
        - Avoid showing diagram in volcano plot tooltips if event cannot be parsed
        - Minor copy-editing

    commit 2ac31028e0d646c3a706c908688770bd82280920
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Jul 20 11:39:09 2020 +0100

        Fix suggested attributes in group creation not being updated when changing to datasets with no attributes

    commit b5605b22ce54ba396cfb54819c54b6d855982f0d
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Jul 20 11:35:50 2020 +0100

        Support SRA metadata automatically

        - Update user-provided data loading tutorial

    commit 0a6ef1ea0a509671a2fcc10d2483d1fadeb3f75d
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Sat Jul 18 14:17:52 2020 +0100

        Fix expected events type from a VAST-TOOLS PSI table

    commit d8d18f3ba2177cc1565f8a2d2245022106df5d65
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Sat Jul 18 13:59:25 2020 +0100

        Support loading PSI tables with arbitrary (i.e. unparsable) events

        - Expect warning (instead of error) from `parseSplicingEvent()` only when running in the R console

    commit 1d43fac671ca8e72872eb59f73c5fceece715dc5
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Sat Jul 18 11:12:24 2020 +0100

        Use cache for inclusion level summary plots

    commit 0333d6e65c6df9391286504b7bee022c87c7f824
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Sat Jul 18 11:00:34 2020 +0100

        Minor improvements

        - Fix gene expression summary plots not showing in specific situations
        - Fix legend not hiding in plotRowStats
        - Minor copy-editing

    commit 796838fe55a3f30ce877350526af91f0dd23ecf9
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Jul 17 16:55:43 2020 +0100

        Alternative splicing quantification filtering

    commit b66f2d762dc6cbcb0bcffe044de207767bcf68ee
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Jul 17 16:51:02 2020 +0100

        Avoid leaving missing values in type when there is subtype information

    commit 7787bd2caa9a73da856d624dcb1af3a38048cac1
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Jul 17 15:35:23 2020 +0100

        Improve data loading visual interface

        - Discard file browser input selection
        - Show helpful context messages in panel interfaces
        - Minor copy-editing
        - Avoid re-matching subject to their samples

    commit d076540dec323a59e38e17d2684e37226b4fb62c
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Jul 17 15:29:01 2020 +0100

        Use fan as loading icon for AS event selectize element

    commit b41f94365b0754e95f905c600ae1d7dc19224906
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Jul 2 17:46:01 2020 +0100

        Improve gene annotation page

        - Persistent user tags when querying PubMed
        - Allow to select more species/assemblies and freely add more
        - Fix no AS event plot diagram in information
        - Minor code copy-editing

    commit 0fc04c8c5df2501789d5f0553dd68dcfc5c816ad
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Jul 2 13:57:12 2020 +0100

        Fix rug plots in the middle of density plots

    commit c2e1d5babcfd4ca370ec70f85064773c4e89f3f1
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Jul 2 13:43:00 2020 +0100

        Use group colours in density plots of differential expression table

    commit 9d1ea065b6a16820965b0e3ae1dea7ae81b31910
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Jul 2 10:24:59 2020 +0100

        Improve differential analyses and other fixes

        - Correctly set splicing event when clicking in PCA loadings or in differential analysis table
        - Remove deprecated psi argument from diffAnalyses
        - Avoid plot issues with plot titles
        - Avoid errors when parsing event ID
        - Correct issues when plotting event diagrams in information
        - Copy-edit code and minor changes

    commit 4b1c028128094288811c0eeaffa437f9f9e59ab5
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Jul 1 19:29:18 2020 +0100

        Allow to search using an event ID directly

    commit 623951ee40cc71090debea80b18cf45e47a938fa
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Jun 30 23:28:45 2020 +0100

        Improve volcano plots' tooltips

        - Fix tooltip position
        - Include diagram of AS event

    commit 4d7fff2fe3a0b849dba599cd184ee0dc79fd887b
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Jun 30 17:06:20 2020 +0100

        Improve relevance of PubMed article results

    commit 1f4ff7e5d6e01659afaffab9c6aa79bd9ab5ed30
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Jun 26 20:13:10 2020 +0100

        Fix crash when changing to a PSI dataset without selected AS event

    commit 16aab679e2b369a2d38baf9b3cdfce0528d93604
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Jun 26 20:10:57 2020 +0100

        Improve "gene, transcript and protein information"

        - Select species and assembly directly in annotation (automatically picked based on loaded datasets)
        - Suggest genes based on loaded datasets

    commit 105a405b3af2c15453ff58b48259aa5144fa70df
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Jun 26 13:28:25 2020 +0100

        Fix issues with plotting VAST-TOOLS A3SS and A5SS events

        - Improve searching AS events in AS event selectize, including unhighlighting search results when no query is typed and avoid including SVG code (from diagrams) when searching for AS events
        - Avoid plotting AS event regions if events could not be parsed
        - Copy-edit code

    commit 94c19167715f7acfa56a1e397a462e636584c49e
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Jun 26 12:45:59 2020 +0100

        Avoid searching SVG code from AS event diagrams

    commit a6c38080eb07cdad11c3688a05fbb08af4dac76d
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Jun 26 09:58:03 2020 +0100

        Fix plotting A3SS and A5SS events and always show full coordinates of unsupported diagram events

    commit 312c0b4ddb73880f176b93e9e896c06086953462
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Jun 25 19:11:03 2020 +0100

        Simplify group selection interface

        - Replace button to edit groups with a greyed out dropdown item, simplifying the design of the group selectize element
        - Copy-edit interface

    commit 3713216a46a2496f9317305b76f5547e9f6e6802
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Jun 25 12:28:23 2020 +0100

        Rename vignettes

    commit 2107da0d81411a3b68c6796ae29dddad24206bde
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Jun 25 12:27:25 2020 +0100

        Fix progress bar not animating

    commit d0498355caa2bfd90d3cbb8f54791f6fc5de4a38
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Jun 24 15:46:43 2020 +0100

        Fix problem with geom_density_2d

    commit 2aa7fe5a22d783a55d413137d276dbb7a618cfb9
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Jun 24 15:43:55 2020 +0100

        Fix unexpected VAST-TOOLS types

    commit c32bf742128c44616c9c78479fccbc9878e38b8b
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Jun 23 17:33:45 2020 +0100

        Hide message about filtering gene expression

    commit f5ed4139e81a187e68745c6b054feb02ee3815f7
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Jun 23 16:45:15 2020 +0100

        Show loading indicator when searching for events

    commit bcf4b99ee598fd37db903c97594a5a77b889b5d2
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Jun 23 16:42:45 2020 +0100

        Improve printing of gene list object

    commit 5d38f45edab0f266e3de62b405c69aa9cd049512
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Jun 16 09:43:29 2020 +0100

        Allow to import VAST-TOOLS' inclusion levels table

        - Add attribute "rowData" to inclusion levels containing AS event information, allowing to parse and plot alternative splicing event identifiers from VAST-TOOLS
        - In the visual interface, if plotting is not supported for some event, show its full coordinates
        - Use attribute "rowData" when quantifying psichomics' inclusion levels
        - Improve gene parsing when quantifying splicing with psichomics
        - Create "sticky" objects to preserve their attributes even when extracting data
        - Rename "intron retention" to "retained intron" for consistency
        - Copy-edit code and documentation

    commit 49ca48915fca6612b372e6222fca1d1f75fa3922
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Jun 16 10:42:28 2020 +0100

        Fix unit tests for R 4.0 (#408)

        - Update required R version

    commit c3f588538530c7707c9a109fe821a1488abb1953
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Jun 12 16:56:18 2020 +0100

        Print AS event diagrams

        - Export functions to print AS event diagrams
        - Only print AS event diagram if possible (instead of table)

    commit 205a30a34f065a1227e46df636cb9ddf57d4030c
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Jun 3 22:59:31 2020 +0100

        Improve custom alternative splicing annotation

        - Include gene symbols in custom annotations if available
        - Support more flexible filenames for VAST-TOOLS, rMATS, SUPPA and MISO

    commit 4340f89b9af23a6dd1d47d604510e4b122fbc0ce
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Jun 3 13:31:49 2020 +0100

        Copy-edit NEWS

    commit 635ea7f799c4e572686ca959f3c7531a246a8776
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Jun 2 17:44:16 2020 +0100

        Fix settings not showing for alternative splicing quantification

        - Display filename of gene expression and alternative splicing quantification from recount

    commit 026ce50e441453d4dd0e19e9955b9aa81470b6d5
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Jun 2 10:52:51 2020 +0100

        Improve TCGA code

        - Copy-edit function names
        - Correctly take the most recent Firebrowse data

    commit dea5e14c85289cba3c9a22f9a33329d8a939b9a9
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Jun 1 12:16:45 2020 +0100

        Improve rendering of summary plots

    commit d49a5805bdfef5bd76a8a28bc861843cbc2d3752
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri May 29 17:43:57 2020 +0100

        Parse gene symbols containing underscores

    commit b179ec03939d22a80388765cc0ef576f008f322d
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu May 28 15:00:08 2020 +0100

        Copy-edit code and function documentation

        - Fix unit tests regarding changes in R 4.0

    commit 947ed62290a80b7cec9fed50b1e136e14dd4af74
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu May 28 14:43:29 2020 +0100

        Allow to create Docker images based on code revisions

        - Improve startup message to include psichomics version
        - Avoid unneeded functions that may mask other package functions (rowMeans and rowVars)

    commit c360449e0d364afc1b39e3184c2c3c8fa91be413
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue May 26 15:37:32 2020 +0100

        Create function `plotLibrarySize`

        - Fix library size plot not working properly
        - Improve function documentation of plotRowStats and minor copy-edits

    commit 19ab1733af38042a9df952faa59b70e778cb1d93
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon May 25 15:39:35 2020 +0100

        Fix file browser dialog not opening and warn about selecting mandatory GTEx data options

    commit 5d94ba4f7e5aabb58d762ee9531bd89f54b69857
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri May 22 16:06:56 2020 +0100

        Support GTEx V8 and older releases

        - Improve loading of GTEx data and local files

    commit dd4feaf7f443bce01109dbcb487a046e9043bf30
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Mar 31 15:51:58 2020 +0100

        Try to load cached AS annotations if a timeout is reached

    commit 97023f2a69897f86e2c446563f104b096d7bb287
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Mar 5 12:03:33 2020 +0000

        Fix HTML sanitization in popovers

    commit cf9fc483aa2267caa6b87690c0b22fb1f254c3ba
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Mar 5 10:56:27 2020 +0000

        When plotting density plots, hide Y axis when only showing their rug plots

    commit da7404c3a21434453055cddda867465852167945
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Feb 25 11:07:53 2020 +0000

        Include search in pkgdown website

    commit e0df41302b0dceb0e55ba982b400bb804a72454e
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Feb 7 14:28:45 2020 +0000

        Include search in pkgdown site

    commit 2ae72bf49708a8d63f4ae8ecb435b9893d1b5ad4
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Feb 4 14:16:32 2020 +0000

        Simplify Travis CI config

        - Include link to GitHub page in pkgdown site
        - Fix warnings from Travis CI config validator
        - Use Linux with bioc-release for code coverage and
        - Start code coverage and deployment as soon as possible

    commit a9bb71aff254442561f5ae25d43596a50a9d2b02
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Feb 4 10:06:34 2020 +0000

        Minor changes to pkgdown and function documentation

        - Include link to GitHub page
        - Improve pkgdown reference
        - Copy-edit function documentation

    commit 8ea7f504b74a2c4a18f482e468421e846ac2a754
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Jan 31 13:59:34 2020 +0000

        Update pkgdown

    commit 27587d6647229f8ba513a60b8bad0ccbc7b0e7a4
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Jan 31 13:31:01 2020 +0000

        Copy-edit tutorial, NEWS.md and README.md

    commit 9d956f1685543ecae353c30257999375889b7dfc
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Jan 31 11:02:23 2020 +0000

        Fix warning of Unicode symbol translation in Windows

        R CMD check raises the warning: "unable to translate '<U+2206>' to native encoding". Column names are translated to native encoding if directly set.

    commit c7b18c7c55bdad08cc6f9d8b5841ea739be66d33
    Merge: 415a02f6 52f3b141
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Jan 30 13:14:11 2020 +0000

        Merge branch 'master' into dev

    commit 415a02f6eebed57472516438edf3f2dc87892f13
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Jan 30 13:11:44 2020 +0000

        Avoid Bioconductor warnings when comparing signed and unsigned ints

    commit 52f3b141d985ab2d2de50867953090fc4ed0ce9b
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Jan 29 21:50:46 2020 +0000

        Dev (#403)

        * Improve Travis CI

        - Run jobs through steps
        - Add words to spell checker
        - Test code coverage and deploy even if bioc-devel or macOS jobs fail
        - Only deploy on master branch

    commit d9bfab3374682ea450bdb41d4d34e5ea01cae899
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Jan 29 21:31:31 2020 +0000

        Only deploy on master branch

    commit d4a68aaeb9e3aa255152f5ab016c4cbbe693520e
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Jan 29 19:04:44 2020 +0000

        Add newline

    commit 002dd77093673121994dba9db00e49a9205beb56
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Jan 29 19:02:48 2020 +0000

        Test code coverage and deploy even if bioc-devel or macOS jobs fail

    commit e20bf5344b947aa74a7c14836cb55a7d2cd017ac
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Jan 29 19:01:45 2020 +0000

        Add words to spell checker

    commit bb6fa2cf973f794d5d9ee2b21767bf14cb7fbde4
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Jan 29 18:16:32 2020 +0000

        R in Windows still not supported at Travis CI

    commit 3cb8dcdc1786559c3ae83b3d931a94ca11819395
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Jan 29 18:13:18 2020 +0000

        Improve Travis CI

        - Test on Windows
        - Run jobs through steps

    commit bfb6318485cf3216c93b0ccfedb10a6cd93ebf41
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Jan 29 15:40:34 2020 +0000

        Update NEWS.md

    commit b4e13768bb28355901c8ec0c50785ff11493200e
    Merge: 8e5fc8aa 1b6fc0da
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Jan 29 15:35:51 2020 +0000

        Merge pull request #402 from nuno-agostinho/dev

        Improve usage of pkgdown site

    commit 1b6fc0da6070527caf29c9eee97c556ce7c3257f
    Merge: 98996ded 8e5fc8aa
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Jan 29 15:34:51 2020 +0000

        Merge branch 'master' into dev

    commit 98996ded5f67ffdb9b329f5b11467c6c344a7b92
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Jan 29 10:38:36 2020 +0000

        Improve usage of pkgdown site

        - Include links to MiMB chapter
        - Replace vignette links from RPubs to pkgdown
        - Direct to quick reference instead of listing
        - Update license to current year
        - Copy-edit welcome message

    commit 8e5fc8aa362f97fd97156ad46ff3cc317fc0b919
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Jan 29 00:21:19 2020 +0000

        Revert last commit (did not solve Travis issues)

    commit 64919795f1ebf9111aa2c2c82ef10da3e56f9490
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Jan 28 23:48:48 2020 +0000

        Set up SSH keys between Travis CI and GitHub

        Following tutorial on: https://github.com/alrra/travis-scripts/blob/master/docs/github-deploy-keys.md

    commit b0ce9cf85a1541909f6043072d00639418af8758
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Jan 28 18:54:08 2020 +0000

        Ask for verbose deployment of pkgdown site

    commit 0a9c9d2c59348c90591edb3e4233d0df25cf9bbc
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Jan 28 18:16:18 2020 +0000

        Import shiny::fluidPage

    commit 82767daa06239159bf7a2e9febc5688d0369e681
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Jan 28 17:16:18 2020 +0000

        Fix AppVeyor using release version of R

    commit ab0189024fde749153c28982ae86a7dfc803c35d
    Merge: c2cd46b2 bdc1e3c9
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Jan 28 17:07:55 2020 +0000

        Merge pull request #401 from nuno-agostinho/dev

        psichomics 1.12.1

    commit bdc1e3c90cd8ac7fb70acafb04d0989c608d8c1a
    Merge: 7f1a9834 c2cd46b2
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Jan 28 17:05:42 2020 +0000

        Merge branch 'master' into dev

    commit c2cd46b237b06dd61a2bba714220b7d370708a78
    Merge: 27b677b4 7c933a20
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Jan 28 16:55:10 2020 +0000

        Merge pull request #400 from nuno-agostinho/imgbot

        [ImgBot] Optimize images

    commit 7f1a9834e8faaed78558eb56fb05461f2d07dec9
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Jan 28 16:29:48 2020 +0000

        Avoid test failure by skipping it on CI tools

    commit e23f89dae16a1f10f627a560795d0a43127abe23
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Jan 28 15:02:03 2020 +0000

        Minor changes

        - Fix unit test issues
        - Fix error when using `plotDistribution()` for a single value
        - Copy-edit NEWS.md

    commit 475b712449f5db139901453e85356ebdf74b228f
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Jan 28 14:38:35 2020 +0000

        Browse list of AS event diagrams

    commit e038ea32fc8c01066d7117ffa40cd3b89afe35f7
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Jan 28 14:37:40 2020 +0000

        Filter AS annotation list

    commit f7477f5e51ee57e7c67fd9f9bdfdf8eae04a9184
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Jan 27 23:57:32 2020 +0000

        Fix issues with R CMD build/check

    commit e3c650251cdf2023ea275d6b897ccba2331995d6
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Jan 27 21:34:13 2020 +0000

        Correct spelling issues

    commit 983944d3b0cf7f975021b81700d6efc9804c5551
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Jan 27 21:22:59 2020 +0000

        Fix issues with taking into account another exon as reference

    commit ce61e2c7ecf183ce11be7284d9b7acdaca3b605b
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Jan 21 17:18:25 2020 +0000

        Fix UCSC external link not working based on gene position

    commit 38d61368a649e870f93d061d0fe5f24d96b8feb8
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Jan 21 16:58:51 2020 +0000

        Fix SRA project not loading if extra information fills only one extra column

    commit 4e4ebdd510d70ff8022dbd05e1a95b5c699d0164
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Jan 20 16:35:40 2020 +0000

        Show available annotation information and query PubMed even if Ensembl is down

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    Date:   Sat Jan 18 12:11:22 2020 +0000

        [ImgBot] Optimize images

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        /vignettes/img/NUMB_exon_12_inclusion.png -- 110.03kb -> 66.18kb (39.85%)
        /vignettes/img/UHRF2_exon_10_inclusion_differential_splicing.png -- 77.23kb -> 47.89kb (37.98%)
        /vignettes/img/UHRF2_differential_expression.png -- 170.04kb -> 108.91kb (35.95%)
        /vignettes/img/3_quantify_splicing.png -- 89.61kb -> 58.73kb (34.46%)
        /vignettes/img/5_pca.png -- 146.58kb -> 97.32kb (33.61%)
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        /inst/shiny/www/set-operations/fonts/set-operations.svg -- 28.02kb -> 27.75kb (0.98%)

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    commit 9cbef932c55f8edf806cee6be9822af8c13aedd0
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Jan 17 18:02:25 2020 +0000

        Fix tooltip colour when hovering rug plot points

    commit 6dc691bd1a13937d8b4775f2d5b6abc5d06f33a2
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Jan 17 15:38:06 2020 +0000

        Create pkgdown site

        - Copy-edit README, documentation, etc.
        - Improve alternative splicing annotation tutorial

    commit ac83c06f7f2950f6cb8762447f1fe35208bcfff1
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Jan 17 14:12:24 2020 +0000

        Add automatic spell checker and copy-edit documentation

    commit 8450709045cd166beefe3a4c19c37984a7fa1cae
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Jan 17 11:29:02 2020 +0000

        Minor improvements

        - Fix plotSurvivalPvaluesByCutoff example
        - Rename vignettes
        - Copy-edit CLI tutorial
        - Fix R CMD build/check/BiocCheck issues
        - Copy-edit function documentation
        - Add unit tests for SRA metadata loading

    commit 85c54c9e052ca61ad76c4d823046ab85ca091afe
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Jan 17 10:11:56 2020 +0000

        Add AS event diagram to distribution plots and annotation page

        - Avoid app crashing when searching for PubMed articles to many times

    commit 28ee94df2c70355fb76f71bb7748a799eaf20429
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Jan 16 13:07:32 2020 +0000

        Copy-edit NEWS

    commit e5ddf7c9e37160c77ba689f283dbf99562061442
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Jan 16 11:48:36 2020 +0000

        Fix R CMD build issues and copy-edit code

    commit 726a5adbbeb3db4f8d9eb53a21ed01764e887ccd
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Jan 16 11:48:03 2020 +0000

        Fix package dependencies

    commit 08555fabd4260d005c14cbd531e42b24271a43c0
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Jan 16 10:10:41 2020 +0000

        Fix: add code for subset plot

    commit 81f6f1174ad6339d34a7bae00ab8e7b9af9b94fe
    Merge: de9d66b5 94f39514
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Jan 15 19:41:12 2020 +0000

        Merge branch 'dev2' into dev

    commit de9d66b54ded617f41bf29a2dc60673a079939d0
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Jan 15 19:38:01 2020 +0000

        Remove unused function

    commit f2c47bdb34cd80c71d85cf82b506d5ff0f9d2358
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Jan 15 13:47:52 2020 +0000

        Improve data grouping

        - Improve import/export of data groups from/to a file, including colour support
        - Fix discarding of samples not associated with any subject when exporting groups
        - Fix issues related with importing groups based on a file with groups of splicing events and/or genes
        - Inform user when groups are successfully loaded from a file and whether any group elements are discarded in the process
        - Show number of genes in pre-made gene lists
        - When creating group of genes based on pre-made gene lists, discard genes that are not loaded

    commit 04b163d7f1c72f8ee713913db8b3f287079fbd82
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Jan 8 17:02:03 2020 +0000

        Copy-edit code and NEWS

    commit 20e61243055c4d63b32672bf3611f8b04bb2c258
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Jan 8 16:56:29 2020 +0000

        Fix slow preparation of diagram representations of AS events

    commit f9c74c8e4a69a9628d0166e8d8222efa619a7489
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Jan 8 16:50:33 2020 +0000

        Fix error when trying to set page_size for Firebrowse web API

    commit a379bb5798e60bc6e61c3cca34bbacb1e73b89fa
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Jan 7 11:29:06 2020 +0000

        Update documentation regarding survdiffTerms

    commit fa33d46c6f897ee868a1c8c5a1ceedef7a5ec837
    Merge: 1d7116ec 27b677b4
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Jan 7 11:26:13 2020 +0000

        Merge branch 'master' into dev

    commit 94f395143e5a5a4ef2d1075f97ed6854275e8b4a
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Jan 7 11:20:28 2020 +0000

        Fix 0 (valid) rows error

    commit 1d7116ecb67fdbfb43db06d78c23b9ca897e1f87
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Jan 7 11:19:29 2020 +0000

        Include reshape2

    commit f95f8e20c99ecd90fd35844f5f121025bd5f3222
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Jan 7 11:11:21 2020 +0000

        Diagram representation of alternative splicing events

        - Redesign AS event selection; highlight search results using jquery.mark.min.js (built-in highlighter has many bugs)
        - Rename internal CSS/JS files
        - Update jquery-template from 1.3.4 (2016-04-19) to 1.8.5 (2019-02-17)
        - Remove validator.min.js (not being used)

    commit 6806235f5404304cb749b6693cfbd87054acdbbf
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Jan 7 10:53:40 2020 +0000

        Copy-edit code and function documentation

        - Separate utils into different, related scripts
        - Update Roxygen to 7.0.2

    commit f58c252a9c739899ca4d9c4c9fa062fca939de1e
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Jan 7 10:22:14 2020 +0000

        Improve density plot

        - Fix visual bug when plotting a group with only one sample (if one data point is available for a group, only the rug plot is drawn)
        - After hiding all plot series, rug plots of the different groups can be distinguished based on the Y axis (different arbitrary Y values are given to each rug plot series)
        - Rug plot labels now show data values if sample names are not provided
        - Rug plot labels can now be rotated (rotation is not enabled by default given Highcharts issues that may occur at different zoom levels and depending on proximity between different sample values)
        - Fix misguiding example in function documentation

    commit 84f9ec3b0f69b8729c5c3176fb0cf7e66206cc0e
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Dec 20 17:41:20 2019 +0000

        Fix loading of a portion of TCGA data if too many cohorts are selected

    commit 91c46c3a69363d5d98b36a111b02dcc7d773c98b
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Dec 20 13:34:08 2019 +0000

        Improve function documentation

        - Include information on function family
        - Clean up documentation of aliases and deprecated functions
        - Change patient to subject where appropriate
        - Copy-edit CLI tutorial

    commit c569febbc2f8f77a8003f6c4b9dd6304db5d1bcd
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Dec 19 16:43:17 2019 +0000

        Fix issues with junction quantification files

        - Improve tutorial on loading user-provided data
        - Warn when discarding rows with duplicated rownames
        - Warn when discarding rows containing random, alt and Un (unknown) chromosomes
        - Fix error when returning NULL dataset after processing
        - Copy-edit code
        - Test junction quantification file loading

    commit 5fbc5bdc8ab3de2aec982a9b3c8febfe94809b5a
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Dec 17 15:08:42 2019 +0000

        Support junction coordinates from chromosomes M, Z and W

        - When loading custom junction quantification files
        - Copy-edit information on the format of custom files

    commit e4e8e918cd6b4830b31ed7b0a07abdb462481042
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Nov 7 14:46:07 2019 +0000

        Add ORCID identifiers

    commit 27b677b4d6929ab5a0690b3abc21a77077a13736
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Oct 7 18:18:58 2019 +0100

        Update README.md

    commit 77ff8427f0f4a810ece914cbc99db54a646df4a8
    Merge: 50ebb496 4550109a
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Oct 7 18:16:59 2019 +0100

        Fix Windows warnings in CI tools

    commit 4550109aac0d2180d44e45b01598f7552517c569
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Oct 4 13:49:29 2019 +0100

        Avoid using Bioconductor-devel (wrongly trying to use R-devel)

    commit 05dec272fdc65906c1c73c7e37e69eff1317cd3d
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Oct 4 13:45:19 2019 +0100

        Bump version to 1.10.2

    commit f403ca10dd6f9595af5e7ed534a6101efbb760d1
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Oct 4 10:05:40 2019 +0100

        Install r-lib/remotes from CRAN instead of GitHub

    commit 7f4ad886741271dc774ce750222dda1b0b03eb94
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Oct 4 09:59:53 2019 +0100

        Fix link to ggrepel::geom_label_repel not being found on Windows CI tools

    commit 50ebb4961783ce4751ef4b492c8428b837802a65
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Sep 19 13:13:38 2019 +0100

        Bump version to 1.10.1

    commit 2e2abe34478ccf8fb14d177f2ce0eeaae817996b
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Sep 19 13:04:23 2019 +0100

        Avoid test timeouts in CI tools and Bioconductor

    commit 3f3f8872b35e321f524599ae8913aa3ca4a40eaf
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Sep 16 19:20:58 2019 +0100

        Fix AppVeyor (#387)

        Install *org.Hs.eg.db* and *GenomeInfoDbData* packages via source (instead of binary which is unavailable)

    commit 6f41576364d55a3dd9a0299a78d08c8c3069c62a
    Merge: 8711c313 6d9f0824
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Sep 16 16:34:43 2019 +0100

        Merge pull request #388 from nuno-agostinho/travis-mac

        Support macOS testing via Travis-CI

    commit 6d9f08241245a75c1469c7ad1d5fac455ab2fbf7
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Sep 16 15:46:34 2019 +0100

        Support macOS testing via Travis-CI

    commit f912e3d65be79c9bd52e38e58cff285bd2d8cd94
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Jun 24 17:17:46 2019 +0100

        Improve dialog when trying to load a local folder without any supported files available

    commit 6f714d3578ce7a6d2f89a400f10907b6c88acc1b
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Jun 19 17:33:17 2019 +0100

        Improve GTEx data loading

        - Export getGtexDataTypes()
        - Improve available examples

    commit a1ca8d232ff76a824fd935f2690e4628d5cdfdba
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Jun 19 14:51:22 2019 +0100

        Fix alerts crashing the app

    commit e07766a3583da3c318be50eaa3477b9322a96658
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Jun 19 14:06:35 2019 +0100

        Improve AS annotation loading

    commit d0745def60c2469178b0341697c110b086497040
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Jun 3 13:54:24 2019 +0100

        Fix prepareGeneQuant not working for stranded datasets

    commit 4fc0ed6e3872a15a6091f5c656164be7fa806e77
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri May 3 14:05:13 2019 +0100

        Fix Firebrowse function not loading all expected data

    commit 8711c313fd02fb095c496a2b9242193d5d1e7b4d
    Merge: e87a817f 15236616
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Sun Apr 21 18:33:33 2019 +0100

        Merge pull request #384 from nuno-agostinho/evalWithTimeout

        Replace usage of deprecated function

    commit 1523661611913ceef6a3f3bd6e1b89c9ce3ac716
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Sun Apr 21 18:08:51 2019 +0100

        Replace usage of deprecated function

    commit b952a879b3bf23f3759312c86677ad8b0a16f764
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Apr 2 14:26:14 2019 +0100

        Fix p-value plot bugs

    commit e87a817f84eb88df17a3a4f53fef2b94e7a560c1
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Mar 27 16:20:05 2019 +0000

        Update .travis.yml

        Based on https://github.com/Bioconductor/BiocManager/blob/master/.travis.yml

    commit f15ab1875b318554d568022228f33a8a3e3def20
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Mar 27 16:16:02 2019 +0000

        Fix appveyor.yml

        Based on https://raw.githubusercontent.com/Bioconductor/BiocManager/master/appveyor.yml

    commit 3cf6a9b743356485fd354175173440fb270a35f8
    Merge: cad23d89 1f121b7a
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Mar 27 13:24:40 2019 +0000

        Merge branch 'dev'

    commit 1f121b7a9263a9bc1348fe95ed10a32f93b4113b
    Merge: db6c24f4 6ab7ab5b
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Mar 26 17:53:02 2019 +0000

        Merge branch 'dev-2' into dev

    commit 6ab7ab5b7faf8f0755df4585415f0cb281ed1aea
    Merge: b91903c6 cad23d89
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Mar 26 17:52:17 2019 +0000

        Merge branch 'master' into dev-2

        # Conflicts:
        #	NEWS

    commit b91903c6b07bf50e1cbe67bf46b06343a39d9320
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Mar 26 17:51:23 2019 +0000

        Fix R CMD check and BiocCheck issues

    commit db6c24f4af2b371c061b96577479a59aca9097ce
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Mar 26 17:45:11 2019 +0000

        Fix R CMD check and BiocCheck issues

    commit 71e896c1c008fce02fbad5de282327816ef39a33
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Mar 26 17:28:24 2019 +0000

        Improve and fix function examples

    commit e29243d6e5d2783019182604c4ada9b96dba7582
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Mar 26 13:47:16 2019 +0000

        Fix issues in R CMD build/check

    commit db83ac6395086c9ab0d244fff1eced5734c41965
    Merge: 17e2fbd3 1deea8a5
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Mar 26 13:31:49 2019 +0000

        Merge branch 'dev' of github.com:nuno-agostinho/psichomics into dev

    commit 17e2fbd3026f133b864b60a08bbb742a373b2f53
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Mar 26 11:25:15 2019 +0000

        Fix issues in R CMD build/check

    commit 1deea8a5ceb0c77ff269cffe6e4762d205433468
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Mar 26 11:25:15 2019 +0000

        Copy-editing

    commit 1190319ef6dab35921c8fb3c9870a29c5befe51a
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Mar 26 10:04:36 2019 +0000

        Fix issues using EList's gene expression for correlation analyses

    commit d6ecc35918e88ce390a51026234c38824cd18581
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Mar 25 16:00:29 2019 +0000

        Code copy-editing

    commit 0fefbe1d1cc79a2c554321ef62af02ce37647cb8
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Mar 25 15:58:12 2019 +0000

        Make it clearer that TCGA data is loaded from Downloads folder by default

    commit 885ed2cc3315d2efaa7795679597f7b2e29f4810
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Mar 22 09:22:18 2019 +0000

        Plot p-values by cutoff

    commit 388aef18906d504e4edfef4294d8152935b63322
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Mar 22 09:14:01 2019 +0000

        Minor bug fixes and improvements

        - Allow to edit path in file/directory browser elements
        - Automatically set dropdown width for group attribute selection
        - Fix warning when displaying group preview only based on subjects or samples
        - Prepare for code escaping in newer JavaScript versions

    commit 37a0afa77baec0645d9378d24cd0acb57d1af1de
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Mar 21 15:11:35 2019 +0000

        Fix issues with R CMD check

    commit d1246e4b8322f3cce87fcacb76894dc2e34ccb56
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Mar 21 14:55:48 2019 +0000

        Require human gene annotation

    commit 87a2d3d83d46f2660576f905222a3c1df1638da7
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Mar 21 11:21:05 2019 +0000

        Fix table filtering based on plotted points

    commit 3cb42cf98e05b35bd2006ab9ae5f85833e707032
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Mar 18 15:43:04 2019 +0000

        Improve and fix plotting of gene expression and alternative splicing quantification data

    commit 1caf8bada79c40a23afb39422050550f2c9aae6d
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Mar 15 16:22:27 2019 +0100

        Plot specific combinations of gene and alternative splicing events after performing correlation analyses

    commit 387d63051f11ccee7856271f8369b38570b3d556
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Mar 8 14:24:35 2019 +0000

        Improve AS and GE filtering

        - Present PSI filtering settings in the visual interface
        - Minor interface tweaks
        - Fix plot PSI error

    commit 0a094a868e124e5ec115d1f5f3c169ae057fdafe
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Mar 8 13:45:24 2019 +0000

        Update citation details

    commit b6d0909be72ed3d54fabd3378aae050e14ec4082
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Mar 7 15:27:54 2019 +0000

        Allow to use selected splicing event in correlation analysis

    commit 1fb75cbb1f6de14bbcff49a1fa2ed1f942a0e3ce
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Mar 6 18:58:47 2019 +0000

        Fix error when subsetting edgeR::DGEList

    commit b0be91e288bab1d1a3f2917dc4ea0a917400382d
    Merge: 47bee247 76ba81ea
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Mar 6 14:50:34 2019 +0000

        Merge branch 'dev' of https://github.com/nuno-agostinho/psichomics into dev

        # Conflicts:
        #	NEWS
        #	R/data.R

    commit 47bee24752a09aae6052235133a41d5c30e71f14
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Mar 6 03:01:52 2019 +0000

        Minor copy-editing

    commit 972e5582a5cc7664a89542dc37edf926e7b27e65
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Mar 6 02:59:35 2019 +0000

        Improve correlation plots

    commit 25ece479739d264f1f86898a98b703b6355ffbe6
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Mar 6 00:36:02 2019 +0000

        Fix missing attributes of gene expression normalised via voom

    commit a949e3a91ad0a650c39a57e0351e9bae1f702b73
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Mar 6 00:34:12 2019 +0000

        Fix error when creating groups containing only samples and no matching subjects

    commit a063ae9c3e8485ec8321719898a43a2e1eced67b
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Mar 5 15:54:02 2019 +0000

        Improve GTEx and other data loading

        - Automatically download and load GTEx data
        - Only display at most the first 100 columns for performance reasons
        - Improve data loading titles
        - Default to load clinical, junction quantification and gene expression data when selecting TCGA data
        - Minor copyediting

    commit 76ba81ea5f6d3f13761ab733550daa2e703252bc
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Mar 5 15:54:02 2019 +0000

        Improve GTEx and other data loading

        - Automatically download and load GTEx data
        - Only display at most the first 100 columns for performance reasons
        - Improve data loading titles
        - Minor copyediting

    commit f344fc0607fdf20cf78e91ecaf4e40f8ff337493
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Mar 5 15:50:28 2019 +0000

        Fix article title formatting

    commit ad81788ad9241386b34349bb6d912824a7ff51e8
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Feb 28 11:57:54 2019 +0000

        Improve gene expression filtering and normalisation and PSI filtering

        - Plot distribution of gene expression per sample
        - Plot distribution of library sizes
        - Plot gene-wise expression mean and variance across samples
        - Plot PSI mean, variance and range
        - Filter PSI values
        - Perform voom and respective normalisation if desired
        - Sample filtering
        - Filter lowly expressed genes using edgeR::filterByExpr
        - Convert ENSEMBL identifiers to gene symbols
        - Show labels for distribution plots

        Bug fixes:
        - Fix distribution plots requiring all samples in a group
        - Show sample names in distribution plots
        - Fix inconsistency of delta median and variance

    commit 795d17597f7d639681aa2cf33937ecd8a0c7eea8
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Feb 18 11:15:56 2019 +0000

        Improve SRA data loading

        - Accept a vector of files as the first argument (easier to use with `list.files()`)
        - Ask to overwrite file if one exists with the same name as the output file

    commit 161f9c2da7bf5139bda1a56c0bd8aebf76268b9e
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Feb 18 11:03:53 2019 +0000

        Minor copyediting

    commit 2fb74587d87c9a8a6fc2e85c1c429faf4ea1d3b6
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Feb 18 11:02:33 2019 +0000

        Update copyright references to 2019

    commit 808b219acfb5b317afc0fe232cb268a49a51cd52
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Feb 13 17:05:57 2019 +0000

        Fix colours/opacity in the rug plot within the distribution plot

    commit 7536285cb2fcea357ff945ce96192b6aff815396
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Feb 7 17:46:53 2019 +0000

        Fix wrong information in table of differential splicing results

    commit cad23d89b8f07420b6cd90067b9ede60a4651881
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Dec 3 14:59:22 2018 +0000

        Add tag ImmunoOncology to BiocViews

    commit a1510c15977c36b6c9863b0a0ba0140243b9b8c5
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Dec 3 11:54:33 2018 +0000

        Add tag ImmunoOncology to BiocViews

    commit 676ecb0b64f593ce3a9b4d3d5fbc4adae17fd1d2
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Nov 29 23:10:02 2018 +0000

        Fix crash when loading psichomics with test data that is not locally available

    commit 5bf83e4e96ac73180b6187239c7d2f570da21c1e
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Nov 8 16:59:39 2018 +0000

        Fix R CMD check and BiocCheck errors and warnings

    commit bb78b2be6e8c9457b5772435a574e728c870504e
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Nov 8 16:59:27 2018 +0000

        Fix progress bar when quantifying alternative splicing

    commit 19fea9e64f53c3e0479b61db08adee359ced772d
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Nov 7 15:46:13 2018 +0000

        Improve documentation of exported and internal functions

        - Minor code copy-editing
        - Minor tutorial copy-editing

    commit 23e38acd50866c16438a4dc6399173d98e52259b
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Nov 7 11:47:25 2018 +0000

        Minor improvements

        - Bump version number
        - Allow to show dataset icons in "Data"
        - Improve data grouping interface
        - Fix inconsistent group names when creating groups based on pre-made gene lists
        - Avoid error when user cancels file browser dialog to load groups from a file
        - Copy-editing code and documentation

    commit 65cc716dd58d1ea9a577e34d898c24b92308853a
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Nov 7 11:25:38 2018 +0000

        Ask before replacing correlation analyses

    commit 661a73a2bc12c54227a97c0003eccb022dfdab28
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Nov 7 11:24:40 2018 +0000

        Copy-edit tutorial on custom alternative splicing annotation preparation

    commit 09210d45c4a69f37355299acff1d074e3e3c2349
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Nov 7 11:21:38 2018 +0000

        Improve console logging of alerts

    commit e81cee95712934e4ba04b8100e7cee13d99874cb
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Nov 6 15:44:19 2018 +0000

        Decrease loading time after alternative splicing quantification

    commit d65138081a2c0f25c4c4f59e8cac3aa99fe68cf2
    Merge: 950fead2 0166a557
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Nov 5 17:45:15 2018 +0000

        Merge branch 'dev' of https://github.com/nuno-agostinho/psichomics into dev

    commit 950fead2c87b45eef1c57ba0ecc5221405648e07
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Nov 5 17:43:56 2018 +0000

        Change which AS event types are quantified by default

    commit af7d87997ca811bc3dae0c9bca5e964eb92ff713
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Oct 31 17:37:25 2018 +0000

        Load pre-made gene lists and improvements to correlation analyses

        - Display correlation results in a table
        - Display correlation analyses progress
        - Load those groups by default and allow to create them in the group interface
        - Initial support for RBPs in Sebestyen et al. 2016
        - Allow to use such groups in correlation analyses
        - Improvements to interface for correlation analyses
        - Minor copy-editing and interface improvements

    commit 757f821eacadef804a39c948dc8752bec86bba88
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Oct 30 18:37:13 2018 +0000

        Fix link for AS annotation creation and loading

    commit cc0ddc5999ac10060c83dcff1cdf35356e5e5aa7
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Oct 30 18:29:53 2018 +0000

        Fix word break-related visual issues

    commit f59713d9a5b76005ca392b10477376fa3fb4c941
    Merge: 650c0bcd 0166a557
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Oct 2 09:44:32 2018 +0100

        Merge pull request #366 from nuno-agostinho/dev

        Update citation link

    commit 0166a5578b61fcb0af3c4a9643402d3ac886869c
    Merge: c78f8054 650c0bcd
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Oct 2 09:44:13 2018 +0100

        Merge branch 'master' into dev

    commit c78f80540dbb9a3bef754317251d16403c57c8df
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Oct 2 09:42:49 2018 +0100

        Update citations to link to article in Nucleic Acids Research

    commit 650c0bcdc1728a113a1a11e095c16b07c3a10881
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Oct 2 09:22:01 2018 +0100

        Update NEWS date

    commit ebb47d9cc359f8539e319b67ee7512dd55a92eb9
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Oct 2 08:56:29 2018 +0100

        Minor changes

        - Update LICENSE for current year
        - Update clinical dataset used in vignettes

    commit ed1ad926df259ee936a9c0175a3f59024595895e
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Sep 20 16:53:57 2018 +0100

        Improve TCGA data download modal and minor changes

    commit 1614e3e3a35a4c8f15a05a45623584d234c98f20
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Sep 20 16:51:43 2018 +0100

        Add metadata regarding loaded and created datasets

    commit fbb70cc6b0a0a892716fd4fe6b0e7a9734bf1aff
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Sep 18 17:56:21 2018 +0100

        Fix errors, warnings and notes from R CMD check/build

    commit ae48e0e42ecd7c2217e7e5acc6ef1af5514aadaf
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Sep 18 16:50:37 2018 +0100

        Fix allowing to select a directory when requesting a file

    commit ad6777fd7a401b37b659bb5440449a79b8450545
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Sep 18 16:49:38 2018 +0100

        Fix allowing to select a directory when requesting a file

    commit e08b64dd60fa56ee697557beb2090724f8f28896
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Sep 18 15:49:59 2018 +0100

        Minor changes and code copyediting

    commit 3229d8ce5f23237f67119ce45eb23e545aabc4c3
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Sep 18 15:45:49 2018 +0100

        Improve file browser dialog in remote server

        - Allow to directly input a path without using the file browser dialog
        - Display warning when calling the file browser dialog in RStudio Server or in an unsupported system

    commit 9953f4f41d7b573653e23bb4ac45df864cbab160
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Sep 18 15:17:31 2018 +0100

        Fix issues in downstream analyses when using GTEx data subset by tissues

    commit 5fc56fd9162549d11daf7aa6271274b9c2323112
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Sep 17 16:19:46 2018 +0100

        Inform of sequencing technology used to obtain gene expression data from TCGA

    commit f7921b88d00b7da95c5acd379abd56d14088cf5c
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Sep 17 15:40:24 2018 +0100

        Improve console logging of error and warning messages

        - Check if files exist before loading local data
        - Check if any projects are selected and if given directory exists before downloading recount2 data

    commit c9fa821990d83f6fe223aa97de8b9265d2050ab1
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Sep 5 15:19:03 2018 +0100

        Improve group selection and correlation analyses

        Group selection:
        - Show group colour in group selection element
        - Avoid moving "Create groups" due to group creation preview

        Correlation analysis plot:
        - Colour samples by group
        - Render contour based on a density estimate
        - Interface changes to make it more intuitive
        - Fix Loess curve gaussian fitting regardless of the fitting argument

    commit 4f4cd0fe701f891d536bd13d227a908878b8e722
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Aug 30 15:51:42 2018 +0100

        Fix forced axis limit of density plot

        When plotting values within 0 and 1, limit X axis to 0 and 1; otherwise, do not limit X axis

    commit 54dea1bdb5f19a49683e3a24cc6f33964657e9fb
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Aug 15 21:43:50 2018 +0100

        Fix data group display when Patients or Samples are unavailable

        Minor changes:
        - Copyediting

    commit 8b5e1b106d6b4a3556bd6c57dd1bd1786053a660
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Aug 15 21:43:50 2018 +0100

        Fix data group display when Patients or Samples are unavailable

        Minor changes:
        - Copyediting

    commit b4fcaeaef1238f77a19b6262a6bbbea88e265940
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Aug 15 20:18:02 2018 +0100

        Improvements to data loading

        - Fix wrong parsing of recount's sampe metadata when fields across samples are not the same
        - Fix GTEx data loading as numeric instead of factor when filtering by tissues
        - Check if GTEx data files exist before attempting to load them
        - Copyedit code and user messages

    commit 2a2c46a84954e56ae792f075207a1fc7c6eb1f74
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Aug 15 20:13:53 2018 +0100

        Search PubMed instead of PMC

    commit ad607e31af37c0a65de674140e4f45ba04cef0e2
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Aug 13 18:07:50 2018 +0100

        Updated roxygen version

    commit 2e29f55d2a884216e4eb623772018a6f61683624
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Sun Jul 15 18:29:13 2018 +0100

        Minor improvements)

        - Update screenshot
        - Allow to select hg38 assembly when loading PSI quantification
        - Improve correlation's interface
        - Improve selection of icons used
        - Copy-editing

    commit 4593c1ffe040e390b5ec049c449a82ad725c6dcb
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Jul 9 19:30:46 2018 +0100

        Clean code for differential analyses

    commit 2f7c7e695f269a454f0a7de1e17872ec6c835217
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Jul 9 19:30:46 2018 +0100

        Clean code for differential analyses

    commit d3218e2997a5c238827332cf8d1e16a33fbbf496
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Jul 9 16:52:52 2018 +0100

        Copy-edit

    commit 327bf525aeb1fb599f400b05c5ae51074db77c44
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Jul 6 17:56:24 2018 +0100

        Allow to input formulas when highlighting points

        Other minor changes:
        - Fix filenames of exported tables mentioning differential splicing analysis instead of differential expression analysis
        - Minor style changes

    commit dace8973cd449c327d17e068fa680c1af0851bc5
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Jul 6 17:25:25 2018 +0100

        Copy-edit README and update screen shot

    commit 8c6e49459bf060426fd4dec5c97a0437b9fb8295
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Oct 2 09:22:01 2018 +0100

        Update NEWS date

    commit 9f57a89e0a585cf095b39298c276a3a5385afd0a
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Oct 2 08:56:29 2018 +0100

        Minor changes

        - Update LICENSE for current year
        - Update clinical dataset used in vignettes

    commit a766175c2c1814c06ae700cefc2dbedf54e09272
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Sep 20 16:53:57 2018 +0100

        Improve TCGA data download modal and minor changes

    commit 72c7322885372c86ec86a7160ff366549f1e7c04
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Sep 20 16:51:43 2018 +0100

        Add metadata regarding loaded and created datasets

    commit 6ef892922d492ea1b23bd36ddd970bb72c27caca
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Sep 18 17:56:21 2018 +0100

        Fix errors, warnings and notes from R CMD check/build

    commit 644b5514e8ddc046e3ea9b4db38a25928da50ef3
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Sep 18 16:50:37 2018 +0100

        Fix allowing to select a directory when requesting a file

    commit 4ba02ed2c43d15f44f7c04a68c9c04f6b854536b
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Sep 18 16:49:38 2018 +0100

        Fix allowing to select a directory when requesting a file

    commit 4d7e49cf6e5884f7b70bd31cf5809b7ad407f3b8
    Merge: 193ac794 660ff9d8
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Sep 18 15:50:12 2018 +0100

        Merge branch 'dev' of https://github.com/nuno-agostinho/psichomics into dev

    commit 193ac794afb5ba5ecc87a8434e6d98a8ad5b264e
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Sep 18 15:49:59 2018 +0100

        Minor changes and code copyediting

    commit 826edf1ecb8a4d56472cf35392919ae485e53a6b
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Sep 18 15:45:49 2018 +0100

        Improve file browser dialog in remote server

        - Allow to directly input a path without using the file browser dialog
        - Display warning when calling the file browser dialog in RStudio Server or in an unsupported system

    commit d2a64dbf7f7ab3189334b6de72623685b47f920d
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Sep 18 15:17:31 2018 +0100

        Fix issues in downstream analyses when using GTEx data subset by tissues

    commit 10cb3df4c0304152629e18fec97a1fa880bcef8b
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Sep 17 16:19:46 2018 +0100

        Inform of sequencing technology used to obtain gene expression data from TCGA

    commit 486d43c20f70f1f18f4b6ea3988c31558f719940
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Sep 17 15:40:24 2018 +0100

        Improve console logging of error and warning messages

        - Check if files exist before loading local data
        - Check if any projects are selected and if given directory exists before downloading recount2 data

    commit bddf111e81a70a988d8c06c31147518592098412
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Sep 5 15:19:03 2018 +0100

        Improve group selection and correlation analyses

        Group selection:
        - Show group colour in group selection element
        - Avoid moving "Create groups" due to group creation preview

        Correlation analysis plot:
        - Colour samples by group
        - Render contour based on a density estimate
        - Interface changes to make it more intuitive
        - Fix Loess curve gaussian fitting regardless of the fitting argument

    commit eae64553ff843b09a8013c6565f9a75bb47f9876
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Aug 30 15:51:42 2018 +0100

        Fix forced axis limit of density plot

        When plotting values within 0 and 1, limit X axis to 0 and 1; otherwise, do not limit X axis

    commit 48189e1b1a8a49b2f45816c448da9b0cc5e71149
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Aug 15 21:43:50 2018 +0100

        Fix data group display when Patients or Samples are unavailable

        Minor changes:
        - Copyediting

    commit 660ff9d802bd2f9d7eb920b519dfe0d74906904b
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Aug 15 21:43:50 2018 +0100

        Fix data group display when Patients or Samples are unavailable

        Minor changes:
        - Copyediting

    commit 788366fff3a0e37fd5a4bb7f5829b7c3fde6a9d5
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Aug 15 20:18:02 2018 +0100

        Improvements to data loading

        - Fix wrong parsing of recount's sampe metadata when fields across samples are not the same
        - Fix GTEx data loading as numeric instead of factor when filtering by tissues
        - Check if GTEx data files exist before attempting to load them
        - Copyedit code and user messages

    commit d7792511a47552b836047659736db4cf7fc1462b
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Aug 15 20:13:53 2018 +0100

        Search PubMed instead of PMC

    commit d5f8c587115cc23b4a07e496c8f07a5ba86bfe58
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Aug 13 18:07:50 2018 +0100

        Updated roxygen version

    commit 40aeed67aa0e24588ab126f7fd03537583d09ac4
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Sun Jul 15 18:29:13 2018 +0100

        Minor improvements)

        - Update screenshot
        - Allow to select hg38 assembly when loading PSI quantification
        - Improve correlation's interface
        - Improve selection of icons used
        - Copy-editing

    commit ca61fe24d1f043edd937be09e816f40ed1f0c9c7
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Jul 9 19:30:46 2018 +0100

        Clean code for differential analyses

    commit 455faf68c9dc1ebee8bd1cba8d0f0e6743b5154a
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Jul 9 19:30:46 2018 +0100

        Clean code for differential analyses

    commit 7e2e449e90b11da3ff93247ccbc58e33dfb6218e
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Jul 9 16:52:52 2018 +0100

        Copy-edit

    commit 8b4a7e91d71b858ea16b763d6929643d1b216f04
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Jul 6 17:56:24 2018 +0100

        Allow to input formulas when highlighting points

        Other minor changes:
        - Fix filenames of exported tables mentioning differential splicing analysis instead of differential expression analysis
        - Minor style changes

    commit 3b246807f63fa611d8ace55e3245965aaccac351
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Jul 6 17:25:25 2018 +0100

        Copy-edit README and update screen shot

    commit e392f34ebc314e4e7360ccbb3685fe4119734718
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Jul 5 20:09:09 2018 +0100

        Update README.md

    commit bf424d7bc72d8c9eff2cf92c920b883ec7ea9552
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Jul 5 20:01:13 2018 +0100

        Update README.md

    commit 66e932b545d0e533d7a3025de1216fb989465321
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Jul 5 19:57:39 2018 +0100

        Update README.md

    commit 946af16ddbe473f074e560ba248e40b54f8359c6
    Merge: 0aac8a4d 9ea793f8
    Author: Nuno Agostinho <danielagostinho@sapo.pt>
    Date:   Thu Jul 5 16:45:04 2018 +0100

        Merge pull request #361 from nuno-agostinho/dev

        Version 1.6.1

    commit 9ea793f87b94f1d916200d7431eea90e90bcf2d7
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Jul 5 15:59:26 2018 +0100

        Add placeholder

    commit 99e7b05fd75667a856b3d7254d2444b5063430b8
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Jul 5 15:11:47 2018 +0100

        Add more options when plotting gene expression versus PSI values

        - Change font size
        - Change plot height
        - Improve presentation of scatterplot options

    commit c4cbb939fdc4f0c0eb83e5a556895650974fb285
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Jul 5 14:26:46 2018 +0100

        Simplify code for file format recognition

    commit 0f976abc5570ae7407fdd0ea19af92ee62a15f13
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Jul 5 14:09:37 2018 +0100

        Improve group creation and manipulation

        - Greatly improve speed at which a big file is marked as incorrect (by loading just the first row instead of the first six rows of a file...)
        - Fix error alerts not appearing when trying to create groups based on invalid parameters
        - Add error alert when trying to load file without group information when such data is expected
        - Improve style of group preview table

    commit 864fd363e59a050aa89f5dc614c207d130d998a0
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Jul 5 11:45:03 2018 +0100

        Fix unit tests for parsing splicing events

    commit cd795942df7123e959bef96c36c03a0c8d956b4c
    Merge: cb459489 0aac8a4d
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Jul 5 00:11:41 2018 +0100

        Merge branch 'master' into dev

    commit cb459489889a9f185d4b15ee792bb3cd6becf05f
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Jul 5 00:06:35 2018 +0100

        Minor changes

        - Copy-edit NEWS
        - Change order of analyses (makes more sense this way)

    commit 09c0622f25d775e282d415c20a0bdb828a5669bb
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Jul 4 18:18:57 2018 +0100

        Display alternative splicing events in transcript plot

    commit 0aac8a4d1f5f9e3352612a1d3b901faacc7723b7
    Author: Nuno Agostinho <danielagostinho@sapo.pt>
    Date:   Wed Jun 27 17:21:32 2018 +0100

        Travis-CI and AppVeyor fix (#360)

        * Fix issues with GenomeInfoDbData and DelayedArray installation in AppVeyor
        * Use binary packages to speed up Travis-CI builds

    commit 47cd9d40d6b374ad1ffd5f397a4b7920bd4fcf4c
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Jun 26 18:58:47 2018 +0100

        Fix issues in R CMD check and BiocCheck

    commit 9de9492c581732f7cfd296f9f44478eb4b7cf699
    Merge: 92236436 30ff9e8a
    Author: Nuno Agostinho <danielagostinho@sapo.pt>
    Date:   Tue Jun 26 17:45:49 2018 +0100

        Merge pull request #359

        Version 1.6.1

    commit 30ff9e8aa73036e42a2a0203de606787729574fc
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Jun 26 17:40:46 2018 +0100

        Rollback to before introducing event-wise Cox models (re-think if this is the best solution or not)

    commit 36d3163410f32578a195eec7d204d6334ddcbe65
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Jun 26 17:02:34 2018 +0100

        Improve data grouping

        - Preview groups based on selected attribute before creation, closes
        #218
        - Correctly suggest how to select variables in subset expression and
        give more examples on how to use this feature, closes #220
        - Fix subject/sample attributes not being updated for selection for the
        GREP interface
        - Minor copy-editing

    commit dfdcb3fdfb06591c0a050e22bbdac8d1fef33f9e
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Jun 26 16:59:31 2018 +0100

        Update NEWS

    commit 5de4ee0251eab26e9f205d793190dec57f2aed4a
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Jun 25 16:26:12 2018 +0100

        Recommend installing psichomics through BiocManager

    commit 2a9f6ab5820cb39fffbb470a1b92e20a635ce394
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Sun Jun 3 23:26:17 2018 +0100

        Fix error if named samples are given

    commit b3cd480ba9acd37f5948be7532f5923ab6fbc335
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Sun Jun 3 15:47:28 2018 +0100

        Minor improvements

        - Improve display of filtered genes
        - Update default minimum samples used based on available samples
        - Render position of splicing event when plotting transcripts

    commit a155800df9380649e461bbd5aa8d0bbe8711d451
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Sun Jun 3 15:20:07 2018 +0100

        Improve support for loading custom data

        - Prepare gene and junction quantifications (STAR output) and SRA metadata to be loaded into psichomics
        - Add tutorial on how to analyse SRA and user-owned data
        - Update other tutorials
        - Fix data not being loaded when fread returns a warning related to issues with previous fread commands

    commit fb347b1842f935e9251f60f1cf8d8c4ff5131e1a
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Sun Jun 3 10:33:20 2018 +0100

        Fix warning when using deprecated function limma::toptable

    commit a79e15837ca633766d0397432f1704ecd1de30ae
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Sun Jun 3 10:30:14 2018 +0100

        Fix crash when quantifying splicing for a single sample

    commit ba626a461dbdc236499392d798564c3b53a04eac
    Merge: caa07c20 9c1b3da2
    Author: Nuno Agostinho <danielagostinho@sapo.pt>
    Date:   Sun May 20 16:49:14 2018 +0100

        Merge pull request #356 from nuno-agostinho/recount2

        Add support for recount2/SRA data

    commit 9c1b3da2306a4a60b3f97c5a0fe6e54262f4f50e
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Sun May 20 16:40:48 2018 +0100

        Minor improvements

        - Bump version
        - Update NEWS
        - Fix issues with R CMD check
        - Hide close button in progress notification

    commit 203a0fd493387983ce8f50caa2cf9118b62f0d7f
    Merge: 6702d93c 32213531
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Sun May 20 15:54:53 2018 +0100

        Merge branch 'recount2' of https://github.com/nuno-agostinho/psichomics into recount2

        # Conflicts:
        #	R/data_recount.R

    commit 6702d93c929e7818ec2a8f992936032d583f5dee
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed May 16 14:46:22 2018 +0100

        Load SRA data using recount R package

        - Load gene expression, junction quantification and sample metadata from SRA projects
        - Update documentation (including copyediting)
        - Improve hg38 splicing annotation

    commit 3221353188fa26be22296c0fa596efa5040e8c6b
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed May 16 14:46:22 2018 +0100

        Load SRA data using recount R package

        - Load gene expression, junction quantification and sample metadata from SRA projects

    commit b22a2ca081d095d87fd7581f6a9384f6575ed6f3
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu May 10 15:18:36 2018 +0100

        Minor revisions to survival

        - Add link to survival page from Cox regression results withing the table containing the results from exploratory differential splicing analysis
        - Use minimal p-value to decide the optimal PSI cutoff (makes more sense)
        - Improve p-value plot, including labelled line with the p-value threshold and
        - Minor copy-editing

    commit d0304ffd165e31e25cc665c3067db3877b4a5b4c
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue May 8 15:29:57 2018 +0100

        Perform event-wise Cox models using PSI values

    commit 20e84802e4827d7161276129577bd2fcc626b08a
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue May 8 15:10:34 2018 +0100

        Fix crash when inputting non-sense as the axes for the splicing scatter plot

        For instance, discard:
        - Non-numeric values
        - Numeric values when min > max

    commit f3645f0247f8e01f6e5873f09ac8c765fe3904d3
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue May 8 14:51:32 2018 +0100

        Allow to start app with test data (for dev purposes)

    commit caa07c20f35289f48fdf0deeecd3f8437a16bbb6
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Apr 12 14:17:41 2018 +0100

        Fix TCGA sample metadata not showing samples from all junction quantification files

    commit 2fa6cf42035a2c62fd03fd910a9d5fbf203d834a
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Apr 12 14:15:29 2018 +0100

        Fix TCGA sample metadata not being shown when loading TCGA files from local folder

    commit 92236436b040442b484060209e959af947d76503
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Apr 4 16:29:05 2018 +0100

        Bump to version 1.4.5

        - Update NEWS
        - Add links to original article in bioRxiv
        - Update package description within the GUI
        - Update mentions to NMorais Lab and iMM
        - Update copyright years to include 2018
        - Minor copy-editing

    commit b4d0e8748a3160e6838b6f68bc2a11795be92de2
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Apr 4 15:30:06 2018 +0100

        Copy-edit GUI tutorial

    commit b25b9124e57cf2758b710e980e1dde74f30b4a66
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Apr 4 15:16:38 2018 +0100

        Replace dataset no longer distributed with car package with a built-in R dataset

    commit a09c8ee50a9ae185438c2b37e554ef9086a24655
    Author: Nuno Agostinho <danielagostinho@sapo.pt>
    Date:   Mon Mar 12 11:37:29 2018 +0000

        Update Contributor Covenant Code to version 1.4

    commit 58a1f137b2985b97d188f87e67f14437dec757f3
    Author: Nuno Agostinho <danielagostinho@sapo.pt>
    Date:   Mon Mar 12 11:35:17 2018 +0000

        Update README.md

        - Direct article link to the latest version available
        - Direct reference to original article (instead of references)

    commit 7783adb3be5bf6a1095a9f1cdc4b7fb899ba05ff
    Author: Nuno Agostinho <danielagostinho@sapo.pt>
    Date:   Mon Feb 12 17:28:12 2018 +0000

        Update README.md

    commit 584cce4cf4da01e3da5450c4ec889e15d3cb8ddb
    Author: Nuno Agostinho <danielagostinho@sapo.pt>
    Date:   Mon Feb 12 17:06:00 2018 +0000

        Update README.md

    commit 751e3f52c2539032b615c2e10e3d3fbb774e1455
    Author: Nuno Agostinho <danielagostinho@sapo.pt>
    Date:   Mon Feb 12 01:54:53 2018 +0000

        Update NEWS

    commit ccecd6b7c2a1164470fa3e23bec53a7f876c24be
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Feb 12 01:28:11 2018 +0000

        Fix R CMD check issues

    commit 26b3e0d375f4916ad2570f8421ab344286986e34
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Feb 12 01:13:08 2018 +0000

        Improve differential analyses

        - Fix highlighted events not filtering table for differential expression
        - Update selected gene in gene information according to selected
        splicing event
        - Select splicing events or genes for differential analysis
        - Set selected gene when performing survival analysis

    commit 5fef2819224bfc3cd3af6aefadc34cba94ca66d0
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Feb 12 01:06:45 2018 +0000

        Fix problems related with DT versions >= 0.3

    commit ac6dfae6e30064dd2f8ccf1aac9c1e58091ba676
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Feb 8 16:04:23 2018 +0000

        Update vignettes to include case studies

        - Correctly export required functions
        - Copy-edit documentation
        - Rank variable that most contribute to selected principal components
        - Update CITATION file to direct to bioRxiv article
        - Update information in welcome message
        - Show number of contained items for selected groups
        - Update authors and bump version to 1.4.4
        - Update .gitignore

    commit 882eb627227e20e61ce9b4379d493fa06c5820ae
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Feb 8 16:03:04 2018 +0000

        Fix optimisation problem when calculating optimal PSI cutoff for survival by extending search bounds

    commit 860ce90adea912abdaa7da6d775060748499e457
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Sun Feb 4 23:30:52 2018 +0000

        Select samples to be used for survival analysis

        - Automatically select primary solid tumour samples (if available) when using TCGA data

    commit 8c2cd8af6f5fff32f63174e0f3f459db9140df7e
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Sun Feb 4 13:51:55 2018 +0000

        Automatically set sample types as groups when loading TCGA data (GUI)

        - Fix potential issues when dropping matrices
        - Show groups after creating groups based on clusters

    commit 8311aa1488253356b25e7f98285fc4b18526e7e2
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Sat Feb 3 19:26:23 2018 +0000

        Improve gene expression pipeline (perform limma-trend by default)

        - Improve gene filtering
        - Copy-editing

    commit bace4ac2e6dcec6df18e3131ae7e94db95cd9773
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Sat Feb 3 17:58:24 2018 +0000

        Stratify patients for survival analysis based on optimal gene expression cutoff

    commit f55dcfbf6af1719efc8aff413bf0fd4624d17f72
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Sat Feb 3 15:00:13 2018 +0000

        Quantify AFE and ALE events through AS-centric and exon-centric methods

    commit 8451fe2aad4865b20cb35ecd548771326b31028d
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Sat Feb 3 14:41:38 2018 +0000

        Tolerate 5% of missing values for both PCA and ICA (by default)

commit 6b5f77d6f59186ce1084e92c9deb44198f9f6515
Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
Date:   Fri Jun 4 16:50:07 2021 +0100

    Squashed commit of the following:

    commit 4a6f72fdec02c7be120bd60845aed7112bfc0c75
    Merge: 5e58444d 15d5a462
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Jun 4 16:47:19 2021 +0100

        Merge pull request #425 from nuno-agostinho/dev

        1.18.2

    commit 15d5a4621e4b88316f7667cbdd80b8ec97dd0b85
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Jun 4 16:46:36 2021 +0100

        Bump version to 1.18.2

    commit b781bd868ec318caf3cdeb01f925b9642377af2d
    Merge: cb6c0347 caf4bbe7
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Jun 4 16:45:52 2021 +0100

        Merge branch 'dev' of github.com:nuno-agostinho/psichomics into dev

    commit cb6c03478d4484d221a26155193f745705eb1d70
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Jun 4 12:29:06 2021 +0100

        Fix issues with Bioconductor build system

    commit 5e58444d4202f4a3f872735541138d22ea55c1a0
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Jun 3 11:18:47 2021 +0100

        Update docker.yml

    commit caf4bbe7b433adbdd9ad04927f220dd5f0225dc1
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Jun 2 21:30:28 2021 +0100

        Update docker.yml

    commit be79fc80b7052f2e4734c427e2102bb3a045b515
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Jun 2 16:44:50 2021 +0100

        Fix issues with Bioconductor build system

    commit c585cecdc180a789d46cde82c5f52b3642a5d623
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu May 27 16:48:10 2021 +0100

        Fix link to Bioconductor Docker

    commit f25daead424f1abdb9587df8ca9521e859643a98
    Merge: 800a9497 b09a55ce
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu May 27 10:42:35 2021 +0100

        Merge pull request #424 from nuno-agostinho/dev

        Bump version to 1.18.1

    commit b09a55ce3133b85fa7d664dfcaa0c73b2025a61b
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed May 26 15:50:21 2021 +0100

        Bump version to 1.18.1

    commit a136b3277c7cd6345d09e0e5b182cbbbec341e35
    Merge: 4ed660dd 800a9497
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed May 26 15:43:58 2021 +0100

        Merge branch 'master' into dev

    commit 4ed660dd456eec62d194aa51054d52490f30fd23
    Merge: 7af5ed78 08d79a95
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed May 26 15:36:42 2021 +0100

        Merge branch 'dev' of github.com:nuno-agostinho/psichomics into dev

    commit 7af5ed7815f903863eca6be95ee75c7a54754c1e
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed May 26 15:36:35 2021 +0100

        Rename custom data tutorial

        - Minor copy-editing

    commit 800a9497227a2952a51962819840d4029f57a9b7
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon May 24 21:37:01 2021 +0100

        Fix Docker install instructions

    commit 3d89ab07e2870eedec3558c73cbc2ec9f041e18f
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon May 24 13:19:52 2021 +0100

        Use GitHub Container Registry

        - Release `latest` tag
        - Update Docker action versions

    commit 5ce0e06d24febbc6a000db17ab540b779f2c6c36
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon May 24 13:17:04 2021 +0100

        Simplify dependencies install in Dockerfile

    commit 31adf199ce9b5abde5f3cd5e51349848d832ce74
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon May 24 13:14:57 2021 +0100

        GitHub and Docker install instructions

    commit 08d79a95acdd38bca6367b2b35295e66c513aea8
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Sat May 22 17:29:58 2021 +0100

        Update README.md

    commit 72dd83cc5ffdce789cba11c17d09149032972ac1
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Sat May 22 16:01:24 2021 +0100

        Update docker.yml

    commit 02fa0bb25c07eb9b7d9660a00bf1cd3cd09b7433
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Sat May 22 15:58:00 2021 +0100

        Update Dockerfile

    commit 046ccaa16ccbb0196e83d13638bd637e82334e4e
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Sat May 22 15:57:17 2021 +0100

        Include cache in docker.yml

    commit 6b6eea05c1c25febfc53ca1229836fefe6b878e0
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Sat May 22 15:53:19 2021 +0100

        Update docker.yml

    commit b4dfaa5c8bec6e5bee8c13bb88227ce89c895be5
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Sat May 22 15:52:27 2021 +0100

        Temporary test

    commit b0ed55070f7225db992becd6eab75cf15951cac9
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Sat May 22 14:46:56 2021 +0100

        Update docker.yml

    commit 729c0ec030f8301fa1dd87d0ab13fd81a97b1566
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Sat May 22 11:42:24 2021 +0100

        Update docker.yml

    commit c72aa7cb9ec3f4cb83d2a1b5a7faaaa12bdb2145
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri May 21 15:50:44 2021 +0100

        Simplify Dockerfile to the bare minimum

    commit 409d56b0289259d2aa6405dd5cb77d6b983176f2
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri May 21 15:16:34 2021 +0100

        Revert to working docker.yml with new registry

    commit 247013fb0d49dab26cec19d1f3d8eb43bb0de622
    Merge: 09d3d385 debcc26e
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri May 21 15:08:48 2021 +0100

        Merge branch 'dev' of github.com:nuno-agostinho/psichomics into dev

    commit 09d3d385a633832b71391aeb006aa0f97f6c1ec9
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri May 21 15:08:42 2021 +0100

        Fix spelling issues

    commit debcc26e145239d23368ab36ed8ad5d6995ad1df
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri May 21 11:54:40 2021 +0100

        Update docker.yml

    commit 7bdfbd87b2579f5d63f5b7cdae0e6f44723f7c49
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri May 21 10:43:13 2021 +0100

        Update docker.yml

    commit fd6dd049b71f72d21f6ac3a899574137697eada9
    Merge: b5380673 ba7412e1
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu May 20 19:22:09 2021 +0100

        Merge pull request #422 from nuno-agostinho/master

        Update dev from master

    commit b53806731c44ff936b200238e00375023da76dd3
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu May 20 18:51:51 2021 +0100

        Update docker.yml

    commit ba7412e14ae3aac94fa6bb70e404db554bcace7c
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu May 20 18:16:45 2021 +0100

        Update check-bioc.yml

    commit 95ca4df14220a184de1b4c713fbe4712143028ce
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu May 20 16:58:50 2021 +0100

        Update check-bioc.yml

        Update usage of environment variable

    commit ff60092684c225f8da7daa5ca74d61eda8ffc851
    Merge: 3c039cf6 32205d23
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu May 20 14:48:47 2021 +0100

        Merge pull request #421 from nuno-agostinho/dev

        Dev

    commit 32205d23dd284807e79c26e65c68a095e6d87cd6
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon May 17 20:23:41 2021 +0100

        Avoid problematic unit tests in Bioconductor

    commit 2e7b506736eb923a4ea6229f58b3464f731cd205
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon May 17 12:48:38 2021 +0100

        Update NEWS.md

    commit 08302a37027e18169519859fa435014b25a5987f
    Merge: e2f0ae2c 3c039cf6
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu May 13 17:35:12 2021 +0100

        Merge branch 'master' into dev

    commit e2f0ae2c838d418bfc01245afcaf8f7d9eb62bf5
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu May 13 17:24:49 2021 +0100

        Bump version to 1.18.0

    commit e5003caf9a98ab9981e0c8c02448d232ebf6f9e2
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu May 13 17:24:34 2021 +0100

        Fix issues with R CMD build/check

    commit b846abece509ea86a1998f8bd5bc31eeba16ef81
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu May 13 16:18:43 2021 +0100

        Update documentation and resolve minor issues

    commit 445dacade2d8745957b2a42dbc5663159f98861b
    Merge: de048440 2ea05d6f
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu May 13 15:38:38 2021 +0100

        Merge branch 'dev' of github.com:nuno-agostinho/psichomics into dev

    commit de048440a477c16339030886703ac2d1f9417021
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu May 13 15:38:19 2021 +0100

        Fix `plotDistribution()` for listed groups (e.g. in the CLI tutorial)

        - Fix issues with unit tests

    commit 2ea05d6f66a31aadc63fd81efbaab2e4d655734b
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu May 13 14:09:56 2021 +0100

        Avoid using set-env to set environment variables

    commit 2e536f9e4573549df3a1af7f5b0991e2aec7364b
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu May 13 13:45:23 2021 +0100

        Only animate spinning wheel when effectively loading data

    commit a9362fe77814ff22f8b092fd4a804becc2f8bc81
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu May 13 13:29:26 2021 +0100

        Improve plotting of AS events

        - Allow to use `plotSplicingEvent()` directly with a PSI table
        - Improve support diagrams for IR events
        - Fix IR diagrams in distribution plots not displaying introns
        - Fix parsing of VAST-TOOLS IR events as SE for certain annotations
        - When searching particular splicing events, fix results based on the wrong genomic coordinates
        - Fix other AS events display in Y axis for distribution plots
        - Minor copy-editing

    commit 283e137bcca44e07a451296dab8c44655184748b
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue May 11 19:28:03 2021 +0100

        Improve distribution plots

        - Allow to invert axes
        - Avoid redundant code
        - Render event diagram based on axis containing PSI distribution values

    commit 0e9e88251500d9d4a063d641240090b118ef3be2
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue May 11 13:01:27 2021 +0100

        Suppress snapshot date message

    commit 5dd040a4800f71e4bc93ca86b4fb45d1d58ffc64
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon May 10 19:28:24 2021 +0100

        Minor improvements

        - Place distribution plots on top of event diagrams
        - Timeout GTEx data retrieval after 3 seconds without server response
        - Avoid unnecessary messages when loading Firebrowse interface
        - Avoid "Matching subjects to their samples/Matching process concluded" loop

    commit 28b2c303bad579cd2a25093bb9f0388a4150991a
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon May 10 19:18:53 2021 +0100

        Support gene symbol conversion for any species with OrgDb

        - Remove 'org.Hs.eg.db' dependency
        - Allow to select OrgDb species to use for gene symbol conversion
        - Minor code copy-editting

    commit efb0bd138e1abb07cab0034bab8bca749f860b91
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Apr 8 11:00:36 2021 +0100

        Bump version to 1.16.1

    commit 74cc2347872c24788419a3ccb96b3ec7851b53c6
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Apr 8 10:59:49 2021 +0100

        Fix parsing of VAST-TOOLS intron retention events as skipped exons

    commit d651dd530ea5e05e987b7f12f342de4dda51d5f8
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Feb 19 13:37:06 2021 +0000

        Improve distribution plots

        - Allow to plot violin and box plots
        - Hide rug plots with 500 or more values (by default) for performance reasons
        - Add jitter to rug plot (helps to discern multiple numerous points)
        - Display IQR per group in tooltip
        - Easily add subtitles to distribution plots
        - Avoid redundant code
        - Reorganise code

    commit 3c039cf6f68722e0a1def624c607aca18c8910ec
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Nov 23 12:33:22 2020 +0000

        Fix setting environment variable

    commit a6feeadad42e93163d6614d1fb89a50ac5f30faa
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Nov 23 12:05:11 2020 +0000

        Avoid bioc-devel while R-devel is not available

    commit 35b2cc0dcb02e20eacd1a4a8c2594945cd1322fd
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Oct 9 18:35:05 2020 +0100

        Fix comments in bash commands

    commit f159bdc8ea2800c6482e439ea8f495575b52db1c
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Oct 8 14:50:53 2020 +0100

        Fix unit test function

    commit bdc246c1708d7ed3957cf74bd830467c42ab9f23
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Oct 8 14:19:13 2020 +0100

        Move unit tests to correct folder

    commit 87344cdc4a8e92eb6a3fa3c0857cd7e559986e01
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Oct 7 15:26:06 2020 +0100

        Minor changes

        * Warn about discarded events when quantifying/loading PSI data
        * Print elapsed time of loading local files
        * Improve verbosity when quantifying or loading PSI values
        * Add dev/ dir to add files of interest to the project
        * Copy-edit CLI tutorial, code and documentation

    commit 37f209a0799b21c71faffb6c21c101f115c27ba0
    Merge: a84aeb84 13b0d736
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Sep 25 18:41:27 2020 +0100

        Update NEWS from origin

        Merge branch 'dev' of github.com:nuno-agostinho/psichomics into dev

        # Conflicts:
        #	NEWS.md

    commit a84aeb84b669683aa20fddc20852b9599cc0b845
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Sep 25 17:39:49 2020 +0100

        Improve performance of `discardLowCoveragePSIvalues()`

        - Move reusable `progressBar()` C++ function to header file

    commit 15c4e2712d424ce0e3835e30fbf8c6be1c77fda8
    Merge: 3cfc873d 13b0d736
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Sun Aug 30 12:52:54 2020 +0100

        Merge pull request #415 from nuno-agostinho/dev

        1.14.4

    commit 13b0d736d14f623658fffad4da31be115624dee4
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Sun Aug 30 12:52:12 2020 +0100

        Update NEWS.md

    commit 358819f2127b3340d2624489d06c1135f5808d50
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Sat Aug 29 17:15:14 2020 +0100

        Correct spelling

    commit 230f03f3e6704626e13d60417d340a1aa3adbe60
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Sat Aug 29 16:33:23 2020 +0100

        Improve file/directory browser dialog

    commit 18344b16cc4bcd251c9c01b23011e10b20750ffd
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Sat Aug 29 14:59:37 2020 +0100

        Improve file/directory browser dialog

    commit 989b5aac54dc7799b9f187349a901370b402beea
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Aug 28 18:54:44 2020 +0100

        Improve file/directory browser dialog

    commit e37c62c848e3dc0091076d7dd7894aa4f9fe62da
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Aug 27 15:13:58 2020 +0100

        Bump version to 1.14.4

    commit 1bb928810f71d63daf7ae3f840b6c59f06d79d8f
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Aug 27 09:18:27 2020 +0100

        Fix file browser dialog selection of single file in macOS

    commit cc63bdb5a69a6e0c9fbdd2cb860629a6bfec404c
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Aug 26 19:02:54 2020 +0100

        Improve data loading

        - Speed up loading of GZ and BZ2 files
        - Increase verbosity while loading files
        - Speed up loading of VAST-TOOLS' inclusion levels
        - Fix loading of VAST-TOOLS' inclusion levels sometimes returning an error regarding duplicated row names
        - Fix issues with missing values as alternative splicing event complexity in VAST-TOOLS' inclusion levels

    commit cae16fb330bf82aff77ac9b6beda26e4f5462519
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Aug 24 18:17:36 2020 +0100

        Copy-edit tutorials

    commit 3cfc873db5f20c82d408f71b0522f52d7c3bf2b4
    Merge: 0db81dd6 b766d090
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Aug 21 17:41:29 2020 +0100

        Merge pull request #414 from nuno-agostinho/dev

        Expect to contain "ensembl_havena_gene" in logic_name

    commit b766d0908894fb121a93ccb575037741e22967e8
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Aug 21 17:41:05 2020 +0100

        Expect to contain "ensembl_havena_gene" in logic_name

    commit 0db81dd670f572886d9398b38bbbea7f536e3400
    Merge: b31fc62a ed83e8a1
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Aug 21 15:21:00 2020 +0100

        Merge pull request #413 from nuno-agostinho/dev

        1.14.3

    commit ed83e8a169ccaf55867e225c4e236ccd7aa1b232
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Aug 21 15:02:32 2020 +0100

        Bump version to 1.14.3

    commit 91198ec580ae300566c318391287d7e9540f83a1
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Aug 21 11:48:36 2020 +0100

        Fix upstream changes from Ensembl API response

    commit 339e0d6f658074fb96e9996014c8d9da84271d0c
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Aug 21 11:47:32 2020 +0100

        Run R CMD check regularly

    commit c04f25193841c87d7a9df28ad37bc4c7af682f97
    Merge: 548ae1f5 b31fc62a
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Aug 21 11:30:40 2020 +0100

        Merge branch 'master' into dev

    commit 548ae1f5984a6858b777a4dadc474b482bc44ca4
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Aug 21 00:33:07 2020 +0100

        Fix undefined global variables on renderBoxplot

    commit 616f2804081e240a1cedf920164015a178dfc998
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Aug 12 16:32:08 2020 +0100

        Fix incomplete final line

    commit f7f34ccde450d5666d2253c36e7436d350580771
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Aug 12 16:13:24 2020 +0100

        Pass codecov even with 1% of differences

    commit 21864c25fb5dc270d6f4d0eee9cf84aaf5a5d3e2
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Aug 12 15:17:15 2020 +0100

        Publish Docker images based on dev branch

    commit 278f77ebe6bc1b50861df5c6cad21d8f3b279609
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Aug 12 10:05:50 2020 +0100

        Minor copy-edit

    commit b31fc62a23d4a2eeb8f993baa0cadce22d3b89b1
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Aug 12 01:29:36 2020 +0100

        Avoid publishing Docker image on master push

    commit 75706aac561c5cee7e2bccb911187e7a78940df1
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Aug 12 01:26:33 2020 +0100

        Update README.md

    commit f9d0f85e50aae13d81e4394d4c85d60c35fa60b1
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Aug 12 00:24:03 2020 +0100

        Fix pkgdown deployment

    commit 96942cc2abc3e3bd8a835c0f0807be8cd13a96f1
    Merge: 49ca4891 14364a71
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Aug 11 23:26:58 2020 +0100

        Merge pull request #412 from nuno-agostinho/dev

        1.14.2

    commit 14364a719e271169cc4198cdf66974cb06606d2c
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Aug 11 21:49:36 2020 +0100

        Fix unit tests for VAST-TOOLS' data loading

    commit 40d7f93c716a914200f456c12d4013234721975b
    Merge: 31fc5ac5 140ab018
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Aug 11 21:01:28 2020 +0100

        Merge branch 'dev' of github.com:nuno-agostinho/psichomics into dev

    commit 140ab01862eb4e021430593492a0799a0f3c6333
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Aug 11 21:00:42 2020 +0100

        Update NEWS.md

    commit 31fc5ac577e056bee88e00c3565f29f2fab52291
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Aug 11 13:29:27 2020 +0100

        Improve loading of VAST-TOOLS' inclusion levels

    commit 48cc9ee5617d5a4b08e21ba7954b3e11eb719fd2
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Aug 11 13:27:58 2020 +0100

        Fix asking multiple paths in file browser on macOS

    commit cfa5ec8e6c08baf3374545828f59470038d7a2ee
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Aug 10 10:16:59 2020 +0100

        Table with supported file formats in psichomics

        - Include more information on manually loading FireBrowse and GTEx data
        - Reorganise information

    commit a3f81cfa4816ab3bdc1b3185a025d0a8d9d6a83e
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Sat Aug 8 23:19:54 2020 +0100

        Copy-edit NEWS.md

    commit 3f2a23257ed3f8735c8ea07e3f8f892378a7f80a
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Sat Aug 8 23:12:55 2020 +0100

        Publish Docker image in GitHub Packages

    commit 88b307d9598e608666281bd135c2b09ae3a92550
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Sat Aug 8 20:51:07 2020 +0100

        Fix VAST-TOOLS data loading unit tests

    commit 1977f5fe2f9038998c81577edbe0ecf745e43a39
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Aug 7 19:27:58 2020 +0100

        Test VAST-TOOLS data loading

    commit c56b728553c133747c685f7b1112555a6aa48a6e
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Aug 7 12:11:23 2020 +0100

        Fix testing expected error

    commit e751c549cfb39d44e4ff69891b94d7f3304c005e
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Aug 7 11:46:05 2020 +0100

        Fix returning only one data column for loaded data

    commit f4e6750492448d5bdd6193ada0c342cb0bf72c35
    Merge: 1301be60 23881204
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Aug 7 11:25:04 2020 +0100

        Merge branch 'vast' into dev

    commit 2388120475c3f585440dd15cc320863b6109ed13
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Aug 7 11:24:47 2020 +0100

        Replace CI tools with GitHub Actions

    commit d78cef99c576bc6922310245055b37a544cfe375
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Aug 7 11:22:39 2020 +0100

        Avoid using deprecated boxplot function

    commit 1301be607968ea9febcec01adba5dfa5873da8f5
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Aug 7 10:28:16 2020 +0100

        Avoid running interactive example

    commit 30a9b4786c606cf013d766b6a3d20538ab2c36b0
    Merge: 8d83c327 75748c4f
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Aug 5 09:37:29 2020 +0100

        Merge branch 'vast' of github.com:nuno-agostinho/psichomics into vast

    commit 8d83c327e7e37f4e4fc69ebbf9adff3d66724b34
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Aug 5 08:05:12 2020 +0100

        Minor copy-edit

        - Allow US spelling for normaliseGeneExpression()
        - Use cRPKM (singular), not cRPKMs whenever talking about the cRPKM dataset
        - Copy-edit CLI tutorial
        - Use Gene (singular), not Genes in calculateLoadingsContribution()
        - custom_data.Rm: Show usage of both gene read counts and cRPKMs in CLI

    commit 75748c4f9610e6aa078e1034dc0a2b5488f55025
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Aug 5 08:05:12 2020 +0100

        Minor copy-edit

        - Allow US spelling for normaliseGeneExpression()
        - Use cRPKM (singular), not cRPKMs
        - Copy-edit CLI tutorial

    commit 49d76fd13e0e57205efc684d3194a9eb67b14ae7
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Aug 5 08:03:09 2020 +0100

        Raise error (instead of capturing it) when perfoming PCA/ICA

    commit 03e69817e4dfe7bfbbf03d9e714c8e65cde0ffb0
    Merge: 2f41e2dd 1804e4f3
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Aug 5 01:06:16 2020 +0100

        Merge branch 'vast' of github.com:nuno-agostinho/psichomics into vast

        # Conflicts:
        #	R/data_geNormalisationFiltering.R
        #	man/normaliseGeneExpression.Rd

    commit 2f41e2ddc9aef85bbe70dc2424b3ba9d0f72df9f
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Aug 5 01:02:48 2020 +0100

        Replace label of `plotLibrarySize()` from "Gene expression" to "log10(library size)"

    commit 26beab6c7291874fa2fadeca79940017079fcea3
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Aug 4 12:24:35 2020 +0100

        Load both VAST-TOOLS' cRPKMs and gene read counts when available

        - Allow to load multiple datasets from a single file format by returning a list of data frames (for compatibility reasons, only return the first dataset unless explicitely requested otherwise)
        - All gene expression loading elements now support loading more than one gene expression file
        - Toggle specific statistics based on gene expression values when filtering
        -
        - Allow to change object attributes to unset attributes only
        - Improve gene expression documentation
        - Copy-editing

    commit 1804e4f38074cc9fb07a2db616f7c78e78f89fed
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Aug 4 12:24:35 2020 +0100

        Load both VAST-TOOLS' cRPKMs and gene read counts when available

        - Allow to load multiple datasets from a single file format by returning a list of data frames (for compatibility reasons, only return the first dataset unless explicitely requested otherwise)
        - All gene expression loading elements now support loading more than one gene expression file
        - Allow to change object attributes to unset attributes only
        - Copy-editing

    commit 868139d711321b01d291c9e6eacb8f5daff6fad6
    Merge: 364bbe0b 49ca4891
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Aug 3 11:57:18 2020 +0100

        Update with master and fix conflict

    commit 364bbe0bd4201884f093aee244667e0925d6bcbf
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Aug 3 11:30:10 2020 +0100

        Copy-edit

        - Keep event data on PCA results
        - Copy-edit welcome screen
        - Rename exported function `getSplicingEventInformation()` to `getSplicingEventData()`
        - Rename internal function `getEventData()` to `findEventData()`
        - Put group creation table preview above other elements in the page
        - Minor copy-editing code and documentation

    commit 68770871054fbe55172a3b7ebe683e37cf782002
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Jul 30 14:08:25 2020 +0100

        Copy-edit documentation

    commit a86b1bbd7b7a934767b413f51d7dfca26e8b8ac7
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Jul 30 13:54:35 2020 +0100

        Fix cognate genes when creating groups from differential splicing results

        - Change group title depending on creating group from differential splicing or expression results

    commit 2c2cbfdc5f19a4fd403f344736c75dfd3650d418
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Jul 29 19:14:09 2020 +0100

        Minor changes to visual interface

        - Improve groups interface, including larger margin between buttons when decreasing window width
        - Copy-edit text of GTEx tissue selection context

    commit 3ca2e456984732b1d3fbcde5e68d5e0829f71033
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Jul 29 17:43:55 2020 +0100

        Toggle individual parameters when filtering PSI data

        - Fix filtering settings not being reported after quantifying PSI

    commit 769e05e499d88cde8b892b93d7f7f3a9bb09229c
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Jul 29 17:06:27 2020 +0100

        Improve interface for group preview

    commit cde100637ec21e0ef51b05540ec5f1bde2bd367f
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Jul 29 11:53:19 2020 +0100

        Copy-edit custom data tutorial

    commit 231a81728c4145517d3abc2739faff64992c0076
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Jul 28 23:06:30 2020 +0100

        Improve group creation and correlation interface

        - Show an alert when there is no data to create groups
        - When creating groups by sample index/identifiers, suggest sample names not only obtained from sample information, but also from alternative splicing quantification and gene expression datasets
        - Fix suggested attributes and index/identifiers in group creation not being cleared when changing to datasets where such data is unavailable (thus showing the attributes/index/identifiers of the previous dataset)
        - Warn when selecting genes that are not available in the selected gene expression dataset (instead of crashing the app) when performing correlation
        - Avoid creating automatic groups based on gene lists when respective genes are not available
        - Rename RBPs to make it clear they are human RBPs
        - Minor copy-editing

    commit 8b018cc96486b55f95ff3f75c00382269607cded
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Jul 28 15:44:53 2020 +0100

        Preserve eventData for results from differentialAnalyses

    commit 916e3f257bd71754b6824811fd266b335410130f
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Jul 28 15:38:05 2020 +0100

        Copy-edit

        - Improve information on loading user-provided data and include it in the custom data loading tutorial
        - Improve function documentation
        - Copy-edit tutorials

    commit b4a187d34e2db7bea482648ec1d839b3c1f3029e
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Jul 28 11:02:56 2020 +0100

        Fix warning in Roxygen regarding link to unknown function

    commit 594df5196876340607c3ce0ecd94062706328d7e
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Jul 27 23:59:21 2020 +0100

        Fix issues in R CMD BiocCheck

    commit c16c21c691dc8dd40bd651d9a570efea0621ff76
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Jul 27 21:47:21 2020 +0100

        Fix R CMD check issues

    commit 671b9de8b6be89484540f15655695a052e454432
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Jul 27 21:17:01 2020 +0100

        Fix unit test issues

        - Fix plot distribution of single values
        - Fix wrong results when calculating fast row-wise stats of vectors
        - Fix error when quantifying splicing with no genes in the annotation

    commit 2ee32f8f8b25deb90bab250ae96f4d4dc53895fd
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Jul 27 19:35:36 2020 +0100

        Minor copy-editing

        - Replace icons for consistency
        - Improve vertical distance of primary buttons when window width is small
        - Avoid permanent progress bar after loading list of GTEx tissues

    commit 4ae464c767abd9b4a8c15d7a01200fd669f10912
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Jul 27 19:18:53 2020 +0100

        Fix issues with PSI filtering

        - Fix not filtering by event type events quantified via psichomics
        - Fix error when calculating stats for a single row containing missing values
        - Fix not being able to search for event types in selectize input

    commit a897e1f734a1c60ce7620f818be513959f79c6fa
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Jul 27 17:28:26 2020 +0100

        Fix not filtering splicing event (sub)types if stat filtering is disabled

        - Improve speed of filtering VAST-TOOLS by reordering steps
        - Improve filtering settings attribute
        - Copy-edit

    commit 06fb9cacdc5f74e0268536861d084842b6f1ef14
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Sat Jul 25 10:20:50 2020 +0100

        Improvements on parsing and directing user to differential page

        - Improve speed of joining all coordinates
        - Ensure groups are NULL when going to differential page from PCA loadings
        - Ensure AS events are correctly parsed by setting the alternative splicing quantification information when setting the event
        - Load test data with unparsable events
        - Correctly identify alternative splicing events: consider a string as splicing event if data's attribute dataType is "Inclusion levels"
        - Improve tooltips of PCA and volcano plots (loading plots now show cognate gene, event subtype and event position in tooltips)
        - Show AS event identifier at all times in the selectize event input and tables below volcano plots
        - Fix crash when there's no splicing event information
        - Copy-editing

    commit 850d2f7b2f27629b2276aae18f16817b5ac2fca2
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Jul 23 16:20:18 2020 +0100

        Improve PSI filtering interface

        - Filter by min/max individual PSI values
        - Discard VAST-TOOLS values based on quality scores

    commit 0cf47d34fc134ad02ec377317733d3e8b150228d
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Jul 23 14:02:36 2020 +0100

        Copy-edit documentation

    commit 6feb0f564baeb49857528bb7f685f3a39eac1756
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Jul 23 14:00:44 2020 +0100

        Remove redundant datasets from loaded data (ignoring attributes)

    commit fb0a764d4995dd34167af81be9cb1c813ade6802
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Jul 23 13:58:48 2020 +0100

        Correclty discard events containing only missing values

    commit eeb388ee789460220b0f4c214abef95ce2635811
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Jul 23 13:58:20 2020 +0100

        Fix VAST-TOOLS' IR-S event type not being parsed

    commit 4337b2452869d07fdb5ae47db7d8d413ad1d4ef9
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Jul 23 13:56:29 2020 +0100

        Vastly improve preparation of alternative text when there are no AS event diagrams

    commit 3b7414ee228b4502fc6ce9899729637a50d10392
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Jul 22 18:40:59 2020 +0100

        Improve filtering of PSI values

        - Discard low coverage PSIs from VAST-TOOLS
        - Allow to filter by event type or subtype
        - Use faster calculation of row-wise max and min
        - Improve code for row-/col-wise stats

    commit e8a0538af6cb0e523d73f59f51e0557854ce5021
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Jul 22 18:38:51 2020 +0100

        Get splicing event types from a given dataset

    commit 0c7b1fa05e2d707ce82d2c512ec38eab34b722ff
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Jul 22 18:37:20 2020 +0100

        Improve VAST-TOOLS file support

        - Support loading output from `vast-tools tidy`
        - Use ENSEMBL gene names when gene symbols are ambiguous
        - Correctly name RI events as expected in psichomics

    commit 17e5e2c819c3a99523066ccee1a86591f342516a
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Jul 22 18:32:12 2020 +0100

        Fix eventData passing from transposed PSI for dimensionality reduction

    commit 4be272d9bc5f531d68d5056b50fad6efcea08c6c
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Jul 22 18:12:04 2020 +0100

        Add exported function getSplicingEventInformation()

    commit adfc058c6ca8f0b2ad283e290a5f4b81ea1f20d3
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Jul 21 11:53:09 2020 +0100

        Improve calculation time of row- and column-wise statistics

    commit 0589f7a51f76de753fab53ad954c50f2845a6fea
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Jul 21 10:24:35 2020 +0100

        Improve consistency of function names

    commit 1e02261a0891870725ad2749528304d2ae4e8a9a
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Jul 21 09:36:36 2020 +0100

        Improve file loading and parsing

        - Import VAST-TOOLS gene expression data
        - Check if folder exists before loading files
        - Add verbosity to file loading functions
        - Return only TRUE/FALSE when checking file formats
        - Minor copy-editing

    commit 07addf93e43abf273be6596944d176bd71ba0e51
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Jul 20 11:42:28 2020 +0100

        Copy-edit NEWS

    commit 5567fcf5a6c19ba34c4b75f2d1c71425f52c260c
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Jul 20 11:42:14 2020 +0100

        Process psichomics PSI tables the same way as any other generic PSI tables

    commit b124bb55472c429167a5f63239a5739ee4458420
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Jul 20 11:39:26 2020 +0100

        Fix misc issues

        - Correctly parse AS events (major issue)
        - Try to put tooltip always on top of every element (still problematic...)
        - Avoid showing diagram in volcano plot tooltips if event cannot be parsed
        - Minor copy-editing

    commit 2ac31028e0d646c3a706c908688770bd82280920
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Jul 20 11:39:09 2020 +0100

        Fix suggested attributes in group creation not being updated when changing to datasets with no attributes

    commit b5605b22ce54ba396cfb54819c54b6d855982f0d
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Jul 20 11:35:50 2020 +0100

        Support SRA metadata automatically

        - Update user-provided data loading tutorial

    commit 0a6ef1ea0a509671a2fcc10d2483d1fadeb3f75d
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Sat Jul 18 14:17:52 2020 +0100

        Fix expected events type from a VAST-TOOLS PSI table

    commit d8d18f3ba2177cc1565f8a2d2245022106df5d65
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Sat Jul 18 13:59:25 2020 +0100

        Support loading PSI tables with arbitrary (i.e. unparsable) events

        - Expect warning (instead of error) from `parseSplicingEvent()` only when running in the R console

    commit 1d43fac671ca8e72872eb59f73c5fceece715dc5
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Sat Jul 18 11:12:24 2020 +0100

        Use cache for inclusion level summary plots

    commit 0333d6e65c6df9391286504b7bee022c87c7f824
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Sat Jul 18 11:00:34 2020 +0100

        Minor improvements

        - Fix gene expression summary plots not showing in specific situations
        - Fix legend not hiding in plotRowStats
        - Minor copy-editing

    commit 796838fe55a3f30ce877350526af91f0dd23ecf9
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Jul 17 16:55:43 2020 +0100

        Alternative splicing quantification filtering

    commit b66f2d762dc6cbcb0bcffe044de207767bcf68ee
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Jul 17 16:51:02 2020 +0100

        Avoid leaving missing values in type when there is subtype information

    commit 7787bd2caa9a73da856d624dcb1af3a38048cac1
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Jul 17 15:35:23 2020 +0100

        Improve data loading visual interface

        - Discard file browser input selection
        - Show helpful context messages in panel interfaces
        - Minor copy-editing
        - Avoid re-matching subject to their samples

    commit d076540dec323a59e38e17d2684e37226b4fb62c
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Jul 17 15:29:01 2020 +0100

        Use fan as loading icon for AS event selectize element

    commit b41f94365b0754e95f905c600ae1d7dc19224906
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Jul 2 17:46:01 2020 +0100

        Improve gene annotation page

        - Persistent user tags when querying PubMed
        - Allow to select more species/assemblies and freely add more
        - Fix no AS event plot diagram in information
        - Minor code copy-editing

    commit 0fc04c8c5df2501789d5f0553dd68dcfc5c816ad
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Jul 2 13:57:12 2020 +0100

        Fix rug plots in the middle of density plots

    commit c2e1d5babcfd4ca370ec70f85064773c4e89f3f1
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Jul 2 13:43:00 2020 +0100

        Use group colours in density plots of differential expression table

    commit 9d1ea065b6a16820965b0e3ae1dea7ae81b31910
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Jul 2 10:24:59 2020 +0100

        Improve differential analyses and other fixes

        - Correctly set splicing event when clicking in PCA loadings or in differential analysis table
        - Remove deprecated psi argument from diffAnalyses
        - Avoid plot issues with plot titles
        - Avoid errors when parsing event ID
        - Correct issues when plotting event diagrams in information
        - Copy-edit code and minor changes

    commit 4b1c028128094288811c0eeaffa437f9f9e59ab5
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Jul 1 19:29:18 2020 +0100

        Allow to search using an event ID directly

    commit 623951ee40cc71090debea80b18cf45e47a938fa
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Jun 30 23:28:45 2020 +0100

        Improve volcano plots' tooltips

        - Fix tooltip position
        - Include diagram of AS event

    commit 4d7fff2fe3a0b849dba599cd184ee0dc79fd887b
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Jun 30 17:06:20 2020 +0100

        Improve relevance of PubMed article results

    commit 1f4ff7e5d6e01659afaffab9c6aa79bd9ab5ed30
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Jun 26 20:13:10 2020 +0100

        Fix crash when changing to a PSI dataset without selected AS event

    commit 16aab679e2b369a2d38baf9b3cdfce0528d93604
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Jun 26 20:10:57 2020 +0100

        Improve "gene, transcript and protein information"

        - Select species and assembly directly in annotation (automatically picked based on loaded datasets)
        - Suggest genes based on loaded datasets

    commit 105a405b3af2c15453ff58b48259aa5144fa70df
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Jun 26 13:28:25 2020 +0100

        Fix issues with plotting VAST-TOOLS A3SS and A5SS events

        - Improve searching AS events in AS event selectize, including unhighlighting search results when no query is typed and avoid including SVG code (from diagrams) when searching for AS events
        - Avoid plotting AS event regions if events could not be parsed
        - Copy-edit code

    commit 94c19167715f7acfa56a1e397a462e636584c49e
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Jun 26 12:45:59 2020 +0100

        Avoid searching SVG code from AS event diagrams

    commit a6c38080eb07cdad11c3688a05fbb08af4dac76d
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Jun 26 09:58:03 2020 +0100

        Fix plotting A3SS and A5SS events and always show full coordinates of unsupported diagram events

    commit 312c0b4ddb73880f176b93e9e896c06086953462
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Jun 25 19:11:03 2020 +0100

        Simplify group selection interface

        - Replace button to edit groups with a greyed out dropdown item, simplifying the design of the group selectize element
        - Copy-edit interface

    commit 3713216a46a2496f9317305b76f5547e9f6e6802
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Jun 25 12:28:23 2020 +0100

        Rename vignettes

    commit 2107da0d81411a3b68c6796ae29dddad24206bde
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Jun 25 12:27:25 2020 +0100

        Fix progress bar not animating

    commit d0498355caa2bfd90d3cbb8f54791f6fc5de4a38
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Jun 24 15:46:43 2020 +0100

        Fix problem with geom_density_2d

    commit 2aa7fe5a22d783a55d413137d276dbb7a618cfb9
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Jun 24 15:43:55 2020 +0100

        Fix unexpected VAST-TOOLS types

    commit c32bf742128c44616c9c78479fccbc9878e38b8b
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Jun 23 17:33:45 2020 +0100

        Hide message about filtering gene expression

    commit f5ed4139e81a187e68745c6b054feb02ee3815f7
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Jun 23 16:45:15 2020 +0100

        Show loading indicator when searching for events

    commit bcf4b99ee598fd37db903c97594a5a77b889b5d2
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Jun 23 16:42:45 2020 +0100

        Improve printing of gene list object

    commit 5d38f45edab0f266e3de62b405c69aa9cd049512
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Jun 16 09:43:29 2020 +0100

        Allow to import VAST-TOOLS' inclusion levels table

        - Add attribute "rowData" to inclusion levels containing AS event information, allowing to parse and plot alternative splicing event identifiers from VAST-TOOLS
        - In the visual interface, if plotting is not supported for some event, show its full coordinates
        - Use attribute "rowData" when quantifying psichomics' inclusion levels
        - Improve gene parsing when quantifying splicing with psichomics
        - Create "sticky" objects to preserve their attributes even when extracting data
        - Rename "intron retention" to "retained intron" for consistency
        - Copy-edit code and documentation

    commit 49ca48915fca6612b372e6222fca1d1f75fa3922
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Jun 16 10:42:28 2020 +0100

        Fix unit tests for R 4.0 (#408)

        - Update required R version

    commit c3f588538530c7707c9a109fe821a1488abb1953
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Jun 12 16:56:18 2020 +0100

        Print AS event diagrams

        - Export functions to print AS event diagrams
        - Only print AS event diagram if possible (instead of table)

    commit 205a30a34f065a1227e46df636cb9ddf57d4030c
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Jun 3 22:59:31 2020 +0100

        Improve custom alternative splicing annotation

        - Include gene symbols in custom annotations if available
        - Support more flexible filenames for VAST-TOOLS, rMATS, SUPPA and MISO

    commit 4340f89b9af23a6dd1d47d604510e4b122fbc0ce
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Jun 3 13:31:49 2020 +0100

        Copy-edit NEWS

    commit 635ea7f799c4e572686ca959f3c7531a246a8776
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Jun 2 17:44:16 2020 +0100

        Fix settings not showing for alternative splicing quantification

        - Display filename of gene expression and alternative splicing quantification from recount

    commit 026ce50e441453d4dd0e19e9955b9aa81470b6d5
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Jun 2 10:52:51 2020 +0100

        Improve TCGA code

        - Copy-edit function names
        - Correctly take the most recent Firebrowse data

    commit dea5e14c85289cba3c9a22f9a33329d8a939b9a9
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Jun 1 12:16:45 2020 +0100

        Improve rendering of summary plots

    commit d49a5805bdfef5bd76a8a28bc861843cbc2d3752
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri May 29 17:43:57 2020 +0100

        Parse gene symbols containing underscores

    commit b179ec03939d22a80388765cc0ef576f008f322d
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu May 28 15:00:08 2020 +0100

        Copy-edit code and function documentation

        - Fix unit tests regarding changes in R 4.0

    commit 947ed62290a80b7cec9fed50b1e136e14dd4af74
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu May 28 14:43:29 2020 +0100

        Allow to create Docker images based on code revisions

        - Improve startup message to include psichomics version
        - Avoid unneeded functions that may mask other package functions (rowMeans and rowVars)

    commit c360449e0d364afc1b39e3184c2c3c8fa91be413
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue May 26 15:37:32 2020 +0100

        Create function `plotLibrarySize`

        - Fix library size plot not working properly
        - Improve function documentation of plotRowStats and minor copy-edits

    commit 19ab1733af38042a9df952faa59b70e778cb1d93
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon May 25 15:39:35 2020 +0100

        Fix file browser dialog not opening and warn about selecting mandatory GTEx data options

    commit 5d94ba4f7e5aabb58d762ee9531bd89f54b69857
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri May 22 16:06:56 2020 +0100

        Support GTEx V8 and older releases

        - Improve loading of GTEx data and local files

    commit dd4feaf7f443bce01109dbcb487a046e9043bf30
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Mar 31 15:51:58 2020 +0100

        Try to load cached AS annotations if a timeout is reached

    commit 97023f2a69897f86e2c446563f104b096d7bb287
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Mar 5 12:03:33 2020 +0000

        Fix HTML sanitization in popovers

    commit cf9fc483aa2267caa6b87690c0b22fb1f254c3ba
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Mar 5 10:56:27 2020 +0000

        When plotting density plots, hide Y axis when only showing their rug plots

    commit da7404c3a21434453055cddda867465852167945
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Feb 25 11:07:53 2020 +0000

        Include search in pkgdown website

    commit e0df41302b0dceb0e55ba982b400bb804a72454e
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Feb 7 14:28:45 2020 +0000

        Include search in pkgdown site

    commit 2ae72bf49708a8d63f4ae8ecb435b9893d1b5ad4
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Feb 4 14:16:32 2020 +0000

        Simplify Travis CI config

        - Include link to GitHub page in pkgdown site
        - Fix warnings from Travis CI config validator
        - Use Linux with bioc-release for code coverage and
        - Start code coverage and deployment as soon as possible

    commit a9bb71aff254442561f5ae25d43596a50a9d2b02
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Feb 4 10:06:34 2020 +0000

        Minor changes to pkgdown and function documentation

        - Include link to GitHub page
        - Improve pkgdown reference
        - Copy-edit function documentation

    commit 8ea7f504b74a2c4a18f482e468421e846ac2a754
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Jan 31 13:59:34 2020 +0000

        Update pkgdown

    commit 27587d6647229f8ba513a60b8bad0ccbc7b0e7a4
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Jan 31 13:31:01 2020 +0000

        Copy-edit tutorial, NEWS.md and README.md

    commit 9d956f1685543ecae353c30257999375889b7dfc
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Jan 31 11:02:23 2020 +0000

        Fix warning of Unicode symbol translation in Windows

        R CMD check raises the warning: "unable to translate '<U+2206>' to native encoding". Column names are translated to native encoding if directly set.

    commit c7b18c7c55bdad08cc6f9d8b5841ea739be66d33
    Merge: 415a02f6 52f3b141
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Jan 30 13:14:11 2020 +0000

        Merge branch 'master' into dev

    commit 415a02f6eebed57472516438edf3f2dc87892f13
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Jan 30 13:11:44 2020 +0000

        Avoid Bioconductor warnings when comparing signed and unsigned ints

    commit 52f3b141d985ab2d2de50867953090fc4ed0ce9b
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Jan 29 21:50:46 2020 +0000

        Dev (#403)

        * Improve Travis CI

        - Run jobs through steps
        - Add words to spell checker
        - Test code coverage and deploy even if bioc-devel or macOS jobs fail
        - Only deploy on master branch

    commit d9bfab3374682ea450bdb41d4d34e5ea01cae899
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Jan 29 21:31:31 2020 +0000

        Only deploy on master branch

    commit d4a68aaeb9e3aa255152f5ab016c4cbbe693520e
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Jan 29 19:04:44 2020 +0000

        Add newline

    commit 002dd77093673121994dba9db00e49a9205beb56
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Jan 29 19:02:48 2020 +0000

        Test code coverage and deploy even if bioc-devel or macOS jobs fail

    commit e20bf5344b947aa74a7c14836cb55a7d2cd017ac
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Jan 29 19:01:45 2020 +0000

        Add words to spell checker

    commit bb6fa2cf973f794d5d9ee2b21767bf14cb7fbde4
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Jan 29 18:16:32 2020 +0000

        R in Windows still not supported at Travis CI

    commit 3cb8dcdc1786559c3ae83b3d931a94ca11819395
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Jan 29 18:13:18 2020 +0000

        Improve Travis CI

        - Test on Windows
        - Run jobs through steps

    commit bfb6318485cf3216c93b0ccfedb10a6cd93ebf41
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Jan 29 15:40:34 2020 +0000

        Update NEWS.md

    commit b4e13768bb28355901c8ec0c50785ff11493200e
    Merge: 8e5fc8aa 1b6fc0da
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Jan 29 15:35:51 2020 +0000

        Merge pull request #402 from nuno-agostinho/dev

        Improve usage of pkgdown site

    commit 1b6fc0da6070527caf29c9eee97c556ce7c3257f
    Merge: 98996ded 8e5fc8aa
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Jan 29 15:34:51 2020 +0000

        Merge branch 'master' into dev

    commit 98996ded5f67ffdb9b329f5b11467c6c344a7b92
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Jan 29 10:38:36 2020 +0000

        Improve usage of pkgdown site

        - Include links to MiMB chapter
        - Replace vignette links from RPubs to pkgdown
        - Direct to quick reference instead of listing
        - Update license to current year
        - Copy-edit welcome message

    commit 8e5fc8aa362f97fd97156ad46ff3cc317fc0b919
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Jan 29 00:21:19 2020 +0000

        Revert last commit (did not solve Travis issues)

    commit 64919795f1ebf9111aa2c2c82ef10da3e56f9490
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Jan 28 23:48:48 2020 +0000

        Set up SSH keys between Travis CI and GitHub

        Following tutorial on: https://github.com/alrra/travis-scripts/blob/master/docs/github-deploy-keys.md

    commit b0ce9cf85a1541909f6043072d00639418af8758
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Jan 28 18:54:08 2020 +0000

        Ask for verbose deployment of pkgdown site

    commit 0a9c9d2c59348c90591edb3e4233d0df25cf9bbc
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Jan 28 18:16:18 2020 +0000

        Import shiny::fluidPage

    commit 82767daa06239159bf7a2e9febc5688d0369e681
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Jan 28 17:16:18 2020 +0000

        Fix AppVeyor using release version of R

    commit ab0189024fde749153c28982ae86a7dfc803c35d
    Merge: c2cd46b2 bdc1e3c9
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Jan 28 17:07:55 2020 +0000

        Merge pull request #401 from nuno-agostinho/dev

        psichomics 1.12.1

    commit bdc1e3c90cd8ac7fb70acafb04d0989c608d8c1a
    Merge: 7f1a9834 c2cd46b2
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Jan 28 17:05:42 2020 +0000

        Merge branch 'master' into dev

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    Merge: 27b677b4 7c933a20
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Jan 28 16:55:10 2020 +0000

        Merge pull request #400 from nuno-agostinho/imgbot

        [ImgBot] Optimize images

    commit 7f1a9834e8faaed78558eb56fb05461f2d07dec9
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Jan 28 16:29:48 2020 +0000

        Avoid test failure by skipping it on CI tools

    commit e23f89dae16a1f10f627a560795d0a43127abe23
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Jan 28 15:02:03 2020 +0000

        Minor changes

        - Fix unit test issues
        - Fix error when using `plotDistribution()` for a single value
        - Copy-edit NEWS.md

    commit 475b712449f5db139901453e85356ebdf74b228f
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Jan 28 14:38:35 2020 +0000

        Browse list of AS event diagrams

    commit e038ea32fc8c01066d7117ffa40cd3b89afe35f7
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Jan 28 14:37:40 2020 +0000

        Filter AS annotation list

    commit f7477f5e51ee57e7c67fd9f9bdfdf8eae04a9184
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Jan 27 23:57:32 2020 +0000

        Fix issues with R CMD build/check

    commit e3c650251cdf2023ea275d6b897ccba2331995d6
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Jan 27 21:34:13 2020 +0000

        Correct spelling issues

    commit 983944d3b0cf7f975021b81700d6efc9804c5551
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Jan 27 21:22:59 2020 +0000

        Fix issues with taking into account another exon as reference

    commit ce61e2c7ecf183ce11be7284d9b7acdaca3b605b
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Jan 21 17:18:25 2020 +0000

        Fix UCSC external link not working based on gene position

    commit 38d61368a649e870f93d061d0fe5f24d96b8feb8
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Jan 21 16:58:51 2020 +0000

        Fix SRA project not loading if extra information fills only one extra column

    commit 4e4ebdd510d70ff8022dbd05e1a95b5c699d0164
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Jan 20 16:35:40 2020 +0000

        Show available annotation information and query PubMed even if Ensembl is down

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    Date:   Sat Jan 18 12:11:22 2020 +0000

        [ImgBot] Optimize images

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        /vignettes/img/pca_results.png -- 347.44kb -> 197.16kb (43.25%)
        /vignettes/img/NUMB_exon_12_inclusion.png -- 110.03kb -> 66.18kb (39.85%)
        /vignettes/img/UHRF2_exon_10_inclusion_differential_splicing.png -- 77.23kb -> 47.89kb (37.98%)
        /vignettes/img/UHRF2_differential_expression.png -- 170.04kb -> 108.91kb (35.95%)
        /vignettes/img/3_quantify_splicing.png -- 89.61kb -> 58.73kb (34.46%)
        /vignettes/img/5_pca.png -- 146.58kb -> 97.32kb (33.61%)
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        /vignettes/img/4_group_tables.png -- 64.14kb -> 45.53kb (29.01%)
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    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Jan 17 18:02:25 2020 +0000

        Fix tooltip colour when hovering rug plot points

    commit 6dc691bd1a13937d8b4775f2d5b6abc5d06f33a2
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Jan 17 15:38:06 2020 +0000

        Create pkgdown site

        - Copy-edit README, documentation, etc.
        - Improve alternative splicing annotation tutorial

    commit ac83c06f7f2950f6cb8762447f1fe35208bcfff1
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Jan 17 14:12:24 2020 +0000

        Add automatic spell checker and copy-edit documentation

    commit 8450709045cd166beefe3a4c19c37984a7fa1cae
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Jan 17 11:29:02 2020 +0000

        Minor improvements

        - Fix plotSurvivalPvaluesByCutoff example
        - Rename vignettes
        - Copy-edit CLI tutorial
        - Fix R CMD build/check/BiocCheck issues
        - Copy-edit function documentation
        - Add unit tests for SRA metadata loading

    commit 85c54c9e052ca61ad76c4d823046ab85ca091afe
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Jan 17 10:11:56 2020 +0000

        Add AS event diagram to distribution plots and annotation page

        - Avoid app crashing when searching for PubMed articles to many times

    commit 28ee94df2c70355fb76f71bb7748a799eaf20429
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Jan 16 13:07:32 2020 +0000

        Copy-edit NEWS

    commit e5ddf7c9e37160c77ba689f283dbf99562061442
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Jan 16 11:48:36 2020 +0000

        Fix R CMD build issues and copy-edit code

    commit 726a5adbbeb3db4f8d9eb53a21ed01764e887ccd
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Jan 16 11:48:03 2020 +0000

        Fix package dependencies

    commit 08555fabd4260d005c14cbd531e42b24271a43c0
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Jan 16 10:10:41 2020 +0000

        Fix: add code for subset plot

    commit 81f6f1174ad6339d34a7bae00ab8e7b9af9b94fe
    Merge: de9d66b5 94f39514
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Jan 15 19:41:12 2020 +0000

        Merge branch 'dev2' into dev

    commit de9d66b54ded617f41bf29a2dc60673a079939d0
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Jan 15 19:38:01 2020 +0000

        Remove unused function

    commit f2c47bdb34cd80c71d85cf82b506d5ff0f9d2358
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Jan 15 13:47:52 2020 +0000

        Improve data grouping

        - Improve import/export of data groups from/to a file, including colour support
        - Fix discarding of samples not associated with any subject when exporting groups
        - Fix issues related with importing groups based on a file with groups of splicing events and/or genes
        - Inform user when groups are successfully loaded from a file and whether any group elements are discarded in the process
        - Show number of genes in pre-made gene lists
        - When creating group of genes based on pre-made gene lists, discard genes that are not loaded

    commit 04b163d7f1c72f8ee713913db8b3f287079fbd82
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Jan 8 17:02:03 2020 +0000

        Copy-edit code and NEWS

    commit 20e61243055c4d63b32672bf3611f8b04bb2c258
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Jan 8 16:56:29 2020 +0000

        Fix slow preparation of diagram representations of AS events

    commit f9c74c8e4a69a9628d0166e8d8222efa619a7489
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Jan 8 16:50:33 2020 +0000

        Fix error when trying to set page_size for Firebrowse web API

    commit a379bb5798e60bc6e61c3cca34bbacb1e73b89fa
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Jan 7 11:29:06 2020 +0000

        Update documentation regarding survdiffTerms

    commit fa33d46c6f897ee868a1c8c5a1ceedef7a5ec837
    Merge: 1d7116ec 27b677b4
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Jan 7 11:26:13 2020 +0000

        Merge branch 'master' into dev

    commit 94f395143e5a5a4ef2d1075f97ed6854275e8b4a
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Jan 7 11:20:28 2020 +0000

        Fix 0 (valid) rows error

    commit 1d7116ecb67fdbfb43db06d78c23b9ca897e1f87
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Jan 7 11:19:29 2020 +0000

        Include reshape2

    commit f95f8e20c99ecd90fd35844f5f121025bd5f3222
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Jan 7 11:11:21 2020 +0000

        Diagram representation of alternative splicing events

        - Redesign AS event selection; highlight search results using jquery.mark.min.js (built-in highlighter has many bugs)
        - Rename internal CSS/JS files
        - Update jquery-template from 1.3.4 (2016-04-19) to 1.8.5 (2019-02-17)
        - Remove validator.min.js (not being used)

    commit 6806235f5404304cb749b6693cfbd87054acdbbf
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Jan 7 10:53:40 2020 +0000

        Copy-edit code and function documentation

        - Separate utils into different, related scripts
        - Update Roxygen to 7.0.2

    commit f58c252a9c739899ca4d9c4c9fa062fca939de1e
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Jan 7 10:22:14 2020 +0000

        Improve density plot

        - Fix visual bug when plotting a group with only one sample (if one data point is available for a group, only the rug plot is drawn)
        - After hiding all plot series, rug plots of the different groups can be distinguished based on the Y axis (different arbitrary Y values are given to each rug plot series)
        - Rug plot labels now show data values if sample names are not provided
        - Rug plot labels can now be rotated (rotation is not enabled by default given Highcharts issues that may occur at different zoom levels and depending on proximity between different sample values)
        - Fix misguiding example in function documentation

    commit 84f9ec3b0f69b8729c5c3176fb0cf7e66206cc0e
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Dec 20 17:41:20 2019 +0000

        Fix loading of a portion of TCGA data if too many cohorts are selected

    commit 91c46c3a69363d5d98b36a111b02dcc7d773c98b
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Dec 20 13:34:08 2019 +0000

        Improve function documentation

        - Include information on function family
        - Clean up documentation of aliases and deprecated functions
        - Change patient to subject where appropriate
        - Copy-edit CLI tutorial

    commit c569febbc2f8f77a8003f6c4b9dd6304db5d1bcd
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Dec 19 16:43:17 2019 +0000

        Fix issues with junction quantification files

        - Improve tutorial on loading user-provided data
        - Warn when discarding rows with duplicated rownames
        - Warn when discarding rows containing random, alt and Un (unknown) chromosomes
        - Fix error when returning NULL dataset after processing
        - Copy-edit code
        - Test junction quantification file loading

    commit 5fbc5bdc8ab3de2aec982a9b3c8febfe94809b5a
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Dec 17 15:08:42 2019 +0000

        Support junction coordinates from chromosomes M, Z and W

        - When loading custom junction quantification files
        - Copy-edit information on the format of custom files

    commit e4e8e918cd6b4830b31ed7b0a07abdb462481042
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Nov 7 14:46:07 2019 +0000

        Add ORCID identifiers

    commit 27b677b4d6929ab5a0690b3abc21a77077a13736
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Oct 7 18:18:58 2019 +0100

        Update README.md

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    Merge: 50ebb496 4550109a
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Oct 7 18:16:59 2019 +0100

        Fix Windows warnings in CI tools

    commit 4550109aac0d2180d44e45b01598f7552517c569
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Oct 4 13:49:29 2019 +0100

        Avoid using Bioconductor-devel (wrongly trying to use R-devel)

    commit 05dec272fdc65906c1c73c7e37e69eff1317cd3d
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Oct 4 13:45:19 2019 +0100

        Bump version to 1.10.2

    commit f403ca10dd6f9595af5e7ed534a6101efbb760d1
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Oct 4 10:05:40 2019 +0100

        Install r-lib/remotes from CRAN instead of GitHub

    commit 7f4ad886741271dc774ce750222dda1b0b03eb94
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Oct 4 09:59:53 2019 +0100

        Fix link to ggrepel::geom_label_repel not being found on Windows CI tools

    commit 50ebb4961783ce4751ef4b492c8428b837802a65
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Sep 19 13:13:38 2019 +0100

        Bump version to 1.10.1

    commit 2e2abe34478ccf8fb14d177f2ce0eeaae817996b
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Sep 19 13:04:23 2019 +0100

        Avoid test timeouts in CI tools and Bioconductor

    commit 3f3f8872b35e321f524599ae8913aa3ca4a40eaf
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Sep 16 19:20:58 2019 +0100

        Fix AppVeyor (#387)

        Install *org.Hs.eg.db* and *GenomeInfoDbData* packages via source (instead of binary which is unavailable)

    commit 6f41576364d55a3dd9a0299a78d08c8c3069c62a
    Merge: 8711c313 6d9f0824
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Sep 16 16:34:43 2019 +0100

        Merge pull request #388 from nuno-agostinho/travis-mac

        Support macOS testing via Travis-CI

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    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Sep 16 15:46:34 2019 +0100

        Support macOS testing via Travis-CI

    commit f912e3d65be79c9bd52e38e58cff285bd2d8cd94
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Jun 24 17:17:46 2019 +0100

        Improve dialog when trying to load a local folder without any supported files available

    commit 6f714d3578ce7a6d2f89a400f10907b6c88acc1b
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Jun 19 17:33:17 2019 +0100

        Improve GTEx data loading

        - Export getGtexDataTypes()
        - Improve available examples

    commit a1ca8d232ff76a824fd935f2690e4628d5cdfdba
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Jun 19 14:51:22 2019 +0100

        Fix alerts crashing the app

    commit e07766a3583da3c318be50eaa3477b9322a96658
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Jun 19 14:06:35 2019 +0100

        Improve AS annotation loading

    commit d0745def60c2469178b0341697c110b086497040
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Jun 3 13:54:24 2019 +0100

        Fix prepareGeneQuant not working for stranded datasets

    commit 4fc0ed6e3872a15a6091f5c656164be7fa806e77
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri May 3 14:05:13 2019 +0100

        Fix Firebrowse function not loading all expected data

    commit 8711c313fd02fb095c496a2b9242193d5d1e7b4d
    Merge: e87a817f 15236616
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Sun Apr 21 18:33:33 2019 +0100

        Merge pull request #384 from nuno-agostinho/evalWithTimeout

        Replace usage of deprecated function

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    Date:   Sun Apr 21 18:08:51 2019 +0100

        Replace usage of deprecated function

    commit b952a879b3bf23f3759312c86677ad8b0a16f764
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    Date:   Tue Apr 2 14:26:14 2019 +0100

        Fix p-value plot bugs

    commit e87a817f84eb88df17a3a4f53fef2b94e7a560c1
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Mar 27 16:20:05 2019 +0000

        Update .travis.yml

        Based on https://github.com/Bioconductor/BiocManager/blob/master/.travis.yml

    commit f15ab1875b318554d568022228f33a8a3e3def20
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Mar 27 16:16:02 2019 +0000

        Fix appveyor.yml

        Based on https://raw.githubusercontent.com/Bioconductor/BiocManager/master/appveyor.yml

    commit 3cf6a9b743356485fd354175173440fb270a35f8
    Merge: cad23d89 1f121b7a
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Mar 27 13:24:40 2019 +0000

        Merge branch 'dev'

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    Merge: db6c24f4 6ab7ab5b
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Mar 26 17:53:02 2019 +0000

        Merge branch 'dev-2' into dev

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    Merge: b91903c6 cad23d89
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Mar 26 17:52:17 2019 +0000

        Merge branch 'master' into dev-2

        # Conflicts:
        #	NEWS

    commit b91903c6b07bf50e1cbe67bf46b06343a39d9320
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Mar 26 17:51:23 2019 +0000

        Fix R CMD check and BiocCheck issues

    commit db6c24f4af2b371c061b96577479a59aca9097ce
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Mar 26 17:45:11 2019 +0000

        Fix R CMD check and BiocCheck issues

    commit 71e896c1c008fce02fbad5de282327816ef39a33
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Mar 26 17:28:24 2019 +0000

        Improve and fix function examples

    commit e29243d6e5d2783019182604c4ada9b96dba7582
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Mar 26 13:47:16 2019 +0000

        Fix issues in R CMD build/check

    commit db83ac6395086c9ab0d244fff1eced5734c41965
    Merge: 17e2fbd3 1deea8a5
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Mar 26 13:31:49 2019 +0000

        Merge branch 'dev' of github.com:nuno-agostinho/psichomics into dev

    commit 17e2fbd3026f133b864b60a08bbb742a373b2f53
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Mar 26 11:25:15 2019 +0000

        Fix issues in R CMD build/check

    commit 1deea8a5ceb0c77ff269cffe6e4762d205433468
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Mar 26 11:25:15 2019 +0000

        Copy-editing

    commit 1190319ef6dab35921c8fb3c9870a29c5befe51a
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Mar 26 10:04:36 2019 +0000

        Fix issues using EList's gene expression for correlation analyses

    commit d6ecc35918e88ce390a51026234c38824cd18581
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Mar 25 16:00:29 2019 +0000

        Code copy-editing

    commit 0fefbe1d1cc79a2c554321ef62af02ce37647cb8
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Mar 25 15:58:12 2019 +0000

        Make it clearer that TCGA data is loaded from Downloads folder by default

    commit 885ed2cc3315d2efaa7795679597f7b2e29f4810
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Mar 22 09:22:18 2019 +0000

        Plot p-values by cutoff

    commit 388aef18906d504e4edfef4294d8152935b63322
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Mar 22 09:14:01 2019 +0000

        Minor bug fixes and improvements

        - Allow to edit path in file/directory browser elements
        - Automatically set dropdown width for group attribute selection
        - Fix warning when displaying group preview only based on subjects or samples
        - Prepare for code escaping in newer JavaScript versions

    commit 37a0afa77baec0645d9378d24cd0acb57d1af1de
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Mar 21 15:11:35 2019 +0000

        Fix issues with R CMD check

    commit d1246e4b8322f3cce87fcacb76894dc2e34ccb56
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Mar 21 14:55:48 2019 +0000

        Require human gene annotation

    commit 87a2d3d83d46f2660576f905222a3c1df1638da7
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Mar 21 11:21:05 2019 +0000

        Fix table filtering based on plotted points

    commit 3cb42cf98e05b35bd2006ab9ae5f85833e707032
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Mar 18 15:43:04 2019 +0000

        Improve and fix plotting of gene expression and alternative splicing quantification data

    commit 1caf8bada79c40a23afb39422050550f2c9aae6d
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Mar 15 16:22:27 2019 +0100

        Plot specific combinations of gene and alternative splicing events after performing correlation analyses

    commit 387d63051f11ccee7856271f8369b38570b3d556
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Mar 8 14:24:35 2019 +0000

        Improve AS and GE filtering

        - Present PSI filtering settings in the visual interface
        - Minor interface tweaks
        - Fix plot PSI error

    commit 0a094a868e124e5ec115d1f5f3c169ae057fdafe
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Mar 8 13:45:24 2019 +0000

        Update citation details

    commit b6d0909be72ed3d54fabd3378aae050e14ec4082
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Mar 7 15:27:54 2019 +0000

        Allow to use selected splicing event in correlation analysis

    commit 1fb75cbb1f6de14bbcff49a1fa2ed1f942a0e3ce
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Mar 6 18:58:47 2019 +0000

        Fix error when subsetting edgeR::DGEList

    commit b0be91e288bab1d1a3f2917dc4ea0a917400382d
    Merge: 47bee247 76ba81ea
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Mar 6 14:50:34 2019 +0000

        Merge branch 'dev' of https://github.com/nuno-agostinho/psichomics into dev

        # Conflicts:
        #	NEWS
        #	R/data.R

    commit 47bee24752a09aae6052235133a41d5c30e71f14
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Mar 6 03:01:52 2019 +0000

        Minor copy-editing

    commit 972e5582a5cc7664a89542dc37edf926e7b27e65
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Mar 6 02:59:35 2019 +0000

        Improve correlation plots

    commit 25ece479739d264f1f86898a98b703b6355ffbe6
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Mar 6 00:36:02 2019 +0000

        Fix missing attributes of gene expression normalised via voom

    commit a949e3a91ad0a650c39a57e0351e9bae1f702b73
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Mar 6 00:34:12 2019 +0000

        Fix error when creating groups containing only samples and no matching subjects

    commit a063ae9c3e8485ec8321719898a43a2e1eced67b
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Mar 5 15:54:02 2019 +0000

        Improve GTEx and other data loading

        - Automatically download and load GTEx data
        - Only display at most the first 100 columns for performance reasons
        - Improve data loading titles
        - Default to load clinical, junction quantification and gene expression data when selecting TCGA data
        - Minor copyediting

    commit 76ba81ea5f6d3f13761ab733550daa2e703252bc
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Mar 5 15:54:02 2019 +0000

        Improve GTEx and other data loading

        - Automatically download and load GTEx data
        - Only display at most the first 100 columns for performance reasons
        - Improve data loading titles
        - Minor copyediting

    commit f344fc0607fdf20cf78e91ecaf4e40f8ff337493
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Mar 5 15:50:28 2019 +0000

        Fix article title formatting

    commit ad81788ad9241386b34349bb6d912824a7ff51e8
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Feb 28 11:57:54 2019 +0000

        Improve gene expression filtering and normalisation and PSI filtering

        - Plot distribution of gene expression per sample
        - Plot distribution of library sizes
        - Plot gene-wise expression mean and variance across samples
        - Plot PSI mean, variance and range
        - Filter PSI values
        - Perform voom and respective normalisation if desired
        - Sample filtering
        - Filter lowly expressed genes using edgeR::filterByExpr
        - Convert ENSEMBL identifiers to gene symbols
        - Show labels for distribution plots

        Bug fixes:
        - Fix distribution plots requiring all samples in a group
        - Show sample names in distribution plots
        - Fix inconsistency of delta median and variance

    commit 795d17597f7d639681aa2cf33937ecd8a0c7eea8
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Feb 18 11:15:56 2019 +0000

        Improve SRA data loading

        - Accept a vector of files as the first argument (easier to use with `list.files()`)
        - Ask to overwrite file if one exists with the same name as the output file

    commit 161f9c2da7bf5139bda1a56c0bd8aebf76268b9e
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Feb 18 11:03:53 2019 +0000

        Minor copyediting

    commit 2fb74587d87c9a8a6fc2e85c1c429faf4ea1d3b6
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Feb 18 11:02:33 2019 +0000

        Update copyright references to 2019

    commit 808b219acfb5b317afc0fe232cb268a49a51cd52
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Feb 13 17:05:57 2019 +0000

        Fix colours/opacity in the rug plot within the distribution plot

    commit 7536285cb2fcea357ff945ce96192b6aff815396
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Feb 7 17:46:53 2019 +0000

        Fix wrong information in table of differential splicing results

    commit cad23d89b8f07420b6cd90067b9ede60a4651881
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Dec 3 14:59:22 2018 +0000

        Add tag ImmunoOncology to BiocViews

    commit a1510c15977c36b6c9863b0a0ba0140243b9b8c5
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Dec 3 11:54:33 2018 +0000

        Add tag ImmunoOncology to BiocViews

    commit 676ecb0b64f593ce3a9b4d3d5fbc4adae17fd1d2
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Nov 29 23:10:02 2018 +0000

        Fix crash when loading psichomics with test data that is not locally available

    commit 5bf83e4e96ac73180b6187239c7d2f570da21c1e
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Nov 8 16:59:39 2018 +0000

        Fix R CMD check and BiocCheck errors and warnings

    commit bb78b2be6e8c9457b5772435a574e728c870504e
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Nov 8 16:59:27 2018 +0000

        Fix progress bar when quantifying alternative splicing

    commit 19fea9e64f53c3e0479b61db08adee359ced772d
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Nov 7 15:46:13 2018 +0000

        Improve documentation of exported and internal functions

        - Minor code copy-editing
        - Minor tutorial copy-editing

    commit 23e38acd50866c16438a4dc6399173d98e52259b
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Nov 7 11:47:25 2018 +0000

        Minor improvements

        - Bump version number
        - Allow to show dataset icons in "Data"
        - Improve data grouping interface
        - Fix inconsistent group names when creating groups based on pre-made gene lists
        - Avoid error when user cancels file browser dialog to load groups from a file
        - Copy-editing code and documentation

    commit 65cc716dd58d1ea9a577e34d898c24b92308853a
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Nov 7 11:25:38 2018 +0000

        Ask before replacing correlation analyses

    commit 661a73a2bc12c54227a97c0003eccb022dfdab28
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Nov 7 11:24:40 2018 +0000

        Copy-edit tutorial on custom alternative splicing annotation preparation

    commit 09210d45c4a69f37355299acff1d074e3e3c2349
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Nov 7 11:21:38 2018 +0000

        Improve console logging of alerts

    commit e81cee95712934e4ba04b8100e7cee13d99874cb
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Nov 6 15:44:19 2018 +0000

        Decrease loading time after alternative splicing quantification

    commit d65138081a2c0f25c4c4f59e8cac3aa99fe68cf2
    Merge: 950fead2 0166a557
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Nov 5 17:45:15 2018 +0000

        Merge branch 'dev' of https://github.com/nuno-agostinho/psichomics into dev

    commit 950fead2c87b45eef1c57ba0ecc5221405648e07
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Nov 5 17:43:56 2018 +0000

        Change which AS event types are quantified by default

    commit af7d87997ca811bc3dae0c9bca5e964eb92ff713
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Oct 31 17:37:25 2018 +0000

        Load pre-made gene lists and improvements to correlation analyses

        - Display correlation results in a table
        - Display correlation analyses progress
        - Load those groups by default and allow to create them in the group interface
        - Initial support for RBPs in Sebestyen et al. 2016
        - Allow to use such groups in correlation analyses
        - Improvements to interface for correlation analyses
        - Minor copy-editing and interface improvements

    commit 757f821eacadef804a39c948dc8752bec86bba88
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Oct 30 18:37:13 2018 +0000

        Fix link for AS annotation creation and loading

    commit cc0ddc5999ac10060c83dcff1cdf35356e5e5aa7
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Oct 30 18:29:53 2018 +0000

        Fix word break-related visual issues

    commit f59713d9a5b76005ca392b10477376fa3fb4c941
    Merge: 650c0bcd 0166a557
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Oct 2 09:44:32 2018 +0100

        Merge pull request #366 from nuno-agostinho/dev

        Update citation link

    commit 0166a5578b61fcb0af3c4a9643402d3ac886869c
    Merge: c78f8054 650c0bcd
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Oct 2 09:44:13 2018 +0100

        Merge branch 'master' into dev

    commit c78f80540dbb9a3bef754317251d16403c57c8df
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Oct 2 09:42:49 2018 +0100

        Update citations to link to article in Nucleic Acids Research

    commit 650c0bcdc1728a113a1a11e095c16b07c3a10881
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Oct 2 09:22:01 2018 +0100

        Update NEWS date

    commit ebb47d9cc359f8539e319b67ee7512dd55a92eb9
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Oct 2 08:56:29 2018 +0100

        Minor changes

        - Update LICENSE for current year
        - Update clinical dataset used in vignettes

    commit ed1ad926df259ee936a9c0175a3f59024595895e
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Sep 20 16:53:57 2018 +0100

        Improve TCGA data download modal and minor changes

    commit 1614e3e3a35a4c8f15a05a45623584d234c98f20
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Sep 20 16:51:43 2018 +0100

        Add metadata regarding loaded and created datasets

    commit fbb70cc6b0a0a892716fd4fe6b0e7a9734bf1aff
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Sep 18 17:56:21 2018 +0100

        Fix errors, warnings and notes from R CMD check/build

    commit ae48e0e42ecd7c2217e7e5acc6ef1af5514aadaf
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Sep 18 16:50:37 2018 +0100

        Fix allowing to select a directory when requesting a file

    commit ad6777fd7a401b37b659bb5440449a79b8450545
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Sep 18 16:49:38 2018 +0100

        Fix allowing to select a directory when requesting a file

    commit e08b64dd60fa56ee697557beb2090724f8f28896
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Sep 18 15:49:59 2018 +0100

        Minor changes and code copyediting

    commit 3229d8ce5f23237f67119ce45eb23e545aabc4c3
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Sep 18 15:45:49 2018 +0100

        Improve file browser dialog in remote server

        - Allow to directly input a path without using the file browser dialog
        - Display warning when calling the file browser dialog in RStudio Server or in an unsupported system

    commit 9953f4f41d7b573653e23bb4ac45df864cbab160
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Sep 18 15:17:31 2018 +0100

        Fix issues in downstream analyses when using GTEx data subset by tissues

    commit 5fc56fd9162549d11daf7aa6271274b9c2323112
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Sep 17 16:19:46 2018 +0100

        Inform of sequencing technology used to obtain gene expression data from TCGA

    commit f7921b88d00b7da95c5acd379abd56d14088cf5c
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Sep 17 15:40:24 2018 +0100

        Improve console logging of error and warning messages

        - Check if files exist before loading local data
        - Check if any projects are selected and if given directory exists before downloading recount2 data

    commit c9fa821990d83f6fe223aa97de8b9265d2050ab1
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Sep 5 15:19:03 2018 +0100

        Improve group selection and correlation analyses

        Group selection:
        - Show group colour in group selection element
        - Avoid moving "Create groups" due to group creation preview

        Correlation analysis plot:
        - Colour samples by group
        - Render contour based on a density estimate
        - Interface changes to make it more intuitive
        - Fix Loess curve gaussian fitting regardless of the fitting argument

    commit 4f4cd0fe701f891d536bd13d227a908878b8e722
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Aug 30 15:51:42 2018 +0100

        Fix forced axis limit of density plot

        When plotting values within 0 and 1, limit X axis to 0 and 1; otherwise, do not limit X axis

    commit 54dea1bdb5f19a49683e3a24cc6f33964657e9fb
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Aug 15 21:43:50 2018 +0100

        Fix data group display when Patients or Samples are unavailable

        Minor changes:
        - Copyediting

    commit 8b5e1b106d6b4a3556bd6c57dd1bd1786053a660
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Aug 15 21:43:50 2018 +0100

        Fix data group display when Patients or Samples are unavailable

        Minor changes:
        - Copyediting

    commit b4fcaeaef1238f77a19b6262a6bbbea88e265940
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Aug 15 20:18:02 2018 +0100

        Improvements to data loading

        - Fix wrong parsing of recount's sampe metadata when fields across samples are not the same
        - Fix GTEx data loading as numeric instead of factor when filtering by tissues
        - Check if GTEx data files exist before attempting to load them
        - Copyedit code and user messages

    commit 2a2c46a84954e56ae792f075207a1fc7c6eb1f74
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Aug 15 20:13:53 2018 +0100

        Search PubMed instead of PMC

    commit ad607e31af37c0a65de674140e4f45ba04cef0e2
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Aug 13 18:07:50 2018 +0100

        Updated roxygen version

    commit 2e29f55d2a884216e4eb623772018a6f61683624
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Sun Jul 15 18:29:13 2018 +0100

        Minor improvements)

        - Update screenshot
        - Allow to select hg38 assembly when loading PSI quantification
        - Improve correlation's interface
        - Improve selection of icons used
        - Copy-editing

    commit 4593c1ffe040e390b5ec049c449a82ad725c6dcb
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Jul 9 19:30:46 2018 +0100

        Clean code for differential analyses

    commit 2f7c7e695f269a454f0a7de1e17872ec6c835217
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Jul 9 19:30:46 2018 +0100

        Clean code for differential analyses

    commit d3218e2997a5c238827332cf8d1e16a33fbbf496
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Jul 9 16:52:52 2018 +0100

        Copy-edit

    commit 327bf525aeb1fb599f400b05c5ae51074db77c44
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Jul 6 17:56:24 2018 +0100

        Allow to input formulas when highlighting points

        Other minor changes:
        - Fix filenames of exported tables mentioning differential splicing analysis instead of differential expression analysis
        - Minor style changes

    commit dace8973cd449c327d17e068fa680c1af0851bc5
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Jul 6 17:25:25 2018 +0100

        Copy-edit README and update screen shot

    commit 8c6e49459bf060426fd4dec5c97a0437b9fb8295
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Oct 2 09:22:01 2018 +0100

        Update NEWS date

    commit 9f57a89e0a585cf095b39298c276a3a5385afd0a
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Oct 2 08:56:29 2018 +0100

        Minor changes

        - Update LICENSE for current year
        - Update clinical dataset used in vignettes

    commit a766175c2c1814c06ae700cefc2dbedf54e09272
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Sep 20 16:53:57 2018 +0100

        Improve TCGA data download modal and minor changes

    commit 72c7322885372c86ec86a7160ff366549f1e7c04
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Sep 20 16:51:43 2018 +0100

        Add metadata regarding loaded and created datasets

    commit 6ef892922d492ea1b23bd36ddd970bb72c27caca
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Sep 18 17:56:21 2018 +0100

        Fix errors, warnings and notes from R CMD check/build

    commit 644b5514e8ddc046e3ea9b4db38a25928da50ef3
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Sep 18 16:50:37 2018 +0100

        Fix allowing to select a directory when requesting a file

    commit 4ba02ed2c43d15f44f7c04a68c9c04f6b854536b
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Sep 18 16:49:38 2018 +0100

        Fix allowing to select a directory when requesting a file

    commit 4d7e49cf6e5884f7b70bd31cf5809b7ad407f3b8
    Merge: 193ac794 660ff9d8
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Sep 18 15:50:12 2018 +0100

        Merge branch 'dev' of https://github.com/nuno-agostinho/psichomics into dev

    commit 193ac794afb5ba5ecc87a8434e6d98a8ad5b264e
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Sep 18 15:49:59 2018 +0100

        Minor changes and code copyediting

    commit 826edf1ecb8a4d56472cf35392919ae485e53a6b
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Sep 18 15:45:49 2018 +0100

        Improve file browser dialog in remote server

        - Allow to directly input a path without using the file browser dialog
        - Display warning when calling the file browser dialog in RStudio Server or in an unsupported system

    commit d2a64dbf7f7ab3189334b6de72623685b47f920d
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Sep 18 15:17:31 2018 +0100

        Fix issues in downstream analyses when using GTEx data subset by tissues

    commit 10cb3df4c0304152629e18fec97a1fa880bcef8b
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Sep 17 16:19:46 2018 +0100

        Inform of sequencing technology used to obtain gene expression data from TCGA

    commit 486d43c20f70f1f18f4b6ea3988c31558f719940
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Sep 17 15:40:24 2018 +0100

        Improve console logging of error and warning messages

        - Check if files exist before loading local data
        - Check if any projects are selected and if given directory exists before downloading recount2 data

    commit bddf111e81a70a988d8c06c31147518592098412
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Sep 5 15:19:03 2018 +0100

        Improve group selection and correlation analyses

        Group selection:
        - Show group colour in group selection element
        - Avoid moving "Create groups" due to group creation preview

        Correlation analysis plot:
        - Colour samples by group
        - Render contour based on a density estimate
        - Interface changes to make it more intuitive
        - Fix Loess curve gaussian fitting regardless of the fitting argument

    commit eae64553ff843b09a8013c6565f9a75bb47f9876
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Aug 30 15:51:42 2018 +0100

        Fix forced axis limit of density plot

        When plotting values within 0 and 1, limit X axis to 0 and 1; otherwise, do not limit X axis

    commit 48189e1b1a8a49b2f45816c448da9b0cc5e71149
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Aug 15 21:43:50 2018 +0100

        Fix data group display when Patients or Samples are unavailable

        Minor changes:
        - Copyediting

    commit 660ff9d802bd2f9d7eb920b519dfe0d74906904b
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Aug 15 21:43:50 2018 +0100

        Fix data group display when Patients or Samples are unavailable

        Minor changes:
        - Copyediting

    commit 788366fff3a0e37fd5a4bb7f5829b7c3fde6a9d5
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Aug 15 20:18:02 2018 +0100

        Improvements to data loading

        - Fix wrong parsing of recount's sampe metadata when fields across samples are not the same
        - Fix GTEx data loading as numeric instead of factor when filtering by tissues
        - Check if GTEx data files exist before attempting to load them
        - Copyedit code and user messages

    commit d7792511a47552b836047659736db4cf7fc1462b
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Aug 15 20:13:53 2018 +0100

        Search PubMed instead of PMC

    commit d5f8c587115cc23b4a07e496c8f07a5ba86bfe58
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Aug 13 18:07:50 2018 +0100

        Updated roxygen version

    commit 40aeed67aa0e24588ab126f7fd03537583d09ac4
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Sun Jul 15 18:29:13 2018 +0100

        Minor improvements)

        - Update screenshot
        - Allow to select hg38 assembly when loading PSI quantification
        - Improve correlation's interface
        - Improve selection of icons used
        - Copy-editing

    commit ca61fe24d1f043edd937be09e816f40ed1f0c9c7
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Jul 9 19:30:46 2018 +0100

        Clean code for differential analyses

    commit 455faf68c9dc1ebee8bd1cba8d0f0e6743b5154a
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Jul 9 19:30:46 2018 +0100

        Clean code for differential analyses

    commit 7e2e449e90b11da3ff93247ccbc58e33dfb6218e
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Jul 9 16:52:52 2018 +0100

        Copy-edit

    commit 8b4a7e91d71b858ea16b763d6929643d1b216f04
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Jul 6 17:56:24 2018 +0100

        Allow to input formulas when highlighting points

        Other minor changes:
        - Fix filenames of exported tables mentioning differential splicing analysis instead of differential expression analysis
        - Minor style changes

    commit 3b246807f63fa611d8ace55e3245965aaccac351
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Jul 6 17:25:25 2018 +0100

        Copy-edit README and update screen shot

    commit e392f34ebc314e4e7360ccbb3685fe4119734718
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Jul 5 20:09:09 2018 +0100

        Update README.md

    commit bf424d7bc72d8c9eff2cf92c920b883ec7ea9552
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Jul 5 20:01:13 2018 +0100

        Update README.md

    commit 66e932b545d0e533d7a3025de1216fb989465321
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Jul 5 19:57:39 2018 +0100

        Update README.md

    commit 946af16ddbe473f074e560ba248e40b54f8359c6
    Merge: 0aac8a4d 9ea793f8
    Author: Nuno Agostinho <danielagostinho@sapo.pt>
    Date:   Thu Jul 5 16:45:04 2018 +0100

        Merge pull request #361 from nuno-agostinho/dev

        Version 1.6.1

    commit 9ea793f87b94f1d916200d7431eea90e90bcf2d7
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Jul 5 15:59:26 2018 +0100

        Add placeholder

    commit 99e7b05fd75667a856b3d7254d2444b5063430b8
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Jul 5 15:11:47 2018 +0100

        Add more options when plotting gene expression versus PSI values

        - Change font size
        - Change plot height
        - Improve presentation of scatterplot options

    commit c4cbb939fdc4f0c0eb83e5a556895650974fb285
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Jul 5 14:26:46 2018 +0100

        Simplify code for file format recognition

    commit 0f976abc5570ae7407fdd0ea19af92ee62a15f13
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Jul 5 14:09:37 2018 +0100

        Improve group creation and manipulation

        - Greatly improve speed at which a big file is marked as incorrect (by loading just the first row instead of the first six rows of a file...)
        - Fix error alerts not appearing when trying to create groups based on invalid parameters
        - Add error alert when trying to load file without group information when such data is expected
        - Improve style of group preview table

    commit 864fd363e59a050aa89f5dc614c207d130d998a0
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Jul 5 11:45:03 2018 +0100

        Fix unit tests for parsing splicing events

    commit cd795942df7123e959bef96c36c03a0c8d956b4c
    Merge: cb459489 0aac8a4d
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Jul 5 00:11:41 2018 +0100

        Merge branch 'master' into dev

    commit cb459489889a9f185d4b15ee792bb3cd6becf05f
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Jul 5 00:06:35 2018 +0100

        Minor changes

        - Copy-edit NEWS
        - Change order of analyses (makes more sense this way)

    commit 09c0622f25d775e282d415c20a0bdb828a5669bb
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Jul 4 18:18:57 2018 +0100

        Display alternative splicing events in transcript plot

    commit 0aac8a4d1f5f9e3352612a1d3b901faacc7723b7
    Author: Nuno Agostinho <danielagostinho@sapo.pt>
    Date:   Wed Jun 27 17:21:32 2018 +0100

        Travis-CI and AppVeyor fix (#360)

        * Fix issues with GenomeInfoDbData and DelayedArray installation in AppVeyor
        * Use binary packages to speed up Travis-CI builds

    commit 47cd9d40d6b374ad1ffd5f397a4b7920bd4fcf4c
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Jun 26 18:58:47 2018 +0100

        Fix issues in R CMD check and BiocCheck

    commit 9de9492c581732f7cfd296f9f44478eb4b7cf699
    Merge: 92236436 30ff9e8a
    Author: Nuno Agostinho <danielagostinho@sapo.pt>
    Date:   Tue Jun 26 17:45:49 2018 +0100

        Merge pull request #359

        Version 1.6.1

    commit 30ff9e8aa73036e42a2a0203de606787729574fc
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Jun 26 17:40:46 2018 +0100

        Rollback to before introducing event-wise Cox models (re-think if this is the best solution or not)

    commit 36d3163410f32578a195eec7d204d6334ddcbe65
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Jun 26 17:02:34 2018 +0100

        Improve data grouping

        - Preview groups based on selected attribute before creation, closes
        #218
        - Correctly suggest how to select variables in subset expression and
        give more examples on how to use this feature, closes #220
        - Fix subject/sample attributes not being updated for selection for the
        GREP interface
        - Minor copy-editing

    commit dfdcb3fdfb06591c0a050e22bbdac8d1fef33f9e
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Jun 26 16:59:31 2018 +0100

        Update NEWS

    commit 5de4ee0251eab26e9f205d793190dec57f2aed4a
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Jun 25 16:26:12 2018 +0100

        Recommend installing psichomics through BiocManager

    commit 2a9f6ab5820cb39fffbb470a1b92e20a635ce394
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Sun Jun 3 23:26:17 2018 +0100

        Fix error if named samples are given

    commit b3cd480ba9acd37f5948be7532f5923ab6fbc335
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Sun Jun 3 15:47:28 2018 +0100

        Minor improvements

        - Improve display of filtered genes
        - Update default minimum samples used based on available samples
        - Render position of splicing event when plotting transcripts

    commit a155800df9380649e461bbd5aa8d0bbe8711d451
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Sun Jun 3 15:20:07 2018 +0100

        Improve support for loading custom data

        - Prepare gene and junction quantifications (STAR output) and SRA metadata to be loaded into psichomics
        - Add tutorial on how to analyse SRA and user-owned data
        - Update other tutorials
        - Fix data not being loaded when fread returns a warning related to issues with previous fread commands

    commit fb347b1842f935e9251f60f1cf8d8c4ff5131e1a
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Sun Jun 3 10:33:20 2018 +0100

        Fix warning when using deprecated function limma::toptable

    commit a79e15837ca633766d0397432f1704ecd1de30ae
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Sun Jun 3 10:30:14 2018 +0100

        Fix crash when quantifying splicing for a single sample

    commit ba626a461dbdc236499392d798564c3b53a04eac
    Merge: caa07c20 9c1b3da2
    Author: Nuno Agostinho <danielagostinho@sapo.pt>
    Date:   Sun May 20 16:49:14 2018 +0100

        Merge pull request #356 from nuno-agostinho/recount2

        Add support for recount2/SRA data

    commit 9c1b3da2306a4a60b3f97c5a0fe6e54262f4f50e
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Sun May 20 16:40:48 2018 +0100

        Minor improvements

        - Bump version
        - Update NEWS
        - Fix issues with R CMD check
        - Hide close button in progress notification

    commit 203a0fd493387983ce8f50caa2cf9118b62f0d7f
    Merge: 6702d93c 32213531
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Sun May 20 15:54:53 2018 +0100

        Merge branch 'recount2' of https://github.com/nuno-agostinho/psichomics into recount2

        # Conflicts:
        #	R/data_recount.R

    commit 6702d93c929e7818ec2a8f992936032d583f5dee
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed May 16 14:46:22 2018 +0100

        Load SRA data using recount R package

        - Load gene expression, junction quantification and sample metadata from SRA projects
        - Update documentation (including copyediting)
        - Improve hg38 splicing annotation

    commit 3221353188fa26be22296c0fa596efa5040e8c6b
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed May 16 14:46:22 2018 +0100

        Load SRA data using recount R package

        - Load gene expression, junction quantification and sample metadata from SRA projects

    commit b22a2ca081d095d87fd7581f6a9384f6575ed6f3
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu May 10 15:18:36 2018 +0100

        Minor revisions to survival

        - Add link to survival page from Cox regression results withing the table containing the results from exploratory differential splicing analysis
        - Use minimal p-value to decide the optimal PSI cutoff (makes more sense)
        - Improve p-value plot, including labelled line with the p-value threshold and
        - Minor copy-editing

    commit d0304ffd165e31e25cc665c3067db3877b4a5b4c
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue May 8 15:29:57 2018 +0100

        Perform event-wise Cox models using PSI values

    commit 20e84802e4827d7161276129577bd2fcc626b08a
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue May 8 15:10:34 2018 +0100

        Fix crash when inputting non-sense as the axes for the splicing scatter plot

        For instance, discard:
        - Non-numeric values
        - Numeric values when min > max

    commit f3645f0247f8e01f6e5873f09ac8c765fe3904d3
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue May 8 14:51:32 2018 +0100

        Allow to start app with test data (for dev purposes)

    commit caa07c20f35289f48fdf0deeecd3f8437a16bbb6
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Apr 12 14:17:41 2018 +0100

        Fix TCGA sample metadata not showing samples from all junction quantification files

    commit 2fa6cf42035a2c62fd03fd910a9d5fbf203d834a
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Apr 12 14:15:29 2018 +0100

        Fix TCGA sample metadata not being shown when loading TCGA files from local folder

    commit 92236436b040442b484060209e959af947d76503
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Apr 4 16:29:05 2018 +0100

        Bump to version 1.4.5

        - Update NEWS
        - Add links to original article in bioRxiv
        - Update package description within the GUI
        - Update mentions to NMorais Lab and iMM
        - Update copyright years to include 2018
        - Minor copy-editing

    commit b4d0e8748a3160e6838b6f68bc2a11795be92de2
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Apr 4 15:30:06 2018 +0100

        Copy-edit GUI tutorial

    commit b25b9124e57cf2758b710e980e1dde74f30b4a66
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Apr 4 15:16:38 2018 +0100

        Replace dataset no longer distributed with car package with a built-in R dataset

    commit a09c8ee50a9ae185438c2b37e554ef9086a24655
    Author: Nuno Agostinho <danielagostinho@sapo.pt>
    Date:   Mon Mar 12 11:37:29 2018 +0000

        Update Contributor Covenant Code to version 1.4

    commit 58a1f137b2985b97d188f87e67f14437dec757f3
    Author: Nuno Agostinho <danielagostinho@sapo.pt>
    Date:   Mon Mar 12 11:35:17 2018 +0000

        Update README.md

        - Direct article link to the latest version available
        - Direct reference to original article (instead of references)

    commit 7783adb3be5bf6a1095a9f1cdc4b7fb899ba05ff
    Author: Nuno Agostinho <danielagostinho@sapo.pt>
    Date:   Mon Feb 12 17:28:12 2018 +0000

        Update README.md

    commit 584cce4cf4da01e3da5450c4ec889e15d3cb8ddb
    Author: Nuno Agostinho <danielagostinho@sapo.pt>
    Date:   Mon Feb 12 17:06:00 2018 +0000

        Update README.md

    commit 751e3f52c2539032b615c2e10e3d3fbb774e1455
    Author: Nuno Agostinho <danielagostinho@sapo.pt>
    Date:   Mon Feb 12 01:54:53 2018 +0000

        Update NEWS

    commit ccecd6b7c2a1164470fa3e23bec53a7f876c24be
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Feb 12 01:28:11 2018 +0000

        Fix R CMD check issues

    commit 26b3e0d375f4916ad2570f8421ab344286986e34
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Feb 12 01:13:08 2018 +0000

        Improve differential analyses

        - Fix highlighted events not filtering table for differential expression
        - Update selected gene in gene information according to selected
        splicing event
        - Select splicing events or genes for differential analysis
        - Set selected gene when performing survival analysis

    commit 5fef2819224bfc3cd3af6aefadc34cba94ca66d0
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Feb 12 01:06:45 2018 +0000

        Fix problems related with DT versions >= 0.3

    commit ac6dfae6e30064dd2f8ccf1aac9c1e58091ba676
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Feb 8 16:04:23 2018 +0000

        Update vignettes to include case studies

        - Correctly export required functions
        - Copy-edit documentation
        - Rank variable that most contribute to selected principal components
        - Update CITATION file to direct to bioRxiv article
        - Update information in welcome message
        - Show number of contained items for selected groups
        - Update authors and bump version to 1.4.4
        - Update .gitignore

    commit 882eb627227e20e61ce9b4379d493fa06c5820ae
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Feb 8 16:03:04 2018 +0000

        Fix optimisation problem when calculating optimal PSI cutoff for survival by extending search bounds

    commit 860ce90adea912abdaa7da6d775060748499e457
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Sun Feb 4 23:30:52 2018 +0000

        Select samples to be used for survival analysis

        - Automatically select primary solid tumour samples (if available) when using TCGA data

    commit 8c2cd8af6f5fff32f63174e0f3f459db9140df7e
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Sun Feb 4 13:51:55 2018 +0000

        Automatically set sample types as groups when loading TCGA data (GUI)

        - Fix potential issues when dropping matrices
        - Show groups after creating groups based on clusters

    commit 8311aa1488253356b25e7f98285fc4b18526e7e2
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Sat Feb 3 19:26:23 2018 +0000

        Improve gene expression pipeline (perform limma-trend by default)

        - Improve gene filtering
        - Copy-editing

    commit bace4ac2e6dcec6df18e3131ae7e94db95cd9773
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Sat Feb 3 17:58:24 2018 +0000

        Stratify patients for survival analysis based on optimal gene expression cutoff

    commit f55dcfbf6af1719efc8aff413bf0fd4624d17f72
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Sat Feb 3 15:00:13 2018 +0000

        Quantify AFE and ALE events through AS-centric and exon-centric methods

    commit 8451fe2aad4865b20cb35ecd548771326b31028d
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Sat Feb 3 14:41:38 2018 +0000

        Tolerate 5% of missing values for both PCA and ICA (by default)

commit 8cb09af05681a0b4a38c61be9f2969c2419b02e7
Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
Date:   Thu May 27 10:37:35 2021 +0100

    Remove problematic Bioconductor unit test

commit 5f10dc44f55f0a29679a2de5e821ce09a0d0620b
Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
Date:   Thu May 27 10:34:13 2021 +0100

    Squashed commit of the following:

    commit b09a55ce3133b85fa7d664dfcaa0c73b2025a61b
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed May 26 15:50:21 2021 +0100

        Bump version to 1.18.1

    commit a136b3277c7cd6345d09e0e5b182cbbbec341e35
    Merge: 4ed660dd 800a9497
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed May 26 15:43:58 2021 +0100

        Merge branch 'master' into dev

    commit 4ed660dd456eec62d194aa51054d52490f30fd23
    Merge: 7af5ed78 08d79a95
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed May 26 15:36:42 2021 +0100

        Merge branch 'dev' of github.com:nuno-agostinho/psichomics into dev

    commit 7af5ed7815f903863eca6be95ee75c7a54754c1e
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed May 26 15:36:35 2021 +0100

        Rename custom data tutorial

        - Minor copy-editing

    commit 800a9497227a2952a51962819840d4029f57a9b7
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon May 24 21:37:01 2021 +0100

        Fix Docker install instructions

    commit 3d89ab07e2870eedec3558c73cbc2ec9f041e18f
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon May 24 13:19:52 2021 +0100

        Use GitHub Container Registry

        - Release `latest` tag
        - Update Docker action versions

    commit 5ce0e06d24febbc6a000db17ab540b779f2c6c36
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon May 24 13:17:04 2021 +0100

        Simplify dependencies install in Dockerfile

    commit 31adf199ce9b5abde5f3cd5e51349848d832ce74
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon May 24 13:14:57 2021 +0100

        GitHub and Docker install instructions

    commit 08d79a95acdd38bca6367b2b35295e66c513aea8
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Sat May 22 17:29:58 2021 +0100

        Update README.md

    commit 72dd83cc5ffdce789cba11c17d09149032972ac1
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Sat May 22 16:01:24 2021 +0100

        Update docker.yml

    commit 02fa0bb25c07eb9b7d9660a00bf1cd3cd09b7433
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Sat May 22 15:58:00 2021 +0100

        Update Dockerfile

    commit 046ccaa16ccbb0196e83d13638bd637e82334e4e
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Sat May 22 15:57:17 2021 +0100

        Include cache in docker.yml

    commit 6b6eea05c1c25febfc53ca1229836fefe6b878e0
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Sat May 22 15:53:19 2021 +0100

        Update docker.yml

    commit b4dfaa5c8bec6e5bee8c13bb88227ce89c895be5
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Sat May 22 15:52:27 2021 +0100

        Temporary test

    commit b0ed55070f7225db992becd6eab75cf15951cac9
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Sat May 22 14:46:56 2021 +0100

        Update docker.yml

    commit 729c0ec030f8301fa1dd87d0ab13fd81a97b1566
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Sat May 22 11:42:24 2021 +0100

        Update docker.yml

    commit c72aa7cb9ec3f4cb83d2a1b5a7faaaa12bdb2145
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri May 21 15:50:44 2021 +0100

        Simplify Dockerfile to the bare minimum

    commit 409d56b0289259d2aa6405dd5cb77d6b983176f2
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri May 21 15:16:34 2021 +0100

        Revert to working docker.yml with new registry

    commit 247013fb0d49dab26cec19d1f3d8eb43bb0de622
    Merge: 09d3d385 debcc26e
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri May 21 15:08:48 2021 +0100

        Merge branch 'dev' of github.com:nuno-agostinho/psichomics into dev

    commit 09d3d385a633832b71391aeb006aa0f97f6c1ec9
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri May 21 15:08:42 2021 +0100

        Fix spelling issues

    commit debcc26e145239d23368ab36ed8ad5d6995ad1df
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri May 21 11:54:40 2021 +0100

        Update docker.yml

    commit 7bdfbd87b2579f5d63f5b7cdae0e6f44723f7c49
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri May 21 10:43:13 2021 +0100

        Update docker.yml

    commit fd6dd049b71f72d21f6ac3a899574137697eada9
    Merge: b5380673 ba7412e1
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu May 20 19:22:09 2021 +0100

        Merge pull request #422 from nuno-agostinho/master

        Update dev from master

    commit b53806731c44ff936b200238e00375023da76dd3
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu May 20 18:51:51 2021 +0100

        Update docker.yml

    commit ba7412e14ae3aac94fa6bb70e404db554bcace7c
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu May 20 18:16:45 2021 +0100

        Update check-bioc.yml

    commit 95ca4df14220a184de1b4c713fbe4712143028ce
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu May 20 16:58:50 2021 +0100

        Update check-bioc.yml

        Update usage of environment variable

    commit ff60092684c225f8da7daa5ca74d61eda8ffc851
    Merge: 3c039cf6 32205d23
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu May 20 14:48:47 2021 +0100

        Merge pull request #421 from nuno-agostinho/dev

        Dev

    commit 32205d23dd284807e79c26e65c68a095e6d87cd6
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon May 17 20:23:41 2021 +0100

        Avoid problematic unit tests in Bioconductor

    commit 2e7b506736eb923a4ea6229f58b3464f731cd205
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon May 17 12:48:38 2021 +0100

        Update NEWS.md

    commit 08302a37027e18169519859fa435014b25a5987f
    Merge: e2f0ae2c 3c039cf6
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu May 13 17:35:12 2021 +0100

        Merge branch 'master' into dev

    commit e2f0ae2c838d418bfc01245afcaf8f7d9eb62bf5
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu May 13 17:24:49 2021 +0100

        Bump version to 1.18.0

    commit e5003caf9a98ab9981e0c8c02448d232ebf6f9e2
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu May 13 17:24:34 2021 +0100

        Fix issues with R CMD build/check

    commit b846abece509ea86a1998f8bd5bc31eeba16ef81
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu May 13 16:18:43 2021 +0100

        Update documentation and resolve minor issues

    commit 445dacade2d8745957b2a42dbc5663159f98861b
    Merge: de048440 2ea05d6f
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu May 13 15:38:38 2021 +0100

        Merge branch 'dev' of github.com:nuno-agostinho/psichomics into dev

    commit de048440a477c16339030886703ac2d1f9417021
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu May 13 15:38:19 2021 +0100

        Fix `plotDistribution()` for listed groups (e.g. in the CLI tutorial)

        - Fix issues with unit tests

    commit 2ea05d6f66a31aadc63fd81efbaab2e4d655734b
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu May 13 14:09:56 2021 +0100

        Avoid using set-env to set environment variables

    commit 2e536f9e4573549df3a1af7f5b0991e2aec7364b
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu May 13 13:45:23 2021 +0100

        Only animate spinning wheel when effectively loading data

    commit a9362fe77814ff22f8b092fd4a804becc2f8bc81
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu May 13 13:29:26 2021 +0100

        Improve plotting of AS events

        - Allow to use `plotSplicingEvent()` directly with a PSI table
        - Improve support diagrams for IR events
        - Fix IR diagrams in distribution plots not displaying introns
        - Fix parsing of VAST-TOOLS IR events as SE for certain annotations
        - When searching particular splicing events, fix results based on the wrong genomic coordinates
        - Fix other AS events display in Y axis for distribution plots
        - Minor copy-editing

    commit 283e137bcca44e07a451296dab8c44655184748b
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue May 11 19:28:03 2021 +0100

        Improve distribution plots

        - Allow to invert axes
        - Avoid redundant code
        - Render event diagram based on axis containing PSI distribution values

    commit 0e9e88251500d9d4a063d641240090b118ef3be2
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue May 11 13:01:27 2021 +0100

        Suppress snapshot date message

    commit 5dd040a4800f71e4bc93ca86b4fb45d1d58ffc64
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon May 10 19:28:24 2021 +0100

        Minor improvements

        - Place distribution plots on top of event diagrams
        - Timeout GTEx data retrieval after 3 seconds without server response
        - Avoid unnecessary messages when loading Firebrowse interface
        - Avoid "Matching subjects to their samples/Matching process concluded" loop

    commit 28b2c303bad579cd2a25093bb9f0388a4150991a
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon May 10 19:18:53 2021 +0100

        Support gene symbol conversion for any species with OrgDb

        - Remove 'org.Hs.eg.db' dependency
        - Allow to select OrgDb species to use for gene symbol conversion
        - Minor code copy-editting

    commit efb0bd138e1abb07cab0034bab8bca749f860b91
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Apr 8 11:00:36 2021 +0100

        Bump version to 1.16.1

    commit 74cc2347872c24788419a3ccb96b3ec7851b53c6
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Apr 8 10:59:49 2021 +0100

        Fix parsing of VAST-TOOLS intron retention events as skipped exons

    commit d651dd530ea5e05e987b7f12f342de4dda51d5f8
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Feb 19 13:37:06 2021 +0000

        Improve distribution plots

        - Allow to plot violin and box plots
        - Hide rug plots with 500 or more values (by default) for performance reasons
        - Add jitter to rug plot (helps to discern multiple numerous points)
        - Display IQR per group in tooltip
        - Easily add subtitles to distribution plots
        - Avoid redundant code
        - Reorganise code

    commit 3c039cf6f68722e0a1def624c607aca18c8910ec
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Nov 23 12:33:22 2020 +0000

        Fix setting environment variable

    commit a6feeadad42e93163d6614d1fb89a50ac5f30faa
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Nov 23 12:05:11 2020 +0000

        Avoid bioc-devel while R-devel is not available

    commit 35b2cc0dcb02e20eacd1a4a8c2594945cd1322fd
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Oct 9 18:35:05 2020 +0100

        Fix comments in bash commands

    commit f159bdc8ea2800c6482e439ea8f495575b52db1c
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Oct 8 14:50:53 2020 +0100

        Fix unit test function

    commit bdc246c1708d7ed3957cf74bd830467c42ab9f23
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Oct 8 14:19:13 2020 +0100

        Move unit tests to correct folder

    commit 87344cdc4a8e92eb6a3fa3c0857cd7e559986e01
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Oct 7 15:26:06 2020 +0100

        Minor changes

        * Warn about discarded events when quantifying/loading PSI data
        * Print elapsed time of loading local files
        * Improve verbosity when quantifying or loading PSI values
        * Add dev/ dir to add files of interest to the project
        * Copy-edit CLI tutorial, code and documentation

    commit 37f209a0799b21c71faffb6c21c101f115c27ba0
    Merge: a84aeb84 13b0d736
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Sep 25 18:41:27 2020 +0100

        Update NEWS from origin

        Merge branch 'dev' of github.com:nuno-agostinho/psichomics into dev

        # Conflicts:
        #	NEWS.md

    commit a84aeb84b669683aa20fddc20852b9599cc0b845
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Sep 25 17:39:49 2020 +0100

        Improve performance of `discardLowCoveragePSIvalues()`

        - Move reusable `progressBar()` C++ function to header file

    commit 15c4e2712d424ce0e3835e30fbf8c6be1c77fda8
    Merge: 3cfc873d 13b0d736
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Sun Aug 30 12:52:54 2020 +0100

        Merge pull request #415 from nuno-agostinho/dev

        1.14.4

    commit 13b0d736d14f623658fffad4da31be115624dee4
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Sun Aug 30 12:52:12 2020 +0100

        Update NEWS.md

    commit 358819f2127b3340d2624489d06c1135f5808d50
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Sat Aug 29 17:15:14 2020 +0100

        Correct spelling

    commit 230f03f3e6704626e13d60417d340a1aa3adbe60
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Sat Aug 29 16:33:23 2020 +0100

        Improve file/directory browser dialog

    commit 18344b16cc4bcd251c9c01b23011e10b20750ffd
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Sat Aug 29 14:59:37 2020 +0100

        Improve file/directory browser dialog

    commit 989b5aac54dc7799b9f187349a901370b402beea
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Aug 28 18:54:44 2020 +0100

        Improve file/directory browser dialog

    commit e37c62c848e3dc0091076d7dd7894aa4f9fe62da
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Aug 27 15:13:58 2020 +0100

        Bump version to 1.14.4

    commit 1bb928810f71d63daf7ae3f840b6c59f06d79d8f
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Aug 27 09:18:27 2020 +0100

        Fix file browser dialog selection of single file in macOS

    commit cc63bdb5a69a6e0c9fbdd2cb860629a6bfec404c
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Aug 26 19:02:54 2020 +0100

        Improve data loading

        - Speed up loading of GZ and BZ2 files
        - Increase verbosity while loading files
        - Speed up loading of VAST-TOOLS' inclusion levels
        - Fix loading of VAST-TOOLS' inclusion levels sometimes returning an error regarding duplicated row names
        - Fix issues with missing values as alternative splicing event complexity in VAST-TOOLS' inclusion levels

    commit cae16fb330bf82aff77ac9b6beda26e4f5462519
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Aug 24 18:17:36 2020 +0100

        Copy-edit tutorials

    commit 3cfc873db5f20c82d408f71b0522f52d7c3bf2b4
    Merge: 0db81dd6 b766d090
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Aug 21 17:41:29 2020 +0100

        Merge pull request #414 from nuno-agostinho/dev

        Expect to contain "ensembl_havena_gene" in logic_name

    commit b766d0908894fb121a93ccb575037741e22967e8
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Aug 21 17:41:05 2020 +0100

        Expect to contain "ensembl_havena_gene" in logic_name

    commit 0db81dd670f572886d9398b38bbbea7f536e3400
    Merge: b31fc62a ed83e8a1
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Aug 21 15:21:00 2020 +0100

        Merge pull request #413 from nuno-agostinho/dev

        1.14.3

    commit ed83e8a169ccaf55867e225c4e236ccd7aa1b232
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Aug 21 15:02:32 2020 +0100

        Bump version to 1.14.3

    commit 91198ec580ae300566c318391287d7e9540f83a1
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Aug 21 11:48:36 2020 +0100

        Fix upstream changes from Ensembl API response

    commit 339e0d6f658074fb96e9996014c8d9da84271d0c
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Aug 21 11:47:32 2020 +0100

        Run R CMD check regularly

    commit c04f25193841c87d7a9df28ad37bc4c7af682f97
    Merge: 548ae1f5 b31fc62a
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Aug 21 11:30:40 2020 +0100

        Merge branch 'master' into dev

    commit 548ae1f5984a6858b777a4dadc474b482bc44ca4
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Aug 21 00:33:07 2020 +0100

        Fix undefined global variables on renderBoxplot

    commit 616f2804081e240a1cedf920164015a178dfc998
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Aug 12 16:32:08 2020 +0100

        Fix incomplete final line

    commit f7f34ccde450d5666d2253c36e7436d350580771
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Aug 12 16:13:24 2020 +0100

        Pass codecov even with 1% of differences

    commit 21864c25fb5dc270d6f4d0eee9cf84aaf5a5d3e2
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Aug 12 15:17:15 2020 +0100

        Publish Docker images based on dev branch

    commit 278f77ebe6bc1b50861df5c6cad21d8f3b279609
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Aug 12 10:05:50 2020 +0100

        Minor copy-edit

    commit b31fc62a23d4a2eeb8f993baa0cadce22d3b89b1
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Aug 12 01:29:36 2020 +0100

        Avoid publishing Docker image on master push

    commit 75706aac561c5cee7e2bccb911187e7a78940df1
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Aug 12 01:26:33 2020 +0100

        Update README.md

    commit f9d0f85e50aae13d81e4394d4c85d60c35fa60b1
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Aug 12 00:24:03 2020 +0100

        Fix pkgdown deployment

    commit 96942cc2abc3e3bd8a835c0f0807be8cd13a96f1
    Merge: 49ca4891 14364a71
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Aug 11 23:26:58 2020 +0100

        Merge pull request #412 from nuno-agostinho/dev

        1.14.2

    commit 14364a719e271169cc4198cdf66974cb06606d2c
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Aug 11 21:49:36 2020 +0100

        Fix unit tests for VAST-TOOLS' data loading

    commit 40d7f93c716a914200f456c12d4013234721975b
    Merge: 31fc5ac5 140ab018
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Aug 11 21:01:28 2020 +0100

        Merge branch 'dev' of github.com:nuno-agostinho/psichomics into dev

    commit 140ab01862eb4e021430593492a0799a0f3c6333
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Aug 11 21:00:42 2020 +0100

        Update NEWS.md

    commit 31fc5ac577e056bee88e00c3565f29f2fab52291
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Aug 11 13:29:27 2020 +0100

        Improve loading of VAST-TOOLS' inclusion levels

    commit 48cc9ee5617d5a4b08e21ba7954b3e11eb719fd2
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Aug 11 13:27:58 2020 +0100

        Fix asking multiple paths in file browser on macOS

    commit cfa5ec8e6c08baf3374545828f59470038d7a2ee
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Aug 10 10:16:59 2020 +0100

        Table with supported file formats in psichomics

        - Include more information on manually loading FireBrowse and GTEx data
        - Reorganise information

    commit a3f81cfa4816ab3bdc1b3185a025d0a8d9d6a83e
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Sat Aug 8 23:19:54 2020 +0100

        Copy-edit NEWS.md

    commit 3f2a23257ed3f8735c8ea07e3f8f892378a7f80a
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Sat Aug 8 23:12:55 2020 +0100

        Publish Docker image in GitHub Packages

    commit 88b307d9598e608666281bd135c2b09ae3a92550
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Sat Aug 8 20:51:07 2020 +0100

        Fix VAST-TOOLS data loading unit tests

    commit 1977f5fe2f9038998c81577edbe0ecf745e43a39
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Aug 7 19:27:58 2020 +0100

        Test VAST-TOOLS data loading

    commit c56b728553c133747c685f7b1112555a6aa48a6e
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Aug 7 12:11:23 2020 +0100

        Fix testing expected error

    commit e751c549cfb39d44e4ff69891b94d7f3304c005e
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Aug 7 11:46:05 2020 +0100

        Fix returning only one data column for loaded data

    commit f4e6750492448d5bdd6193ada0c342cb0bf72c35
    Merge: 1301be60 23881204
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Aug 7 11:25:04 2020 +0100

        Merge branch 'vast' into dev

    commit 2388120475c3f585440dd15cc320863b6109ed13
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Aug 7 11:24:47 2020 +0100

        Replace CI tools with GitHub Actions

    commit d78cef99c576bc6922310245055b37a544cfe375
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Aug 7 11:22:39 2020 +0100

        Avoid using deprecated boxplot function

    commit 1301be607968ea9febcec01adba5dfa5873da8f5
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Aug 7 10:28:16 2020 +0100

        Avoid running interactive example

    commit 30a9b4786c606cf013d766b6a3d20538ab2c36b0
    Merge: 8d83c327 75748c4f
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Aug 5 09:37:29 2020 +0100

        Merge branch 'vast' of github.com:nuno-agostinho/psichomics into vast

    commit 8d83c327e7e37f4e4fc69ebbf9adff3d66724b34
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Aug 5 08:05:12 2020 +0100

        Minor copy-edit

        - Allow US spelling for normaliseGeneExpression()
        - Use cRPKM (singular), not cRPKMs whenever talking about the cRPKM dataset
        - Copy-edit CLI tutorial
        - Use Gene (singular), not Genes in calculateLoadingsContribution()
        - custom_data.Rm: Show usage of both gene read counts and cRPKMs in CLI

    commit 75748c4f9610e6aa078e1034dc0a2b5488f55025
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Aug 5 08:05:12 2020 +0100

        Minor copy-edit

        - Allow US spelling for normaliseGeneExpression()
        - Use cRPKM (singular), not cRPKMs
        - Copy-edit CLI tutorial

    commit 49d76fd13e0e57205efc684d3194a9eb67b14ae7
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Aug 5 08:03:09 2020 +0100

        Raise error (instead of capturing it) when perfoming PCA/ICA

    commit 03e69817e4dfe7bfbbf03d9e714c8e65cde0ffb0
    Merge: 2f41e2dd 1804e4f3
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Aug 5 01:06:16 2020 +0100

        Merge branch 'vast' of github.com:nuno-agostinho/psichomics into vast

        # Conflicts:
        #	R/data_geNormalisationFiltering.R
        #	man/normaliseGeneExpression.Rd

    commit 2f41e2ddc9aef85bbe70dc2424b3ba9d0f72df9f
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Aug 5 01:02:48 2020 +0100

        Replace label of `plotLibrarySize()` from "Gene expression" to "log10(library size)"

    commit 26beab6c7291874fa2fadeca79940017079fcea3
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Aug 4 12:24:35 2020 +0100

        Load both VAST-TOOLS' cRPKMs and gene read counts when available

        - Allow to load multiple datasets from a single file format by returning a list of data frames (for compatibility reasons, only return the first dataset unless explicitely requested otherwise)
        - All gene expression loading elements now support loading more than one gene expression file
        - Toggle specific statistics based on gene expression values when filtering
        -
        - Allow to change object attributes to unset attributes only
        - Improve gene expression documentation
        - Copy-editing

    commit 1804e4f38074cc9fb07a2db616f7c78e78f89fed
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Aug 4 12:24:35 2020 +0100

        Load both VAST-TOOLS' cRPKMs and gene read counts when available

        - Allow to load multiple datasets from a single file format by returning a list of data frames (for compatibility reasons, only return the first dataset unless explicitely requested otherwise)
        - All gene expression loading elements now support loading more than one gene expression file
        - Allow to change object attributes to unset attributes only
        - Copy-editing

    commit 868139d711321b01d291c9e6eacb8f5daff6fad6
    Merge: 364bbe0b 49ca4891
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Aug 3 11:57:18 2020 +0100

        Update with master and fix conflict

    commit 364bbe0bd4201884f093aee244667e0925d6bcbf
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Aug 3 11:30:10 2020 +0100

        Copy-edit

        - Keep event data on PCA results
        - Copy-edit welcome screen
        - Rename exported function `getSplicingEventInformation()` to `getSplicingEventData()`
        - Rename internal function `getEventData()` to `findEventData()`
        - Put group creation table preview above other elements in the page
        - Minor copy-editing code and documentation

    commit 68770871054fbe55172a3b7ebe683e37cf782002
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Jul 30 14:08:25 2020 +0100

        Copy-edit documentation

    commit a86b1bbd7b7a934767b413f51d7dfca26e8b8ac7
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Jul 30 13:54:35 2020 +0100

        Fix cognate genes when creating groups from differential splicing results

        - Change group title depending on creating group from differential splicing or expression results

    commit 2c2cbfdc5f19a4fd403f344736c75dfd3650d418
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Jul 29 19:14:09 2020 +0100

        Minor changes to visual interface

        - Improve groups interface, including larger margin between buttons when decreasing window width
        - Copy-edit text of GTEx tissue selection context

    commit 3ca2e456984732b1d3fbcde5e68d5e0829f71033
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Jul 29 17:43:55 2020 +0100

        Toggle individual parameters when filtering PSI data

        - Fix filtering settings not being reported after quantifying PSI

    commit 769e05e499d88cde8b892b93d7f7f3a9bb09229c
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Jul 29 17:06:27 2020 +0100

        Improve interface for group preview

    commit cde100637ec21e0ef51b05540ec5f1bde2bd367f
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Jul 29 11:53:19 2020 +0100

        Copy-edit custom data tutorial

    commit 231a81728c4145517d3abc2739faff64992c0076
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Jul 28 23:06:30 2020 +0100

        Improve group creation and correlation interface

        - Show an alert when there is no data to create groups
        - When creating groups by sample index/identifiers, suggest sample names not only obtained from sample information, but also from alternative splicing quantification and gene expression datasets
        - Fix suggested attributes and index/identifiers in group creation not being cleared when changing to datasets where such data is unavailable (thus showing the attributes/index/identifiers of the previous dataset)
        - Warn when selecting genes that are not available in the selected gene expression dataset (instead of crashing the app) when performing correlation
        - Avoid creating automatic groups based on gene lists when respective genes are not available
        - Rename RBPs to make it clear they are human RBPs
        - Minor copy-editing

    commit 8b018cc96486b55f95ff3f75c00382269607cded
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Jul 28 15:44:53 2020 +0100

        Preserve eventData for results from differentialAnalyses

    commit 916e3f257bd71754b6824811fd266b335410130f
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Jul 28 15:38:05 2020 +0100

        Copy-edit

        - Improve information on loading user-provided data and include it in the custom data loading tutorial
        - Improve function documentation
        - Copy-edit tutorials

    commit b4a187d34e2db7bea482648ec1d839b3c1f3029e
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Jul 28 11:02:56 2020 +0100

        Fix warning in Roxygen regarding link to unknown function

    commit 594df5196876340607c3ce0ecd94062706328d7e
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Jul 27 23:59:21 2020 +0100

        Fix issues in R CMD BiocCheck

    commit c16c21c691dc8dd40bd651d9a570efea0621ff76
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Jul 27 21:47:21 2020 +0100

        Fix R CMD check issues

    commit 671b9de8b6be89484540f15655695a052e454432
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Jul 27 21:17:01 2020 +0100

        Fix unit test issues

        - Fix plot distribution of single values
        - Fix wrong results when calculating fast row-wise stats of vectors
        - Fix error when quantifying splicing with no genes in the annotation

    commit 2ee32f8f8b25deb90bab250ae96f4d4dc53895fd
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Jul 27 19:35:36 2020 +0100

        Minor copy-editing

        - Replace icons for consistency
        - Improve vertical distance of primary buttons when window width is small
        - Avoid permanent progress bar after loading list of GTEx tissues

    commit 4ae464c767abd9b4a8c15d7a01200fd669f10912
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Jul 27 19:18:53 2020 +0100

        Fix issues with PSI filtering

        - Fix not filtering by event type events quantified via psichomics
        - Fix error when calculating stats for a single row containing missing values
        - Fix not being able to search for event types in selectize input

    commit a897e1f734a1c60ce7620f818be513959f79c6fa
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Jul 27 17:28:26 2020 +0100

        Fix not filtering splicing event (sub)types if stat filtering is disabled

        - Improve speed of filtering VAST-TOOLS by reordering steps
        - Improve filtering settings attribute
        - Copy-edit

    commit 06fb9cacdc5f74e0268536861d084842b6f1ef14
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Sat Jul 25 10:20:50 2020 +0100

        Improvements on parsing and directing user to differential page

        - Improve speed of joining all coordinates
        - Ensure groups are NULL when going to differential page from PCA loadings
        - Ensure AS events are correctly parsed by setting the alternative splicing quantification information when setting the event
        - Load test data with unparsable events
        - Correctly identify alternative splicing events: consider a string as splicing event if data's attribute dataType is "Inclusion levels"
        - Improve tooltips of PCA and volcano plots (loading plots now show cognate gene, event subtype and event position in tooltips)
        - Show AS event identifier at all times in the selectize event input and tables below volcano plots
        - Fix crash when there's no splicing event information
        - Copy-editing

    commit 850d2f7b2f27629b2276aae18f16817b5ac2fca2
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Jul 23 16:20:18 2020 +0100

        Improve PSI filtering interface

        - Filter by min/max individual PSI values
        - Discard VAST-TOOLS values based on quality scores

    commit 0cf47d34fc134ad02ec377317733d3e8b150228d
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Jul 23 14:02:36 2020 +0100

        Copy-edit documentation

    commit 6feb0f564baeb49857528bb7f685f3a39eac1756
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Jul 23 14:00:44 2020 +0100

        Remove redundant datasets from loaded data (ignoring attributes)

    commit fb0a764d4995dd34167af81be9cb1c813ade6802
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Jul 23 13:58:48 2020 +0100

        Correclty discard events containing only missing values

    commit eeb388ee789460220b0f4c214abef95ce2635811
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Jul 23 13:58:20 2020 +0100

        Fix VAST-TOOLS' IR-S event type not being parsed

    commit 4337b2452869d07fdb5ae47db7d8d413ad1d4ef9
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Jul 23 13:56:29 2020 +0100

        Vastly improve preparation of alternative text when there are no AS event diagrams

    commit 3b7414ee228b4502fc6ce9899729637a50d10392
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Jul 22 18:40:59 2020 +0100

        Improve filtering of PSI values

        - Discard low coverage PSIs from VAST-TOOLS
        - Allow to filter by event type or subtype
        - Use faster calculation of row-wise max and min
        - Improve code for row-/col-wise stats

    commit e8a0538af6cb0e523d73f59f51e0557854ce5021
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Jul 22 18:38:51 2020 +0100

        Get splicing event types from a given dataset

    commit 0c7b1fa05e2d707ce82d2c512ec38eab34b722ff
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Jul 22 18:37:20 2020 +0100

        Improve VAST-TOOLS file support

        - Support loading output from `vast-tools tidy`
        - Use ENSEMBL gene names when gene symbols are ambiguous
        - Correctly name RI events as expected in psichomics

    commit 17e5e2c819c3a99523066ccee1a86591f342516a
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Jul 22 18:32:12 2020 +0100

        Fix eventData passing from transposed PSI for dimensionality reduction

    commit 4be272d9bc5f531d68d5056b50fad6efcea08c6c
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Jul 22 18:12:04 2020 +0100

        Add exported function getSplicingEventInformation()

    commit adfc058c6ca8f0b2ad283e290a5f4b81ea1f20d3
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Jul 21 11:53:09 2020 +0100

        Improve calculation time of row- and column-wise statistics

    commit 0589f7a51f76de753fab53ad954c50f2845a6fea
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Jul 21 10:24:35 2020 +0100

        Improve consistency of function names

    commit 1e02261a0891870725ad2749528304d2ae4e8a9a
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Jul 21 09:36:36 2020 +0100

        Improve file loading and parsing

        - Import VAST-TOOLS gene expression data
        - Check if folder exists before loading files
        - Add verbosity to file loading functions
        - Return only TRUE/FALSE when checking file formats
        - Minor copy-editing

    commit 07addf93e43abf273be6596944d176bd71ba0e51
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Jul 20 11:42:28 2020 +0100

        Copy-edit NEWS

    commit 5567fcf5a6c19ba34c4b75f2d1c71425f52c260c
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Jul 20 11:42:14 2020 +0100

        Process psichomics PSI tables the same way as any other generic PSI tables

    commit b124bb55472c429167a5f63239a5739ee4458420
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Jul 20 11:39:26 2020 +0100

        Fix misc issues

        - Correctly parse AS events (major issue)
        - Try to put tooltip always on top of every element (still problematic...)
        - Avoid showing diagram in volcano plot tooltips if event cannot be parsed
        - Minor copy-editing

    commit 2ac31028e0d646c3a706c908688770bd82280920
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Jul 20 11:39:09 2020 +0100

        Fix suggested attributes in group creation not being updated when changing to datasets with no attributes

    commit b5605b22ce54ba396cfb54819c54b6d855982f0d
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Jul 20 11:35:50 2020 +0100

        Support SRA metadata automatically

        - Update user-provided data loading tutorial

    commit 0a6ef1ea0a509671a2fcc10d2483d1fadeb3f75d
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Sat Jul 18 14:17:52 2020 +0100

        Fix expected events type from a VAST-TOOLS PSI table

    commit d8d18f3ba2177cc1565f8a2d2245022106df5d65
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Sat Jul 18 13:59:25 2020 +0100

        Support loading PSI tables with arbitrary (i.e. unparsable) events

        - Expect warning (instead of error) from `parseSplicingEvent()` only when running in the R console

    commit 1d43fac671ca8e72872eb59f73c5fceece715dc5
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Sat Jul 18 11:12:24 2020 +0100

        Use cache for inclusion level summary plots

    commit 0333d6e65c6df9391286504b7bee022c87c7f824
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Sat Jul 18 11:00:34 2020 +0100

        Minor improvements

        - Fix gene expression summary plots not showing in specific situations
        - Fix legend not hiding in plotRowStats
        - Minor copy-editing

    commit 796838fe55a3f30ce877350526af91f0dd23ecf9
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Jul 17 16:55:43 2020 +0100

        Alternative splicing quantification filtering

    commit b66f2d762dc6cbcb0bcffe044de207767bcf68ee
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Jul 17 16:51:02 2020 +0100

        Avoid leaving missing values in type when there is subtype information

    commit 7787bd2caa9a73da856d624dcb1af3a38048cac1
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Jul 17 15:35:23 2020 +0100

        Improve data loading visual interface

        - Discard file browser input selection
        - Show helpful context messages in panel interfaces
        - Minor copy-editing
        - Avoid re-matching subject to their samples

    commit d076540dec323a59e38e17d2684e37226b4fb62c
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Jul 17 15:29:01 2020 +0100

        Use fan as loading icon for AS event selectize element

    commit b41f94365b0754e95f905c600ae1d7dc19224906
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Jul 2 17:46:01 2020 +0100

        Improve gene annotation page

        - Persistent user tags when querying PubMed
        - Allow to select more species/assemblies and freely add more
        - Fix no AS event plot diagram in information
        - Minor code copy-editing

    commit 0fc04c8c5df2501789d5f0553dd68dcfc5c816ad
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Jul 2 13:57:12 2020 +0100

        Fix rug plots in the middle of density plots

    commit c2e1d5babcfd4ca370ec70f85064773c4e89f3f1
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Jul 2 13:43:00 2020 +0100

        Use group colours in density plots of differential expression table

    commit 9d1ea065b6a16820965b0e3ae1dea7ae81b31910
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Jul 2 10:24:59 2020 +0100

        Improve differential analyses and other fixes

        - Correctly set splicing event when clicking in PCA loadings or in differential analysis table
        - Remove deprecated psi argument from diffAnalyses
        - Avoid plot issues with plot titles
        - Avoid errors when parsing event ID
        - Correct issues when plotting event diagrams in information
        - Copy-edit code and minor changes

    commit 4b1c028128094288811c0eeaffa437f9f9e59ab5
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Jul 1 19:29:18 2020 +0100

        Allow to search using an event ID directly

    commit 623951ee40cc71090debea80b18cf45e47a938fa
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Jun 30 23:28:45 2020 +0100

        Improve volcano plots' tooltips

        - Fix tooltip position
        - Include diagram of AS event

    commit 4d7fff2fe3a0b849dba599cd184ee0dc79fd887b
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Jun 30 17:06:20 2020 +0100

        Improve relevance of PubMed article results

    commit 1f4ff7e5d6e01659afaffab9c6aa79bd9ab5ed30
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Jun 26 20:13:10 2020 +0100

        Fix crash when changing to a PSI dataset without selected AS event

    commit 16aab679e2b369a2d38baf9b3cdfce0528d93604
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Jun 26 20:10:57 2020 +0100

        Improve "gene, transcript and protein information"

        - Select species and assembly directly in annotation (automatically picked based on loaded datasets)
        - Suggest genes based on loaded datasets

    commit 105a405b3af2c15453ff58b48259aa5144fa70df
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Jun 26 13:28:25 2020 +0100

        Fix issues with plotting VAST-TOOLS A3SS and A5SS events

        - Improve searching AS events in AS event selectize, including unhighlighting search results when no query is typed and avoid including SVG code (from diagrams) when searching for AS events
        - Avoid plotting AS event regions if events could not be parsed
        - Copy-edit code

    commit 94c19167715f7acfa56a1e397a462e636584c49e
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Jun 26 12:45:59 2020 +0100

        Avoid searching SVG code from AS event diagrams

    commit a6c38080eb07cdad11c3688a05fbb08af4dac76d
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Jun 26 09:58:03 2020 +0100

        Fix plotting A3SS and A5SS events and always show full coordinates of unsupported diagram events

    commit 312c0b4ddb73880f176b93e9e896c06086953462
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Jun 25 19:11:03 2020 +0100

        Simplify group selection interface

        - Replace button to edit groups with a greyed out dropdown item, simplifying the design of the group selectize element
        - Copy-edit interface

    commit 3713216a46a2496f9317305b76f5547e9f6e6802
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Jun 25 12:28:23 2020 +0100

        Rename vignettes

    commit 2107da0d81411a3b68c6796ae29dddad24206bde
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Jun 25 12:27:25 2020 +0100

        Fix progress bar not animating

    commit d0498355caa2bfd90d3cbb8f54791f6fc5de4a38
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Jun 24 15:46:43 2020 +0100

        Fix problem with geom_density_2d

    commit 2aa7fe5a22d783a55d413137d276dbb7a618cfb9
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Jun 24 15:43:55 2020 +0100

        Fix unexpected VAST-TOOLS types

    commit c32bf742128c44616c9c78479fccbc9878e38b8b
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Jun 23 17:33:45 2020 +0100

        Hide message about filtering gene expression

    commit f5ed4139e81a187e68745c6b054feb02ee3815f7
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Jun 23 16:45:15 2020 +0100

        Show loading indicator when searching for events

    commit bcf4b99ee598fd37db903c97594a5a77b889b5d2
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Jun 23 16:42:45 2020 +0100

        Improve printing of gene list object

    commit 5d38f45edab0f266e3de62b405c69aa9cd049512
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Jun 16 09:43:29 2020 +0100

        Allow to import VAST-TOOLS' inclusion levels table

        - Add attribute "rowData" to inclusion levels containing AS event information, allowing to parse and plot alternative splicing event identifiers from VAST-TOOLS
        - In the visual interface, if plotting is not supported for some event, show its full coordinates
        - Use attribute "rowData" when quantifying psichomics' inclusion levels
        - Improve gene parsing when quantifying splicing with psichomics
        - Create "sticky" objects to preserve their attributes even when extracting data
        - Rename "intron retention" to "retained intron" for consistency
        - Copy-edit code and documentation

    commit 49ca48915fca6612b372e6222fca1d1f75fa3922
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Jun 16 10:42:28 2020 +0100

        Fix unit tests for R 4.0 (#408)

        - Update required R version

    commit c3f588538530c7707c9a109fe821a1488abb1953
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Jun 12 16:56:18 2020 +0100

        Print AS event diagrams

        - Export functions to print AS event diagrams
        - Only print AS event diagram if possible (instead of table)

    commit 205a30a34f065a1227e46df636cb9ddf57d4030c
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Jun 3 22:59:31 2020 +0100

        Improve custom alternative splicing annotation

        - Include gene symbols in custom annotations if available
        - Support more flexible filenames for VAST-TOOLS, rMATS, SUPPA and MISO

    commit 4340f89b9af23a6dd1d47d604510e4b122fbc0ce
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Jun 3 13:31:49 2020 +0100

        Copy-edit NEWS

    commit 635ea7f799c4e572686ca959f3c7531a246a8776
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Jun 2 17:44:16 2020 +0100

        Fix settings not showing for alternative splicing quantification

        - Display filename of gene expression and alternative splicing quantification from recount

    commit 026ce50e441453d4dd0e19e9955b9aa81470b6d5
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Jun 2 10:52:51 2020 +0100

        Improve TCGA code

        - Copy-edit function names
        - Correctly take the most recent Firebrowse data

    commit dea5e14c85289cba3c9a22f9a33329d8a939b9a9
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Jun 1 12:16:45 2020 +0100

        Improve rendering of summary plots

    commit d49a5805bdfef5bd76a8a28bc861843cbc2d3752
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri May 29 17:43:57 2020 +0100

        Parse gene symbols containing underscores

    commit b179ec03939d22a80388765cc0ef576f008f322d
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu May 28 15:00:08 2020 +0100

        Copy-edit code and function documentation

        - Fix unit tests regarding changes in R 4.0

    commit 947ed62290a80b7cec9fed50b1e136e14dd4af74
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu May 28 14:43:29 2020 +0100

        Allow to create Docker images based on code revisions

        - Improve startup message to include psichomics version
        - Avoid unneeded functions that may mask other package functions (rowMeans and rowVars)

    commit c360449e0d364afc1b39e3184c2c3c8fa91be413
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue May 26 15:37:32 2020 +0100

        Create function `plotLibrarySize`

        - Fix library size plot not working properly
        - Improve function documentation of plotRowStats and minor copy-edits

    commit 19ab1733af38042a9df952faa59b70e778cb1d93
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon May 25 15:39:35 2020 +0100

        Fix file browser dialog not opening and warn about selecting mandatory GTEx data options

    commit 5d94ba4f7e5aabb58d762ee9531bd89f54b69857
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri May 22 16:06:56 2020 +0100

        Support GTEx V8 and older releases

        - Improve loading of GTEx data and local files

    commit dd4feaf7f443bce01109dbcb487a046e9043bf30
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Mar 31 15:51:58 2020 +0100

        Try to load cached AS annotations if a timeout is reached

    commit 97023f2a69897f86e2c446563f104b096d7bb287
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Mar 5 12:03:33 2020 +0000

        Fix HTML sanitization in popovers

    commit cf9fc483aa2267caa6b87690c0b22fb1f254c3ba
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Mar 5 10:56:27 2020 +0000

        When plotting density plots, hide Y axis when only showing their rug plots

    commit da7404c3a21434453055cddda867465852167945
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Feb 25 11:07:53 2020 +0000

        Include search in pkgdown website

    commit e0df41302b0dceb0e55ba982b400bb804a72454e
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Feb 7 14:28:45 2020 +0000

        Include search in pkgdown site

    commit 2ae72bf49708a8d63f4ae8ecb435b9893d1b5ad4
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Feb 4 14:16:32 2020 +0000

        Simplify Travis CI config

        - Include link to GitHub page in pkgdown site
        - Fix warnings from Travis CI config validator
        - Use Linux with bioc-release for code coverage and
        - Start code coverage and deployment as soon as possible

    commit a9bb71aff254442561f5ae25d43596a50a9d2b02
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Feb 4 10:06:34 2020 +0000

        Minor changes to pkgdown and function documentation

        - Include link to GitHub page
        - Improve pkgdown reference
        - Copy-edit function documentation

    commit 8ea7f504b74a2c4a18f482e468421e846ac2a754
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Jan 31 13:59:34 2020 +0000

        Update pkgdown

    commit 27587d6647229f8ba513a60b8bad0ccbc7b0e7a4
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Jan 31 13:31:01 2020 +0000

        Copy-edit tutorial, NEWS.md and README.md

    commit 9d956f1685543ecae353c30257999375889b7dfc
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Jan 31 11:02:23 2020 +0000

        Fix warning of Unicode symbol translation in Windows

        R CMD check raises the warning: "unable to translate '<U+2206>' to native encoding". Column names are translated to native encoding if directly set.

    commit c7b18c7c55bdad08cc6f9d8b5841ea739be66d33
    Merge: 415a02f6 52f3b141
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Jan 30 13:14:11 2020 +0000

        Merge branch 'master' into dev

    commit 415a02f6eebed57472516438edf3f2dc87892f13
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Jan 30 13:11:44 2020 +0000

        Avoid Bioconductor warnings when comparing signed and unsigned ints

    commit 52f3b141d985ab2d2de50867953090fc4ed0ce9b
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Jan 29 21:50:46 2020 +0000

        Dev (#403)

        * Improve Travis CI

        - Run jobs through steps
        - Add words to spell checker
        - Test code coverage and deploy even if bioc-devel or macOS jobs fail
        - Only deploy on master branch

    commit d9bfab3374682ea450bdb41d4d34e5ea01cae899
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Jan 29 21:31:31 2020 +0000

        Only deploy on master branch

    commit d4a68aaeb9e3aa255152f5ab016c4cbbe693520e
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Jan 29 19:04:44 2020 +0000

        Add newline

    commit 002dd77093673121994dba9db00e49a9205beb56
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Jan 29 19:02:48 2020 +0000

        Test code coverage and deploy even if bioc-devel or macOS jobs fail

    commit e20bf5344b947aa74a7c14836cb55a7d2cd017ac
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Jan 29 19:01:45 2020 +0000

        Add words to spell checker

    commit bb6fa2cf973f794d5d9ee2b21767bf14cb7fbde4
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Jan 29 18:16:32 2020 +0000

        R in Windows still not supported at Travis CI

    commit 3cb8dcdc1786559c3ae83b3d931a94ca11819395
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Jan 29 18:13:18 2020 +0000

        Improve Travis CI

        - Test on Windows
        - Run jobs through steps

    commit bfb6318485cf3216c93b0ccfedb10a6cd93ebf41
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Jan 29 15:40:34 2020 +0000

        Update NEWS.md

    commit b4e13768bb28355901c8ec0c50785ff11493200e
    Merge: 8e5fc8aa 1b6fc0da
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Jan 29 15:35:51 2020 +0000

        Merge pull request #402 from nuno-agostinho/dev

        Improve usage of pkgdown site

    commit 1b6fc0da6070527caf29c9eee97c556ce7c3257f
    Merge: 98996ded 8e5fc8aa
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Jan 29 15:34:51 2020 +0000

        Merge branch 'master' into dev

    commit 98996ded5f67ffdb9b329f5b11467c6c344a7b92
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Jan 29 10:38:36 2020 +0000

        Improve usage of pkgdown site

        - Include links to MiMB chapter
        - Replace vignette links from RPubs to pkgdown
        - Direct to quick reference instead of listing
        - Update license to current year
        - Copy-edit welcome message

    commit 8e5fc8aa362f97fd97156ad46ff3cc317fc0b919
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Jan 29 00:21:19 2020 +0000

        Revert last commit (did not solve Travis issues)

    commit 64919795f1ebf9111aa2c2c82ef10da3e56f9490
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Jan 28 23:48:48 2020 +0000

        Set up SSH keys between Travis CI and GitHub

        Following tutorial on: https://github.com/alrra/travis-scripts/blob/master/docs/github-deploy-keys.md

    commit b0ce9cf85a1541909f6043072d00639418af8758
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Jan 28 18:54:08 2020 +0000

        Ask for verbose deployment of pkgdown site

    commit 0a9c9d2c59348c90591edb3e4233d0df25cf9bbc
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Jan 28 18:16:18 2020 +0000

        Import shiny::fluidPage

    commit 82767daa06239159bf7a2e9febc5688d0369e681
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Jan 28 17:16:18 2020 +0000

        Fix AppVeyor using release version of R

    commit ab0189024fde749153c28982ae86a7dfc803c35d
    Merge: c2cd46b2 bdc1e3c9
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Jan 28 17:07:55 2020 +0000

        Merge pull request #401 from nuno-agostinho/dev

        psichomics 1.12.1

    commit bdc1e3c90cd8ac7fb70acafb04d0989c608d8c1a
    Merge: 7f1a9834 c2cd46b2
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Jan 28 17:05:42 2020 +0000

        Merge branch 'master' into dev

    commit c2cd46b237b06dd61a2bba714220b7d370708a78
    Merge: 27b677b4 7c933a20
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Jan 28 16:55:10 2020 +0000

        Merge pull request #400 from nuno-agostinho/imgbot

        [ImgBot] Optimize images

    commit 7f1a9834e8faaed78558eb56fb05461f2d07dec9
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Jan 28 16:29:48 2020 +0000

        Avoid test failure by skipping it on CI tools

    commit e23f89dae16a1f10f627a560795d0a43127abe23
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Jan 28 15:02:03 2020 +0000

        Minor changes

        - Fix unit test issues
        - Fix error when using `plotDistribution()` for a single value
        - Copy-edit NEWS.md

    commit 475b712449f5db139901453e85356ebdf74b228f
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Jan 28 14:38:35 2020 +0000

        Browse list of AS event diagrams

    commit e038ea32fc8c01066d7117ffa40cd3b89afe35f7
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Jan 28 14:37:40 2020 +0000

        Filter AS annotation list

    commit f7477f5e51ee57e7c67fd9f9bdfdf8eae04a9184
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Jan 27 23:57:32 2020 +0000

        Fix issues with R CMD build/check

    commit e3c650251cdf2023ea275d6b897ccba2331995d6
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Jan 27 21:34:13 2020 +0000

        Correct spelling issues

    commit 983944d3b0cf7f975021b81700d6efc9804c5551
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Jan 27 21:22:59 2020 +0000

        Fix issues with taking into account another exon as reference

    commit ce61e2c7ecf183ce11be7284d9b7acdaca3b605b
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Jan 21 17:18:25 2020 +0000

        Fix UCSC external link not working based on gene position

    commit 38d61368a649e870f93d061d0fe5f24d96b8feb8
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Jan 21 16:58:51 2020 +0000

        Fix SRA project not loading if extra information fills only one extra column

    commit 4e4ebdd510d70ff8022dbd05e1a95b5c699d0164
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Jan 20 16:35:40 2020 +0000

        Show available annotation information and query PubMed even if Ensembl is down

    commit 7c933a202268984ba77b179faba66e8b7d9be8a6
    Author: ImgBotApp <ImgBotHelp@gmail.com>
    Date:   Sat Jan 18 12:11:22 2020 +0000

        [ImgBot] Optimize images

        *Total -- 2,817.81kb -> 2,014.38kb (28.51%)

        /vignettes/img/UHRF2_expression_prognosis.png -- 97.26kb -> 46.80kb (51.88%)
        /vignettes/img/UHRF2_exon_10_inclusion_prognosis.png -- 47.44kb -> 23.25kb (50.99%)
        /vignettes/img/pca_results.png -- 347.44kb -> 197.16kb (43.25%)
        /vignettes/img/NUMB_exon_12_inclusion.png -- 110.03kb -> 66.18kb (39.85%)
        /vignettes/img/UHRF2_exon_10_inclusion_differential_splicing.png -- 77.23kb -> 47.89kb (37.98%)
        /vignettes/img/UHRF2_differential_expression.png -- 170.04kb -> 108.91kb (35.95%)
        /vignettes/img/3_quantify_splicing.png -- 89.61kb -> 58.73kb (34.46%)
        /vignettes/img/5_pca.png -- 146.58kb -> 97.32kb (33.61%)
        /vignettes/img/4_survival.png -- 84.17kb -> 56.04kb (33.41%)
        /vignettes/img/2_normalise_gene_expression.png -- 70.54kb -> 49.50kb (29.82%)
        /vignettes/img/4_group_tables.png -- 64.14kb -> 45.53kb (29.01%)
        /screenshot.png -- 293.99kb -> 209.80kb (28.64%)
        /vignettes/img/4_data_grouping.png -- 50.17kb -> 36.50kb (27.25%)
        /vignettes/img/1_load_data.png -- 55.78kb -> 41.42kb (25.73%)
        /vignettes/img/diff_expression.png -- 525.58kb -> 421.29kb (19.84%)
        /vignettes/img/diff_analyses.png -- 327.87kb -> 265.16kb (19.13%)
        /vignettes/img/4_save_groups.png -- 42.34kb -> 34.70kb (18.05%)
        /vignettes/img/Correlation_NUMB_exon_12_and_QKI_GE.png -- 189.59kb -> 180.42kb (4.84%)
        /inst/shiny/www/set-operations/fonts/set-operations.svg -- 28.02kb -> 27.75kb (0.98%)

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    commit 9cbef932c55f8edf806cee6be9822af8c13aedd0
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Jan 17 18:02:25 2020 +0000

        Fix tooltip colour when hovering rug plot points

    commit 6dc691bd1a13937d8b4775f2d5b6abc5d06f33a2
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Jan 17 15:38:06 2020 +0000

        Create pkgdown site

        - Copy-edit README, documentation, etc.
        - Improve alternative splicing annotation tutorial

    commit ac83c06f7f2950f6cb8762447f1fe35208bcfff1
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Jan 17 14:12:24 2020 +0000

        Add automatic spell checker and copy-edit documentation

    commit 8450709045cd166beefe3a4c19c37984a7fa1cae
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Jan 17 11:29:02 2020 +0000

        Minor improvements

        - Fix plotSurvivalPvaluesByCutoff example
        - Rename vignettes
        - Copy-edit CLI tutorial
        - Fix R CMD build/check/BiocCheck issues
        - Copy-edit function documentation
        - Add unit tests for SRA metadata loading

    commit 85c54c9e052ca61ad76c4d823046ab85ca091afe
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Jan 17 10:11:56 2020 +0000

        Add AS event diagram to distribution plots and annotation page

        - Avoid app crashing when searching for PubMed articles to many times

    commit 28ee94df2c70355fb76f71bb7748a799eaf20429
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Jan 16 13:07:32 2020 +0000

        Copy-edit NEWS

    commit e5ddf7c9e37160c77ba689f283dbf99562061442
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Jan 16 11:48:36 2020 +0000

        Fix R CMD build issues and copy-edit code

    commit 726a5adbbeb3db4f8d9eb53a21ed01764e887ccd
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Jan 16 11:48:03 2020 +0000

        Fix package dependencies

    commit 08555fabd4260d005c14cbd531e42b24271a43c0
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Jan 16 10:10:41 2020 +0000

        Fix: add code for subset plot

    commit 81f6f1174ad6339d34a7bae00ab8e7b9af9b94fe
    Merge: de9d66b5 94f39514
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Jan 15 19:41:12 2020 +0000

        Merge branch 'dev2' into dev

    commit de9d66b54ded617f41bf29a2dc60673a079939d0
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Jan 15 19:38:01 2020 +0000

        Remove unused function

    commit f2c47bdb34cd80c71d85cf82b506d5ff0f9d2358
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Jan 15 13:47:52 2020 +0000

        Improve data grouping

        - Improve import/export of data groups from/to a file, including colour support
        - Fix discarding of samples not associated with any subject when exporting groups
        - Fix issues related with importing groups based on a file with groups of splicing events and/or genes
        - Inform user when groups are successfully loaded from a file and whether any group elements are discarded in the process
        - Show number of genes in pre-made gene lists
        - When creating group of genes based on pre-made gene lists, discard genes that are not loaded

    commit 04b163d7f1c72f8ee713913db8b3f287079fbd82
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Jan 8 17:02:03 2020 +0000

        Copy-edit code and NEWS

    commit 20e61243055c4d63b32672bf3611f8b04bb2c258
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Jan 8 16:56:29 2020 +0000

        Fix slow preparation of diagram representations of AS events

    commit f9c74c8e4a69a9628d0166e8d8222efa619a7489
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Jan 8 16:50:33 2020 +0000

        Fix error when trying to set page_size for Firebrowse web API

    commit a379bb5798e60bc6e61c3cca34bbacb1e73b89fa
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Jan 7 11:29:06 2020 +0000

        Update documentation regarding survdiffTerms

    commit fa33d46c6f897ee868a1c8c5a1ceedef7a5ec837
    Merge: 1d7116ec 27b677b4
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Jan 7 11:26:13 2020 +0000

        Merge branch 'master' into dev

    commit 94f395143e5a5a4ef2d1075f97ed6854275e8b4a
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Jan 7 11:20:28 2020 +0000

        Fix 0 (valid) rows error

    commit 1d7116ecb67fdbfb43db06d78c23b9ca897e1f87
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Jan 7 11:19:29 2020 +0000

        Include reshape2

    commit f95f8e20c99ecd90fd35844f5f121025bd5f3222
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Jan 7 11:11:21 2020 +0000

        Diagram representation of alternative splicing events

        - Redesign AS event selection; highlight search results using jquery.mark.min.js (built-in highlighter has many bugs)
        - Rename internal CSS/JS files
        - Update jquery-template from 1.3.4 (2016-04-19) to 1.8.5 (2019-02-17)
        - Remove validator.min.js (not being used)

    commit 6806235f5404304cb749b6693cfbd87054acdbbf
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Jan 7 10:53:40 2020 +0000

        Copy-edit code and function documentation

        - Separate utils into different, related scripts
        - Update Roxygen to 7.0.2

    commit f58c252a9c739899ca4d9c4c9fa062fca939de1e
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Jan 7 10:22:14 2020 +0000

        Improve density plot

        - Fix visual bug when plotting a group with only one sample (if one data point is available for a group, only the rug plot is drawn)
        - After hiding all plot series, rug plots of the different groups can be distinguished based on the Y axis (different arbitrary Y values are given to each rug plot series)
        - Rug plot labels now show data values if sample names are not provided
        - Rug plot labels can now be rotated (rotation is not enabled by default given Highcharts issues that may occur at different zoom levels and depending on proximity between different sample values)
        - Fix misguiding example in function documentation

    commit 84f9ec3b0f69b8729c5c3176fb0cf7e66206cc0e
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Dec 20 17:41:20 2019 +0000

        Fix loading of a portion of TCGA data if too many cohorts are selected

    commit 91c46c3a69363d5d98b36a111b02dcc7d773c98b
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Dec 20 13:34:08 2019 +0000

        Improve function documentation

        - Include information on function family
        - Clean up documentation of aliases and deprecated functions
        - Change patient to subject where appropriate
        - Copy-edit CLI tutorial

    commit c569febbc2f8f77a8003f6c4b9dd6304db5d1bcd
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Dec 19 16:43:17 2019 +0000

        Fix issues with junction quantification files

        - Improve tutorial on loading user-provided data
        - Warn when discarding rows with duplicated rownames
        - Warn when discarding rows containing random, alt and Un (unknown) chromosomes
        - Fix error when returning NULL dataset after processing
        - Copy-edit code
        - Test junction quantification file loading

    commit 5fbc5bdc8ab3de2aec982a9b3c8febfe94809b5a
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Dec 17 15:08:42 2019 +0000

        Support junction coordinates from chromosomes M, Z and W

        - When loading custom junction quantification files
        - Copy-edit information on the format of custom files

    commit e4e8e918cd6b4830b31ed7b0a07abdb462481042
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Nov 7 14:46:07 2019 +0000

        Add ORCID identifiers

    commit 27b677b4d6929ab5a0690b3abc21a77077a13736
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Oct 7 18:18:58 2019 +0100

        Update README.md

    commit 77ff8427f0f4a810ece914cbc99db54a646df4a8
    Merge: 50ebb496 4550109a
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Oct 7 18:16:59 2019 +0100

        Fix Windows warnings in CI tools

    commit 4550109aac0d2180d44e45b01598f7552517c569
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Oct 4 13:49:29 2019 +0100

        Avoid using Bioconductor-devel (wrongly trying to use R-devel)

    commit 05dec272fdc65906c1c73c7e37e69eff1317cd3d
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Oct 4 13:45:19 2019 +0100

        Bump version to 1.10.2

    commit f403ca10dd6f9595af5e7ed534a6101efbb760d1
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Oct 4 10:05:40 2019 +0100

        Install r-lib/remotes from CRAN instead of GitHub

    commit 7f4ad886741271dc774ce750222dda1b0b03eb94
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Oct 4 09:59:53 2019 +0100

        Fix link to ggrepel::geom_label_repel not being found on Windows CI tools

    commit 50ebb4961783ce4751ef4b492c8428b837802a65
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Sep 19 13:13:38 2019 +0100

        Bump version to 1.10.1

    commit 2e2abe34478ccf8fb14d177f2ce0eeaae817996b
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Sep 19 13:04:23 2019 +0100

        Avoid test timeouts in CI tools and Bioconductor

    commit 3f3f8872b35e321f524599ae8913aa3ca4a40eaf
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Sep 16 19:20:58 2019 +0100

        Fix AppVeyor (#387)

        Install *org.Hs.eg.db* and *GenomeInfoDbData* packages via source (instead of binary which is unavailable)

    commit 6f41576364d55a3dd9a0299a78d08c8c3069c62a
    Merge: 8711c313 6d9f0824
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Sep 16 16:34:43 2019 +0100

        Merge pull request #388 from nuno-agostinho/travis-mac

        Support macOS testing via Travis-CI

    commit 6d9f08241245a75c1469c7ad1d5fac455ab2fbf7
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Sep 16 15:46:34 2019 +0100

        Support macOS testing via Travis-CI

    commit f912e3d65be79c9bd52e38e58cff285bd2d8cd94
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Jun 24 17:17:46 2019 +0100

        Improve dialog when trying to load a local folder without any supported files available

    commit 6f714d3578ce7a6d2f89a400f10907b6c88acc1b
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Jun 19 17:33:17 2019 +0100

        Improve GTEx data loading

        - Export getGtexDataTypes()
        - Improve available examples

    commit a1ca8d232ff76a824fd935f2690e4628d5cdfdba
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Jun 19 14:51:22 2019 +0100

        Fix alerts crashing the app

    commit e07766a3583da3c318be50eaa3477b9322a96658
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Jun 19 14:06:35 2019 +0100

        Improve AS annotation loading

    commit d0745def60c2469178b0341697c110b086497040
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Jun 3 13:54:24 2019 +0100

        Fix prepareGeneQuant not working for stranded datasets

    commit 4fc0ed6e3872a15a6091f5c656164be7fa806e77
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri May 3 14:05:13 2019 +0100

        Fix Firebrowse function not loading all expected data

    commit 8711c313fd02fb095c496a2b9242193d5d1e7b4d
    Merge: e87a817f 15236616
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Sun Apr 21 18:33:33 2019 +0100

        Merge pull request #384 from nuno-agostinho/evalWithTimeout

        Replace usage of deprecated function

    commit 1523661611913ceef6a3f3bd6e1b89c9ce3ac716
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Sun Apr 21 18:08:51 2019 +0100

        Replace usage of deprecated function

    commit b952a879b3bf23f3759312c86677ad8b0a16f764
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Apr 2 14:26:14 2019 +0100

        Fix p-value plot bugs

    commit e87a817f84eb88df17a3a4f53fef2b94e7a560c1
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Mar 27 16:20:05 2019 +0000

        Update .travis.yml

        Based on https://github.com/Bioconductor/BiocManager/blob/master/.travis.yml

    commit f15ab1875b318554d568022228f33a8a3e3def20
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Mar 27 16:16:02 2019 +0000

        Fix appveyor.yml

        Based on https://raw.githubusercontent.com/Bioconductor/BiocManager/master/appveyor.yml

    commit 3cf6a9b743356485fd354175173440fb270a35f8
    Merge: cad23d89 1f121b7a
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Mar 27 13:24:40 2019 +0000

        Merge branch 'dev'

    commit 1f121b7a9263a9bc1348fe95ed10a32f93b4113b
    Merge: db6c24f4 6ab7ab5b
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Mar 26 17:53:02 2019 +0000

        Merge branch 'dev-2' into dev

    commit 6ab7ab5b7faf8f0755df4585415f0cb281ed1aea
    Merge: b91903c6 cad23d89
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Mar 26 17:52:17 2019 +0000

        Merge branch 'master' into dev-2

        # Conflicts:
        #	NEWS

    commit b91903c6b07bf50e1cbe67bf46b06343a39d9320
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Mar 26 17:51:23 2019 +0000

        Fix R CMD check and BiocCheck issues

    commit db6c24f4af2b371c061b96577479a59aca9097ce
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Mar 26 17:45:11 2019 +0000

        Fix R CMD check and BiocCheck issues

    commit 71e896c1c008fce02fbad5de282327816ef39a33
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Mar 26 17:28:24 2019 +0000

        Improve and fix function examples

    commit e29243d6e5d2783019182604c4ada9b96dba7582
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Mar 26 13:47:16 2019 +0000

        Fix issues in R CMD build/check

    commit db83ac6395086c9ab0d244fff1eced5734c41965
    Merge: 17e2fbd3 1deea8a5
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Mar 26 13:31:49 2019 +0000

        Merge branch 'dev' of github.com:nuno-agostinho/psichomics into dev

    commit 17e2fbd3026f133b864b60a08bbb742a373b2f53
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Mar 26 11:25:15 2019 +0000

        Fix issues in R CMD build/check

    commit 1deea8a5ceb0c77ff269cffe6e4762d205433468
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Mar 26 11:25:15 2019 +0000

        Copy-editing

    commit 1190319ef6dab35921c8fb3c9870a29c5befe51a
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Mar 26 10:04:36 2019 +0000

        Fix issues using EList's gene expression for correlation analyses

    commit d6ecc35918e88ce390a51026234c38824cd18581
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Mar 25 16:00:29 2019 +0000

        Code copy-editing

    commit 0fefbe1d1cc79a2c554321ef62af02ce37647cb8
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Mar 25 15:58:12 2019 +0000

        Make it clearer that TCGA data is loaded from Downloads folder by default

    commit 885ed2cc3315d2efaa7795679597f7b2e29f4810
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Mar 22 09:22:18 2019 +0000

        Plot p-values by cutoff

    commit 388aef18906d504e4edfef4294d8152935b63322
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Mar 22 09:14:01 2019 +0000

        Minor bug fixes and improvements

        - Allow to edit path in file/directory browser elements
        - Automatically set dropdown width for group attribute selection
        - Fix warning when displaying group preview only based on subjects or samples
        - Prepare for code escaping in newer JavaScript versions

    commit 37a0afa77baec0645d9378d24cd0acb57d1af1de
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Mar 21 15:11:35 2019 +0000

        Fix issues with R CMD check

    commit d1246e4b8322f3cce87fcacb76894dc2e34ccb56
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Mar 21 14:55:48 2019 +0000

        Require human gene annotation

    commit 87a2d3d83d46f2660576f905222a3c1df1638da7
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Mar 21 11:21:05 2019 +0000

        Fix table filtering based on plotted points

    commit 3cb42cf98e05b35bd2006ab9ae5f85833e707032
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Mar 18 15:43:04 2019 +0000

        Improve and fix plotting of gene expression and alternative splicing quantification data

    commit 1caf8bada79c40a23afb39422050550f2c9aae6d
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Mar 15 16:22:27 2019 +0100

        Plot specific combinations of gene and alternative splicing events after performing correlation analyses

    commit 387d63051f11ccee7856271f8369b38570b3d556
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Mar 8 14:24:35 2019 +0000

        Improve AS and GE filtering

        - Present PSI filtering settings in the visual interface
        - Minor interface tweaks
        - Fix plot PSI error

    commit 0a094a868e124e5ec115d1f5f3c169ae057fdafe
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Mar 8 13:45:24 2019 +0000

        Update citation details

    commit b6d0909be72ed3d54fabd3378aae050e14ec4082
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Mar 7 15:27:54 2019 +0000

        Allow to use selected splicing event in correlation analysis

    commit 1fb75cbb1f6de14bbcff49a1fa2ed1f942a0e3ce
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Mar 6 18:58:47 2019 +0000

        Fix error when subsetting edgeR::DGEList

    commit b0be91e288bab1d1a3f2917dc4ea0a917400382d
    Merge: 47bee247 76ba81ea
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Mar 6 14:50:34 2019 +0000

        Merge branch 'dev' of https://github.com/nuno-agostinho/psichomics into dev

        # Conflicts:
        #	NEWS
        #	R/data.R

    commit 47bee24752a09aae6052235133a41d5c30e71f14
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Mar 6 03:01:52 2019 +0000

        Minor copy-editing

    commit 972e5582a5cc7664a89542dc37edf926e7b27e65
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Mar 6 02:59:35 2019 +0000

        Improve correlation plots

    commit 25ece479739d264f1f86898a98b703b6355ffbe6
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Mar 6 00:36:02 2019 +0000

        Fix missing attributes of gene expression normalised via voom

    commit a949e3a91ad0a650c39a57e0351e9bae1f702b73
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Mar 6 00:34:12 2019 +0000

        Fix error when creating groups containing only samples and no matching subjects

    commit a063ae9c3e8485ec8321719898a43a2e1eced67b
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Mar 5 15:54:02 2019 +0000

        Improve GTEx and other data loading

        - Automatically download and load GTEx data
        - Only display at most the first 100 columns for performance reasons
        - Improve data loading titles
        - Default to load clinical, junction quantification and gene expression data when selecting TCGA data
        - Minor copyediting

    commit 76ba81ea5f6d3f13761ab733550daa2e703252bc
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Mar 5 15:54:02 2019 +0000

        Improve GTEx and other data loading

        - Automatically download and load GTEx data
        - Only display at most the first 100 columns for performance reasons
        - Improve data loading titles
        - Minor copyediting

    commit f344fc0607fdf20cf78e91ecaf4e40f8ff337493
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Mar 5 15:50:28 2019 +0000

        Fix article title formatting

    commit ad81788ad9241386b34349bb6d912824a7ff51e8
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Feb 28 11:57:54 2019 +0000

        Improve gene expression filtering and normalisation and PSI filtering

        - Plot distribution of gene expression per sample
        - Plot distribution of library sizes
        - Plot gene-wise expression mean and variance across samples
        - Plot PSI mean, variance and range
        - Filter PSI values
        - Perform voom and respective normalisation if desired
        - Sample filtering
        - Filter lowly expressed genes using edgeR::filterByExpr
        - Convert ENSEMBL identifiers to gene symbols
        - Show labels for distribution plots

        Bug fixes:
        - Fix distribution plots requiring all samples in a group
        - Show sample names in distribution plots
        - Fix inconsistency of delta median and variance

    commit 795d17597f7d639681aa2cf33937ecd8a0c7eea8
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Feb 18 11:15:56 2019 +0000

        Improve SRA data loading

        - Accept a vector of files as the first argument (easier to use with `list.files()`)
        - Ask to overwrite file if one exists with the same name as the output file

    commit 161f9c2da7bf5139bda1a56c0bd8aebf76268b9e
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Feb 18 11:03:53 2019 +0000

        Minor copyediting

    commit 2fb74587d87c9a8a6fc2e85c1c429faf4ea1d3b6
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Feb 18 11:02:33 2019 +0000

        Update copyright references to 2019

    commit 808b219acfb5b317afc0fe232cb268a49a51cd52
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Feb 13 17:05:57 2019 +0000

        Fix colours/opacity in the rug plot within the distribution plot

    commit 7536285cb2fcea357ff945ce96192b6aff815396
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Feb 7 17:46:53 2019 +0000

        Fix wrong information in table of differential splicing results

    commit cad23d89b8f07420b6cd90067b9ede60a4651881
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Dec 3 14:59:22 2018 +0000

        Add tag ImmunoOncology to BiocViews

    commit a1510c15977c36b6c9863b0a0ba0140243b9b8c5
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Dec 3 11:54:33 2018 +0000

        Add tag ImmunoOncology to BiocViews

    commit 676ecb0b64f593ce3a9b4d3d5fbc4adae17fd1d2
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Nov 29 23:10:02 2018 +0000

        Fix crash when loading psichomics with test data that is not locally available

    commit 5bf83e4e96ac73180b6187239c7d2f570da21c1e
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Nov 8 16:59:39 2018 +0000

        Fix R CMD check and BiocCheck errors and warnings

    commit bb78b2be6e8c9457b5772435a574e728c870504e
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Nov 8 16:59:27 2018 +0000

        Fix progress bar when quantifying alternative splicing

    commit 19fea9e64f53c3e0479b61db08adee359ced772d
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Nov 7 15:46:13 2018 +0000

        Improve documentation of exported and internal functions

        - Minor code copy-editing
        - Minor tutorial copy-editing

    commit 23e38acd50866c16438a4dc6399173d98e52259b
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Nov 7 11:47:25 2018 +0000

        Minor improvements

        - Bump version number
        - Allow to show dataset icons in "Data"
        - Improve data grouping interface
        - Fix inconsistent group names when creating groups based on pre-made gene lists
        - Avoid error when user cancels file browser dialog to load groups from a file
        - Copy-editing code and documentation

    commit 65cc716dd58d1ea9a577e34d898c24b92308853a
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Nov 7 11:25:38 2018 +0000

        Ask before replacing correlation analyses

    commit 661a73a2bc12c54227a97c0003eccb022dfdab28
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Nov 7 11:24:40 2018 +0000

        Copy-edit tutorial on custom alternative splicing annotation preparation

    commit 09210d45c4a69f37355299acff1d074e3e3c2349
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Nov 7 11:21:38 2018 +0000

        Improve console logging of alerts

    commit e81cee95712934e4ba04b8100e7cee13d99874cb
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Nov 6 15:44:19 2018 +0000

        Decrease loading time after alternative splicing quantification

    commit d65138081a2c0f25c4c4f59e8cac3aa99fe68cf2
    Merge: 950fead2 0166a557
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Nov 5 17:45:15 2018 +0000

        Merge branch 'dev' of https://github.com/nuno-agostinho/psichomics into dev

    commit 950fead2c87b45eef1c57ba0ecc5221405648e07
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Nov 5 17:43:56 2018 +0000

        Change which AS event types are quantified by default

    commit af7d87997ca811bc3dae0c9bca5e964eb92ff713
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Oct 31 17:37:25 2018 +0000

        Load pre-made gene lists and improvements to correlation analyses

        - Display correlation results in a table
        - Display correlation analyses progress
        - Load those groups by default and allow to create them in the group interface
        - Initial support for RBPs in Sebestyen et al. 2016
        - Allow to use such groups in correlation analyses
        - Improvements to interface for correlation analyses
        - Minor copy-editing and interface improvements

    commit 757f821eacadef804a39c948dc8752bec86bba88
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Oct 30 18:37:13 2018 +0000

        Fix link for AS annotation creation and loading

    commit cc0ddc5999ac10060c83dcff1cdf35356e5e5aa7
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Oct 30 18:29:53 2018 +0000

        Fix word break-related visual issues

    commit f59713d9a5b76005ca392b10477376fa3fb4c941
    Merge: 650c0bcd 0166a557
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Oct 2 09:44:32 2018 +0100

        Merge pull request #366 from nuno-agostinho/dev

        Update citation link

    commit 0166a5578b61fcb0af3c4a9643402d3ac886869c
    Merge: c78f8054 650c0bcd
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Oct 2 09:44:13 2018 +0100

        Merge branch 'master' into dev

    commit c78f80540dbb9a3bef754317251d16403c57c8df
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Oct 2 09:42:49 2018 +0100

        Update citations to link to article in Nucleic Acids Research

    commit 650c0bcdc1728a113a1a11e095c16b07c3a10881
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Oct 2 09:22:01 2018 +0100

        Update NEWS date

    commit ebb47d9cc359f8539e319b67ee7512dd55a92eb9
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Oct 2 08:56:29 2018 +0100

        Minor changes

        - Update LICENSE for current year
        - Update clinical dataset used in vignettes

    commit ed1ad926df259ee936a9c0175a3f59024595895e
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Sep 20 16:53:57 2018 +0100

        Improve TCGA data download modal and minor changes

    commit 1614e3e3a35a4c8f15a05a45623584d234c98f20
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Sep 20 16:51:43 2018 +0100

        Add metadata regarding loaded and created datasets

    commit fbb70cc6b0a0a892716fd4fe6b0e7a9734bf1aff
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Sep 18 17:56:21 2018 +0100

        Fix errors, warnings and notes from R CMD check/build

    commit ae48e0e42ecd7c2217e7e5acc6ef1af5514aadaf
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Sep 18 16:50:37 2018 +0100

        Fix allowing to select a directory when requesting a file

    commit ad6777fd7a401b37b659bb5440449a79b8450545
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Sep 18 16:49:38 2018 +0100

        Fix allowing to select a directory when requesting a file

    commit e08b64dd60fa56ee697557beb2090724f8f28896
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Sep 18 15:49:59 2018 +0100

        Minor changes and code copyediting

    commit 3229d8ce5f23237f67119ce45eb23e545aabc4c3
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Sep 18 15:45:49 2018 +0100

        Improve file browser dialog in remote server

        - Allow to directly input a path without using the file browser dialog
        - Display warning when calling the file browser dialog in RStudio Server or in an unsupported system

    commit 9953f4f41d7b573653e23bb4ac45df864cbab160
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Sep 18 15:17:31 2018 +0100

        Fix issues in downstream analyses when using GTEx data subset by tissues

    commit 5fc56fd9162549d11daf7aa6271274b9c2323112
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Sep 17 16:19:46 2018 +0100

        Inform of sequencing technology used to obtain gene expression data from TCGA

    commit f7921b88d00b7da95c5acd379abd56d14088cf5c
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Sep 17 15:40:24 2018 +0100

        Improve console logging of error and warning messages

        - Check if files exist before loading local data
        - Check if any projects are selected and if given directory exists before downloading recount2 data

    commit c9fa821990d83f6fe223aa97de8b9265d2050ab1
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Sep 5 15:19:03 2018 +0100

        Improve group selection and correlation analyses

        Group selection:
        - Show group colour in group selection element
        - Avoid moving "Create groups" due to group creation preview

        Correlation analysis plot:
        - Colour samples by group
        - Render contour based on a density estimate
        - Interface changes to make it more intuitive
        - Fix Loess curve gaussian fitting regardless of the fitting argument

    commit 4f4cd0fe701f891d536bd13d227a908878b8e722
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Aug 30 15:51:42 2018 +0100

        Fix forced axis limit of density plot

        When plotting values within 0 and 1, limit X axis to 0 and 1; otherwise, do not limit X axis

    commit 54dea1bdb5f19a49683e3a24cc6f33964657e9fb
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Aug 15 21:43:50 2018 +0100

        Fix data group display when Patients or Samples are unavailable

        Minor changes:
        - Copyediting

    commit 8b5e1b106d6b4a3556bd6c57dd1bd1786053a660
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Aug 15 21:43:50 2018 +0100

        Fix data group display when Patients or Samples are unavailable

        Minor changes:
        - Copyediting

    commit b4fcaeaef1238f77a19b6262a6bbbea88e265940
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Aug 15 20:18:02 2018 +0100

        Improvements to data loading

        - Fix wrong parsing of recount's sampe metadata when fields across samples are not the same
        - Fix GTEx data loading as numeric instead of factor when filtering by tissues
        - Check if GTEx data files exist before attempting to load them
        - Copyedit code and user messages

    commit 2a2c46a84954e56ae792f075207a1fc7c6eb1f74
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Aug 15 20:13:53 2018 +0100

        Search PubMed instead of PMC

    commit ad607e31af37c0a65de674140e4f45ba04cef0e2
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Aug 13 18:07:50 2018 +0100

        Updated roxygen version

    commit 2e29f55d2a884216e4eb623772018a6f61683624
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Sun Jul 15 18:29:13 2018 +0100

        Minor improvements)

        - Update screenshot
        - Allow to select hg38 assembly when loading PSI quantification
        - Improve correlation's interface
        - Improve selection of icons used
        - Copy-editing

    commit 4593c1ffe040e390b5ec049c449a82ad725c6dcb
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Jul 9 19:30:46 2018 +0100

        Clean code for differential analyses

    commit 2f7c7e695f269a454f0a7de1e17872ec6c835217
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Jul 9 19:30:46 2018 +0100

        Clean code for differential analyses

    commit d3218e2997a5c238827332cf8d1e16a33fbbf496
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Jul 9 16:52:52 2018 +0100

        Copy-edit

    commit 327bf525aeb1fb599f400b05c5ae51074db77c44
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Jul 6 17:56:24 2018 +0100

        Allow to input formulas when highlighting points

        Other minor changes:
        - Fix filenames of exported tables mentioning differential splicing analysis instead of differential expression analysis
        - Minor style changes

    commit dace8973cd449c327d17e068fa680c1af0851bc5
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Jul 6 17:25:25 2018 +0100

        Copy-edit README and update screen shot

    commit 8c6e49459bf060426fd4dec5c97a0437b9fb8295
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Oct 2 09:22:01 2018 +0100

        Update NEWS date

    commit 9f57a89e0a585cf095b39298c276a3a5385afd0a
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Oct 2 08:56:29 2018 +0100

        Minor changes

        - Update LICENSE for current year
        - Update clinical dataset used in vignettes

    commit a766175c2c1814c06ae700cefc2dbedf54e09272
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Sep 20 16:53:57 2018 +0100

        Improve TCGA data download modal and minor changes

    commit 72c7322885372c86ec86a7160ff366549f1e7c04
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Sep 20 16:51:43 2018 +0100

        Add metadata regarding loaded and created datasets

    commit 6ef892922d492ea1b23bd36ddd970bb72c27caca
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Sep 18 17:56:21 2018 +0100

        Fix errors, warnings and notes from R CMD check/build

    commit 644b5514e8ddc046e3ea9b4db38a25928da50ef3
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Sep 18 16:50:37 2018 +0100

        Fix allowing to select a directory when requesting a file

    commit 4ba02ed2c43d15f44f7c04a68c9c04f6b854536b
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Sep 18 16:49:38 2018 +0100

        Fix allowing to select a directory when requesting a file

    commit 4d7e49cf6e5884f7b70bd31cf5809b7ad407f3b8
    Merge: 193ac794 660ff9d8
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Sep 18 15:50:12 2018 +0100

        Merge branch 'dev' of https://github.com/nuno-agostinho/psichomics into dev

    commit 193ac794afb5ba5ecc87a8434e6d98a8ad5b264e
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Sep 18 15:49:59 2018 +0100

        Minor changes and code copyediting

    commit 826edf1ecb8a4d56472cf35392919ae485e53a6b
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Sep 18 15:45:49 2018 +0100

        Improve file browser dialog in remote server

        - Allow to directly input a path without using the file browser dialog
        - Display warning when calling the file browser dialog in RStudio Server or in an unsupported system

    commit d2a64dbf7f7ab3189334b6de72623685b47f920d
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Sep 18 15:17:31 2018 +0100

        Fix issues in downstream analyses when using GTEx data subset by tissues

    commit 10cb3df4c0304152629e18fec97a1fa880bcef8b
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Sep 17 16:19:46 2018 +0100

        Inform of sequencing technology used to obtain gene expression data from TCGA

    commit 486d43c20f70f1f18f4b6ea3988c31558f719940
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Sep 17 15:40:24 2018 +0100

        Improve console logging of error and warning messages

        - Check if files exist before loading local data
        - Check if any projects are selected and if given directory exists before downloading recount2 data

    commit bddf111e81a70a988d8c06c31147518592098412
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Sep 5 15:19:03 2018 +0100

        Improve group selection and correlation analyses

        Group selection:
        - Show group colour in group selection element
        - Avoid moving "Create groups" due to group creation preview

        Correlation analysis plot:
        - Colour samples by group
        - Render contour based on a density estimate
        - Interface changes to make it more intuitive
        - Fix Loess curve gaussian fitting regardless of the fitting argument

    commit eae64553ff843b09a8013c6565f9a75bb47f9876
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Aug 30 15:51:42 2018 +0100

        Fix forced axis limit of density plot

        When plotting values within 0 and 1, limit X axis to 0 and 1; otherwise, do not limit X axis

    commit 48189e1b1a8a49b2f45816c448da9b0cc5e71149
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Aug 15 21:43:50 2018 +0100

        Fix data group display when Patients or Samples are unavailable

        Minor changes:
        - Copyediting

    commit 660ff9d802bd2f9d7eb920b519dfe0d74906904b
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Aug 15 21:43:50 2018 +0100

        Fix data group display when Patients or Samples are unavailable

        Minor changes:
        - Copyediting

    commit 788366fff3a0e37fd5a4bb7f5829b7c3fde6a9d5
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Aug 15 20:18:02 2018 +0100

        Improvements to data loading

        - Fix wrong parsing of recount's sampe metadata when fields across samples are not the same
        - Fix GTEx data loading as numeric instead of factor when filtering by tissues
        - Check if GTEx data files exist before attempting to load them
        - Copyedit code and user messages

    commit d7792511a47552b836047659736db4cf7fc1462b
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Aug 15 20:13:53 2018 +0100

        Search PubMed instead of PMC

    commit d5f8c587115cc23b4a07e496c8f07a5ba86bfe58
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Aug 13 18:07:50 2018 +0100

        Updated roxygen version

    commit 40aeed67aa0e24588ab126f7fd03537583d09ac4
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Sun Jul 15 18:29:13 2018 +0100

        Minor improvements)

        - Update screenshot
        - Allow to select hg38 assembly when loading PSI quantification
        - Improve correlation's interface
        - Improve selection of icons used
        - Copy-editing

    commit ca61fe24d1f043edd937be09e816f40ed1f0c9c7
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Jul 9 19:30:46 2018 +0100

        Clean code for differential analyses

    commit 455faf68c9dc1ebee8bd1cba8d0f0e6743b5154a
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Jul 9 19:30:46 2018 +0100

        Clean code for differential analyses

    commit 7e2e449e90b11da3ff93247ccbc58e33dfb6218e
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Jul 9 16:52:52 2018 +0100

        Copy-edit

    commit 8b4a7e91d71b858ea16b763d6929643d1b216f04
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Jul 6 17:56:24 2018 +0100

        Allow to input formulas when highlighting points

        Other minor changes:
        - Fix filenames of exported tables mentioning differential splicing analysis instead of differential expression analysis
        - Minor style changes

    commit 3b246807f63fa611d8ace55e3245965aaccac351
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Jul 6 17:25:25 2018 +0100

        Copy-edit README and update screen shot

    commit e392f34ebc314e4e7360ccbb3685fe4119734718
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Jul 5 20:09:09 2018 +0100

        Update README.md

    commit bf424d7bc72d8c9eff2cf92c920b883ec7ea9552
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Jul 5 20:01:13 2018 +0100

        Update README.md

    commit 66e932b545d0e533d7a3025de1216fb989465321
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Jul 5 19:57:39 2018 +0100

        Update README.md

    commit 946af16ddbe473f074e560ba248e40b54f8359c6
    Merge: 0aac8a4d 9ea793f8
    Author: Nuno Agostinho <danielagostinho@sapo.pt>
    Date:   Thu Jul 5 16:45:04 2018 +0100

        Merge pull request #361 from nuno-agostinho/dev

        Version 1.6.1

    commit 9ea793f87b94f1d916200d7431eea90e90bcf2d7
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Jul 5 15:59:26 2018 +0100

        Add placeholder

    commit 99e7b05fd75667a856b3d7254d2444b5063430b8
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Jul 5 15:11:47 2018 +0100

        Add more options when plotting gene expression versus PSI values

        - Change font size
        - Change plot height
        - Improve presentation of scatterplot options

    commit c4cbb939fdc4f0c0eb83e5a556895650974fb285
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Jul 5 14:26:46 2018 +0100

        Simplify code for file format recognition

    commit 0f976abc5570ae7407fdd0ea19af92ee62a15f13
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Jul 5 14:09:37 2018 +0100

        Improve group creation and manipulation

        - Greatly improve speed at which a big file is marked as incorrect (by loading just the first row instead of the first six rows of a file...)
        - Fix error alerts not appearing when trying to create groups based on invalid parameters
        - Add error alert when trying to load file without group information when such data is expected
        - Improve style of group preview table

    commit 864fd363e59a050aa89f5dc614c207d130d998a0
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Jul 5 11:45:03 2018 +0100

        Fix unit tests for parsing splicing events

    commit cd795942df7123e959bef96c36c03a0c8d956b4c
    Merge: cb459489 0aac8a4d
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Jul 5 00:11:41 2018 +0100

        Merge branch 'master' into dev

    commit cb459489889a9f185d4b15ee792bb3cd6becf05f
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Jul 5 00:06:35 2018 +0100

        Minor changes

        - Copy-edit NEWS
        - Change order of analyses (makes more sense this way)

    commit 09c0622f25d775e282d415c20a0bdb828a5669bb
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Jul 4 18:18:57 2018 +0100

        Display alternative splicing events in transcript plot

    commit 0aac8a4d1f5f9e3352612a1d3b901faacc7723b7
    Author: Nuno Agostinho <danielagostinho@sapo.pt>
    Date:   Wed Jun 27 17:21:32 2018 +0100

        Travis-CI and AppVeyor fix (#360)

        * Fix issues with GenomeInfoDbData and DelayedArray installation in AppVeyor
        * Use binary packages to speed up Travis-CI builds

    commit 47cd9d40d6b374ad1ffd5f397a4b7920bd4fcf4c
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Jun 26 18:58:47 2018 +0100

        Fix issues in R CMD check and BiocCheck

    commit 9de9492c581732f7cfd296f9f44478eb4b7cf699
    Merge: 92236436 30ff9e8a
    Author: Nuno Agostinho <danielagostinho@sapo.pt>
    Date:   Tue Jun 26 17:45:49 2018 +0100

        Merge pull request #359

        Version 1.6.1

    commit 30ff9e8aa73036e42a2a0203de606787729574fc
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Jun 26 17:40:46 2018 +0100

        Rollback to before introducing event-wise Cox models (re-think if this is the best solution or not)

    commit 36d3163410f32578a195eec7d204d6334ddcbe65
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Jun 26 17:02:34 2018 +0100

        Improve data grouping

        - Preview groups based on selected attribute before creation, closes
        #218
        - Correctly suggest how to select variables in subset expression and
        give more examples on how to use this feature, closes #220
        - Fix subject/sample attributes not being updated for selection for the
        GREP interface
        - Minor copy-editing

    commit dfdcb3fdfb06591c0a050e22bbdac8d1fef33f9e
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Jun 26 16:59:31 2018 +0100

        Update NEWS

    commit 5de4ee0251eab26e9f205d793190dec57f2aed4a
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Jun 25 16:26:12 2018 +0100

        Recommend installing psichomics through BiocManager

    commit 2a9f6ab5820cb39fffbb470a1b92e20a635ce394
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Sun Jun 3 23:26:17 2018 +0100

        Fix error if named samples are given

    commit b3cd480ba9acd37f5948be7532f5923ab6fbc335
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Sun Jun 3 15:47:28 2018 +0100

        Minor improvements

        - Improve display of filtered genes
        - Update default minimum samples used based on available samples
        - Render position of splicing event when plotting transcripts

    commit a155800df9380649e461bbd5aa8d0bbe8711d451
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Sun Jun 3 15:20:07 2018 +0100

        Improve support for loading custom data

        - Prepare gene and junction quantifications (STAR output) and SRA metadata to be loaded into psichomics
        - Add tutorial on how to analyse SRA and user-owned data
        - Update other tutorials
        - Fix data not being loaded when fread returns a warning related to issues with previous fread commands

    commit fb347b1842f935e9251f60f1cf8d8c4ff5131e1a
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Sun Jun 3 10:33:20 2018 +0100

        Fix warning when using deprecated function limma::toptable

    commit a79e15837ca633766d0397432f1704ecd1de30ae
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Sun Jun 3 10:30:14 2018 +0100

        Fix crash when quantifying splicing for a single sample

    commit ba626a461dbdc236499392d798564c3b53a04eac
    Merge: caa07c20 9c1b3da2
    Author: Nuno Agostinho <danielagostinho@sapo.pt>
    Date:   Sun May 20 16:49:14 2018 +0100

        Merge pull request #356 from nuno-agostinho/recount2

        Add support for recount2/SRA data

    commit 9c1b3da2306a4a60b3f97c5a0fe6e54262f4f50e
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Sun May 20 16:40:48 2018 +0100

        Minor improvements

        - Bump version
        - Update NEWS
        - Fix issues with R CMD check
        - Hide close button in progress notification

    commit 203a0fd493387983ce8f50caa2cf9118b62f0d7f
    Merge: 6702d93c 32213531
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Sun May 20 15:54:53 2018 +0100

        Merge branch 'recount2' of https://github.com/nuno-agostinho/psichomics into recount2

        # Conflicts:
        #	R/data_recount.R

    commit 6702d93c929e7818ec2a8f992936032d583f5dee
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed May 16 14:46:22 2018 +0100

        Load SRA data using recount R package

        - Load gene expression, junction quantification and sample metadata from SRA projects
        - Update documentation (including copyediting)
        - Improve hg38 splicing annotation

    commit 3221353188fa26be22296c0fa596efa5040e8c6b
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed May 16 14:46:22 2018 +0100

        Load SRA data using recount R package

        - Load gene expression, junction quantification and sample metadata from SRA projects

    commit b22a2ca081d095d87fd7581f6a9384f6575ed6f3
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu May 10 15:18:36 2018 +0100

        Minor revisions to survival

        - Add link to survival page from Cox regression results withing the table containing the results from exploratory differential splicing analysis
        - Use minimal p-value to decide the optimal PSI cutoff (makes more sense)
        - Improve p-value plot, including labelled line with the p-value threshold and
        - Minor copy-editing

    commit d0304ffd165e31e25cc665c3067db3877b4a5b4c
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue May 8 15:29:57 2018 +0100

        Perform event-wise Cox models using PSI values

    commit 20e84802e4827d7161276129577bd2fcc626b08a
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue May 8 15:10:34 2018 +0100

        Fix crash when inputting non-sense as the axes for the splicing scatter plot

        For instance, discard:
        - Non-numeric values
        - Numeric values when min > max

    commit f3645f0247f8e01f6e5873f09ac8c765fe3904d3
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue May 8 14:51:32 2018 +0100

        Allow to start app with test data (for dev purposes)

    commit caa07c20f35289f48fdf0deeecd3f8437a16bbb6
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Apr 12 14:17:41 2018 +0100

        Fix TCGA sample metadata not showing samples from all junction quantification files

    commit 2fa6cf42035a2c62fd03fd910a9d5fbf203d834a
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Apr 12 14:15:29 2018 +0100

        Fix TCGA sample metadata not being shown when loading TCGA files from local folder

    commit 92236436b040442b484060209e959af947d76503
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Apr 4 16:29:05 2018 +0100

        Bump to version 1.4.5

        - Update NEWS
        - Add links to original article in bioRxiv
        - Update package description within the GUI
        - Update mentions to NMorais Lab and iMM
        - Update copyright years to include 2018
        - Minor copy-editing

    commit b4d0e8748a3160e6838b6f68bc2a11795be92de2
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Apr 4 15:30:06 2018 +0100

        Copy-edit GUI tutorial

    commit b25b9124e57cf2758b710e980e1dde74f30b4a66
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Apr 4 15:16:38 2018 +0100

        Replace dataset no longer distributed with car package with a built-in R dataset

    commit a09c8ee50a9ae185438c2b37e554ef9086a24655
    Author: Nuno Agostinho <danielagostinho@sapo.pt>
    Date:   Mon Mar 12 11:37:29 2018 +0000

        Update Contributor Covenant Code to version 1.4

    commit 58a1f137b2985b97d188f87e67f14437dec757f3
    Author: Nuno Agostinho <danielagostinho@sapo.pt>
    Date:   Mon Mar 12 11:35:17 2018 +0000

        Update README.md

        - Direct article link to the latest version available
        - Direct reference to original article (instead of references)

    commit 7783adb3be5bf6a1095a9f1cdc4b7fb899ba05ff
    Author: Nuno Agostinho <danielagostinho@sapo.pt>
    Date:   Mon Feb 12 17:28:12 2018 +0000

        Update README.md

    commit 584cce4cf4da01e3da5450c4ec889e15d3cb8ddb
    Author: Nuno Agostinho <danielagostinho@sapo.pt>
    Date:   Mon Feb 12 17:06:00 2018 +0000

        Update README.md

    commit 751e3f52c2539032b615c2e10e3d3fbb774e1455
    Author: Nuno Agostinho <danielagostinho@sapo.pt>
    Date:   Mon Feb 12 01:54:53 2018 +0000

        Update NEWS

    commit ccecd6b7c2a1164470fa3e23bec53a7f876c24be
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Feb 12 01:28:11 2018 +0000

        Fix R CMD check issues

    commit 26b3e0d375f4916ad2570f8421ab344286986e34
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Feb 12 01:13:08 2018 +0000

        Improve differential analyses

        - Fix highlighted events not filtering table for differential expression
        - Update selected gene in gene information according to selected
        splicing event
        - Select splicing events or genes for differential analysis
        - Set selected gene when performing survival analysis

    commit 5fef2819224bfc3cd3af6aefadc34cba94ca66d0
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Feb 12 01:06:45 2018 +0000

        Fix problems related with DT versions >= 0.3

    commit ac6dfae6e30064dd2f8ccf1aac9c1e58091ba676
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Feb 8 16:04:23 2018 +0000

        Update vignettes to include case studies

        - Correctly export required functions
        - Copy-edit documentation
        - Rank variable that most contribute to selected principal components
        - Update CITATION file to direct to bioRxiv article
        - Update information in welcome message
        - Show number of contained items for selected groups
        - Update authors and bump version to 1.4.4
        - Update .gitignore

    commit 882eb627227e20e61ce9b4379d493fa06c5820ae
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Feb 8 16:03:04 2018 +0000

        Fix optimisation problem when calculating optimal PSI cutoff for survival by extending search bounds

    commit 860ce90adea912abdaa7da6d775060748499e457
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Sun Feb 4 23:30:52 2018 +0000

        Select samples to be used for survival analysis

        - Automatically select primary solid tumour samples (if available) when using TCGA data

    commit 8c2cd8af6f5fff32f63174e0f3f459db9140df7e
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Sun Feb 4 13:51:55 2018 +0000

        Automatically set sample types as groups when loading TCGA data (GUI)

        - Fix potential issues when dropping matrices
        - Show groups after creating groups based on clusters

    commit 8311aa1488253356b25e7f98285fc4b18526e7e2
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Sat Feb 3 19:26:23 2018 +0000

        Improve gene expression pipeline (perform limma-trend by default)

        - Improve gene filtering
        - Copy-editing

    commit bace4ac2e6dcec6df18e3131ae7e94db95cd9773
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Sat Feb 3 17:58:24 2018 +0000

        Stratify patients for survival analysis based on optimal gene expression cutoff

    commit f55dcfbf6af1719efc8aff413bf0fd4624d17f72
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Sat Feb 3 15:00:13 2018 +0000

        Quantify AFE and ALE events through AS-centric and exon-centric methods

    commit 8451fe2aad4865b20cb35ecd548771326b31028d
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Sat Feb 3 14:41:38 2018 +0000

        Tolerate 5% of missing values for both PCA and ICA (by default)

Package: ORFik
Commit: a5a44e1cdb66d5658313133f64468cb76ddfa42b
Author: Roleren <hauken_heyken@hotmail.com>
Date: 2021-06-11 16:12:36 +0200
Commit message:

 Updated docs

Package: ORFik
Commit: 245b6e35bf576939e23e78738aaa82ba6ff4af39
Author: Roleren <hauken_heyken@hotmail.com>
Date: 2021-06-11 14:03:09 +0200
Commit message:

 Added verbose option for experiment syntax

Package: ORFik
Commit: fe86d85d45367db1f22943be84bc04f6a4456d68
Author: Roleren <hauken_heyken@hotmail.com>
Date: 2021-06-11 12:00:45 +0200
Commit message:

 Added more options for detection of p-site when verbose is TRUE

Package: ORFik
Commit: 47f2e9696c8fc85f32a9d64fd014fffefaf5a156
Author: Roleren <hauken_heyken@hotmail.com>
Date: 2021-06-10 15:40:33 +0200
Commit message:

 Added verbose option for p-site detection

Package: ORFik
Commit: 08d3e2f47d59a1f4ca04f5af47153a87a33ee2af
Author: Roleren <hauken_heyken@hotmail.com>
Date: 2021-06-10 13:19:28 +0200
Commit message:

 Starting test of improved pshifting

Package: UMI4Cats
Commit: d3a7908c52a609fab3937ab1064d36cfa4c0a43d
Author: mireia-bioinfo <mireiarr9@gmail.com>
Date: 2021-06-11 14:57:40 +0200
Commit message:

 Update CITATION

Package: biomaRt
Commit: 2a075947822e3b9cc294cf8d313a81f3a39af636
Author: Mike Smith <grimbough@gmail.com>
Date: 2021-06-11 14:21:56 +0200
Commit message:

 Does this help fix the test failing on the builders?

Package: MsBackendMgf
Commit: f78047bdf3e5ddcffa269686515fe062f3673a09
Author: Johannes Rainer <5506112+jorainer@users.noreply.github.com>
Date: 2021-06-11 14:03:07 +0200
Commit message:

 Merge pull request #15 from rformassspectrometry/jomaster

Add example on how to selectively export variables to MGF (issue #14)

Package: MsBackendMgf
Commit: 09123b1b32461882d45a9f5761551c9e3760166b
Author: jorainer <johannes.rainer@gmail.com>
Date: 2021-06-11 11:26:02 +0200
Commit message:

 ci: fix CI

Package: MsBackendMgf
Commit: 3fc658e54f1457809937c65028ace70152a6a2c8
Author: jorainer <johannes.rainer@gmail.com>
Date: 2021-06-11 10:42:57 +0200
Commit message:

 docs: add description for selective field export (issue #14)

- Add an example to the vignette describing export of only selected spectra
  variables to the MGF file.

Package: MsBackendMgf
Commit: ae3e4f891787925a0f80a331ebc4de8f7d5a1dc7
Author: Johannes Rainer <5506112+jorainer@users.noreply.github.com>
Date: 2021-05-28 11:57:00 +0200
Commit message:

 Merge pull request #13 from rformassspectrometry/jomaster

Add logo and update CI

Package: MsBackendMgf
Commit: f82f5cf2664572c3f0155cbda6b93cd492ffa557
Author: jorainer <johannes.rainer@gmail.com>
Date: 2021-05-28 10:58:11 +0200
Commit message:

 Add logo and update CI

Package: MsBackendMgf
Commit: 129599f2a7f05b77ab9c97dbdfc47be2cfdc6c1f
Author: jorainer <johannes.rainer@gmail.com>
Date: 2021-05-21 08:59:21 +0200
Commit message:

 Merge branch 'master' into jomaster

Package: MsBackendMgf
Commit: b7db9d10accd835d5c234c1f09dda73f5d554c35
Author: jorainer <johannes.rainer@gmail.com>
Date: 2021-05-21 08:58:50 +0200
Commit message:

 Merge remote-tracking branch 'upstream/master'

Package: MsBackendMgf
Commit: ae7293759249aba85e9e287318f206c823f40951
Author: jorainer <johannes.rainer@gmail.com>
Date: 2021-03-19 11:43:59 +0100
Commit message:

 ci: update correct CI result link in README

Package: MsBackendMgf
Commit: 4a43a9279177b6b6ce519918151a08bc55306860
Author: jorainer <johannes.rainer@gmail.com>
Date: 2021-03-19 09:12:46 +0100
Commit message:

 ci: add github actions

Package: MsBackendMgf
Commit: f8f991f6dc1f6f20c804a93bb102c93504c35fe5
Author: jorainer <johannes.rainer@gmail.com>
Date: 2021-03-19 09:08:46 +0100
Commit message:

 Add package sticker to README

Package: MsBackendMgf
Commit: f5bc620aacca582804b4fc64010f27f388e854e0
Author: jorainer <johannes.rainer@gmail.com>
Date: 2021-03-04 19:46:45 +0100
Commit message:

 Change to R 4.0

Package: TimiRGeN
Commit: 097eda2a019afc644224dfa35c2e6aaa539c2152
Author: Krutik Patel <krutik@hotmail.co.uk>
Date: 2021-06-11 11:09:40 +0100
Commit message:

 git merged

Package: TimiRGeN
Commit: c513f1b0418b8ec6056a52a2b454abd93717e24b
Author: Krutik Patel <krutik@hotmail.co.uk>
Date: 2021-06-11 10:56:41 +0100
Commit message:

 suppressing Warnings

Package: rawrr
Commit: 7a706128758bd265a0d3d857e306fa91e907faa8
Author: Christian Panse <cp@fgcz.ethz.ch>
Date: 2021-06-11 11:55:54 +0200
Commit message:

 version bump

Package: ViSEAGO
Commit: 7363350791a08208d7cf5c202343fac4632b598e
Author: Aurelien Brionne <aurelien.brionne@inrae.fr>
Date: 2021-06-11 11:36:44 +0200
Commit message:

 merge_enrich_terms update for Ensembl

Package: ggtreeExtra
Commit: 00672729e73d1a01d4a57c504d8bcb8c576e248d
Author: xiangpin <xshuangbin@163.com>
Date: 2021-06-11 16:23:59 +0800
Commit message:

 update news and bump version

Package: ggtreeExtra
Commit: 9f4982bee55b53e2f0e9e076e8242fb38c3a759e
Author: xiangpin <xshuangbin@163.com>
Date: 2021-06-11 16:21:33 +0800
Commit message:

 fix vector logical check

Package: ggtreeExtra
Commit: b6437a111b4d4e4863452f478d34dde0a201e6dc
Author: xiangpin <xshuangbin@163.com>
Date: 2021-06-11 10:14:19 +0800
Commit message:

 update reference

Package: coMethDMR
Commit: 76736cb40cf4dd756915cb6d7de9292d08aae290
Author: Gabriel J. Odom <gabriel.odom@fiu.edu>
Date: 2021-06-08 19:03:40 -0400
Commit message:

 Moving calls to sesameData:: functions to .onLoad(). Made other miscellaneous edits per Issue #1.

Package: coMethDMR
Commit: fdda3e80db58dc0d68326bc6dc1b2cc24747aa46
Author: Fernanda Veitzman <fveit001@fiu.edu>
Date: 2021-06-08 17:46:58 -0400
Commit message:

 Updated Description, Vignettes 1 and 2.

Package: coMethDMR
Commit: 57d697afcf9c6d19cee67018cb24abcf0cfc127c
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2021-06-04 16:03:20 -0400
Commit message:

 Removing comments from travis

Package: coMethDMR
Commit: 7dc05da3587c93d949ca61a6313070958391fe43
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2021-06-04 14:29:22 -0400
Commit message:

 Update travis

Package: coMethDMR
Commit: bdcdbafcef70e3dbfdb40f388c57a86df1f5b372
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2021-06-04 14:27:46 -0400
Commit message:

 small changes to travis

Package: coMethDMR
Commit: 73259dcb1b9b72c69c27b43e3525d4bffec116df
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2021-06-04 13:50:56 -0400
Commit message:

 Updating travis

Package: coMethDMR
Commit: 707ff83c6f2102df5a5935cc3fa2d72592152280
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2021-06-04 12:03:09 -0400
Commit message:

 Add travis CI config

Package: coMethDMR
Commit: cb42e2250f01654d6d88f31ded4d23f862babf67
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2021-06-04 11:43:54 -0400
Commit message:

 Adding cache download before data access

Package: biodb
Commit: 5f6a85d6b6720136d6e329697f49d57178b8a937
Author: Pierrick Roger <pk.roger@icloud.com>
Date: 2021-06-10 17:29:29 +0200
Commit message:

 Bump version.

Package: biodb
Commit: c0abf623adddaf826f3695c7f5dde7035bd63519
Author: Pierrick Roger <pk.roger@icloud.com>
Date: 2021-06-10 16:54:58 +0200
Commit message:

 Improve r front (#563)

* Use current R if version number match with --r-version.

* Add --no-current option to forbid using R installed on system.

* Make downloading versions file an option.

* Use new R_front options.

Package: biodb
Commit: fa8ce375d77a2214dc4696afc5745af69f6ce55d
Author: Pierrick Roger <pk.roger@icloud.com>
Date: 2021-06-10 12:16:33 +0200
Commit message:

 Check entries argument to functions.

Package: biodb
Commit: 54ce7baeedef6696cf228d1057f893338471aca6
Author: Pierrick Roger <pk.roger@icloud.com>
Date: 2021-06-10 12:16:06 +0200
Commit message:

 Add quotes param in CSV entry class.

Package: biodb
Commit: 03b7137257c2ddc8cda82d198596dc727ee84dfd
Author: Pierrick Roger <pk.roger@icloud.com>
Date: 2021-06-09 11:20:40 +0200
Commit message:

 Disable travis file generation/upgrade by default.

Package: PoDCall
Commit: 03c9a14db4bcbf30c879fd7969a5786eb4533f34
Author: Hans Petter Brodal <habrod@ad.medicalresearch.no>
Date: 2021-06-10 13:22:17 +0200
Commit message:

 Added 'rmarkdown' to Suggests, bumped version.

Package: PoDCall
Commit: 569034028b7a6f628d6f7d4d23cad62ee51b1a75
Author: Hans Petter Brodal <habrod@ad.medicalresearch.no>
Date: 2021-06-10 13:05:30 +0200
Commit message:

 Bumped version

Package: PoDCall
Commit: 549687bba0ab6d1398a7ca89353462261e43b658
Author: Hans Petter Brodal <habrod@ad.medicalresearch.no>
Date: 2021-06-10 13:01:38 +0200
Commit message:

 Resolved git merge conflict

Merge remote-tracking branch 'upstream/master'

# Conflicts:
#	DESCRIPTION

Package: PoDCall
Commit: 322497e84d201c6fe90e5666ff65e43d9e4eb8e3
Author: Hans Petter Brodal <habrod@ad.medicalresearch.no>
Date: 2021-06-10 12:53:38 +0200
Commit message:

 Implemented use of reference well for channel 2 and some minor fixes.

Package: PoDCall
Commit: 31bc034012a17d1ca06768f4a96e96c3301d1237
Author: Hans Petter Brodal <habrod@ad.medicalresearch.no>
Date: 2021-04-08 11:28:04 +0200
Commit message:

 Fixed typos is NEWS.rd

Package: MutationalPatterns
Commit: 524128e046fff673fca8ca1deba82d6642f0d362
Author: mroosmalen <m.j.vanroosmalen-3@prinsesmaximacentrum.nl>
Date: 2021-06-10 12:48:06 +0200
Commit message:

 Merge from github

Package: ORFik
Commit: c488670affbefea98d30c9320b6561769327454f
Author: Roleren <hauken_heyken@hotmail.com>
Date: 2021-06-10 11:28:04 +0200
Commit message:

 Check fixes

Package: ORFik
Commit: c68d107dc69266f622bfecb53072d659b1d56fe6
Author: Roleren <hauken_heyken@hotmail.com>
Date: 2021-06-09 16:12:13 +0200
Commit message:

 Added isoform option for heatmaps

Package: ORFik
Commit: 9d8988ef868afc44e684dd600528f9a6abeeea08
Author: Roleren <hauken_heyken@hotmail.com>
Date: 2021-06-09 01:37:04 +0200
Commit message:

 Added seqlength safeguard for extendTrailers and extendLeaders. Added tests.

Package: ORFik
Commit: b87c2b2ef359287dbe1466ee039f931c3d1cc444
Author: Roleren <hauken_heyken@hotmail.com>
Date: 2021-06-08 16:54:15 +0200
Commit message:

 Added better auto search for library type

Package: ORFik
Commit: ac852c8449f6a4738931f84faab61a41dece6e38
Author: Roleren <hauken_heyken@hotmail.com>
Date: 2021-06-08 16:35:54 +0200
Commit message:

 Added more auto-detection options for library type

Package: ORFik
Commit: a6153efd49992b8363e01d16582942d537a5d94a
Author: Roleren <hauken_heyken@hotmail.com>
Date: 2021-06-08 15:05:33 +0200
Commit message:

 Added more safety tests for SRA metadata download

Package: rnaseqGene
Commit: 36b9e050cfef5d8d2f3712215ed9bd00d9afce40
Author: mikelove <michaelisaiahlove@gmail.com>
Date: 2021-06-10 10:38:42 +0200
Commit message:

 fix doi

Package: ClassifyR
Commit: 354813f34ff5dfb3c8611358f84b114cb5d0dedc
Author: Dario Strbenac <dario@maths.usyd.edu.au>
Date: 2021-06-10 15:42:44 +1000
Commit message:

 - Increased version.

Package: ClassifyR
Commit: 66d365d944f60c64d7e9d0007c0a9e1535d6f757
Author: Dario Strbenac <dario@maths.usyd.edu.au>
Date: 2021-06-10 15:33:02 +1000
Commit message:

 - Package load moved to correct location in vignette.

Package: FLAMES
Commit: 679e451e462c3bcf1bd67c85565b6604a585d353
Author: Oliver Voogd <olivervoogd@gmail.com>
Date: 2021-06-10 11:35:00 +1000
Commit message:

 version bump

Package: FLAMES
Commit: 628fe510c5844b47d3c43e256573e8808ead001f
Author: Oliver Voogd <olivervoogd@gmail.com>
Date: 2021-06-10 11:34:00 +1000
Commit message:

 modified vignette

Package: FLAMES
Commit: e5fc783647f01c2f387d1f39ae4605b28b693c5f
Author: Oliver Voogd <olivervoogd@gmail.com>
Date: 2021-06-02 13:01:41 +1000
Commit message:

 extended vignette with high level description, workflow image, reference to minimap2. Changed README

Package: FLAMES
Commit: 3ed33bb0cd068ac1cb104014ebff04cdfd849000
Author: Oliver Voogd <olivervoogd@gmail.com>
Date: 2021-06-01 14:30:48 +1000
Commit message:

 initial server commit

Package: FLAMES
Commit: ced19f58fcfa199db944052829fc61df8dc96977
Author: Oliver Voogd <olivervoogd@gmail.com>
Date: 2021-06-01 13:37:19 +1000
Commit message:

 improve clarity of function documentation

Package: CTCF
Commit: e6880e4c8249c388b9c0407be4fd9e3edcfe67f5
Author: Mikhail Dozmorov <mikhail.dozmorov@gmail.com>
Date: 2021-06-09 16:47:26 -0400
Commit message:

 Move AnnotationHub to Suggests

Package: sesame
Commit: a4c6ae42341fe542933a94510aa69dfc69a6133f
Author: Wanding Zhou <zhouwanding@gmail.com>
Date: 2021-06-09 15:56:48 -0400
Commit message:

 bump to 1.11.4

Package: sesame
Commit: 7e4679bb5bfa95b2241f16907c73626229dbbc6a
Author: Wanding Zhou <zhouwanding@gmail.com>
Date: 2021-06-09 06:46:27 -0400
Commit message:

 fix to qc/QC.html issue in vignette linking

Package: HPAStainR
Commit: 78b58dd1c34520356ae7936e381a23c7acd0df4c
Author: 32tim32 <tnieuwe1@jhmi.edu>
Date: 2021-06-09 14:43:20 -0400
Commit message:

 Fixed error caused by limieted data: if  column isn't there error thrown, this is now fixed

Package: HPAStainR
Commit: 7ad4119be94602c8c1439d44a915c4ea61e874cf
Author: 32tim32 <tnieuwe1@jhmi.edu>
Date: 2021-06-09 14:37:23 -0400
Commit message:

 updating

Package: HPAStainR
Commit: 861fd2a2c2d9137c5873a1c156820b1316078303
Author: Tim Nieuwenhuis <40697504+tnieuwe@users.noreply.github.com>
Date: 2021-06-09 14:21:36 -0400
Commit message:

 Merge pull request #3 from tnieuwe/future_updates

Added code that caught sitautions where the not detected column is no…

Package: HPAStainR
Commit: c44763d8ad22226e2e633d93f71e2ae22f5f71e5
Author: tnieuwe <40697504+tnieuwe@users.noreply.github.com>
Date: 2021-06-09 10:50:44 -0400
Commit message:

 Added code that caught sitautions where the not detected column is not created

Package: HPAStainR
Commit: fe5fdac4723f31351a5ea00bafbddbf550b32e06
Author: tnieuwe <40697504+tnieuwe@users.noreply.github.com>
Date: 2021-05-24 15:35:00 -0400
Commit message:

 minor grammatical errors

Package: BiocCheck
Commit: 154fc290bdcec9c0ccf3cdb908801d1be27d61e8
Author: LiNk-NY <mramos09@gmail.com>
Date: 2021-06-09 13:58:13 -0400
Commit message:

 update NEWS

Package: BiocCheck
Commit: 82f7e43b9f1108bae62895332962e0578361066d
Author: LiNk-NY <mramos09@gmail.com>
Date: 2021-06-09 13:56:29 -0400
Commit message:

 version bump 1.29.8

Package: BiocCheck
Commit: afdf4deb17d42ecf134f2ac4e44d5f3faed73632
Author: LiNk-NY <mramos09@gmail.com>
Date: 2021-06-09 13:51:49 -0400
Commit message:

 add session_info check

Package: BiocCheck
Commit: e315de458559da63655dbd8d0f22f415d45da0cf
Author: LiNk-NY <mramos09@gmail.com>
Date: 2021-06-09 13:51:33 -0400
Commit message:

 bug fix: use filename after removing empty results

Package: BiocCheck
Commit: 072359b4ff98091055f20d885aa632475c571691
Author: LiNk-NY <mramos09@gmail.com>
Date: 2021-06-09 13:49:15 -0400
Commit message:

 avoid stats::setNames

Package: RTCGAToolbox
Commit: e36855bb9bdd7813512497b4458151ddf4c49a29
Author: LiNk-NY <mramos09@gmail.com>
Date: 2021-06-09 11:20:29 -0400
Commit message:

 version bump 2.23.2

Package: RTCGAToolbox
Commit: bf302448b781a9cfa6cdaa2e5b507fb66ed4b36c
Author: LiNk-NY <mramos09@gmail.com>
Date: 2021-06-09 11:20:24 -0400
Commit message:

 update NEWS

Package: RTCGAToolbox
Commit: 5b4e88b52b696983a46b198329be294d058dda4d
Author: LiNk-NY <mramos09@gmail.com>
Date: 2021-06-09 11:20:15 -0400
Commit message:

 move deprecated vignette to analysis folder

Package: RnBeads
Commit: 40f9807e6d5de6560461402d6331fc7fa45c008d
Author: Michael Scherer <mscherer@mpi-inf.mpg.de>
Date: 2021-06-09 16:55:11 +0200
Commit message:

 Fixed typo in greedycut

Package: VAExprs
Commit: 0dce1ff1f8ece165703691867b98c1376331a2b4
Author: dongminjung <dongminjung@Dongmins-MacBook-Pro.local>
Date: 2021-06-09 22:52:37 +0900
Commit message:

 update

Package: fishpond
Commit: 4a4ebf99ffc3f9b2a573c383d12b497382b382a7
Author: mikelove <michaelisaiahlove@gmail.com>
Date: 2021-06-09 14:20:48 +0200
Commit message:

 more work on importAllelicCounts

Package: VAExprs
Commit: d95f8a3c7ee16af27d42536d3a215fc4d1dc4110
Author: dongminjung <dongminjung@Dongmins-MacBook-Pro.local>
Date: 2021-06-09 20:31:46 +0900
Commit message:

 update

Package: sesame
Commit: 50d40fe9cac1648f25d32836a22ba42e7eae569c
Author: Wanding Zhou <zhouwanding@gmail.com>
Date: 2021-06-09 06:29:17 -0400
Commit message:

 bump to 1.11.3

Package: sesame
Commit: 9d5447ab351d49188d2073098d15bb8c4693f5df
Author: Wanding Zhou <zhouwanding@gmail.com>
Date: 2021-06-08 23:02:56 -0400
Commit message:

 fix to DML non-standard group level name

Package: RnBeads
Commit: d5e0d50ac5e8edcf9bc4e5b4d3804b62c9f36f4f
Author: Michael Scherer <mscherer@mpi-inf.mpg.de>
Date: 2021-06-09 12:05:30 +0200
Commit message:

 Merge branch 'master' of git.bioconductor.org:packages/RnBeads

Package: RnBeads
Commit: 405ad8d28837489df11787a1dd4bb56b27ca45e1
Author: lutsik <pavlo.lutsik@gmail.com>
Date: 2021-06-09 11:40:20 +0200
Commit message:

 temp disabled bead count-based threshold in greedycut for array data

Package: RnBeads
Commit: 5ccd77f0a47a0cec03507918813214c36c878385
Author: lutsik <pavlo.lutsik@gmail.com>
Date: 2021-06-09 11:28:36 +0200
Commit message:

 hotfix option name in greedycut

Package: iSEE
Commit: 26c71eb56efd438a173302196da5ca4ba9226c4b
Author: Kevin Rue-Albrecht <kevinrue67@gmail.com>
Date: 2021-06-07 13:16:26 +0100
Commit message:

 update version of R in configuration matrix

Package: iSEE
Commit: 3c8006f2fa37187f3e0b0587daaed3837d22f361
Author: Charlotte Soneson <charlottesoneson@gmail.com>
Date: 2021-06-07 13:30:25 +0200
Commit message:

 Bump version and date, update NEWS

Package: iSEE
Commit: 657bdf743282807e758265fe3eab8e9caf03a466
Author: Charlotte Soneson <charlottesoneson@gmail.com>
Date: 2021-06-07 13:25:54 +0200
Commit message:

 Avoid double rendering of height/width UI

Package: iSEE
Commit: 7b4762075afed987ab5914106993c0e4d99b5956
Author: Charlotte Soneson <charlottesoneson@gmail.com>
Date: 2021-06-04 20:25:40 +0200
Commit message:

 Update panel selectize also when removing panels.

Package: ReactomeGSA
Commit: beba40ce5ef4e3bea6b49c1a2b76f69cbd04edcd
Author: Johannes Griss <jgriss8@yahoo.com>
Date: 2021-06-09 11:52:17 +0200
Commit message:

 Merged Bioconductor version change

Package: ReactomeGSA
Commit: 355e1db403eb5d5f571278cd6d12ce81a1b99eaf
Author: Johannes Griss <jgriss8@yahoo.com>
Date: 2021-06-09 11:50:19 +0200
Commit message:

 Fixed typo in scRNA-seq vignette

Package: segmenter
Commit: a236104ebc025d017551bd3a1adf88c131eba144
Author: Mahmoud Ahmed <mahshaaban2@gmail.com>
Date: 2021-06-09 18:41:49 +0900
Commit message:

 import method in namespace

Package: VAExprs
Commit: 26d813a79876e0ce0f39b916504af9fce14c263f
Author: dongminjung <dongminjung@Dongmins-MacBook-Pro.local>
Date: 2021-06-09 17:42:17 +0900
Commit message:

 update

Package: biodb
Commit: 61c5f5b1de77ea51c1b2fd5e0f6fea7de010f12c
Author: Pierrick Roger <pk.roger@icloud.com>
Date: 2021-06-09 10:22:24 +0200
Commit message:

 Bug fix: correct logTrace() call in cache class.

Package: biodb
Commit: f23c4a0c68adb449b45a925e3facb6add1a692d8
Author: Pierrick Roger <pk.roger@icloud.com>
Date: 2021-06-09 09:11:48 +0200
Commit message:

 Correct test of return type of searchForEntries(). (#561)

Package: biodb
Commit: 1e7803a74728c83829b876742217d4fc15016293
Author: Pierrick Roger <pk.roger@icloud.com>
Date: 2021-06-09 08:49:31 +0200
Commit message:

 Correct test.searchCompound(). (#560)

searchForEntries() returns now an empty character vector instead of
NULL.

Package: biodb
Commit: b27307556f8708d40ebadf84ac5059cbacce19ce
Author: Pierrick Roger <pk.roger@icloud.com>
Date: 2021-06-02 13:11:15 +0200
Commit message:

 Debug longtests (#559)

* Pass checks. Update long tests in make file.

* Factorize test targets.

Package: biodb
Commit: 2545f9c9fbfdc09e75a90b7d3a291eb6b5491ac4
Author: Pierrick Roger <pk.roger@icloud.com>
Date: 2021-06-02 11:25:48 +0200
Commit message:

 Move tests/long folder to longtests. Enable long tests for Bioconductor building system. (#558)

Package: biodb
Commit: 2abccf7ca8c57cec1670996f7b4478e86ab8b95a
Author: Pierrick Roger <pk.roger@icloud.com>
Date: 2021-05-28 12:16:15 +0200
Commit message:

 Remove .Rhistory when cleaning. (#557)

Package: biodb
Commit: 0f5095c6df3a351c4c333a4fb988ee9f8b189512
Author: Pierrick Roger <pk.roger@icloud.com>
Date: 2021-05-28 12:12:18 +0200
Commit message:

 Skip some searchable fields in generic tests (#556)

* Use option to skip test on some searchable fields.

* Reduce showed vector length when showing field's values.

* Update NEWS file.

Package: biodb
Commit: ec9ca4a2ce6122dba61a9ad7cc42a27132cb99f0
Author: Pierrick Roger <pk.roger@icloud.com>
Date: 2021-05-26 11:37:12 +0200
Commit message:

 Bug fix: correct generic test of searchForEntries. (#553)

Allows testing with NA value.

Package: biodb
Commit: 9b8eb7daad5028092a73d066e3e2c32ddd3203fd
Author: Pierrick Roger <pk.roger@icloud.com>
Date: 2021-05-25 10:58:47 +0200
Commit message:

 Improve test msg. (#552)

Package: biodb
Commit: 49e7f30e4ace1779918a0a7fb0495d090a0926a9
Author: Pierrick Roger <pk.roger@icloud.com>
Date: 2021-05-23 12:04:29 +0200
Commit message:

 Bugfix return type of search for entries (#550)

* Correct return type of searchForEntries().

* Remove result check based on searchable fields.

* Remove spaces.

* Add new line.

Package: biodb
Commit: 6e48a16477a26d6258a8613fa08d137751cd401d
Author: Pierrick Roger <pk.roger@icloud.com>
Date: 2021-05-20 18:42:06 +0200
Commit message:

 Use r beta (#547)

* Use template inside makefile.

* Use R_ver_select script.

* Set R 4.1 as dependency.

* Set R version explicitly for Travis-CI.

* Set full R version.

* Use devel for R version.

* Try R release.

* Use bioc-devel for R version in Travis-CI.

* Set all 4 versions of R.

* BiocCheck should be installed with R version bioc-devel.

* Try with embedded R_front.

* Use R_FRONT also to get R bin path.

* Switch to bash.

* Force using R_front

* Add debug info for R_FRONT

* Use official release also in R_front.

* Stop running tests on Travis-CI.

Since now tests are already run on Bioconductor.

* Remove Travis-CI build status.

* Install R_front script along with Makefile in ext pkg.

Package: biodb
Commit: 3922ca914df19273bae5a663ea91e6162425ae23
Author: Pierrick Roger <pk.roger@icloud.com>
Date: 2021-05-20 12:54:10 +0200
Commit message:

 bug fix: correct typos in some logger calls.

Package: VAExprs
Commit: 36698a7b4334ffb86347a6d82861a922721654d2
Author: dongminjung <dongminjung@Dongmins-MacBook-Pro.local>
Date: 2021-06-09 17:09:16 +0900
Commit message:

 update

Package: VAExprs
Commit: 07aeab3188afea155383bbe7ed85d4b613f37006
Author: dongminjung <dongminjung@Dongmins-MacBook-Pro.local>
Date: 2021-06-09 16:52:42 +0900
Commit message:

 update

Package: segmenter
Commit: 8b9775490b1c275efb289c65482e0b6d743c0345
Author: Mahmoud Ahmed <mahshaaban2@gmail.com>
Date: 2021-06-09 15:31:41 +0900
Commit message:

 changes for bioc review, Bioconductor/Contributions#2056
	- update description and namespace
	- import chromhmmData and methods
	- add toc and remove uneval code in vignette
	- remove data-raw
	- add inst/script s to document/generate data and inst/extdata
	- update the data objects

Package: chromhmmData
Commit: 8df27c4e8c8fb85c65bf8e7722396f3cb44dc0ba
Author: Mahmoud Ahmed <mahshaaban2@gmail.com>
Date: 2021-06-09 11:06:02 +0900
Commit message:

 changes for bioc review, Bioconductor/Contributions#2056
	- update to R 4.1
	- add bug reports
	- add installation and sessioninfo to vignette

Package: VAExprs
Commit: 2b336cb4cd96bb11fe2fbecf27837746b1082542
Author: dongminjung <dongminjung@Dongmins-MacBook-Pro.local>
Date: 2021-06-09 15:22:24 +0900
Commit message:

 update

Package: VAExprs
Commit: 766365c5149e54a909033b8b71c7ba991ff05e81
Author: dongminjung <dongminjung@Dongmins-MacBook-Pro.local>
Date: 2021-06-09 15:02:25 +0900
Commit message:

 update

Package: VAExprs
Commit: e18f60819b60bce772cb95d5162bdc7d7eae870c
Author: dongminjung <dongminjung@Dongmins-MacBook-Pro.local>
Date: 2021-06-09 14:39:25 +0900
Commit message:

 update

Package: VAExprs
Commit: 78c84b3e8835029eecd729b2ea21bc24b8b92ffa
Author: dongminjung <dongminjung@Dongmins-MacBook-Pro.local>
Date: 2021-06-09 12:56:17 +0900
Commit message:

 update

Package: MicrobiotaProcess
Commit: 42d3821f1783020bddda101883145ce3a951e1a0
Author: xiangpin <xshuangbin@163.com>
Date: 2021-06-09 11:31:47 +0800
Commit message:

 bump version

Package: MicrobiotaProcess
Commit: a50879687f3a2b4a580744c2df16cd9260715391
Author: xiangpin <xshuangbin@163.com>
Date: 2021-06-08 21:38:56 +0800
Commit message:

 update news

Package: MicrobiotaProcess
Commit: ec0e47b4b1fe9b75e7fbea1ff6384586a30ae50c
Author: xiangpin <xshuangbin@163.com>
Date: 2021-06-08 21:38:30 +0800
Commit message:

 add get_NRT_NTI

Package: MicrobiotaProcess
Commit: 816553be9af2085eab125bdfc9108538a65db443
Author: xiangpin <xshuangbin@163.com>
Date: 2021-06-07 15:17:37 +0800
Commit message:

 update news

Package: MicrobiotaProcess
Commit: b0d9676a6822008db3534d8184e376119da1e59b
Author: xiangpin <xshuangbin@163.com>
Date: 2021-06-07 15:09:40 +0800
Commit message:

 more accessor

Package: MicrobiotaProcess
Commit: f80730782c018b6b78b8a76343561455bcb49349
Author: xiangpin <xshuangbin@163.com>
Date: 2021-06-07 11:41:08 +0800
Commit message:

 update doc

Package: MicrobiotaProcess
Commit: 437edf08c847d1f3e1947c86d69a9de023038d6b
Author: xiangpin <xshuangbin@163.com>
Date: 2021-06-07 11:40:50 +0800
Commit message:

 add filter fucntion for result of diff_analysis

Package: MicrobiotaProcess
Commit: 80057d7124a0047d17273498716feda02b5ecbdf
Author: xiangpin <xshuangbin@163.com>
Date: 2021-06-06 22:24:33 +0800
Commit message:

 add mean and median for comparision when the samples is too few

Package: MicrobiotaProcess
Commit: 1bba1acd1edca64ff0933d76a3197c03c962c5e3
Author: xiangpin <xshuangbin@163.com>
Date: 2021-05-24 14:28:26 +0800
Commit message:

 update doc

Package: MicrobiotaProcess
Commit: fc0c27865f57e28e4bd68f4c522e80777c0d9aca
Author: xiangpin <xshuangbin@163.com>
Date: 2021-05-24 14:23:55 +0800
Commit message:

 add ellipse_linewd and ellipse_lty in ggordpoint

Package: MicrobiotaProcess
Commit: 896ce3179c22033c42aafc1bffc623b51fe25645
Author: xiangpin <xshuangbin@163.com>
Date: 2021-05-20 17:30:38 +0800
Commit message:

 new release

Package: VAExprs
Commit: 491a807738862eb826c05fc7af09eb67b90c6607
Author: dongminjung <dongminjung@Dongmins-MacBook-Pro.local>
Date: 2021-06-09 11:37:02 +0900
Commit message:

 update

Package: Rsubread
Commit: 8d0427f3a18507bbd9fa8b797cdde705beee0a43
Author: Yang Liao <liao_y@svr2672.licr.unimelb.edu.au>
Date: 2021-06-09 12:23:40 +1000
Commit message:

 fixed a bug

Package: VAExprs
Commit: d61f44facb62a3dcaefedaddcd9fc51211d6692b
Author: dongminjung <dongminjung@Dongmins-MacBook-Pro.local>
Date: 2021-06-09 11:20:53 +0900
Commit message:

 update

Package: cBioPortalData
Commit: e943ab64b3bdaa4bff813806d17e0fd6b6191baa
Author: LiNk-NY <mramos09@gmail.com>
Date: 2021-06-08 21:35:22 -0400
Commit message:

 version bump 2.5.4

Package: cBioPortalData
Commit: 870a040e6d81d70e69e5812745acedf2855969d2
Author: LiNk-NY <mramos09@gmail.com>
Date: 2021-06-08 21:35:20 -0400
Commit message:

 update NEWS

Package: cBioPortalData
Commit: 1c4fcf6eee5d8c7ae8a3a94f0667ce35c65f6208
Author: LiNk-NY <mramos09@gmail.com>
Date: 2021-06-08 15:57:26 -0400
Commit message:

 partial loading of MultiAssayExperiment objects

- when a file fails to import, a warning is produced
- reason is also given

Package: cBioPortalData
Commit: c5c2c909778d14e03862711b946782b12b897448
Author: LiNk-NY <mramos09@gmail.com>
Date: 2021-06-08 15:56:53 -0400
Commit message:

 pass the ask argument

Package: VAExprs
Commit: 4b371de60668114a75112b3e50a80eaa3b371118
Author: dongminjung <dongminjung@Dongmins-MacBook-Pro.local>
Date: 2021-06-09 10:19:09 +0900
Commit message:

 update

Package: airpart
Commit: c0a1d2aeb8e164faa662d8a9d58c313a206a3821
Author: Wancen <42752661+Wancen@users.noreply.github.com>
Date: 2021-06-08 17:23:05 -0400
Commit message:

 add step function in vignette

Package: hca
Commit: 35dead8d668ad0837522f263992c5188f0d2d3af
Author: MRMcD <49954418+reed-mcdaniel-716@users.noreply.github.com>
Date: 2021-06-08 10:27:50 -0400
Commit message:

 Merge pull request #17 from Bioconductor/1.1.1_changes

fix in filter validation

Package: hca
Commit: 8f1be7eb0f2d1f7095217e3799110d148707d458
Author: Maya Reed McDaniel <maya.mcdaniel@roswellpark.org>
Date: 2021-06-08 10:27:03 -0400
Commit message:

 fix in filter validation

Package: airpart
Commit: 5bff448b192a8444601f41edbceda8645625bcca
Author: Wancen <42752661+Wancen@users.noreply.github.com>
Date: 2021-06-08 17:02:21 -0400
Commit message:

 add step plot and extract result function

Package: SpatialExperiment
Commit: d42e6a40b78df440b6c994fa54fdde0be7c086e0
Author: dario righelli <dario.righelli@gmail.com>
Date: 2021-06-06 17:38:43 +0200
Commit message:

 Merge pull request #68 from drighelli/colData_duplicate_cols

Merge branch to fix duplicated colData columns issue

Package: SpatialExperiment
Commit: 70cb5ba654a01b33fb46c3db99fa95a3e08a3bb9
Author: Lukas Weber <lukas.weber.edu@gmail.com>
Date: 2021-06-04 17:05:12 -0400
Commit message:

 version bump

Package: SpatialExperiment
Commit: c072ad9f2823201beee7b9ace96dfa139391a286
Author: Lukas Weber <lukas.weber.edu@gmail.com>
Date: 2021-06-04 17:04:49 -0400
Commit message:

 remove Bioc 3.14 from GitHub Actions for now

Package: SpatialExperiment
Commit: 80436b886ad56dda15a6695016b00bed043a24e3
Author: Lukas Weber <lukas.weber.edu@gmail.com>
Date: 2021-06-04 16:54:31 -0400
Commit message:

 unit test for no duplicated columns from spatialData in colData

Package: SpatialExperiment
Commit: 62014b389dc03a23168de33bed5f7a30d1c0606f
Author: Lukas Weber <lukas.weber.edu@gmail.com>
Date: 2021-06-04 16:34:28 -0400
Commit message:

 change bugfix to check spatialDataNames instead of spatialCoordsNames

Package: SpatialExperiment
Commit: 10a24036fe2acfcdd0b10bd8c04ff816da0d8e79
Author: dario righelli <dario.righelli@gmail.com>
Date: 2021-06-04 17:02:05 +0200
Commit message:

 Update R-cmd-check.yaml

Package: SpatialExperiment
Commit: 8594a47fcf187e9c1d4bd2d6d7f5911d83629176
Author: dario righelli <dario.righelli@gmail.com>
Date: 2021-06-04 16:57:53 +0200
Commit message:

 Update R-cmd-check.yaml

Package: SpatialExperiment
Commit: 1c428351a7ba0db61cb046c2d75c24de7f1dc0ff
Author: dario righelli <dario.righelli@gmail.com>
Date: 2021-06-04 16:56:15 +0200
Commit message:

 Update R-cmd-check.yaml

Package: SpatialExperiment
Commit: f41045b2b178793a3ed1137d58ffa6b5bcce2129
Author: dario righelli <dario.righelli@gmail.com>
Date: 2021-06-04 16:51:30 +0200
Commit message:

 Update R-cmd-check.yaml

Package: SpatialExperiment
Commit: c5d5f8970334cca216396bfa51c93dad54df7230
Author: Dario Righelli <dario.righelli@gmail.com>
Date: 2021-06-04 16:06:44 +0200
Commit message:

 passing checks

Package: SpatialExperiment
Commit: 9bdb900c0e5ac4be8e4a712e93b739dc31d40949
Author: Dario Righelli <dario.righelli@gmail.com>
Date: 2021-06-04 15:48:42 +0200
Commit message:

 solving issue #66

Package: SpatialExperiment
Commit: 64dd16573f5c47a88108b569bbf5d10c95b1bbce
Author: Lukas Weber <lukas.weber.edu@gmail.com>
Date: 2021-05-24 15:50:43 -0400
Commit message:

 partial attempt at overwriting colData show method

Package: flowViz
Commit: 1a10c6cafedfe5e0e8d11d6f188d6f1bfc7363d4
Author: mikejiang <mike@ozette.ai>
Date: 2021-06-08 12:07:33 -0700
Commit message:

 add rmarkdown to Suggests

Package: Rsubread
Commit: 7488a931af661a1755de060d440dde6f7eb087af
Author: Yang Liao <liao_y@svr2672.licr.unimelb.edu.au>
Date: 2021-06-09 05:00:25 +1000
Commit message:

 Fixed Rstudio bug

Package: RProtoBufLib
Commit: 9b5b2d6aa0d5f74a100d7c7640ee8dbe9e5ba32a
Author: mikejiang <mike@ozette.ai>
Date: 2021-06-08 11:57:58 -0700
Commit message:

 Merge branch 'master' into devel

Package: RProtoBufLib
Commit: 2184b494e7e7399d246428a806d6ea50a27d2e34
Author: mikejiang <mike@ozette.ai>
Date: 2021-06-08 11:57:48 -0700
Commit message:

 add rmarkdown to Suggests

Package: RProtoBufLib
Commit: e9b86ff29bcc9a069a042c5fc46137aa0f43ff6e
Author: mikejiang <mike@ozette.ai>
Date: 2021-05-27 10:55:42 -0700
Commit message:

 Merge branch 'master' into devel

Package: RProtoBufLib
Commit: b35d83acf3a38a66ec32404e8bc56a775b368c6d
Author: Nitesh Turaga <nitesh.turaga@gmail.com>
Date: 2021-05-19 16:28:30 +0000
Commit message:

 bump x.y.z version to odd y following creation of RELEASE_3_13 branch

Package: RProtoBufLib
Commit: 59a233cebcdbf93c854b8d6645146b7efe1c2880
Author: Nitesh Turaga <nitesh.turaga@gmail.com>
Date: 2021-05-19 16:28:30 +0000
Commit message:

 bump x.y.z version to even y prior to creation of RELEASE_3_13 branch

Package: openCyto
Commit: 4399a9f5fc8f9c9702110402452644c64b58affa
Author: mikejiang <mike@ozette.ai>
Date: 2021-06-08 11:57:02 -0700
Commit message:

 add rmarkdown to Suggests

Package: CytoML
Commit: a1c6ddbdee4b804e00dc0b6869b831d1426e522b
Author: mikejiang <mike@ozette.ai>
Date: 2021-06-08 11:56:28 -0700
Commit message:

 Merge branch 'master' into devel

Package: CytoML
Commit: a6d96b6eeb349ec4644a20516fedd71a587819b4
Author: mikejiang <mike@ozette.ai>
Date: 2021-06-08 11:56:05 -0700
Commit message:

 add rmarkdown to Suggests

Package: flowWorkspace
Commit: 2457e8bfba8a545ee680289648cefef53c96ab41
Author: mikejiang <mike@ozette.ai>
Date: 2021-06-08 11:55:16 -0700
Commit message:

 Merge branch 'master' into devel

Package: flowWorkspace
Commit: 6890d9c7975190a7ac55cf899cfd50aae7d8600b
Author: mikejiang <mike@ozette.ai>
Date: 2021-06-08 11:55:05 -0700
Commit message:

 add rmarkdown to Suggests

Package: cytolib
Commit: d10f814aea839694163116a80bf6e73a39dcd608
Author: mikejiang <mike@ozette.ai>
Date: 2021-06-08 11:53:47 -0700
Commit message:

 add rmarkdown to Suggests

Package: seq2pathway
Commit: 68cf544a831f25182197036ed20d72ed9e3f7c94
Author: Arjun Kinstlick <ajkinstlick@gmail.com>
Date: 2021-06-08 13:40:56 -0500
Commit message:

 updated version number

Package: seq2pathway
Commit: a2fff7b5ba761ebb8c08983c394f865713a54576
Author: Arjun Kinstlick <ajkinstlick@gmail.com>
Date: 2021-06-08 13:40:08 -0500
Commit message:

 resolved merge conflicts

Package: seq2pathway
Commit: a81cac94fee747a5145dc22e7e66673dc6859242
Author: Arjun Kinstlick <ajkinstlick@gmail.com>
Date: 2021-06-08 13:35:20 -0500
Commit message:

 Merge branch 'master' of https://github.com/xyang2uchicago/seq2pathway19

Package: seq2pathway
Commit: 4ea9471c1ecd999081129d2fc18f53b29ed1d0aa
Author: Arjun Kinstlick <ajkinstlick@gmail.com>
Date: 2021-06-08 13:32:30 -0500
Commit message:

 updated vignette to include hg38 and m25

Package: seq2pathway
Commit: 04ba9f541960a2351bb373f05fc706523ac1ff6f
Author: YangGroup <44039446+xyang2uchicago@users.noreply.github.com>
Date: 2021-06-01 20:55:37 -0500
Commit message:

 Add acknowledgement to the original authors

Package: GSEABenchmarkeR
Commit: 689e1df827d1041e934fc83b07c3cdca5aef9c8d
Author: lgeistlinger <ludwig.geistlinger@gmail.com>
Date: 2021-06-08 12:28:24 -0400
Commit message:

 remove cache

Package: cBioPortalData
Commit: 4607fbf227481eb631614a3cc47a489282bcf1de
Author: LiNk-NY <mramos09@gmail.com>
Date: 2021-06-08 11:59:43 -0400
Commit message:

 version bump 2.5.3

Package: cBioPortalData
Commit: dacf4ea7d4b9c6d4d226b5503d669beb3c5d9883
Author: LiNk-NY <mramos09@gmail.com>
Date: 2021-06-08 11:58:47 -0400
Commit message:

 api update

Package: VAExprs
Commit: 9a9b3897f953a080b5c550b4eca3d8298b306928
Author: dongminjung <dongminjung@Dongmins-MacBook-Pro.local>
Date: 2021-06-09 00:08:02 +0900
Commit message:

 update

Package: VAExprs
Commit: 3ce55c580cf8fa4f1e417c6f85246cd7cc8564e9
Author: dongminjung <dongminjung@Dongmins-MacBook-Pro.local>
Date: 2021-06-08 23:48:50 +0900
Commit message:

 update

Package: spbtest3
Commit: 2fd112f07ce6b52857b07c1f8d23426d02479940
Author: Lori Shepherd <lori.shepherd@roswellpark.org>
Date: 2021-06-08 09:13:15 -0400
Commit message:

 Update description

Package: spbtest3
Commit: b87e0a75b72503a67b97d59902b36f36128e2d39
Author: Lori Shepherd <lori.shepherd@roswellpark.org>
Date: 2021-03-10 16:34:05 -0500
Commit message:

 Bump description

Package: ClassifyR
Commit: 5eaf07a0759c29366679237764d6d8073c7da57b
Author: Dario Strbenac <dario@maths.usyd.edu.au>
Date: 2021-06-08 22:38:05 +1000
Commit message:

 - Pre-validation incorporated into runTests function.

Package: EpiXprSData
Commit: 2b4de2ec19083be5dec299988adc55edb403cb46
Author: Loveless <ilovele1@HFHS.ORG>
Date: 2021-06-08 07:58:11 -0400
Commit message:

 Update License

Package: FEVV
Commit: aa96b42475e9f745473774787e8f00bf75c08a56
Author: Isar Nassiri <isar.nassiri@oncology.ox.ac.uk>
Date: 2021-06-08 09:58:43 +0100
Commit message:

 Fixed conflicts in version change

Package: FEVV
Commit: 2512341d001f8ff8036b707f546baf45e631a9e2
Author: Isar Nassiri <isar.nassiri@oncology.ox.ac.uk>
Date: 2021-06-08 09:57:16 +0100
Commit message:

 Merge remote-tracking branch 'upstream/master'

Package: FEVV
Commit: bca6b19f7664ea91714e9d6aa37060740d83d140
Author: Isar Nassiri <isar.nassiri@oncology.ox.ac.uk>
Date: 2018-09-15 16:32:19 +0100
Commit message:

 Monocyte samples annotation

Package: ViSEAGO
Commit: 08efc447178fb1613436da833b18e37cac3a1d02
Author: Aurelien Brionne <aurelien.brionne@inrae.fr>
Date: 2021-06-08 10:07:35 +0200
Commit message:

 remove folder

Package: ViSEAGO
Commit: c5a67f6b9bc6b3078ebaa38d05f365ce1e5a965e
Author: Aurelien Brionne <aurelien.brionne@inrae.fr>
Date: 2021-06-08 10:03:01 +0200
Commit message:

 Ensembl2GO update

Package: BiocSingular
Commit: 01209b851de08f0d0a86db017f89b976a8449c58
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2021-06-07 23:14:49 -0700
Commit message:

 Docfix.

Package: GenomicTuples
Commit: dbee8946936609f3b6d5a52509f8ce89a2e531da
Author: PeteHaitch <peter.hickey@gmail.com>
Date: 2021-06-08 14:57:25 +1000
Commit message:

 Enable `STRICT_R_HEADERS`

- https://github.com/RcppCore/Rcpp/issues/1158

Package: airpart
Commit: 6fc62ed7b697c4a9e2f8110728fc6726b1c5246d
Author: Wancen <42752661+Wancen@users.noreply.github.com>
Date: 2021-06-08 01:42:20 -0400
Commit message:

 add offset for batch

Package: rawrr
Commit: c047112d83178c1d45ed301d0de72922182bd594
Author: Christian Panse <cp@fgcz.ethz.ch>
Date: 2021-06-08 06:59:33 +0200
Commit message:

 roxygen2::roxygenise()

Package: rawrr
Commit: b448f8ecc1727f7003ee5d64f29d25e8a25d3529
Author: Christian Panse <cp@fgcz.ethz.ch>
Date: 2021-06-08 06:58:41 +0200
Commit message:

 man page cosmetics

Package: rawrr
Commit: db8d0a73954f651bf922fa5c56376170fe515347
Author: Christian Panse <cp@fgcz.ethz.ch>
Date: 2021-06-08 06:57:42 +0200
Commit message:

 shorted VignetteIndexEntry

Package: ggtreeExtra
Commit: 93cb2cf4b8530bd4dbaa3af26a635d165a9e684d
Author: xiangpin <xshuangbin@163.com>
Date: 2021-06-08 10:11:32 +0800
Commit message:

 update reference

Package: BUSpaRse
Commit: cb370256cdaea034ee2c4e65cddf81f75e341551
Author: Lambda Moses <dlu2@caltech.edu>
Date: 2021-06-07 18:07:36 -0700
Commit message:

 Forgot about the automated version bump

Merge branch 'master' of git.bioconductor.org:packages/BUSpaRse

# Conflicts:
#	DESCRIPTION

Package: BUSpaRse
Commit: 958ca9bb2520d98651e18c4ca7952c03827dc644
Author: Lambda Moses <dlu2@caltech.edu>
Date: 2021-06-07 18:05:37 -0700
Commit message:

 Got rid of R CMD check error caused by updates in GenomeInfoDB and Ensembl

Package: BiocGenerics
Commit: bd8defbe5d691604954504f3237c00dc0c0cdfc2
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2021-06-07 14:09:22 -0700
Commit message:

 Remove generics based on functions from package parallel

This commit removes the following generics: clusterApply(), clusterCall(),
clusterApplyLB(), clusterEvalQ(), clusterExport(), clusterMap(),
clusterSplit(), parLapply(), parSapply(), parApply(), parRapply(),
parCapply(), parLapplyLB(), and parSapplyLB().

Note that all these generics were added in Oct 2012 and never used (see
commit a47eebcb).

Package: BiocGenerics
Commit: 005e57b458d0c90f9e3577b64399e46cba39e6ef
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2021-06-07 13:57:21 -0700
Commit message:

 BiocGenerics:::updateS4() is now defunct

It has been deprecated in favor of BiocGenerics:::replaceSlots() for
about 6 years!

Package: cBioPortalData
Commit: a55a2c67cf98e0b9f3884702d7da685cb72aeff0
Author: LiNk-NY <mramos09@gmail.com>
Date: 2021-06-07 16:57:59 -0400
Commit message:

 version bump 2.5.2

Package: cBioPortalData
Commit: efb98b11a17d140ee5d8e7ff3c5e850a6a6b769c
Author: LiNk-NY <mramos09@gmail.com>
Date: 2021-06-07 14:31:29 -0400
Commit message:

 add error vignette

Package: cBioPortalData
Commit: a6cb5c41596ce2a9724fe2718ded37b0bb7c247d
Author: LiNk-NY <mramos09@gmail.com>
Date: 2021-06-07 11:50:38 -0400
Commit message:

 update NEWS

Package: cBioPortalData
Commit: 2bb7c49ccecf018e326508ec3de124306d459c63
Author: LiNk-NY <mramos09@gmail.com>
Date: 2021-06-07 11:45:14 -0400
Commit message:

 add helper to check study builds

Package: AnnotationDbi
Commit: 5b26730bc45c0a0488fe6f0a406d3564ec0e31f1
Author: Jim MacDonald <jmacdon@vector.deohs.washington.edu>
Date: 2021-06-07 09:10:50 -0700
Commit message:

 Removed outdated warning about Blast2GO sources - we use UniProt for that now, and have for a long time (Marc made the changes...).

Package: AnVILPublish
Commit: 8c71edde8520b67b718d8bc882ba58c71340431b
Author: Martin Morgan <Martin.Morgan@RoswellPark.org>
Date: 2021-06-07 10:08:31 -0400
Commit message:

 bug fixes to .set_tables

- use inst/tables (plural) as path
- pass package path to .set_tables

Package: AnVILPublish
Commit: 0204cad157e3c2424d1e4449a26e6e959c09eb68
Author: Martin Morgan <Martin.Morgan@RoswellPark.org>
Date: 2021-06-06 10:38:52 -0400
Commit message:

 Merge remote-tracking branch 'upstream/master'

Package: AnVILPublish
Commit: 814374ea2f4a13abd8120d35b2cbb21d4de5c07b
Author: Martin Morgan <Martin.Morgan@RoswellPark.org>
Date: 2021-04-20 14:23:46 -0400
Commit message:

 add .set_tables() to populate DATA TABLES from inst/tables/*csv

Package: iSEEu
Commit: 57f18a372eeabd424ef20323064d3ce987bc29ad
Author: Kevin Rue-Albrecht <kevinrue67@gmail.com>
Date: 2021-06-07 14:27:34 +0100
Commit message:

 Add biocthis GitHub Action workflow (#97)

* set up biothis gha template

* enable testthat, covr, and pkgdown

* workflow should _not_ error on warning

Package: animalcules
Commit: 6d94ed8aa26da0faa16c9bcad84307acac31d3f7
Author: jasonzhao0307 <jasonzhao0307@gmail.com>
Date: 2021-06-07 08:29:10 -0400
Commit message:

 comment out tsne in vignette

Package: rawrr
Commit: 7a821dd8d655022783a75efbc87f1c2a9bce959f
Author: Christian Panse <cp@fgcz.ethz.ch>
Date: 2021-06-07 13:41:34 +0200
Commit message:

 Merge branch 'master' of git.bioconductor.org:packages/rawrr

Package: rawrr
Commit: 8a602133e8c9e3206ae527a584c22d6000968869
Author: Christian Panse <cp@fgcz.ethz.ch>
Date: 2021-06-07 13:40:49 +0200
Commit message:

 cosmetics in yIonSeries code snippet

Package: rawrr
Commit: 6ecd918eeeb11c379a082fd7a1969813b3057b41
Author: Christian Panse <cp@fgcz.ethz.ch>
Date: 2021-06-07 13:40:49 +0200
Commit message:

 cosmetics of yIonSeries  code snippet

Package: BiocStyle
Commit: 3fa692f8aec8329e95f313fd18559e5d90f9d3ca
Author: Mike Smith <grimbough@gmail.com>
Date: 2021-06-07 12:17:27 +0200
Commit message:

 Version bump

Package: BiocStyle
Commit: 42d9cd89d89baf43144b9677acee4ca00ec488aa
Author: Mike Smith <grimbough@gmail.com>
Date: 2021-06-07 12:17:18 +0200
Commit message:

 Still trying to fix issue with code block padding.  Differences between build system vignettes and local knitting

Package: iSEEu
Commit: 08771423e44c87adf40d33c330645a677d1ad467
Author: Kevin Rue-Albrecht <kevinrue67@gmail.com>
Date: 2021-06-07 11:00:37 +0100
Commit message:

 Fix spelling typo in man page (#95)

* fix spelling typo in man page; roxygenise

* update version bump after bioc release

Package: Spectra
Commit: a50e09f394a54612a7e8cf756d9bce89b74c4aca
Author: jorainer <johannes.rainer@gmail.com>
Date: 2021-06-07 10:06:51 +0200
Commit message:

 tests: drop comparison of processing log to fix unit test

Package: Spectra
Commit: 25a2bfb24adf9b62745e52176db211c75639fcce
Author: jorainer <johannes.rainer@gmail.com>
Date: 2021-06-07 09:23:03 +0200
Commit message:

 ci: fix CI

Package: Spectra
Commit: 771c430505f711511a5427787328b02ea1a2124a
Author: Johannes Rainer <5506112+jorainer@users.noreply.github.com>
Date: 2021-06-07 09:21:42 +0200
Commit message:

 Merge pull request #203 from rformassspectrometry/jomain

feat: add estimatePrecursorIntensity (issue #202)

Package: Spectra
Commit: 4c76c17992463e1ee241fb8d32a20b2abcbf5119
Author: jorainer <johannes.rainer@gmail.com>
Date: 2021-06-07 09:06:46 +0200
Commit message:

 Merge remote-tracking branch 'origin/jomain' into jomain

Package: Spectra
Commit: 2d41b9e40ad167ab38a7cd0aeb6f9dab5302fcac
Author: jorainer <johannes.rainer@gmail.com>
Date: 2021-06-07 09:06:21 +0200
Commit message:

 Merge remote-tracking branch 'origin' into jomain

Package: Spectra
Commit: ccc773b1f54f2c0126eef1fe03dc0fc686da7f8d
Author: Johannes Rainer <5506112+jorainer@users.noreply.github.com>
Date: 2021-06-07 08:46:22 +0200
Commit message:

 Update R/Spectra.R

Co-authored-by: Sebastian Gibb <mail@sebastiangibb.de>

Package: Spectra
Commit: 6e9983b6afb291c18a59847046138af870132658
Author: Laurent Gatto <laurent.gatto@gmail.com>
Date: 2021-05-28 07:48:50 +0200
Commit message:

 Update check-bioc.yml

Package: Spectra
Commit: adcb5dcb731c7fb39ff1f4666d8c8f76af58945d
Author: Laurent Gatto <laurent.gatto@gmail.com>
Date: 2021-05-27 17:11:56 +0200
Commit message:

 Merge pull request #205 from lgatto/master

Add package logo

Package: Spectra
Commit: 9ceede7340396c87f4b4404d7d2a8cb723b0ff67
Author: Laurent Gatto <laurent.gatto@uclouvain.be>
Date: 2021-05-27 17:11:19 +0200
Commit message:

 ci: bump version

Package: Spectra
Commit: 47b05707a5d2ecde89537a7e0efc3e46c44020f4
Author: Laurent Gatto <laurent.gatto@uclouvain.be>
Date: 2021-05-27 17:10:44 +0200
Commit message:

 build: ignore logo when building package

Package: Spectra
Commit: 37f6c42b75a08f883625409d5cb5eb207dbd47e2
Author: Laurent Gatto <laurent.gatto@uclouvain.be>
Date: 2021-05-27 17:06:39 +0200
Commit message:

 add package logo

Package: Spectra
Commit: 5590dacf712cf74e9df882a84c28b465deded8db
Author: jorainer <johannes.rainer@gmail.com>
Date: 2021-05-21 09:05:49 +0200
Commit message:

 bump version

Package: Spectra
Commit: 90247451423ec49bd405b4ca1cb0a6ee636bb64a
Author: jorainer <johannes.rainer@gmail.com>
Date: 2021-05-21 09:04:45 +0200
Commit message:

 Merge branch 'master' into jomain

Package: Spectra
Commit: 49bf2ecd8c7101cc10232bdaea9340f4993196ef
Author: jorainer <johannes.rainer@gmail.com>
Date: 2021-05-07 14:56:15 +0200
Commit message:

 feat: add estimatePrecursorIntensity (issue #202)

Package: MethylSeekR
Commit: c54eba4472a9052ea9c27e2eb6aa71dd440608cc
Author: burgerlu <lukas.burger@fmi.ch>
Date: 2021-06-07 11:39:17 +0200
Commit message:

 Fixed conflicts in version change

Package: MethylSeekR
Commit: 967bb863bc49d31c0d746d9ea00e1eb8889660eb
Author: burgerlu <lukas.burger@fmi.ch>
Date: 2021-06-07 11:27:14 +0200
Commit message:

 bumped up version number

Package: MethylSeekR
Commit: bd6623ebd2ed17cf6317e82016924c55e24aec1d
Author: burgerlu <lukas.burger@fmi.ch>
Date: 2021-06-07 11:20:33 +0200
Commit message:

 more precise description of input file

Package: MethylSeekR
Commit: 140143912c568da643a068487f28cfaa9c6aa2f1
Author: mbstadler <stadler.michael@gmail.com>
Date: 2021-01-15 14:02:35 +0100
Commit message:

 control deployment using config variable; switch off deployment for the moment

Package: MethylSeekR
Commit: 0e30caf236100feac9403168295b4e828e7fe267
Author: mbstadler <stadler.michael@gmail.com>
Date: 2021-01-15 12:45:56 +0100
Commit message:

 add bioc variable to container config

Package: MethylSeekR
Commit: 5888a26a613646c8b2c5194882394d935b2dbf0f
Author: mbstadler <stadler.michael@gmail.com>
Date: 2021-01-15 12:38:51 +0100
Commit message:

 deploy from macOS

Package: MethylSeekR
Commit: de4eea4891e208d4003d0f0500c00b4753e2ba09
Author: mbstadler <stadler.michael@gmail.com>
Date: 2021-01-15 12:16:44 +0100
Commit message:

 try not installing latex packages in bioc container (has a full tex installation)

Package: MethylSeekR
Commit: 47a9ae20fd587d31c94ccb229ac42cff81d0e37c
Author: mbstadler <stadler.michael@gmail.com>
Date: 2021-01-15 12:06:47 +0100
Commit message:

 re-enable macOS and install gfortran

Package: MethylSeekR
Commit: 164ebcd2f854a03d16724789a2b50cbda91ddeba
Author: mbstadler <stadler.michael@gmail.com>
Date: 2021-01-15 11:45:48 +0100
Commit message:

 initialize tex user tree

Package: MethylSeekR
Commit: 45373869ba97717b9f4500c0f8a70c6bff7783d2
Author: mbstadler <stadler.michael@gmail.com>
Date: 2021-01-15 11:33:36 +0100
Commit message:

 replace tabs with spaces

Package: MethylSeekR
Commit: 5ceb7f7a5c3b73fd25d6c0ae1456c5dbe21438eb
Author: mbstadler <stadler.michael@gmail.com>
Date: 2021-01-15 11:29:17 +0100
Commit message:

 fix another syntax error

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