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Bioconductor has moved to GIT for contributed packages; the subversion logs are no longer active.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 devel(development) branch of the Bioconductor GIT repository.

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

Package: BEclear
Commit: ce25f01e0f65c114ef0a2276369970e25a804958
Author: Livia Rasp <livia.rasp@gmail.com>
Date: 2026-01-08 20:48:34 +0100
Commit message:

 exchanged package in import statements

Package: MOFA2
Commit: db029665dbd85412b5b2c04af4c5e225751bbcd7
Author: Jan Sprengel <jansprengel@web.de>
Date: 2026-01-08 15:55:55 +0100
Commit message:

 increment version to 1.21.2

Package: MOFA2
Commit: 07b20a4be3b191300081c684d0a30560825083cf
Author: Jan Sprengel <jansprengel@web.de>
Date: 2026-01-05 16:17:52 +0100
Commit message:

 comment plot_mutliple_factors function

Package: MOFA2
Commit: 76801df2fc5501fe2efb7ab2381f7b948abd295f
Author: Jan Sprengel <136387767+jan-spr@users.noreply.github.com>
Date: 2026-01-05 15:40:58 +0100
Commit message:

 Merge pull request #105 from ilia-kats/fix_factor_plot_colorscale

plot_factors: fix continuous color scale when plotting >2 factors

Package: MOFA2
Commit: 7360cf43c1b21b503a71980574e121f4f1825349
Author: Jan Sprengel <136387767+jan-spr@users.noreply.github.com>
Date: 2026-01-05 15:39:29 +0100
Commit message:

 Merge branch 'main-dev' into fix_factor_plot_colorscale

Package: MOFA2
Commit: f95fb5a31cd01d53594066d5d71e41494aa96536
Author: Jan Sprengel <jansprengel@web.de>
Date: 2025-12-17 13:57:03 +0100
Commit message:

 fix typo in plot_factors (#172), update man

Package: MOFA2
Commit: d8c7aa2c3de554f9e20f5cbe5f9183da8b9fa3ce
Author: Ilia Kats <ilia-kats@gmx.net>
Date: 2022-09-22 16:16:29 +0200
Commit message:

 plot_factors: fix continuous color scale when plotting >2 factors

Package: BayesSpace
Commit: ba8b42211ef1581d31a659766559bd6e42be3acc
Author: Senbai Kang <30857702+senbaikang@users.noreply.github.com>
Date: 2026-01-08 16:39:36 +0100
Commit message:

 User-defined nthreads for xgboost (#157)

* feat: user-defined nthread for xgb

* version bump devel

Package: BayesSpace
Commit: 8f25ca4e0c8d58e5b55851ef67bb1d837ba8e128
Author: Senbai Kang <30857702+senbaikang@users.noreply.github.com>
Date: 2026-01-08 14:43:59 +0100
Commit message:

 fix: compatibility issues with xgb 3+ (#156)

This PR fixes the compatibility issues with xgboost v3+.

Package: scFeatures
Commit: aa0f2c89542de66c6649757266c1bedf99705583
Author: Yue Cao <yue.cao@sydney.edu.au>
Date: 2026-01-08 20:06:09 +1100
Commit message:

 Make CellChat optional

Package: scFeatures
Commit: 23835874e9d8421429f2179c2da9f7ea09b7c993
Author: Yue Cao <yue.cao@sydney.edu.au>
Date: 2026-01-08 16:25:27 +1100
Commit message:

 Merge GitHub devel into Bioconductor devel

Package: scFeatures
Commit: 2a17fd3446206c6385705da5c768b6d105cb8ba7
Author: Yue Cao <yue.cao.au@gmail.com>
Date: 2025-12-23 19:37:05 +1100
Commit message:

 Suppress messages in bplapply call

Wrap bplapply call in capture.output to suppress messages.

Package: scFeatures
Commit: 3d0aa934fa67440e8171213f817655be006f6297
Author: Yue Cao <yue.cao.au@gmail.com>
Date: 2025-12-23 19:26:04 +1100
Commit message:

 error handling of empty CCI result

Ensured proper handling of empty results.

Package: scFeatures
Commit: 3d9eafef88b9197d3ab2d4d68fe09ce7578a26a5
Author: Yue Cao <yue.cao.au@gmail.com>
Date: 2025-12-23 17:05:15 +1100
Commit message:

 replace human with homo sapiens

for consistency

Package: scFeatures
Commit: 96ddaa8ce8d73a2903f5589979f2816397b4cec4
Author: Yue Cao <yue.cao.au@gmail.com>
Date: 2025-12-23 17:03:52 +1100
Commit message:

 import cellchat database

import cellchat database

Package: scFeatures
Commit: 5352e2518ccc41e05f3e2099803bbc2376f18783
Author: Yue Cao <yue.cao.au@gmail.com>
Date: 2025-12-23 16:40:21 +1100
Commit message:

 replace SingleCellSignalR import with CellChat from NAMESPACE

replace SingleCellSignalR import with CellChat from NAMESPACE

Package: scFeatures
Commit: 7f009018e3eafb45d06ea710da6562996e7b3d0e
Author: Yue Cao <yue.cao.au@gmail.com>
Date: 2025-12-23 16:39:04 +1100
Commit message:

 Replace SingleCellSignalR import with CellChat

Package: scFeatures
Commit: c5b2264877a543c8ee5e506a1375b7f1f42e5ac8
Author: Yue Cao <yue.cao.au@gmail.com>
Date: 2025-12-23 16:30:51 +1100
Commit message:

 replace singlecellsignalR with CellChat  

Updated DESCRIPTION file to include CellChat and its remote repository.

Package: scFeatures
Commit: 66b22cdb53f063addf63fc0a52c55a7255071c9b
Author: Yue Cao <yue.cao.au@gmail.com>
Date: 2025-12-23 16:29:32 +1100
Commit message:

 cellchat allows human and mouse database

Package: scFeatures
Commit: 0e08639ec6259e74369a4290c9e80b34d9cfcf9d
Author: Yue Cao <yue.cao.au@gmail.com>
Date: 2025-12-23 16:28:02 +1100
Commit message:

 cellchat allows human and mouse database

Package: scFeatures
Commit: 38f4a9ece6b7f2efac8eaae8f592aa21898afe8e
Author: Yue Cao <yue.cao.au@gmail.com>
Date: 2025-12-23 16:27:04 +1100
Commit message:

 use cellchat instead of singlecellsignalR

to avoid installation issue with singlecellsignalR and bulksignalR

Package: scFeatures
Commit: 72c0770918eba9f301990e5adb8eda4a9bff348b
Author: Yue Cao <yue.cao.au@gmail.com>
Date: 2025-10-07 18:14:28 +1100
Commit message:

 Merge pull request #15 from SydneyBioX/mattshu0410-patch-1

Update helper_pathway.R

Package: scFeatures
Commit: fbc75e38c04df3995fb755833357e6c8f5f4c1d3
Author: Matthew Shu <62276229+mattshu0410@users.noreply.github.com>
Date: 2025-10-06 12:08:43 +1100
Commit message:

 Update helper_pathway.R 

When greater than 30000 cells, the final set upper bound index is incorrectly set to be 1 less than the true length. This causes an index mismatch.

Package: scFeatures
Commit: d308df2c6f1ecb0e2f930ce97ef6367b536dd1f9
Author: Yue Cao <yue.cao.au@gmail.com>
Date: 2025-06-11 15:14:31 +1000
Commit message:

 Update run_scfeatures.R

default to aucell instead of ssgsea

Package: scFeatures
Commit: 48c58ebf6d7921d47f2d18b4c621fc2984491403
Author: Yue Cao <yue.cao.au@gmail.com>
Date: 2025-05-05 23:17:17 +1000
Commit message:

 fix compatibility with sparse matrix

Package: scFeatures
Commit: b24dde52d0899641c014ee13a2557fbad14a76fb
Author: Yue Cao <yue.cao.au@gmail.com>
Date: 2024-11-29 10:16:54 +1100
Commit message:

 Update helper_spatial_metrics.R

remove starting from 0 in spatial coordinate

Package: scFeatures
Commit: 28d38da24d697926af33f1cb0dc90787542a80b7
Author: Yue Cao <yue.cao.au@gmail.com>
Date: 2024-11-25 10:28:29 +1100
Commit message:

 remove x and y coordinates starting from 0 in L function

remove x and y coordinates starting from 0 in L function

Package: scFeatures
Commit: 78ef5592fe659713d5ef59464f6bce0a2951f130
Author: Yue Cao <yue.cao.au@gmail.com>
Date: 2024-08-26 20:16:06 +1000
Commit message:

 Add files via upload

Package: scFeatures
Commit: 5646fad16427bee9455ea7e8be7fe6f5cf908c86
Author: Yue Cao <yue.cao.au@gmail.com>
Date: 2024-08-26 20:13:16 +1000
Commit message:

 Add files via upload

Package: scFeatures
Commit: 2a5f13f6e539c31fe62be567bc8af32bcddc6a0f
Author: Yue Cao <yue.cao.au@gmail.com>
Date: 2024-08-26 20:13:04 +1000
Commit message:

 update readme to include more examples

Package: mitch
Commit: 560f5e5fa7d3a487f0cbbc889e6d31b39f619baf
Author: markziemann <markziemann@gmail.com>
Date: 2026-01-08 19:35:19 +1100
Commit message:

 bump

Package: mitch
Commit: 062e4881d338ed0dbe016911252961719aadde6d
Author: markziemann <markziemann@gmail.com>
Date: 2026-01-08 19:34:28 +1100
Commit message:

 merge

Package: mitch
Commit: ed9abbbe767a452e4ea22955daccf3171c897436
Author: markziemann <markziemann@gmail.com>
Date: 2026-01-08 19:30:58 +1100
Commit message:

 got an error with vignette generation due to availability of web file. fixed now but need to bump anyway.

Package: augere.core
Commit: 555f0a5f688e21e3162a5ca39f5d0c5e8c456db9
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2026-01-08 18:23:03 +1100
Commit message:

 Minor improvements to pass Bioc review, mostly to flesh out details.

Package: QTLExperiment
Commit: e9b1b31b6fe6fa349487941e750efacbccc4c575
Author: dunstone-a <amelia.dunstone@gmail.com>
Date: 2026-01-08 15:05:06 +1100
Commit message:

 Remove warning
- Update documentation so that \linkS4class{} isn't used for classes outside the package itself. These are replaced with \code{\link[package]{class}}

Package: knowYourCG
Commit: 51b323e5d52332bbd5ad21cce2a520a0a907f023
Author: Wanding Zhou <zhouwanding@gmail.com>
Date: 2026-01-07 22:24:50 -0500
Commit message:

 bump to 1.7.11, attempting to address the warning on bioc

Package: knowYourCG
Commit: e1b6adad29064db26634a082c0beea59cff1a2e5
Author: Wanding Zhou <zhouwanding@gmail.com>
Date: 2026-01-07 22:17:30 -0500
Commit message:

 bump to 1.7.10

Package: epiSeeker
Commit: f0aec403375059808e6c3ea35b03d5357abf369a
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2026-01-07 14:41:08 +0800
Commit message:

 update

Package: multiWGCNA
Commit: 42c77b53d06c54aa321e19f9316cedb3ecee78bb
Author: dariotommasini <dtommasini0@gmail.com>
Date: 2026-01-07 16:41:10 -0800
Commit message:

 1.9.3

Package: multiWGCNA
Commit: 5f218a371f31688c7520e373feecf8643cad9353
Author: dariotommasini <dtommasini0@gmail.com>
Date: 2026-01-07 16:40:48 -0800
Commit message:

 adding everything

Package: multiWGCNA
Commit: 602a5b6b89c4c19f436ef5e9acb913ab2619c4dc
Author: dariotommasini <dtommasini0@gmail.com>
Date: 2026-01-07 16:39:17 -0800
Commit message:

 dont test diffCoexpression

Package: knowYourCG
Commit: fe1446c4883626879e05151d918aab33f2445ae7
Author: Wanding Zhou <zhouwanding@gmail.com>
Date: 2026-01-07 16:48:09 -0500
Commit message:

 bump to 1.7.9

Package: knowYourCG
Commit: 6a7d0a66df3ed40e2bc1173fc703a96174654e95
Author: Wanding Zhou <zhouwanding@gmail.com>
Date: 2026-01-07 16:47:53 -0500
Commit message:

 bump to 1.7.9, more removal of github links

Package: knowYourCG
Commit: 9dcbb6869e53935da81f45ad867a6d47e37431b6
Author: Wanding Zhou <zhouwanding@gmail.com>
Date: 2026-01-07 15:32:04 -0500
Commit message:

 bump to 1.7.8, removed github links

Package: igblastr
Commit: 7ccc8a940cc85aaeb48ef95c9be92876373f8c1f
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2026-01-07 13:14:46 -0800
Commit message:

 Add annotate_heavy_V_alleles() and annotate_light_V_alleles()

Package: memes
Commit: 7c48d1debc2c5709b2f4ab1a125da929dfa1a675
Author: Spencer Nystrom <snystrom@users.noreply.github.com>
Date: 2026-01-06 18:00:21 -0800
Commit message:

 plot nomatch with universalmotif

Package: orthogene
Commit: 3569148c78b81aec65651ddd90d019ac084051a1
Author: bschilder <brian_schilder@alumni.brown.edu>
Date: 2026-01-07 00:17:38 -0500
Commit message:

 Update benchmarks. Chunk gprofiler queries

Package: orthogene
Commit: ecf7c3669431c2ce4e9c412bad9982dc2e62f6bd
Author: bschilder <brian_schilder@alumni.brown.edu>
Date: 2026-01-05 01:09:31 -0500
Commit message:

 upgrade hex [skipci]

Package: orthogene
Commit: 9a51222af4454d0df05d1c1d19c0c2ed7dca9e04
Author: bschilder <brian_schilder@alumni.brown.edu>
Date: 2026-01-03 21:43:01 -0500
Commit message:

 Fix planarian tests

Package: orthogene
Commit: 7fd6db13945eb2c8834465b7e09b5c4ba6fa8e8c
Author: bschilder <brian_schilder@alumni.brown.edu>
Date: 2026-01-03 21:06:10 -0500
Commit message:

 trigger GHA [nocache]

Package: orthogene
Commit: 61e510c5b96c76aded16cb07befdf43c44414452
Author: bschilder <brian_schilder@alumni.brown.edu>
Date: 2026-01-03 20:38:05 -0500
Commit message:

 Fix version number

Package: bedbaser
Commit: 20ad1adca71972be37988a871117ca689aa78c0e
Author: A Wokaty <awokaty@users.noreply.github.com>
Date: 2026-01-07 12:08:53 -0500
Commit message:

 Bump version, update NEWS

Package: bedbaser
Commit: 198b21ec4aff47bcc1121914b9915ab8edbe8664
Author: A Wokaty <awokaty@users.noreply.github.com>
Date: 2026-01-07 12:08:17 -0500
Commit message:

 Change maintainer email

Package: bedbaser
Commit: 380398c021446a61e991fe5b345bfd1e71c3980c
Author: A Wokaty <awokaty@users.noreply.github.com>
Date: 2026-01-07 12:00:16 -0500
Commit message:

 Update api to 0.12.1, fix test for search, replace download.file

- Update api to 0.12.1
- Fix test for bb_bed_text_search
- Replace download.file with curl::curl_download

Package: tidyexposomics
Commit: d83a8e0b4c4fe957dad0643cec770d24ec00b8d3
Author: BioNomad <jlaird1@binghamton.edu>
Date: 2026-01-07 12:38:33 -0500
Commit message:

 0.99.12 changes removing .Rproj.user dir

Package: qPLEXanalyzer
Commit: a9f40f91098e7e5f5aaf631f70d436e8afe776c8
Author: Ashley Sawle <ads2202cu@gmail.com>
Date: 2026-01-07 16:35:10 +0000
Commit message:

 Updates and version bump

Package: qPLEXanalyzer
Commit: 03c9057a66287b05e45dcdf8ed5c0a59ff32e33c
Author: Ashley Sawle <ads2202cu@gmail.com>
Date: 2026-01-07 15:28:53 +0000
Commit message:

 Merge conflicts resolved

Package: qPLEXanalyzer
Commit: 89f3a805f7b2c26c0be8989045fba0dc5a3fc73e
Author: Ashley Sawle <ads2202cu@gmail.com>
Date: 2026-01-07 15:25:45 +0000
Commit message:

 Update to new ROxygen

Package: qPLEXanalyzer
Commit: 0320d03d61e08d22a7fe3fcc623a55b41de7aa7c
Author: Ashley Sawle <ads2202cu@gmail.com>
Date: 2026-01-07 15:25:28 +0000
Commit message:

 Change man pages to reflect switch to using name for congtrast

Package: qPLEXanalyzer
Commit: 6716487e8c37bb2ae033d7cd7edb018b48e7ceaa
Author: Ashley Sawle <ads2202cu@gmail.com>
Date: 2026-01-07 15:25:05 +0000
Commit message:

 Change to using name for contrasts

Package: qPLEXanalyzer
Commit: bcc7cbe2869f6510e4f7a0f658f5525c7f94021f
Author: Ashley Sawle <ads2202cu@gmail.com>
Date: 2026-01-07 15:24:39 +0000
Commit message:

 Fix for limma 3.66.0 switching to using the names for the contrasts

Package: qPLEXanalyzer
Commit: 03d740e3c610a158bc2af5c54ae6af9f4195200c
Author: kamalfartiyal84 <kamal.fartiyal84@gmail.com>
Date: 2025-04-23 15:24:55 +0100
Commit message:

 Updated qPLEXanalyzer.Rmd

Updated the Tutorial code at the Uniprot.ws section to extract annotation

Package: qPLEXanalyzer
Commit: 89a97dd02e9bacf9e00274c3dfd4b38b36be619c
Author: AshKernow <AshKernow@users.noreply.github.com>
Date: 2024-09-18 15:17:32 +0100
Commit message:

 Merge pull request #22 from crukci-bioinformatics/RELEASE_3_19

Release 3 19

Package: qPLEXanalyzer
Commit: e9ff9dda065c2a0c257a89263071d395b711df14
Author: Ashley Sawle <ads2202cu@gmail.com>
Date: 2024-09-18 14:31:31 +0100
Commit message:

 Update NEWS

Package: qPLEXanalyzer
Commit: bc5aa0f0de3816bff7e5521bb1d096b5cac46486
Author: Ashley Sawle <ads2202cu@gmail.com>
Date: 2024-09-18 14:30:28 +0100
Commit message:

 Update everything with roxygen and version bump

Package: qPLEXanalyzer
Commit: b70897a821494e1758d07658fb1e5279c6278eba
Author: Ashley Sawle <ads2202cu@gmail.com>
Date: 2024-09-18 14:28:36 +0100
Commit message:

 Switch from gridExtra to patchwork in vignette

Package: qPLEXanalyzer
Commit: b17fe600cd1c44fe3d6136136cfd4a6377b71c35
Author: Ashley Sawle <ads2202cu@gmail.com>
Date: 2024-09-18 14:28:20 +0100
Commit message:

 Update so that user can omit labels on PCA plot

Package: scds
Commit: 3f70cadec32eff3f5e8d07037638d886a22a685d
Author: Dennis Kostka <kostka@Denniss-MacBook-Pro-2.local>
Date: 2026-01-07 10:39:07 -0500
Commit message:

 Resolve merge conflict and bump version for BioC

Package: scds
Commit: c9054c2637dfab28d726f0a346d049080e25f84f
Author: kostkalab <47754848+kostkalab@users.noreply.github.com>
Date: 2026-01-06 10:48:09 -0500
Commit message:

 Bump version from 1.13.2 to 1.99.0

Package: scds
Commit: f8fc5d30edc970de2f939af6c598f8bd96f4ffda
Author: kostkalab <47754848+kostkalab@users.noreply.github.com>
Date: 2026-01-06 10:47:03 -0500
Commit message:

 Merge pull request #10 from joshua-d-campbell/master

Fix xgboost compatibility

Package: scds
Commit: de9b9a5feae38f252035b9542e38c9d4d379f822
Author: kostkalab <47754848+kostkalab@users.noreply.github.com>
Date: 2026-01-06 10:46:24 -0500
Commit message:

 Merge branch 'master' into master

Package: scds
Commit: 6ca01688beb5ce236c9fec85c4b4c41e03956157
Author: kostkalab <47754848+kostkalab@users.noreply.github.com>
Date: 2026-01-06 10:45:10 -0500
Commit message:

 Bump version from 1.13.1 to 1.13.2

Package: scds
Commit: 9265e5d12c396c4a9a296be491447010c80d6a4d
Author: Joshua D. Campbell <joshua.d.campbell@gmail.com>
Date: 2025-12-30 17:11:06 -0500
Commit message:

 Removed old license file

Package: scds
Commit: ea946113b0bb6249d3637220cfec17bfe54b00a3
Author: Joshua D. Campbell <joshua.d.campbell@gmail.com>
Date: 2025-12-30 17:07:29 -0500
Commit message:

 added gitignore

Package: scds
Commit: 07d86d65c3e6e7e8cad059b2fd8ec155d0697c92
Author: Joshua D. Campbell <joshua.d.campbell@gmail.com>
Date: 2025-12-30 17:05:29 -0500
Commit message:

 Update docs

Package: scds
Commit: 38178c635a8f0df3ee0618f0ed902150f11015dc
Author: Joshua D. Campbell <joshua.d.campbell@gmail.com>
Date: 2025-12-30 17:05:14 -0500
Commit message:

 Remove usage statement to get rid of R CMD check warning

Package: scds
Commit: 136055dbe3ccc7b6d6807c82c1bb2a79d59199ca
Author: Joshua D. Campbell <joshua.d.campbell@gmail.com>
Date: 2025-12-30 16:55:30 -0500
Commit message:

 fixed parameter matching

Package: scds
Commit: 47ec1760c34f30d9cabf27b13c35042f75887aff
Author: Joshua D. Campbell <joshua.d.campbell@gmail.com>
Date: 2025-12-30 16:41:35 -0500
Commit message:

 version bump

Package: scds
Commit: 21f73acd24abcfcc379a4558423e4a5ad7bd151d
Author: Joshua D. Campbell <joshua.d.campbell@gmail.com>
Date: 2025-12-30 16:23:46 -0500
Commit message:

 Handle new xgboost syntax. Now handles both prior and current versions of xgboost

Package: famat
Commit: 6608014a5bd023ae8a545ce21adb49bd673a38be
Author: MathieuCharlesINRAE <mathieu.charles@inrae.fr>
Date: 2026-01-07 15:57:05 +0100
Commit message:

 Fix for change in KEGGrest not supporting Chebi anymore

Package: famat
Commit: be1fd64249a5f729f382b2347bd1a731cb8c01bd
Author: MathieuCharlesINRAE <mathieu.charles@inrae.fr>
Date: 2025-12-01 10:16:10 +0100
Commit message:

 Last fix following the change in KEGGrest around keggconv

Package: famat
Commit: 669099e9bf8f3ae97cd748e54b67fee276b0b3ab
Author: MathieuCharlesINRAE <mathieu.charles@inrae.fr>
Date: 2025-11-27 17:25:01 +0100
Commit message:

 fix for KEGGREST not supporting chebi in keggconv

Package: hmdbQuery
Commit: 14be67dc724b1c169209d02a6034837e6d06e351
Author: lshep <lori.shepherd@roswellpark.org>
Date: 2026-01-07 09:18:34 -0500
Commit message:

 requested deprecation

Package: scater
Commit: db4b85873c6300a1c46f780f6fe635862f70295b
Author: Alan O'Callaghan <alan.ocallaghan@outlook.com>
Date: 2026-01-07 13:24:31 +0000
Commit message:

 Version

Package: scater
Commit: 0fd4a7380fc2764395a26c9ae73ce55dd03669d6
Author: Alan O'Callaghan <alan.ocallaghan@outlook.com>
Date: 2026-01-07 13:24:12 +0000
Commit message:

 Merge branch 'devel' of git.bioconductor.org:packages/scater into devel

Package: scater
Commit: ef10509acec572790f6991fffc76f713af45baeb
Author: Aaron Lun <infinite.monkeys.with.keyboards@gmail.com>
Date: 2026-01-08 00:23:41 +1100
Commit message:

 Simple addition of per-category horizontal line segments to a plot. (#222)

* Added utility to easily add per-category hlines to a ggplot.

* More robust mapping to x-axes, yet more cryptic and disturbing.

Package: plaid
Commit: ec5caa563158ff2776ef70a6b9487f0b7ba33202
Author: ESCRI11 <xavier.escriba.montagut@gmail.com>
Date: 2026-01-07 13:44:24 +0100
Commit message:

 bump version

Package: plaid
Commit: edc7de61d245a725eafedf0769d9d7b527f64a9b
Author: ESCRI11 <xavier.escriba.montagut@gmail.com>
Date: 2026-01-07 13:43:53 +0100
Commit message:

 move sparsematrixstats to suggests

Package: psichomics
Commit: 70c9e2e81ddeb06f70e0b07cadeb9be74c92bbf6
Author: Nuno Agostinho <nuno.agostinho@crg.eu>
Date: 2026-01-07 12:09:05 +0100
Commit message:

 Squashed commit of the following:

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        Fix GTEx URLs

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        docs(license): update copyright year(s)

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        docs(license): update copyright year(s)

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        Update NEWS.md

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        Update NEWS.md

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        1.22.1

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        Update changelog date

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    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Jul 11 17:15:02 2022 +0000

        Fix loading GTEx v8 data

    commit dc70999b0ccb9ed58d317c1e0d66f29479e84e9a
    Author: Nuno Agostinho <nuno@ebi.ac.uk>
    Date:   Mon Jun 20 19:10:07 2022 +0100

        Bump version

    commit d25c0ca418c7b7a25346e0c359657e1ad0ba4047
    Merge: 08247299 f3fe8f33
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Jun 20 19:06:48 2022 +0100

        Merge pull request #448 from nuno-agostinho/fix/tutorial-surv-plot-list

        Update CLI_tutorial.Rmd

    commit 0824729992cec87dc2b238d338d3a66eba0ec4cf
    Author: Nuno Agostinho <nuno@ebi.ac.uk>
    Date:   Mon Jun 20 19:05:49 2022 +0100

        Fix GTEx data loading

    commit b609d8d8ad645a3b9af8239e9003c18f6fb5810e
    Merge: 9a6bc51d c4b63557
    Author: Nuno Agostinho <nuno@ebi.ac.uk>
    Date:   Thu May 19 13:26:23 2022 +0100

        Merge pull request #449 from nuno-agostinho:dev

        Custom Codespace container

    commit c4b63557ff5ab2c58ce85a637069ff07c4301757
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu May 19 12:23:41 2022 +0000

        Custom Codespace container

    commit f3fe8f33605a513c9c81f04516fef1369d342c18
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Sat May 7 21:12:39 2022 +0100

        Update CLI_tutorial.Rmd

    commit 9a6bc51dcbe1adf7e71b02a17a7c7be25a6b27d3
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Sun Mar 13 13:59:56 2022 +0000

        Fix missing topics from pkgdown

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    Merge: 5b443011 c79b8fd5
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Sun Mar 13 02:48:59 2022 +0000

        Merge pull request #439 from nuno-agostinho/fix/limmaTrend

        Fix limma-trend when using newer versions of limma

    commit 5b4430113074848e90b5169834da7ef1e0ee5d4e
    Author: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
    Date:   Sun Mar 13 02:47:55 2022 +0000

        Update license copyright year(s) (#443)

    commit 2ea84960801becee014c1dc80c7555ef2fe4b863
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Sun Mar 13 02:45:46 2022 +0000

        Update update-license-year.yml (#445)

    commit 991b060d25cf8b3d3f5fb3e52787e05b0b3e9d5e
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Sun Mar 13 02:43:01 2022 +0000

        Update update-license-year.yml (#444)

    commit d8bf3c5add70774446475763346a37b343470488
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Sun Mar 13 02:39:50 2022 +0000

        Update update-license-year.yml (#442)

    commit 5149c2a1069294b150a4db58bdb766a40dce5fda
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Sun Mar 13 02:38:25 2022 +0000

        Fix auto-update of copyright year (#441)

    commit 21fbf34b6fdd0686150a0a3ec808e52f04db25d0
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Sun Mar 13 02:34:55 2022 +0000

        Auto-update license year (#440)

    commit c79b8fd5e0d82bbe5ed49c4e4ebab8481963cf2d
    Author: Nuno Agostinho <nuno@ebi.ac.uk>
    Date:   Sun Mar 13 02:13:23 2022 +0000

        Fix limma-trend bug when using newer versions of limma to calculate average gene expression

    commit 5160e701985f6441d71efef51b918dfcb4b247fe
    Merge: 96b67336 6e1ef6ff
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Mar 11 17:55:14 2022 +0000

        Merge pull request #438 from nuno-agostinho/nuno-agostinho-patch-1

        Update pkgdown.yaml

    commit 6e1ef6ff18bfa69d275c769981cecf27dcbae17e
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Mar 11 17:53:42 2022 +0000

        Update pkgdown.yaml

    commit 96b67336960edb62e45f89420e5e7c7dcafd3708
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Mar 11 17:46:29 2022 +0000

        Update pkgdown.yaml

    commit 89672d62235a5a4762695613a1b8f30379117bc0
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Jan 25 20:59:08 2022 +0000

        Update README.md

    commit 30929b077b136356b18a73661ef5d3a30efa94b7
    Merge: 6b958b84 8ccc8660
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Jan 25 20:46:49 2022 +0000

        Merge pull request #437 from nuno-agostinho/fix/corr

        Allow to analyse correlation more than once in GUI

    commit 8ccc8660ee14f5ee25d2b3d942b1568c5538e866
    Author: Nuno Agostinho <nuno@ebi.ac.uk>
    Date:   Tue Jan 25 09:12:41 2022 +0000

        Allow to analyse correlation more than once in GUI

    commit 6b958b848fdc0308e44a13510827030a32eee488
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Dec 27 12:02:30 2021 +0000

        Update testDiscardLowCoveragePSIs.R

    commit 9bdab27c376201a8061114890ca39f54dde1a5ca
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Dec 27 09:08:11 2021 +0000

        Update testDiscardLowCoveragePSIs.R

    commit 1296c70a4d52813c2cfc5ce3210908d5318e0221
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Dec 24 09:19:16 2021 +0000

        Update pkgdown.yaml

    commit 9fc9299f34afb48971788e753d540948507ba929
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Dec 22 23:41:16 2021 +0000

        Revert to pkgdown 1.6.1

    commit 846031b61499f7e0d5d6445e171f59321b56bbac
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Dec 22 22:18:44 2021 +0000

        Fix using template tag twice

    commit 923c64f1b29863711ecbc0238e423b2155aaa309
    Merge: 02cd795c ff7d8f27
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Dec 22 22:01:21 2021 +0000

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

    commit 02cd795cbbd9e873d02bfb36072d23d3928503bf
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Dec 22 22:01:05 2021 +0000

        Isolate GitHub Action to deploy package

    commit ff7d8f27558f202678f49f574f9b393218187081
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Nov 3 16:30:37 2021 +0000

        Avoid Docker cache

        Doesn't update newer images?

    commit 99b289e5b61ce5280a5d6323b63ddb2ba2c71db6
    Merge: 7c8e8fac 0a22b26d
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Oct 28 00:10:19 2021 +0100

        Merge pull request #434 from nuno-agostinho/dev

        1.20.0

    commit 0a22b26dbf09e39aabc3e8bfc352ab95c4ea7254
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Oct 28 00:09:31 2021 +0100

        Bump version to 1.20.0

    commit 1a4f5ec9a3c559507da5109abcc524cf49db3bf9
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Oct 19 17:06:33 2021 +0100

        Update date of release based on Bioc 3.14

    commit 873f63b8decb2be1e0df4de9ba120bbd61b23330
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Oct 18 20:30:28 2021 +0100

        Support new AS annotations

        - Create AnnotationHub cache directory on first run of psichomics and allow to set cache path
        - Improve species/genome selection
        - Add loading bar when looking for AS annotation list
        - Change option used to evaluate shinyproxy support
        - Code copy-editing

    commit 7c8e8fac14d0087fff3e1b21d56b875d1436da00
    Merge: 654122c7 ed375ca8
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Oct 4 18:39:11 2021 +0100

        Merge pull request #431 from nuno-agostinho/dev

        1.18.6

    commit ed375ca8c6010dac6b9e0f837d4df60725144041
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Oct 4 17:06:05 2021 +0100

        Update Rcpp

    commit 1b3e34c4273ebb23e6c239201dfa633dc488e30a
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Oct 4 17:05:52 2021 +0100

        Fix issues with R CMD check

    commit 253eecb02608ad1ef94a9d8c1cdcff77da5c6472
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Oct 4 16:29:55 2021 +0100

        Minor UI improvements

        - Show tutorial link for user-provided data loading in welcome screen
        - Show psichomics version in welcome screen and help section
        - Update current year in copyright

    commit de8fde9fdfa31c9457f6d35c5aab8df4ff0965f2
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Oct 4 16:27:55 2021 +0100

        Upload ZIP folder instead of folder for Shinyproxy

    commit 638e900915afb29925fd893d10f30a5bfd3ebc25
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Oct 4 15:26:21 2021 +0100

        Suppress data's selectize input warnings for too much choices

    commit 9c2ab0cfc611a984bb550321774bce6dd22e657b
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Oct 1 18:00:18 2021 +0100

        Bump version to 1.18.6

    commit 9ba66a3a42041cc0a5f7b2cb5c60d643f8c2bd0c
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Oct 1 17:57:27 2021 +0100

        Clean-up survival analysis code

    commit 0989a6ea0de8c8498553a82fe5389aa7801a7d0c
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Oct 1 17:56:47 2021 +0100

        Update function documentation based on third-party libraries

    commit 607c36ab3c5e4593c1221edd29afa70cd4e6083d
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Oct 1 17:56:13 2021 +0100

        Improve plots and small UI enhancements

        - Show category icons for gene expression, junction quantification, clinical data and sample metadata
        - Minor changes to plot code for more uniformity

    commit b3ffddef7e6485aa482e6800017e2e50f2178158
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Oct 1 17:40:34 2021 +0100

        Select hg38 with GTEx v8 data

    commit 2a05d7f48a2279310307af4e628b1777d9051b98
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Oct 1 17:14:40 2021 +0100

        Fix issues with shiny 1.7.0

        - Change icon names as required by newest versions of font-awesome
        - Avoid modifying Shiny tags using generic positions

    commit 51f3082b7f7303107b0d9eaca798395ca4e98534
    Merge: e3b948c6 654122c7
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Aug 25 03:10:22 2021 +0100

        Merge branch 'master' into dev

    commit 654122c761d823ddc7dbcf7b5f45227dff652ef6
    Merge: bfe3bb28 a59acc08
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Aug 24 23:28:54 2021 +0100

        Merge pull request #430 from nuno-agostinho/diagram-fix

        AS event diagram fix

    commit a59acc08438f848f91bdfb58e5f8ccf0b1215291
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Aug 24 13:34:25 2021 +0100

        Avoid alternative regions from overlapping

    commit e2af9d36405c3d07824cff1f16b352cf2f6c2ce5
    Merge: e144419f bd575a9b
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Aug 24 13:31:39 2021 +0100

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

        # Conflicts:
        #	dev/event_diagrams.R

    commit e144419f14a7de096c9aab86ee1b4ecb0da189f5
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Aug 23 19:07:55 2021 +0100

        Test AS event plots

    commit bd575a9ba1eed989856e1a86606a5afc094c610b
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Aug 23 19:07:55 2021 +0100

        Test AS event plots

    commit dd57c2982e1bb2cf184637047be8cd1a3cedc229
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Aug 23 12:11:25 2021 +0100

        Fix AS event plots

        - Fix wrong colouring of reference exon in AFE and A5SS event diagrams
        - Fix colour order stack in transcript plots (reference exon in orange now on top of others)
        - Fix loading twice transcript plots when selecting a new event in the visual interface

    commit e3b948c6500e48bd5322a6c4d545577b06922eee
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Aug 23 12:02:01 2021 +0100

        Update NEWS.md

    commit 07ff16a97593b3c959f2952e84da8921e3b635fb
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Aug 23 11:59:04 2021 +0100

        Automatically plot PCA after calculating PCA scores

        - Copy-edit text

    commit 865e5f68c5c2c91797b9cdce9271ae67319d3e89
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Aug 23 11:54:57 2021 +0100

        Fix wrong coloring of reference exon in AFE and A5SS event diagrams

        - Change order of colour stack in transcript plots
        - Avoid loading transcript plot twice when selecting AS event
        - Improve unit testing

    commit b268627c9f758589731c4b50f3d329dc0f308674
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Aug 23 11:42:46 2021 +0100

        Load AS annotation only when opening the splicing quantification tab

    commit f5b9d8fc2148aaa343211c2703f1419aa40a1d77
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Mon Aug 23 11:40:29 2021 +0100

        Improve responsiveness of recount project selection

    commit bcb4e0f0d637873de7d79c67eead324b186a8657
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Aug 20 20:06:43 2021 +0100

        Rename JS file based on proper nomenclature

    commit 493b66fc8d42799c625e3ad7eb59bfb9f06121b8
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Aug 20 20:06:06 2021 +0100

        Fix issues with progress bar in ShinyProxy

    commit 015087f22d8090036253dd589ad89978bb29755e
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Aug 19 18:17:18 2021 +0100

        Fix shinyBS.js not loading

    commit c5699a51ed407a67d4b71264adab8bcc302f703c
    Merge: 68110bf2 4e888e4e
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Aug 19 17:43:28 2021 +0100

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

        # Conflicts:
        #	R/utils_interface.R

    commit 68110bf2e51a763b08c59c0363367364358c6933
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Aug 19 17:40:17 2021 +0100

        Add ShinyBS JS library (useful for ShinyProxy)

        - Update animate CSS library

    commit beb347789ac00b51cd1cd51e06ec0e5deb9de2cb
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Tue Aug 17 17:37:19 2021 +0100

        Fix PCA-related bug when plotting only one group

    commit 3ec5ff2f8a4eb285f4838d116c3526f827da5831
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Aug 13 20:59:44 2021 +0100

        shinyproxy: try closing progress bar

    commit 4e888e4e6b85539cb045b96e0e1d027ee7531ec3
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Aug 13 20:59:44 2021 +0100

        shinyproxy: try closing progress bar

    commit 7d55513d4ab47e3ec437b75d405c5015c0678844
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Aug 13 18:53:16 2021 +0100

        Fix getting environemnt option

    commit b0426cb505454a82f87d2e92edf440fad45f7cdc
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Aug 13 17:04:49 2021 +0100

        Add support to run in ShinyProxy

    commit bfe3bb28ad05f3366448ff0f477af3cbb566d4e9
    Merge: 147ae112 e1681cdd
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Jul 22 19:58:42 2021 +0100

        Merge pull request #428 from nuno-agostinho/dev

        Dev

    commit e1681cdd89689f71055713f3cc20724fb098b20d
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Jul 22 19:49:46 2021 +0100

        Bump to 1.18.4

    commit 3988b7694aced91154a8815faf0855bc1427c135
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Jul 22 19:47:35 2021 +0100

        Update orgDB only when loading gene expression

    commit 705ceba254f5c0b34f2b0fe586a76912837cc91e
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Jul 22 19:24:49 2021 +0100

        Fix `psichomics()` not launching

    commit 7fbb69303785b55b40c682248ba203c4687bc8d9
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Thu Jul 22 19:22:03 2021 +0100

        Remove MD5 hash check for TCGA data

    commit 147ae11217673e94ce7612c7b6c99a8e0ad11123
    Merge: 81a7850e c106b63b
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Jun 11 15:57:44 2021 +0100

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

    commit 81a7850e7d9c77677daab27ce2d47ebf99dd9c97
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Jun 11 15:57:34 2021 +0100

        Fix pkgdown error while running examples

    commit 5b3d216809ed1ecb0aca25b05fbf2ce1ba0e82c4
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Jun 11 15:40:54 2021 +0100

        Cache Docker image steps

    commit c106b63b18d224090df407a7b5a216dab76a7fc4
    Merge: 4a6f72fd 4c35844a
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Jun 11 15:26:31 2021 +0100

        Merge pull request #427 from nuno-agostinho/dev

        Push Docker images to DockerHub

    commit 4c35844a410e4b23fc5117df90d45d7410c2ecc1
    Merge: 2d1118e1 58f13e96
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Jun 11 13:40:38 2021 +0100

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

    commit 2d1118e1189ded2a2524c7ade77daebe4197461e
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Fri Jun 11 13:40:34 2021 +0100

        `plotSplicingEvent()`: avoid opening browser window in non-interactive contexts

        - Fix Bioconductor build report for Windows

    commit 58f13e9633d207991f318333943a50023653131f
    Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
    Date:   Wed Jun 9 11:18:21 2021 +0100

        Push Docker images to DockerHub

    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

    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: singIST
Commit: 8d9d6bab0563255fbee363bdee37c51fea2ece53
Author: Aitor Moruno Cuenca <amoruno@almirall.com>
Date: 2026-01-07 10:44:12 +0100
Commit message:

 Solve error

Package: FLAMES
Commit: 17de9d9a5c57c7c36af5d0832fa4880dc946bc36
Author: Changqing Wang <wang.ch@wehi.edu.au>
Date: 2026-01-07 20:35:37 +1100
Commit message:

 bump GHA BioC version

Package: FLAMES
Commit: 3205d767b591743fb83c169ae9c977c2b8281fea
Author: Changqing Wang <wang.ch@wehi.edu.au>
Date: 2026-01-07 20:28:24 +1100
Commit message:

 version bump

Package: FLAMES
Commit: a8faffcd31a75b299ccf71f1d2bd68f253401203
Author: Changqing Wang <wang.ch@wehi.edu.au>
Date: 2026-01-07 20:21:31 +1100
Commit message:

 Merge branch 'fix_bioc_cargo' into devel

Package: FLAMES
Commit: 93697495e1216441b01faefd2dc84ed5af7b93de
Author: Changqing Wang <wang.ch@wehi.edu.au>
Date: 2026-01-07 19:30:05 +1100
Commit message:

 fix: BLAZE not outputting to outdir

Package: FLAMES
Commit: f76e56f45c7f5f2675eb729c12e741a1a7832afe
Author: Changqing Wang <wang.ch@wehi.edu.au>
Date: 2026-01-07 16:14:04 +1100
Commit message:

 fix: find_isoform_bambu unzip error if file exists

Package: FLAMES
Commit: d1ed30d63800683471a9b06e41cadf6c95ee0241
Author: Changqing Wang <wang.ch@wehi.edu.au>
Date: 2026-01-06 16:44:26 +1100
Commit message:

 Add rustc 1.85.0 minimal version check

Package: plyinteractions
Commit: 7865d8736897e6d0b1f87c0294f87659de1877cb
Author: js2264 <jacquesserizay@gmail.com>
Date: 2026-01-07 10:10:37 +0100
Commit message:

 bump to 1.9.1

Package: plyinteractions
Commit: 6c40293028c54943e24896c1563fef7f921bc936
Author: js2264 <jacquesserizay@gmail.com>
Date: 2026-01-07 09:31:25 +0100
Commit message:

 fix: pkgdown material

Package: plyinteractions
Commit: 9d1c42fe31bad3886ef7ab83138a0ccb98b74f23
Author: js2264 <jacquesserizay@gmail.com>
Date: 2026-01-07 07:48:10 +0100
Commit message:

 fix: library imports order in vignettes

Package: plyinteractions
Commit: ea06d65dacdc515cc3beb8cf7c936106409801b7
Author: js2264 <jacquesserizay@gmail.com>
Date: 2026-01-07 07:11:27 +0100
Commit message:

 fix: update after plyranges changes (stopped exporting dplyr verbs)

Package: EventPointer
Commit: cf1b090d40226d37f730b7ee7c0017e15657fb9a
Author: JFerrer-B <jafhernandez@tecnun.es>
Date: 2026-01-07 09:11:58 +0100
Commit message:

 gub in examples

Package: tidyprint
Commit: db7905639f5a3255eba4d090ac4bbb9c26ec5f04
Author: Chen Zhan <chen.zhan@adelaide.edu.au>
Date: 2026-01-07 13:29:09 +1030
Commit message:

 fix bioconductor check error

Package: tidyprint
Commit: 2c53bc5582c680790a53268aea282500ac38bba7
Author: Chen Zhan <chen.zhan@adelaide.edu.au>
Date: 2026-01-07 13:27:33 +1030
Commit message:

 fix error in check

Package: tidyprint
Commit: b94ba58e73bdb927716ad739d5863d7d9ed4e2a9
Author: Stefano Mangiola <mangiolastefano@gmail.com>
Date: 2026-01-07 12:14:45 +1030
Commit message:

 Enhance README and Introduction vignette with tidy print options

- Updated README.md to clarify the opt-in and opt-out functionality for tidy print format in SummarizedExperiment.
- Added detailed examples for enabling and disabling tidy print, including persistent settings.
- Modified Introduction vignette to reflect the new tidy print options and ensure clarity in usage.
- Included additional warnings for package versions in examples to improve user experience.

Package: sesameData
Commit: b2d12f0a6fc22f8d7e951dc8a29abfb0baf722e3
Author: Wanding Zhou <zhouwanding@gmail.com>
Date: 2026-01-06 21:50:16 -0500
Commit message:

 bump to 1.29.8

Package: tidyprint
Commit: 70f6f21b2bff4a9d677adf0744a7b39012bf7a42
Author: Stefano Mangiola <mangiolastefano@gmail.com>
Date: 2026-01-07 11:47:58 +1030
Commit message:

 Update tidy_print functions to use 'remember' parameter instead of 'permanent'

- Renamed 'permanent' parameter to 'remember' in tidy_print_on and tidy_print_off functions for clarity.
- Updated documentation and examples to reflect the new parameter name.
- Adjusted test cases to ensure compatibility with the updated parameter name.

Package: tidyprint
Commit: 586aaf18e46ba849cf7804c3020a6f19b03091ce
Author: Stefano Mangiola <mangiolastefano@gmail.com>
Date: 2026-01-07 11:41:20 +1030
Commit message:

 Refactor print method to directly call SummarizedExperiment's show method

- Updated print.SummarizedExperiment to retrieve and call the original show method from the SummarizedExperiment namespace when tidy print is not enabled.
- Improved clarity of the method's functionality by ensuring the correct method is invoked.

Package: tidyprint
Commit: 991919e09e45b25b2c5f417fa21aaada99132e24
Author: Stefano Mangiola <mangiolastefano@gmail.com>
Date: 2026-01-07 11:29:39 +1030
Commit message:

 Introduce tidy print functionality for SummarizedExperiment

- Added functions to enable and check tidy print format
- Updated print.SummarizedExperiment method to conditionally use tidy print format
- Enhanced documentation to reflect new features and usage instructions

Package: tidyprint
Commit: 5a34a80bbafdf9446fe05a52a9e7ae7825d0b67f
Author: Stefano Mangiola <mangiolastefano@gmail.com>
Date: 2025-10-25 17:55:10 +1030
Commit message:

 Merge pull request #27 from tidyomics/remove-alternative-prints

Simplified codebase

Package: tidyprint
Commit: 5557add267f2e6377b8876ba919bcfcd04d078c4
Author: Stefano Mangiola <mangiolastefano@gmail.com>
Date: 2025-10-25 17:43:49 +1030
Commit message:

 Update README and Introduction vignette to enhance package overview and clarify display features for SummarizedExperiment objects. Removed deprecated visualizations and streamlined content for better accessibility and user experience.

Package: tidyprint
Commit: 8921f3a7e85d2c5cfb7ef2f94cad31f4bd0f59df
Author: Stefano Mangiola <mangiolastefano@gmail.com>
Date: 2025-10-25 17:40:55 +1030
Commit message:

 Merge pull request #29 from tidyomics/use-n-print-argument

Refactor print.SummarizedExperiment function

Package: tidyprint
Commit: c00600c49e6853eada062ea7fcd123efeb87dc94
Author: Stefano Mangiola <mangiolastefano@gmail.com>
Date: 2025-10-25 17:38:19 +1030
Commit message:

 Refactor print.SummarizedExperiment function

- Updated internal logic to replace n_print with n for improved clarity and consistency
- Adjusted row and column slicing logic to accommodate the new parameter
- Enhanced separator row handling for better output formatting
- Maintained attribute management for the output tibble

Package: tidyprint
Commit: 79a8f0105f022f427b59a98e5b0956d5fd7e1a8e
Author: Stefano Mangiola <mangiolastefano@gmail.com>
Date: 2025-10-25 17:28:43 +1030
Commit message:

 Merge pull request #28 from tidyomics/use-n-print-argument

Update print method parameter from n_print to n

Package: tidyprint
Commit: 0c52cf195b3b97669974546732694992d1a3c95b
Author: Stefano Mangiola <mangiolastefano@gmail.com>
Date: 2025-10-25 17:26:37 +1030
Commit message:

 Bump version to 0.99.7 - Update print method parameter from n_print to n

- Changed parameter name in print.SummarizedExperiment function for clarity
- Updated documentation and examples to reflect the new parameter name
- Adjusted internal logic to use the new parameter name consistently
- Updated tests to verify functionality with the new parameter name

Package: tidyprint
Commit: 264d90f9e9af3c6f779d5066023c47ad384d575b
Author: Stefano Mangiola <mangiolastefano@gmail.com>
Date: 2025-10-25 17:17:03 +1030
Commit message:

 Simplified codebase
- Removed design parameter from print.SummarizedExperiment function
- Updated print method to streamline functionality
- Adjusted documentation to reflect changes in print method
- Updated RoxygenNote to 7.3.3
- Added import for dplyr's all_of function in NAMESPACE

Package: epiSeeker
Commit: d0cfcad230aaf7fb995f803b862b3ece1dde3fa5
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2026-01-07 08:59:20 +0800
Commit message:

 r 4.6.0

Package: tidyCoverage
Commit: 8a0985f61f089bc666f1fcd6195df655f1d9fc70
Author: js2264 <jacquesserizay@gmail.com>
Date: 2026-01-07 01:57:18 +0100
Commit message:

 bump to v1.7.1

Package: tidyCoverage
Commit: bf8c7828ccbc26b47bcbb9646ec81064a6c2274e
Author: js2264 <jacquesserizay@gmail.com>
Date: 2025-12-22 11:39:22 +0100
Commit message:

 fix: no more reexports, attach tidyverse packages on load, tidy up expand and as_tibble methods

Package: tidyCoverage
Commit: 4a2d337a43b1c1e5eceab87c7c118a2f7e45fe64
Author: js2264 <jacquesserizay@gmail.com>
Date: 2025-12-20 16:55:21 +0100
Commit message:

 fix: args and doc

Package: tidyCoverage
Commit: 44a877c60101b2ce76b91293ecbc5a95fb0e0596
Author: js2264 <jacquesserizay@gmail.com>
Date: 2025-12-20 16:52:24 +0100
Commit message:

 deps: add ggratr

Package: tidyCoverage
Commit: 3758f3076db53c9c448ab80b2cf08fa6ffbb547e
Author: js2264 <jacquesserizay@gmail.com>
Date: 2025-12-20 16:50:43 +0100
Commit message:

 docs: update vignette to reflect changes in theme/geoms

Package: tidyCoverage
Commit: 2182aeecb5bc0dcf489428564a63de38410a5202
Author: js2264 <jacquesserizay@gmail.com>
Date: 2025-12-20 16:50:40 +0100
Commit message:

 feat: improve geom_coverage

Package: tidyCoverage
Commit: fc2a34a2622e3daaaca22ce0899293b57d17eb8e
Author: js2264 <jacquesserizay@gmail.com>
Date: 2025-10-23 10:17:54 +0200
Commit message:

 ci: update GHA

Package: tidyCoverage
Commit: 1422e0452a52f3cc957a30363147c637fdbede2a
Author: js2264 <jacquesserizay@gmail.com>
Date: 2025-10-23 10:12:02 +0200
Commit message:

 doc: improve documentation for geoms

Package: knowYourCG
Commit: 1c218d9c3dac73ad51c153a60f080e412a03f92e
Author: Wanding Zhou <zhouwanding@gmail.com>
Date: 2026-01-06 15:39:19 -0500
Commit message:

 bump to 1.7.7

Package: Biostrings
Commit: 790340a4c90258c7755744163787c22b4405c711
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2026-01-06 12:07:47 -0800
Commit message:

 Bump version to 2.79.4

Package: Biostrings
Commit: bf39e5875836ae69bd7d27416a7449baffae792a
Author: Felix Ernst <felix.gm.ernst@outlook.com>
Date: 2026-01-06 19:38:41 +0100
Commit message:

 Add "DotBracket" seqtype as compatible "B" seqtype (#134)

Package: singIST
Commit: 64bdb693a879692a4f7fdbd904d650a668ed80dd
Author: Aitor Moruno Cuenca <amoruno@almirall.com>
Date: 2026-01-06 21:01:57 +0100
Commit message:

 Reduce OXA object size

Package: MungeSumstats
Commit: 00858593a7584225fe525630810300417077c244
Author: Al-Murphy <alanmurph94@hotmail.com>
Date: 2026-01-06 13:18:11 -0500
Commit message:

 Bug Fix Unit Test

Package: knowYourCG
Commit: 4913e798e3bb7ab4b6316a391a19aa67db40698e
Author: Wanding Zhou <zhouwanding@gmail.com>
Date: 2026-01-06 12:28:47 -0500
Commit message:

 bump to 1.7.7

Package: knowYourCG
Commit: 334894941f267bacb198ae9ad6f22f6b8f5525fa
Author: Wanding Zhou <zhouwanding@gmail.com>
Date: 2026-01-06 12:13:59 -0500
Commit message:

 fix getDBs for MSA knowledgebases

Package: singIST
Commit: f3f80f2f2430bc7c254ed579a5bad585d5829bb3
Author: Aitor Moruno Cuenca <amoruno@almirall.com>
Date: 2026-01-06 18:11:01 +0100
Commit message:

 Remove unused dependencies

Package: singIST
Commit: c90e2450bebc82197cc316e943cefe52abdede2b
Author: Aitor Moruno Cuenca <amoruno@almirall.com>
Date: 2026-01-06 15:55:08 +0100
Commit message:

 Trigger build minor reviews

Package: QTLExperiment
Commit: 032578468376253f5163274117b0a72c1df7eb78
Author: dunstone-a <amelia.dunstone@gmail.com>
Date: 2026-01-06 17:58:17 +1100
Commit message:

 Update sumstats2qtle() documentation
- Added an otherFields argument
- Added a test for gene_filter

Package: QTLExperiment
Commit: ed3459cdac0865e6c5f02257dff25705814ced62
Author: dunstone-a <amelia.dunstone@gmail.com>
Date: 2025-12-17 12:56:38 +1100
Commit message:

 Merge branch 'devel' of git.bioconductor.org:packages/QTLExperiment into devel

Package: QTLExperiment
Commit: d95b81a426273bcf65cea4b94f4ca13e8f395f8c
Author: dunstone-a <amelia.dunstone@gmail.com>
Date: 2025-12-17 12:52:44 +1100
Commit message:

 Fix bad formatting in vignette and NEWS

Package: damidBind
Commit: b185a6daadab3a37508ee2f8a173b529a6227871
Author: Owen Marshall <owen.marshall@utas.edu.au>
Date: 2026-01-06 05:50:07 +0000
Commit message:

 Improved example code

Package: damidBind
Commit: a09e26785e158cddbae48850be9f607184f7c17d
Author: Owen Marshall <owen.marshall@utas.edu.au>
Date: 2026-01-06 05:49:16 +0000
Commit message:

 Updated to v0.99.12

Package: damidBind
Commit: 98e7ff2ea987868438d7f2321ffc1cf212ac66c9
Author: Owen Marshall <owen.marshall@utas.edu.au>
Date: 2026-01-06 04:17:38 +0000
Commit message:

 Updated to v0.99.12

Package: damidBind
Commit: 43c600eb606016776eb37d8c734b4f7c8ce5c1b1
Author: Owen Marshall <owen.marshall@utas.edu.au>
Date: 2026-01-06 04:17:25 +0000
Commit message:

 Added vignette R intermediary to the ignore list

Package: damidBind
Commit: 8592d98305a901cc3e85dc9b49f5da421ce8652e
Author: Owen Marshall <owen.marshall@utas.edu.au>
Date: 2026-01-05 13:10:30 +0000
Commit message:

 Updated vignette

Package: damidBind
Commit: e7fabfa668960ebb96f1fa30c974c2ceb9aff2fc
Author: Owen Marshall <owen.marshall@utas.edu.au>
Date: 2026-01-05 13:10:10 +0000
Commit message:

 Updated unit tests

Package: damidBind
Commit: 968451b34c2a8d5a3621c354f8d945c1a88284e8
Author: Owen Marshall <owen.marshall@utas.edu.au>
Date: 2026-01-05 13:09:34 +0000
Commit message:

 Updated documentation

Package: damidBind
Commit: ff3145ef27a371a236c7fe2759d7f7f69bb5e5cd
Author: Owen Marshall <owen.marshall@utas.edu.au>
Date: 2026-01-05 13:08:30 +0000
Commit message:

 New occupancy FDR logic

Package: damidBind
Commit: 228ea2d8f8a5d9f0d2291acb7ef7447d7e5d0321
Author: Owen Marshall <owen.marshall@utas.edu.au>
Date: 2026-01-05 13:08:09 +0000
Commit message:

 Minor documentation changes

Package: damidBind
Commit: 8e45b5554fa89a96ab6f42295c650e8b14f67f0e
Author: Owen Marshall <owen.marshall@utas.edu.au>
Date: 2026-01-05 13:07:50 +0000
Commit message:

 Fixed issues with universe handling

Package: damidBind
Commit: 23acc55f1d2e829e5d8f038fc4d4c9f23e53eded
Author: Owen Marshall <owen.marshall@utas.edu.au>
Date: 2026-01-05 13:07:28 +0000
Commit message:

 New occupancy FDR logic

Package: damidBind
Commit: 57e8a4ffecd9a03d8568f30a5345a5918eee3e66
Author: Owen Marshall <owen.marshall@utas.edu.au>
Date: 2026-01-05 13:07:10 +0000
Commit message:

 New occupancy FDR logic

Package: damidBind
Commit: 5aa5e1c510ffc3e1c18d9df8801b9ee30a8c51f4
Author: Owen Marshall <owen.marshall@utas.edu.au>
Date: 2026-01-05 13:06:50 +0000
Commit message:

 Updated with new internal condition naming logic

Package: damidBind
Commit: c687ed622b73ffef98039a9d7d804abeb3d5c085
Author: Owen Marshall <owen.marshall@utas.edu.au>
Date: 2026-01-05 13:06:39 +0000
Commit message:

 New occupancy FDR logic; new internal condition naming logic

Package: damidBind
Commit: 42a1fc3f8a85a5c52b8ad6327a4c6742407e1c71
Author: Owen Marshall <owen.marshall@utas.edu.au>
Date: 2026-01-05 13:05:43 +0000
Commit message:

 Major rewrite of occupancy FDR logic

Package: damidBind
Commit: db1dda8f598a5b10a60d6dcb911e1423c840cf62
Author: Owen Marshall <owen.marshall@utas.edu.au>
Date: 2026-01-05 13:05:05 +0000
Commit message:

 Updated with new occupancy FDR diagnostic plots

Package: damidBind
Commit: ce9b2c1926d42fc410575ba9be9c5a5aa8a1981e
Author: Owen Marshall <owen.marshall@utas.edu.au>
Date: 2026-01-05 13:03:52 +0000
Commit message:

 Minor changes to example code

Package: damidBind
Commit: def4162f692404f94d49acf9123bc1880ceddb00
Author: Owen Marshall <owen.marshall@utas.edu.au>
Date: 2026-01-05 13:03:23 +0000
Commit message:

 Updated with new internal condition naming logic

Package: damidBind
Commit: cfb75667960c8dc05e18f6b5d294f3fc074a2a93
Author: Owen Marshall <owen.marshall@utas.edu.au>
Date: 2026-01-05 13:02:24 +0000
Commit message:

 Updated with new occupancy FDR options

Package: damidBind
Commit: dbac97ecd9d465faa0fbffa4fc0817e78f36f8e4
Author: Owen Marshall <owen.marshall@utas.edu.au>
Date: 2026-01-04 13:17:11 +0000
Commit message:

 Updated to v0.99.12

Package: damidBind
Commit: c9c224c50c9367b26d8c9d90b940e9efaefe636e
Author: Owen Marshall <owen.marshall@utas.edu.au>
Date: 2025-12-14 02:50:47 +0000
Commit message:

 Added bookdown as a suggest for pkgdown documentation creation

Package: damidBind
Commit: c4a56d3f48aed4eb5df4f1c9709202b48aa1950d
Author: Owen Marshall <owen.marshall@utas.edu.au>
Date: 2025-12-14 02:49:53 +0000
Commit message:

 Wrapped \dontrun{} tags around code example to prevent execution during pkgdown creation.

Package: damidBind
Commit: 48fd2a705e2d4909ba690c151c689e8a2360643b
Author: Owen Marshall <owen.marshall@utas.edu.au>
Date: 2025-12-14 02:48:57 +0000
Commit message:

 Minor changes for readability

Package: PLSDAbatch
Commit: f1c3e0c7c62982428994be32e74638fca9cc2dc6
Author: Yiwen (Eva) Wang <anjiwangyiwen@gmail.com>
Date: 2026-01-06 16:22:10 +1100
Commit message:

 Fix the figure display issue

Package: PLSDAbatch
Commit: dfd8b6f515acbe85e688d409803237520a06fcb1
Author: Yiwen (Eva) Wang <anjiwangyiwen@gmail.com>
Date: 2026-01-06 16:17:30 +1100
Commit message:

 Fix the figure display issue

Package: LOLA
Commit: 5459337f3c13709006f65f44b27a308e248ffbdb
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2026-01-05 19:20:06 -0800
Commit message:

 LOLA 1.41.1: Add XVector to Suggests

The XVector package is needed by the buildRestrictedUniverse() function.
This function calls the disjoin() method for GRanges objects which calls the
range() method for CompressedIRangesList objects which requires XVector.

Package: IWTomics
Commit: 22ec111e1c82cfb15d99734c4daa57dfd5461608
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2026-01-05 19:04:01 -0800
Commit message:

 IWTomics 1.35.1: Add XVector to Suggests

The XVector package is needed by the IWTomicsData#GRangesList#list method.
This method calls the disjoin() method for GRanges objects which calls the
range() method for CompressedIRangesList objects which requires XVector.

Package: igblastr
Commit: 9b941e6cb1dd710640072822e024ffdc1ec38256
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2026-01-05 16:17:08 -0800
Commit message:

 Add IMGT data conditions of use and license to man page for
install_IMGT_germline_db(). Also display them when the user
selects an IMGT db with use_germline_db() or use_c_region_db().

Package: tidyexposomics
Commit: c510a2af65e0351b7a1f993d3bcd82bd7cc23cd6
Author: BioNomad <jlaird1@binghamton.edu>
Date: 2026-01-05 18:44:54 -0500
Commit message:

 0.99.11 updates

Package: igblastr
Commit: 061babbd03d988e8bad19b21787f1a501527693b
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2026-01-05 13:42:46 -0800
Commit message:

 igblastr 1.1.9

Document (and add unit tests for) the new utilities to access and
manipulate IgBLAST internal data.

Package: carnation
Commit: a1f999424eed3da9cd84a96b9f52d754289016b3
Author: Apratim Mitra <16709900+mitraak@users.noreply.github.com>
Date: 2026-01-05 15:50:31 -0500
Commit message:

 Merge pull request #22 from NICHD-BSPC/bioc_timing2

tweak examples to reduce R CMD check times

- revert to using non-package data for some examples
- switch entire examples blocks for module server/ui to using examplesIf interactive()

Package: carnation
Commit: e65d079b63f48343fbfa4a326c8ff5d8fd53a67a
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2026-01-05 15:29:07 -0500
Commit message:

 version bump

Package: carnation
Commit: c537ac23645a8edba20320eb25aa985a3297916a
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2026-01-05 15:07:17 -0500
Commit message:

 add back --as-cran to check cmd

Package: carnation
Commit: d081fa941ae2c19179bf69958a1123ffb23bda76
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2026-01-05 14:52:45 -0500
Commit message:

 updt R CMD check args; mv env pinned bld

Package: carnation
Commit: 0c59e7e29110df09da6b369028b3795da87779e2
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2026-01-05 14:50:45 -0500
Commit message:

 switch mod ex to examplesIf interactive

Package: carnation
Commit: 26a018344e0832446d06953c94d243a33eebe0ce
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2026-01-05 14:19:38 -0500
Commit message:

 repl donttest w examplesIf interactive

Package: carnation
Commit: 15124b4727d32046c90615cda01fcffa8b4c8bd7
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2026-01-05 13:46:25 -0500
Commit message:

 revert to non-package data

Package: TrIdent
Commit: eef799682a2a34098dcfe50c47e04dfa1b927362
Author: jlmaier <jlmaier@ncsu.edu>
Date: 2026-01-05 15:28:41 -0500
Commit message:

 Fixed conflicts in version change

Package: TrIdent
Commit: ce414593acc02617c7d41568b9e9a523d3da4ecd
Author: jlmaier <jlmaier@ncsu.edu>
Date: 2026-01-05 14:45:55 -0500
Commit message:

 Update minSlopeSize parameter, fix bug, and remove out of date tests

Package: TrIdent
Commit: 8249ae3bd99a9dfdde5c26945f5ec5b13a5e670d
Author: jlmaier <jlmaier@ncsu.edu>
Date: 2025-11-25 16:57:42 -0500
Commit message:

 minor update to variable options

Package: ClustIRR
Commit: 57d62e884824e74b5a04fced4ce3000f69625e46
Author: snaketron <simo.kitanovski@proton.me>
Date: 2026-01-05 17:09:58 +0100
Commit message:

 fix group model, bump ersion, add another vignette, simplify models

Package: SingleR
Commit: 40ff41ae2387b3de6673ea516f437266caa08ace
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2026-01-05 21:05:14 +1100
Commit message:

 Don't suggest aggr.ref=TRUE if it was already set.

Package: singIST
Commit: 3df77ca640acea38aa44fcad4d6a6c05e3d17f97
Author: Aitor Moruno Cuenca <amoruno@almirall.com>
Date: 2026-01-05 11:26:55 +0100
Commit message:

 Minor review

Package: SingleR
Commit: f6615e5d18712d03c183fc39967c8daf67365134
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2026-01-05 20:01:00 +1100
Commit message:

 Updated NEWS, bumped version and date.

Package: SingleR
Commit: 7f945df47d6d12f3389d740e7dd754d5ffc752ad
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2026-01-05 19:54:55 +1100
Commit message:

 Hint for the recommended de.method= and aggr.ref= for SCE inputs.

This avoids the use of inappropriate defaults for single-cell references.

Package: SingleR
Commit: d0b97f7e274463fa5e53bb9d39244cafe82e1973
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2026-01-05 14:21:58 +1100
Commit message:

 Replace scuttle with scrapper in the vignette.

Package: mastR
Commit: 95bae610a3c98a2d1583289f760c911c062080d2
Author: Gene233 <chen_jj97@163.com>
Date: 2026-01-05 14:02:30 +1100
Commit message:

 Fix bioc check size.

Package: mastR
Commit: 7aa74329c71f0f1f79d824eb8c9b5c245743cc99
Author: Gene233 <chen_jj97@163.com>
Date: 2026-01-05 13:42:12 +1100
Commit message:

 Add Glimma for new vignette.

Package: mastR
Commit: 4554f0c63cffa2e7466ac722a8eb667acc3e10cd
Author: Gene233 <chen_jj97@163.com>
Date: 2026-01-05 13:29:20 +1100
Commit message:

 Fix bioc check.

Package: mastR
Commit: 40130f7ce391d41d0fa27b0c5fdb80b4a891a98c
Author: Gene233 <chen_jj97@163.com>
Date: 2026-01-05 13:13:08 +1100
Commit message:

 Fix bioc check.

Package: mastR
Commit: a6bc1d0240e7dc7deac1490add0f6c1df0c7b90a
Author: Gene233 <chen_jj97@163.com>
Date: 2026-01-05 13:03:40 +1100
Commit message:

 Fix bioc check.

Package: mastR
Commit: 36e52d55951251eb89c5b46ff9f14630153c2831
Author: Gene233 <chen_jj97@163.com>
Date: 2026-01-05 12:37:59 +1100
Commit message:

 Fix bioc check.

Package: mastR
Commit: a930499d8a718bb9b3437f41386d87499ca63610
Author: Gene233 <chen_jj97@163.com>
Date: 2026-01-05 12:23:34 +1100
Commit message:

 Fix bioc check.

Package: mastR
Commit: 114700555a60b7bebe68544101e1d900e516f329
Author: Gene233 <chen_jj97@163.com>
Date: 2026-01-05 12:16:39 +1100
Commit message:

 Set upper bound for SeuratObject and add new vignette.

Merge remote-tracking branch 'origin/main'

# Conflicts:
#	DESCRIPTION

Package: mastR
Commit: 32da4ae181fb42a2e715644426c3f3b6c8244704
Author: Gene233 <chen_jj97@163.com>
Date: 2026-01-05 11:58:08 +1100
Commit message:

 Fix Seurat v5 problems and add new vignette.

Package: SingleR
Commit: 13cfc313ad9f2917a50e3281b31f5259f59ced9b
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2026-01-05 14:08:45 +1100
Commit message:

 Merge remote-tracking branch 'upstream/devel'

Package: SingleR
Commit: 365aaca8f61f32c30a206f57b992953485268d25
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2026-01-05 13:42:46 +1100
Commit message:

 Removed the scuttle dependency from examples and tests.

- Cleaned up code for partitioning the reference into two smaller datasets for
  combineRecomputedResults tests and examples.
- Make sure that the chosen markers actually have increased expression above
  the baseline in .mockRefData.

Package: SingleR
Commit: b0adc3ca2afd137263e792fbe2101821fa0ac252
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2026-01-05 12:43:32 +1100
Commit message:

 Add a warning if the names of 'trained' and 'results' are different.

Because if any names are present, they should really be the same.

Package: SingleR
Commit: d11205d93365cf465c21057164227903dcca5f4f
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2025-10-19 01:44:29 -0700
Commit message:

 Strip out version number when installing dependencies for GHA.

Package: scrapper
Commit: 94857a9e419c87beadd5f49912bfc626c38db3ab
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2026-01-05 13:26:16 +1100
Commit message:

 Pass additional arguments from normalization wrappers to normalizeCounts.

Package: immReferent
Commit: 77dc25dd1ac8b77fa1fbf1d6045e22e928860164
Author: theHumanBorch <ncborch@gmail.com>
Date: 2026-01-04 15:00:15 -0600
Commit message:

 correcting version

Package: immReferent
Commit: c3bf59c93a4fa8ccc1b3ba2ee02269c73e8e6cca
Author: theHumanBorch <ncborch@gmail.com>
Date: 2026-01-04 14:50:50 -0600
Commit message:

 Merge pull request #11 from BorchLab/export-functionality

Export functionality

Package: immReferent
Commit: 2d6a73337637a155c434743f91ab95f6e1e58ef2
Author: theHumanBorch <ncborch@gmail.com>
Date: 2026-01-04 14:42:27 -0600
Commit message:

 remove snapshot check

Package: immReferent
Commit: 412616acd4dc8ec470f616b70db44d7e2c673b76
Author: theHumanBorch <ncborch@gmail.com>
Date: 2026-01-04 14:35:05 -0600
Commit message:

 remove message testing

Package: immReferent
Commit: d0e191a2c8d607d95fff7cce040f7af3628c0b96
Author: theHumanBorch <ncborch@gmail.com>
Date: 2026-01-04 14:11:07 -0600
Commit message:

 Update test-mainOGRDB.R

Package: immReferent
Commit: b6c1a17393b68e6774b5e7863eefabb4c58b14d3
Author: theHumanBorch <ncborch@gmail.com>
Date: 2026-01-04 12:48:06 -0600
Commit message:

 OGRDB export support

#7 Allowing for both IMGT and OGRDB support for export

Improved overall documentation

Package: immReferent
Commit: 06d6f0ec9a88f4696615f8dd17a7b1ae0b1a1931
Author: theHumanBorch <ncborch@gmail.com>
Date: 2026-01-04 11:15:45 -0600
Commit message:

 export functions

#7

Package: methodical
Commit: e40174f7012334a8b447243cbf5b58622afa0d4c
Author: Richard Heery <richardheery@gmail.com>
Date: 2026-01-04 20:48:58 +0000
Commit message:

 Fixed issue in .write_chunks_to_hdf5 with fread where all values in a column are NA results in colimn being logical rather than numeric

Package: methodical
Commit: cd319c02dd636f8630a25727cc54a5f70bb132a5
Author: Richard Heery <richardheery@gmail.com>
Date: 2026-01-01 21:13:20 +0000
Commit message:

 Updated .set_meth_df_columns to use with for meth_files_columns

Package: methodical
Commit: 2dbb9a7220c56e39ef5476cedbaff280d1067c92
Author: Richard Heery <richardheery@gmail.com>
Date: 2026-01-01 20:06:18 +0000
Commit message:

 make_meth_rse.R updated

Package: methodical
Commit: c05edd2f601bfcb601258f930939a2e30c9b9158
Author: Richard Heery <richardheery@gmail.com>
Date: 2026-01-01 13:32:39 +0000
Commit message:

 Fixed setup to use final GRanges

Package: methodical
Commit: e0b7ccb768ccce59ba2ba468cea55b426277e551
Author: Richard Heery <richardheery@gmail.com>
Date: 2025-12-31 18:50:00 +0000
Commit message:

 Further changes to make_meth_rse.R

Package: methodical
Commit: 93a7b26a15b1fef0c07dab037562f020d10eb265
Author: Richard Heery <richardheery@gmail.com>
Date: 2025-12-30 21:48:18 +0000
Commit message:

 Cleaned make_meth_rse helper functions

Package: methodical
Commit: c0f70c2b40f1dad392bf71cf369053eeec472774
Author: Richard Heery <richardheery@gmail.com>
Date: 2025-12-29 21:17:37 +0000
Commit message:

 Updated make_meth_rse to add coverage

Package: methodical
Commit: 503d8aa73a9857d42c5abb0928697ef9cae615b4
Author: Richard Heery <richardheery@gmail.com>
Date: 2025-12-29 19:44:44 +0000
Commit message:

 udpate

Package: methodical
Commit: 8ef330b5cb6c32811b0619f29391585f5b4c05de
Author: Richard Heery <richardheery@gmail.com>
Date: 2025-12-29 12:33:13 +0000
Commit message:

 Updated extractMethSitesFromGenome to search both strands with a DNAStringSet

Package: methodical
Commit: 111fd6af5f2676857bf46058e3933a29ddaabe26
Author: Richard Heery <richardheery@gmail.com>
Date: 2025-12-29 11:36:59 +0000
Commit message:

 Updated extractMethSitesFromGenome

Package: methodical
Commit: c8c50e7901da6b722ef984b6165f7b4cfdc4621d
Author: Richard Heery <richardheery@gmail.com>
Date: 2025-12-28 18:07:10 +0000
Commit message:

 Updated make_meth_rse_accessory_functions2.R

Package: methodical
Commit: 4f283ca0738c8edd05c57580baf529dca881299e
Author: Richard Heery <richardheery@gmail.com>
Date: 2025-12-28 18:05:26 +0000
Commit message:

 Updated make_meth_rse_accessory_functions2.R

Package: methodical
Commit: ca2080fa7b7cd056cd46e05a4aaf4fbee9666af2
Author: Richard Heery <richardheery@gmail.com>
Date: 2025-12-28 18:04:07 +0000
Commit message:

 Updated make_meth_rse_accessory_functions2.R

Package: escape
Commit: f1d30416a2df05d3b69dbd433e61700562da40cc
Author: theHumanBorch <ncborch@gmail.com>
Date: 2026-01-04 14:39:15 -0600
Commit message:

 Merge branch 'master' into devel

Package: escape
Commit: 4c5c36566fec3f4234c5f940dcc8d07f2d096b6e
Author: theHumanBorch <ncborch@gmail.com>
Date: 2026-01-04 09:14:21 -0600
Commit message:

 Update README.md

Package: escape
Commit: ade846644b6596ac0b62e7a2a82e6dcf1e8d692f
Author: theHumanBorch <ncborch@gmail.com>
Date: 2026-01-04 09:12:23 -0600
Commit message:

 Merge pull request #176 from BorchLab/fix-seurat-assay

updated documentation and assay utilization

Package: escape
Commit: b9f178d84cff1d941d194eb471ae740cd5be925c
Author: theHumanBorch <ncborch@gmail.com>
Date: 2026-01-04 07:55:04 -0600
Commit message:

 updated documentation

Package: escape
Commit: 5ca67b1b5f89c56dcbfbb0238dfb8dd6696c7fe4
Author: theHumanBorch <ncborch@gmail.com>
Date: 2025-11-24 08:51:14 -0600
Commit message:

 Update README.md

Package: escape
Commit: 5eae8bd7dd210274da32afd150f304281b493586
Author: theHumanBorch <ncborch@gmail.com>
Date: 2025-10-31 09:19:59 -0500
Commit message:

 v2.6.1

Small bug from GSVA in unit tests fix

Package: lcmsPlot
Commit: 6c31e2db8199b35dacc067fd383905f24388a137
Author: Ossama Edbali <ossedb@gmail.com>
Date: 2026-01-04 12:53:39 +0000
Commit message:

 chore: Add titles to code chunks

Package: lcmsPlot
Commit: 4acaf22a534f47dfda66f5ec7093065dd1f8ae2e
Author: Ossama Edbali <ossedb@gmail.com>
Date: 2026-01-04 12:20:51 +0000
Commit message:

 chore: Add runnable examples to MZmine and MS-DIAL data sources

Package: lcmsPlot
Commit: 7935b9badbbc34a7ac949c3f7bda847092799cc0
Author: Ossama Edbali <ossedb@gmail.com>
Date: 2026-01-04 02:48:39 +0000
Commit message:

 feat: Update vignettes and docs, and enable support for MZmine and MS-DIAL

Package: ggcyto
Commit: 8ac30c492c938e4b66cfaa72137548969d8f57ba
Author: Mike Jiang <mike@ozette.com>
Date: 2026-01-03 17:07:57 -0800
Commit message:

 bump

Package: ggcyto
Commit: 4e7589c838c3fb8e3f56e467566bef1c1efb1b3e
Author: Mike Jiang <mike@ozette.com>
Date: 2026-01-03 17:02:06 -0800
Commit message:

 downcast plot class #109

Package: ggcyto
Commit: 29b7c4eed99768116ad7d31bf96fa14cedafc369
Author: Mike Jiang <mike@ozette.com>
Date: 2026-01-03 17:00:56 -0800
Commit message:

 Merge remote-tracking branch 'conductor/devel' into devel

Package: ggcyto
Commit: bf660652034edaaf022ff2a01d8dcb7fae804ee5
Author: Mike Jiang <mike@ozette.com>
Date: 2025-09-14 17:26:03 -0700
Commit message:

 Merge remote-tracking branch 'conductor/devel' into devel

Package: ggcyto
Commit: 9653aa647c1f4ca19cf790c7b69a852a76395849
Author: Mike Jiang <wenxin.jiang@gmail.com>
Date: 2025-07-03 21:18:51 -0700
Commit message:

 Merge pull request #103 from teunbrand/compat_ggplot2_400

Compatibility with future ggplot2 version

Package: orthogene
Commit: e1cf945b3af29414d59049d9ff9f6eb7c4269e3a
Author: bschilder <brian_schilder@alumni.brown.edu>
Date: 2026-01-03 15:31:36 -0500
Commit message:

 Rm usage from gprofiler_orgs/gprofiler_namespace

Package: systemPipeR
Commit: cc2e63a777630bb047b58e62139bb14e1f05638b
Author: tgirke <tgirke@citrus.ucr.edu>
Date: 2026-01-03 10:56:16 -0800
Commit message:

 some meaningful message

Package: systemPipeR
Commit: 9e3f9ed4039b905d97a0e051c4acf2b07ffbacef
Author: tgirke <tgirke@citrus.ucr.edu>
Date: 2026-01-02 18:25:43 -0800
Commit message:

 DESC file fix

Package: systemPipeR
Commit: 802825fc5506d129c8c36196e2804cd1d61f6e20
Author: Thomas Girke <tgirke@citrus.ucr.edu>
Date: 2026-01-02 18:04:24 -0800
Commit message:

 Merge pull request #88 from lz100/devel

fix: auto cwl sample replacement

Package: systemPipeR
Commit: 154609cedb87dc7b96667e9d8ad8f660ca2e0e42
Author: Le Zhang <35240440+lz100@users.noreply.github.com>
Date: 2025-12-19 02:22:11 -0800
Commit message:

 Merge branch 'tgirke:devel' into devel

Package: systemPipeR
Commit: 7c9f60a875aeaf4cd5f51abcd70fe469ca9d90a4
Author: Le Zhang <35240440+lz100@users.noreply.github.com>
Date: 2025-08-27 17:21:04 -0700
Commit message:

 fix: auto cwl sample replacement

Package: systemPipeR
Commit: f0c615418c69baaf1c04c1ca791227726921c03d
Author: Thomas Girke <tgirke@citrus.ucr.edu>
Date: 2025-06-21 16:49:12 -0700
Commit message:

 Merge pull request #87 from lz100/devel

fix: Add extraction of special variables to YAML input in write.yml

Package: systemPipeR
Commit: 0b45c1484ad8a9113ba8640365083ba8910c518c
Author: Le Zhang <35240440+lz100@users.noreply.github.com>
Date: 2025-06-04 22:02:11 -0700
Commit message:

 fix: Add extraction of special variables to YAML input in write.yml function

Package: orthogene
Commit: 4b1505f04fd49b6f5f56c0fb71dda4ebcedf3efb
Author: bschilder <brian_schilder@alumni.brown.edu>
Date: 2026-01-03 13:39:30 -0500
Commit message:

 use extract() from magrittr

Package: orthogene
Commit: 9e31c54862c8ed057befee033e19e0e492c12938
Author: bschilder <brian_schilder@alumni.brown.edu>
Date: 2026-01-03 13:26:51 -0500
Commit message:

 Merge grr fixes #47 and push to bioc devel

Package: orthogene
Commit: a19dd67ad7aa7281e31461d2fe538e0a082d54c8
Author: bschilder <brian_schilder@alumni.brown.edu>
Date: 2026-01-03 13:26:20 -0500
Commit message:

 Merge grr fixes #47

Package: orthogene
Commit: cb24853e8fa59793a50e9a982895aed560e6b590
Author: bschilder <brian_schilder@alumni.brown.edu>
Date: 2026-01-03 13:17:47 -0500
Commit message:

 Fix 7

Package: knowYourCG
Commit: cb6361e61cde77e38f18a359308d67d29bb17dbc
Author: Wanding Zhou <zhouwanding@gmail.com>
Date: 2026-01-03 13:19:08 -0500
Commit message:

 bump to 1.7.6

Package: knowYourCG
Commit: 9023c38fe2063ac62e5802bcae4b26baf25a0192
Author: Wanding Zhou <zhouwanding@gmail.com>
Date: 2026-01-03 10:03:33 -0500
Commit message:

 improved sequencing data analysis vignette

Package: knowYourCG
Commit: c87aa9baf991ca8b73664188150e82b3f4e17d45
Author: Wanding Zhou <zhouwanding@gmail.com>
Date: 2026-01-03 09:13:04 -0500
Commit message:

 refactored testEnrichment

Package: scrapper
Commit: 113db3f5e071bef47c4705e6cb19c0fd6b4c470f
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2026-01-03 15:48:22 +1100
Commit message:

 Updated NEWS, bumped version and date.

Package: scrapper
Commit: b9bdece2af7b633aa2b2109635c71bb6d59e8926
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2026-01-03 15:28:56 +1100
Commit message:

 Minor testfix to avoid unnecessary warnings about capped k.

Because CRISPR QC filtering is too aggressive on a random matrix.

Package: scrapper
Commit: b2904f927243f8622e67b38e79d5d2305400f63d
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2026-01-03 15:06:36 +1100
Commit message:

 Ignore num.neighbors= if it isn't the same as the supplied neighbor results.

The warning is unnecessary if the user has already implicitly told us the number
of neighbors that they want via the pre-computed search results.

The only exception is that of t-SNE, where the number of neighbors is tied to
the perplexity; we retain the warning when these two are inconsistent, though
we also add a NULL option to easily suppress the warning.

We replace the num.neighbors= check with a check that the dimensionality of
the neighbor distance matrix is the same as that of the neighbor indices.

Package: scrapper
Commit: 5f359470b71d0c243b063284d347b8122ad534e3
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2026-01-03 14:57:27 +1100
Commit message:

 Only subset the neighbor search results if there are enough observations.

Package: scrapper
Commit: 1e4feb97dec666af4e97246b290bc61586cf7462
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2026-01-02 12:31:14 +1100
Commit message:

 Improvements to the docs and tests for analyze.se().

In particular, we test that internal updates to the choice of target embedding
(e.g., after MNN correction) are actually respected in downstream steps.

Package: scrapper
Commit: ecd8df039f57c597597ef48f24eceb30a4b507bc
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2026-01-01 02:22:59 +1100
Commit message:

 Testfix for scoreMarkers with newly added fields.

Package: scrapper
Commit: c8e7b67bc7201b2405e362dc8f201a22f5ecaaac
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2025-12-31 21:26:33 +1100
Commit message:

 Fleshed out the man page for getTest*Data.se().

Package: scrapper
Commit: 7f08cb1bdcbd2b0c9745a584c05f7d880877d3bf
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2025-12-31 21:12:32 +1100
Commit message:

 Accept a string in include.order.by= to support custom colnames.

Package: scrapper
Commit: 2f658218d41a6668b16fc66f40fad6ac6b26d64c
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2025-12-30 12:21:05 +1100
Commit message:

 Report number of rows, row names and group IDs explicitly from scoreMarkers.

This makes it easier to assemble results in scoreMarkers.se without having to
guess the dims or dimnames from potentially missing fields. In particular, we
can still make the DF if no marker statistics are computed at all.

Package: scrapper
Commit: ac3c96496a8034ddb996809998bcd5b7cf1642e9
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2025-12-30 12:00:06 +1100
Commit message:

 Report block IDs with the same type as the input for easier matching.

This only applies to functions that report some kind of per-block result, where
the user might want to extract a result for a specific block without coercing
the block identity to a string to match the row/colnames.

We already do this for the QC functions but we rename the field to 'block.ids',
which is easier to understand than 'block.levels'.

Package: scrapper
Commit: f4a9b065e5b30d2942fc211b4bde358cdbdc195a
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2025-12-29 12:06:39 +1100
Commit message:

 Emit a warning when k-means fails to converge.

Package: scrapper
Commit: 235b832bc10f05cf2561d3aa3df2b7971f4d754f
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2025-12-29 11:55:20 +1100
Commit message:

 testEnrichment now returns a DataFrame for consistency with other functions.

Package: scrapper
Commit: a4a11fdf8bf5b224026b6b92014d6dfd47b19b9b
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2025-12-28 16:32:46 +1100
Commit message:

 Simplify the auto-added names for unnamed factors in combineFactors.

Package: scrapper
Commit: 4dafde7e174d617816046b3e171532375a191407
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2025-12-28 15:39:16 +1100
Commit message:

 Replace most references to base data.frames with S4Vectors::DataFrame in the docs.

Package: scrapper
Commit: 8b133edb1556d17b7790e5258f8ddc1225330c2e
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2025-12-28 15:29:33 +1100
Commit message:

 scoreMarkers(), summarizeEffects() now returns DataFrames instead of the base df.

Package: scrapper
Commit: c2ccc784a9db754c30296d1ac7bbe8c1f0ab70ba
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2025-12-28 13:45:54 +1100
Commit message:

 Remove namespacing for S4Vectors:: in all remaining functions.

Package: scrapper
Commit: bdca1317ccd2e8a557b8bb7c891a5dfb3cc0998f
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2025-12-28 13:25:13 +1100
Commit message:

 Fixed examples for DFrame outputs to pass check.

Package: scrapper
Commit: c17142a4e349f19c03a71a71ca7670e87587bcce
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2025-12-28 11:59:21 +1100
Commit message:

 Preserve the type of the blocking factor in .transformFactor.

This is useful for QC functions, to ensure that the block= for filter*
functions can be correctly matched to the block= used in suggest*.

Package: scrapper
Commit: a8f50462b19ca752356eb188ae15d0a806052edb
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2025-12-28 11:46:12 +1100
Commit message:

 aggregateAcrossCells now returns combinations as a DFrame, for convenience.

We also remove S4Vectors:: namespacing for aggregateAcrossCells.se, given that
we have to import it anywway.

Package: scrapper
Commit: 3a01326d55a1a19efb38d8500fb90279149c7d69
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2025-12-28 00:37:02 +1100
Commit message:

 Report DataFrame directly from modelGeneVariances, for convenience.

Package: scrapper
Commit: d04f52d54e8ee1ae697a08faeaf910791a5c4d53
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2025-12-28 00:29:40 +1100
Commit message:

 Report QC metrics as a DataFrame for improved ergonomics.

We already import S4Vectors, so we might as well make full use of it.

We also store the subset statistics as a nested DataFrame. We mandate names for
the supplied subsets= to ensure that the nested DF has proper colnames.

Package: scrapper
Commit: bc64da6dd2f2269d5720198a2e4d9dd516ecc6b7
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2025-12-27 15:22:28 +1100
Commit message:

 Simplify logic for reporting the ordering statistic by previewMarkers.

Package: scrapper
Commit: 5a56564997db93c460b063ff496ad63102316006
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2025-12-27 14:39:31 +1100
Commit message:

 Don't reset order.by within the loop in formatScoreMarkersResults.

Probably doesn't really matter as each group should have the same columns in
the data frame, but we might as well avoid the extra work where possible.

Package: scrapper
Commit: 4cfa13a901299521245ae05f4ac71f95d7785d45
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2025-12-27 13:49:12 +1100
Commit message:

 Report quantiles in the scoreMarkers.se results.

Package: igblastr
Commit: 4ca5eacec537095b75f1c14286ae1c1381e4d241
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2026-01-02 20:29:47 -0800
Commit message:

 Add utilities to access and manipulate IgBLAST internal data.

Package: knowYourCG
Commit: 0149fecd992f424601042cdfee2c6409f96c5365
Author: Wanding Zhou <zhouwanding@gmail.com>
Date: 2026-01-02 23:27:58 -0500
Commit message:

 fix two-sided pvalue, bump to 1.7.5

Package: knowYourCG
Commit: 15d6d050d377950638516e74019c8e76b5edd81d
Author: Wanding Zhou <zhouwanding@gmail.com>
Date: 2026-01-02 22:01:21 -0500
Commit message:

 bump to 1.7.4

Package: knowYourCG
Commit: 0ecbe0fa826dc3ce75d0c9f25de2f8f844a470b6
Author: Wanding Zhou <zhouwanding@gmail.com>
Date: 2026-01-02 20:10:35 -0500
Commit message:

 fix to cdata.h

Package: multiWGCNA
Commit: a011afed65be01dc66ed3ad7e2f74d6fffb14376
Author: dariotommasini <dtommasini0@gmail.com>
Date: 2026-01-02 13:31:44 -0800
Commit message:

 increased version to 1.9.1

Package: multiWGCNA
Commit: be9c910cd6a5af42f950f6a1e58bb81ca89308a0
Author: dariotommasini <dtommasini0@gmail.com>
Date: 2025-11-26 09:53:15 -0800
Commit message:

 Merge branch 'master' of https://github.com/fogellab/multiWGCNA

Package: multiWGCNA
Commit: aeb6a91728f0c6beac988aea742445218a212cdb
Author: dariotommasini <dtommasini0@gmail.com>
Date: 2025-11-26 09:53:08 -0800
Commit message:

 ModuleFlowPlot

Fixed issues with ggraph. Namely, needed to specify the guide. Also added a check for the column names in the trait cor function.

Package: multiWGCNA
Commit: 78b48728d39b5a57d2e670ef2a4118276630790e
Author: Dario Tommasini <103676484+dariotommasini@users.noreply.github.com>
Date: 2025-10-06 15:43:39 -0700
Commit message:

 Update README.md

Package: multiWGCNA
Commit: f71548e657ea352396fbb156474d05a88a4ec303
Author: Dario Tommasini <103676484+dariotommasini@users.noreply.github.com>
Date: 2025-10-06 15:43:10 -0700
Commit message:

 Added original WGCNA citation

Package: multiWGCNA
Commit: fd54e5886a495c44db4db1e927baaa783da507da
Author: dariotommasini <dtommasini0@gmail.com>
Date: 2025-08-24 17:12:43 -0700
Commit message:

 Update DESCRIPTION

Package: multiWGCNA
Commit: d1118af9dafe8f5cad7ae259635740c89b8ab66c
Author: dariotommasini <dtommasini0@gmail.com>
Date: 2025-08-24 17:12:07 -0700
Commit message:

 Added scale.by.size

Package: multiWGCNA
Commit: 852e7e286606429784ca1e6121507fde9563f76c
Author: dariotommasini <dtommasini0@gmail.com>
Date: 2025-08-19 09:30:13 -0700
Commit message:

 Print statement deleted

Package: multiWGCNA
Commit: f7c3e1a35d29bf0726618121b40d8e64a2d31ae9
Author: dariotommasini <dtommasini0@gmail.com>
Date: 2025-08-19 08:55:51 -0700
Commit message:

 Added ModuleFlowPlot function

Package: multiWGCNA
Commit: da9b83eb91ce23778a7de6a33783d9dfbda199e1
Author: Dario Tommasini <103676484+dariotommasini@users.noreply.github.com>
Date: 2025-06-18 09:24:08 -0700
Commit message:

 Merge pull request #30 from OumaeKaede/OumaeKaede-patch-1

Update overlaps.R

Package: multiWGCNA
Commit: 45d813db711cbf74098cb9608e7a77f56dc03575
Author: OumaeKaede <152619226+OumaeKaede@users.noreply.github.com>
Date: 2025-05-31 17:03:12 +0800
Commit message:

 Update overlaps.R

I have conducted thorough tests and successfully build a function which can create with no limits. But noticed that when the number of genes exceeds 10k, this function may cause excessive memory usage and might fail to export the graph. 
In addition, for security considerations, a "for" loop was not used to construct !!sym -like functions in rlang package. Therefore, currently, only 2 to 5 networks are supported for overlap.

Package: multiWGCNA
Commit: 77ac9c2d3d81e57ff5f23c047aeef187dbe8d88a
Author: dariotommasini <dtommasini0@gmail.com>
Date: 2025-05-26 10:38:36 -0700
Commit message:

 Added getModule function

Package: multiWGCNA
Commit: 34cd989f1af594d867d8281502cfde824d945a17
Author: dariotommasini <dtommasini0@gmail.com>
Date: 2025-04-27 19:53:05 -0700
Commit message:

 Update overlaps.R

Minor tweaks to module comparison plotting functions.

Package: multiWGCNA
Commit: a824b66c4fd488f22e2176c7049a019f54315bc4
Author: dariotommasini <dtommasini0@gmail.com>
Date: 2025-04-27 19:23:29 -0700
Commit message:

 Modified findBestTrait

Made compatible with having no trait variance by adding an NA check

Package: multiWGCNA
Commit: 63ec7cc25c34aba5097390a597fdd478af48772e
Author: dariotommasini <dtommasini0@gmail.com>
Date: 2025-02-07 15:38:46 -0800
Commit message:

 Added Sample check to constructNetworks

Package: multiWGCNA
Commit: 0ded1fcb31a46736d9deabda5cf77b8adffbaa2a
Author: dariotommasini <dtommasini0@gmail.com>
Date: 2024-08-05 11:11:04 -0400
Commit message:

 Added description to autism vignette

Package: multiWGCNA
Commit: c2e4d3ed2974154a5607ad9945bb634047c56272
Author: dariotommasini <dtommasini0@gmail.com>
Date: 2024-07-30 14:56:47 -0700
Commit message:

 Added messages to constructNetworks

Package: scRNAseqApp
Commit: c6fc76779597e1aa5ee1b8c483e6a1dd115231c6
Author: Jianhong Ou <jianhong.ou@gmail.com>
Date: 2026-01-02 14:51:15 -0500
Commit message:

 fix the bug when subset the cells by percentage.

Package: COTAN
Commit: 0293be8091bd7c66b68131d519f9085d70029cd3
Author: trinetra75 <marco.fantozzi@gmail.com>
Date: 2026-01-02 18:12:23 +0100
Commit message:

 =Bumped-up version and updated NEWS.md

Package: COTAN
Commit: 450c87107de7486ba6e491f6f183ddcb5370cc35
Author: Marco Fantozzi <57561972+trinetra75@users.noreply.github.com>
Date: 2026-01-02 11:16:15 +0100
Commit message:

 Fixed funtion `isCoexAvailable()` (#129)

* Fixed funtion `isCoexAvailable()`

for cases when global meta-data have more columns

Fixed dispersion function error output

* Updated tests about multi-valued global data

* Added navigation comments

Package: COTAN
Commit: 2515a3ce4ac65bec4b35ce9888752326c85ee3c3
Author: Marco Fantozzi <57561972+trinetra75@users.noreply.github.com>
Date: 2026-01-01 19:00:33 +0100
Commit message:

 Solve issue with Dispersion solver (#128)

* Added consistency checks

* Solved minor issues related to genes'/cells' names not being unique

* Solved issue with Dispersion solver

When Newton method fails uses bisection as fall-back

* Updated NEWS.md

Package: COTAN
Commit: a34dfab26016cc6bd0ad58013e8f67b1fdb7d8ac
Author: Marco Fantozzi <57561972+trinetra75@users.noreply.github.com>
Date: 2026-01-01 18:10:44 +0100
Commit message:

 Bugfix: drop `gghalves` package (#127)

* Dropped use og gghalves and some plots clean-up

* Solved operator conflict for zeallot's `%<-%`

Improved vignette coding style

Package: BEclear
Commit: 36e57b04c6ccfbc4a2affddaa0d08759d2138f6a
Author: David Rasp <d.rasp@lacdr.leidenuniv.nl>
Date: 2026-01-02 14:09:57 +0100
Commit message:

 version bump

Package: BEclear
Commit: 49f3a618537d0cacc651d460cb0decdd8880f66b
Author: David Rasp <d.rasp@lacdr.leidenuniv.nl>
Date: 2026-01-02 14:04:01 +0100
Commit message:

 migration from dependency futile.logger to logger

Package: PIUMA
Commit: a2a72a772a9a217dae7d5ad0ebdffa6268f155a0
Author: BioinfoMonzino <mattia.chiesa@cardiologicomonzino.it>
Date: 2026-01-02 10:14:35 +0100
Commit message:

 updates for PIUMA 1.7.2_

Package: PIUMA
Commit: 257e720cb8de8ab1d8e3bdec7dbb7a1f2b1e7459
Author: BioinfoMonzino <mattia.chiesa@cardiologicomonzino.it>
Date: 2026-01-02 10:07:31 +0100
Commit message:

 updates for PIUMA 1.7.2

Package: fgsea
Commit: 1a82392e409d58a3c24ebf29699218e198af344d
Author: Alexey Sergushichev <alsergbox@gmail.com>
Date: 2026-01-01 20:47:45 -0600
Commit message:

 version bump

Package: fgsea
Commit: 6919c5268faff1da4b2540866355f8b4f1435371
Author: Vladimir Sukhov <vdsukhov@ya.ru>
Date: 2025-12-31 22:32:13 -0600
Commit message:

 retrigger checks

Package: fgsea
Commit: 207aa7015a9f211b88516af7d7dfcceb1642c7a2
Author: Vladimir Sukhov <vdsukhov@ya.ru>
Date: 2025-12-30 14:55:34 -0600
Commit message:

 Update Visium object link after rebuilding with Seurat v5

Package: systemPipeRdata
Commit: e294bcb709e9b3f59b9e153defddfd5454c29aa6
Author: tgirke <tgirke@citrus.ucr.edu>
Date: 2026-01-01 18:15:45 -0800
Commit message:

 Le's changes

Package: systemPipeRdata
Commit: 55b819a604d37c6a9a68cc9abcd8892cae8d8bdc
Author: tgirke <tgirke@citrus.ucr.edu>
Date: 2026-01-01 17:00:34 -0800
Commit message:

 Merge branch 'devel' of git.bioconductor.org:packages/systemPipeRdata into devel

Package: systemPipeRdata
Commit: df1fda3232f2155abb6210f7e3ff92f49c19081e
Author: tgirke <tgirke@citrus.ucr.edu>
Date: 2026-01-01 16:27:46 -0800
Commit message:

 Normalize line endings to LF for Bioconductor compliance

Package: systemPipeRdata
Commit: 42dc699348d2e88502b63995b269e2b0b2c77825
Author: Thomas Girke <tgirke@citrus.ucr.edu>
Date: 2026-01-01 16:26:24 -0800
Commit message:

 Merge pull request #21 from systemPipeR/devel

find . -type f -not -path '*/.*' -exec dos2unix {} +
git add --renormalize .
git commit -m "Normalize line endings to LF for Bioconductor compliance"

Package: systemPipeRdata
Commit: 9cd926def3956feaf540b428427cb108f587210d
Author: lz100 <35240440+lz100@users.noreply.github.com>
Date: 2025-12-20 03:06:48 -0800
Commit message:

 Add new visualizations and update documentation in systemPipeVARseq workflow

Package: systemPipeRdata
Commit: a18c58e39e792824077db992b96f3ab54221b74c
Author: lz100 <35240440+lz100@users.noreply.github.com>
Date: 2025-11-24 01:41:32 -0800
Commit message:

 Fix figure caption formatting and enable tool listing in report

Package: systemPipeRdata
Commit: 2f41b38a14225390cb2bffa870881ad9db96fa89
Author: lz100 <35240440+lz100@users.noreply.github.com>
Date: 2025-11-24 01:27:00 -0800
Commit message:

 feat: varseq related-files

Package: systemPipeRdata
Commit: 636409c2d203d7c26fbd4a6d70d239a74ee749d6
Author: lz <lz@DESKTOP-MP3UQ3S.localdomain>
Date: 2025-11-24 01:01:09 -0800
Commit message:

 feat: update cwl params for varseq

Package: flowWorkspace
Commit: 2783e5cecdda7ac3e7d4b80185245293e6d9d728
Author: Mike Jiang <mike@ozette.com>
Date: 2026-01-01 14:42:44 -0800
Commit message:

 bump

Package: flowWorkspace
Commit: 2f7d3e7dd0f1242f19fc0bbcfbf935d5fd8faafd
Author: Mike Jiang <mike@ozette.com>
Date: 2026-01-01 14:39:55 -0800
Commit message:

 update

Package: flowCore
Commit: 4f0009e837ef3778e7eae7a434aa936fb08663f2
Author: Mike Jiang <mike@ozette.com>
Date: 2026-01-01 14:33:10 -0800
Commit message:

 bump

Package: flowCore
Commit: 3357cd8111b76d991af43cdc1497e80809adc931
Author: Mike Jiang <mike@ozette.com>
Date: 2026-01-01 14:32:25 -0800
Commit message:

 update description

Package: flowCore
Commit: da0721cfb340549c1b14ca5bfefd585e56bfb2bf
Author: Mike Jiang <mike@ozette.com>
Date: 2026-01-01 14:21:16 -0800
Commit message:

 merge

Package: flowCore
Commit: 152b8e4903039aceb32e7393a98ee2dc69f89759
Author: Mike Jiang <mike@ozette.com>
Date: 2024-08-22 15:10:31 -0700
Commit message:

 bump

Package: flowCore
Commit: 903b5b31ed17d2b239267a518ad512a475e2d120
Author: Mike Jiang <mike@ozette.com>
Date: 2024-08-22 15:09:32 -0700
Commit message:

 fix #272

Package: EventPointer
Commit: 7218d8ad83a2876dfd810a9aa2d644ac60fb6f21
Author: JFerrer-B <jafhernandez@tecnun.es>
Date: 2026-01-01 15:25:49 +0100
Commit message:

 bug in ResultTable function

Package: CNVMetrics
Commit: f9a36a2d54a159d87a107e1a81b3f9c7973fa2fd
Author: adeschen <adeschen@hotmail.com>
Date: 2025-12-31 19:50:22 -0500
Commit message:

 Version bump in devel

Package: CNVMetrics
Commit: 84dd7ea7845728b10a73626d27203aa6f77402c0
Author: adeschen <adeschen@hotmail.com>
Date: 2025-12-31 19:26:55 -0500
Commit message:

 Add XVector library

Package: CNVMetrics
Commit: f052e97072c284929cd5433a7ceba41aed85d739
Author: adeschen <adeschen@hotmail.com>
Date: 2025-12-31 19:15:49 -0500
Commit message:

 Update github action check-bioc

Package: CNVMetrics
Commit: c92eea698aa45aa7639cab8aed84858e10ad2a89
Author: adeschen <adeschen@hotmail.com>
Date: 2025-12-31 19:12:06 -0500
Commit message:

 Fix conflict

Package: CNVMetrics
Commit: 9135482ad17deeccdbad9dabd1300aad48c7d3c5
Author: adeschen <adeschen@hotmail.com>
Date: 2025-12-31 19:10:45 -0500
Commit message:

 Update github action check-bioc

Package: CNVMetrics
Commit: 7c21b01855fdc9bb01d3633e308b395541ff6eeb
Author: Astrid Deschênes <adeschen@users.noreply.github.com>
Date: 2025-12-31 19:05:36 -0500
Commit message:

 Update check-bioc.yaml

Package: CNVMetrics
Commit: 5f76e21d8909eca510bf680247dba6b9259e6c4d
Author: adeschen <adeschen@hotmail.com>
Date: 2025-12-31 18:59:55 -0500
Commit message:

 Update parameters of the generatic is.CNVMetic()

Package: enrichViewNet
Commit: 9d4d7b1538e167099a5f380f0935f633ad8a7385
Author: adeschen <adeschen@hotmail.com>
Date: 2025-12-31 18:03:47 -0500
Commit message:

 Bump version in devel

Package: enrichViewNet
Commit: 0ada9a7e9d1396ebbf6c1f4d181e409d8729d7ab
Author: Astrid Deschênes <adeschen@users.noreply.github.com>
Date: 2025-12-31 16:59:37 -0500
Commit message:

 Merge pull request #27 from adeschen/adeschen-patch-3

Update check-bioc.yml

Package: enrichViewNet
Commit: 5f9a0bf43d2598e129756e6855712b9b7b2a860f
Author: Astrid Deschênes <adeschen@users.noreply.github.com>
Date: 2025-12-31 16:34:39 -0500
Commit message:

 Update check-bioc.yml

Package: enrichViewNet
Commit: d29831daa461622160cc058efd6e133913f2c7d7
Author: Astrid Deschênes <adeschen@users.noreply.github.com>
Date: 2025-12-31 15:27:49 -0500
Commit message:

 Merge pull request #26 from adeschen/adeschen-patch-3

Update check-bioc.yml

Package: enrichViewNet
Commit: 811bccac959d798a2303ebf609693a01a039d258
Author: Astrid Deschênes <adeschen@users.noreply.github.com>
Date: 2025-12-31 15:00:06 -0500
Commit message:

 Update check-bioc.yml

Package: enrichViewNet
Commit: 63fee37218e4a56f0bd88f002a5de2a04057f027
Author: Astrid Deschênes <adeschen@users.noreply.github.com>
Date: 2025-12-31 13:56:05 -0500
Commit message:

 Update check-bioc.yml

Package: enrichViewNet
Commit: 9634ef85f82e7f6c964341db88092ba7d67ed30b
Author: Astrid Deschênes <adeschen@users.noreply.github.com>
Date: 2025-12-31 13:43:12 -0500
Commit message:

 Update check-bioc.yml

Package: enrichViewNet
Commit: a0889cd63bca0b0dfad4cc05e93631d2975e9c8f
Author: Astrid Deschênes <adeschen@users.noreply.github.com>
Date: 2025-12-31 13:32:19 -0500
Commit message:

 Update check-bioc.yml

Package: enrichViewNet
Commit: 888ecfb04e242b5d013bf7c3b1e522e8fc60812c
Author: adeschen <adeschen@hotmail.com>
Date: 2025-12-31 13:26:49 -0500
Commit message:

 Remove groupCategory parameter as it is not used anymore by emapplot() function

Package: pathlinkR
Commit: bac4a673c706dc95ba868fed97680611c77ed8fd
Author: Travis Blimkie <travis.m.blimkie@gmail.com>
Date: 2025-12-31 11:19:45 -0800
Commit message:

 Made pathwayEnrichment test generic to prevent erroneous errors

Package: pathlinkR
Commit: a63c047ea5825746e3972d267a20968935305d6c
Author: Travis Blimkie <travis.m.blimkie@gmail.com>
Date: 2025-12-31 10:52:54 -0800
Commit message:

 Updated vignette

Package: pathlinkR
Commit: 812f91ccfafa2f1f97b63675012680feba37825f
Author: Travis Blimkie <travis.m.blimkie@gmail.com>
Date: 2025-12-31 10:03:52 -0800
Commit message:

 Fixed to test to prevent failure

Package: pathlinkR
Commit: d24d216a2239293b442f05d36ca29b67b2179037
Author: Travis Blimkie <travis.m.blimkie@gmail.com>
Date: 2025-12-31 09:58:25 -0800
Commit message:

 Updated sigoraDatabase data object

Package: pathlinkR
Commit: 93a1373b82576365007c7c93db48937c929b3294
Author: Travis Blimkie <travis.m.blimkie@gmail.com>
Date: 2025-12-31 09:56:56 -0800
Commit message:

 Updated reactomeDatabase data object

Package: pathlinkR
Commit: f3866b1cadf400fe8daff1d8b9fae74174df831d
Author: Travis Blimkie <travis.m.blimkie@gmail.com>
Date: 2025-12-31 09:55:34 -0800
Commit message:

 Updated mappingFile data object

Package: pathlinkR
Commit: 2de1b039b4dd41ef8c64f06f46fb8dd26747f22d
Author: Travis Blimkie <travis.m.blimkie@gmail.com>
Date: 2025-12-31 09:54:28 -0800
Commit message:

 Updated keggDatabase data object

Package: pathlinkR
Commit: 3fd84473a62c4ae930f7d9811d1ef2f864d674ac
Author: Travis Blimkie <travis.m.blimkie@gmail.com>
Date: 2025-12-31 09:53:33 -0800
Commit message:

 Updated innateDbPPI data object

Package: pathlinkR
Commit: a654db56cbdf9da227194cc4b6eec006f7d0b9ea
Author: Travis Blimkie <travis.m.blimkie@gmail.com>
Date: 2025-12-31 09:52:38 -0800
Commit message:

 Updated hallmarkDatabase data object

Package: pathlinkR
Commit: 8867bcbaab684a72e2078a396d950fe15b3bdb35
Author: Travis Blimkie <travis.m.blimkie@gmail.com>
Date: 2025-12-31 09:50:49 -0800
Commit message:

 Updated groupedPathwayColours data object

Package: pathlinkR
Commit: 61b277f1a973435edf8f7eb7f03f2531601294a5
Author: Travis Blimkie <travis.m.blimkie@gmail.com>
Date: 2025-12-31 09:49:52 -0800
Commit message:

 Updated pathwayCategories data object

Package: pathlinkR
Commit: 7a8d2c185691aa67bac2790d40bc878a4f34941c
Author: Travis Blimkie <travis.m.blimkie@gmail.com>
Date: 2025-12-31 08:24:49 -0800
Commit message:

 Switched from ggforce to patchwork for combining pathwayPlot outputs

Package: pathlinkR
Commit: fbe2227138eaaf80e3844c122cd685d7cd842466
Author: Travis Blimkie <travis.m.blimkie@gmail.com>
Date: 2025-12-31 08:24:07 -0800
Commit message:

 Changed factor column to character in sigoraExamples

Package: PIUMA
Commit: 5ec02ede9ec802b040efad8082721d92877f8935
Author: BioinfoMonzino <mattia.chiesa@cardiologicomonzino.it>
Date: 2025-12-31 16:30:46 +0100
Commit message:

 updates for PIUMA 1.7.1

Package: CTCF
Commit: 193d94ec069089c199190250a5959f305e34fee3
Author: Mikhail Dozmorov <mikhail.dozmorov@gmail.com>
Date: 2025-12-31 12:41:46 +0000
Commit message:

 Comment out plyranges

Package: spatialHeatmap
Commit: 38d22d674e5f6347d3cfb26b65276add332b537e
Author: jianhaizhang <jzhan067@ucr.edu>
Date: 2025-12-31 16:52:38 +0800
Commit message:

 Merge branch 'devel' of git.bioconductor.org:packages/spatialHeatmap into devel

Package: spatialHeatmap
Commit: 3ca3e109dffd3f3bb75f411363dcc4805e4064a2
Author: jianhaizhang <jzhan067@ucr.edu>
Date: 2025-12-31 16:11:52 +0800
Commit message:

 Version bump.

Package: spatialHeatmap
Commit: d15109a03a3012a38ef8687fd1a00ffffadb1c70
Author: jianhaizhang <jzhan067@ucr.edu>
Date: 2025-12-31 16:10:04 +0800
Commit message:

 Small update.

Package: spatialHeatmap
Commit: 72c815bdea92cfb199998d2013ea5fa63478a086
Author: jianhaizhang <jzhan067@ucr.edu>
Date: 2025-12-31 16:09:34 +0800
Commit message:

 Re-created srt_sc.rds to address the error related to "VisiumV1" object.

Package: annoLinker
Commit: f358cb55c3b16ab8744badc00890800b1ebadd0e
Author: Jianhong Ou <jianhong.ou@gmail.com>
Date: 2025-12-30 11:37:10 -0500
Commit message:

 update the code style.

Package: annoLinker
Commit: 63bb8f9a4400390c700b141dd1d328382a964748
Author: Jianhong Ou <jianhong.ou@gmail.com>
Date: 2025-12-30 08:22:43 -0500
Commit message:

 update code style.

Package: annoLinker
Commit: c94978291c84a195b2c43fcad1925bb90b502f0e
Author: Jianhong Ou <jianhong.ou@gmail.com>
Date: 2025-12-30 08:19:11 -0500
Commit message:

 update the installation instructions.

Package: singIST
Commit: 5c3ed38a2b102ce0d9bd0d9cf60c6c4c0f9fecba
Author: Aitor Moruno Cuenca <amoruno@almirall.com>
Date: 2025-12-30 13:19:43 +0100
Commit message:

 Solve error

Package: lcmsPlot
Commit: 3da402e8ec979d60fde680704a0989710d7fd4b5
Author: Ossama Edbali <ossedb@gmail.com>
Date: 2025-12-29 21:34:44 +0000
Commit message:

 chore: Increase pre-release version

Package: lcmsPlot
Commit: 7c378f887c9f1f5dfbe7a68bd8bea79a439eb030
Author: Ossama Edbali <ossedb@gmail.com>
Date: 2025-12-29 21:34:03 +0000
Commit message:

 feat: Enable Compound Discoverer support

Package: singIST
Commit: ecf12f0b87472cedca99be9f41616274ecc2961a
Author: Aitor Moruno Cuenca <amoruno@almirall.com>
Date: 2025-12-29 21:34:04 +0100
Commit message:

 Vignette aesthetics and version
git push upstream HEAD:devel

Package: singIST
Commit: 499c8d9b7f03e28fafe1cd1bc647694b87ef2879
Author: Aitor Moruno Cuenca <amoruno@almirall.com>
Date: 2025-12-29 21:32:13 +0100
Commit message:

 Vignette aesthetics

Package: gwascat
Commit: 47c8928af65175ec78bd8a9d31b81bf9a7a4d006
Author: vjcitn <stvjc@channing.harvard.edu>
Date: 2025-12-29 14:40:18 -0500
Commit message:

 introduce new URL for updated gwas catalog from EBI

Package: spammR
Commit: 7fcc35fc970f18fca7fb3dfa23a2507ff2cf7f9f
Author: Sara JC Gosline <sara.gosline@pnnl.gov>
Date: 2025-12-29 11:26:22 -0800
Commit message:

 version bump

Package: spammR
Commit: e649626a30a49881ac45f7feb7aec98855223846
Author: Sara JC Gosline <sara.gosline@pnnl.gov>
Date: 2025-12-23 18:14:37 -0800
Commit message:

 Merge pull request #73 from PNNL-CompBio/reticulate_fix

Reticulate fix

Package: spammR
Commit: 284b4777574a1ce6d80316ff8e8cd35cf5edcdce
Author: Yannick Mahlich <yannick.mahlich@pnnl.gov>
Date: 2025-12-23 14:35:09 -0800
Commit message:

 added comment to explain name difference between `py_module_available()` & `py_install`

Package: spammR
Commit: 8be8dba489003ec7893b6bafe74add81d14cc0b9
Author: Yannick Mahlich <yannick.mahlich@pnnl.gov>
Date: 2025-12-23 14:33:03 -0800
Commit message:

 reverted change to python module availability check to reference correct module import name

Package: spammR
Commit: ab2e04bb4e9618f492a9e1687ee3f79938b63e84
Author: Sara JC Gosline <sara.gosline@pnnl.gov>
Date: 2025-12-23 12:33:56 -0800
Commit message:

 Merge pull request #72 from PNNL-CompBio/metab-prot-integ

thanks for the comments!

Package: spammR
Commit: 30ef682a0d41292808bbbbd9b97aed9d913618a4
Author: Sara JC Gosline <sara.gosline@pnnl.gov>
Date: 2025-12-23 12:33:28 -0800
Commit message:

 Update retrieve_metaspace_data.R

Package: spammR
Commit: cd0b4f53d2d84ac212f9c7631152fc5dda55bcf8
Author: Sara JC Gosline <sara.gosline@pnnl.gov>
Date: 2025-12-23 12:32:28 -0800
Commit message:

 Update DESCRIPTION

i think depends is more stringent than imports

Package: spammR
Commit: 8e0b09e2eacb34f2c50630e282c4c935402abc4b
Author: Sara JC Gosline <sara.gosline@pnnl.gov>
Date: 2025-12-19 13:37:42 -0800
Commit message:

 added more to confirm build

Package: spammR
Commit: a5491ec51f7d6d5a774bc96f462bf6ab81f4d852
Author: Sara JC Gosline <sara.gosline@pnnl.gov>
Date: 2025-12-19 10:28:59 -0800
Commit message:

 added manuscript figure script

Package: spammR
Commit: 555e6690bb8a33620fa32047c345c24c6fedece1
Author: Sara JC Gosline <sara.gosline@pnnl.gov>
Date: 2025-12-15 08:56:33 -0800
Commit message:

 refining package vignettes

Package: spammR
Commit: be852fb5d2c907478a0b2e937da45be2aecdbdb8
Author: Sara JC Gosline <sara.gosline@pnnl.gov>
Date: 2025-12-10 12:05:45 -0800
Commit message:

 Merge pull request #71 from PNNL-CompBio/metab-prot-integ

Metab prot integ

Package: spammR
Commit: dbef57c2c924efc01dd2b093ccf3afb19716a02d
Author: Sara JC Gosline <sara.gosline@pnnl.gov>
Date: 2025-12-10 10:04:40 -0800
Commit message:

 update for package building

Package: spammR
Commit: 5f2e66d29176cbeafe8e105fa43b433e14d600d4
Author: Sara JC Gosline <sara.gosline@pnnl.gov>
Date: 2025-12-07 18:36:33 -0800
Commit message:

 maybe we need vignette files?

Package: spammR
Commit: 9d1af329d6a2735b93ef6f18bfbae2d2a303b6be
Author: Sara JC Gosline <sara.gosline@pnnl.gov>
Date: 2025-12-05 22:00:02 -0800
Commit message:

 hopefully last updates

Package: spammR
Commit: 86557a3393da96b2f1f42fabdc6b26917e4fe6eb
Author: Sara JC Gosline <sara.gosline@pnnl.gov>
Date: 2025-12-05 15:39:36 -0800
Commit message:

 updated to make better sense of data

Package: spammR
Commit: 8bf97e1892fe3fb81abbe46393b0945b51985326
Author: Sara JC Gosline <sara.gosline@pnnl.gov>
Date: 2025-12-04 15:47:11 -0800
Commit message:

 updated with new bug find!

Package: spammR
Commit: 6e59073b19a043808cbb838f26738f4089107d19
Author: Sara JC Gosline <sara.gosline@pnnl.gov>
Date: 2025-12-04 15:29:02 -0800
Commit message:

 new changes

Package: spammR
Commit: a82c65fd1040a6fb0710e05363b6f65766fd2582
Author: Sara JC Gosline <sara.gosline@pnnl.gov>
Date: 2025-12-01 17:00:19 -0800
Commit message:

 Merge pull request #70 from PNNL-CompBio/metab-prot-integ

added dependency checking, small PR allowing vignette to run. as i forgot a file download.

Package: spammR
Commit: 612fcfd2332444d90a170b84fef0a988082f1de6
Author: Sara JC Gosline <sara.gosline@pnnl.gov>
Date: 2025-12-01 17:00:02 -0800
Commit message:

 last updates

Package: spammR
Commit: 3d31b265e4cae086a6cdb697d0cd5cd948c2f37b
Author: Sara JC Gosline <sara.gosline@pnnl.gov>
Date: 2025-12-01 15:46:24 -0800
Commit message:

 added dependency checking

Package: spammR
Commit: dfb517c3f38c854f7f1cbe86d0f60e091cede935
Author: Sara JC Gosline <sara.gosline@pnnl.gov>
Date: 2025-12-01 15:30:40 -0800
Commit message:

 Merge pull request #69 from PNNL-CompBio/metab-prot-integ

addition of a lipid/protein example

Package: spammR
Commit: 2eb3a7a4efde8598dec8831bee88429f46e40737
Author: Sara JC Gosline <sara.gosline@pnnl.gov>
Date: 2025-12-01 15:29:06 -0800
Commit message:

 passes build check

Package: spammR
Commit: 07010ef285f154071645a181717825a4274ad2e5
Author: Sara JC Gosline <sara.gosline@pnnl.gov>
Date: 2025-12-01 12:51:12 -0800
Commit message:

 more updates to the vignette

Package: spammR
Commit: 092a6427a4739a141e0097290d370a1525817e2c
Author: Sara JC Gosline <sara.gosline@pnnl.gov>
Date: 2025-12-01 11:23:45 -0800
Commit message:

 working on updated vignettes and network

Package: spammR
Commit: 143c1525359b3d83260f9c9214e9c9613251cb4e
Author: Sara JC Gosline <sara.gosline@pnnl.gov>
Date: 2025-11-13 15:01:53 -0800
Commit message:

 Merge pull request #68 from PNNL-CompBio/metab-prot-integ

Added outline of lipid/proteomic integration

Package: spammR
Commit: 774ae8e319649ddce9565b69ee552edd3c1c32e9
Author: Sara JC Gosline <sara.gosline@pnnl.gov>
Date: 2025-11-13 13:46:40 -0800
Commit message:

 reduced file size and made updates to pass build/check

Package: spammR
Commit: b511621aa2d00e8d1ca07aa25d2905d8929c09a7
Author: Sara JC Gosline <sara.gosline@pnnl.gov>
Date: 2025-11-12 12:02:59 -0800
Commit message:

 working on  package building with vignette

Package: spammR
Commit: 0c9498073b7a404e0495ad20909ced12da144273
Author: Sara JC Gosline <sara.gosline@pnnl.gov>
Date: 2025-11-11 11:24:35 -0800
Commit message:

 added updates to markdown

Package: spammR
Commit: fe0c97f206a004c130275e158b9756e684e9b83e
Author: Sara JC Gosline <sara.gosline@pnnl.gov>
Date: 2025-11-11 11:07:01 -0800
Commit message:

 added reduce function

Package: spammR
Commit: 1ee9ce042404bd84e24a3c68ed8793aec8b82f93
Author: Sara JC Gosline <sara.gosline@pnnl.gov>
Date: 2025-11-11 09:58:38 -0800
Commit message:

 updated with new plotting

Package: spammR
Commit: 06d6f917e0455aa20ce689da30c4fa5190f62204
Author: Sara JC Gosline <sara.gosline@pnnl.gov>
Date: 2025-11-09 15:16:39 -0800
Commit message:

 Added updated function to get metspace data

Package: spammR
Commit: 407055517fe3178f7b8f37d7ad232b8587535d6f
Author: Sara JC Gosline <sara.gosline@pnnl.gov>
Date: 2025-11-05 09:52:25 -0800
Commit message:

 slight updates to ideas/thoughts

Package: spammR
Commit: 0008fc7fb08f3b92c8390fa84dd1eae11fa8e16a
Author: Sara JC Gosline <sara.gosline@pnnl.gov>
Date: 2025-11-05 09:24:39 -0800
Commit message:

 updated spatial diffex fro counts

added support for voom.

Package: spammR
Commit: 78bbd1835801384ed2c3004cd24df9220997c870
Author: Sara JC Gosline <sara.gosline@pnnl.gov>
Date: 2025-11-05 09:06:23 -0800
Commit message:

 removed this for now

Package: spammR
Commit: 9b38ae8c1348fbea3ff646a72693102066630e7e
Author: Sara JC Gosline <sara.gosline@pnnl.gov>
Date: 2025-11-05 08:37:34 -0800
Commit message:

 kept this in separate branch for now

Package: spammR
Commit: bff2877d0f101ed86f2e3da05b91392d00119bff
Author: Sara JC Gosline <sara.gosline@pnnl.gov>
Date: 2025-11-05 08:35:07 -0800
Commit message:

 added some draft files

Package: spammR
Commit: 6ca0ffc68f392f0e614eddd2c8bf4003788b6551
Author: Sara JC Gosline <sara.gosline@pnnl.gov>
Date: 2025-11-04 10:48:43 -0800
Commit message:

 testing out metabolomic/proteomic integration

Package: spammR
Commit: d95eb222194f6bdfe0d97c023f95ad9281fc6313
Author: Sara JC Gosline <sara.gosline@pnnl.gov>
Date: 2025-11-04 10:48:08 -0800
Commit message:

 trying out some code for SFE

Package: spammR
Commit: 8298328c34b7a50a24954748215460d878cb9cfc
Author: Sara JC Gosline <sara.gosline@pnnl.gov>
Date: 2025-10-22 20:16:57 -0700
Commit message:

 cleaned up line ending

Package: spammR
Commit: e466bf4acce32d4ddc35d0fa72c63165522c03ee
Author: Sara JC Gosline <sara.gosline@pnnl.gov>
Date: 2025-10-22 14:45:15 -0700
Commit message:

 updating spacing here

Package: spammR
Commit: 92ef380100d875a4faa3efc1b7e115fa0caf4601
Author: Sara JC Gosline <sara.gosline@pnnl.gov>
Date: 2025-10-22 08:43:04 -0700
Commit message:

 Merge pull request #62 from PNNL-CompBio/new-bioc-sub

Major bioconductor updates, trying to get ahead after seeing the leapR comments

Package: spammR
Commit: 3b8729dc9a00a88656086a662380c9eb06b9ed99
Author: Sara JC Gosline <sara.gosline@pnnl.gov>
Date: 2025-10-14 15:36:47 -0700
Commit message:

 more udpates

Package: spammR
Commit: 7a7ff005f9881440af15ae1bbed6929c1428b7bd
Author: Sara JC Gosline <sara.gosline@pnnl.gov>
Date: 2025-10-14 14:48:17 -0700
Commit message:

 updated ahead of new bioconductor version prep

Package: spammR
Commit: 91c317588bd70376d4ff140e94352f6f57bdb63e
Author: Sara JC Gosline <sara.gosline@pnnl.gov>
Date: 2025-09-30 13:15:33 -0700
Commit message:

 Update README.md

Package: spammR
Commit: 78cc7d4e29ef9a7196435acb7510da8878d05266
Author: Sara JC Gosline <sara.gosline@pnnl.gov>
Date: 2025-09-30 10:40:07 -0700
Commit message:

 Update README.md

Package: spammR
Commit: 77e136f7fb6190a2cb75fcb6d1e9b1deb2c41b42
Author: Sara JC Gosline <sara.gosline@pnnl.gov>
Date: 2025-08-26 15:18:50 -0700
Commit message:

 Merge pull request #61 from PNNL-CompBio/edge-detection

updated vignette

Package: spammR
Commit: 1c5f016abb42282c6b5bb60d2243831bd625cc8d
Author: Sara JC Gosline <sara.gosline@pnnl.gov>
Date: 2025-08-26 15:18:19 -0700
Commit message:

 updated vignette

Package: spammR
Commit: a65ee25fbf3c62de9b9862242b53612e6ae0f4c0
Author: Sara JC Gosline <sara.gosline@pnnl.gov>
Date: 2025-08-21 18:11:15 -0700
Commit message:

 Merge pull request #57 from PNNL-CompBio/edge-detection

Added non-square edge detection script

Package: spammR
Commit: 0e27ee2964079b3aa7f6d25c2c46697f05d640d2
Author: Sara JC Gosline <sara.gosline@pnnl.gov>
Date: 2025-08-15 10:15:07 -0700
Commit message:

 updated vignette

Package: spammR
Commit: f2d6e845f75eb30cf47c5cfbb58debfabe90eb9c
Author: Sara JC Gosline <sara.gosline@pnnl.gov>
Date: 2025-08-14 16:03:25 -0700
Commit message:

 added python code for edge detection.

still need to integrate via reticulate and provide example

Package: spammR
Commit: 1fa9a71c53c53592e5e6ff5ecd8c8e285844dcea
Author: Sara JC Gosline <sara.gosline@pnnl.gov>
Date: 2025-08-08 10:18:40 -0700
Commit message:

 added python script to process edges of image automatically

Package: spammR
Commit: 8f6708960bb8ee3258bc32729bf06bc9d79004c0
Author: Sara JC Gosline <sara.gosline@pnnl.gov>
Date: 2025-08-07 14:59:24 -0700
Commit message:

 Merge pull request #54 from PNNL-CompBio/split-impute

added ability to calculate missingness

Package: spammR
Commit: bf52846989030f1e602146b9bf3b9396b75ffb0b
Author: Sara JC Gosline <sara.gosline@pnnl.gov>
Date: 2025-08-07 14:58:44 -0700
Commit message:

 fixed issue

Package: spammR
Commit: fe10c50c7dd1e35c94efd2d1280bd1ebdff10313
Author: Sara JC Gosline <sara.gosline@pnnl.gov>
Date: 2025-08-07 14:51:04 -0700
Commit message:

 added ability to calculate misingness

Package: spammR
Commit: b02c8d1936d2cf764204ed2f83979845dfb8d282
Author: Sara JC Gosline <sara.gosline@pnnl.gov>
Date: 2025-08-07 13:02:54 -0700
Commit message:

 Merge pull request #53 from PNNL-CompBio/split-impute

Split impute

Package: spammR
Commit: 5ecf2bcec2a77f44f377ff6c192433c306ba46c7
Author: Sara JC Gosline <sara.gosline@pnnl.gov>
Date: 2025-08-07 13:02:42 -0700
Commit message:

 more doc corrections

Package: spammR
Commit: 1c7b72471ca0697f12936a062d89a30f2fc48781
Author: Sara JC Gosline <sara.gosline@pnnl.gov>
Date: 2025-08-07 12:35:05 -0700
Commit message:

 cleaned up more issues

Package: spammR
Commit: 203125f8136cac3c7a4530fdd2a1e03a33b2af4b
Author: Sara JC Gosline <sara.gosline@pnnl.gov>
Date: 2025-08-07 12:29:00 -0700
Commit message:

 cleaning up more functionality of the imputation function

Package: spammR
Commit: e80808e09b9c360da228f49c9992a408cb86afa7
Author: Sara JC Gosline <sara.gosline@pnnl.gov>
Date: 2025-08-07 12:03:33 -0700
Commit message:

 updated documentation

Package: spammR
Commit: f6291dcce7a963e43e11e0df970e37c5cdf76caa
Author: Sara JC Gosline <sara.gosline@pnnl.gov>
Date: 2025-08-07 12:01:47 -0700
Commit message:

 bug present in group code

Package: spammR
Commit: a9693e4b2a83f05ddc878871ba8a7612ad9637a6
Author: Sara JC Gosline <sara.gosline@pnnl.gov>
Date: 2025-08-06 17:21:12 -0700
Commit message:

 Merge pull request #52 from PNNL-CompBio/split-impute

updated split function

Package: spammR
Commit: db3892bcb71c2777a6c8a04eff7cb7607e928006
Author: Sara JC Gosline <sara.gosline@pnnl.gov>
Date: 2025-08-06 17:20:48 -0700
Commit message:

 updated split function

Package: spammR
Commit: e48ef81b23cdb0fabb76fe79ca1f3392885f408d
Author: Sara JC Gosline <sara.gosline@pnnl.gov>
Date: 2025-08-06 17:01:42 -0700
Commit message:

 Merge pull request #51 from PNNL-CompBio/split-impute

Added split functionality and more methods to imputation

Package: spammR
Commit: e95ef73960a33a11c92f7a5a2e17218eac8edf89
Author: Sara JC Gosline <sara.gosline@pnnl.gov>
Date: 2025-08-06 16:54:40 -0700
Commit message:

 updated vignette

Package: spammR
Commit: 83f1db51fc32c556989fad8fafefd8ee9712345d
Author: Sara JC Gosline <sara.gosline@pnnl.gov>
Date: 2025-08-06 16:48:14 -0700
Commit message:

 slight fix to vignette

Package: spammR
Commit: d741498147ef711184ffa4256a13da8cb5fbc186
Author: Sara JC Gosline <sara.gosline@pnnl.gov>
Date: 2025-08-06 16:46:23 -0700
Commit message:

 Delete spammR.Rproj

Package: spammR
Commit: 566eb0811cf8cd1a8d55604008df98d87bf5bf62
Author: Sara JC Gosline <sara.gosline@pnnl.gov>
Date: 2025-08-06 16:45:44 -0700
Commit message:

 updated ignore

Package: spammR
Commit: 84783a78509b6df6c95ba99173e0f64458a1b904
Author: Sara JC Gosline <sara.gosline@pnnl.gov>
Date: 2025-08-06 16:44:18 -0700
Commit message:

 updated files to pass test

Package: spammR
Commit: 603d51bd9a42ffd928bf0ca91073aecd2395548a
Author: Sara JC Gosline <sara.gosline@pnnl.gov>
Date: 2025-08-06 16:25:05 -0700
Commit message:

 fixed imputation and aded ability to split

added split functionality to help with RA anlsysi, fixed imputation.

Package: spammR
Commit: d2e114fbaee203886b2e04ef4883a9c807d90f04
Author: Sara JC Gosline <sara.gosline@pnnl.gov>
Date: 2025-07-24 17:34:11 -0700
Commit message:

 updated to account for subtle leapR changes

Package: singIST
Commit: c0f1484000663001ba02e1e60c3e54faf6a713ce
Author: Aitor Moruno Cuenca <amoruno@almirall.com>
Date: 2025-12-29 20:14:48 +0100
Commit message:

 First reviewed version of Bioconductor submission

Package: BiocCheck
Commit: 927dc6465e8a83d3081b46dc648c70802db4772a
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-12-29 13:47:04 -0500
Commit message:

 version bump 1.47.8

Package: BiocCheck
Commit: f78bb19a3edb02cd8c0c0989804cbc08b8c5ab56
Author: Jeroen Ooms <jeroenooms@gmail.com>
Date: 2025-12-28 13:45:38 +0100
Commit message:

 Add error message to output

Package: BiocCheck
Commit: 9817476c9a6c3561b47151c3c9a38c7f8a5a086a
Author: Jeroen Ooms <jeroenooms@gmail.com>
Date: 2025-12-27 15:12:40 +0100
Commit message:

 Add commonmark to DESCRIPTION dependencies

The `commonmark` and `xml2` packages are required for parsing the `NEWS.md` file, see `help('news', package = 'utils')`.

Fixes https://github.com/r-universe-org/help/issues/649

Package: BiocCheck
Commit: 0d5022b9139e4f46b31173ce65cc1f469d913278
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-12-10 17:25:28 -0500
Commit message:

 version bump 1.47.7

Package: BiocCheck
Commit: 6c6c3610c74ec25ed78f35ad1987ba6573a97df6
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-12-10 17:25:24 -0500
Commit message:

 add exception to checkWatchedTag for maintainer@bioconductor.org

Package: BiocCheck
Commit: 4be4595e58ae1086bdc0f18b44ff930c59d6103d
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-12-09 14:17:08 -0500
Commit message:

 version bump 1.47.6

Package: BiocCheck
Commit: 8e6bd2c922aa5e3b1f2b6d9bd59c4f6082958ff9
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-12-09 14:17:01 -0500
Commit message:

 bug fix use stop instead of non-existent error()

Package: pathlinkR
Commit: 7f27e55c0689be90366bd4ad9edcf873eb9c2628
Author: Travis Blimkie <travis.m.blimkie@gmail.com>
Date: 2025-12-29 09:20:05 -0800
Commit message:

 Tweaked test to support release and development versions

Package: pathlinkR
Commit: abc980a4423434009c6a10f81c496a9ddb434b26
Author: Travis Blimkie <travis.m.blimkie@gmail.com>
Date: 2025-12-29 07:52:45 -0800
Commit message:

 Fixed test for development version.

Package: panoramic
Commit: 97f8c07ef6514e354f9752b584dd887d0b183e06
Author: Jacob Chang <jacobchang@Jacobs-MacBook-Pro-2.local>
Date: 2025-12-29 09:21:07 -0800
Commit message:

 Bump version to 0.99.1 for Bioconductor build

Package: panoramic
Commit: d0104d55f5fc4a41abfbac5cc853c6a73cd0a496
Author: Jacob (Jake) Chang <69719427+chang-jacob@users.noreply.github.com>
Date: 2025-12-23 12:44:09 -0800
Commit message:

 Update README.md

Package: panoramic
Commit: 64002875a1ad5a6d40e5ebf6dcaec87923c9a4c7
Author: Jacob (Jake) Chang <69719427+chang-jacob@users.noreply.github.com>
Date: 2025-12-23 12:43:47 -0800
Commit message:

 Add files via upload

Package: panoramic
Commit: af1533aa895c3fa2dc9041aff3aa4ebbddd9f3ac
Author: Jacob (Jake) Chang <69719427+chang-jacob@users.noreply.github.com>
Date: 2025-12-23 12:42:45 -0800
Commit message:

 Add files via upload

Package: panoramic
Commit: 0d606e9a544177e6c9a538f623649983fc889776
Author: Jacob (Jake) Chang <69719427+chang-jacob@users.noreply.github.com>
Date: 2025-12-23 12:42:25 -0800
Commit message:

 Delete panoramic_graphic.png

Package: panoramic
Commit: 41da1b59cd4512e8dac0f0875fc435b932f097ec
Author: Jacob (Jake) Chang <69719427+chang-jacob@users.noreply.github.com>
Date: 2025-12-23 12:41:47 -0800
Commit message:

 Add files via upload

Package: panoramic
Commit: ad394c437f60b102414ad8f47a5ebc703be3ccc3
Author: Jacob (Jake) Chang <69719427+chang-jacob@users.noreply.github.com>
Date: 2025-12-23 12:41:26 -0800
Commit message:

 Delete panoramic_graphic.png

Package: panoramic
Commit: 0798a1169aebdb0d9c5b41ffb4a81548f4568204
Author: Jacob (Jake) Chang <69719427+chang-jacob@users.noreply.github.com>
Date: 2025-12-23 12:40:03 -0800
Commit message:

 Add files via upload

Package: bugsigdbr
Commit: 6348069535e9f3d5209d80acecfe3a4f3a13129c
Author: lgeistlinger <ludwig.geistlinger@gmail.com>
Date: 2025-12-29 08:57:03 -0500
Commit message:

 fixed cache issue

Package: HPiP
Commit: 68bd9a14f4c0c5b6e13a5d100e79734445cff800
Author: Matineh Rahmatbakhsh <matinerb.94@gmail.com>
Date: 2025-12-28 17:34:02 -0600
Commit message:

 version bump

Package: HPiP
Commit: 4c07334225832ae84813b7fd0d1d1410ba92d5b6
Author: Matineh Rahmatbakhsh <matinerb.94@gmail.com>
Date: 2025-12-28 17:31:13 -0600
Commit message:

 fix namespacee

Package: methodical
Commit: 68b0dfb95a39954fc617b65365ea03b63dde95dc
Author: Richard Heery <richardheery@gmail.com>
Date: 2025-12-28 17:43:12 +0000
Commit message:

 Updated make_meth_rse_accessory_functions2.R

Package: zellkonverter
Commit: 0b30029f56ea445d66a013c591c465fc89aa8c9f
Author: Luke Zappia <lazappi@users.noreply.github.com>
Date: 2025-12-28 13:46:54 +0100
Commit message:

 Bump version to 1.20.1

Package: zellkonverter
Commit: bb352916e44e623ece0559525a9d9f9d82a92a9b
Author: Luke Zappia <lazappi@users.noreply.github.com>
Date: 2025-12-28 13:45:39 +0100
Commit message:

 Fix documentation links

Package: zellkonverter
Commit: 5f76c3bd132a216f9e418cb6859f6f26ea378f40
Author: Luke Zappia <lazappi@users.noreply.github.com>
Date: 2025-12-28 10:51:25 +0100
Commit message:

 Fix expectation in validation tests

Package: zellkonverter
Commit: 0127f9b004fff00f73dc7c839a5109287a46e802
Author: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Date: 2025-11-25 07:33:36 +0100
Commit message:

 Bump actions/checkout from 5 to 6 (#155)

Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

Package: zellkonverter
Commit: 8a5a5a2a19cbbb84ed22f77d420e920de5ca10ee
Author: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Date: 2025-11-11 07:24:25 +0100
Commit message:

 Bump JamesIves/github-pages-deploy-action from 4.7.3 to 4.7.4 (#154)

Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

Package: fluentGenomics
Commit: c296633b332a65253b6c86148d1b30954bf160a8
Author: sa-lee <stuart.andrew.lee@gmail.com>
Date: 2025-12-17 12:37:24 +1100
Commit message:

 correct package name

Package: memes
Commit: bb7e7dc7d2f8775f91fb08a5b70113d51d8c89e4
Author: Spencer Nystrom <snystrom@users.noreply.github.com>
Date: 2025-06-14 02:48:04 -0400
Commit message:

 Merge pull request #124 from karawoo/gha

update cache action

Package: memes
Commit: 3aa940302f33de0a8b5956f6174d22c51d25b4f3
Author: Kara Woo <woo.kara@gmail.com>
Date: 2025-06-13 23:43:23 -0700
Commit message:

 update cache action

Package: CPSM
Commit: dc1acc4718df35de2591069c12414332f9c19674
Author: Harpreet Kaur <hks04180@gmail.com>
Date: 2025-12-26 17:29:30 -0500
Commit message:

 CPSM 1.3.1: Update in DESCRIPTION and NEWS.md, cross-validation updates, feature stability metrics, and documentation

Package: CPSM
Commit: 7d04cc634cbc988c55bde4e3d28856fe94ba89c5
Author: Harpreet Kaur <hks04180@gmail.com>
Date: 2025-12-26 16:46:42 -0500
Commit message:

 CPSM 1.1.4: cross-validation updates, feature stability metrics, and documentation

Package: Rigraphlib
Commit: 7cfc7f9f925ac74025a15308ded3554b1d42bbc5
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2025-12-07 17:44:21 +1100
Commit message:

 Streamline configure script when the output directories already exist.

Package: scrapper
Commit: d28799af985eed1bef0910e5e74eeec468fe65cb
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2025-12-27 00:13:54 +1100
Commit message:

 More realistic example for fitVarianceTrend.

Package: scrapper
Commit: 0c67ab2ba01430088a11c9da913dbecfc6364893
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2025-12-27 00:05:36 +1100
Commit message:

 Added seealso links to the SE wrappers for each non-SE function.

Package: scrapper
Commit: a30e01d814c93b968cedd71eb982a6865e377572
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2025-12-26 21:13:11 +1100
Commit message:

 Elaborated on the tests in scaleByNeighbors.se.

- Added some tests for deduplication of the reddims.
- Added tests for correct names of the scaling factors.
- Removed some extraneous scrapper:: namespace.

Package: scrapper
Commit: 90dcc7acd3d038e658ccf7a34dfd18e3fb3afae8
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2025-12-26 16:42:29 +1100
Commit message:

 Removed some extraneous scrapple references.

Package: scrapper
Commit: a90702e9a39a0bfc3fdc731b0fb532b3b4860658
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2025-12-26 14:48:16 +1100
Commit message:

 Updated NEWS file and bumped version.

Package: scrapper
Commit: f0a22ee71278fef0ea1f0ba906d46c4de131f1de
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2025-12-26 14:00:02 +1100
Commit message:

 Collapse the neighbor search for greater speed by default.

Package: scrapper
Commit: 04b49036ff26af842867d631f9a45a5e97f7ebfb
Author: Aaron Lun <infinite.monkeys.with.keyboards@gmail.com>
Date: 2025-12-26 13:51:17 +1100
Commit message:

 Integrate SE-compatible wrappers from scrapple back into scrapper. (#19)

As it turns out, there wasn't much point in keeping the packages separate
because it's become increasingly unlikely that I'll get any resources for
separate maintainership. So, we might as well merge everything into one package
and keep things simple for the end-user.

We deprecate the analyze() function in favor of analyze.se(). We also direct
readers of the vignette to the analyze.se() function.

Package: lcmsPlot
Commit: f5001e2c2ffc6700d142ca8f5bcdf999d34fbaf9
Author: Ossama Edbali <ossedb@gmail.com>
Date: 2025-12-25 22:51:06 +0000
Commit message:

 chore: Update lcmsPlotClass documentation

Package: lcmsPlot
Commit: 5ae024c773b9f35d8993dc89c39cd9717de341ae
Author: Ossama Edbali <ossedb@gmail.com>
Date: 2025-12-25 22:41:16 +0000
Commit message:

 chore: Remove lcmsPlotClass example

Package: lcmsPlot
Commit: fc6a71420ac5c60e12660b436b6927a11a0c84a9
Author: Ossama Edbali <ossedb@gmail.com>
Date: 2025-12-25 22:22:30 +0000
Commit message:

 feat: Codebase improvements for Bioconductor standards

Package: ClustIRR
Commit: fedad9771dc85fa705375e4df060f6dea2a65cb5
Author: snaketron <simo.kitanovski@uni-due.de>
Date: 2025-12-25 20:56:29 +0100
Commit message:

 minor updates

Package: ClustIRR
Commit: 4e2c28612f22837d525c81438a317dab7be4e4dd
Author: snaketron <simo.kitanovski@uni-due.de>
Date: 2025-12-25 20:37:16 +0100
Commit message:

 bugfix namespace, simplify .stan models

Package: ClustIRR
Commit: f1c549b3d48ff88e107b0c98833dcdb6617d68ad
Author: snaketron <simo.kitanovski@uni-due.de>
Date: 2025-12-25 18:55:20 +0100
Commit message:

 merge

Package: ClustIRR
Commit: 5ea3a3db95927643e15f2e64d22a5eca5448c8ed
Author: snaketron <simo.kitanovski@uni-due.de>
Date: 2025-12-25 18:46:17 +0100
Commit message:

 merge

Package: ClustIRR
Commit: 3ca7164000fa8f8ee426de9305ab693dffdbc3da
Author: snaketron <simo.kitanovski@proton.me>
Date: 2025-12-25 16:49:14 +0100
Commit message:

 faster community summary

Package: ClustIRR
Commit: 60afd60f8e9652120ed6cc1a608b0881491e5a2a
Author: snaketron <simo.kitanovski@proton.me>
Date: 2025-12-05 16:26:50 +0100
Commit message:

 KNN implementation

Package: PLSDAbatch
Commit: 50c28a1d75729dd659588f18a573cc8a6e18dbd7
Author: Yiwen (Eva) Wang <anjiwangyiwen@gmail.com>
Date: 2025-12-26 03:28:53 +1100
Commit message:

 improve usability

Package: PLSDAbatch
Commit: 77b91a664366ccf76213eb28eba2ab29ae8b3817
Author: Yiwen (Eva) Wang <anjiwangyiwen@gmail.com>
Date: 2025-11-06 11:20:14 +1100
Commit message:

 Merge remote-tracking branch 'upstream/devel'

Package: PLSDAbatch
Commit: e5d2954225d057e5c7a5bf72693193f36444b858
Author: Yiwen (Eva) Wang <anjiwangyiwen@gmail.com>
Date: 2025-05-05 17:02:58 +1000
Commit message:

 Merge remote-tracking branch 'upstream/devel'

Package: VisiumIO
Commit: f81ae8ecdd3fd0a31d6e8e1c0229fbb85bc06c07
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-12-24 11:10:25 -0500
Commit message:

 version bump 1.7.6

Package: VisiumIO
Commit: 7e55a9d5fddfb793651cfd60ff9368982a697692
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-12-24 11:10:19 -0500
Commit message:

 re-add spatialCoordsNames input to .import_binsize, closes #21

Package: Modstrings
Commit: f830d42b85d1dbbc9d408d471277b2b2d8476621
Author: FelixErnst <felix.gm.ernst@outlook.com>
Date: 2025-12-24 14:33:31 +0100
Commit message:

 Updated comparison to work with Biostrings 2.79.3

comparable_seqtypes was changed in Biostrings to allow for seqtypes "ModRNA" and "ModDNA" to be used efficiently. Performance improvements by avoiding the constructor calls as suggested by Herve Pages were implemented.

Package: StatescopeR
Commit: 65ab0011084c7152e8ac25e8050b18e1faa02c97
Author: MSteketee <m.f.b.steketee@amsterdamumc.nl>
Date: 2025-12-24 14:04:06 +0100
Commit message:

 Merge branch 'devel' of github.com:tgac-vumc/StatescopeR into devel

Package: StatescopeR
Commit: 911ddba7ce55cd45322dd2f58807e0513076c14c
Author: MSteketee <m.f.b.steketee@amsterdamumc.nl>
Date: 2025-12-24 14:02:21 +0100
Commit message:

 Added function to fetch signatures from https://github.com/tgac-vumc/StatescopeData and did some code cleaning

Package: StatescopeR
Commit: 164ff5adba1b1e654643a4c8188ad0725df71206
Author: MSteketee <m.f.b.steketee@amsterdamumc.nl>
Date: 2025-12-24 14:02:21 +0100
Commit message:

 Added function to fetch signatures from https://github.com/tgac-vumc/StatescopeData and did some code cleaning

Package: StatescopeR
Commit: 1bebb97a17a59fac24c3d43bce44f51ae97c3c1b
Author: MSteketee <m.f.b.steketee@amsterdamumc.nl>
Date: 2025-12-23 16:36:13 +0100
Commit message:

 Merge branch 'devel' of github.com:tgac-vumc/StatescopeR into devel

Package: StatescopeR
Commit: d44ee627e8babed4a901093f9b0ba81245540f42
Author: MSteketee <70577986+MSteketee@users.noreply.github.com>
Date: 2025-12-23 16:35:28 +0100
Commit message:

 Remove all check bioc.yml differences again

didn't end up doing anyhing

Package: StatescopeR
Commit: 91a2681c9e6fa375e81fd7ab4aceeb0f5cc889e6
Author: MSteketee <70577986+MSteketee@users.noreply.github.com>
Date: 2025-12-23 16:29:40 +0100
Commit message:

 Update check-bioc.yml

Package: StatescopeR
Commit: 814c27fc38346d6cc87922c9ca4d23a09012204c
Author: MSteketee <70577986+MSteketee@users.noreply.github.com>
Date: 2025-12-23 16:26:48 +0100
Commit message:

 Update check-bioc.yml

Package: StatescopeR
Commit: 5570bd142ff686e9668604346b64dff9c3810f7f
Author: MSteketee <70577986+MSteketee@users.noreply.github.com>
Date: 2025-12-23 16:25:33 +0100
Commit message:

 Update check-bioc.yml

Package: StatescopeR
Commit: 10e5df580a4552690c49826fb54d5b577c98b975
Author: MSteketee <70577986+MSteketee@users.noreply.github.com>
Date: 2025-12-23 16:10:37 +0100
Commit message:

 Update check-bioc.yml

Package: StatescopeR
Commit: ec2a7da87fdbe2ed06620737bb9d2a6641397501
Author: MSteketee <70577986+MSteketee@users.noreply.github.com>
Date: 2025-12-23 15:51:08 +0100
Commit message:

 Update check-bioc.yml

Package: StatescopeR
Commit: 3820ef3a7c6493127cc5520747867147a86de04f
Author: MSteketee <70577986+MSteketee@users.noreply.github.com>
Date: 2025-12-23 15:42:43 +0100
Commit message:

 Update check-bioc.yml

Next try

Package: StatescopeR
Commit: ff094108284bbf6c08b1027cb15b809bbddc450f
Author: MSteketee <70577986+MSteketee@users.noreply.github.com>
Date: 2025-12-23 15:31:58 +0100
Commit message:

 Update check-bioc.yml

Switched to newer free disk space fork

Package: StatescopeR
Commit: 81f8028eca0d833ad5283e5903ea4d2073c1e0ad
Author: MSteketee <70577986+MSteketee@users.noreply.github.com>
Date: 2025-12-23 15:12:47 +0100
Commit message:

 Update check-bioc.yml

New variation of freeing up space