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GIT Logs

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

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Package: SingleR
Commit: d06e65f7b03ef61b7c7b1a670e718ea7900d21ca
Author: Daniel Bunis <daniel.bunis@ucsf.edu>
Date: 2022-01-25 22:49:53 -0800
Commit message:

 Add 'rows.order' input to 'plotScoreHeatmap()' (#209)

Co-authored-by: LTLA <infinite.monkeys.with.keyboards@gmail.com> 
Package: SingleR
Commit: b30ccd0d2f6b9e79d6b2bd261428b71238dc7915
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2022-01-25 22:46:31 -0800
Commit message:

 Rebuilt the Rcpp bindings.
 
Package: GenomeInfoDb
Commit: 5177c9013cae28ea8755f818c51c39442682362c
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2022-01-25 22:27:14 -0800
Commit message:

 Small get_Ensembl_FTP_core_db_url() improvement and code reorganization
 
Package: scATAC.Explorer
Commit: 49a6df0a3e912653ad894103f8e9752e9b26804c
Author: Arrian Gibson-Khademi <agibsonk@uwo.ca>
Date: 2022-01-26 00:01:27 -0500
Commit message:

 fixing bioconductor versioning
 
Package: scATAC.Explorer
Commit: d739a0a3bf77b04cb242b965662fd57bf6d49028
Author: Arrian Gibson-Khademi <agibsonk@uwo.ca>
Date: 2022-01-25 22:34:48 -0500
Commit message:

 fixing bioconductor versioning
 
Package: gpuMagic
Commit: 81993479faea079307e34d15729d9e45c591baa0
Author: Jiefei-Wang <szwjf08@gmail.com>
Date: 2022-01-25 22:36:02 -0500
Commit message:

 update authorship
 
Package: GCSFilesystem
Commit: 7facd05ee26b3faf1a638956998ac72ea0905cdc
Author: Jiefei-Wang <szwjf08@gmail.com>
Date: 2022-01-25 22:34:42 -0500
Commit message:

 update authorship
 
Package: GCSConnection
Commit: e0a314a5beb2af2f6c46b9725cade8c2700ae281
Author: Jiefei-Wang <szwjf08@gmail.com>
Date: 2022-01-25 22:34:17 -0500
Commit message:

 update authorship
 
Package: Travel
Commit: 1a6f8a88c94177bd19311c6a7d866c7a509b811d
Author: Jiefei-Wang <szwjf08@gmail.com>
Date: 2022-01-25 22:33:29 -0500
Commit message:

 update authorship
 
Package: SharedObject
Commit: cf0140ab255894961df593b70fa831f0f88eefdc
Author: Jiefei-Wang <szwjf08@gmail.com>
Date: 2022-01-25 22:33:14 -0500
Commit message:

 update authorship
 
Package: Travel
Commit: 7164b843df72d58887359c5fc19c1cfcd32eba9a
Author: Jiefei-Wang <szwjf08@gmail.com>
Date: 2022-01-25 22:31:29 -0500
Commit message:

 update authorship
 
Package: scATAC.Explorer
Commit: 768cca021ac52248e9d00986f286d5f6d50e4858
Author: Arrian Gibson-Khademi <agibsonk@uwo.ca>
Date: 2022-01-25 22:27:46 -0500
Commit message:

 fixing bioconductor versioning
 
Package: scATAC.Explorer
Commit: e4cdba519375f86e154470ce0b2e94f24aa1c91d
Author: Arrian Gibson-Khademi <agibsonk@uwo.ca>
Date: 2022-01-25 22:26:17 -0500
Commit message:

 fixing bioconductor package versioning
 
Package: scATAC.Explorer
Commit: c7d2cbbcf2f91406cc92f8652ce639871231c91c
Author: Arrian Gibson-Khademi <agibsonk@uwo.ca>
Date: 2022-01-25 21:59:48 -0500
Commit message:

 fixed error in Domcke dataset cluster and cell type metadata counts
 
Package: cytolib
Commit: 3b906bcb9d5cdac70598c32c480afcf33d493dd4
Author: mikejiang <mike@ozette.ai>
Date: 2022-01-25 14:36:30 -0800
Commit message:

 Merge branch 'master' into devel
 
Package: cytolib
Commit: 1d48b5243dad13c394c606811991a1e691afb3d8
Author: mikejiang <mike@ozette.ai>
Date: 2022-01-25 14:35:56 -0800
Commit message:

 add Makevars.ucrt
 
Package: psichomics
Commit: a8739058bfbbe6757c2b08aa563db9e00d5e7e2d
Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
Date: 2022-01-25 20:52:54 +0000
Commit message:

 Squashed commit of the following:

commit 12dca96a3a4d8ded9b3a89deba0dc8e62d35cac9
Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
Date:   Tue Jan 25 20:52:08 2022 +0000

    Squashed commit of the following:

    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: atena
Commit: 776d611f294841dfff88fa7348c71d4ff3cfbf2f
Author: beacalvo <beacalvo96@gmail.com>
Date: 2022-01-25 20:29:59 +0100
Commit message:

 Fixed small errors and updated documentation
 
Package: atena
Commit: b73353560999efa8ee5f31467a91e7a399d3a23f
Author: beacalvo <beacalvo96@gmail.com>
Date: 2022-01-25 19:54:15 +0100
Commit message:

 Fixed small errors and updated documentation
 
Package: atena
Commit: 703f23f356081d2a1153aa31fd4f41b7c39a5d7f
Author: beacalvo <beacalvo96@gmail.com>
Date: 2022-01-25 19:43:38 +0100
Commit message:

 Fixed small error
 
Package: atena
Commit: 4383f98fb6430e60959bddc27df39a6a8c445732
Author: beacalvo <beacalvo96@gmail.com>
Date: 2022-01-25 19:38:40 +0100
Commit message:

 Increased package version
 
Package: atena
Commit: 107e0ca105b6fc54c52922bbe50ec8430ebf1803
Author: beacalvo <beacalvo96@gmail.com>
Date: 2022-01-25 18:37:50 +0100
Commit message:

 Adapting Telescope and TEtranscripts for when no secondary alignments are present in the BAM file
 
Package: atena
Commit: 5cb2a670d24e73b1947c242505633e33cb57c60b
Author: beacalvo <beacalvo96@gmail.com>
Date: 2022-01-25 16:58:34 +0100
Commit message:

 Added stop when no overlaps are found
 
Package: atena
Commit: 3ff4b8708ae09cfc928bfc47088e5c3e73ec304b
Author: beacalvo <beacalvo96@gmail.com>
Date: 2022-01-25 15:53:48 +0100
Commit message:

 Minor modification in error message
 
Package: atena
Commit: 47815af11a9aa8c3ea53cda7acfc4cb3ad9ddc1c
Author: beacalvo <beacalvo96@gmail.com>
Date: 2022-01-25 12:41:17 +0100
Commit message:

 Implementation of average read length in case of GAlignmentsList
 
Package: atena
Commit: 0bd7c1dd091403e95143b5959fc36c3623fbd974
Author: beacalvo <beacalvo96@gmail.com>
Date: 2022-01-25 10:35:05 +0100
Commit message:

 Changed rowSums and colSums for rowSums2 and colSums2
 
Package: pRolocGUI
Commit: 3302c93b653a7ce8f99b65aea242edc53ede6b9b
Author: Lisa Breckels <lms79@cam.ac.uk>
Date: 2022-01-25 17:12:50 +0000
Commit message:

 increment pkg version
 
Package: pRolocGUI
Commit: 825d92df2bb00f55adf532ef816f49c14e511e28
Author: Lisa Breckels <lms79@cam.ac.uk>
Date: 2022-01-25 17:09:00 +0000
Commit message:

 fixing #110
 
Package: pRolocGUI
Commit: ae7d92f159e570ec92a5340da7a102ab3a8b6f00
Author: Lisa Breckels <lms79@cam.ac.uk>
Date: 2022-01-21 20:56:19 +0000
Commit message:

 fontawesome deprecated switch to cogs
 
Package: DepInfeR
Commit: 923851a1340a6f7230bf892a29ac5825a5583bbf
Author: lujunyan1118 <jylu1118@gmail.com>
Date: 2022-01-25 18:02:46 +0100
Commit message:

 bump up version
 
Package: mzR
Commit: 458704d680a2eead5acb0a4aa224b6e48ff170a6
Author: Steffen Neumann <sneumann@ipb-halle.de>
Date: 2022-01-25 17:51:47 +0100
Commit message:

 Merge pull request #253 from sneumann/feature/updatePwiz_3_0_21263

Feature/update pwiz 3 0 21263 
Package: mzR
Commit: f9a44238772c82acff4d35811464491f1cc0930c
Author: Steffen Neumann <sneumann@ipb-halle.de>
Date: 2022-01-25 17:30:31 +0100
Commit message:

 Merge branch 'master' into feature/updatePwiz_3_0_21263 
Package: mzR
Commit: e43067df3f8634b9491f661d2b98122ca168534d
Author: Steffen Neumann <sneumann@ipb-halle.de>
Date: 2022-01-25 10:42:19 +0100
Commit message:

 Cleanup ZLIB from Makevars, enable other arches and disable error on warning in GitHub action, update DESCRIPTION and NEWS
 
Package: mzR
Commit: 9b60d772032ac53dcf56af3fadc16c030a9dd40d
Author: uly55e5 <uly55e5@web.de>
Date: 2022-01-24 18:18:46 +0100
Commit message:

 Fix compile errors by win_check()
 
Package: mzR
Commit: d51b668984ed73cb669d4cb60fe936335a62cf98
Author: uly55e5 <uly55e5@web.de>
Date: 2022-01-19 01:30:42 +0100
Commit message:

 fixed iostream.cpp
 
Package: mzR
Commit: d2f5476d83fa9fd57767a22a46215d8548c97331
Author: Steffen Neumann <sneumann@ipb-halle.de>
Date: 2022-01-18 12:59:27 +0100
Commit message:

 Add iostream.cpp
 
Package: mzR
Commit: d49b824da6a88693c6245c78972302e65d89aba0
Author: Steffen Neumann <sneumann@ipb-halle.de>
Date: 2022-01-18 12:27:30 +0100
Commit message:

 Add winthreads, adopt to changed location of iostream.cpp
 
Package: mzR
Commit: 54422cf9770f0135d6e2f6a069d744d0360c5b46
Author: Steffen Neumann <sneumann@ipb-halle.de>
Date: 2022-01-18 11:55:21 +0100
Commit message:

 Adding algo
 
Package: mzR
Commit: d8aa09b2f35dadfa5c3282035d840151b6fa1d40
Author: Steffen Neumann <sneumann@ipb-halle.de>
Date: 2022-01-18 11:29:09 +0100
Commit message:

 Add more headers for unordered
 
Package: mzR
Commit: 3cb3c128c7344c54fd0db1e87e140c2e8143e8b7
Author: Steffen Neumann <sneumann@ipb-halle.de>
Date: 2022-01-18 10:43:12 +0100
Commit message:

 Add more headers
 
Package: mzR
Commit: 11faef7a98d01d7ae42ba5104797b80b5f3034c6
Author: Steffen Neumann <sneumann@ipb-halle.de>
Date: 2022-01-18 09:33:38 +0100
Commit message:

 Adding IPC detail on windows
 
Package: mzR
Commit: 828c534b878bac9b70fff7519adb667410d041f9
Author: Steffen Neumann <sneumann@ipb-halle.de>
Date: 2022-01-17 14:33:38 +0100
Commit message:

 Adding stream on windows
 
Package: mzR
Commit: 3e92e812232c9c44a621687fa35f1042517ab48a
Author: Steffen Neumann <sneumann@ipb-halle.de>
Date: 2022-01-17 14:07:22 +0100
Commit message:

 Add spinlock on windows
 
Package: mzR
Commit: e07abc799335c05be609b3cbda7fbb8ae6ec45af
Author: Steffen Neumann <sneumann@ipb-halle.de>
Date: 2022-01-17 13:28:34 +0100
Commit message:

 Fix path of windows includes
 
Package: mzR
Commit: a4600bb328f9e1005ec54e1b233a158f075003a1
Author: Steffen Neumann <sneumann@ipb-halle.de>
Date: 2022-01-17 13:00:22 +0100
Commit message:

 Add IPB on windows
 
Package: mzR
Commit: bdfb826b0b0a7ac5e597c5c0f7dd08904c6085d0
Author: Steffen Neumann <sneumann@ipb-halle.de>
Date: 2022-01-14 10:04:24 +0100
Commit message:

 Move disabling INSTALL patches
 
Package: mzR
Commit: 4c79687123dccce1d390489b3f5bfa2bc2f9a510
Author: Steffen Neumann <sneumann@ipb-halle.de>
Date: 2022-01-14 09:22:15 +0100
Commit message:

 Fix env var against install time patches again
 
Package: mzR
Commit: 60306fb03a6e5ba8aef762f20f64a377e2d11290
Author: Steffen Neumann <sneumann@ipb-halle.de>
Date: 2022-01-14 08:05:56 +0100
Commit message:

 Fix Avoid install time patching in github actions
 
Package: mzR
Commit: 8af49c07de1e027ae3babe62cad81c72fb111291
Author: Steffen Neumann <sneumann@ipb-halle.de>
Date: 2022-01-14 07:34:11 +0100
Commit message:

 Avoid install time patching in github actions
 
Package: mzR
Commit: 0132be366bcee9ba850d3c6b76b07aaa0ecd03a7
Author: Steffen Neumann <sneumann@ipb-halle.de>
Date: 2022-01-13 22:44:30 +0100
Commit message:

 avoid use of find in Makevars, breaking windows builds
 
Package: mzR
Commit: 3d7449c099be1f812977afbe8063d3ffe272279a
Author: Steffen Neumann <sneumann@ipb-halle.de>
Date: 2022-01-13 09:17:12 +0100
Commit message:

 Merge remote-tracking branch 'drauh/feature/updatePwiz_3_0_21263' into feature/updatePwiz_3_0_21263
 
Package: mzR
Commit: 942bd2aeaea14b5ca794a1f01464a9074edc683e
Author: uly55e5 <uly55e5@web.de>
Date: 2021-12-09 08:53:32 +0100
Commit message:

 Fix problems with Filesystem.cpp from pwiz #253
 
Package: mzR
Commit: 87322ebb0c6362032626fcc371e83a6d1f3c8108
Author: uly55e5 <uly55e5@web.de>
Date: 2021-12-09 08:51:46 +0100
Commit message:

 Change DESCRIPTION to work with devtools::check_win()
 
Package: mzR
Commit: fbfaeb1a14d5fdd0bb36b90aa43d400d5a9329b7
Author: Steffen Neumann <sneumann@ipb-halle.de>
Date: 2021-11-27 19:51:13 +0100
Commit message:

 don't install dependencies originally added for xcms github action
 
Package: mzR
Commit: a3475bfd58f8e23d87e700b9f7cb62d2d1f686d8
Author: Steffen Neumann <sneumann@ipb-halle.de>
Date: 2021-11-27 18:52:21 +0100
Commit message:

 Revert d76a1fe3601ffdcf4b8a30a535a1e2a442f894e2 and change preprocessor check instead
 
Package: mzR
Commit: 86b5dcddca1e6bb52cc9bbb1ec28dbc6aed5a8a5
Author: Steffen Neumann <sneumann@ipb-halle.de>
Date: 2021-11-27 18:37:38 +0100
Commit message:

 Add some mac stuff
 
Package: mzR
Commit: f8316567b0a97665dc780e8137321be8413ad744
Author: Steffen Neumann <sneumann@ipb-halle.de>
Date: 2021-11-27 17:17:55 +0100
Commit message:

 Adding more win stuff
 
Package: mzR
Commit: a0ee32b052636ffe996dd68c4598f7b463c1c420
Author: Steffen Neumann <sneumann@ipb-halle.de>
Date: 2021-11-27 14:24:19 +0100
Commit message:

 Adding more win stuff
 
Package: mzR
Commit: d76a1fe3601ffdcf4b8a30a535a1e2a442f894e2
Author: Steffen Neumann <sneumann@ipb-halle.de>
Date: 2021-11-27 13:35:29 +0100
Commit message:

 Explicitly and manually define _MSC_VER on Windows
 
Package: mzR
Commit: 1aeecc6485aa9efa42d92ec5f1d8a230184d2076
Author: Steffen Neumann <sneumann@ipb-halle.de>
Date: 2021-11-27 12:11:29 +0100
Commit message:

 Adding more win stuff
 
Package: mzR
Commit: 17ebe8ec2f85696cabe2e103e9d74ec7265a51fd
Author: Steffen Neumann <sneumann@ipb-halle.de>
Date: 2021-11-27 11:23:50 +0100
Commit message:

 Adding more win stuff
 
Package: mzR
Commit: d9219a9ac163b8fc0a7cd3797615d06db9ded315
Author: Steffen Neumann <sneumann@ipb-halle.de>
Date: 2021-11-26 23:31:46 +0100
Commit message:

 Adding winapi
 
Package: mzR
Commit: cfe0e67aa8c2b17a1fe9cf3c8182c2a866211b0a
Author: Steffen Neumann <sneumann@ipb-halle.de>
Date: 2021-11-26 22:38:42 +0100
Commit message:

 Add github actions
 
Package: mzR
Commit: 6f8ec1746d245962784ec666808a8a19501bfe4c
Author: Steffen Neumann <sneumann@ipb-halle.de>
Date: 2021-11-26 18:00:54 +0100
Commit message:

 Merge pull request #254 from jorainer/feature/updatePwiz_3_0_21263

refactor: header always returns a `data.frame` (PR #253) 
Package: mzR
Commit: ee9c964e8fea5787bef034c480a6d5d0b1e2ecc8
Author: jorainer <johannes.rainer@gmail.com>
Date: 2021-11-25 09:27:02 +0100
Commit message:

 refactor: header always returns a `data.frame` (PR #253)

- Fix header for pwiz backend to always return a `data.frame`.
- Update documentation.
 
Package: mzR
Commit: f95a952bc7eaed8073b96a1c35a6b6e04e371f8e
Author: Steffen Neumann <sneumann@ipb-halle.de>
Date: 2021-11-24 17:31:22 +0100
Commit message:

 Merge branch 'master' into feature/updatePwiz_3_0_21263 
Package: mzR
Commit: 899e9e0c6cce52f3d13b5fc49e7678b10f7bc3fe
Author: Steffen Neumann <sneumann@ipb-halle.de>
Date: 2021-11-20 12:19:02 +0100
Commit message:

 Add News
 
Package: mzR
Commit: 7ff9196cddb430fa629acc72c7224687fd980fea
Author: Steffen Neumann <sneumann@ipb-halle.de>
Date: 2021-09-23 17:21:20 +0200
Commit message:

 remove (hopefully) unused directories
 
Package: mzR
Commit: 72fef926d839a747c54664d5735a7b978db59b72
Author: Steffen Neumann <sneumann@ipb-halle.de>
Date: 2021-09-23 14:34:25 +0200
Commit message:

 Updating pwiz to 3_0_21263
 
Package: mzR
Commit: d6c9b8db08bfa61e4a5d3da92cccab196fe53e97
Author: Steffen Neumann <sneumann@ipb-halle.de>
Date: 2021-09-22 12:40:31 +0200
Commit message:

 Removed old pwiz code
 
Package: mzR
Commit: 5fbb9facff8b0888470b365cba141957b4b10f98
Author: Steffen Neumann <sneumann@ipb-halle.de>
Date: 2021-09-20 20:55:47 +0200
Commit message:

 Merge pull request #251 from jorainer/without_ramp

Remove Ramp backend with dependencies 
Package: mzR
Commit: e3f79ff5f7c2a3a52eba6fd416ab11b138a2dd77
Author: jorainer <johannes.rainer@gmail.com>
Date: 2021-09-20 14:19:56 +0200
Commit message:

 Remove Ramp backend with dependencies
 
Package: PhyloProfile
Commit: 745559dd939da14a911bec88fc5e53b5714973e1
Author: trvinh <trvinh@gmail.com>
Date: 2022-01-25 17:47:05 +0100
Commit message:

 added fn for exporting plot settings
 
Package: sesameData
Commit: b5607f01431615043f358736c7341ad2c41c81f1
Author: Wanding Zhou <zhouwanding@gmail.com>
Date: 2022-01-25 11:02:36 -0500
Commit message:

 bump to 1.13.14, caching returns invisible
 
Package: sesameData
Commit: 7e4030fe6f6271316c91c772d547cb8d0070a53a
Author: Wanding Zhou <zhouwanding@gmail.com>
Date: 2022-01-24 10:42:36 -0500
Commit message:

 minor, message omitted
 
Package: MatrixQCvis
Commit: aa48779ad36b70c43498a3056b7ecb6300571c34
Author: tnaake <thomasnaake@gmx.de>
Date: 2022-01-25 16:39:26 +0100
Commit message:

 bump version to 1.3.3
 
Package: MatrixQCvis
Commit: 0b6f4c9e4eab7aa84a97112eea06fb639aab2d8e
Author: tnaake <thomasnaake@gmx.de>
Date: 2022-01-25 15:05:39 +0100
Commit message:

 Update tab_values.R
 
Package: MatrixQCvis
Commit: 54d6a72262b2818ae073db68d58c16426d8a5141
Author: tnaake <thomasnaake@gmx.de>
Date: 2022-01-25 14:56:11 +0100
Commit message:

 add clustering for columns in distSample (heatmap)
 
Package: MatrixQCvis
Commit: b36e9a680cb493952c694f937ac59670f8f12702
Author: tnaake <thomasnaake@gmx.de>
Date: 2022-01-24 11:35:47 +0100
Commit message:

 update biocrates with make.names for colnames
 
Package: mnem
Commit: ca0ad2792229a81a45c8936e4b992b78c99437a3
Author: mpirkl <martinpirkl@yahoo.de>
Date: 2022-01-20 17:05:31 +0100
Commit message:

 fixed a bug for matrix input to plotDnf (edge labels); some internal boxplot adjustments
 
Package: protGear
Commit: 8fe88100aaa155cebfd1bbcbafef572971253b16
Author: Keniajin <keniajin@gmail.com>
Date: 2022-01-25 16:40:43 +0300
Commit message:

 updated the package version
 
Package: monaLisa
Commit: 99fa570a047bc5c01c57bccfcab2eb911448f20e
Author: Michael Stadler <stadler.michael@gmail.com>
Date: 2022-01-25 07:53:25 +0100
Commit message:

 Merge pull request #54 from fmicompbio/add_preprint_to_readme

Updates to monaLisa for revision 
Package: monaLisa
Commit: 0eacd2224921e3777a5ffc9930a3a9dcd0f1c274
Author: machlabd <dania.machlab@gmail.com>
Date: 2022-01-24 17:02:56 +0100
Commit message:

 upadte `NEWS.md` file
 
Package: monaLisa
Commit: b3c8941ed5e900b6deacff6f31f1e0ec080845ba
Author: machlabd <dania.machlab@gmail.com>
Date: 2022-01-24 16:58:01 +0100
Commit message:

 updated `.rds` results file
 
Package: monaLisa
Commit: c8bc658c24aa55fb4a86611e4f2d6e617711b219
Author: machlabd <dania.machlab@gmail.com>
Date: 2022-01-24 16:36:24 +0100
Commit message:

 rephrase variable co-selection in regression vignette
 
Package: monaLisa
Commit: db9ada67e750fd2f4589aa75a7ce8ae32b4f14d9
Author: burgerlu <lukas.burger@fmi.ch>
Date: 2022-01-24 15:12:43 +0100
Commit message:

 small rewordings
 
Package: monaLisa
Commit: dc402d5886579cf3c7d645d087e9d0c3816e35cf
Author: mbstadler <stadler.michael@gmail.com>
Date: 2022-01-24 14:56:42 +0100
Commit message:

 reword KLF result in vignette
 
Package: monaLisa
Commit: f610cd98e787dfd6cd9da4626b30ae388c476db3
Author: machlabd <dania.machlab@gmail.com>
Date: 2022-01-24 14:05:35 +0100
Commit message:

 more main vignette fixes
 
Package: monaLisa
Commit: 3953949ab8aaff9164ac90ab61b01979aae4f0f1
Author: machlabd <dania.machlab@gmail.com>
Date: 2022-01-24 13:40:14 +0100
Commit message:

 fix main vignette
 
Package: monaLisa
Commit: c55fdb00b365af88afbcd5fcd61277b1412bcd56
Author: machlabd <dania.machlab@gmail.com>
Date: 2022-01-24 11:44:30 +0100
Commit message:

 fixed merge conflicts

Merge branch 'add_preprint_to_readme' of github.com:fmicompbio/monaLisa into add_preprint_to_readme

Conflicts:
	vignettes/selecting_motifs_with_randLassoStabSel.Rmd
 
Package: monaLisa
Commit: 8fb6e695bce316e81cf25ee069ed809afb4c8928
Author: machlabd <dania.machlab@gmail.com>
Date: 2022-01-24 11:34:54 +0100
Commit message:

 stabsel vignette fix links to packages and add a sentence on the barplot
 
Package: monaLisa
Commit: 18a8c35195e16a5da49162c64cb7d238b4ee9b98
Author: mbstadler <stadler.michael@gmail.com>
Date: 2022-01-24 11:28:28 +0100
Commit message:

 fix multiline inline r code
 
Package: monaLisa
Commit: 8377cfc3fb508e25ad7c542b6dd02735e877cbe1
Author: mbstadler <stadler.michael@gmail.com>
Date: 2022-01-24 10:55:17 +0100
Commit message:

 minor edits to selecting_motifs_with_randLassoStabSel.Rmd
 
Package: monaLisa
Commit: b6f5359a0effd22aedba498d783d52f75f8473ba
Author: mbstadler <stadler.michael@gmail.com>
Date: 2022-01-24 10:36:09 +0100
Commit message:

 fix RSAT bibtex entry (did not render correctly in vignette)
 
Package: monaLisa
Commit: 048e06516d40e4217f575dfa10191c0dab7e4edd
Author: mbstadler <stadler.michael@gmail.com>
Date: 2022-01-24 10:04:59 +0100
Commit message:

 minor edits to monaLisa.Rmd
 
Package: monaLisa
Commit: 2dc0a73eabe9a8b4c2394a3a739bb6fd7b836498
Author: Charlotte Soneson <charlottesoneson@gmail.com>
Date: 2022-01-23 17:52:58 +0100
Commit message:

 Correct linebreaks in vignettes
 
Package: monaLisa
Commit: aca02917b7258a86c9253117871fb632f77503ca
Author: burgerlu <lukas.burger@fmi.ch>
Date: 2022-01-21 11:43:47 +0100
Commit message:

 sentence in intro with respect to single-set or two-set comparisons
 
Package: monaLisa
Commit: 21d29843ada8affade7919d0a07c594fa02843e6
Author: burgerlu <lukas.burger@fmi.ch>
Date: 2022-01-21 11:34:49 +0100
Commit message:

 rewording some sentences
 
Package: monaLisa
Commit: 14fe99f3427a84e92ebb36bbb40164cb747bfdd9
Author: machlabd <dania.machlab@gmail.com>
Date: 2022-01-20 16:46:28 +0100
Commit message:

 re-arrange text on collinearity and update `NEWS.md`
 
Package: monaLisa
Commit: 500ee1326ca7d89f10862c1f31ef3ba7671c3cc8
Author: machlabd <dania.machlab@gmail.com>
Date: 2022-01-20 14:42:37 +0100
Commit message:

 main vignette: typos, consistency in `package::`, adjust heatmap widths
 
Package: monaLisa
Commit: cfdd6762bd4851a5d1b09baeccfe9fce3896ac0c
Author: mbstadler <stadler.michael@gmail.com>
Date: 2022-01-19 15:31:01 +0100
Commit message:

 fix seeding of random number generator
 
Package: monaLisa
Commit: 29553dc90df82f93e1e68e73488914234c30a6ae
Author: mbstadler <stadler.michael@gmail.com>
Date: 2022-01-19 14:37:45 +0100
Commit message:

 add binary and single-set enrichment analysis examples to vignette
 
Package: monaLisa
Commit: 9d43b954cda8be92a5a79918d8a068c70af56634
Author: machlabd <dania.machlab@gmail.com>
Date: 2022-01-17 19:47:29 +0100
Commit message:

 add comment on the parameter values for stability selection in the vignette
 
Package: monaLisa
Commit: ab614727a6594f147dd9665fd162528fcb3a586b
Author: machlabd <dania.machlab@gmail.com>
Date: 2022-01-17 19:13:15 +0100
Commit message:

 expand on collinearity in stabsel vignette
 
Package: monaLisa
Commit: 7771784b8226f2093a220c0820039abe5787534a
Author: mbstadler <stadler.michael@gmail.com>
Date: 2022-01-17 15:03:31 +0100
Commit message:

 show alternative input example code in eval=FALSE blocks instead of comments; mention how to get scores from bed files
 
Package: monaLisa
Commit: ab0bdc022b62775f4c3a44ef000a104b3947eee2
Author: mbstadler <stadler.michael@gmail.com>
Date: 2022-01-17 14:09:21 +0100
Commit message:

 Merge branch 'add_preprint_to_readme' of github.com:fmicompbio/monaLisa into add_preprint_to_readme
 
Package: monaLisa
Commit: 87afda6f4e1a24f92a7c19d8651dd79d56411e6c
Author: mbstadler <stadler.michael@gmail.com>
Date: 2022-01-17 14:09:16 +0100
Commit message:

 expand discussion of GC-bias in specific bins
 
Package: monaLisa
Commit: 0e75f05d6de6dfae4960b023142b382cb24724f6
Author: machlabd <dania.machlab@gmail.com>
Date: 2022-01-17 13:47:21 +0100
Commit message:

 remove full heatmap in stabsel vignette
 
Package: monaLisa
Commit: 195bf3e1a13526e23b1b55d33a4665483a7f0f2d
Author: machlabd <dania.machlab@gmail.com>
Date: 2022-01-17 13:23:40 +0100
Commit message:

 small fix to main vignette on reading in bed and fasta files
 
Package: monaLisa
Commit: 50ccc780f4870b50a36dcf14ee7af0f5f5bed6b5
Author: mbstadler <stadler.michael@gmail.com>
Date: 2022-01-17 13:15:44 +0100
Commit message:

 Merge branch 'add_preprint_to_readme' of github.com:fmicompbio/monaLisa into add_preprint_to_readme
 
Package: monaLisa
Commit: 58eb1c048c6cad576482c9b743bf5b119000a1ef
Author: machlabd <dania.machlab@gmail.com>
Date: 2022-01-17 12:09:21 +0100
Commit message:

 Merge branch 'add_preprint_to_readme' of github.com:fmicompbio/monaLisa into add_preprint_to_readme
 
Package: monaLisa
Commit: 4e53cdb56a2fe18120fda94297beadd56f346933
Author: machlabd <dania.machlab@gmail.com>
Date: 2022-01-17 12:09:15 +0100
Commit message:

 added unrun code in main vignette showing how to read in bed and fasta files
 
Package: monaLisa
Commit: a89bfecbdb9a89ac6727f92ba6da6183a55085df
Author: mbstadler <stadler.michael@gmail.com>
Date: 2022-01-17 11:59:05 +0100
Commit message:

 Merge branch 'add_preprint_to_readme' of github.com:fmicompbio/monaLisa into add_preprint_to_readme
 
Package: monaLisa
Commit: 4d4fd8eb63e0712eabf82d2664686f4b0a088618
Author: mbstadler <stadler.michael@gmail.com>
Date: 2022-01-17 11:59:01 +0100
Commit message:

 expand description of zero-bin boundary adjustment
 
Package: monaLisa
Commit: d2378144b3901230d2917415a80deba07a065cc2
Author: burgerlu <lukas.burger@fmi.ch>
Date: 2022-01-17 11:45:32 +0100
Commit message:

 small change
 
Package: monaLisa
Commit: df43ba2082b7578bf13f435cbc606c5cb5553889
Author: mbstadler <stadler.michael@gmail.com>
Date: 2022-01-17 11:41:09 +0100
Commit message:

 Merge branch 'add_preprint_to_readme' of github.com:fmicompbio/monaLisa into add_preprint_to_readme
 
Package: monaLisa
Commit: d48a13522d94acf644c0ac3c1da37d4a78965f1b
Author: mbstadler <stadler.michael@gmail.com>
Date: 2022-01-17 11:41:04 +0100
Commit message:

 add reference to AME
 
Package: monaLisa
Commit: 20e46b476babcc3e99983bbf0731b00875c1b110
Author: burgerlu <lukas.burger@fmi.ch>
Date: 2022-01-17 11:40:17 +0100
Commit message:

 changed wording
 
Package: monaLisa
Commit: a4ffddc8a282cc24c156b4666ee51f365dbe608d
Author: burgerlu <lukas.burger@fmi.ch>
Date: 2022-01-17 11:23:45 +0100
Commit message:

 sentence about motif clustering
 
Package: monaLisa
Commit: 165e7244e8cc031f59190229e2d72ea2dcb7ac44
Author: burgerlu <lukas.burger@fmi.ch>
Date: 2022-01-17 10:30:50 +0100
Commit message:

 rewording
 
Package: monaLisa
Commit: 848ae23ce9f9ba98618750de553cc89030abf4eb
Author: Charlotte Soneson <charlottesoneson@gmail.com>
Date: 2022-01-17 09:36:31 +0100
Commit message:

 Add note on database size to vignette
 
Package: monaLisa
Commit: 9ccdea64ca0c6b6c1858382dfc710a0e13185e42
Author: Charlotte Soneson <charlottesoneson@gmail.com>
Date: 2022-01-17 09:21:25 +0100
Commit message:

 Capitalization in README
 
Package: monaLisa
Commit: b5892cff4942226acffaf56813c3eef4207a893c
Author: burgerlu <lukas.burger@fmi.ch>
Date: 2022-01-14 17:06:30 +0100
Commit message:

 Added sentence regarding the minimal number of sequences per bin
 
Package: monaLisa
Commit: 57cd639af5df4c420c10dbcaec046acbc0231435
Author: machlabd <dania.machlab@gmail.com>
Date: 2022-01-11 16:58:20 +0100
Commit message:

 updated `NEWS.md` file
 
Package: monaLisa
Commit: b862deebe3340e40031f02892efa470a0d4ad1ce
Author: machlabd <dania.machlab@gmail.com>
Date: 2022-01-11 15:47:59 +0100
Commit message:

 added `LICENSE.md` file
 
Package: monaLisa
Commit: f6e79ffbbe10c27f3b4fd29e9a5960550df02696
Author: mbstadler <stadler.michael@gmail.com>
Date: 2022-01-11 12:58:49 +0100
Commit message:

 update NEWS.md and bump version
 
Package: monaLisa
Commit: a6a37d27366b432f63a5cc567026a80048932615
Author: mbstadler <stadler.michael@gmail.com>
Date: 2022-01-11 12:52:46 +0100
Commit message:

 add doPlot argument to plotMotifHeatmaps
 
Package: monaLisa
Commit: aaf163608d4e69d29fdbc61843d9819568c3c7c5
Author: mbstadler <stadler.michael@gmail.com>
Date: 2022-01-11 10:44:20 +0100
Commit message:

 warn if zero bin breaks are adjusted more than 20% of minAbsX
 
Package: monaLisa
Commit: d541bbcb48e652cabc05cc3a06fb3a67f791b1c6
Author: machlabd <dania.machlab@gmail.com>
Date: 2022-01-07 10:04:05 +0100
Commit message:

 added `News` section in `README.md` with links
 
Package: monaLisa
Commit: 90b96befd80ab3f113c775e1ba1972e161f98d43
Author: mbstadler <stadler.michael@gmail.com>
Date: 2021-11-12 17:26:21 +0100
Commit message:

 install harfbuzz and fribidi libs on macOS and linux runners
 
Package: monaLisa
Commit: 350c507a20b77a49a3a849cb49cc2c0b1f2e2651
Author: Michael Stadler <stadler.michael@gmail.com>
Date: 2021-11-08 11:34:21 +0100
Commit message:

 Merge pull request #53 from fmicompbio/use_r_devel_on_gha

use R devel on GHA 
Package: monaLisa
Commit: e95216b09a6c41e72d12f4ffff1fd3fb3bfcc418
Author: mbstadler <stadler.michael@gmail.com>
Date: 2021-11-01 08:42:26 +0100
Commit message:

 use R devel on GHA
 
Package: protGear
Commit: bedcceaf777bde8712451288ba64605f0003d681
Author: Keniajin <keniajin@gmail.com>
Date: 2022-01-25 16:28:18 +0300
Commit message:

 updated the package version
 
Package: protGear
Commit: c6556819d8e9d2d166b837a7a73c7761d08e6995
Author: Keniajin <keniajin@gmail.com>
Date: 2022-01-25 12:40:39 +0300
Commit message:

 removed gitignore files
 
Package: synergyfinder
Commit: 557d5fc376f99f1a77cdb8079079274e5cb96f90
Author: Shuyu <shuyu.zheng@helsinki.fi>
Date: 2022-01-25 14:36:49 +0200
Commit message:

 Update version number to 3.3.5
 
Package: synergyfinder
Commit: 20fe317fe10d00309be391f7fac23f33187a645e
Author: Shuyu <shuyu.zheng@helsinki.fi>
Date: 2022-01-25 14:30:44 +0200
Commit message:

 Let user to set random "seed" for imputation in ReshapeData function
 
Package: synergyfinder
Commit: 19d36fc4e5d2ccd023305c14c44f32c895ed8760
Author: Shuyu <shuyu.zheng@helsinki.fi>
Date: 2022-01-13 19:41:31 +0200
Commit message:

 Update version to 3.2.4
 
Package: synergyfinder
Commit: 1995448fbe20d289b6ff193fee2f90a7afcffd82
Author: Shuyu <shuyu.zheng@helsinki.fi>
Date: 2022-01-05 16:43:11 +0200
Commit message:

 Update version number to 3.2.3
 
Package: synergyfinder
Commit: a315d608a5ff99ef1975d6e368ec25223fadb8cb
Author: Shuyu <shuyu.zheng@helsinki.fi>
Date: 2021-10-28 13:05:42 +0300
Commit message:

 update version number to 3.2.2
 
Package: synergyfinder
Commit: 9bf552a06c4355d933afd80e9e26c405192447a0
Author: Shuyu <shuyu.zheng@helsinki.fi>
Date: 2021-10-27 16:49:54 +0300
Commit message:

 update version number to 3.2.1
 
Package: Rhdf5lib
Commit: 1a1a86e7ace1c7e2dda25f9ac976d075a06c2e82
Author: Mike Smith <grimbough@gmail.com>
Date: 2022-01-25 11:33:22 +0100
Commit message:

 Configure linux runner with libcurl
 
Package: Rhdf5lib
Commit: 8cd8613161daa0d7c04d91cc56b98f7db57f51ab
Author: Mike Smith <grimbough@gmail.com>
Date: 2022-01-25 10:49:43 +0100
Commit message:

 Update NEWS
 
Package: Rhdf5lib
Commit: 51253447408e8a223a2a080e8a1ccb3cec60180f
Author: Mike Smith <grimbough@gmail.com>
Date: 2022-01-25 10:45:42 +0100
Commit message:

 Update NEWS
 
Package: Rhdf5lib
Commit: f2bdcc76ebb5d9ce0fd94ae4a941cb58e50cc641
Author: Mike Smith <grimbough@gmail.com>
Date: 2022-01-25 10:43:44 +0100
Commit message:

 Version bump
 
Package: Rhdf5lib
Commit: acbff6248872c05f43130004d05bb61a29a6e353
Author: Mike Smith <grimbough@gmail.com>
Date: 2022-01-25 10:43:21 +0100
Commit message:

 Fix libaec autotools settings
 
Package: Rhdf5lib
Commit: a26bbda1b5d5cc95c2a17f8c6278b1fec2f8b8c0
Author: Mike Smith <grimbough@gmail.com>
Date: 2022-01-24 19:20:16 +0100
Commit message:

 Try capturing config log as artifact
 
Package: Rhdf5lib
Commit: b406adedc325b14f8611031fccf430f98bf4e686
Author: Mike Smith <grimbough@gmail.com>
Date: 2022-01-24 17:46:25 +0100
Commit message:

 Add linux rhdf5 test
 
Package: Rhdf5lib
Commit: c14c23d68cdb25306572b1c7b978c99d82b75606
Author: Mike Smith <grimbough@gmail.com>
Date: 2022-01-24 17:46:15 +0100
Commit message:

 Try using libaec instead of libsz
 
Package: protGear
Commit: fd64ad63a2999048ed3b60ce1ee35a0500bf6089
Author: Keniajin <keniajin@gmail.com>
Date: 2022-01-25 11:54:05 +0300
Commit message:

 updated the package version
 
Package: protGear
Commit: 5b66521a8c13cc69e9a4b2647b76104f760e6aa4
Author: Keniajin <keniajin@gmail.com>
Date: 2022-01-25 10:59:38 +0300
Commit message:

 commit bioc
 
Package: ASEB
Commit: 4e78e48eede2b997fde8bca048b40bc6b7d04a1e
Author: Likun Wang <wanglikun@tsinghua.edu.cn>
Date: 2022-01-25 16:50:28 +0800
Commit message:

 Chang email
 
Package: signatureSearch
Commit: 6833e725048beb73e14ddd1ace6fbc438ebdffa3
Author: Yuzhu Duan <yduan004@ucr.edu>
Date: 2022-01-25 00:10:53 -0800
Commit message:

 add cell info 2
 
Package: signatureSearch
Commit: 16e80d65391003fddcc28038c451a71c03391e9b
Author: Yuzhu Duan <yduan004@ucr.edu>
Date: 2022-01-24 22:47:21 -0800
Commit message:

 update lincs_pert_info2
 
Package: ASEB
Commit: a04a8c3f80e597d07af1acd90af2e735c87a433c
Author: Likun Wang <wanglikun@tsinghua.edu.cn>
Date: 2022-01-25 13:18:55 +0800
Commit message:

 Fix a bug (-> as.numeric(indexes[max_y_index+1]))
 
Package: ASEB
Commit: 339c29cd7ec238a57c4796baa7ccf7153acdf15d
Author: Likun Wang <wanglikun@tsinghua.edu.cn>
Date: 2022-01-25 10:48:39 +0800
Commit message:

 Fix a bug -> as.numeric(indexes[max_y_index+1])
 
Package: SCArray
Commit: 05a49f7c40e0dc5b467065bcf41953b2f289b9a3
Author: Xiuwen Zheng <zhengxwen@gmail.com>
Date: 2022-01-24 17:39:01 -0600
Commit message:

 new Overview.Rmd
 
Package: protGear
Commit: e3955eafda850cb57819b07c359a2cca342c4c31
Author: keniajin <keniajin@gmail.com>
Date: 2022-01-20 11:51:01 +0300
Commit message:

 updated vignette file
 
Package: GenomicSuperSignature
Commit: b0852c5ca4c9d540cebb9201bede253c3585a21f
Author: Sehyun Oh <shbrief@hotmail.com>
Date: 2022-01-24 15:14:06 -0500
Commit message:

 version bump
 
Package: GenomicSuperSignature
Commit: 15d4d39532459e63807c651fe0202097fc1c6811
Author: Sehyun Oh <shbrief@hotmail.com>
Date: 2022-01-24 15:10:33 -0500
Commit message:

 new functions to extract basic metadata of study and RAV
 
Package: GenomicSuperSignature
Commit: 212c6f32baf60460d69f0efa67a29b880ef44cbd
Author: Sehyun Oh <shbrief@hotmail.com>
Date: 2022-01-24 15:04:58 -0500
Commit message:

 subsetEnrichedPathways function returns NES
 
Package: GenomicSuperSignature
Commit: 4ce674dd68e49f6b79baf02970154783509ab13b
Author: Sehyun Oh <shbrief@hotmail.com>
Date: 2021-12-16 16:58:11 -0500
Commit message:

 cleaning some accessory scripts
 
Package: MsBackendMassbank
Commit: 72cbbc1d57ffa0fb2d35b7f8252eb5e38277216a
Author: Johannes Rainer <5506112+jorainer@users.noreply.github.com>
Date: 2022-01-24 17:09:15 +0100
Commit message:

 Merge pull request #40 from rformassspectrometry/jomain

Jomain 
Package: MsBackendMassbank
Commit: 1bad846e6ff5517f6850190d9a851704797001b3
Author: jorainer <johannes.rainer@gmail.com>
Date: 2022-01-19 12:14:41 +0100
Commit message:

 fix: adapt to new unit tests
 
Package: MsBackendMassbank
Commit: aa3e56ab433996a48f3449b3f7dd59c4e6e3290b
Author: jorainer <johannes.rainer@gmail.com>
Date: 2022-01-19 10:50:20 +0100
Commit message:

 Merge branch 'master' into jomain
 
Package: MsBackendMassbank
Commit: cc978fbb048085781de327f3e79f96685c583c3d
Author: jorainer <johannes.rainer@gmail.com>
Date: 2021-11-25 14:15:25 +0100
Commit message:

 tests: include unit tests from Spectra
 
Package: MsBackendMgf
Commit: 63b2c7e9c4ce35dd2cad42510074dec07ce41905
Author: jorainer <johannes.rainer@gmail.com>
Date: 2022-01-24 15:51:11 +0100
Commit message:

 ci: switch to R devel and BioC 3.15
 
Package: atena
Commit: 39e3bde52f7ef90b288de8891fe93cd550a2e80f
Author: beacalvo <beacalvo96@gmail.com>
Date: 2022-01-24 18:14:51 +0100
Commit message:

 Added warning when no multi-mapping reads are identified
 
Package: atena
Commit: 3ec77ef9e195cbb237abae78b8c310e3f36f0b52
Author: beacalvo <beacalvo96@gmail.com>
Date: 2022-01-24 17:34:53 +0100
Commit message:

 Improved read length computation when fragments=TRUE
 
Package: atena
Commit: d3af3b32f9dfa6cb321c341f414daf0b8309955f
Author: beacalvo <beacalvo96@gmail.com>
Date: 2022-01-24 16:10:11 +0100
Commit message:

 Modified .correctPreference to avoid error when only 1 read overlaps a TE and a gene
 
Package: atena
Commit: 577a9153b38f42aba00e252573f93cfa482a23a6
Author: beacalvo <beacalvo96@gmail.com>
Date: 2022-01-24 15:20:54 +0100
Commit message:

 Modified .correctPreference to avoid error when only 1 read overlaps a TE and a gene
 
Package: atena
Commit: 790d431d860b4920ce412e614701a3240eec1cbd
Author: beacalvo <beacalvo96@gmail.com>
Date: 2022-01-24 13:25:47 +0100
Commit message:

 Adapting .getOverlapLength for when gene counts are also quantified
 
Package: atena
Commit: 03270bd3722279b2e90a528594afa71ff5f1c61c
Author: beacalvo <beacalvo96@gmail.com>
Date: 2022-01-24 13:20:55 +0100
Commit message:

 Adapting .getOverlapLength for when gene counts are also quantified
 
Package: atena
Commit: 69e104ecd7d310684fbd2d322ebb6c2cbc5e283c
Author: beacalvo <beacalvo96@gmail.com>
Date: 2022-01-24 12:54:43 +0100
Commit message:

 Added error when gene annotations have no identifiers
 
Package: MethReg
Commit: 59d90a9685742e95348ae9f09c3b691c3bff3ed3
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2022-01-24 11:03:38 -0500
Commit message:

 Adding more info in the table: distance and target region
 
Package: sesame
Commit: 29eb4349bad4a653e8af302ce8626202a34a3a1f
Author: Wanding Zhou <zhouwanding@gmail.com>
Date: 2022-01-24 10:44:25 -0500
Commit message:

 bump to 1.13.17
 
Package: sesame
Commit: 31b6deae53e629407e9baf6195efd5c24d61e69e
Author: Wanding Zhou <zhouwanding@gmail.com>
Date: 2022-01-23 21:32:35 -0500
Commit message:

 fix platform caching
 
Package: sesame
Commit: 8b38e112cb82712344b3da7785d7fed131f7c621
Author: Wanding Zhou <zhouwanding@gmail.com>
Date: 2022-01-22 09:55:11 -0500
Commit message:

 fixing a documentation bug
 
Package: sesame
Commit: 62f42682a6ba2115a3db0ec37a3f63bce777a4fb
Author: Wanding Zhou <zhouwanding@gmail.com>
Date: 2022-01-21 22:07:55 -0500
Commit message:

 minor, message omitted
 
Package: sesame
Commit: 654cdfb6c2519073e32879a99ea9b8524470136f
Author: Wanding Zhou <zhouwanding@gmail.com>
Date: 2022-01-21 17:53:15 -0500
Commit message:

 bump to 1.13.16
 
Package: sesame
Commit: d14be0c85c2ac74c6a790d63bcb4abb0549febe7
Author: Wanding Zhou <zhouwanding@gmail.com>
Date: 2022-01-21 11:49:47 -0500
Commit message:

 inferStrain before cleaning
 
Package: sesame
Commit: 6d1ffdb049567ff6b7afb994238a25c1a19d5e3c
Author: Wanding Zhou <zhouwanding@gmail.com>
Date: 2022-01-20 09:28:44 -0500
Commit message:

 performance improvement to inferSpecies
 
Package: sesame
Commit: cb30d7ea3730be5dd1a57edf77c8207bf82db656
Author: Wanding Zhou <zhouwanding@gmail.com>
Date: 2022-01-19 11:48:59 -0500
Commit message:

 minor, message omitted
 
Package: sesameData
Commit: 66b1d684122bfb9e9c9b2d9c600dd586c3f57aa5
Author: Wanding Zhou <zhouwanding@gmail.com>
Date: 2022-01-24 10:40:54 -0500
Commit message:

 bump to 1.13.13
 
Package: sesameData
Commit: 0458aa4f95f7c727ca40b455b3d4a91b29ed1100
Author: Wanding Zhou <zhouwanding@gmail.com>
Date: 2022-01-23 21:25:20 -0500
Commit message:

 bump to 1.13.12
 
Package: compcodeR
Commit: 730c4d010c6bd8bdc820aed90dc5528da8ab2502
Author: Charlotte Soneson <charlottesoneson@gmail.com>
Date: 2022-01-24 12:27:05 +0100
Commit message:

 Merge pull request #14 from csoneson/phylocomp

Phylocomp 
Package: compcodeR
Commit: 361f261adce04e30e9426da32eab3972a5cbc16d
Author: Charlotte Soneson <charlottesoneson@gmail.com>
Date: 2022-01-24 11:21:35 +0100
Commit message:

 Bump version
 
Package: compcodeR
Commit: 406040b0d3a6cf6b2a5a2d446d03f5f5688b9c29
Author: Charlotte Soneson <charlottesoneson@gmail.com>
Date: 2022-01-24 11:16:32 +0100
Commit message:

 Merge pull request #13 from pbastide/toCompcodeR

Update citation with preprint. 
Package: compcodeR
Commit: faffdef98bd9fc35e42bbc52e49646403eb88d91
Author: Paul Bastide <paul.bastide@gmail.com>
Date: 2022-01-24 09:15:02 +0100
Commit message:

 Update citation with preprint.
 
Package: compcodeR
Commit: e646f441fe87234801b1c22db0140aa18bec3143
Author: Charlotte Soneson <charlottesoneson@gmail.com>
Date: 2021-11-30 20:05:50 +0100
Commit message:

 Merge pull request #11 from pbastide/toCompcodeR

Remove flawed rpois_robust 
Package: compcodeR
Commit: 0c1f4e750008fd6f669f38002a50266ce1850663
Author: Paul Bastide <paul.bastide@gmail.com>
Date: 2021-11-30 10:58:17 +0100
Commit message:

 DESeq2.length.results -> DESeq2.results
 
Package: compcodeR
Commit: 82ffb870b41b9cbdcabff577e746d985540ac44b
Author: Paul Bastide <paul.bastide@gmail.com>
Date: 2021-11-25 09:20:06 +0100
Commit message:

 More param inheritance.
 
Package: compcodeR
Commit: 34d9948cece2acab9f99bf425399995fa4bc482e
Author: Paul Bastide <paul.bastide@gmail.com>
Date: 2021-11-25 09:11:10 +0100
Commit message:

 Add nas.as.ones in DESeq2.createRmd and remove some roxygen redundancy.
 
Package: compcodeR
Commit: d7b744477a9f1b34153bcf7ac26e485cdea35e0e
Author: Paul Bastide <paul.bastide@gmail.com>
Date: 2021-11-24 17:03:23 +0100
Commit message:

 nas_as_ones -> nas.as.ones
 
Package: compcodeR
Commit: 3fba209b4379824f84e3f6a7e9e8441bd7dbd0b0
Author: Paul Bastide <paul.bastide@gmail.com>
Date: 2021-11-24 11:08:09 +0100
Commit message:

 Dependency on phytools for tests.
 
Package: compcodeR
Commit: fd26b74c1b9487eee71af4585261ba265574dab2
Author: Paul Bastide <paul.bastide@gmail.com>
Date: 2021-11-24 10:21:37 +0100
Commit message:

 Allow prop.var.tree to be a vector.
 
Package: compcodeR
Commit: ebe2728d549fa6177c86e3f6563dde8b04802868
Author: Paul Bastide <paul.bastide@gmail.com>
Date: 2021-11-22 18:28:23 +0100
Commit message:

 Add message for nas_to_ones argument.
 
Package: compcodeR
Commit: 30f98c4f5f058262c598ad93a94e5224e3ef210f
Author: Paul Bastide <paul.bastide@gmail.com>
Date: 2021-11-22 10:11:33 +0100
Commit message:

 Add an option to set NAs padj to 1 in DESeq2.
 
Package: compcodeR
Commit: 49e6ea8e69995d633ff7f51e71c9728ce51b1587
Author: Paul Bastide <paul.bastide@gmail.com>
Date: 2021-11-22 09:33:09 +0100
Commit message:

 Add some correlation tests
 
Package: compcodeR
Commit: b8778408d7051089faec8c70a2e265a897822b7d
Author: Paul Bastide <paul.bastide@gmail.com>
Date: 2021-11-22 09:12:53 +0100
Commit message:

 rpois_robust is not needed since R 4.0
 
Package: compcodeR
Commit: 3d2c3790c60584219bd1891cbdb3b014506b7441
Author: Paul Bastide <paul.bastide@gmail.com>
Date: 2021-11-22 09:08:54 +0100
Commit message:

 Correct error in rpois_robust
 
Package: compcodeR
Commit: 2554cd8f1de9d6e289f7a82019dc9e45c5e34819
Author: Paul Bastide <paul.bastide@gmail.com>
Date: 2021-11-22 09:07:31 +0100
Commit message:

 Remove dependency to viridis package.
 
Package: compcodeR
Commit: 44a82c9ae36b8feb2d18c8e9df44c51c5c431984
Author: Charlotte Soneson <charlottesoneson@gmail.com>
Date: 2021-11-10 18:05:12 +0100
Commit message:

 Safeguarding in the data summary report
 
Package: compcodeR
Commit: 1648bebad7cc9282a33fd96528b0c96544e5170b
Author: Charlotte Soneson <charlottesoneson@gmail.com>
Date: 2021-11-06 09:16:22 +0100
Commit message:

 Merge pull request #10 from pbastide/toCompcodeR

More tests 
Package: compcodeR
Commit: e5dabd2451f7abd5b0352a92ec6b0bcd6ada7a99
Author: Paul Bastide <paul.bastide@gmail.com>
Date: 2021-11-03 11:45:31 +0100
Commit message:

 Add statmod in suggest, required for correlation modelling in limma.
 
Package: compcodeR
Commit: feb8c2c6ba100d8169e4e4c8e6530fe57a8f9578
Author: Paul Bastide <paul.bastide@gmail.com>
Date: 2021-11-03 09:27:42 +0100
Commit message:

 More tests and correction in covariate handling.
 
Package: compcodeR
Commit: 5d0fb6d1137c4ce8765f30cf442e891df96adaaf
Author: Paul Bastide <paul.bastide@gmail.com>
Date: 2021-11-02 16:07:08 +0100
Commit message:

 More tests.
 
Package: compcodeR
Commit: aef6c7ae5f4d31b611ef7a4c1c2a5e4bb014dde8
Author: Paul Bastide <paul.bastide@gmail.com>
Date: 2021-11-02 16:06:53 +0100
Commit message:

 Test and slight refactor on phyloCompData class checks.
 
Package: compcodeR
Commit: 69d793d065b718b68f2776a018ffe3591cf3d06b
Author: Paul Bastide <paul.bastide@gmail.com>
Date: 2021-11-02 11:49:58 +0100
Commit message:

 Add covr in suggest
 
Package: compcodeR
Commit: a2e847e52958afa1ced32c8ade2be62029923a40
Author: Paul Bastide <paul.bastide@gmail.com>
Date: 2021-11-02 11:00:50 +0100
Commit message:

 Add tests for generateSyntheticData and runDiffExpr with phylo tree.
 
Package: compcodeR
Commit: 67375b349c03b7f743c48cffc0207e85d77862b7
Author: Paul Bastide <paul.bastide@gmail.com>
Date: 2021-11-02 10:01:24 +0100
Commit message:

 Remove deprecated option from phylolm.
 
Package: compcodeR
Commit: 2ef38b14a371bf2fbff5aab3fedf5e30ee6ba659
Author: Charlotte Soneson <charlottesoneson@gmail.com>
Date: 2021-10-30 14:25:32 +0200
Commit message:

 Updates from upstream

Merge branch 'master' into phylocomp

# Conflicts:
#	.github/workflows/R-CMD-check.yaml
#	DESCRIPTION
 
Package: compcodeR
Commit: 7d50e6985a063b72bcf524cdbd9e8935afdd86a8
Author: Charlotte Soneson <charlottesoneson@gmail.com>
Date: 2021-10-30 14:22:29 +0200
Commit message:

 Use ubuntu-latest on GHA
 
Package: compcodeR
Commit: d22c17901497adb2366422bcd90984074c1ffbae
Author: Charlotte Soneson <charlottesoneson@gmail.com>
Date: 2021-10-30 14:20:16 +0200
Commit message:

 Use R devel on GHA
 
Package: compcodeR
Commit: d9683d2505838d47df686ea7755fe9b403e1c922
Author: Charlotte Soneson <charlottesoneson@gmail.com>
Date: 2021-10-24 21:51:41 +0200
Commit message:

 Use ubuntu-latest on GHA
 
Package: compcodeR
Commit: 541ad97e64f362e6e3f1df5c171fa286199175f2
Author: Charlotte Soneson <charlottesoneson@gmail.com>
Date: 2021-10-24 21:48:58 +0200
Commit message:

 Merge pull request #8 from pbastide/toCompcodeR

Add inter-species RNA-Seq data simulation to compcodeR 
Package: compcodeR
Commit: a0911fd9a26925d093919421ad4fb2954a3da013
Author: Paul Bastide <paul.bastide@gmail.com>
Date: 2021-10-22 16:06:05 +0200
Commit message:

 Change version to 1.29.1
 
Package: compcodeR
Commit: b75ae90c4a0fbefba4353adbbdb808342faa126d
Author: Paul Bastide <paul.bastide@gmail.com>
Date: 2021-10-04 12:36:26 +0200
Commit message:

 Skip tests individually
 
Package: compcodeR
Commit: 1b486b27d838a6a2e652492606619edf900c2d3f
Author: Paul Bastide <paul.bastide@gmail.com>
Date: 2021-10-04 10:49:21 +0200
Commit message:

 Authors and news
 
Package: compcodeR
Commit: ce641d2328d0689ca5d077534b344f54fc0d6105
Author: Paul Bastide <paul.bastide@gmail.com>
Date: 2021-10-04 10:48:29 +0200
Commit message:

 Use dedicated functions in getNegativeBinomialParameters
 
Package: compcodeR
Commit: 583153f0b5e17300a1ce9cd9beee04c5405449ae
Author: Paul Bastide <paul.bastide@gmail.com>
Date: 2021-10-01 18:58:20 +0200
Commit message:

 Accessor functions, clarified doc and typos.
 
Package: compcodeR
Commit: c4b2d225b9648f8e8548a5d4868af85eb5e5e2d2
Author: Paul Bastide <paul.bastide@gmail.com>
Date: 2021-10-01 18:22:17 +0200
Commit message:

 Remove un-needed duplicated tree file.
 
Package: compcodeR
Commit: 430bebc72fecccf46ea745dab77113ec39cf1ae8
Author: Paul Bastide <paul.bastide@gmail.com>
Date: 2021-10-01 17:52:35 +0200
Commit message:

 compData to phyloCompData for phylo or length methods.
 
Package: compcodeR
Commit: 3c74a6b7384c20ab03e873c1ad43cf22cc63cac0
Author: Paul Bastide <paul.bastide@gmail.com>
Date: 2021-10-01 17:41:38 +0200
Commit message:

 Change camelCase to dot separeted arguments for consistency.
 
Package: compcodeR
Commit: 55aa274cd296bcec8a63cbafc6c5e087fc486958
Author: Paul Bastide <paul.bastide@gmail.com>
Date: 2021-10-01 17:26:05 +0200
Commit message:

 extraDesignFactor -> extra.design.covariates, with (hopefully) better doc.
 
Package: compcodeR
Commit: ef57471c68a6ba071b32991d0c17533218050b7a
Author: Paul Bastide <paul.bastide@gmail.com>
Date: 2021-10-01 16:56:03 +0200
Commit message:

 Remove "divByLengths" option.
 
Package: compcodeR
Commit: bde34f7243cc244f19cf8ef80d38b3822a41b897
Author: Paul Bastide <paul.bastide@gmail.com>
Date: 2021-09-30 16:37:30 +0200
Commit message:

 Taking CS comments into account in phyloCompData class deffinition, with better doc and examples.
 
Package: compcodeR
Commit: 94dfeae345737fb3631ef408477dc386c64aecad
Author: Paul Bastide <paul.bastide@gmail.com>
Date: 2021-09-20 09:53:13 +0200
Commit message:

 Add some details in the doc.
 
Package: compcodeR
Commit: ab147f6b0ff957c5e3adca570cb2573b790ace20
Author: Paul Bastide <paul.bastide@gmail.com>
Date: 2021-09-17 17:46:33 +0200
Commit message:

 Some spell check.
 
Package: compcodeR
Commit: 74c5af3ed16aa5d19faf25433fe830e03e9bf430
Author: Paul Bastide <paul.bastide@gmail.com>
Date: 2021-09-17 17:32:44 +0200
Commit message:

 Restaure default behaviour deleting the Rmd file.
 
Package: compcodeR
Commit: c636c77bc6192bf156d038f8a1313335740cf2d5
Author: Paul Bastide <paul.bastide@gmail.com>
Date: 2021-09-17 16:52:11 +0200
Commit message:

 Clean up the doc.
 
Package: compcodeR
Commit: 5148395ab283f72a3fe117efeebb8e84f0666044
Author: Paul Bastide <paul.bastide@gmail.com>
Date: 2021-09-17 15:19:04 +0200
Commit message:

 Remove compcodeR from Suggests
 
Package: compcodeR
Commit: 2f0993db29065919031b152ac0b37f88b1539061
Author: Paul Bastide <paul.bastide@gmail.com>
Date: 2021-09-17 15:10:58 +0200
Commit message:

 Rename phylocompcodeR -> compcodeR
 
Package: compcodeR
Commit: 311bae7770546cb5a21ec32d7efdfa7c8694db85
Author: Paul Bastide <paul.bastide@gmail.com>
Date: 2021-09-17 14:06:02 +0200
Commit message:

 Remove dependency to phylolimma
 
Package: compcodeR
Commit: 8f43b1a6347f0b8e66793ec0d64bbc328f109f26
Author: Paul Bastide <paul.bastide@gmail.com>
Date: 2021-09-17 13:41:31 +0200
Commit message:

 Clean up some no longer used functions.
 
Package: compcodeR
Commit: ce466f1058a3db7470f30c3c2a34426f740799b8
Author: Paul Bastide <paul.bastide@gmail.com>
Date: 2021-09-17 13:37:26 +0200
Commit message:

 Clean up some commented code.
 
Package: compcodeR
Commit: 234b498ead9b9989428ee6e9f372a96098379328
Author: Paul Bastide <paul.bastide@gmail.com>
Date: 2021-08-19 17:56:38 +0200
Commit message:

 Add vignette on phylocompcodeR.
 
Package: compcodeR
Commit: 601082d55f63a38835ec75cd07e715e55468d5d7
Author: Paul Bastide <paul.bastide@gmail.com>
Date: 2021-08-18 11:32:32 +0200
Commit message:

 Merge remote-tracking branch 'upstream/master'
 
Package: compcodeR
Commit: c842336d4b4403dc84a713a7ece4f47952bc4c36
Author: Paul Bastide <paul.bastide@gmail.com>
Date: 2021-08-18 11:20:20 +0200
Commit message:

 FiX test.
 
Package: compcodeR
Commit: 1ca7b7bc0439ee01168fe20a1a5baa5594935a70
Author: Paul Bastide <paul.bastide@gmail.com>
Date: 2021-08-18 10:48:58 +0200
Commit message:

 Typo in limma trend
 
Package: compcodeR
Commit: 432350563194f77229d7aa56c29f5afd88986389
Author: Paul Bastide <paul.bastide@gmail.com>
Date: 2021-08-18 10:48:46 +0200
Commit message:

 Add some variance tests.
 
Package: compcodeR
Commit: c2c761215e5105da0df87e25fb12e98d0f7dd6e9
Author: Paul Bastide <paul.bastide@gmail.com>
Date: 2021-04-19 18:37:19 +0200
Commit message:

 Add tests of moments.
 
Package: compcodeR
Commit: 1c8571ab49505221629041f616b0e1c11f7b4095
Author: Paul Bastide <paul.bastide@gmail.com>
Date: 2021-04-01 14:34:52 +0200
Commit message:

 Correct some typos.
 
Package: compcodeR
Commit: b714c64ce3ac69b42ab95f6e340da36ffc6f5840
Author: Paul Bastide <paul.bastide@gmail.com>
Date: 2021-03-24 13:58:10 +0100
Commit message:

 Add trend option for limma.
 
Package: compcodeR
Commit: 14834db2b60b2875c183d993524d7db0b7be5618
Author: Paul Bastide <paul.bastide@gmail.com>
Date: 2021-03-12 18:40:59 +0100
Commit message:

 Get tree correctly.
 
Package: compcodeR
Commit: a80ab55a3856d860e69b5a6ec5d4b602986fc008
Author: Paul Bastide <paul.bastide@gmail.com>
Date: 2021-03-12 18:29:36 +0100
Commit message:

 Stern data.
 
Package: compcodeR
Commit: 1eb409b8c85c12b28c7d3d96705c6aef50ba95b0
Author: Paul Bastide <paul.bastide@gmail.com>
Date: 2021-03-12 16:39:33 +0100
Commit message:

 Add Stern data.
 
Package: compcodeR
Commit: 1f95ec9bb24f95aa73f1c91d31e631da3edb9e91
Author: Paul Bastide <paul.bastide@gmail.com>
Date: 2021-03-12 16:39:14 +0100
Commit message:

 Add "auto" mode for lengths, based on Stern data.
 
Package: compcodeR
Commit: 29a2d17b197a0390dbcc8fc76fe997b93b84e32f
Author: Paul Bastide <paul.bastide@gmail.com>
Date: 2021-03-11 19:03:59 +0100
Commit message:

 Create a "phyloCompData" object.
 
Package: compcodeR
Commit: f3bd5904d1a45ff8775d3e1fcbb85630df2f0ead
Author: Paul Bastide <paul.bastide@gmail.com>
Date: 2021-03-10 16:54:31 +0100
Commit message:

 Skip tests if suggested packages are not installed.
 
Package: compcodeR
Commit: d5029af0805965c915a7e897472f7793f270d444
Author: Paul Bastide <paul.bastide@gmail.com>
Date: 2021-03-10 16:29:42 +0100
Commit message:

 Skip test if phylolimma not installed.
 
Package: compcodeR
Commit: 35ada89b940aee54489b63339d02072571c54f7b
Author: Paul Bastide <paul.bastide@gmail.com>
Date: 2021-03-10 15:46:33 +0100
Commit message:

 Some clean up in Rmd Code Diff Exp.
 
Package: compcodeR
Commit: c0a5045fdba64b25dba75cbb623464e372b6f9c0
Author: Paul Bastide <paul.bastide@gmail.com>
Date: 2021-02-19 14:17:05 +0100
Commit message:

 Test variances in phylolm / Rphylopars comparison.
 
Package: compcodeR
Commit: f56c831987491a642301e6490830d199821405f3
Author: Paul Bastide <paul.bastide@gmail.com>
Date: 2021-02-05 10:18:14 +0100
Commit message:

 use_eBayes option.
 
Package: compcodeR
Commit: 1b8a686aa4c5d9162fbc463ae03e7ee176f68ce2
Author: Paul Bastide <paul.bastide@gmail.com>
Date: 2021-01-29 16:48:13 +0100
Commit message:

 Merge remote-tracking branch 'upstream/master'
 
Package: compcodeR
Commit: 8ec1ba97fef97b7a0556c2ce666e46a543e272a1
Author: Paul Bastide <paul.bastide@gmail.com>
Date: 2021-01-29 16:40:42 +0100
Commit message:

 Few tweaks to function to call phylolimma.
 
Package: compcodeR
Commit: e403881be22fc95ea0c2800d5157cb702e823252
Author: Paul Bastide <paul.bastide@gmail.com>
Date: 2021-01-28 11:32:14 +0100
Commit message:

 Trying to fix GHA on macOS.
 
Package: compcodeR
Commit: 0fc208a937d1362c376567bf2b63b073609e912a
Author: Paul Bastide <paul.bastide@gmail.com>
Date: 2021-01-28 09:57:11 +0100
Commit message:

 Merge remote-tracking branch 'upstream/master'
 
Package: compcodeR
Commit: 597ff500fb250b434e8677dca3c255df2a168cdd
Author: Paul Bastide <paul.bastide@gmail.com>
Date: 2021-01-26 16:53:52 +0100
Commit message:

 Using phylolimma
 
Package: compcodeR
Commit: 724fc382b6470826fd696996c8fcc276500b5426
Author: Paul Bastide <paul.bastide@gmail.com>
Date: 2021-01-18 15:38:24 +0100
Commit message:

 Add possible block structure for species in limma.
 
Package: compcodeR
Commit: f8736f16c1e8255046935c737eb5e0fd765a5aa6
Author: Paul Bastide <paul.bastide@gmail.com>
Date: 2021-01-08 14:52:09 +0100
Commit message:

 Filter length matrix only if it exists.
 
Package: compcodeR
Commit: d3f1d4ac7cb479c6688e360712d7b20277a4f10c
Author: Paul Bastide <paul.bastide@gmail.com>
Date: 2021-01-08 12:21:19 +0100
Commit message:

 Use only TPM in simulation diagnostic plots.
 
Package: compcodeR
Commit: 223b1d11215d41ebdeac04fdf7fb55a9d0eeeabb
Author: Paul Bastide <paul.bastide@gmail.com>
Date: 2021-01-08 11:51:49 +0100
Commit message:

 Bug fix: Filter length matrix to match expression matrix when needed.
 
Package: compcodeR
Commit: b7b1c1ca9dc2c908323513ee425c15b4b421cca2
Author: Paul Bastide <paul.bastide@gmail.com>
Date: 2021-01-06 12:07:12 +0100
Commit message:

 Phylogenetic effective sample size for difference in means estimation.
 
Package: compcodeR
Commit: 88f9e1dab08946f71dcfe3854e328b33beb6931d
Author: Paul Bastide <paul.bastide@gmail.com>
Date: 2020-12-17 17:25:14 +0100
Commit message:

 Do dot scale by million for asin(sqrt).
 
Package: compcodeR
Commit: c8f32f7053844337651c5b1013c9dc2613e5c7b9
Author: Paul Bastide <paul.bastide@gmail.com>
Date: 2020-12-17 17:24:46 +0100
Commit message:

 Remove deprecated functions.
 
Package: compcodeR
Commit: 93475a57205c5beaf0f7b6e765f11b1db75f925f
Author: Paul Bastide <paul.bastide@gmail.com>
Date: 2020-12-17 15:46:17 +0100
Commit message:

 Use asin(sqrt) transformation (and correct typo).
 
Package: compcodeR
Commit: 67d6e8ea477fec86d9005e58f4e047c1dacd9ea7
Author: Paul Bastide <paul.bastide@gmail.com>
Date: 2020-12-04 17:41:44 +0100
Commit message:

 Remove dependency to gdata
 
Package: compcodeR
Commit: 192553eb7c6689b39b3d799ce1a73684d820dc21
Author: Paul Bastide <paul.bastide@gmail.com>
Date: 2020-12-04 17:01:44 +0100
Commit message:

 Finish merge for check to pass.
 
Package: compcodeR
Commit: e5550e1b4d1d9eb1b1ea97f7abf52c98d42ba91b
Author: Paul Bastide <paul.bastide@gmail.com>
Date: 2020-12-04 15:50:45 +0100
Commit message:

 Manually merge remote-tracking branch 'upstream/master'
 
Package: compcodeR
Commit: 40447ba79a09ff9eb6cbfdcc1ea5b552e69ed7fe
Author: Paul Bastide <paul.bastide@gmail.com>
Date: 2020-09-29 16:22:08 +0200
Commit message:

 VST transformation with length for limma and phylolm.
 
Package: compcodeR
Commit: 4d2eefc33ee385f2c11f2b5da5c6bce7ca893d8e
Author: Paul Bastide <paul.bastide@gmail.com>
Date: 2020-09-11 12:42:36 +0200
Commit message:

 Counts per millions and log2 + 1
 
Package: compcodeR
Commit: 20f7feb14092268985e6d88c8c4f79d6bb619e1e
Author: Paul Bastide <paul.bastide@gmail.com>
Date: 2020-09-10 16:06:14 +0200
Commit message:

 More flexible phylolm with non-voom normalisation.
 
Package: compcodeR
Commit: c2b7b706b82713bb568e17141510e2ac5160ec89
Author: Paul Bastide <paul.bastide@gmail.com>
Date: 2020-09-10 16:05:40 +0200
Commit message:

 Correct TPM computation in voom.
 
Package: compcodeR
Commit: 55d8801cc3f20697f44bc3eaf63b247601930085
Author: Paul Bastide <paul.bastide@gmail.com>
Date: 2020-07-17 11:24:33 +0200
Commit message:

 Add sqrtTPM normalisation method.
 
Package: compcodeR
Commit: f088f374ac87707fe4117acfa79e52239a46aa6e
Author: Paul Bastide <paul.bastide@gmail.com>
Date: 2020-07-07 09:36:37 +0200
Commit message:

 Save result table for further plotting
 
Package: compcodeR
Commit: cb3127f2234d6145a70aa2863d720e26a061561a
Author: Paul Bastide <paul.bastide@gmail.com>
Date: 2020-06-30 17:22:01 +0200
Commit message:

 Move sm from Depends to Imports
 
Package: compcodeR
Commit: aae6aeab6857c0c3cedf44d9e74364f25fda82c4
Author: Paul Bastide <paul.bastide@gmail.com>
Date: 2020-06-30 15:24:45 +0200
Commit message:

 Unique name for tempcode.Rmd for parallelization.
 
Package: compcodeR
Commit: 3a8508744e03b16547599e131a49ee56d7b91bb2
Author: Paul Bastide <paul.bastide@gmail.com>
Date: 2020-06-24 14:53:37 +0200
Commit message:

 Fix phytools dependency and rpois behaviour in R 4.0
 
Package: compcodeR
Commit: 48a882b7c3bbc8185e87adf33c27201832970827
Author: Paul Bastide <paul.bastide@gmail.com>
Date: 2020-06-24 14:20:54 +0200
Commit message:

 Try to fix tests by correcting name.
 
Package: compcodeR
Commit: f626b33e5c5b497baaf92f0fdf680f14fcb4046b
Author: Paul Bastide <paul.bastide@gmail.com>
Date: 2020-06-24 13:49:20 +0200
Commit message:

 Clean dependency on phytools and set _R_CHECK_FORCE_SUGGESTS_="false"
 
Package: compcodeR
Commit: 18a9aa1ec4d92f7ba9812c3295e276b881d092d3
Author: Paul Bastide <paul.bastide@gmail.com>
Date: 2020-06-24 11:11:49 +0200
Commit message:

 Remote setting for DESeq and NOISeq
 
Package: compcodeR
Commit: bdd548920ad2ff9ecdb37ecf5e7e78d8b9349691
Author: Paul Bastide <paul.bastide@gmail.com>
Date: 2020-06-24 09:47:04 +0200
Commit message:

 Change name to "phylocompcodeR"
 
Package: compcodeR
Commit: 1292b3efabdc4a33e3038b5e0f85feb36495d96e
Author: Paul Bastide <paul.bastide@gmail.com>
Date: 2020-06-24 09:45:55 +0200
Commit message:

 Merge remote-tracking branch 'upstream/master'
 
Package: compcodeR
Commit: 0fe29bedc008b517bacb0f121a60e17969fbf91d
Author: Paul Bastide <paul.bastide@gmail.com>
Date: 2020-06-24 09:19:24 +0200
Commit message:

 Typo.
 
Package: compcodeR
Commit: 4acc403f0619a8bde13f128efeab5170738dee4a
Author: Paul Bastide <paul.bastide@gmail.com>
Date: 2020-06-23 09:59:27 +0200
Commit message:

 More robust delta fisher computations.
 
Package: compcodeR
Commit: 3d8f98254c879ce0f66bbe7483c72d8048bcf165
Author: Paul Bastide <paul.bastide@gmail.com>
Date: 2020-06-19 18:07:44 +0200
Commit message:

 Missing condition.
 
Package: compcodeR
Commit: 5399781cf31a56848b76b3446b33ba24c3d02aaf
Author: Paul Bastide <paul.bastide@gmail.com>
Date: 2020-06-19 17:39:46 +0200
Commit message:

 Correct for OU model in student factor computation.
 
Package: compcodeR
Commit: 77fdb7d96893c8007927125143f8fa1f8f6bb0fa
Author: Paul Bastide <paul.bastide@gmail.com>
Date: 2020-06-19 16:56:39 +0200
Commit message:

 Re-organize length normalization in analysis functions.
 
Package: compcodeR
Commit: d7d817a981afeb1423cfded13fa27c31e0cd9ffe
Author: Paul Bastide <paul.bastide@gmail.com>
Date: 2020-06-19 16:56:14 +0200
Commit message:

 Use tree to simulate lengths only if tree exists.
 
Package: compcodeR
Commit: 21e07522720393879727f5c2fac15e2e65b8b780
Author: Paul Bastide <paul.bastide@gmail.com>
Date: 2020-06-19 16:43:14 +0200
Commit message:

 Add vanilla power computation.
 
Package: compcodeR
Commit: 18239a0cbfe9badb6dc2fd50b1630020ce3bb55e
Author: Paul Bastide <paul.bastide@gmail.com>
Date: 2020-06-17 16:07:20 +0200
Commit message:

 Use the tree to simulate the lengths.
 
Package: compcodeR
Commit: aabcec76a9c3cb07faea75206b1370b655bc7343
Author: Paul Bastide <paul.bastide@gmail.com>
Date: 2020-06-08 19:33:26 +0200
Commit message:

 extraDesignFactor in voom+limma.
 
Package: compcodeR
Commit: 3a15effec3263549ec3cb79fc25911c3f0832fe8
Author: Paul Bastide <paul.bastide@gmail.com>
Date: 2020-06-08 19:32:56 +0200
Commit message:

 Make sure factors are consistently named in phylolm analyses.
 
Package: compcodeR
Commit: 076dbfd6c07437857dde72ebe9281f4542cb05c8
Author: Paul Bastide <paul.bastide@gmail.com>
Date: 2020-05-29 16:50:52 +0200
Commit message:

 Add check on the tree for compData object.
 
Package: compcodeR
Commit: 8da8c58b772d9c37ed0615a8d996e99be575b124
Author: Paul Bastide <paul.bastide@gmail.com>
Date: 2020-05-25 18:32:06 +0200
Commit message:

 Student factor difficulty index.
 
Package: compcodeR
Commit: 0fab52760f0454523ea37afeea9e16ddb371f288
Author: Paul Bastide <paul.bastide@gmail.com>
Date: 2020-05-25 18:31:43 +0200
Commit message:

 Fix build.
 
Package: compcodeR
Commit: 0c22814e70fc8524acf68fbbe6156310b18c4c36
Author: Paul Bastide <paul.bastide@gmail.com>
Date: 2020-05-25 14:32:12 +0200
Commit message:

 Change length normalization in diagnostic MA plot.
 
Package: compcodeR
Commit: 81e7629d0e9b2e8559ff93fa6b37f15dd1228c5c
Author: Paul Bastide <paul.bastide@gmail.com>
Date: 2020-05-25 09:59:34 +0200
Commit message:

 Functions to correct for length in DESeq2 and voom analyses.
 
Package: compcodeR
Commit: 67335f961a3a3187115c3377d52903bf42ccf875
Author: Paul Bastide <paul.bastide@gmail.com>
Date: 2020-05-07 12:00:16 +0200
Commit message:

 Move length.matrix to its own data slot.
 
Package: compcodeR
Commit: 024c3c8260bca5743482764754cb1b537a4e500a
Author: Paul Bastide <paul.bastide@gmail.com>
Date: 2020-05-07 10:35:29 +0200
Commit message:

 Avoid storing large matrices when not necessary.
 
Package: compcodeR
Commit: caae730e599d8759c194f3b5c2ff41d9a9145b73
Author: Paul Bastide <paul.bastide@gmail.com>
Date: 2020-05-07 09:24:00 +0200
Commit message:

 Save lengths and plots.
 
Package: compcodeR
Commit: fb53bdb51afaf88e81d03af8e7f70297bad6c696
Author: Paul Bastide <paul.bastide@gmail.com>
Date: 2020-04-30 18:12:01 +0200
Commit message:

 Simulate lengths.
 
Package: compcodeR
Commit: cdb90d49c46c95145c438506867586d7eee5b5e9
Author: Paul Bastide <paul.bastide@gmail.com>
Date: 2020-04-30 18:11:12 +0200
Commit message:

 Ensure tree is ultrametric in analyses.
 
Package: compcodeR
Commit: 06e89c18c59fca309ff6f4a63127a5eafe6aec97
Author: Paul Bastide <paul.bastide@gmail.com>
Date: 2020-04-20 14:21:38 +0200
Commit message:

 Ultrametric tree in phylolm analysis when no tree is provided.
 
Package: compcodeR
Commit: b734c713464d44bb467623a5206bf956c80947e7
Author: Paul Bastide <paul.bastide@gmail.com>
Date: 2020-04-20 14:15:44 +0200
Commit message:

 Simulate with OU process.
 
Package: compcodeR
Commit: b7a80651a90b384c447057dd4b763bd268813ffb
Author: Paul Bastide <paul.bastide@gmail.com>
Date: 2020-04-14 15:51:20 +0200
Commit message:

 Typo in phylo heatmap plot: take log2 only once.
 
Package: compcodeR
Commit: 6ffa4992d42027628a150e1b2782b5784510d016
Author: Paul Bastide <paul.bastide@gmail.com>
Date: 2020-04-14 15:07:41 +0200
Commit message:

 Add voom + phylolm analysis method.
 
Package: compcodeR
Commit: 6c4a6853305d8ad0077830752c6dea6904add41e
Author: Paul Bastide <paul.bastide@gmail.com>
Date: 2020-04-14 15:06:40 +0200
Commit message:

 Add heatmap plot to diagnostic
 
Package: compcodeR
Commit: 519b4f35b8b94fffa7280cfb28ccacc597ae6e5f
Author: Paul Bastide <paul.bastide@gmail.com>
Date: 2020-04-13 12:55:20 +0200
Commit message:

 Robust rpois simulation for large numbers.
 
Package: compcodeR
Commit: 62be414e8308a52ebbf5afe250428e95186244fe
Author: Paul Bastide <paul.bastide@gmail.com>
Date: 2020-04-10 19:19:25 +0200
Commit message:

 New function for DESeq2 analysis with added factor and normalizing matrix.
 
Package: compcodeR
Commit: e0c95d9f0f4c0176a3e3a079959d04f09d7c0dd2
Author: Paul Bastide <paul.bastide@gmail.com>
Date: 2020-04-09 18:08:54 +0200
Commit message:

 Generating parameters is now its own function.
 
Package: compcodeR
Commit: 6210ea823afe323578a672853ec7080c70ce2d0d
Author: Paul Bastide <paul.bastide@gmail.com>
Date: 2020-04-09 18:08:09 +0200
Commit message:

 Handle intermediate md file in runComparison.
 
Package: compcodeR
Commit: 587725f5353f2b47c4aa09954705d69ffcdf486d
Author: Paul Bastide <paul.bastide@gmail.com>
Date: 2020-04-08 17:11:54 +0200
Commit message:

 Get rid of intermediate md file.
 
Package: compcodeR
Commit: f587f3ec3cf6364496aae5a3eaec0d3a48a18fc9
Author: Paul Bastide <paul.bastide@gmail.com>
Date: 2020-04-08 15:34:49 +0200
Commit message:

 Add phylogenetic heatmap to rmd report.
 
Package: compcodeR
Commit: c0cad743c64936de93a0bd7f3b73a2f82eb7c833
Author: Paul Bastide <paul.bastide@gmail.com>
Date: 2020-03-27 16:26:31 +0100
Commit message:

 Clean documentation and imports.
 
Package: compcodeR
Commit: f23d03021056568eb9f7a615d2190de693b62bcd
Author: Paul Bastide <paul.bastide@gmail.com>
Date: 2020-03-27 15:18:12 +0100
Commit message:

 Adapt simulation function to work with phylogenetic poisson log normal model.
 
Package: atena
Commit: 51aa29a5f95e0139f5d46641d0149b3564f3c23b
Author: beacalvo <beacalvo96@gmail.com>
Date: 2022-01-24 11:29:32 +0100
Commit message:

 Version bump after implementation of paired-end in Telescope
 
Package: uncoverappLib
Commit: 18e4c675fcaf9f0565cea43fd72c3449d9cd87d3
Author: eiovino <emanuelaiovino.87@gmail.com>
Date: 2022-01-24 11:11:33 +0100
Commit message:

 change rename
 
Package: GeneTonic
Commit: 334cc30103ec1a31e98b86da3f1cd8e3303a90f1
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2022-01-24 08:56:46 +0100
Commit message:

 Version bump, 1.7.3
 
Package: GeneTonic
Commit: 11fdf5facbe7d51d17caf26e4fe44827bafb5879
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2022-01-19 17:23:14 +0100
Commit message:

 namespace fix
 
Package: GeneTonic
Commit: 4ceeef3c37e6516593b1ace3256b28113c39bbe9
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2022-01-19 17:23:05 +0100
Commit message:

 updated manpages
 
Package: GeneTonic
Commit: 744c2eed940c3737a978a0429e22c0d26175fd7a
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2022-01-19 17:22:34 +0100
Commit message:

 backbone functions update - hyperg replaced by fixedrow
 
Package: sesameData
Commit: 0bccad0a256a096a9721e03b1b6858d2d69c758f
Author: Wanding Zhou <zhouwanding@gmail.com>
Date: 2022-01-23 21:17:48 -0500
Commit message:

 bump to 1.13.11, removed platform specific caching
 
Package: bugsigdbr
Commit: 4d2f9b2f27141d1b6fba0646005aa226ebbab35b
Author: lgeistlinger <ludwig.geistlinger@gmail.com>
Date: 2022-01-23 15:28:45 -0500
Commit message:

 fix import issues
 
Package: HiCDCPlus
Commit: af4f4869059993cb56eca4a1a2d6882643f6f6db
Author: Merrick Usta <m0u00pf@m-c02cf3lymd6r.fios-router.home>
Date: 2022-01-23 12:36:08 -0500
Commit message:

 fix bug that prevents using variable window sizes and accessing function documentation
 
Package: beer
Commit: 4774750a8962b8d9ef36700db2164cf0b8ac05fe
Author: Athena Chen <achen70@jhu.edu>
Date: 2022-01-23 12:18:26 -0500
Commit message:

 added link to bioRxiv manuscript
 
Package: Rhdf5lib
Commit: 24823db15bb9b40035f474cebcd4297ab6672e6d
Author: Mike Smith <grimbough@gmail.com>
Date: 2022-01-23 15:53:50 +0100
Commit message:

 Updates to configure scripts
 
Package: weitrix
Commit: b9b2107865e1de62e63ca6a0065010dffd18e879
Author: pfh <pfh@logarithmic.net>
Date: 2022-01-23 17:29:15 +1100
Commit message:

 Version bump for typecast argument
 
Package: weitrix
Commit: 10782bfa88c5fcb68061f64260f83e8dfd17ec51
Author: pfh <pfh@logarithmic.net>
Date: 2022-01-23 17:27:18 +1100
Commit message:

 Merge remote-tracking branch 'upstream/master'
 
Package: weitrix
Commit: 7c877c0142eb320a4979b381dde788a6021fb7ac
Author: pfh <pfh@logarithmic.net>
Date: 2022-01-23 17:26:58 +1100
Commit message:

 Remove travis status
 
Package: weitrix
Commit: b60e86a02e1d69ee626caa23e39f2b4d87620262
Author: Paul Harrison <paul.harrison@monash.edu>
Date: 2021-06-15 14:02:48 +1000
Commit message:

 add typecast argument to counts_shift and counts_proportions
 
Package: sesameData
Commit: 200ec456532d9650fd12ed157ea1bba6eb3a80c7
Author: Wanding Zhou <zhouwanding@gmail.com>
Date: 2022-01-22 21:57:07 -0500
Commit message:

 bump to 1.13.10
 
Package: sesameData
Commit: d29cdd7b743795cf60f6ecda171ff6c8e46a536c
Author: Wanding Zhou <zhouwanding@gmail.com>
Date: 2022-01-22 20:47:25 -0500
Commit message:

 bump to 1.13.9
 
Package: sesameData
Commit: c0ac3a47e3c68db58559abfd763bac4906467e60
Author: Wanding Zhou <zhouwanding@gmail.com>
Date: 2022-01-22 20:46:14 -0500
Commit message:

 more meta update
 
Package: sesameData
Commit: bfcafef67ece5c6739dc7c48cb992e267fa6f7bb
Author: Wanding Zhou <zhouwanding@gmail.com>
Date: 2022-01-22 19:47:28 -0500
Commit message:

 bump to 1.13.8, updated metadata
 
Package: sesameData
Commit: 62cb7d484c3dcad8a09b3ec3bc64548cc48f4954
Author: Wanding Zhou <zhouwanding@gmail.com>
Date: 2022-01-22 19:27:48 -0500
Commit message:

 minor, message omitted
 
Package: sesameData
Commit: f1f1f6b22d59f922bd782661fad3c84cb9abda5e
Author: Wanding Zhou <zhouwanding@gmail.com>
Date: 2022-01-22 19:18:30 -0500
Commit message:

 update to data sheet
 
Package: TRESS
Commit: 3db1c7fb28d1b91fd039cb7b63abc7a148fd5834
Author: Zhenxing Guo <zhenxingguo@Zhenxings-MacBook-Pro.local>
Date: 2022-01-22 13:12:39 -0500
Commit message:

 bump version
 
Package: TRESS
Commit: 5fb6f89c4bda2009b3159e628c5b1ae7ad886b20
Author: Zhenxing Guo <zhenxingguo@Zhenxings-MacBook-Pro.local>
Date: 2022-01-22 13:11:34 -0500
Commit message:

 remove systematic  files
 
Package: TRESS
Commit: 6b897139b97e6c52a783eb44cd7749e343e4b496
Author: Zhenxing Guo <zhenxingguo@Zhenxings-MacBook-Pro.local>
Date: 2022-01-22 13:09:54 -0500
Commit message:

 updates
 
Package: TRESS
Commit: 70514240468ec61a43d131babf6bb0e1a5b87216
Author: Zhenxing Guo <zhenxingguo@Zhenxings-MacBook-Pro.local>
Date: 2022-01-22 13:07:37 -0500
Commit message:

 bump version
 
Package: TRESS
Commit: 5d732fc40129ef20d993330ee4ceaac0ac931e47
Author: Zhenxing Guo <zhenxingguo@Zhenxings-MacBook-Pro.local>
Date: 2022-01-22 13:01:33 -0500
Commit message:

 update CallPeaks.oneRep.R
 
Package: TRESS
Commit: d6bbbdddfccd37976725d0515639ae9b87084c60
Author: Zhenxing Guo <zhenxingguo@Zhenxings-MacBook-Pro.local>
Date: 2022-01-22 12:59:08 -0500
Commit message:

 debug old CallPeaks.oneRep.R
 
Package: GenProSeq
Commit: d336da01de55bbcd513a3345af099f82e9f9f6bd
Author: dongminjung <dongminjung@Dongmins-MacBook-Pro.local>
Date: 2022-01-22 20:29:10 +0900
Commit message:

 update
 
Package: GenProSeq
Commit: 84ffb42ac1a5fec2d9500bc37fc485d27ec803a0
Author: dongminjung <dongminjung@Dongmins-MacBook-Pro.local>
Date: 2022-01-22 20:11:48 +0900
Commit message:

 update
 
Package: GenProSeq
Commit: 9456fd1e9e198c3a11bbda0fe3fdf1d8ae0b2407
Author: dongminjung <dongminjung@Dongmins-MacBook-Pro.local>
Date: 2022-01-22 19:49:22 +0900
Commit message:

 update
 
Package: metapone
Commit: 937317d263e48fb684651b4a0642a3e293c91cc2
Author: tianwei-yu <tianwei.yu@outlook.com>
Date: 2022-01-22 15:58:34 +0800
Commit message:

 fixed some plotting issues
 
Package: metapone
Commit: 9735faf904932316ff9753d42d70c71f49e8ed13
Author: tianwei-yu <tianwei.yu@outlook.com>
Date: 2022-01-22 15:56:37 +0800
Commit message:

 added gsea type test, and fixed some plotting issues
 
Package: metapone
Commit: 0990f7975570de9548c51c0e65cb6ab974333761
Author: tianwei-yu <tianwei.yu@outlook.com>
Date: 2022-01-22 15:54:12 +0800
Commit message:

 fixed some plotting issue
 
Package: metapone
Commit: e562b5e51351f4ab8b591d17f1908607051192c4
Author: tianwei-yu <tianwei.yu@outlook.com>
Date: 2022-01-22 15:52:17 +0800
Commit message:

 fixed some plotting issues
 
Package: metapone
Commit: dd7838972d4f18b6d2f44d6d9605db2640c2eeda
Author: tianwei-yu <tianwei.yu@outlook.com>
Date: 2022-01-22 15:51:10 +0800
Commit message:

 fixed some plotting issue
 
Package: metapone
Commit: 3cdc96921f88af7d71b76fd6ccda487cbb15ed70
Author: tianwei-yu <tianwei.yu@outlook.com>
Date: 2022-01-22 15:47:54 +0800
Commit message:

 fixed some plotting issues
 
Package: ASEB
Commit: e83093727f80bb6efd266c4b24d1f5e820ac40b4
Author: Wang Likun <wanglk@bjmu.edu.cn>
Date: 2022-01-22 13:23:19 +0800
Commit message:

 Fix a bug indexes[1,1]->indexes[1]

Fix a bug indexes[1,1]->indexes[1]
 
Package: SeqArray
Commit: 2372fc165e51555eee518e4a78ab6585fbd883e5
Author: Xiuwen Zheng <zhengxwen@gmail.com>
Date: 2022-01-21 21:12:06 -0600
Commit message:

 sparse matrix in seqGetData()
 
Package: BiocCheck
Commit: 2520de97cf2852c58888d08c5abfabeba2232e6c
Author: LiNk-NY <marcel.ramosperez@roswellpark.org>
Date: 2022-01-21 18:24:04 -0500
Commit message:

 version bump 1.31.29
 
Package: BiocCheck
Commit: f54d1f3da9e9e80722a008365566fa23ebee1e40
Author: LiNk-NY <marcel.ramosperez@roswellpark.org>
Date: 2022-01-21 18:21:35 -0500
Commit message:

 use libdir for R_LIBS_USER in installAndLoad and update CMD
 
Package: cleanUpdTSeq
Commit: a18a44c31aa44c99cd084d36c2a5a914a3217801
Author: JIANHONG OU <jianhong@users.noreply.github.com>
Date: 2022-01-21 13:52:47 -0500
Commit message:

 fix a bug for one line GRanges reported by Haibo
 
Package: atena
Commit: d182fee004f7f90c82a77dc8957e037be908e254
Author: beacalvo <beacalvo96@gmail.com>
Date: 2022-01-21 17:45:42 +0100
Commit message:

 Fixed function to get read length in paired-end
 
Package: Gviz
Commit: 812e4d000c1a285c762d01a52ef33934bdf7bf89
Author: Robert Ivánek <robert.ivanek@unibas.ch>
Date: 2022-01-21 16:52:54 +0100
Commit message:

 Restructured the code, split according to the class, first version of roxygen2 documentation. Bumped the version.
 
Package: TCGAbiolinks
Commit: 812181130cacf2b81872c35fdf6897c1c63bb72b
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2022-01-21 11:15:17 -0500
Commit message:

 Version bump
 
Package: TCGAbiolinks
Commit: 6018d4787ee5d85b127133f5cfa5ac45c2471861
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2022-01-21 11:14:57 -0500
Commit message:

 Fix #425. Update clinical data column names
 
Package: beer
Commit: ef9a02cde46fe17113b9aeeb54ee19eedda6328c
Author: Athena Chen <achen70@jhu.edu>
Date: 2022-01-21 10:21:39 -0500
Commit message:

 removed beer.Rproj file
 
Package: rhdf5
Commit: 9251f5acd719a9716b50758468cc8aee450510e3
Author: Mike Smith <grimbough@gmail.com>
Date: 2022-01-21 15:42:19 +0100
Commit message:

 Version bump
 
Package: rhdf5
Commit: ec16627900de0a0777b5e9c3cf19245a9413f3de
Author: Mike Smith <grimbough@gmail.com>
Date: 2022-01-21 15:41:35 +0100
Commit message:

 Address C compiler warnings
 
Package: rhdf5
Commit: 3b5e029c08a5f51807878e3b8713d28cecaf09dc
Author: Mike Smith <grimbough@gmail.com>
Date: 2022-01-19 14:51:39 +0100
Commit message:

 Make szip test specific to windows versions
 
Package: rhdf5
Commit: 124b14507347cd77ee53a4439fb2f27465aaf8ca
Author: Mike Smith <grimbough@gmail.com>
Date: 2022-01-18 13:54:25 +0100
Commit message:

 Update test
 
Package: rhdf5
Commit: 03fdfca9afef85504e2ab69fec31440f48ae7829
Author: Mike Smith <grimbough@gmail.com>
Date: 2022-01-07 14:36:30 +0100
Commit message:

 Address some "unused variable" warnings
 
Package: rhdf5
Commit: 2201c4f0d6e6b272f41bbd6bca85f4a51cf37823
Author: Mike Smith <grimbough@gmail.com>
Date: 2022-01-07 13:36:07 +0100
Commit message:

 Version bump
 
Package: rhdf5
Commit: 7fea60a9eaeff457b4c95fe0e4de6b90de99fb51
Author: Mike Smith <grimbough@gmail.com>
Date: 2022-01-07 13:35:59 +0100
Commit message:

 Fix uninitialized value usage in h5dump()
 
Package: rhdf5
Commit: e5cbe3314fcfd2168daa7350a501d270a9a66383
Author: Mike Smith <grimbough@gmail.com>
Date: 2021-12-21 17:41:56 +0100
Commit message:

 Documentation typo
 
Package: rhdf5
Commit: 1055187819569e34668329f8ed268f5e732c8521
Author: Mike Smith <grimbough@gmail.com>
Date: 2021-12-21 16:22:35 +0100
Commit message:

 Version bump
 
Package: rhdf5
Commit: b395077665b34f8ef554c6ae91bab3da68bedd78
Author: Mike Smith <grimbough@gmail.com>
Date: 2021-12-21 16:20:35 +0100
Commit message:

 Update workflow
 
Package: rhdf5
Commit: 7446ec4b5dec3816e388ca3b4dbba96c502c454a
Author: Mike Smith <grimbough@gmail.com>
Date: 2021-12-16 16:42:35 +0100
Commit message:

 Unit tests for N-bit filter and datatype
 
Package: rhdf5
Commit: c4f94ff6635c8efa255c4df73cc5171622a18368
Author: Mike Smith <grimbough@gmail.com>
Date: 2021-12-15 17:20:11 +0100
Commit message:

 Add more parts to N-bit filter
 
Package: rhdf5
Commit: 7466425c9c2147b8da17ee061cc284015ee08f90
Author: Mike Smith <grimbough@gmail.com>
Date: 2021-12-15 17:19:32 +0100
Commit message:

 Still playing with configure and .Rprofile
 
Package: rhdf5
Commit: e35387817383b88ca88c1af2ab7d2c59ceb14b6e
Author: Mike Smith <grimbough@gmail.com>
Date: 2021-12-09 17:32:26 +0100
Commit message:

 Merge branch 'master' into nbit-datatype
 
Package: rhdf5
Commit: fbb3f7b1ac05a6ee8cd8f54f78f490ddd461fc97
Author: Mike Smith <grimbough@gmail.com>
Date: 2021-12-09 17:23:52 +0100
Commit message:

 New attempt at robust detection of rhdf5filters package
 
Package: rhdf5
Commit: 4187cf869e8ec219c8cb677b66c2ed0a239abcf2
Author: Mike Smith <grimbough@gmail.com>
Date: 2021-12-09 12:14:11 +0100
Commit message:

 Add n-bit filter support
 
Package: beer
Commit: d4dd69f1b06ebbc70f1a95eb45d0a4c048418a55
Author: Athena Chen <achen70@jhu.edu>
Date: 2022-01-21 09:57:05 -0500
Commit message:

 version bump to trigger bioc build
 
Package: Spectra
Commit: 68fce99f267d36152bf15a887440838ce9658882
Author: jorainer <johannes.rainer@gmail.com>
Date: 2022-01-21 15:47:54 +0100
Commit message:

 fix: add missing export of filterPrecursorMz
 
Package: AnnotationHubData
Commit: 4c3b0e4e16f5bc14462f2ca5f7485b5ce9a7ae4c
Author: lshep <lori.shepherd@roswellpark.org>
Date: 2022-01-21 09:18:13 -0500
Commit message:

 Add helper function upload_to_azure
 
Package: AnnotationHubData
Commit: b81587bbb21d47a34716d8a6fa63e8dc144a75f1
Author: lshep <lori.shepherd@roswellpark.org>
Date: 2022-01-21 07:38:53 -0500
Commit message:

 remove whitespace
 
Package: AnnotationHubData
Commit: c10cee3bfb75db16346ee694cbb97f49beb7121b
Author: lshep <lori.shepherd@roswellpark.org>
Date: 2022-01-19 13:38:02 -0500
Commit message:

 Add check for azcopy install
 
Package: AnnotationHubData
Commit: 11a31e4c04b2b4acb8b28e8951e87d5b07e07035
Author: lshep <lori.shepherd@roswellpark.org>
Date: 2022-01-19 09:56:26 -0500
Commit message:

 Add shell for azure upload function
 
Package: PhyloProfile
Commit: c548b6e380740dbc45bc2bb95455c5192eb86806
Author: trvinh <trvinh@gmail.com>
Date: 2022-01-21 15:12:12 +0100
Commit message:

 added fn for import and export tax DB
 
Package: qsea
Commit: 6e6352f685d62b0edac90c8b45162594d6b1c7e1
Author: Matthias Lienhard <mali270484@gmail.com>
Date: 2022-01-21 14:50:44 +0100
Commit message:

 Merge pull request #9 from SPPearce/SPPearce

Allow upper bound for a in enrichment optimisation to go above 3 
Package: qsea
Commit: 983e03b21f2d5a16167141b4f41b8bcda56cd1f2
Author: Simon Pearce <simon.pearce@cruk.manchester.ac.uk>
Date: 2022-01-20 11:29:56 +0000
Commit message:

 Allow upper bound for a in enrichment optimisation to go above 3
 
Package: iSEEu
Commit: 965aca815f14cea7932db108d44258320a54be54
Author: Kevin Rue-Albrecht <kevinrue67@gmail.com>
Date: 2022-01-21 13:46:17 +0000
Commit message:

 Restore windows build (#102)

 
Package: atena
Commit: 1a4179ff2dcd44cf41631ae7bac369a8b62716ce
Author: beacalvo <beacalvo96@gmail.com>
Date: 2022-01-21 09:57:23 +0100
Commit message:

 Modified alignment length computation for paired-end, and finished implementation of paired-end in Telescope
 
Package: atena
Commit: 7217d6029b8b4a864e6c45217e03a19c7504796d
Author: beacalvo <beacalvo96@gmail.com>
Date: 2022-01-20 10:22:37 +0100
Commit message:

 Implemented AS and alignment length getter for paired-end
 
Package: MultiBaC
Commit: 71e9c82ea067a42533a3d5c995612ebb7f85c059
Author: manuelUgidos <martaperezsanchez@MacBook-Pro-de-Marta.local>
Date: 2022-01-21 11:33:07 +0100
Commit message:

 Error correction
 
Package: iSEEu
Commit: b4de7b10f964bfe6d67ef0e934f4791dd6f5c517
Author: Kevin Rue-Albrecht <kevinrue67@gmail.com>
Date: 2022-01-21 10:25:15 +0000
Commit message:

 Bug fix for DynamicMarkerTable (#101)

* getTableExtraFields returns empty vector instead of NULL

* udpdate version of R and bioconductor in action

* update biocthis action

* R CMD check error on error not warning

* version bump

* run covr on all branches

* temporarily disable window to pass build 
Package: universalmotif
Commit: 6db6213919871a87565c393a071144666702d9e9
Author: Benjamin Jean-Marie Tremblay <benjmtremblay@gmail.com>
Date: 2022-01-21 10:23:51 +0100
Commit message:

 v1.12.3 bugfix
 
Package: universalmotif
Commit: c58a1508fa7d3c171e8ddbb3a58379fba22d582c
Author: Benjamin Jean-Marie Tremblay <benjmtremblay@gmail.com>
Date: 2022-01-21 10:07:48 +0100
Commit message:

 Fix dup seqnames in scanning
 
Package: universalmotif
Commit: 5c6a32f7e73f723ffb73c1a8a591abba33e0a126
Author: Benjamin Jean-Marie Tremblay <benjmtremblay@gmail.com>
Date: 2022-01-20 22:53:24 +0100
Commit message:

 todo item
 
Package: universalmotif
Commit: 4dd9d633110e44e7c42280dd4455040c4c1af4eb
Author: Benjamin Jean-Marie Tremblay <benjmtremblay@gmail.com>
Date: 2022-01-20 22:47:59 +0100
Commit message:

 todo item
 
Package: OSCA.multisample
Commit: e3e60fd3980f307910d7f2f62c6f0e387827d55a
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2022-01-20 20:54:25 -0800
Commit message:

 Segue to the next chapter.
 
Package: GenProSeq
Commit: c2d14a597c41cee4cb9a8708921ea87414c2f905
Author: dongminjung <dongminjung@Dongmins-MacBook-Pro.local>
Date: 2022-01-21 10:30:17 +0900
Commit message:

 update
 
Package: GenomicDistributions
Commit: 37e8c306537db84a6c7283004b56f3ae97964e70
Author: Kristyna Kupkova <kristynakupkova@gmail.com>
Date: 2022-01-20 19:36:49 -0500
Commit message:

 Merge remote-tracking branch 'upstream/master'
 
Package: GenomicDistributions
Commit: 68e6acac8b08608568786e39b161d67afe42bd46
Author: Kristyna Kupkova <kristynakupkova@gmail.com>
Date: 2022-01-20 19:33:47 -0500
Commit message:

 Merge pull request #186 from databio/dev

increase version number - correct 
Package: GenomicDistributions
Commit: 142461ec29dc53101ab774282d08bcb32d80b967
Author: Kristyna Kupkova <kristynakupkova@gmail.com>
Date: 2022-01-20 19:33:25 -0500
Commit message:

 increase version number - correct
 
Package: GenomicDistributions
Commit: 4e9b7a76481d790e54547e9bc243d913eafcd19f
Author: Kristyna Kupkova <kristynakupkova@gmail.com>
Date: 2022-01-20 19:24:22 -0500
Commit message:

 Merge pull request #185 from databio/dev

Update full-power.Rmd 
Package: GenomicDistributions
Commit: eb336615b570a2e49e63904d86d4a0c229d1d9b4
Author: Kristyna Kupkova <kristynakupkova@gmail.com>
Date: 2022-01-20 19:23:36 -0500
Commit message:

 Update full-power.Rmd
 
Package: GenomicDistributions
Commit: 67664d997cc6245c5c52a04d910973d7426449e6
Author: Kristyna Kupkova <kristynakupkova@gmail.com>
Date: 2022-01-20 19:00:32 -0500
Commit message:

 Merge pull request #184 from databio/dev

1.3.1 update NEWS 
Package: GenomicDistributions
Commit: 304e7b4b93cbcd6bee1cf11c114e758fa3b84f59
Author: Kristyna Kupkova <kristynakupkova@gmail.com>
Date: 2022-01-20 18:59:44 -0500
Commit message:

 Update NEWS
 
Package: GenomicDistributions
Commit: 000a81f23d88b819ecaac9a94619eb69b7e657ca
Author: Kristyna Kupkova <kristynakupkova@gmail.com>
Date: 2022-01-20 18:58:51 -0500
Commit message:

 Update NEWS
 
Package: GenomicDistributions
Commit: 496d06b9c093fc8bb2a16f125c3c206de6f9f29a
Author: Kristyna Kupkova <kristynakupkova@gmail.com>
Date: 2022-01-20 18:57:32 -0500
Commit message:

 Merge pull request #183 from databio/dev

Version 1.3.1 
Package: GenomicDistributions
Commit: dd07ad9e1a89fb3ee6b202a7cdd7ed5759f9ace9
Author: Kristyna Kupkova <kristynakupkova@gmail.com>
Date: 2022-01-20 18:56:00 -0500
Commit message:

 Update DESCRIPTION
 
Package: GenomicDistributions
Commit: e03f1005b60c24d3e9765bb8735dffea0741419a
Author: Kristyna Kupkova <kristynakupkova@gmail.com>
Date: 2022-01-20 18:55:15 -0500
Commit message:

 biocheck notes fix
 
Package: GenomicDistributions
Commit: fa332328e6996bdd5138bcfe7847cf10c1bd46bf
Author: Kristyna Kupkova <kristynakupkova@gmail.com>
Date: 2022-01-20 18:37:35 -0500
Commit message:

 edits to pass check
 
Package: GenomicDistributions
Commit: 15f9b17fbd20d1260d4eda0c8eb3f62b9865c371
Author: Kristyna Kupkova <kristynakupkova@gmail.com>
Date: 2022-01-20 17:51:29 -0500
Commit message:

 Updated example datasets for building gene models from custom genomes
 
Package: GenomicDistributions
Commit: 2b875d8d2b5e9e99a6751bfeae37af2ef0eca9ce
Author: Jose E. Verdezoto Mosquera <j.esiempreliga@hotmail.com>
Date: 2022-01-19 16:29:46 -0500
Commit message:

 Merge pull request #182 from databio/dev_jose

Dev jose 
Package: GenomicDistributions
Commit: 23e61fb48cda086b7f5db4e2a9fb7740fcdf8a54
Author: joseverdezoto <j.esiempreliga@hotmail.com>
Date: 2022-01-19 16:12:34 -0500
Commit message:

 updated NEWS
 
Package: GenomicDistributions
Commit: 66df18ae5079dccfea0e694e43c0451835e2df49
Author: joseverdezoto <j.esiempreliga@hotmail.com>
Date: 2022-01-18 12:26:53 -0500
Commit message:

 fixed arg in plotQThist, added pvals plot, updated descript
 
Package: GenomicDistributions
Commit: 46542ff91277ddbc073985bf4e1e42baa8700664
Author: Jose E. Verdezoto Mosquera <j.esiempreliga@hotmail.com>
Date: 2022-01-18 10:33:01 -0500
Commit message:

 Merge pull request #181 from databio/dev_jose

Dev jose 
Package: GenomicDistributions
Commit: b58bf8880539931b696d7eb4578acfc8d5de5787
Author: Kristyna Kupkova <kristynakupkova@gmail.com>
Date: 2022-01-14 16:35:33 -0500
Commit message:

 biocheck guidelines
 
Package: GenomicDistributions
Commit: 3166946c917fe388d1dc78c747fccc670f89704d
Author: Kristyna Kupkova <kristynakupkova@gmail.com>
Date: 2022-01-13 20:44:40 -0500
Commit message:

 paramater description update
 
Package: GenomicDistributions
Commit: c9037e3d9bec03bed55ef714dcf064fb5eb0a9a2
Author: Kristyna Kupkova <kristynakupkova@gmail.com>
Date: 2022-01-13 20:23:24 -0500
Commit message:

 #178 parameter quantile replaced with quantThresh

examples relevant to quantile function (function had dist to TSS example)
 
Package: GenomicDistributions
Commit: b2af9848d731f2cc3876273923006025f189e3c0
Author: Kristyna Kupkova <kristynakupkova@gmail.com>
Date: 2022-01-13 19:47:36 -0500
Commit message:

 #176 fixed guides(fill = "none")
 
Package: GenomicDistributions
Commit: 56d969a6a473f16d449ac3ca991b89cfbc484d24
Author: Kristyna Kupkova <kristynakupkova@gmail.com>
Date: 2022-01-13 19:38:43 -0500
Commit message:

 #174 <- removed where possible
 
Package: GenomicDistributions
Commit: d3d85fb96289c657ae4d1bc5d693b466c6ef101c
Author: nsheff <nsheff@users.noreply.github.com>
Date: 2022-01-08 14:29:27 -0500
Commit message:

 Merge branch 'dev' of github.com:databio/GenomicDistributions into dev
 
Package: GenomicDistributions
Commit: f04e6b27b8f273f3831ceb358ad2d09d41b9a302
Author: nsheff <nsheff@users.noreply.github.com>
Date: 2022-01-08 14:28:37 -0500
Commit message:

 Make QTHist consistent

now QThist will show percentages, rather then frequencies,
for single distributions as well as multi-distributions.
Also, the numbers param now works in both cases. Fix #179
 
Package: GenomicDistributions
Commit: 12b5090e0844d6900adbfd99ed11cc74d80d6e7f
Author: nsheff <nsheff@users.noreply.github.com>
Date: 2022-01-08 14:28:37 -0500
Commit message:

 Make QTHist consistent

now QThist will show percentages, rather then frequencies,
for single distributions as well as multi-distributions.
Also, the numbers param now works in both cases. Fix #176
 
Package: GenomicDistributions
Commit: 3f4129954ca0415d31737e0f22caf0aeb3f375dc
Author: Nathan Sheffield <nsheff@users.noreply.github.com>
Date: 2022-01-08 10:20:40 -0500
Commit message:

 Merge pull request #171 from tgstoecker/master

plotChromBins - option to change limit of y-axes 
Package: GenomicDistributions
Commit: 9b34a6c49f5a0d176deb150de412f0660ae51ced
Author: nsheff <nsheff@users.noreply.github.com>
Date: 2022-01-08 10:09:48 -0500
Commit message:

 Update chrom bins plots
 
Package: GenomicDistributions
Commit: e0a113a7163cc3c6e6508422d0fa0f4beb07efc1
Author: nsheff <nsheff@users.noreply.github.com>
Date: 2022-01-07 17:54:00 -0500
Commit message:

 Merge branch 'dev' of github.com:databio/GenomicDistributions into dev
 
Package: GenomicDistributions
Commit: cf49252085a5813b41af4e84e947cb9a44523857
Author: nsheff <nsheff@users.noreply.github.com>
Date: 2022-01-07 17:53:56 -0500
Commit message:

 Add new, faster implementation of calcCChromBinsRef
 
Package: GenomicDistributions
Commit: 5abe04ceacdc3457c2bd639bd8f459a4195b927e
Author: joseverdezoto <j.esiempreliga@hotmail.com>
Date: 2022-01-07 11:01:05 -0500
Commit message:

 add stars for p vals instead of numbers
 
Package: GenomicDistributions
Commit: 9cdfada1e6f01a2c0bcd8f5ab3c023ad02920f22
Author: Kristyna Kupkova <kristynakupkova@gmail.com>
Date: 2022-01-05 15:52:52 -0500
Commit message:

 fix partition overlap frequency count - multi input
 
Package: GenomicDistributions
Commit: a7f0bd119f6a81b38e715b698422fe91f1497ded
Author: Kristyna Kupkova <kristynakupkova@gmail.com>
Date: 2022-01-03 13:29:24 -0500
Commit message:

 updated cell specificity function to more flexible use
 
Package: GenomicDistributions
Commit: b510a0b1984acd660f52b69983dc2f9304c5177c
Author: joseverdezoto <j.esiempreliga@hotmail.com>
Date: 2022-01-03 12:54:11 -0500
Commit message:

 change size/position of pval labels
 
Package: GenomicDistributions
Commit: e36563ef357fb091a28060c08cf3807c7ef6f94d
Author: joseverdezoto <j.esiempreliga@hotmail.com>
Date: 2021-12-28 14:08:05 -0500
Commit message:

 update pval sig figs, make exp plot pvals optional, update doc
 
Package: GenomicDistributions
Commit: 9655c7da154b1c95c0733f2a49415bf143a2c43d
Author: joseverdezoto <j.esiempreliga@hotmail.com>
Date: 2021-12-28 10:50:34 -0500
Commit message:

 use tidy directly from broom
 
Package: GenomicDistributions
Commit: fde1bd4d43ca0c4db9797a337079579cd82c0ef7
Author: joseverdezoto <j.esiempreliga@hotmail.com>
Date: 2021-12-28 10:43:03 -0500
Commit message:

 add p-vals for exp part calc, import broom, update doc
 
Package: GenomicDistributions
Commit: c3b2d03b6d3dec00ed8ccb6f64b7a516cae0d23b
Author: Kristyna Kupkova <kristynakupkova@gmail.com>
Date: 2021-11-30 18:39:06 -0500
Commit message:

 today date
 
Package: GenomicDistributions
Commit: d2707a01761124a2b7538df95d561b4f9e0e39a9
Author: Kristyna Kupkova <kristynakupkova@gmail.com>
Date: 2021-11-30 18:19:22 -0500
Commit message:

 Update DESCRIPTION
 
Package: GenomicDistributions
Commit: db9ada5c1c4351efc7ab33ddcabc160c8f3dd33b
Author: Kristyna Kupkova <kristynakupkova@gmail.com>
Date: 2021-11-30 18:14:34 -0500
Commit message:

 update version for next release
 
Package: GenomicDistributions
Commit: b9ef8c399903651cc7bba1191e56d4708e7b7e86
Author: Tyll Stöcker <53227400+tgstoecker@users.noreply.github.com>
Date: 2021-11-24 21:06:54 +0100
Commit message:

 Merge pull request #1 from tgstoecker/tgstoecker-contribs

Added option to set ylim in plotChromBins 
Package: GenomicDistributions
Commit: 54e25ddff0313aa365fa495afa91c52aec786ad1
Author: Tyll Stöcker <53227400+tgstoecker@users.noreply.github.com>
Date: 2021-11-24 21:06:34 +0100
Commit message:

 Added option to set ylim in plotChromBins

- even one extreme bin size makes the plotChromBins output less usable
  - e.g. if most bins N ~10-100 and one is 8000 everything is scaled for this one bar (ran into this twice now in my work)
- instead of having to manually remove data one can simply set the ylim manually using the new ylim option 
Package: GenomicDistributions
Commit: d279427a5e58355f0af31b46a4e4792518870a55
Author: Jose E. Verdezoto Mosquera <j.esiempreliga@hotmail.com>
Date: 2021-09-28 13:13:51 -0400
Commit message:

 Merge pull request #169 from databio/jose_dev

Add corrected neighbor dist, nearestNeighbors, doc changes 
Package: GenomicDistributions
Commit: 60e2cd09abdc97e5d7abdf789f788883e2e88dc2
Author: joseverdezoto <j.esiempreliga@hotmail.com>
Date: 2021-06-04 19:53:14 -0400
Commit message:

 Add corrected neighbor dist, nearestNeighbors, doc changes
 
Package: octad.db
Commit: 59b1f7a0e12d8acb436760877d06a002be68cd99
Author: Lionir <eygen.chekalin@gmail.com>
Date: 2022-01-20 19:30:23 -0500
Commit message:

 0.21 partial responce to review
 
Package: octad.db
Commit: b78c1c93927de3a3ba28e7dbdc3cb768509ba818
Author: Lionir <eygen.chekalin@gmail.com>
Date: 2022-01-20 19:21:06 -0500
Commit message:

 0.20 partial responce to review
 
Package: octad.db
Commit: 7ce5a494ca60756607f997fa39b6f74b3dc46f8b
Author: Lionir <eygen.chekalin@gmail.com>
Date: 2022-01-20 19:15:40 -0500
Commit message:

 0.19 partial responce to review
 
Package: octad.db
Commit: 8b880d7872515cff97adb31468ceace19061d9e2
Author: Lionir <eygen.chekalin@gmail.com>
Date: 2022-01-20 19:13:19 -0500
Commit message:

 0.19 partial responce to review
 
Package: octad.db
Commit: 0ed03daaf2feb1242a5290c0a41d035064f26236
Author: Lionir <eygen.chekalin@gmail.com>
Date: 2022-01-20 19:03:28 -0500
Commit message:

 0.19 partial responce to review
 
Package: octad.db
Commit: 45578a92179292eb65d9defcc22afa54cdb8addd
Author: Lionir <eygen.chekalin@gmail.com>
Date: 2022-01-20 19:03:03 -0500
Commit message:

 0.19 partial responce to review
 
Package: octad.db
Commit: 9404a74fa61a815e80093ce2c7e2ef9e69677cd2
Author: Lionir <eygen.chekalin@gmail.com>
Date: 2022-01-20 19:01:06 -0500
Commit message:

 0.18 partial responce to review
 
Package: octad.db
Commit: dcd3016c0bfdbc3c01ebacfd22aff5aa8d788c88
Author: Lionir <eygen.chekalin@gmail.com>
Date: 2022-01-20 18:59:02 -0500
Commit message:

 0.18 partial responce to review
 
Package: octad.db
Commit: 032c8f077c133dc2bc035884f7dd2c42ba4e4604
Author: Lionir <eygen.chekalin@gmail.com>
Date: 2022-01-20 18:55:50 -0500
Commit message:

 0.41 partial responce to review
 
Package: octad.db
Commit: 74a70b62a811a67f0d569b41cf971164345c23dc
Author: Lionir <eygen.chekalin@gmail.com>
Date: 2022-01-20 18:38:02 -0500
Commit message:

 0.40 partial responce to review
 
Package: octad.db
Commit: 8c1e42a0461524ffba073110ed04c09b8aaff3df
Author: Lionir <eygen.chekalin@gmail.com>
Date: 2021-11-17 13:57:25 -0500
Commit message:

 0.39 author list update
 
Package: octad.db
Commit: f2e89c4a2e91c3c5bc517ed03e4d77e0dd0c7ddc
Author: Lionir <eygen.chekalin@gmail.com>
Date: 2021-11-12 13:17:15 -0500
Commit message:

 0.38 tidy up
 
Package: octad.db
Commit: f0cd38ae27fe79c4afc8e20704b0f482a5328e04
Author: Lionir <eygen.chekalin@gmail.com>
Date: 2021-11-12 12:51:43 -0500
Commit message:

 0.37 tidy up
 
Package: octad.db
Commit: bf5867abb9ff5e25e043daa8a15a2ef64c6b462d
Author: Lionir <eygen.chekalin@gmail.com>
Date: 2021-11-12 12:28:05 -0500
Commit message:

 0.36 tidy up
 
Package: octad.db
Commit: 5014a58576fb6c10f87cf2aa15b680208b66b6c8
Author: Lionir <eygen.chekalin@gmail.com>
Date: 2021-11-12 00:46:36 -0500
Commit message:

 removed 32-bit support 0.35
 
Package: octad.db
Commit: 5072bb896a671e3a1165a6622a70190762c66525
Author: Lionir <eygen.chekalin@gmail.com>
Date: 2021-11-11 17:00:49 -0500
Commit message:

 looking for the bottleneck 0.34
 
Package: octad.db
Commit: 8008680b901e250ae0610ea03f06b3f52db83b64
Author: Lionir <eygen.chekalin@gmail.com>
Date: 2021-11-11 14:27:17 -0500
Commit message:

 looking for the bottleneck
 
Package: octad.db
Commit: 6a5943f7d9c4b474d8fde25b5bbecfd23b253d0f
Author: Lionir <eygen.chekalin@gmail.com>
Date: 2021-11-11 13:59:58 -0500
Commit message:

 v0.99.32
 
Package: octad.db
Commit: ed6b7e409add11db2f04ffddb4462afd2f02542f
Author: Lionir <eygen.chekalin@gmail.com>
Date: 2021-11-11 13:14:40 -0500
Commit message:

 v0.99.31
 
Package: octad.db
Commit: d7ee8bd03af9bd9591860d08e9159c9ac42d9199
Author: Lionir <eygen.chekalin@gmail.com>
Date: 2021-11-11 12:44:48 -0500
Commit message:

 v0.99.30
 
Package: octad.db
Commit: b274c4fe9db428eaf62006c49f5b1d0da150ea1a
Author: Lionir <eygen.chekalin@gmail.com>
Date: 2021-11-11 12:44:12 -0500
Commit message:

 v0.99.30
 
Package: octad.db
Commit: 7360f8d93836602b3e6ccba5b88f60629e5fd03c
Author: Lionir <eygen.chekalin@gmail.com>
Date: 2021-11-09 14:28:47 -0500
Commit message:

 v0.99.29
 
Package: octad.db
Commit: 8179437270ae2bc02b98c27ee2e581b8aeed1364
Author: Lionir <eygen.chekalin@gmail.com>
Date: 2021-11-09 14:07:30 -0500
Commit message:

 v0.99.30
 
Package: octad.db
Commit: cd5198365ee719c18dd14cad50bec69733d94960
Author: Lionir <eygen.chekalin@gmail.com>
Date: 2021-11-09 13:11:14 -0500
Commit message:

 v0.99.29
 
Package: octad.db
Commit: d27e509fac730b752c793044e186cd75ea1b8063
Author: Lionir <eygen.chekalin@gmail.com>
Date: 2021-11-09 13:10:25 -0500
Commit message:

 v0.99.29
 
Package: octad.db
Commit: e9a1a9e819f509d81636a9295fc61d51b776eb84
Author: Lionir <eygen.chekalin@gmail.com>
Date: 2021-11-09 13:05:17 -0500
Commit message:

 v0.99.29
 
Package: octad.db
Commit: 8674abaeba928d40096aa188866532cac391353f
Author: Lionir <eygen.chekalin@gmail.com>
Date: 2021-11-09 11:38:25 -0500
Commit message:

 v0.99.28
 
Package: octad.db
Commit: 390311db4fa122bdfe3dce8da078c9fc7b6c2779
Author: Lionir <eygen.chekalin@gmail.com>
Date: 2021-11-09 11:30:27 -0500
Commit message:

 v0.99.27
 
Package: octad.db
Commit: 20111439399516806c98238763c019e3b2cb75cb
Author: Lionir <eygen.chekalin@gmail.com>
Date: 2021-11-08 19:58:41 -0500
Commit message:

 v0.99.26
 
Package: octad.db
Commit: 944778d670d4465a1207ed336f403b60855f39cd
Author: Lionir <eygen.chekalin@gmail.com>
Date: 2021-11-08 18:59:01 -0500
Commit message:

 v0.99.25
 
Package: octad.db
Commit: 87d3333051f972a26c0b262e6685fb79b52034eb
Author: Lionir <eygen.chekalin@gmail.com>
Date: 2021-11-08 18:10:44 -0500
Commit message:

 v0.99.24
 
Package: octad.db
Commit: 330a4c6db5cf7c58aecb10ce1ff9f98808ab3e9c
Author: Lionir <eygen.chekalin@gmail.com>
Date: 2021-11-08 16:44:26 -0500
Commit message:

 v0.99.23
 
Package: octad.db
Commit: 97e9337a643cda7eade8f15d7b721bc2240193de
Author: Lionir <eygen.chekalin@gmail.com>
Date: 2021-11-08 16:33:43 -0500
Commit message:

 v0.99.24
 
Package: octad.db
Commit: 5ce3487710ea38e55039416b850675adc6d978b0
Author: Lionir <eygen.chekalin@gmail.com>
Date: 2021-11-08 16:32:12 -0500
Commit message:

 v0.99.23
 
Package: octad.db
Commit: e547c1f4a83ab898fad4c018e3188ab63ab3e730
Author: Lionir <eygen.chekalin@gmail.com>
Date: 2021-11-08 12:34:15 -0500
Commit message:

 v0.99.22
 
Package: octad.db
Commit: 1bcd66bd36d4017c68fda9678ac28ea862ae5a60
Author: Lionir <eygen.chekalin@gmail.com>
Date: 2021-11-08 12:07:03 -0500
Commit message:

 v0.99.21
 
Package: octad.db
Commit: 4e54b1d916421ea096cc9495b2b7af64ce2657d2
Author: Lionir <eygen.chekalin@gmail.com>
Date: 2021-11-08 12:06:08 -0500
Commit message:

 v0.99.20
 
Package: octad.db
Commit: 449e5e9df47c9e288ee2a3fe072a16d1dc897b06
Author: Lionir <eygen.chekalin@gmail.com>
Date: 2021-11-07 12:01:57 -0500
Commit message:

 v0.99.19
 
Package: octad.db
Commit: 13fc02fb0d84ad9ab3ce26977ca874295b382102
Author: Lionir <eygen.chekalin@gmail.com>
Date: 2021-11-07 11:42:26 -0500
Commit message:

 v0.99.18
 
Package: octad.db
Commit: e3f193f3cacefd578902602ad81b00faf26de19c
Author: Lionir <eygen.chekalin@gmail.com>
Date: 2021-11-07 10:51:24 -0500
Commit message:

 v0.99.17
 
Package: octad.db
Commit: 1e217fc18c1b85270f8f1eabe75ca7d08004f9e1
Author: Lionir <eygen.chekalin@gmail.com>
Date: 2021-11-06 23:48:05 -0400
Commit message:

 v0.99.16
 
Package: octad.db
Commit: fc66fbfd0c224c2b6ab2b5fee811d47b39e3e0a8
Author: Lionir <eygen.chekalin@gmail.com>
Date: 2021-11-06 23:10:53 -0400
Commit message:

 v0.99.15
 
Package: octad.db
Commit: b1f80f983c4e7eaa8a3019ac6bd44cba31a3e040
Author: Lionir <eygen.chekalin@gmail.com>
Date: 2021-11-06 22:37:13 -0400
Commit message:

 v0.99.14
 
Package: octad.db
Commit: 8ee7d2abc4925ea4d8b4bf2c686465c600bf42c5
Author: Lionir <eygen.chekalin@gmail.com>
Date: 2021-11-06 22:01:01 -0400
Commit message:

 v0.99.13
 
Package: octad.db
Commit: 91deceed5df932bfd9344fad37ef6827cc4c336a
Author: Lionir <eygen.chekalin@gmail.com>
Date: 2021-11-06 14:41:54 -0400
Commit message:

 v0.99.9
 
Package: octad.db
Commit: 328519c0f23bb5f74f3d9db2a1444a86a58d6ce8
Author: Lionir <eygen.chekalin@gmail.com>
Date: 2021-11-06 13:16:15 -0400
Commit message:

 v0.99.9
 
Package: octad.db
Commit: 1df358a73c316ed90fb55bd880b03b1c2954e252
Author: Lionir <eygen.chekalin@gmail.com>
Date: 2021-11-06 13:01:39 -0400
Commit message:

 v0.99.9
 
Package: octad.db
Commit: 2a81ac2615073c26fab1385348eb305779d8a10a
Author: Lionir <eygen.chekalin@gmail.com>
Date: 2021-11-06 11:27:15 -0400
Commit message:

 v0.99.9
 
Package: octad.db
Commit: a1747daf41078c46ab099a7f7eb6452e2e13f7e2
Author: Lionir <eygen.chekalin@gmail.com>
Date: 2021-11-06 09:17:35 -0400
Commit message:

 v0.99.8
 
Package: octad.db
Commit: e640a1b3e2645587d28773fed5d62aa6e846ab3f
Author: Lionir <eygen.chekalin@gmail.com>
Date: 2021-11-05 21:43:35 -0400
Commit message:

 v0.99.7
 
Package: octad.db
Commit: 1581553f22a738c8203c8cd3f5abaf60f307cf9e
Author: Lionir <eygen.chekalin@gmail.com>
Date: 2021-11-05 17:29:50 -0400
Commit message:

 v0.99.6
 
Package: octad.db
Commit: 3728e08dcd1928fb7803f4b224e717a3f8b29f43
Author: Lionir <eygen.chekalin@gmail.com>
Date: 2021-11-05 17:11:54 -0400
Commit message:

 v0.99.5
 
Package: octad.db
Commit: 3e84b07f8c02ce9450a4d5c7671aa1dcfcd7e679
Author: Lionir <eygen.chekalin@gmail.com>
Date: 2021-11-05 15:54:52 -0400
Commit message:

 v0.99.4
 
Package: octad.db
Commit: 9fc8f3c8f86e460fc00be6ecfaf8b68d2d51efd5
Author: Lionir <eygen.chekalin@gmail.com>
Date: 2021-11-01 19:56:00 -0400
Commit message:

 v0.99.3
 
Package: octad.db
Commit: c6ff8aa750e89704d88142522a81fde48ff17baa
Author: Lionir <eygen.chekalin@gmail.com>
Date: 2021-11-01 19:41:49 -0400
Commit message:

 v0.99.2
 
Package: octad.db
Commit: 8731193c05c9a1c59fa00c357a35cf63bc7fa54d
Author: Lionir <eygen.chekalin@gmail.com>
Date: 2021-11-01 19:40:17 -0400
Commit message:

 v0.99.1
 
Package: octad.db
Commit: ce42d281724c5c1789c53e99b249769e224a9d5f
Author: Lionir <eygen.chekalin@gmail.com>
Date: 2021-11-01 19:37:39 -0400
Commit message:

 v0.99.1
 
Package: octad.db
Commit: 0f9e8f4685e0a9a9d608878cb41456b94afbf253
Author: Lionir <eygen.chekalin@gmail.com>
Date: 2021-11-01 19:33:34 -0400
Commit message:

 v0.99.1
 
Package: octad.db
Commit: a74aa78ddadb23ab4b51f107f16ed68318ba0c67
Author: Lionir <eygen.chekalin@gmail.com>
Date: 2021-11-01 19:13:07 -0400
Commit message:

 v0.99.1
 
Package: octad.db
Commit: 68d115523f3a5bbb28d155358ac704b3b9e2583a
Author: Lionir <eygen.chekalin@gmail.com>
Date: 2021-10-25 14:50:30 -0400
Commit message:

 v0.99.0
 

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