Bioconductor has moved to GIT for contributed packages; the subversion logs are no longer active.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

GIT Logs

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

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

Package: zellkonverter
Commit: e4fc11792b1b600f52acf6b3384a1eda46362b4c
Author: Luke Zappia <lazappi@users.noreply.github.com>
Date: 2021-10-20 21:57:26 +0200
Commit message:

 Update NEWS.Rd for release
Package: zellkonverter
Commit: 9aba6a1a76d6005f076d27f5a1c32012a4d00b80
Author: Luke Zappia <lazappi@users.noreply.github.com>
Date: 2021-10-20 21:48:41 +0200
Commit message:

 Bump version
Package: zellkonverter
Commit: 8ca691b37128b76ad69b064c4191df1a5f811f43
Author: Luke Zappia <lazappi@users.noreply.github.com>
Date: 2021-10-20 21:47:24 +0200
Commit message:

 Merge branch 'raw'

* raw:
  Update NEWS
  Add test for raw conversion
  Add support for converting raw to atlExp
Package: zellkonverter
Commit: aaa3b09c02a3262fa10d5bad2ece5ef9043f32ac
Author: Luke Zappia <lazappi@users.noreply.github.com>
Date: 2021-10-20 21:47:09 +0200
Commit message:

 Update NEWS
Package: zellkonverter
Commit: ca8ccdc2d6c170bcce5614f52b47fd6462889e9f
Author: Luke Zappia <lazappi@users.noreply.github.com>
Date: 2021-10-20 21:36:11 +0200
Commit message:

 Add test for raw conversion

Uses scanpy PBMC3K dataset, will have to see if that causes issues
Package: zellkonverter
Commit: 5125ca57ab623d6399253cc26c122d3e7bca69f6
Author: Luke Zappia <lazappi@users.noreply.github.com>
Date: 2021-10-20 21:19:15 +0200
Commit message:

 Add support for converting raw to atlExp
Package: zellkonverter
Commit: d5b018024ff8d236d8e35762721663d19ae593b8
Author: Luke Zappia <lazappi@users.noreply.github.com>
Date: 2021-10-20 20:31:20 +0200
Commit message:

 Merge branch 'selection'

* selection:
  Update NEWS
  Adjust slot argument documentation
  Add some minimal slot arguments tests for writeH5AD
  Add slot selection arguments to SCE2AnnData
  Add tests for slot arguments in AnnData2SCE
  Add slot selection arguments to AnnData2SCE
Package: zellkonverter
Commit: 530ab9ca4cc563689a4602dd346423f5f61ec796
Author: Luke Zappia <lazappi@users.noreply.github.com>
Date: 2021-10-20 20:30:49 +0200
Commit message:

 Update NEWS
Package: zellkonverter
Commit: e1e95b153b51441e07eb38a91832994a1ed68c48
Author: Luke Zappia <lazappi@users.noreply.github.com>
Date: 2021-10-20 20:27:23 +0200
Commit message:

 Adjust slot argument documentation
Package: zellkonverter
Commit: e3e160226e32c36eb2425fa85ebfe5e2ce022916
Author: Luke Zappia <lazappi@users.noreply.github.com>
Date: 2021-10-20 20:19:00 +0200
Commit message:

 Add some minimal slot arguments tests for writeH5AD
Package: zellkonverter
Commit: b4abb7e363efe2b124bfa20cb9e6fb13701747e0
Author: Luke Zappia <lazappi@users.noreply.github.com>
Date: 2021-10-20 20:07:21 +0200
Commit message:

 Add slot selection arguments to SCE2AnnData
Package: zellkonverter
Commit: 8859e146b8df0d0f7161551ffdc42e8d93092020
Author: Luke Zappia <lazappi@users.noreply.github.com>
Date: 2021-10-20 14:10:50 +0200
Commit message:

 Add tests for slot arguments in AnnData2SCE

Pretty basic, could do with improving
Package: zellkonverter
Commit: 016d00427993f4d51c4f0b6719a3768fa3c95387
Author: Luke Zappia <lazappi@users.noreply.github.com>
Date: 2021-10-19 16:54:55 +0200
Commit message:

 Add slot selection arguments to AnnData2SCE
Package: zellkonverter
Commit: ab36fc74bd70c3ab0a084c1abe9c6e438ea4b176
Author: Luke Zappia <lazappi@users.noreply.github.com>
Date: 2021-10-19 15:11:26 +0200
Commit message:

 Split konverter.R into two files

Separate AnnData2SCE and SCE2AnnData functions. The file was getting
long and hard to find things.
Package: zellkonverter
Commit: c8ec7b3badb14fc871ed2be24b1e17cc389a9f8a
Author: Luke Zappia <lazappi@users.noreply.github.com>
Date: 2021-10-19 15:04:07 +0200
Commit message:

 Merge branch 'verbose'

* verbose:
  Update spellcheck wordlist
  Add section about progress messages to vignette
  Minor fix to checks
  Finish adding progress messages
  Add progress messages to readH5AD and AnnData2SCE
Package: zellkonverter
Commit: 19f08f9aaf6380731bd9313368fffc3cc387dbd2
Author: Luke Zappia <lazappi@users.noreply.github.com>
Date: 2021-10-19 15:03:14 +0200
Commit message:

 Update spellcheck wordlist
Package: zellkonverter
Commit: 214189af96304cbb3638c4046645a5addaafe3ba
Author: Luke Zappia <lazappi@users.noreply.github.com>
Date: 2021-10-19 15:02:19 +0200
Commit message:

 Add section about progress messages to vignette
Package: zellkonverter
Commit: 04fcaf727a68c2c554b3bfa7fbf9cd66705aa988
Author: Luke Zappia <lazappi@users.noreply.github.com>
Date: 2021-10-19 14:44:28 +0200
Commit message:

 Minor fix to checks
Package: zellkonverter
Commit: fa813b0da5af82f2c1595f8946a62ee3f6eebb88
Author: Luke Zappia <lazappi@users.noreply.github.com>
Date: 2021-10-19 14:22:30 +0200
Commit message:

 Finish adding progress messages

Could still be improved but good enough for now
Package: zellkonverter
Commit: 6c67f786799fd02b46408fdc998e3d5370ce9b56
Author: Luke Zappia <lazappi@users.noreply.github.com>
Date: 2021-09-14 14:56:53 +0200
Commit message:

 Add progress messages to readH5AD and AnnData2SCE
Package: DepecheR
Commit: 8333cc18964323d9b96122eb34aa7ce2dff441a5
Author: Jakob Theorell <jakob.theorell@ki.se>
Date: 2021-10-20 21:49:09 +0200
Commit message:

 Change of email addresses
Package: BioNERO
Commit: 00f2f76f7ab26d49fc6f40071cdd58dfff7d621c
Author: almeidasilvaf <fabricio_almeidasilva@hotmail.com>
Date: 2021-10-20 16:36:04 -0300
Commit message:

 Bug fix: changes in igraph were not committed
Package: orthogene
Commit: 64e87637adf6ee7809ff191bc2aa882632b0e675
Author: Brian M. Schilder <34280215+bschilder@users.noreply.github.com>
Date: 2021-10-20 15:25:58 -0400
Commit message:

 Enable all_genes to keep NAs
Package: BSgenome
Commit: 4c2a49e981474741bac3d4e7b3d4aaa712f2bfcb
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2021-10-20 11:52:30 -0700
Commit message:

 bump BSgenome.Hsapiens.UCSC.hg38 version
Package: attract
Commit: ff46ef70d1044856f01c2a4c2f04ffdd4a23acba
Author: szimmerman92 <samuel.e.zimmerman@gmail.com>
Date: 2021-10-20 14:51:22 -0400
Commit message:

 fix bug when pathway name is missing
Package: BSgenome
Commit: 29ac6272656d6f7d640fac847e1ffa19c6c2a1e2
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2021-10-20 11:34:03 -0700
Commit message:

 Resync BSgenome.Hsapiens.UCSC.hg38 with GRCh38.p13 (was based on GRCh38.p12)
Package: nullranges
Commit: d9211c442efaee2cd808695874a5082d8dee216d
Author: mikelove <michaelisaiahlove@gmail.com>
Date: 2021-10-20 14:15:53 -0400
Commit message:

 updating github actions and docs
Package: matter
Commit: 1a27cb89a6be63df0aa5c771bcaacae02ef4b93c
Author: Kylie Bemis <k.bemis@northeastern.edu>
Date: 2021-10-20 13:19:54 -0400
Commit message:

 v1.19.1 fix error in cbind() on matter_vec objs
Package: BioNERO
Commit: 3f47e05d01c0c35e66ed1adfe9ccbd958938e89a
Author: almeidasilvaf <fabricio_almeidasilva@hotmail.com>
Date: 2021-10-20 14:59:05 -0300
Commit message:

 bug fix: fixed bug in check_SFT() resulting from change in {igraph} when the degree distribution contains only a single integer
Package: QDNAseq
Commit: a32bf44181d83810690e3bd13f76d7c994ce0b97
Author: Henrik Bengtsson <hb@aroma-project.org>
Date: 2021-10-20 10:07:57 -0700
Commit message:

 Merge branch 'release/1.29.5'
Package: QDNAseq
Commit: b7bde5d344f865c0dd60432ae5e4769d8a2288fa
Author: Henrik Bengtsson <hb@aroma-project.org>
Date: 2021-10-20 10:07:49 -0700
Commit message:

 QDNAseq 1.29.5
Package: QDNAseq
Commit: 5cb16f5f57ff9b1106ada76631d1916e8d4bdf98
Author: Henrik Bengtsson <hb@aroma-project.org>
Date: 2021-10-20 09:56:48 -0700
Commit message:

 CODE CLEANUP: TABs -> SPACEs + drop '# EOF' comment in some source files
Package: QDNAseq
Commit: a91b9a51b857e87dee1ebbacb86326661cf9a0bb
Author: Henrik Bengtsson <hb@aroma-project.org>
Date: 2021-10-20 09:48:54 -0700
Commit message:

 PERFORMANCE: Use useNames=FALSE in all matrixStats calls (fixes #98)
Package: QDNAseq
Commit: 49d024bada6aa2b6a00c327befadbecf8c8067e5
Author: Henrik Bengtsson <hb@aroma-project.org>
Date: 2021-10-20 09:10:38 -0700
Commit message:

 Moved 'future' from Imports to Suggests (fixes #97)
Package: QDNAseq
Commit: 5643963bd16fea29418dc514861f4a7b3374811a
Author: Henrik Bengtsson <hb@aroma-project.org>
Date: 2021-10-16 09:58:49 -0700
Commit message:

 Bump develop version [ci skip]
Package: QDNAseq
Commit: 1145d6edaab72be88f40519ecd194da19d9c3ed9
Author: Henrik Bengtsson <hb@aroma-project.org>
Date: 2021-10-16 09:57:30 -0700
Commit message:

 Merge tag '1.29.4' into develop

QDNAseq 1.29.4
Package: nullranges
Commit: 39f1c68c26a31523dec8a150a137525e06e04347
Author: mikelove <michaelisaiahlove@gmail.com>
Date: 2021-10-20 13:39:01 -0400
Commit message:

 version bump
Package: nullranges
Commit: 83a346f2749933ab2bf3de220d17ed05e3e153d3
Author: mikelove <michaelisaiahlove@gmail.com>
Date: 2021-10-20 13:29:45 -0400
Commit message:

 renaming boot arguments and re-arranging
Package: IgGeneUsage
Commit: b5be920fa76ed495f16fefd76c44ba2d09afabf1
Author: sktron <simo.kitanovski@uni-due.de>
Date: 2021-10-20 19:20:30 +0200
Commit message:

 bugfix, tests
Package: ISAnalytics
Commit: b8680040eda527fc5c48bee3799e81bc5f3b0647
Author: Giulia Pais <giuliapais1@gmail.com>
Date: 2021-10-20 19:04:55 +0200
Commit message:

 [UPDATE] Update to version 1.3.7
Package: ISAnalytics
Commit: a422401417d2e3691d4c1644f8b8c97623ea3692
Author: Giulia Pais <giuliapais1@gmail.com>
Date: 2021-10-14 11:19:20 +0200
Commit message:

 [FIX] Fixed issue in murine refGenes
Package: ISAnalytics
Commit: 0e802df3cf62b246f682e4a0cfa29bc30bda52cb
Author: Giulia Pais <giuliapais1@gmail.com>
Date: 2021-10-07 10:51:09 +0200
Commit message:

 [HOTFIX] Fixed minor issue in recalibration function
Package: ISAnalytics
Commit: a4c41d12e9ba373dcb62aa8c1e2eefdf53c0335d
Author: Giulia Pais <giuliapais1@gmail.com>
Date: 2021-10-06 11:04:40 +0200
Commit message:

 changed readme badge
Package: ISAnalytics
Commit: 062baa27ad846f40276d3599c9a0e02513838665
Author: Giulia Pais <giuliapais1@gmail.com>
Date: 2021-10-06 11:01:44 +0200
Commit message:

 Update README.Rmd
Package: ISAnalytics
Commit: 04a754abf24ed05e71f3c038f8ff0f34a725f5b0
Author: Giulia Pais <giuliapais1@gmail.com>
Date: 2021-10-06 11:00:03 +0200
Commit message:

 [FIX] Minor fixes on readme and pkgdown file
Package: ggmanh
Commit: bec593a78f1c5748a3e654a06b7414a01cae4dbb
Author: Lee, John S <john.lee@abbvie.com>
Date: 2021-10-20 12:01:52 -0500
Commit message:

 Version bump. Resolve NAMESPACE warning issue
Package: ggmanh
Commit: 41be74634999d5e53f682bdf1af8509d70928729
Author: Lee, John S <john.lee@abbvie.com>
Date: 2021-10-20 11:35:44 -0500
Commit message:

 version bump

Split functions to separate files.
Add GRanges support for manhattan_chromosome function. Fixed some bugs.
Package: ggmanh
Commit: 16f1ecef5e35b2795add1c84ee659469dbe30a1b
Author: Lee, John S <john.lee@abbvie.com>
Date: 2021-10-20 10:04:27 -0500
Commit message:

 Go back to using defining functions as S3 Generic
Package: SynExtend
Commit: e9547dcb0fbf634e72e4aabcaeef70209c7c0363
Author: npcooley <npcooley@gmail.com>
Date: 2021-10-20 12:09:47 -0400
Commit message:

 New functions
Package: SynExtend
Commit: 83d6ed2bfa141010e4db431b76a44cd049791f43
Author: npcooley <npcooley@gmail.com>
Date: 2021-09-07 12:15:52 -0400
Commit message:

 Missing Verbose logical added
Package: wateRmelon
Commit: 6bac3c234f12c08b42622cc0a9094a1ac488acb9
Author: Tyler Gorrie-Stone <tyler.gorrie-stone@diamond.ac.uk>
Date: 2021-10-15 09:52:15 +0100
Commit message:

 adding missing methods
Package: wateRmelon
Commit: 863fce0151b8c43de842ec020ba912b77f823bc2
Author: Tyler Gorrie-Stone <tyler.gorrie-stone@diamond.ac.uk>
Date: 2021-10-14 10:58:13 +0100
Commit message:

 typofix
Package: wateRmelon
Commit: dd0fa939f3de37f24ceeb5d234ccda8e1da799f6
Author: Tyler Gorrie-Stone <tyler.gorrie-stone@diamond.ac.uk>
Date: 2021-10-13 15:35:51 +0100
Commit message:

 Final? update
Package: wateRmelon
Commit: 04e53b3a76285d78fbdb1b659e1dfdbfa143b6fe
Author: Tyler Gorrie-Stone <tyler.gorrie-stone@diamond.ac.uk>
Date: 2021-10-13 11:16:56 +0100
Commit message:

 upping version
Package: wateRmelon
Commit: c5ebf2d85378fc0d512a7c13f463c3e3d2e65042
Author: Tyler Gorrie-Stone <tyler.gorrie-stone@diamond.ac.uk>
Date: 2021-10-13 11:12:54 +0100
Commit message:

 remove inst/doc
Package: wateRmelon
Commit: 815e8833a9d59a60f3b4f65f968b9bad523df5a7
Author: Tyler Gorrie-Stone <tyler.gorrie-stone@diamond.ac.uk>
Date: 2021-10-13 11:11:16 +0100
Commit message:

 Adding new vigette - needs more text though
Package: wateRmelon
Commit: 839d3b618c067f25db0eb4ff45effdfee7443d40
Author: Tyler Gorrie-Stone <tyler.gorrie-stone@diamond.ac.uk>
Date: 2021-10-04 14:52:29 +0100
Commit message:

 Update README.md
Package: wateRmelon
Commit: 71226dfe5983fff30239e28e515176e1efc17bf3
Author: Tyler Gorrie-Stone <tyler.gorrie-stone@diamond.ac.uk>
Date: 2021-10-04 14:49:19 +0100
Commit message:

 4 NOTES
Package: wateRmelon
Commit: e892179a3f5fa32e6b7ec65ea1361598fc5268d9
Author: Tyler Gorrie-Stone <tyler.gorrie-stone@diamond.ac.uk>
Date: 2021-10-04 13:36:13 +0100
Commit message:

 Update DESCRIPTION
Package: wateRmelon
Commit: bbe63c86091e8e74b928c5b85df2e5f6e525d3d7
Author: Tyler Gorrie-Stone <tyler.gorrie-stone@diamond.ac.uk>
Date: 2021-10-04 13:34:49 +0100
Commit message:

 Update outlyx.Rd
Package: wateRmelon
Commit: c259c386de97c606a86a98da6973700ee4103835
Author: Tyler Gorrie-Stone <tyler.gorrie-stone@diamond.ac.uk>
Date: 2021-10-04 13:31:57 +0100
Commit message:

 Merge pull request #9 from schalkwyk/Deconvolution-error-branch

Deconvolution error branch
Package: wateRmelon
Commit: bdbe31cfeba939a858979dab1cec98ef655121f0
Author: Tyler Gorrie-Stone <tyler.gorrie-stone@diamond.ac.uk>
Date: 2021-10-04 13:31:30 +0100
Commit message:

 Update agep.Rd
Package: wateRmelon
Commit: 026b1c76cdc0f7b44c1260894e003aa42715998b
Author: Tyler Gorrie-Stone <tyler.gorrie-stone@diamond.ac.uk>
Date: 2021-10-04 13:31:24 +0100
Commit message:

 Update estimateCellCounts.wmln.rd
Package: wateRmelon
Commit: 71546d72d907fd93eccaa90feccae48d14f8e08e
Author: Tyler Gorrie-Stone <tyler.gorrie-stone@diamond.ac.uk>
Date: 2021-10-04 13:25:41 +0100
Commit message:

 Merge pull request #7 from schalkwyk/agep-fixes

Update horv.R
Package: wateRmelon
Commit: 0c139265876c532b045d5d004d92274157c837f6
Author: Tyler Gorrie-Stone <tyler.gorrie-stone@diamond.ac.uk>
Date: 2021-10-04 13:25:26 +0100
Commit message:

 Merge branch 'master' into agep-fixes
Package: wateRmelon
Commit: ba9b83743641b559fad123b6e16f6a1fb4b30122
Author: Tyler Gorrie-Stone <tyler.gorrie-stone@diamond.ac.uk>
Date: 2021-10-04 13:24:47 +0100
Commit message:

 Manual Page
Package: wateRmelon
Commit: ab41c2964d21e2385b6474e57a05c3e0996a13e5
Author: Tyler Gorrie-Stone <tyler.gorrie-stone@diamond.ac.uk>
Date: 2021-08-31 15:35:24 +0100
Commit message:

 bug fix
Package: wateRmelon
Commit: cab1a677c6b3efcaafc2c4f830ecb6f116f3dad2
Author: Tyler Gorrie-Stone <tyler.gorrie-stone@diamond.ac.uk>
Date: 2021-08-26 16:25:40 +0100
Commit message:

 n missing and missing probes
Package: wateRmelon
Commit: 3f688b890ab6426a1309d8ee4d46455cbd58413f
Author: Tyler Gorrie-Stone <tyler.gorrie-stone@diamond.ac.uk>
Date: 2021-08-26 13:22:07 +0100
Commit message:

 Fixing ot nonsense...
Package: wateRmelon
Commit: d2f9185a8aeb500971c78e3c6c96a37e3bc521b2
Author: Tyler Gorrie-Stone <tyler.gorrie-stone@diamond.ac.uk>
Date: 2021-08-26 13:07:19 +0100
Commit message:

 Update y_minfi.R
Package: wateRmelon
Commit: eaa5b7dba47f1d9eec891e3211fbfdaa914651c8
Author: Tyler Gorrie-Stone <tyler.gorrie-stone@diamond.ac.uk>
Date: 2021-08-26 12:54:19 +0100
Commit message:

 Update y_minfi.R
Package: wateRmelon
Commit: cc3ca25feba00ec0aaffb14b372d7e2127c2e5fb
Author: Tyler Gorrie-Stone <tyler.gorrie-stone@diamond.ac.uk>
Date: 2021-08-26 12:53:49 +0100
Commit message:

 Update x_methylumi.R
Package: wateRmelon
Commit: 803157d36c5896ec0859f63cc4306451b2ec20fc
Author: Tyler Gorrie-Stone <tyler.gorrie-stone@diamond.ac.uk>
Date: 2021-08-26 12:41:58 +0100
Commit message:

 Adding minfi methods for estimatecellcounts.wmln 

Incase people need them!
Package: wateRmelon
Commit: 5922fd208e4f72f890ab53cae88ed3281c260f67
Author: Tyler Gorrie-Stone <tyler.gorrie-stone@diamond.ac.uk>
Date: 2021-08-26 12:34:40 +0100
Commit message:

 Update x_methylumi.R
Package: wateRmelon
Commit: fe2d02ea7c920e3fffd3fd3d9c747fc36e11604a
Author: Tyler Gorrie-Stone <tyler.gorrie-stone@diamond.ac.uk>
Date: 2021-08-26 12:34:11 +0100
Commit message:

 Update AllGenerics.R
Package: wateRmelon
Commit: 179e63b1e10af76ae033c8f9554bafe8f8f766b2
Author: Tyler Gorrie-Stone <tyler.gorrie-stone@diamond.ac.uk>
Date: 2021-08-26 12:30:02 +0100
Commit message:

 Update AllGenerics.R
Package: wateRmelon
Commit: 592d8c678699c86e32b0af1613f159bc105822ad
Author: Tyler Gorrie-Stone <tyler.gorrie-stone@diamond.ac.uk>
Date: 2021-08-26 12:29:52 +0100
Commit message:

 Update x_methylumi.R
Package: wateRmelon
Commit: c19acebdbc79c10fc0cc6bd276c9405a585fe1e8
Author: Tyler Gorrie-Stone <tyler.gorrie-stone@diamond.ac.uk>
Date: 2021-08-26 12:29:23 +0100
Commit message:

 Update AllGenerics.R
Package: wateRmelon
Commit: 177a1484b1618a93249ee9f527821546f7d3d782
Author: Tyler Gorrie-Stone <tyler.gorrie-stone@diamond.ac.uk>
Date: 2021-08-26 12:15:19 +0100
Commit message:

 Update AllGenerics.R
Package: wateRmelon
Commit: 4f1f7be3a6bcb0a75438475b73da0c7f0153c3f8
Author: Tyler Gorrie-Stone <tyler.gorrie-stone@diamond.ac.uk>
Date: 2021-08-26 12:14:47 +0100
Commit message:

 Adding Method
Package: wateRmelon
Commit: 0e1ae599dec99142c71a7a23baeb36e89fd33076
Author: Tyler Gorrie-Stone <tyler.gorrie-stone@diamond.ac.uk>
Date: 2021-08-26 12:08:20 +0100
Commit message:

 Removing redundant platform type
Package: wateRmelon
Commit: eda9e67434cccef149916f6136ed2cbb8373741d
Author: Tyler Gorrie-Stone <tyler.gorrie-stone@diamond.ac.uk>
Date: 2021-08-26 11:40:47 +0100
Commit message:

 Update estimateCellCounts.R
Package: wateRmelon
Commit: 8db9afe3a35d695e49172cf47036afee4218c98b
Author: Tyler Gorrie-Stone <tyler.gorrie-stone@diamond.ac.uk>
Date: 2021-08-26 10:34:05 +0100
Commit message:

 Update DESCRIPTION
Package: wateRmelon
Commit: 1fffb539edaeb592bbebdc5e32797ee359a875bb
Author: Tyler Gorrie-Stone <tyler.gorrie-stone@diamond.ac.uk>
Date: 2021-08-26 10:33:31 +0100
Commit message:

 Updating Description to suggest the cell type packages...

Might increase build size but nothing minfi does not bloat anyway.
Package: wateRmelon
Commit: c449a6bda0c2367c74f81c4f52cefe8a53affa52
Author: Tyler Gorrie-Stone <tyler.gorrie-stone@diamond.ac.uk>
Date: 2021-08-26 10:32:05 +0100
Commit message:

 Removing grok so function now looks for FlowSorted.Blood.EPIC
Package: wateRmelon
Commit: 8a4e66280737dad4f3b71e0d99a053416ace3500
Author: Tyler Gorrie-Stone <tyler.gorrie-stone@diamond.ac.uk>
Date: 2021-08-26 09:44:37 +0100
Commit message:

 Update horv.R
Package: wateRmelon
Commit: 213c2d3837786844d4fff28e4d8333b5c0c118fc
Author: Tyler Gorrie-Stone <tyler.gorrie-stone@diamond.ac.uk>
Date: 2021-08-25 20:31:56 +0100
Commit message:

 Update horv.R
Package: wateRmelon
Commit: 61725a541dfc299a6565be750b848933d08d4f10
Author: Tyler Gorrie-Stone <tyler.gorrie-stone@diamond.ac.uk>
Date: 2021-08-25 20:27:56 +0100
Commit message:

 Fixing coifs.
Package: wateRmelon
Commit: 02d6e9f8c070115e7760c05bd315af44c53f1f3a
Author: Tyler Gorrie-Stone <tyler.gorrie-stone@diamond.ac.uk>
Date: 2021-08-25 20:27:35 +0100
Commit message:

 anti trafo skinblood
Package: wateRmelon
Commit: 9bc32629961d08a27e9e7a666da3314112408c32
Author: Tyler Gorrie-Stone <tyler.gorrie-stone@diamond.ac.uk>
Date: 2021-08-25 20:09:50 +0100
Commit message:

 Now it should work...

this is what happens when you don't test the code while writing it...
Package: wateRmelon
Commit: 7e030dbb36aaa2ab2afe1e731a9e303d76f74829
Author: Tyler Gorrie-Stone <tyler.gorrie-stone@diamond.ac.uk>
Date: 2021-08-25 19:54:55 +0100
Commit message:

 Update horv.R
Package: wateRmelon
Commit: 9e375ca12e390683eb50453a49fed49ce37c9219
Author: Tyler Gorrie-Stone <tyler.gorrie-stone@diamond.ac.uk>
Date: 2021-08-25 19:50:32 +0100
Commit message:

 Update horv.R
Package: wateRmelon
Commit: 85e085235467e79dd2101da5513b3777d661dc92
Author: Tyler Gorrie-Stone <tyler.gorrie-stone@diamond.ac.uk>
Date: 2021-08-25 19:48:25 +0100
Commit message:

 All method should now work.
Package: wateRmelon
Commit: 5cfe513211b214d33e1ff07a8cd9fff32f8fa978
Author: Tyler Gorrie-Stone <tyler.gorrie-stone@diamond.ac.uk>
Date: 2021-08-25 19:44:58 +0100
Commit message:

 Now it should work...
Package: wateRmelon
Commit: 1f15c73b70c97abcb461f0d10ae766d7affbebbc
Author: Tyler Gorrie-Stone <tyler.gorrie-stone@diamond.ac.uk>
Date: 2021-08-25 19:41:33 +0100
Commit message:

 Update horv.R
Package: wateRmelon
Commit: 51b7bb24e7f1ba24651d0c5b774c4c01735af0a0
Author: Tyler Gorrie-Stone <tyler.gorrie-stone@diamond.ac.uk>
Date: 2021-08-25 19:37:37 +0100
Commit message:

 Removing silly non-coded line
Package: wateRmelon
Commit: 40f013c75cc0f63b285a4058b27467d420ed3d38
Author: Tyler Gorrie-Stone <tyler.gorrie-stone@diamond.ac.uk>
Date: 2021-08-25 19:35:50 +0100
Commit message:

 Adding the rest of the clocks.
Package: wateRmelon
Commit: 4eb9a0a778fab703e7679dc22c91f16ebc0b8106
Author: Tyler Gorrie-Stone <tyler.gorrie-stone@diamond.ac.uk>
Date: 2021-08-25 19:29:43 +0100
Commit message:

 V bump for Version 2.

Setting to 1.99 so when in BioC dev branch will increment to 2.0 automatically.
Package: wateRmelon
Commit: 8e7696658afbe13429ad6f5c250f332be7bc2972
Author: Tyler Gorrie-Stone <tyler.gorrie-stone@diamond.ac.uk>
Date: 2021-08-25 19:28:43 +0100
Commit message:

 Adding age_coefficients.rda
Package: wateRmelon
Commit: 464912e4c8ac08546de635d791d9f0239ed8bdaf
Author: Tyler Gorrie-Stone <tyler.gorrie-stone@diamond.ac.uk>
Date: 2021-08-24 16:45:31 +0100
Commit message:

 Update horv.R
Package: wateRmelon
Commit: 6f2c68d8cb5d7d8a208e98c22cbcc0b1c263fad7
Author: Tyler Gorrie-Stone <tyler.gorrie-stone@diamond.ac.uk>
Date: 2021-08-12 17:07:28 +0100
Commit message:

 Update horv.R

Refactored and greatly expanded ease of adding new information and coefficient lists if needed...
Package: wateRmelon
Commit: 81c57d54e00707965ef79eb8b7d1078505759357
Author: ds420 <ds420@exeter.ac.uk>
Date: 2021-03-05 09:07:46 +0000
Commit message:

 deconvolution error metric added to estimateCellCounts function
Package: FlowSOM
Commit: 2da26cf76c07b08c45449a3b3f19a92d3d036351
Author: svgassen <sofie.vangassen@ugent.be>
Date: 2021-10-20 17:08:54 +0200
Commit message:

 Upload of missing Rd file
Package: orthogene
Commit: f903a5d7629db98ff8f443643dc85eb8afcf4a27
Author: Brian M. Schilder <34280215+bschilder@users.noreply.github.com>
Date: 2021-10-20 11:02:44 -0400
Commit message:

 Update NEWS
Package: BOBaFIT
Commit: b5fb4082ae5d9231d90d298d83db8c749fbe7a3c
Author: gaia-mazzocchetti <67413031+gaia-mazzocchetti@users.noreply.github.com>
Date: 2021-10-20 17:01:29 +0200
Commit message:

 version 5
Package: BOBaFIT
Commit: 032c6596d2492e577100430e31146ac7791003ba
Author: gaia-mazzocchetti <67413031+gaia-mazzocchetti@users.noreply.github.com>
Date: 2021-10-20 17:01:01 +0200
Commit message:

 TCGA_BRCA_CN_segments
Package: BOBaFIT
Commit: a92c5ba27966ac442a4063f98cd24884bc57d649
Author: gaia-mazzocchetti <67413031+gaia-mazzocchetti@users.noreply.github.com>
Date: 2021-10-20 16:46:20 +0200
Commit message:

 version 4
Package: BOBaFIT
Commit: 4dce6aac59360c59511e0efd7823c20b2c4dd3ef
Author: gaia-mazzocchetti <67413031+gaia-mazzocchetti@users.noreply.github.com>
Date: 2021-10-20 16:45:05 +0200
Commit message:

 Namspace update
Package: BOBaFIT
Commit: 1c969182a89a391fc5902e3132890485ee07cebd
Author: gaia-mazzocchetti <67413031+gaia-mazzocchetti@users.noreply.github.com>
Date: 2021-10-20 15:45:34 +0200
Commit message:

 ComputeNormalChromosome update
Package: BOBaFIT
Commit: 959faf0eaf675364d0d41963d459a4b1bedb8169
Author: andrea-poletti-unibo <andrea.poletti9@unibo.it>
Date: 2021-10-20 13:23:20 +0200
Commit message:

 popeye now is ok
Package: BOBaFIT
Commit: 5f21e9201ad7f324149ab1fd9ab34f718ab16321
Author: andrea-poletti-unibo <andrea.poletti9@unibo.it>
Date: 2021-10-20 13:14:40 +0200
Commit message:

 popeye bugfix
Package: BOBaFIT
Commit: 128399fdc090c44a82b4d6cebbe0bd5eb6cb63ca
Author: gaia-mazzocchetti <67413031+gaia-mazzocchetti@users.noreply.github.com>
Date: 2021-10-20 11:38:08 +0200
Commit message:

 Data Preparation vignette, update DRrefit_plot script
Package: BOBaFIT
Commit: 9ad1a1540e2bb1ba5bbdbfb4d1b22be26581493f
Author: andrea-poletti-unibo <andrea.poletti9@unibo.it>
Date: 2021-10-15 13:06:34 +0200
Commit message:

 Popeye bugfix
Package: BOBaFIT
Commit: 8efe49a12929b58a12747215cb231b4bcb891291
Author: gaia-mazzocchetti <gaia.mazzocchetti95@gmail.com>
Date: 2021-10-13 16:49:30 +0200
Commit message:

 Merge branch 'master' of https://github.com/bioinformatic-seragnoli/BOBaFIT
Package: BOBaFIT
Commit: fc91bd76d6b3128cdcda3c8ec95617df70e6e262
Author: gaia-mazzocchetti <gaia.mazzocchetti95@gmail.com>
Date: 2021-10-13 16:49:26 +0200
Commit message:

 DRrefit plot
Package: BOBaFIT
Commit: 2395ebf40f7e5f52515599a1c6b8aa5bd28d19b9
Author: andrea-poletti-unibo <andrea.poletti9@unibo.it>
Date: 2021-10-13 15:52:19 +0200
Commit message:

 Merge branch 'master' of https://github.com/bioinformatic-seragnoli/BOBaFIT
Package: BOBaFIT
Commit: 8d88ac36ff32bacfdaf10468d4add40e5d0093b7
Author: andrea-poletti-unibo <andrea.poletti9@unibo.it>
Date: 2021-10-13 15:52:15 +0200
Commit message:

 width removed
Package: BOBaFIT
Commit: ed305dd72abf530ab090dd8917047ef2c2b2d748
Author: gaia-mazzocchetti <gaia.mazzocchetti95@gmail.com>
Date: 2021-10-13 15:16:09 +0200
Commit message:

 Popeye script
Package: BOBaFIT
Commit: cd5756547a139a747d49d7a1f093454e6af54b62
Author: gaia-mazzocchetti <gaia.mazzocchetti95@gmail.com>
Date: 2021-10-11 17:24:13 +0200
Commit message:

 Check vignette abstract
Package: BOBaFIT
Commit: 403114d0e3e26ec8c7d33ddd3dcf595ca49ec31c
Author: MM_group <andrea.poletti9@unibo.it>
Date: 2021-10-08 14:56:07 +0200
Commit message:

 .
Package: BOBaFIT
Commit: c89b6d193fa7853c0e5b4ca7b9bd43546e7a74b2
Author: MM_group <andrea.poletti9@unibo.it>
Date: 2021-10-08 14:49:14 +0200
Commit message:

 DESCRIPTION 80 cols and typo tollerance
Package: BOBaFIT
Commit: 4e7f0bae52ffc1c5d5a7ff34e4df38e6a6ead13c
Author: MM_group <andrea.poletti9@unibo.it>
Date: 2021-10-08 14:38:30 +0200
Commit message:

 changed PLOT FORMAT (png, tif, jpg, pdf)
Package: BOBaFIT
Commit: b2e39d39dea0eb5226365caced33185c5896263a
Author: gaia-mazzocchetti <67413031+gaia-mazzocchetti@users.noreply.github.com>
Date: 2021-10-08 12:46:04 +0200
Commit message:

 .md file, print() and 1:n removed
Package: BOBaFIT
Commit: 3d540a98466b059f8faac7e132771f8fa7c41a66
Author: MM_group <andrea.poletti9@unibo.it>
Date: 2021-10-08 10:18:08 +0200
Commit message:

 BioC revision 07/10/21
Package: CNVfilteR
Commit: 0013b5b7a2bd228bb3eedfd56d22bc41da57aaf0
Author: José Marcos Moreno-Cabrera <j.morenoc@idibell.cat>
Date: 2021-10-20 16:37:56 +0200
Commit message:

 Fixed doc: added TorrentVariantCaller
Package: netOmics
Commit: 7ceee66e6ffe801ccee981eb18d2dc6295bfe824
Author: AntoineB <bodein.antoine@gmail.com>
Date: 2021-10-20 16:36:21 +0200
Commit message:

 update vignette
Package: CNVfilteR
Commit: 4bb78e9ba143d23dfa4a8c2fbbd3b95eb7d5aa98
Author: José Marcos Moreno-Cabrera <j.morenoc@idibell.cat>
Date: 2021-10-20 16:32:01 +0200
Commit message:

 Version bump
Package: CNVfilteR
Commit: bfe23aa8bb8ba9d4db91136e59d348f35595be60
Author: Jose Marcos Moreno <jmmoreno@ws-es-totoro.igtpscp.local>
Date: 2021-10-20 16:30:59 +0200
Commit message:

 NEWS updated
Package: CNVfilteR
Commit: 3ad4dc8ffc61600039b4299b5cc84fc77d327aef
Author: Jose Marcos Moreno <jmmoreno@ws-es-totoro.igtpscp.local>
Date: 2021-10-20 16:25:26 +0200
Commit message:

 Minor fix
Package: bambu
Commit: 65fa7d055eeae6e9f2bb937f438717be5aa36d5d
Author: Chen Ying <chen_ying@gis.a-star.edu.sg>
Date: 2021-10-20 22:17:18 +0800
Commit message:

 update version number
Package: bambu
Commit: 24561e83dfd2abdb2f916fd3f8e425a2f2a8ecda
Author: Chen Ying <chen_ying@gis.a-star.edu.sg>
Date: 2021-10-20 22:11:18 +0800
Commit message:

 edit our page description in readme
Package: bambu
Commit: 36da8a094f544c92de619fcf9d1f2757f9859ce8
Author: Chen Ying <chen_ying@gis.a-star.edu.sg>
Date: 2021-10-20 22:09:41 +0800
Commit message:

 add github pages link to readme and remove generated manual from docs
Package: bambu
Commit: efad64339393a9d98b8881446b9213a71f8b10b6
Author: Chen Ying <chen_ying@gis.a-star.edu.sg>
Date: 2021-10-20 21:57:25 +0800
Commit message:

 Merge branch 'master' of https://github.com/GoekeLab/bambu
Package: bambu
Commit: ee604f8ff3f3098f192165a04d88a8b02d48da66
Author: Chen Ying <chen_ying@gis.a-star.edu.sg>
Date: 2021-10-20 21:50:51 +0800
Commit message:

 added pkgdown files
Package: bambu
Commit: d96aace068c8b6120ff0f0070c23c24837dbe43e
Author: Chen Ying <chen_ying@gis.a-star.edu.sg>
Date: 2021-10-20 21:43:01 +0800
Commit message:

 Set theme jekyll-theme-minimal
Package: bambu
Commit: 6fcd277cea56b89df5e1f87efa9bd254752d6094
Author: Chen Ying <chen_ying@gis.a-star.edu.sg>
Date: 2021-10-20 21:21:13 +0800
Commit message:

 added pkgdown files
Package: bambu
Commit: 8fc30d877b76bdb1f1253fa4ebf64ab5e547f5a4
Author: Chen Ying <chen_ying@gis.a-star.edu.sg>
Date: 2021-10-20 21:11:12 +0800
Commit message:

 allow workflow checks on push as well
Package: bambu
Commit: c32770cbccf4a612260dd8cbd569237bf44c63b8
Author: Chen Ying <chen_ying@gis.a-star.edu.sg>
Date: 2021-10-20 21:10:58 +0800
Commit message:

 update code coverage badge to be based on master
Package: bambu
Commit: 27293250fbb7d8e71334a3f20a06c9e367d16ecc
Author: Chen Ying <chen_ying@gis.a-star.edu.sg>
Date: 2021-10-20 21:07:42 +0800
Commit message:

 Merge pull request #229 from GoekeLab/estDistToAnno_patch

update master branch
Package: bambu
Commit: 4c39ae51f75452882b50cab197df32ba951d031a
Author: Chen Ying <chen_ying@gis.a-star.edu.sg>
Date: 2021-10-20 20:54:05 +0800
Commit message:

 try to see if remove travis yml can still see code coverage
Package: bambu
Commit: 0b1204f5f8480bbdc1037a2831117b0bd1fa1c02
Author: Chen Ying <chen_ying@gis.a-star.edu.sg>
Date: 2021-10-20 18:46:06 +0800
Commit message:

 unale to solve the issue for windows, will comment windows test for now
Package: bambu
Commit: 62e9a34a879e4cab8f06067d00b368fd76f378b1
Author: Chen Ying <chen_ying@gis.a-star.edu.sg>
Date: 2021-10-20 18:19:24 +0800
Commit message:

 remove customized r cmd check
Package: bambu
Commit: 59d83ec6c6ba5653787f30a5f93d5e307ed707c7
Author: Chen Ying <chen_ying@gis.a-star.edu.sg>
Date: 2021-10-20 18:05:21 +0800
Commit message:

 update code coverage badge src
Package: bambu
Commit: 1db51fc039318a862bb1dd2888e9d0ff46fa3a33
Author: Chen Ying <chen_ying@gis.a-star.edu.sg>
Date: 2021-10-20 17:58:46 +0800
Commit message:

 remove remotes::install_local in dependent pass 2
Package: bambu
Commit: af414307b210607248c1180f673bf1d816baca48
Author: Chen Ying <chen_ying@gis.a-star.edu.sg>
Date: 2021-10-20 17:06:12 +0800
Commit message:

 fix the typo in check-bioc.yml
Package: bambu
Commit: baec0b73141d04ff2ac8410540de0351ea7c5bc9
Author: Chen Ying <chen_ying@gis.a-star.edu.sg>
Date: 2021-10-20 17:03:50 +0800
Commit message:

 try to install rtools for windows tests
Package: bambu
Commit: 5571aa0ba02c55a57358b6bd2befb2dc706c478a
Author: Chen Ying <chen_ying@gis.a-star.edu.sg>
Date: 2021-10-20 16:44:59 +0800
Commit message:

 use default test coverage workflow
Package: bambu
Commit: afe634df33dd50d042d3197972c02796f4329757
Author: Chen Ying <chen_ying@gis.a-star.edu.sg>
Date: 2021-10-20 16:44:41 +0800
Commit message:

 uncomment windows test
Package: bambu
Commit: c07a827f6a6a91ebee52dfb77d97250236e3b7b9
Author: Chen Ying <chen_ying@gis.a-star.edu.sg>
Date: 2021-10-20 16:39:03 +0800
Commit message:

 add a travis yml for code coverage plot uploading
Package: bambu
Commit: 881ee28f4b9a892a968a5fe93c4595faa9a1b712
Author: Chen Ying <chen_ying@gis.a-star.edu.sg>
Date: 2021-10-20 15:51:56 +0800
Commit message:

 edit depends to test-coverage
Package: bambu
Commit: 5a4bf7c24e1c674d9218eac69a7255cda22bab90
Author: Chen Ying <chen_ying@gis.a-star.edu.sg>
Date: 2021-10-20 15:45:44 +0800
Commit message:

 test another set of code to do code coverage report uploads
Package: bambu
Commit: 63db9345e68099c6f4a4b4613bbf67eabcfab4f3
Author: Chen Ying <chen_ying@gis.a-star.edu.sg>
Date: 2021-10-20 15:27:04 +0800
Commit message:

 remove the section added for upload as it seems to generate upload by itself
Package: bambu
Commit: 4a3379ec4cc2e7745a9a75602eb83cb313b77ae9
Author: Chen Ying <chen_ying@gis.a-star.edu.sg>
Date: 2021-10-20 15:12:30 +0800
Commit message:

 remove tokens
Package: bambu
Commit: 145459b8d5edde64862f8c786b4325d616fd6e76
Author: Chen Ying <chen_ying@gis.a-star.edu.sg>
Date: 2021-10-20 15:10:22 +0800
Commit message:

 add a code cov report upload section in test coverage
Package: bambu
Commit: 0fa40b095879440302e7210ee09bd633b8ff188f
Author: Chen Ying <chen_ying@gis.a-star.edu.sg>
Date: 2021-10-20 15:09:36 +0800
Commit message:

 add a codecov badge that is linked to unit tests
Package: bambu
Commit: 606cccdf2ba87e89f2ca8325ec37a69a9558bfe1
Author: Chen Ying <chen_ying@gis.a-star.edu.sg>
Date: 2021-10-20 13:31:13 +0800
Commit message:

 change workflows to check only PRs
Package: bambu
Commit: eadc9dbb52eb7178922a40d54562b0d82b50822e
Author: Chen Ying <chen_ying@gis.a-star.edu.sg>
Date: 2021-10-20 11:08:30 +0800
Commit message:

 updated links for github issue and prs
Package: bambu
Commit: 1d4ddcb94ef42bb8c8a554c2effdbbb55f661b22
Author: Chen Ying <chen_ying@gis.a-star.edu.sg>
Date: 2021-10-20 10:58:37 +0800
Commit message:

 remove pkgdown workflow first as there is some error in installing the package
Package: bambu
Commit: a5c65557ecc66836f976e144e79d6665303e5af8
Author: Chen Ying <chen_ying@gis.a-star.edu.sg>
Date: 2021-10-20 10:45:38 +0800
Commit message:

 removed check-standard for now
Package: bambu
Commit: 839fe9bf31fff96a2dac1c2979eff7a596e85bb2
Author: Chen Ying <chen_ying@gis.a-star.edu.sg>
Date: 2021-10-20 10:45:27 +0800
Commit message:

 commented failing checks for now
Package: bambu
Commit: 730640d238e0e96c8cb8398917a74919e8098470
Author: Chen Ying <chen_ying@gis.a-star.edu.sg>
Date: 2021-10-20 10:45:13 +0800
Commit message:

 added bioc build badges for both release and development branch, github issues and pulls
Package: bambu
Commit: a2dc1b7b0770dea53c2af8bc8b345e17f037b3a8
Author: Chen Ying <chen_ying@gis.a-star.edu.sg>
Date: 2021-10-20 10:01:55 +0800
Commit message:

 edited the style for major changes and completed the output description
Package: bambu
Commit: fe0cec706805528efa604c1bda5c871358954d4e
Author: Chen Ying <chen_ying@gis.a-star.edu.sg>
Date: 2021-10-20 00:17:21 +0800
Commit message:

 remove test coverage badge for now
Package: bambu
Commit: 6878ed404ba4ef95f94ab69c857a8e4a6fcd38a6
Author: Chen Ying <chen_ying@gis.a-star.edu.sg>
Date: 2021-10-20 00:14:21 +0800
Commit message:

 remove github release badge and add test coverage badge
Package: bambu
Commit: 2e6eaafa562e83d016454fb291d7dd82af03f27b
Author: Chen Ying <chen_ying@gis.a-star.edu.sg>
Date: 2021-10-19 23:40:36 +0800
Commit message:

 update check-bioc workflow file
Package: bambu
Commit: bc27f1e033c7748427a4ff0f1fd2996842851b37
Author: Chen Ying <chen_ying@gis.a-star.edu.sg>
Date: 2021-10-19 23:37:44 +0800
Commit message:

 rm r-cmd-check workflows as check-standard already includes that
Package: bambu
Commit: 6b8b242fa3064f66dfdb11258001527164af6d6c
Author: Chen Ying <chen_ying@gis.a-star.edu.sg>
Date: 2021-10-19 23:29:46 +0800
Commit message:

 update link to manual in readme
Package: bambu
Commit: 8a265989b7c74214743013becb4e01a5b9b34559
Author: Chen Ying <chen_ying@gis.a-star.edu.sg>
Date: 2021-10-19 23:28:26 +0800
Commit message:

 update manual
Package: bambu
Commit: 4c3ed227e682f5126c190b4c45f27557235e070c
Author: Chen Ying <chen_ying@gis.a-star.edu.sg>
Date: 2021-10-19 23:28:06 +0800
Commit message:

 update function rd files and manual
Package: bambu
Commit: b1b5dee281f32ff962933da808b7c5d718650649
Author: Chen Ying <chen_ying@gis.a-star.edu.sg>
Date: 2021-10-19 22:47:56 +0800
Commit message:

 remove rmarkdown
Package: bambu
Commit: 4479b6f9f50742adae4ce6d97baa4021a6725131
Author: Chen Ying <chen_ying@gis.a-star.edu.sg>
Date: 2021-10-19 22:47:38 +0800
Commit message:

 edited the make files where spaces between rules are replaced by tabs
Package: bambu
Commit: e33d0978b2244534310889ffb4d1f972a06c125e
Author: Chen Ying <chen_ying@gis.a-star.edu.sg>
Date: 2021-10-19 22:47:10 +0800
Commit message:

 updated the function docmentation for bambu
Package: bambu
Commit: 845bd2c78d8b4719863f4b32a5ed047f34663b69
Author: Chen Ying <chen_ying@gis.a-star.edu.sg>
Date: 2021-10-19 22:46:37 +0800
Commit message:

 added two more badges(r-cmd-check badge frpom github action and codefatcor badge from codefactor check)
Package: bambu
Commit: ed3caf0be554af9bca571b5fb455cc6fd2011e01
Author: Chen Ying <chen_ying@gis.a-star.edu.sg>
Date: 2021-10-19 22:45:43 +0800
Commit message:

 incorrect indentation removed
Package: bambu
Commit: d32c29dd99638cc29ac8fa42d9c1eea2ee23095f
Author: Chen Ying <chen_ying@gis.a-star.edu.sg>
Date: 2021-10-19 22:45:20 +0800
Commit message:

 add git actions to generate automatic checks
Package: bambu
Commit: 7f1621b09de34a52d2b180591e28d21b79f61fa3
Author: Andre <andre_sim@gis.a-star.edu.sg>
Date: 2021-10-19 11:44:56 +0800
Commit message:

 Merge remote-tracking branch 'origin/estDistToAnno_patch' into estDistToAnno_patch
Package: bambu
Commit: 9906cfa04d41ffb367901b3749701e9a82dadbf4
Author: Chen Ying <chen_ying@gis.a-star.edu.sg>
Date: 2021-10-19 11:42:34 +0800
Commit message:

 Update README.md

Co-authored-by: Jonathan Göke <10560051+jonathangoeke@users.noreply.github.com>
Package: bambu
Commit: fd498e8f0a9dde7165de00dae42a4e2ca13f6841
Author: Chen Ying <chen_ying@gis.a-star.edu.sg>
Date: 2021-10-19 11:42:26 +0800
Commit message:

 Update README.md

Co-authored-by: Jonathan Göke <10560051+jonathangoeke@users.noreply.github.com>
Package: bambu
Commit: 6b4efe30afe6e5963c44371faf4ee2b8645d5e38
Author: Chen Ying <chen_ying@gis.a-star.edu.sg>
Date: 2021-10-19 11:42:20 +0800
Commit message:

 Update README.md

Co-authored-by: Jonathan Göke <10560051+jonathangoeke@users.noreply.github.com>
Package: bambu
Commit: ab78dcfdcf96ce902e7ad2ae24d55373bba6c23f
Author: Andre <andre_sim@gis.a-star.edu.sg>
Date: 2021-10-19 11:42:11 +0800
Commit message:

 Fix some typos
Package: bambu
Commit: 955b8a7ee8bc4e986c9de9d63cee7ae8b343516b
Author: Chen Ying <chen_ying@gis.a-star.edu.sg>
Date: 2021-10-19 11:42:03 +0800
Commit message:

 Update README.md

Co-authored-by: Jonathan Göke <10560051+jonathangoeke@users.noreply.github.com>
Package: bambu
Commit: 05e7200bdbae4cc75bbc9a9ba0713a6bcf606677
Author: Chen Ying <chen_ying@gis.a-star.edu.sg>
Date: 2021-10-19 11:41:57 +0800
Commit message:

 Update NEWS

Co-authored-by: Jonathan Göke <10560051+jonathangoeke@users.noreply.github.com>
Package: bambu
Commit: 4476243ca75caba8ec4b1df51f6d67cb2bcebdb4
Author: Chen Ying <chen_ying@gis.a-star.edu.sg>
Date: 2021-10-19 11:41:52 +0800
Commit message:

 Update NEWS

Co-authored-by: Jonathan Göke <10560051+jonathangoeke@users.noreply.github.com>
Package: bambu
Commit: c131d77128ccc949d198403271b4025a90d8cd8c
Author: Chen Ying <chen_ying@gis.a-star.edu.sg>
Date: 2021-10-19 11:41:46 +0800
Commit message:

 Update NEWS

Co-authored-by: Jonathan Göke <10560051+jonathangoeke@users.noreply.github.com>
Package: bambu
Commit: 3fa6ccc6d01ebc651f2346c1dbc7701f24085b09
Author: Chen Ying <chen_ying@gis.a-star.edu.sg>
Date: 2021-10-19 11:41:41 +0800
Commit message:

 Update NEWS

Co-authored-by: Jonathan Göke <10560051+jonathangoeke@users.noreply.github.com>
Package: bambu
Commit: 3b225888032a19b9fb62add34ae3180884b679b7
Author: Andre <andre_sim@gis.a-star.edu.sg>
Date: 2021-10-19 10:52:59 +0800
Commit message:

 Fix the assignGeneID test
Package: bambu
Commit: 308111169b48cd9519c7e193bcc1bb8d5c9532f2
Author: Andre <andre_sim@gis.a-star.edu.sg>
Date: 2021-10-19 10:04:42 +0800
Commit message:

 Remove duplicate function
Package: bambu
Commit: 90932597462c25299a128368cb3a6d71d4905a5b
Author: Chen Ying <chen_ying@gis.a-star.edu.sg>
Date: 2021-10-19 00:51:10 +0800
Commit message:

 update content outline
Package: InterCellar
Commit: 7f8ce0c23e1ed34b7af40362ca06f6189ce6599f
Author: martaint <marta.interlandi01@gmail.com>
Date: 2021-10-20 15:39:35 +0200
Commit message:

 switched home as first in upload, version 1.99.3
Package: InterCellar
Commit: fe78365089fc3ad622fc07b9be0713abb4263944
Author: martaint <marta.interlandi01@gmail.com>
Date: 2021-10-20 15:34:35 +0200
Commit message:

 updated news and version bump 1.99.2
Package: InterCellar
Commit: 3668a9f2e9bfd41acc485aa216699df4e71d5302
Author: martaint <marta.interlandi01@gmail.com>
Date: 2021-10-20 14:53:21 +0200
Commit message:

 github readme updated docker
Package: InterCellar
Commit: d25ff699114266769788fa550dcafed92a058b3d
Author: martaint <marta.interlandi01@gmail.com>
Date: 2021-10-20 12:02:59 +0200
Commit message:

 updated github readme bioconda
Package: TENxVisiumData
Commit: 8710d60cca735c3b838672480bd77815819f2803
Author: HelenaLC <helena@crowells.eu>
Date: 2021-10-20 15:01:08 +0200
Commit message:

 bug fix in EH accession
Package: MAGAR
Commit: c157c2920e04796c1a0fb07e214428e9159fdd28
Author: Michael Scherer <mscherer@mpi-inf.mpg.de>
Date: 2021-10-20 14:40:31 +0200
Commit message:

 Polished vignette
Package: MAGAR
Commit: 604a145c2b90db4970304e2e346ffb6ffce2990f
Author: Michael Scherer <mscherer@mpi-inf.mpg.de>
Date: 2021-10-20 12:19:06 +0200
Commit message:

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

Conflicts:
	DESCRIPTION
Package: MAGAR
Commit: f6d22deaf186a7fee8af69171ed1f4589f084ebf
Author: Michael Scherer <s9mlscer@gmail.com>
Date: 2021-07-06 17:33:54 +0200
Commit message:

 Fix in import
Package: MAGAR
Commit: b846ba4bf38952028ef356135922285309ff094a
Author: Michael Scherer <s9mlscer@gmail.com>
Date: 2021-03-22 11:40:06 +0100
Commit message:

 Corrected name in DESCRIPTION
Package: SMITE
Commit: 2bc34476285225eb3c5e7e62fa17db133ae8b6a4
Author: Andrew Johnston <Adj38@cornell.edu>
Date: 2021-10-20 08:13:52 -0400
Commit message:

 BiocCheck 2.0
Package: SMITE
Commit: f6b794488c8973aa35dd9cf540ea5fd12f793291
Author: Andrew Johnston <Adj38@cornell.edu>
Date: 2021-10-20 08:12:26 -0400
Commit message:

 BiocCheck works
Package: progeny
Commit: f617cb37e3e76c3c912099081b524eecdc3ee47e
Author: adugourd <aurelien.dugourd@bioquant.uni-heidelberg.de>
Date: 2021-10-20 14:02:58 +0200
Commit message:

 updated version number
Package: progeny
Commit: 3d6cfcdc4a2840e1606e4b2f9f21a77c378812f5
Author: adugourd <aurelien.dugourd@bioquant.uni-heidelberg.de>
Date: 2021-10-20 13:51:57 +0200
Commit message:

 added lazyData compression
Package: progeny
Commit: 48b01d3f3f21e8671d530ed6bdc663ba4c26c723
Author: adugourd <aurelien.dugourd@bioquant.uni-heidelberg.de>
Date: 2021-10-20 13:25:30 +0200
Commit message:

 updated vignette to match transcriptutorial
Package: progeny
Commit: a101e0c8e423e49f2d9ef3d0ae1416630fa6a8a7
Author: adugourd <aurelien.dugourd@bioquant.uni-heidelberg.de>
Date: 2021-10-20 13:25:03 +0200
Commit message:

 updated gitignore
Package: epistack
Commit: bf04a05a8af3d625d9b9f6b32d0cda5155dfc60b
Author: Guillaume Devailly <gdevailly@hotmail.com>
Date: 2021-10-19 17:10:45 +0200
Commit message:

 Merge pull request #17 from GenEpi-GenPhySE/dev

sd in plotAverageProfile
Package: epistack
Commit: 418c8ceef745876a8eb5ed67cf682c9f9762e3d7
Author: Guillaume Devailly <gdevailly@hotmail.com>
Date: 2021-10-19 16:50:41 +0200
Commit message:

 error_type in plotEpistack
Package: epistack
Commit: 1190ed5499054946af6b2041f94a1d7b8964c11f
Author: Guillaume Devailly <gdevailly@hotmail.com>
Date: 2021-10-19 15:32:47 +0200
Commit message:

 sd in plotAverageProfile
sd is now the default in plotAverageProfile (was previously sem)
Package: synergyfinder
Commit: 298322a827a782be2c9bae0e2dbaab630fe12b45
Author: Shuyu <shuyu.zheng@helsinki.fi>
Date: 2021-10-20 13:39:59 +0300
Commit message:

 Modify the introduction for package
Package: CopyNumberPlots
Commit: 75702082e117e5c381bc382d44bd43a0730e1b3e
Author: Bernat <bernatgel@gmail.com>
Date: 2021-10-20 12:21:47 +0200
Commit message:

 Version Bump
Package: CopyNumberPlots
Commit: a7df57e27cf0024f64bdeb8e48737c61d518c15a
Author: Bernat <bernatgel@gmail.com>
Date: 2021-10-20 12:20:53 +0200
Commit message:

 Fixed syntax error in vignette
Package: msa
Commit: 9e7acafdee06be502d3c2f3372f45e4a580e9f9d
Author: UBod <ulrich@bodenhofer.com>
Date: 2021-10-20 10:40:40 +0200
Commit message:

 further fixes of warnings; version number bumped to 1.25.3
Package: pengls
Commit: c23787d12c6246c85387ea0f5fce048e49555aa8
Author: Stijn HAWINKEL <sthaw@psb.ugent.be>
Date: 2021-10-20 09:53:24 +0200
Commit message:

 update readme and figure witdth in vignette
Package: pengls
Commit: a83cec3decd37383660c10cba7454f0bcd92d08c
Author: Stijn HAWINKEL <sthaw@psb.ugent.be>
Date: 2021-10-20 09:50:52 +0200
Commit message:

 Rmeoved github installation instructions
Package: GBScleanR
Commit: b941ce5106c002ec1e2b2c0287f88d96e01d5430
Author: tomoyukif <f.tomoyuki@okayama-u.ac.jp>
Date: 2021-10-20 16:23:32 +0900
Commit message:

 15th correction for Bioc
Package: monaLisa
Commit: 01de8ab3931f9ef515d428cbafe38ce390586aff
Author: Michael Stadler <stadler.michael@gmail.com>
Date: 2021-10-20 09:21:24 +0200
Commit message:

 Merge pull request #51 from fmicompbio/fix-warning

Suppress warnings from matchPWM in regression vignette
Package: monaLisa
Commit: 00b6595a11a01d4b969952626e2c69c95531c2df
Author: Charlotte Soneson <charlottesoneson@gmail.com>
Date: 2021-10-20 08:56:03 +0200
Commit message:

 Move stickers to man/figures
Package: monaLisa
Commit: 0f5b8a163da10a584b29b6b5d71ca3548947535e
Author: Charlotte Soneson <charlottesoneson@gmail.com>
Date: 2021-10-20 08:41:36 +0200
Commit message:

 Revert path change to sticker
Package: monaLisa
Commit: 6d37b8a91b1b2583a63ed749066b99bd0728d4e3
Author: Charlotte Soneson <charlottesoneson@gmail.com>
Date: 2021-10-20 08:35:00 +0200
Commit message:

 Suppress warnings from matchPWM in regression vignette
Package: GBScleanR
Commit: ce16eb59bb3f84af053bf3d592c2b2ef36bf637f
Author: tomoyukif <f.tomoyuki@okayama-u.ac.jp>
Date: 2021-10-20 15:23:17 +0900
Commit message:

 14th correction for Bioc
Package: orthogene
Commit: c25248b12b36cf5508ef8e499652dfc5f90df3b2
Author: Brian M. Schilder <34280215+bschilder@users.noreply.github.com>
Date: 2021-10-20 02:15:39 -0400
Commit message:

 Added create_background and infer_species funcs; Added all_genes method for babelgene
Package: GBScleanR
Commit: e0530eae69defd3346c21ce6c547aaf01870aa0a
Author: tomoyukif <f.tomoyuki@okayama-u.ac.jp>
Date: 2021-10-20 14:56:57 +0900
Commit message:

 13th correction of script to meet Bioc demands
Package: ChIPseeker
Commit: 375f551357d6b5fab8fad0d35b69dab0ce47d240
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2021-10-20 11:25:33 +0800
Commit message:

 bump version
Package: ChIPseeker
Commit: 2472c27eb16d3234442b5a2ff060134ce82f10d7
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2021-10-20 11:21:20 +0800
Commit message:

 Merge pull request #163 from MingLi-929/master

update vignettes
Package: ChIPseeker
Commit: 9eed82780d78344883fb1aab25c15a4aded75028
Author: MingLi-929 <limiang929@gmail.com>
Date: 2021-10-19 19:52:07 +0800
Commit message:

 update vignettes
Package: ChIPseeker
Commit: ff350268a3aa97c3eb6096980df185dbc2826f93
Author: MingLi-929 <limiang929@gmail.com>
Date: 2021-10-19 17:15:44 +0800
Commit message:

 support previous functions
Package: ChIPseeker
Commit: 637f997e0c8773c24c910699120b68f22aae58a9
Author: MingLi-929 <limiang929@gmail.com>
Date: 2021-10-19 17:15:18 +0800
Commit message:

 change default value of nbin
Package: ChIPseeker
Commit: 927c8314763d00587128abf84d104326e5f5cece
Author: MingLi-929 <limiang929@gmail.com>
Date: 2021-10-19 10:31:14 +0800
Commit message:

 add ... parameter to plot functions to support tagCount()
Package: ChIPseeker
Commit: 40bcee8fd0e8d5c0b17d41f00f5b221d17521e34
Author: MingLi-929 <limiang929@gmail.com>
Date: 2021-10-18 17:47:27 +0800
Commit message:

 add support for previous functions
Package: ChIPseeker
Commit: bab3731fe496b8228b41eda42754cbd4bd1b0e2b
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2021-10-15 12:10:43 +0800
Commit message:

 update news
Package: ChIPseeker
Commit: 58f3ae6bba4a7f3594a540dddea3cb7723b59e51
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2021-10-15 00:22:44 +0800
Commit message:

 Merge pull request #162 from MingLi-929/master

Combine functions
Package: ChIPseeker
Commit: edf7bbb8d892661fc26efd2a5a270064095f0b41
Author: MingLi-929 <limiang929@gmail.com>
Date: 2021-10-14 11:28:18 +0800
Commit message:

 modify nbin parameter
Package: ChIPseeker
Commit: 1e1422f86fddd4e3e7acc314ed4b9ef1df960ce3
Author: MingLi-929 <limiang929@gmail.com>
Date: 2021-10-14 11:00:17 +0800
Commit message:

 delete options
Package: ChIPseeker
Commit: 6ef50199d149bfd8047ee26087a4545a8305a6ba
Author: MingLi-929 <limiang929@gmail.com>
Date: 2021-10-12 22:27:49 +0800
Commit message:

 support previous functions
Package: ChIPseeker
Commit: bcca4a24a7febe17dc170294f39b582e257b205a
Author: MingLi-929 <limiang929@gmail.com>
Date: 2021-10-12 15:54:20 +0800
Commit message:

 combine functions
Package: ChIPseeker
Commit: e48e9ac86d3c3c897675c078f923b70cf9ae152d
Author: MingLi-929 <limiang929@gmail.com>
Date: 2021-10-10 19:42:14 +0800
Commit message:

 add option of max_region_length
Package: ChIPseeker
Commit: f5d61ce67a9fecbe7de7ca26138084131bdbffea
Author: MingLi-929 <limiang929@gmail.com>
Date: 2021-10-10 19:39:31 +0800
Commit message:

 improve check_upstream_and_downstream()
Package: ChIPseeker
Commit: c8878bebaf3d7a6081c763d6cd6c70e7b8c637c8
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2021-10-08 10:05:34 +0800
Commit message:

 Merge pull request #161 from MingLi-929/master

solve warnings from check()
Package: ChIPseeker
Commit: fc8a01b7ecf059c133fff9326b30949792673057
Author: MingLi-929 <limiang929@gmail.com>
Date: 2021-10-07 17:05:23 +0800
Commit message:

 solve warnings from check()
Package: ChIPseeker
Commit: 7bf5d64163f75f81d4d8e8c532c18cbda5877501
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2021-10-07 11:41:26 +0800
Commit message:

 update docs
Package: ChIPseeker
Commit: 2f0bc2929174b03cd8f422279e994e318542ffdd
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2021-10-06 23:17:32 +0800
Commit message:

 Merge pull request #160 from MingLi-929/master

Add function of getting TTS region
Package: ChIPseeker
Commit: 5f64ca338541c34569b5604a530f515389c43471
Author: MingLi-929 <limiang929@gmail.com>
Date: 2021-10-06 17:38:58 +0800
Commit message:

 act the internal function
Package: ChIPseeker
Commit: f1d0ec4aa1714789d49528ad095a63c2b9368ef5
Author: MingLi-929 <limiang929@gmail.com>
Date: 2021-10-01 23:49:43 +0800
Commit message:

 attach different issues to annotation
Package: ChIPseeker
Commit: 380742791fb06fb46f9be4e114bf754d04754903
Author: MingLi-929 <limiang929@gmail.com>
Date: 2021-10-01 15:08:54 +0800
Commit message:

 add function of getEndRegion and getTTSregion to get the end site of different region
Package: ChIPseeker
Commit: e13e2b58ab2e3fe3e615f3ec6bd80e3449f1699d
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2021-09-28 15:50:16 +0800
Commit message:

 update docs
Package: ChIPseeker
Commit: 09d50e3027e34b4b43558d4ef58eb65eab08252a
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2021-09-28 15:44:28 +0800
Commit message:

 Merge pull request #156 from MingLi-929/master

Adding function of plotting bioregion by binning
Package: ChIPseeker
Commit: e50c1f08c21e30216041e6b27f7534d9aecf8032
Author: MingLi-929 <limiang929@gmail.com>
Date: 2021-09-28 14:40:18 +0800
Commit message:

 adding function of plotting different start sites of bioregion, including 5UTR, exon.
changing the name of the function.
Package: ChIPseeker
Commit: f368d22b634d7c86c925f06d697da1e4e4ce4a15
Author: MingLi-929 <limiang929@gmail.com>
Date: 2021-09-28 00:23:58 +0800
Commit message:

 delete 'is_TSSregion' parameter
add 'type' attribute
Package: ChIPseeker
Commit: 29878c43fc82fc750b18485394d16a821512c1b7
Author: MingLi-929 <limiang929@gmail.com>
Date: 2021-09-25 23:42:11 +0800
Commit message:

 solve the conflict of ggplot2 and BiocGenerics
Package: ChIPseeker
Commit: ed6c08b071f673098271d0047b856b5b6cf62902
Author: MingLi-929 <limiang929@gmail.com>
Date: 2021-09-25 20:01:50 +0800
Commit message:

 introduce rel() function
Package: ChIPseeker
Commit: 16825a7cc944c3467f8951edb7fbebb9f6cbc5c4
Author: MingLi-929 <limiang929@gmail.com>
Date: 2021-09-25 16:44:30 +0800
Commit message:

 introduce rel object to upstream and downstream parameter
Package: ChIPseeker
Commit: 9c247b95f01f9456a1c7cf98eb0a6f3f204c4640
Author: MingLi-929 <limiang929@gmail.com>
Date: 2021-09-20 12:44:20 +0800
Commit message:

 update
Package: ChIPseeker
Commit: 2e6f77cc523d3ae004e1dc64965a7d1b891a6101
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2021-09-16 10:28:09 +0800
Commit message:

 bioc version
Package: ChIPseeker
Commit: 0b0dfd6213745820911f5f742b596c9fac725728
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2021-09-16 10:24:15 +0800
Commit message:

 bioc version
Package: ChIPseeker
Commit: 60a6dffe45ebd0c0024b7d6153255b6ee00124b6
Author: MingLi-929 <limiang929@gmail.com>
Date: 2021-08-25 11:50:23 +0800
Commit message:

 update
Package: ChIPseeker
Commit: 09d18826f889f8dbc2a2d0069eb8bbfe369b4afa
Author: MingLi-929 <limiang929@gmail.com>
Date: 2021-08-23 16:19:59 +0800
Commit message:

 update
Package: ChIPseeker
Commit: 1ef8fb846582bad985cee66b334429b05e9e56d6
Author: MingLi-929 <limiang929@gmail.com>
Date: 2021-08-23 10:22:53 +0800
Commit message:

 update
Package: ChIPseeker
Commit: 5ae5ccbface6ca921634a94266c966c2ed96fbf2
Author: MingLi-929 <limiang929@gmail.com>
Date: 2021-08-16 18:34:12 +0800
Commit message:

 update
Package: ChIPseeker
Commit: 20936b38662049c38c28dc02f0de5ca7c0860eb7
Author: MingLi-929 <limiang929@gmail.com>
Date: 2021-08-16 14:52:12 +0800
Commit message:

 update
Package: ChIPseeker
Commit: e3e2e6c2c0ae1a7c1c00f4d58d2bf49589f36ecd
Author: MingLi-929 <limiang929@gmail.com>
Date: 2021-08-16 14:49:37 +0800
Commit message:

 update
Package: ChIPseeker
Commit: cff16f581d4d28a4eb1463f04209989e1a1cb94b
Author: MingLi-929 <limiang929@gmail.com>
Date: 2021-08-16 14:19:25 +0800
Commit message:

 update
Package: ChIPseeker
Commit: d6f584e6d76fb332b0138c640285eea458bb6ab6
Author: MingLi-929 <limiang929@gmail.com>
Date: 2021-08-16 14:08:47 +0800
Commit message:

 update
Package: ChIPseeker
Commit: bae1ca7bd1fbc98adc8a0c794c7b655b5e73df95
Author: MingLi-929 <limiang929@gmail.com>
Date: 2021-08-16 13:11:59 +0800
Commit message:

 update
Package: ChIPseeker
Commit: efccd9277e6871840dc7176b9363060dec4d4af8
Author: MingLi-929 <limiang929@gmail.com>
Date: 2021-08-16 13:11:25 +0800
Commit message:

 update
Package: ChIPseeker
Commit: 3f1ee4a19f51c0159ebeb68d57a304701000ec0b
Author: MingLi-929 <limiang929@gmail.com>
Date: 2021-08-16 13:00:29 +0800
Commit message:

 update
Package: ChIPseeker
Commit: 30731c37c2ae47be47a71d0d815b35c22c788d3a
Author: MingLi-929 <limiang929@gmail.com>
Date: 2021-08-16 12:56:18 +0800
Commit message:

 update
Package: ChIPseeker
Commit: 7d0bfdc2e18caeb384bee908c3623946452964f6
Author: MingLi-929 <limiang929@gmail.com>
Date: 2021-08-16 12:48:42 +0800
Commit message:

 update
Package: ChIPseeker
Commit: e6e878580c5ce6e01f4badcf964324d30df256ca
Author: MingLi-929 <limiang929@gmail.com>
Date: 2021-08-16 12:37:49 +0800
Commit message:

 Merge branch 'master' of https://github.com/MingLi-929/ChIPseeker
Package: ChIPseeker
Commit: 63a3b72fe1f0f838815a86ed7b81a38045b94a6c
Author: MingLi-929 <limiang929@gmail.com>
Date: 2021-08-16 11:13:50 +0800
Commit message:

 update
Package: ChIPseeker
Commit: e817a3e3c75a21d79d2a969a418d2822d5c2e5e0
Author: MingLi-929 <limiang929@gmail.com>
Date: 2021-08-16 10:53:50 +0800
Commit message:

 cut the amount of parameters
Package: ChIPseeker
Commit: d3b2fb49a21bbf48a588575bfda3667792f56bc2
Author: MingLi-929 <78794151+MingLi-929@users.noreply.github.com>
Date: 2021-08-03 18:47:53 +0800
Commit message:

 Update tagMatrix.R
Package: ChIPseeker
Commit: d116206675dde2590b79ab21e3241f3f5b9205f2
Author: MingLi-929 <limiang929@gmail.com>
Date: 2021-08-03 18:31:28 +0800
Commit message:

 update
Package: ChIPseeker
Commit: 32f92157764033ef334aef4c7c3daf5ab85ddbe9
Author: MingLi-929 <limiang929@gmail.com>
Date: 2021-08-03 18:04:19 +0800
Commit message:

 update
Package: ChIPseeker
Commit: 1f63cbf72efed8e3946f15f2c68147e206706885
Author: MingLi-929 <limiang929@gmail.com>
Date: 2021-08-03 18:01:50 +0800
Commit message:

 update
Package: ChIPseeker
Commit: a817ccb1029c77e17700c4e12b049411ed29fc4d
Author: MingLi-929 <limiang929@gmail.com>
Date: 2021-08-03 17:15:41 +0800
Commit message:

 update
Package: ChIPseeker
Commit: b41867be222f82b0f8b2ed3dac21f2dd3b59c9bf
Author: MingLi-929 <limiang929@gmail.com>
Date: 2021-08-03 16:39:32 +0800
Commit message:

 update
Package: ChIPseeker
Commit: 15c971903b47ab0578d0182bbf11a21ae8e7fdac
Author: MingLi-929 <limiang929@gmail.com>
Date: 2021-08-03 16:14:59 +0800
Commit message:

 update
Package: ChIPseeker
Commit: 22b91f33baec49daa5d0ee7ee7b856747cd6e801
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2021-05-28 14:53:21 +0800
Commit message:

 Merge pull request #151 from MingLi-929/master

Change color scheme
Package: ChIPseeker
Commit: b4195128bd405897bc624a4448e96a97ba8fe8e3
Author: MingLi-929 <78794151+MingLi-929@users.noreply.github.com>
Date: 2021-05-27 22:07:58 +0800
Commit message:

 Update utilities.R
Package: ChIPseeker
Commit: ee1af6d88703988008655bba289f3f013afba526
Author: MingLi-929 <78794151+MingLi-929@users.noreply.github.com>
Date: 2021-05-27 17:12:10 +0800
Commit message:

 Update utilities.R
Package: ChIPseeker
Commit: f9283aca4826126bab3efaea1ba566f950105e6f
Author: MingLi-929 <78794151+MingLi-929@users.noreply.github.com>
Date: 2021-05-27 15:37:09 +0800
Commit message:

 Update utilities.R
Package: ChIPseeker
Commit: bf2000ad5a8348f93537105a980d019c5d753573
Author: MingLi-929 <78794151+MingLi-929@users.noreply.github.com>
Date: 2021-05-27 15:33:50 +0800
Commit message:

 Update utilities.R
Package: ChIPseeker
Commit: ad5cfda66fa6f546e5554bafc5ba3e39a1e769cc
Author: MingLi-929 <78794151+MingLi-929@users.noreply.github.com>
Date: 2021-05-27 13:00:08 +0800
Commit message:

 Update utilities.R
Package: ChIPseeker
Commit: 31ff212d6b93dfe3b35813cc3def989ef5c28f11
Author: MingLi-929 <78794151+MingLi-929@users.noreply.github.com>
Date: 2021-05-27 12:59:07 +0800
Commit message:

 Update utilities.R
Package: treeio
Commit: b0d4c3d1254fc7a1d9c05154855d652640684add
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2021-10-19 17:33:00 +0800
Commit message:

 Merge pull request #69 from xiangpin/master

fix the issue when outgroup is missing in root function
Package: treeio
Commit: df8f981a93c4d0a2ef6784439967691b5d1a0077
Author: xiangpin <xshuangbin@163.com>
Date: 2021-10-19 16:35:14 +0800
Commit message:

 Merge remote-tracking branch 'upstream/master'
Package: treeio
Commit: d19e647325efa17105a7bfd3fe06570622aa4a72
Author: xiangpin <xshuangbin@163.com>
Date: 2021-10-19 16:35:01 +0800
Commit message:

 fix issue when outgroup is missing
Package: treeio
Commit: 1e16179fbc02967dcab573544ad81fb01858a168
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2021-09-23 09:55:39 +0800
Commit message:

 Merge pull request #68 from xiangpin/master

typo
Package: treeio
Commit: f92b559ac5580ed4d737dd99ecb9d7423c7d2ddc
Author: xiangpin <xshuangbin@163.com>
Date: 2021-09-22 14:04:05 +0800
Commit message:

 typo
Package: treeio
Commit: 0271059a5ac7a2aa168bffbd65da8572091e3c94
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2021-09-18 10:06:18 +0800
Commit message:

 more robust to test whether an object is a tree object
Package: treeio
Commit: 6afe9eadab377bfb8e0a72f4dd76ddd6ebb620e7
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2021-09-10 00:35:55 +0800
Commit message:

 Merge pull request #67 from xiangpin/outgroup_root

fix outgroup (character type) of root for treedata
Package: treeio
Commit: d12734c8fc536aa8e1278a729257b1e8dd92d876
Author: xiangpin <xshuangbin@163.com>
Date: 2021-09-07 20:58:22 +0800
Commit message:

 fix outgroup (character type) of root for treedata
Package: treeio
Commit: 9618bec52d10b01813a763ed8ba24466128d51a0
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2021-08-13 22:17:08 +0800
Commit message:

 Merge pull request #65 from xiangpin/drop_all_tip

fix drop.tip when all tips removed
Package: treeio
Commit: eb397ba6623391362688cc4573a0e9e0c2128c5c
Author: xiangpin <xshuangbin@163.com>
Date: 2021-08-13 15:58:25 +0800
Commit message:

 fix drop.tip when all tips removed
Package: treeio
Commit: 331d40ebcf4a7154d08d080a1be6ee4c2df6be74
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2021-08-08 00:26:39 +0800
Commit message:

 Merge pull request #64 from xiangpin/beast_node.label

fix the add_pseudo_nodelabel when the node.label is not null in beast file
Package: treeio
Commit: 27d05a43047fb933c69565e2cb45b81be84b77e3
Author: xiangpin <xshuangbin@163.com>
Date: 2021-08-07 17:54:50 +0800
Commit message:

 update beast for node.label is not NULL
Package: ReactomePA
Commit: 240298a93d248f609d290c34a446d73e28ea77d3
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2021-07-05 11:37:42 +0800
Commit message:

 correct link
Package: ReactomePA
Commit: 5ce95fd17a1475f4c0589168f931b84e4224f02e
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2021-05-20 13:57:37 +0800
Commit message:

 new release
Package: ggtree
Commit: dd1a460eb26868939e41b9f6d5e3cf52bd3771ed
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2021-10-20 11:11:29 +0800
Commit message:

 Merge branch 'master' of github.com:YuLab-SMU/ggtree
Package: ggtree
Commit: d896fe76347e0ce281a78229396bda4e37a6e32a
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2021-10-15 14:32:02 +0800
Commit message:

 Update NEWS.md
Package: ggtree
Commit: ed2ef15c1624eb00308eccbf55277a19e997cb20
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2021-10-15 14:25:49 +0800
Commit message:

 Update NEWS.md
Package: GOSemSim
Commit: d5e95a888aa8d89b98494387ddd4cf83d35a9c8f
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2021-09-03 09:42:06 +0800
Commit message:

 update docs
Package: ggtree
Commit: 40f8e5b3edde928b188cac319e0ee3f936e50b90
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2021-10-20 11:09:01 +0800
Commit message:

 bump version
Package: ggtree
Commit: 0285e5064aeef0106d00ca4b1cabccca04c533ec
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2021-10-14 09:59:58 +0800
Commit message:

 update news
Package: ggtree
Commit: f54cb8b7404f9fb375174d8a91afbdc6110ecaa3
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2021-10-14 09:54:50 +0800
Commit message:

 Merge pull request #446 from xiangpin/geom_cladelab_extend

geom_cladelab extend
Package: ggtree
Commit: ad15fcf4d06f6e99debe84272dc7629b0c20340e
Author: xiangpin <xshuangbin@163.com>
Date: 2021-10-13 21:14:19 +0800
Commit message:

 emojifont should be load to display emoji font
Package: ggtree
Commit: 75e86bf5d037484c169afc0ffa02d365d35bedc9
Author: xiangpin <xshuangbin@163.com>
Date: 2021-10-13 19:00:26 +0800
Commit message:

 Merge remote-tracking branch 'upstream/master'
Package: ggtree
Commit: 7c32e8f84a784dde1b39046d192abd3ce9e60e36
Author: xiangpin <xshuangbin@163.com>
Date: 2021-10-13 19:00:11 +0800
Commit message:

 extend of geom_cladelab supports two element vector
Package: ggtree
Commit: 15c3faed821928739ff486f7f7ae8c5eaf94f223
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2021-10-13 11:35:13 +0800
Commit message:

 update citatino
Package: ggtree
Commit: 9d807a64d5d1d183a52e22b8eca1cdcb27d6ac31
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2021-10-12 16:54:53 +0800
Commit message:

 update docs
Package: ggtree
Commit: 17e4ed931d4a0bd54b3956897e22b09ce4b29ce5
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2021-10-12 16:50:46 +0800
Commit message:

 clean up code #445
Package: ggtree
Commit: bd8d7bd013760813025cf27787f2bb5e949c8cda
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2021-10-12 16:49:03 +0800
Commit message:

 Merge pull request #445 from xiangpin/edge.lenght_negative

ignore negative edge introduce options(ignore.negative.edge=TRUE)
Package: ggtree
Commit: 31cef4dc6bf6249a76312725e96867be165a0d95
Author: xiangpin <xshuangbin@163.com>
Date: 2021-10-12 16:33:52 +0800
Commit message:

 typo
Package: ggtree
Commit: 1a7273159d29b9c0ed73abd07ca1234654af4aab
Author: xiangpin <xshuangbin@163.com>
Date: 2021-10-12 16:00:40 +0800
Commit message:

 ignore negative edge introduce options(ignore.negative.edge=TRUE)
Package: ggtree
Commit: 7bf5375a23597d6f5e06452e09aa891a1165bcf9
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2021-10-11 14:57:20 +0800
Commit message:

 Merge pull request #444 from xiangpin/hilight_gradient

Hilight gradient and round rectangular high light
Package: ggtree
Commit: 6603a1532461f4f91c05f9539b40a03d54739cfc
Author: xiangpin <xshuangbin@163.com>
Date: 2021-10-11 12:14:52 +0800
Commit message:

 gradient or roundrect hilight
Package: ggtree
Commit: 7c597ac2d336571922a747554ccc30331fd90c69
Author: xiangpin <xshuangbin@163.com>
Date: 2021-10-11 12:14:16 +0800
Commit message:

 show.legend works
Package: ggtree
Commit: 74d1d24cf4e27fc2b1d6b702709f9e980139f244
Author: xiangpin <xshuangbin@163.com>
Date: 2021-10-09 14:33:45 +0800
Commit message:

 hilight gradient
Package: ggtree
Commit: 507c882ad6505e6c09da851d820db86a050c3437
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2021-10-05 14:16:49 +0800
Commit message:

 todo
Package: ggtree
Commit: 4be7f96d545e46ca80661103ee69f8a5a2d34fc0
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2021-09-29 15:39:23 +0800
Commit message:

 update docs
Package: ggtree
Commit: b6965ad01869a01a177b2c84cbd5678ff96ce9b7
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2021-09-29 15:37:47 +0800
Commit message:

 Merge pull request #441 from xiangpin/edge.lenght_negative

fix the issue of negative edge.length
Package: ggtree
Commit: 8e7aa9d2d61d549d5f227b236f1cbd822e9d2307
Author: xiangpin <xshuangbin@163.com>
Date: 2021-09-29 14:38:31 +0800
Commit message:

 fix issue of negative edge.length
Package: enrichplot
Commit: 7ed8d9b1dafcfa9ba5e12fb56a04b2228b3a5000
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2021-10-13 15:23:47 +0800
Commit message:

 import yulab.utils
Package: DOSE
Commit: a016588468fa00bcf7530e58d7abaea3e69fe4d3
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2021-10-20 11:08:02 +0800
Commit message:

 bump version
Package: DOSE
Commit: cd88d1eec0e6a5f02569caa5784074ef613eb1e4
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2021-09-30 18:05:47 +0800
Commit message:

 update citation
Package: DOSE
Commit: 7895e502527770e2195e75338defd9ba918d03c6
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2021-09-03 09:11:50 +0800
Commit message:

 Merge pull request #53 from huerqiang/master

update error message of `enricher_internal`
Package: DOSE
Commit: 230f22ce053dce3235560f98b5bcd28d0e0d64ef
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2021-09-03 09:11:39 +0800
Commit message:

 Update enricher_internal.R
Package: DOSE
Commit: fd3f9c9727e611cbb1206c248855a10dd93146b5
Author: huerqiang <13766876214@163.com>
Date: 2021-09-03 00:43:09 +0800
Commit message:

 update error message of `enricher_internal`
Package: DOSE
Commit: 2f585f7dfb87f2d9bcba0e0d34f7eaddbf57a332
Author: Erqiang Hu <13766876214@163.com>
Date: 2021-09-03 00:36:14 +0800
Commit message:

 Merge pull request #2 from YuLab-SMU/master

merge from YuLab to me
Package: DOSE
Commit: 0f418e7327a2e91872f203fb82a31fbe8f31cff5
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2021-08-16 14:48:11 +0800
Commit message:

 update readme
Package: clusterProfiler
Commit: 8aec6ac7d47090930db08330549b53e7c4a9fc41
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2021-09-18 23:04:44 +0800
Commit message:

 Update gseAnalyzer.R
Package: clusterProfiler
Commit: 1ce6ff56227097d5d2cebe4b89848034bf3fb2d7
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2021-09-18 23:02:43 +0800
Commit message:

 Update gseAnalyzer.R

fixed <https://github.com/Bioconductor/AnnotationDbi/issues/4#issuecomment-677871617>.
Package: scClassify
Commit: 74fe32784b401492da0fd203736f39bcd6f2a2c5
Author: yingxinlin <yingxinlindsay@gmail.com>
Date: 2021-10-20 13:50:28 +1100
Commit message:

 change version
Package: scClassify
Commit: 47f8663b853576500fd9a071d842989aadfffa99
Author: yingxinlin <yingxinlindsay@gmail.com>
Date: 2021-10-20 13:47:40 +1100
Commit message:

 add Cepo
Package: scClassify
Commit: b57ac7a1ba8715d177f2bae31f2066f1d856f502
Author: yingxinlin <yingxinlindsay@gmail.com>
Date: 2021-10-20 13:07:33 +1100
Commit message:

 merge
Package: scClassify
Commit: 1dd034a174ebe05b6d8b39ecc8a4cd6ae4e43a11
Author: YingxinLin <yingxinlindsay@gmail.com>
Date: 2021-07-06 14:18:57 +1000
Commit message:

 fix joint prediction
Package: scClassify
Commit: ec5528db03a841241f9a3c6786a219adfac1aada
Author: yingxinlin <yingxinlindsay@gmail.com>
Date: 2021-01-20 15:26:41 +1100
Commit message:

 update citation
Package: vissE
Commit: 1443ff1603628951bd56865d00342ea723e8e2be
Author: bhuva.d <bhuva.d@wehi.edu.au>
Date: 2021-10-20 12:04:17 +1100
Commit message:

 Changed default word cloud statistic
Package: miaSim
Commit: 4dd44a780f48124e4b656aea0bd20d626cfa7ee1
Author: YagmurSimsekk <yagmur.simsek@hsrw.org>
Date: 2021-10-20 03:44:20 +0300
Commit message:

 bioc
Package: miaSim
Commit: 9eb8080d39940dea3e824143206c5cf1b239598d
Author: YagmurSimsekk <yagmur.simsek@hsrw.org>
Date: 2021-10-20 02:50:59 +0300
Commit message:

 bioc
Package: edgeR
Commit: 7a7dc909373966f2f36d7410613b6ec26a06f221
Author: Yunshun Chen <yuchen@wehi.edu.au>
Date: 2021-10-20 11:18:38 +1100
Commit message:

 Updated edgeR user's guide and the test file.
Package: systemPipeR
Commit: eff39c60b56c6236f1455a49c63469b87d4ffb9c
Author: dcassol <danicassol@gmail.com>
Date: 2021-10-19 17:00:44 -0700
Commit message:

 build_check
Package: systemPipeR
Commit: 61de89884cac2910b26d16d19ac029ba0fb48c79
Author: dcassol <danicassol@gmail.com>
Date: 2021-10-19 17:00:36 -0700
Commit message:

 update pkg version; build_check
Package: systemPipeR
Commit: bab46ac6163ebda976b4d1ce7328b966142fef6e
Author: dcassol <danicassol@gmail.com>
Date: 2021-10-18 06:26:40 +0000
Commit message:

 Bot update cwl description files
Package: systemPipeR
Commit: 39919c81a688449bdd302b2a88e39f02b8409397
Author: dcassol <danicassol@gmail.com>
Date: 2021-10-18 06:19:07 +0000
Commit message:

 Bot update cwl description files
Package: dittoSeq
Commit: d7cfa359a43224a01f2a467735dafdfaf191c7a5
Author: dtm2451 <daniel.bunis@ucsf.edu>
Date: 2021-10-19 16:02:50 -0700
Commit message:

 update README
Package: dittoSeq
Commit: bdb59972f2c2f22b711707f3d465458ea6e5a305
Author: dtm2451 <daniel.bunis@ucsf.edu>
Date: 2021-10-19 15:52:22 -0700
Commit message:

 consolidate NEWS and reformat to md
Package: AnVIL
Commit: 97595d83f67a8e1d22b77f3747228db7e5684d65
Author: Martin Morgan <Martin.Morgan@RoswellPark.org>
Date: 2021-10-19 18:06:24 -0400
Commit message:

 update NEWS file
Package: ggmanh
Commit: 67e5fc2ee293917d5872138cdad87c5dca2ceffd
Author: Lee, John S <john.lee@abbvie.com>
Date: 2021-10-19 17:02:21 -0500
Commit message:

 Version bump

Add GRanges support and updated Vignette
Package: ggmanh
Commit: c8eb39cee761416f59cd5d203fa041034a23bbff
Author: Lee, John S <john.lee@abbvie.com>
Date: 2021-10-19 17:00:57 -0500
Commit message:

 Update vignette with BiocStyle
Package: ggmanh
Commit: e376232d9c2b32a7494d16a15b82d591b9acc67c
Author: Lee, John S <john.lee@abbvie.com>
Date: 2021-10-19 16:26:45 -0500
Commit message:

 Add methods for GRanges object. Reimplement manhattan plotting methods.
Package: igvR
Commit: 85ed021a016e1cdcf784234788fa32dd6901d9cd
Author: paul-shannon <paul.thurmond.shannon@gmail.com>
Date: 2021-10-19 14:56:01 -0700
Commit message:

 using new igv.js, version 2.10.1
Package: OmnipathR
Commit: 1c9cfd383a26a6a386ac033aad7d06d05311db6c
Author: Türei Dénes <turei.denes@gmail.com>
Date: 2021-10-19 22:48:28 +0200
Commit message:

 `kegg_pathway_download`: error handling for failed download
Package: DIAlignR
Commit: e9b4be8850e454cf47baf93a76ef89dc7f716b0c
Author: Shubham <sgupt46@alumni.uwo.ca>
Date: 2021-10-19 16:36:31 -0400
Commit message:

 minor
Package: mina
Commit: e9e5ed42b73b93dc3f428ec6eaad27c766615812
Author: Your Name <you@example.com>
Date: 2021-10-19 22:30:20 +0200
Commit message:

 modify exmaple in R/get_rep.R
Package: mina
Commit: 80e9d0a206dba46dd4bac8c6cf6140a9b36427e0
Author: Your Name <you@example.com>
Date: 2021-10-19 22:24:53 +0200
Commit message:

 modify net_grp_cmp.R
Package: InteractiveComplexHeatmap
Commit: 58346dd8f2790809d98601a503222fcf930fc90d
Author: Zuguang Gu <jokergoo@gmail.com>
Date: 2021-10-19 22:18:53 +0200
Commit message:

 adjust examples
Package: InteractiveComplexHeatmap
Commit: 737c1bc733485996916f50d6c0081a9d9a8f288e
Author: Zuguang Gu <jokergoo@gmail.com>
Date: 2021-10-19 11:33:57 +0200
Commit message:

 update website
Package: InteractiveComplexHeatmap
Commit: fd3ed2fed85115fedbcd14e91e31eb884e76f4bd
Author: Zuguang Gu <jokergoo@gmail.com>
Date: 2021-10-19 11:28:49 +0200
Commit message:

 add a new vignette
Package: InteractiveComplexHeatmap
Commit: f5e78d403bee0b9b94c1756d374d91e73ef9f40b
Author: Zuguang Gu <jokergoo@gmail.com>
Date: 2021-10-08 15:33:36 +0200
Commit message:

 content of js and css is directly added to html
Package: InteractiveComplexHeatmap
Commit: dfdc827328ebefe6e3e8569f80f3eae700a00a61
Author: Zuguang Gu <jokergoo@gmail.com>
Date: 2021-09-29 13:44:00 +0200
Commit message:

 update
Package: InteractiveComplexHeatmap
Commit: e0de547ac18033947e63aa9c8e81a486cb048711
Author: Zuguang Gu <jokergoo@gmail.com>
Date: 2021-09-29 13:07:14 +0200
Commit message:

 also inherit row_names_gp and column_names_gp from the complete heatmap
Package: DIAlignR
Commit: 81dc639678da9f3415c5f880ae5431a90bd9385d
Author: Shubham <sgupt46@alumni.uwo.ca>
Date: 2021-10-19 16:21:36 -0400
Commit message:

 [BugFix] Tests were failing on windows machine
Package: animalcules
Commit: b1ebe5f69f837f82d33e576aae2d49b04d6b1ff5
Author: jasonzhao0307 <jasonzhao0307@gmail.com>
Date: 2021-10-19 16:07:00 -0400
Commit message:

 update for biioc3.14
Package: ORFik
Commit: 337a27db07d8e311d62312292f3297dbbe574968
Author: Roleren <hauken_heyken@hotmail.com>
Date: 2021-10-19 21:53:14 +0200
Commit message:

 All checks pass
Package: ORFik
Commit: 425c40beafc777d2e41cf665c1e727dfabf7b11e
Author: Roleren <hauken_heyken@hotmail.com>
Date: 2021-10-19 20:44:05 +0200
Commit message:

 Fixed tests
Package: ORFik
Commit: c4ff9d8a62f38a4786a05e06ffbbb648a71faeca
Author: Roleren <hauken_heyken@hotmail.com>
Date: 2021-10-19 19:27:28 +0200
Commit message:

 Updated ofst files and made annotation bigger
Package: ORFik
Commit: 70e11aa8c9fad875393b86db7f40a71927f8a850
Author: Roleren <hauken_heyken@hotmail.com>
Date: 2021-10-19 15:55:22 +0200
Commit message:

 New template experiment
Package: ORFik
Commit: 1d097ed9bb043ddc7bfc158822b9d7fd11ff38a0
Author: Roleren <hauken_heyken@hotmail.com>
Date: 2021-10-14 15:59:00 +0200
Commit message:

 Updated docs
Package: ORFik
Commit: 78f7108e60152fb0ecd6df4bc2fe0137821e1356
Author: Roleren <hauken_heyken@hotmail.com>
Date: 2021-10-13 12:28:22 +0200
Commit message:

 Fixed bug heatmapRegion
Package: ORFik
Commit: 34718c87900e35e6547406182b407ad27aca0a57
Author: Roleren <hauken_heyken@hotmail.com>
Date: 2021-10-12 14:59:13 +0200
Commit message:

 Fixed bug in QC
Package: ORFik
Commit: a5f043cfe5d83c80e6bde140c395683d50ed4e47
Author: Roleren <hauken_heyken@hotmail.com>
Date: 2021-10-12 14:16:54 +0200
Commit message:

 Faster run time for heatmapRegion
Package: ORFik
Commit: 6a8ccb2c2cb904bcf8344e6f70fb492156554428
Author: Roleren <hauken_heyken@hotmail.com>
Date: 2021-10-12 11:51:34 +0200
Commit message:

 Improved correlation plot look
Package: ORFik
Commit: a97782171c1d9d2b73e6b47c3ddea92f7c01dbb6
Author: Roleren <hauken_heyken@hotmail.com>
Date: 2021-10-12 10:37:08 +0200
Commit message:

 Corrected bug in tRNA alignment
Package: ORFik
Commit: aec57a94da8669d2191802ab8d640578f2a6e611
Author: Roleren <hauken_heyken@hotmail.com>
Date: 2021-10-12 10:08:47 +0200
Commit message:

 Updated tRNA mapping
Package: ORFik
Commit: e70d35414ab96a7894d51ac1e954e91dacbb7b24
Author: Roleren <hauken_heyken@hotmail.com>
Date: 2021-10-11 11:37:04 +0200
Commit message:

 Updated tRNA alignment to be intron-less
Package: ORFik
Commit: 35c43735e47a032f1b92e2184d5863acf3ff92c1
Author: Roleren <hauken_heyken@hotmail.com>
Date: 2021-10-11 09:09:33 +0200
Commit message:

 Proper function call for threads
Package: ORFik
Commit: cc5360a28b7527f0eb8540726dc6b42d31025c85
Author: Roleren <hauken_heyken@hotmail.com>
Date: 2021-10-11 09:02:29 +0200
Commit message:

 Safer CPU core check
Package: ORFik
Commit: 5f9023d0490e7f74dd20d5a9d3f321d6422a716f
Author: Roleren <hauken_heyken@hotmail.com>
Date: 2021-10-08 14:43:35 +0200
Commit message:

 Updated STAR to allow to keep contaminant reads
Package: ORFik
Commit: 65b57a34a3be28b4e485faf33c0b1cee48c1770e
Author: Roleren <hauken_heyken@hotmail.com>
Date: 2021-10-05 14:38:38 +0200
Commit message:

 Updated docs
Package: AnVIL
Commit: 765def6672f3fa198543fd4252c3c40783632e5e
Author: Martin Morgan <Martin.Morgan@RoswellPark.org>
Date: 2021-10-19 15:50:43 -0400
Commit message:

 drs_cp() works with signed URLs

- more selective about drs_stat() columns returned to user
Package: RiboCrypt
Commit: 9d1418f7562b6279b84f65483b4499ae93db07fd
Author: Miswi <michal.swirski@student.uw.edu.pl>
Date: 2021-10-19 19:20:18 +0000
Commit message:

 bump version
Package: RiboCrypt
Commit: d0b47e615ca3cb342bf100238318162c797f108b
Author: Miswi <michal.swirski@student.uw.edu.pl>
Date: 2021-10-19 19:05:59 +0000
Commit message:

 Vignette redo
Package: AnnotationDbi
Commit: 538101ab561bc3b0b21555979c902ebbedab951d
Author: Jim MacDonald <jmacdon@vector.deohs.washington.edu>
Date: 2021-10-19 10:33:56 -0700
Commit message:

 Bugfix for code to find keys for NOSCHEMA DBs. Just added a simplify = FALSE to an additional sapply() call.
Package: AnnotationDbi
Commit: 4da631bf4f7d553f199af1d25fdfa6aedb2c5c9e
Author: Jim MacDonald <jmacdon@vector.deohs.washington.edu>
Date: 2021-10-19 10:20:12 -0700
Commit message:

 Bugfix for code to find keys for NOSCHEMA DBs. Just added a simplify = FALSE to a sapply() call.
Package: TFutils
Commit: b582b4ec0380a45afabbe7bbeaca3b145d69b2ae
Author: vjcitn <stvjc@channing.harvard.edu>
Date: 2021-10-19 13:10:28 -0400
Commit message:

 updates from Ugo Borelli and blocking windows work on FIMO data in cloud
Package: TFutils
Commit: 9d8e39c5e45755d90f1284e90fe0e888c03a5778
Author: Vince Carey <stvjc@channing.harvard.edu>
Date: 2021-10-13 18:27:27 -0400
Commit message:

 Merge pull request #1 from UgoBor/master

Add updated GO and Lambert human TFs databases
Package: TFutils
Commit: c81b502a00eac3eb6a5922a28731c6988c840165
Author: ugo <ugo@iMac.local>
Date: 2021-10-12 14:38:57 +0200
Commit message:

 Add updated GO and Lambert human TFs databases
Package: ternarynet
Commit: b694ef6ed0ea3dc8b940235e8c87b9aa3ec38b2a
Author: mccallm <mccallm@gmail.com>
Date: 2021-10-19 13:07:07 -0400
Commit message:

 Increase cycle number for tests
Package: GenomeInfoDb
Commit: 57cc3d55766c97cb4bb9a3e02f9b1af36a56244e
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2021-10-19 10:05:07 -0700
Commit message:

 oops, forgot to update unit tests and a couple of man pages
Package: AnVIL
Commit: c4a9efbc60daaf35974e2f4f4a65de2f0be6f360
Author: Martin Morgan <Martin.Morgan@RoswellPark.org>
Date: 2021-10-19 12:45:46 -0400
Commit message:

 install() wraps BiocManager::install()

- more consistency between functionality, e.g., both install github
  repositories
Package: SpidermiR
Commit: ef7a9a6525fe207bde8024c794a7f732c162991b
Author: claudia.cava <claudia.cava@ibfm.cnr.it>
Date: 2021-10-19 18:33:36 +0200
Commit message:

 UP
Package: SpidermiR
Commit: baab671e453b9fcb534432360801f031333edfd1
Author: claudia.cava <claudia.cava@ibfm.cnr.it>
Date: 2021-10-19 18:31:26 +0200
Commit message:

 update
Package: fishpond
Commit: b6238662379c70604e13943b6836b37c0dc7d211
Author: mikelove <michaelisaiahlove@gmail.com>
Date: 2021-10-19 12:41:05 -0400
Commit message:

 updating docs
Package: TargetDecoy
Commit: d2d83d23d4247c99a4845cdde3a04570f0aea8f6
Author: Milan Malfait <milan.malfait94@gmail.com>
Date: 2021-10-19 18:07:44 +0200
Commit message:

 Address Bioc review (#6)

* Split evalTargetDecoys function in 5 functions, replace screenshot by runnable code, delete time stuff

* Split function

* Delete Shiny app and make new R file with the shiny app.

* sys.time section deleted

* Revert "Split function"

  This reverts commit 253bcaa8432167c6347db3613e08ff98e3784483.

* Revert "Delete Shiny app and make new R file with the shiny app."

  This reverts commit 875b3c90ad9231a64b94ea0e82a9cec703291e9e.

* Remove shiny app, move `decoyScoreTable()` to `evalTargetDecoys.R`

* Reoxygenize

* Clean up `decoyScoreTable()`

  * Remove Shiny functionality
  * Combine similar error messages
  * Remove default values for `decoy=` and `score=`

* Clean up `evalTargetDecoys()` and friends

  * Format code
  * Remove default `NULL` values for arguments (this only works with the Shiny app)
  * Move over `.ppPlot()` helper from `plots.R`
  * Simplify `evalTargetDecoys()`: let it call the other functions
  internally
  * Remove `evalTargetDecoysTogether()`. This handled by
  `evalTargetDecoys()`

* Add `zoom=` argument to `evalTargetDecoysPPPlot()` and
  `evalTargetDecoysHist()` instead of separate functions

* Add check for `is.logical(log10)` in `decoyScoreTable()`

* Update `evalTargetDecoys()` documentation

* Update tests for `evalTargetDecoys()`

* Move `plots.R` contents to `utils.R`

* Remove `NULL` default values for `score` and `decoy`
  This requires the Shiny app.

* Reoxygenize

* Return single plots arranged by `ggarrange`

* Update data documentation

* Update vignette

  * Remove Bioc installation instructions, replace by 'devel' installation from GitHub
  * Some typo fixes
  * Use new `evalTargetDecoysHist()` and `evalTargetDecoysPPPlot()` functions in examples
  * Remove Shiny-related stuff
  * Remove `grid.arrange` calls, this is now handled by `createPPlotScores()` and `createPPlotObjects()` internally

* Remove `nBins` argument for `evalTargetsPPPlot()`

* Bump Version and Date

Co-authored-by: ElkeDebrie <ElkeDebrie@users.noreply.github.com>
Package: psichomics
Commit: 68bbd6be3be9200a2a91c1ef32c2f956eec73c46
Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
Date: 2021-10-19 17:30:37 +0100
Commit message:

 Squashed commit of the following:

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 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: Pigengene
Commit: a138f8e1215bd23925cda3de7b69be01e208a6f2
Author: Habil Zare <zare@uthscsa.edu>
Date: 2021-10-19 11:19:43 -0500
Commit message:

 Habil approves Nedas changes.
Package: InterCellar
Commit: 13bc2d2c20aac3bea46842faf816470ca9965716
Author: martaint <marta.interlandi01@gmail.com>
Date: 2021-10-19 18:16:07 +0200
Commit message:

 version bump 1.99.1
Package: InterCellar
Commit: 1104d8fa9fdae06659373c781c4adead883ec985
Author: martaint <marta.interlandi01@gmail.com>
Date: 2021-10-19 18:14:16 +0200
Commit message:

 updated userguide plus passing checks
Package: InterCellar
Commit: 5c17fa7dc91550a938fb454a7ce0f5e3ac01580a
Author: martaint <marta.interlandi01@gmail.com>
Date: 2021-10-19 11:27:07 +0200
Commit message:

 updated about and description
Package: trackViewer
Commit: f1f425f6e8a39570e33584871ff9aad3f7fa0fbb
Author: JIANHONG OU <jianhong@users.noreply.github.com>
Date: 2021-10-19 11:56:55 -0400
Commit message:

 Fix the a typo in read hic data.
Package: xcms
Commit: 105d50393972374c907519174385774c45b5177c
Author: Steffen Neumann <sneumann@ipb-halle.de>
Date: 2021-10-19 17:56:08 +0200
Commit message:

 Merge pull request #583 from sneumann/fix/issue582

Disable testing on windows i386 and Disable parallel processing on Windows
Package: xcms
Commit: 02ddd0dd0ab635bef47149163a9371066df6d925
Author: Steffen Neumann <sneumann@ipb-halle.de>
Date: 2021-10-19 16:52:30 +0200
Commit message:

 Disable testing on windows i386 and Disable parallel processing on Windows
Package: graphite
Commit: 18c6a623e7f565778f3eb41a45db94533a44e3aa
Author: Gabriele Sales <gbrsales@gmail.com>
Date: 2021-10-19 17:36:36 +0200
Commit message:

 Bump minimum R version
Package: graphite
Commit: 08f7c8ee23ecd4e74468a5b1fdfe5acb94f5eb54
Author: Gabriele Sales <gbrsales@gmail.com>
Date: 2021-10-19 17:28:11 +0200
Commit message:

 Add sessionInfo()
Package: graphite
Commit: cdcb447debbdc4d4fab1b33a1c8bfea948109bd6
Author: Gabriele Sales <gbrsales@gmail.com>
Date: 2021-10-19 17:27:53 +0200
Commit message:

 Avoid duplicate chunk name
Package: graphite
Commit: ba81ae83d57de4f4e9b511fa109246aae69ac9fe
Author: Gabriele Sales <gbrsales@gmail.com>
Date: 2021-10-19 15:29:48 +0200
Commit message:

 Update all pathway data
Package: graphite
Commit: 3146db12fe854e5ece033748bea34512c7a700b8
Author: Gabriele Sales <gbrsales@gmail.com>
Date: 2021-10-15 13:15:35 +0200
Commit message:

 Remove intermediate file used by SPIA
Package: Pigengene
Commit: 4b05f84fd40b20bf3e90b72a029eb11c7755bf68
Author: Neda <neda.emami1993@gmail.com>
Date: 2021-10-19 19:10:34 +0330
Commit message:

 Neda added filtering functions!
Package: Pigengene
Commit: d3b17d9128dbd74436bdd16965211e2d1c30ddf6
Author: Neda <neda.emami1993@gmail.com>
Date: 2021-10-14 19:51:25 +0330
Commit message:

 Neda is adding filtering, conflict resolved!!
Package: Pigengene
Commit: 42ada31863cf280f210b7ac60f186cce50b4ed09
Author: Neda <neda.emami1993@gmail.com>
Date: 2021-10-14 19:40:53 +0330
Commit message:

 Neda is adding filtering, conflict resolved!
Package: Pigengene
Commit: b155d01d6595b5fb68f49d06bbc34ce95b0c813b
Author: Neda <neda.emami1993@gmail.com>
Date: 2021-10-14 19:22:06 +0330
Commit message:

 Neda is adding filtering!
Package: DIAlignR
Commit: ae4b5defd3175629fdd47b728af81de25f045f60
Author: Shubham <sgupt46@alumni.uwo.ca>
Date: 2021-10-19 11:26:40 -0400
Commit message:

 Updated Version
Package: DIAlignR
Commit: c620f7c3dd8c4533644ff26f6d0299d1af7f47af
Author: Shubham <sgupt46@alumni.uwo.ca>
Date: 2021-10-19 10:45:32 -0400
Commit message:

 [Fix] Added fractionation for MST
Package: fishpond
Commit: 77154dfd0c71cc12cb967a93c2d5cc3e01c2035d
Author: mikelove <michaelisaiahlove@gmail.com>
Date: 2021-10-19 11:31:41 -0400
Commit message:

 tweak margins
Package: BiocSet
Commit: 183e596d19dd896117ad7540704504783af65890
Author: Kayla-Morrell <kayla.morrell@roswellpark.org>
Date: 2021-10-19 11:27:18 -0400
Commit message:

 bug fix: fixed failing kegg test
Package: fishpond
Commit: 826ce21973bd0a9b851e3d7586e3f94d761dec59
Author: mikelove <michaelisaiahlove@gmail.com>
Date: 2021-10-19 10:43:04 -0400
Commit message:

 stylistic changes
Package: fishpond
Commit: 432bb20f17979f2a668d38db4a5ea9c3b6ea989d
Author: Mike Love <mikelove@users.noreply.github.com>
Date: 2021-10-19 10:27:13 -0400
Commit message:

 Merge pull request #13 from DongzeHE/master

expanded argument nonzero, and changed verbose -> quiet
Package: fishpond
Commit: 1f28e0ec251a236cf4a529d8a162028d6fc47147
Author: DongzeHE <32473855+DongzeHE@users.noreply.github.com>
Date: 2021-10-19 10:16:39 -0400
Commit message:

 expand nonzero in loadFry

also changed verbose -> quiet
Package: fishpond
Commit: 2d2dd0a442ee728d70d7e4337a51b015cf0f4c44
Author: DongzeHE <32473855+DongzeHE@users.noreply.github.com>
Date: 2021-10-19 09:57:12 -0400
Commit message:

 Merge branch 'master' of https://github.com/DongzeHE/fishpond
Package: fishpond
Commit: fd294519140c5fde775eccfd23baf27f7744dda7
Author: DongzeHE <32473855+DongzeHE@users.noreply.github.com>
Date: 2021-10-19 09:07:05 -0400
Commit message:

 Update loadFry.R
Package: maftools
Commit: fb51a88b935289a69e8d3bd582b2d68fb43b76e3
Author: PoisonAlien <anandmt3@gmail.com>
Date: 2021-10-19 16:27:26 +0200
Commit message:

 fix vignette typo
Package: maftools
Commit: af202ed5a590e87fdcc38b61ec559e8f4d235e11
Author: PoisonAlien <anandmt3@gmail.com>
Date: 2021-10-19 16:01:42 +0200
Commit message:

 Address #780
Package: maftools
Commit: 1a42a2fa327fa78929c3410816e8da0a24575ea8
Author: PoisonAlien <anandmt3@gmail.com>
Date: 2021-10-18 09:36:49 +0200
Commit message:

 Add SETD1B structure #779
Package: nullranges
Commit: b47f93ec552865adbe67e6361d691b007c40b4f6
Author: mikelove <michaelisaiahlove@gmail.com>
Date: 2021-10-19 10:14:27 -0400
Commit message:

 updating use of seg in boot
Package: karyoploteR
Commit: 99a47e8e0952a70a121f545891854663644b10c7
Author: Bernat <bernatgel@gmail.com>
Date: 2021-10-19 15:55:29 +0200
Commit message:

 Version Bump
Package: karyoploteR
Commit: 4796dde4f91e7a308af79488333289ad39abd313
Author: Bernat <bernatgel@gmail.com>
Date: 2021-10-19 15:55:01 +0200
Commit message:

 Deactivated example to avoid a warning from rtracklayer

Warning triggered by biovizbase code calling rtracklayer
Package: ChIPpeakAnno
Commit: 3c2c9fb8d3c1af23844754aadf7e0d14ba7afe59
Author: JIANHONG OU <jianhong@users.noreply.github.com>
Date: 2021-10-19 09:12:15 -0400
Commit message:

 Fix the erro "!anyNA(m32) is not TRUE" in seqlevelsStyle is not handled.
Package: fishpond
Commit: eb8e7792d81a528ff22f0531ab6a82d4e5ab943a
Author: mikelove <michaelisaiahlove@gmail.com>
Date: 2021-10-19 09:06:13 -0400
Commit message:

 updating docs for loadFry
Package: biomaRt
Commit: e0b0a3996a34486d4229152b986330d3819a2b4a
Author: Mike Smith <grimbough@gmail.com>
Date: 2021-10-19 14:54:33 +0200
Commit message:

 Fix missing httr_config
Package: AnnotationHubData
Commit: 96af743f08cb0aed396461332242f5c8082ea58c
Author: lshep <lori.shepherd@roswellpark.org>
Date: 2021-10-19 08:43:33 -0400
Commit message:

 Chaning testing endpoint

  ftp tests for access and correct parsing are failing occassionally
  the following has intermittent issues with connectivity
      	"ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_mouse/release_M6/"
  changing teseting endpoint to ensembl which seems more stable to test
  functionality of function
        "ftp://ftp.ensembl.org/pub/release-98/gtf/homo_sapiens/"
Package: treekoR
Commit: d1fa32b0048912bc9961f66344287f46cc72cc24
Author: Adam Chan <adam.s.chan@sydney.edu.au>
Date: 2021-08-23 18:27:03 +1000
Commit message:

 Added  to test formula to avoid errors
Package: DEWSeq
Commit: 5f027330d22e986954301296dcaa199a0b6ab1ca
Author: hentzelab <biohentze@embl.de>
Date: 2021-10-11 09:40:02 +0200
Commit message:

 update version
Package: MsBackendRawFileReader
Commit: d1ca9f8854f2a41a9116615ac79bc03caa16de0b
Author: Christian Panse <cp@fgcz.ethz.ch>
Date: 2021-10-19 13:45:23 +0200
Commit message:

 Cosmitics in vignette file
Package: synergyfinder
Commit: 08042e3e16abcba60713f7d228acf01d33d0bfda
Author: Shuyu <shuyu.zheng@helsinki.fi>
Date: 2021-10-19 14:06:24 +0300
Commit message:

 update version number to 3.1.15
Package: synergyfinder
Commit: 429f1c521abdaadb55207f4585dc4ee185d7aad1
Author: Shuyu <shuyu.zheng@helsinki.fi>
Date: 2021-10-19 14:00:47 +0300
Commit message:

 update documentations
Package: synergyfinder
Commit: 269c5db6b65267c89ca7c4af0d17d55d2c37e4f0
Author: Shuyu <shuyu.zheng@helsinki.fi>
Date: 2021-10-19 13:57:28 +0300
Commit message:

 Update version number to 3.0.15
Package: synergyfinder
Commit: 185e55ee5962b78e54fd58d8d7df331e43a72eb9
Author: Shuyu <shuyu.zheng@helsinki.fi>
Date: 2021-10-19 13:56:32 +0300
Commit message:

 Correct the discription for CalculateSensitivity function
Package: synergyfinder
Commit: b06986803008ed1a9fa436f3f4a6b4106d26b8ef
Author: Shuyu <shuyu.zheng@helsinki.fi>
Date: 2021-10-19 13:53:40 +0300
Commit message:

 Suppress warning messages from FitDoseResponse
Package: synergyfinder
Commit: bc55a356f76c3194a1c2bcbff3ca1ab40cab5a58
Author: Shuyu <shuyu.zheng@helsinki.fi>
Date: 2021-10-19 13:52:40 +0300
Commit message:

 Update .Bootstrap function.
Package: synergyfinder
Commit: 11d2c592f9b7c4be34f889350eb95fa0ecca8955
Author: Shuyu <shuyu.zheng@helsinki.fi>
Date: 2021-10-13 11:02:07 +0300
Commit message:

 Update version number to 3.0.14
Package: synergyfinder
Commit: dbb1e0ad88bc41eb446fbc0dce7b0e1e6f77595b
Author: Shuyu <shuyu.zheng@helsinki.fi>
Date: 2021-07-15 12:07:04 +0300
Commit message:

 Update version number to 3.0.13
Package: synergyfinder
Commit: b6f645abd28724b110e5e3c1817c1e51787f0226
Author: Shuyu <shuyu.zheng@helsinki.fi>
Date: 2021-07-15 11:55:28 +0300
Commit message:

 Enable Plot2DrugHeatmap to show SD (standard deviation)
Package: synergyfinder
Commit: 5b246e8fba4918985ec45a345991bfb5ecc6dfca
Author: Shuyu <shuyu.zheng@helsinki.fi>
Date: 2021-07-15 11:42:41 +0300
Commit message:

 Update version number to 3.0.12
Package: synergyfinder
Commit: f4e2626cb1b523f5e4a44b3d0ba953b99178abef
Author: Shuyu <shuyu.zheng@helsinki.fi>
Date: 2021-07-15 11:41:27 +0300
Commit message:

 Correct the calculation of SEM for synergy score and sensitivity score. Add SD in the output list.
Package: synergyfinder
Commit: 077c03cbabba06cc10e4223a88b26d45ac91355c
Author: Shuyu <shuyu.zheng@helsinki.fi>
Date: 2021-07-12 15:46:01 +0300
Commit message:

 update version number to 3.0.11
Package: synergyfinder
Commit: 41f9a9b2cc9ebff1a8c4992d2a941ef2935206cd
Author: Shuyu <shuyu.zheng@helsinki.fi>
Date: 2021-07-07 15:53:14 +0300
Commit message:

 update version number to 3.0.10
Package: GSEABase
Commit: dff61ea0f995d4b9231bf902381cb87d9e3262b9
Author: Martin Morgan <Martin.Morgan@RoswellPark.org>
Date: 2021-10-19 06:32:58 -0400
Commit message:

 update unit test

- make more robust by calculating expectation from basic operations
  on AnnotationDbi resources
Package: biodb
Commit: c231763f1859072f44e156eac3501ebf503708a9
Author: Pierrick Roger <pk.roger@icloud.com>
Date: 2021-10-19 12:21:44 +0200
Commit message:

 Update doc.
Package: edgeR
Commit: 791233fbea3111b780949db36da57767e009b969
Author: Gordon Smyth <smyth@wehi.edu.au>
Date: 2021-10-19 21:16:39 +1100
Commit message:

 edgeR 3.55.2

- Improve error message from readDGE() when there are repeated gene/tag names.
Package: MsBackendRawFileReader
Commit: 0ace183eaff8769698fb1bedc7a8075f5ba16c17
Author: Christian Panse <cp@fgcz.ethz.ch>
Date: 2021-10-19 10:29:51 +0200
Commit message:

 Merge branch 'master' of git.bioconductor.org:packages/MsBackendRawFileReader
Package: MsBackendRawFileReader
Commit: a66881575fbca3e6bb45aeff40f87a6f6b571454
Author: Christian Panse <cp@fgcz.ethz.ch>
Date: 2021-10-19 10:28:38 +0200
Commit message:

 Add ``courtesy'' in vignette  arch figure caption
Package: MicrobiotaProcess
Commit: c9b5d8d7073009ce8268ddad940fc87df0c18f55
Author: xiangpin <xshuangbin@163.com>
Date: 2021-10-19 16:26:16 +0800
Commit message:

 update news and bump version
Package: MicrobiotaProcess
Commit: 02cdae2b12653c12be1d68f0248b73de00a54638
Author: xiangpin <xshuangbin@163.com>
Date: 2021-10-19 16:17:32 +0800
Commit message:

 add include.rownames to control whether consider the OTU as taxonomy table or tip labels of treedata
Package: MicrobiotaProcess
Commit: cd8b297d2be90ee466476468949ef3d4bf6d124a
Author: xiangpin <xshuangbin@163.com>
Date: 2021-10-17 11:28:34 +0800
Commit message:

 update rd
Package: MicrobiotaProcess
Commit: 4f80e6b888fddfff8b06f342c702787f8e256e35
Author: xiangpin <xshuangbin@163.com>
Date: 2021-10-13 20:16:08 +0800
Commit message:

 update rd of mp_diff_analysis
Package: MicrobiotaProcess
Commit: 14ece0802960f2810e05faf50a8216b36c32df21
Author: xiangpin <xshuangbin@163.com>
Date: 2021-10-12 20:52:57 +0800
Commit message:

 change 'J' index to 'Pielou' index
Package: MicrobiotaProcess
Commit: 0acae51640515c953491e3c6f6ed148f2e4f70e3
Author: xiangpin <xshuangbin@163.com>
Date: 2021-10-12 12:27:52 +0800
Commit message:

 update news
Package: MicrobiotaProcess
Commit: f3a4274cfb606cb85186a218bea250eb616e522d
Author: xiangpin <xshuangbin@163.com>
Date: 2021-10-12 12:25:36 +0800
Commit message:

 fix rename bug
Package: MicrobiotaProcess
Commit: da137ebe136de5dff6a0275aa51169b45debb0bd
Author: xiangpin <xshuangbin@163.com>
Date: 2021-10-11 17:13:01 +0800
Commit message:

 Merge remote-tracking branch 'origin/master'
Package: MicrobiotaProcess
Commit: 55daa1ee1b13c8a23dd3b83352f8426918954ffb
Author: xiangpin <xshuangbin@163.com>
Date: 2021-10-11 17:12:05 +0800
Commit message:

 update news
Package: MicrobiotaProcess
Commit: 3c54b3eb5fbe784a9b793b7aba40db23a7371513
Author: xiangpin <xshuangbin@163.com>
Date: 2021-10-11 17:11:46 +0800
Commit message:

 introduce trimSample parameter in mp_rrarefy
Package: MicrobiotaProcess
Commit: cc76dfb7862c196d7653f22637a78e8107a85cb4
Author: xiangpin <xshuangbin@163.com>
Date: 2021-10-09 21:00:29 +0800
Commit message:

 change action="only" to action="add" in mp_cal_nmds
Package: MicrobiotaProcess
Commit: a3f85510a8ebe39ddd6eac55d4d475164a109d47
Author: xiangpin <xshuangbin@163.com>
Date: 2021-10-08 19:12:10 +0800
Commit message:

 update news
Package: MicrobiotaProcess
Commit: d5d348365b522d8430121e882bdf3be58d171ce4
Author: xiangpin <xshuangbin@163.com>
Date: 2021-10-08 19:07:17 +0800
Commit message:

 update MPSE
Package: pengls
Commit: 4e6345c1fbf171550663f694a11b9f0b312bc857
Author: Stijn HAWINKEL <sthaw@psb.ugent.be>
Date: 2021-10-19 10:17:45 +0200
Commit message:

 WIth title and author for the vignette
Package: MsBackendRawFileReader
Commit: ce51bcf3d1b3d1110f69a9d7ee02cff9ca831bbc
Author: Christian Panse <cp@fgcz.ethz.ch>
Date: 2021-10-19 10:17:41 +0200
Commit message:

 Bump version to 0.99.8
Package: MsBackendRawFileReader
Commit: bf067cbaa057d8ce5022cf09f587308569b6a15d
Author: Christian Panse <cp@fgcz.ethz.ch>
Date: 2021-10-19 10:11:40 +0200
Commit message:

 Add mzR in DESCRIPTION suggest field
Package: structToolbox
Commit: 3f07eb46e0f31dccaf1a56b0174219ab327a59a3
Author: Gavin Rhys Lloyd <grlloyd@users.noreply.github.com>
Date: 2021-10-18 16:54:26 +0100
Commit message:

 fix plotting of group ellipses
Package: structToolbox
Commit: 2baf3bbb4d1ed9597875ad7720f9c4fc513815c5
Author: Gavin Rhys Lloyd <grlloyd@users.noreply.github.com>
Date: 2021-10-07 13:22:49 +0100
Commit message:

 add fold change tests
Package: structToolbox
Commit: 33a0ec907c08d6eebd54673e82193404d0abce11
Author: Gavin Rhys Lloyd <grlloyd@users.noreply.github.com>
Date: 2021-10-07 13:22:38 +0100
Commit message:

 improve NA handling
Package: MsBackendRawFileReader
Commit: c3ff30bff8a9caa150ead220fa625444a6a98538
Author: Christian Panse <cp@fgcz.ethz.ch>
Date: 2021-10-19 09:32:26 +0200
Commit message:

 Add arch.jpg
Package: MsBackendRawFileReader
Commit: 510a35d187abed3ea75ec63187f06bf14dc84c05
Author: Christian Panse <cp@fgcz.ethz.ch>
Date: 2021-10-19 09:30:22 +0200
Commit message:

 Add arch figure in vignette file
Package: MsBackendRawFileReader
Commit: a6d260c76688b3228fc0a38da5a01277a8102858
Author: Christian Panse <cp@fgcz.ethz.ch>
Date: 2021-10-19 09:09:18 +0200
Commit message:

 Fix syntax in vignette
Package: MBQN
Commit: efc593fa0b5d6d5b2909cc10cf8c98a1de81f0e4
Author: Eva Brombacher <ebrombacher@web.de>
Date: 2021-10-14 15:39:59 +0200
Commit message:

 adjusted R version
Package: TENxVisiumData
Commit: 004613a6491a559673e7c7bfcf34c41705d7fd13
Author: HelenaLC <helena@crowells.eu>
Date: 2021-10-13 12:20:01 +0200
Commit message:

 version bump 1.1.2->.3
Package: TENxVisiumData
Commit: 8509d9856c73fc0a4cc38041f77beedcde9f1e38
Author: HelenaLC <helena@crowells.eu>
Date: 2021-10-13 12:19:49 +0200
Commit message:

 bug fix- make accession independent of ID changes
Package: MsBackendRawFileReader
Commit: 99399c807aea219eec00dc7fd97d328e4e83530a
Author: Christian Panse <cp@fgcz.ethz.ch>
Date: 2021-10-19 08:04:07 +0200
Commit message:

 Refactor benchmark code and use

e.g., use it in the vignette file
Package: MsBackendRawFileReader
Commit: 1b588dca42e382f3e56c6b3dd15f9e67144e1959
Author: Christian Panse <cp@fgcz.ethz.ch>
Date: 2021-10-19 07:59:38 +0200
Commit message:

 Add / export benchmark R code
Package: spatialHeatmap
Commit: 638b47e5de6628757f8cfb47a996fc02d075d2d5
Author: jianhaizhang <jzhan067@ucr.edu>
Date: 2021-10-18 22:42:16 -0700
Commit message:

 Small update (Version: 1.99.1/new release Bioc 3.14).
Package: spatialHeatmap
Commit: ccdd96ae0843b021cae255a23262f78a36d36c1f
Author: jianhaizhang <jzhan067@ucr.edu>
Date: 2021-10-18 22:37:39 -0700
Commit message:

 Small update (Version: 1.99.1/new release Bioc 3.14).
Package: RNASeqR
Commit: 3d35a08f6581953fc64fddc4595d62d93105a081
Author: Kuan-Hao Chao <kuanhao.chao@gmail.com>
Date: 2021-10-19 00:11:18 -0400
Commit message:

 Update DESCRIPTION version
Package: DelayedTensor
Commit: 062df83bcd8728e05ebd9ae4337c92412d74c939
Author: kokitsuyuzaki <k.t.the-answer@hotmail.co.jp>
Date: 2021-10-19 12:26:08 +0900
Commit message:

 v-0.99.12
Package: excluderanges
Commit: 699dd28b9edb7ecb0a0aab21ea6db90bfd13eb53
Author: Mikhail Dozmorov <mikhail.dozmorov@gmail.com>
Date: 2021-10-18 21:30:13 -0400
Commit message:

 Add package documentation
Package: excluderanges
Commit: 0310b67043bcf17c15f8e4e2525a65a4f54e7cb3
Author: Mikhail Dozmorov <mikhail.dozmorov@gmail.com>
Date: 2021-10-14 15:32:16 -0400
Commit message:

 Add logo, Mike Love version
Package: VAExprs
Commit: 0363902a0d8fcdc872e4cb406d9dece642bc786e
Author: dongminjung <dongminjung@Dongmins-MacBook-Pro.local>
Date: 2021-10-19 10:16:45 +0900
Commit message:

 update
Package: sccomp
Commit: 36fd3b7448eb2d8f42f378607928cbbec901e4a8
Author: stemangiola <mangiolastefano@gmail.com>
Date: 2021-10-19 10:36:49 +1100
Commit message:

 version UP
Package: sccomp
Commit: 4e4d21cc1915edb128b9578af7257534f6fd6c3d
Author: stemangiola <mangiolastefano@gmail.com>
Date: 2021-10-19 10:21:56 +1100
Commit message:

 try to fix warning DOCS
Package: CyTOFpower
Commit: 0ba3553ad1c288fc35c89bbd25e46c4f1cf76f66
Author: Anne-Maud Ferreira <amferrei@stanford.edu>
Date: 2021-10-18 13:40:35 -0700
Commit message:

 Increase version number +1
Package: CyTOFpower
Commit: a5b1a1587166a2986abd9de6979509bac4c983ce
Author: Anne-Maud Ferreira <amferrei@stanford.edu>
Date: 2021-10-18 13:40:13 -0700
Commit message:

 Add "internal" keyword to make documentation internal for all the functions
Package: CyTOFpower
Commit: b6eeb6de34dbcbeaef0e96d2c27f8d406aea4c90
Author: Anne-Maud Ferreira <amferrei@stanford.edu>
Date: 2021-10-18 13:34:24 -0700
Commit message:

 Correct numbering
Package: CyTOFpower
Commit: e135e63f1011055b4fdd7c0c211ae6f2fb69beee
Author: Anne-Maud Ferreira <amferrei@stanford.edu>
Date: 2021-10-18 13:34:01 -0700
Commit message:

 Add sentence in case power is not precomputed
Package: trena
Commit: 0a4fb8e3c0621e1548da266a1c671e2845bbd42d
Author: paul-shannon <paul.thurmond.shannon@gmail.com>
Date: 2021-10-18 15:54:41 -0700
Commit message:

 removed unbalanced tic character in vignette
Package: tidybulk
Commit: e30b102dd8ddb7be6fad44d281703db7f7a84d93
Author: stemangiola <mangiolastefano@gmail.com>
Date: 2021-10-19 09:53:01 +1100
Commit message:

 avoid example as failing on windows Bioconductor CHECK
Package: biocViews
Commit: 3b25b04c37b1b29dfa11e25e659258e2a87c7bd2
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2021-10-18 14:48:28 -0700
Commit message:

 Explain how to run/debug write_VIEWS() on the central builder
Package: biodbLipidmaps
Commit: 7e71359c36d9607ff6ec732caa04231bbd5f9ba7
Author: Pierrick Roger <pk.roger@icloud.com>
Date: 2021-10-18 23:33:17 +0200
Commit message:

 Increase frequency for sending requests.
Package: ggmanh
Commit: 1f1b852ecb6bc8e1f2e274e076bf9ba424f4a6ce
Author: Lee, John S <john.lee@abbvie.com>
Date: 2021-10-18 16:21:08 -0500
Commit message:

 version bump
Package: ggmanh
Commit: 6046d96e52552a6196d89ded3d672ce82499399c
Author: Lee, John S <john.lee@abbvie.com>
Date: 2021-10-18 15:58:36 -0500
Commit message:

 Changes related to gds file to the package for submission.

Add gds annotation data description.
Manually add man file for gds file.
Provide more detailed documentation on annotation using gds file.
Package: biodbHmdb
Commit: 1a9fb64957db071816030f457a9772bbaed330e0
Author: Pierrick Roger <pk.roger@icloud.com>
Date: 2021-10-18 23:13:53 +0200
Commit message:

 Take single XML available in ZIP file.
Package: biodb
Commit: dbcc6fd63f04dcd464460853eed4cc67d4be6e30
Author: Pierrick Roger <pk.roger@icloud.com>
Date: 2021-10-18 23:01:59 +0200
Commit message:

 Bump version.
Package: biodb
Commit: 1bc2d8332e8c077adeef5c49b8ba294eb45b5194
Author: Pierrick Roger <pk.roger@icloud.com>
Date: 2021-10-18 22:59:57 +0200
Commit message:

 Use binary option in RCurl and after base::url().

Add debug messages for getUrlContent().
Package: ToxicoGx
Commit: 25fbd118ec6a67c21a8914cb9240d11aa11dd400
Author: ChristopherEeles <christopher.eeles@outlook.com>
Date: 2021-10-18 17:07:26 -0400
Commit message:

 Version bump for BioC push
Package: ToxicoGx
Commit: 2248f0f20b2f02b72b5ba49d303eb3d9a1390d13
Author: Christopher Eeles <44755307+ChristopherEeles@users.noreply.github.com>
Date: 2021-10-18 16:07:50 -0400
Commit message:

 Merge pull request #8 from bhklab/development

Fix BioC ERROR by removing bplapply from tests
Package: ToxicoGx
Commit: f4a38f4de93b9354cb6de3a738082b621d7f23cf
Author: ChristopherEeles <christopher.eeles@outlook.com>
Date: 2021-10-18 15:28:14 -0400
Commit message:

 Fix test failure due to use of object instead of name in for loop
Package: ToxicoGx
Commit: a885e000622ebcd7a4d95b903ae642ca9e14685c
Author: ChristopherEeles <christopher.eeles@outlook.com>
Date: 2021-10-18 15:02:38 -0400
Commit message:

 Fix BioC ERROR by removing bplapply from tests
Package: IgGeneUsage
Commit: c6cbde572fd6a9106712b788d61b58fe521edbad
Author: sktron <simo.kitanovski@uni-due.de>
Date: 2021-10-18 22:52:34 +0200
Commit message:

 eval=F
Package: TAPseq
Commit: 782bd36fa4c041e11d6c30e535aa840e8c205217
Author: Andreas Gschwind <andreas.gschwind@stanford.edu>
Date: 2021-10-18 21:43:44 +0200
Commit message:

 Implement BiocStyle styling for vignettes

Implement BiocStyle output style in package vignettes to be consistent with Bioconductor ecosytem. Fix some typos in documentation.
Package: TAPseq
Commit: 9cd13cb11e5c00f545f30b6cc2fa86a9164be06f
Author: Andreas Gschwind <andreas.gschwind@stanford.edu>
Date: 2021-10-17 20:11:36 -0700
Commit message:

 Minor updates to documentation
Package: TAPseq
Commit: 747bd11ccfc1b7e38944da735d7ca2b58e7dbfce
Author: Andreas Gschwind <andreas.gschwind@stanford.edu>
Date: 2021-08-27 17:46:56 -0700
Commit message:

 Fix bug in createPrimerTrack()

Fix sorting of transcripts on negative strand in createPrimerTrack(). This bug created wrong genomic coordinates for primers targeting genes on negative strand. Update tests accordingly. Also make minor changes to other tests. Update NEWS file and add CITATION file.
Package: SpatialDecon
Commit: 897c65def51f4832d21d5a325bea12eb871ff079
Author: patrickjdanaher <patrickjdanaher@gmail.com>
Date: 2021-10-18 12:26:02 -0700
Commit message:

 Merge branch 'master' of git.bioconductor.org:packages/SpatialDecon
Package: SpatialDecon
Commit: b0aaccf0495e92c106d1e87e83e5b989839dd9e2
Author: Patrick Danaher <patrickjdanaher@gmail.com>
Date: 2021-10-18 11:22:56 -0700
Commit message:

 Merge branch 'master' of https://github.com/Nanostring-Biostats/SpatialDecon
Package: SpatialDecon
Commit: 5631c0994707db9ccc3b04ff4dee20eda929beca
Author: Maddy Griswold <40255151+maddygriz@users.noreply.github.com>
Date: 2021-10-18 11:04:36 -0700
Commit message:

 update subminor version
Package: SpatialDecon
Commit: 4d3033d61b4fd6c36208b8e9d2db79e692415f33
Author: Maddy Griswold <40255151+maddygriz@users.noreply.github.com>
Date: 2021-10-13 12:37:30 -0700
Commit message:

 Update DESCRIPTION
Package: SpatialDecon
Commit: 7a4fe84dbd56c8d00c9cc43bf5f9168d3b921be3
Author: Maddy Griswold <40255151+maddygriz@users.noreply.github.com>
Date: 2021-10-13 13:25:07 -0600
Commit message:

 Merge pull request #20 from Nanostring-Biostats/v1.3_release

v1.3 release
Package: SpatialDecon
Commit: 2b9d1e7612bb02b1130367a497f07e5246fada85
Author: Maddy Griswold <40255151+maddygriz@users.noreply.github.com>
Date: 2021-10-13 12:22:05 -0700
Commit message:

 Update DESCRIPTION
Package: SpatialDecon
Commit: c03d7f83f55d178bf58887a3d9c3c74c2fa429e9
Author: Maddy Griswold <40255151+maddygriz@users.noreply.github.com>
Date: 2021-10-13 12:21:00 -0700
Commit message:

 Update NEWS
Package: SpatialDecon
Commit: 9ad6b465f881a35bc7c4601b8996502d37e31f86
Author: Maddy Griswold <40255151+maddygriz@users.noreply.github.com>
Date: 2021-10-13 13:00:58 -0600
Commit message:

 Merge pull request #19 from Nanostring-Biostats/v1.3_release

V1.3 release
Package: SpatialDecon
Commit: e5c562299e356582a5009b0b596a739204b098f9
Author: Maddy Griswold <40255151+maddygriz@users.noreply.github.com>
Date: 2021-10-11 16:22:43 -0700
Commit message:

 remove writing file test
Package: SpatialDecon
Commit: 3b0b32e872d16f4c84ca945cfc73f2a73618af1c
Author: Maddy Griswold <40255151+maddygriz@users.noreply.github.com>
Date: 2021-10-11 14:58:36 -0700
Commit message:

 BiocCheck and devtools::check updates
Package: SpatialDecon
Commit: 71374b3c069fdfb2dffa31b9bcc0b0e11416da39
Author: Maddy Griswold <40255151+maddygriz@users.noreply.github.com>
Date: 2021-10-07 15:31:43 -0700
Commit message:

 remove non-exported man pages
Package: SpatialDecon
Commit: 0fe27dca15268ba442758e4f9d36efc94a17a8fe
Author: Maddy Griswold <40255151+maddygriz@users.noreply.github.com>
Date: 2021-09-30 11:19:22 -0700
Commit message:

 Update NEWS

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