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GIT Logs

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

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Package: GENESIS
Commit: b5ffca7f255612ee27d124863dbc3b37be7edb16
Author: Stephanie M. Gogarten <sdmorris@uw.edu>
Date: 2021-06-22 13:08:40 -0700
Commit message:

 version bump
 
Package: SplicingFactory
Commit: 9603ef5df0fdad29a7c3180261586bc17121c318
Author: Endre Sebestyen <endre.sebestyen@gmail.com>
Date: 2021-06-22 20:51:33 +0200
Commit message:

 bug fix: missing example data added back
Vignette building failed, as example data was missing most of the
columns. Properly structured example data added, and other minor
corrections. Fixes #10
 
Package: MungeSumstats
Commit: 871f8aec64ba3a137114e5768dcebc92a1f26f51
Author: Al-Murphy <alanmurph94@hotmail.com>
Date: 2021-06-22 18:54:01 +0100
Commit message:

 bug fix: add paper for citation
 
Package: glmGamPoi
Commit: 5a5e68e5b6720ca05a32259b2b9ba2396d7faa2c
Author: const-ae <artjom31415@googlemail.com>
Date: 2021-06-22 16:12:19 +0200
Commit message:

 Bump version and update news
 
Package: glmGamPoi
Commit: fa40d0bb5a13de921e524d48f3bee0711372a59e
Author: const-ae <artjom31415@googlemail.com>
Date: 2021-06-22 16:11:43 +0200
Commit message:

 Update NEWS for version 1.4
 
Package: glmGamPoi
Commit: 31f7655b9639c0291b02f5e2c9027e6550f2f07f
Author: const-ae <artjom31415@googlemail.com>
Date: 2021-06-22 16:10:18 +0200
Commit message:

 Choose a more reasonable scale for global overdispersion estimate
 
Package: cosmosR
Commit: 189dbcd3a92bf8cdf5a61559d514626c56ddffaa
Author: Katharina Zirngibl <kzngbl@gmail.com>
Date: 2021-06-22 14:20:33 +0200
Commit message:

 Bug Fix: Vapply return error - Version bump to 1.1.1
 
Package: cosmosR
Commit: 461cf91b51fe7080bebbeb723d7c6558e01431e0
Author: Katharina Zirngibl <kzngbl@gmail.com>
Date: 2021-06-22 14:06:47 +0200
Commit message:

 Merge remote-tracking branch 'upstream/master'
 
Package: cosmosR
Commit: be64e70c389815f1ef3195a658d6b13194a8de21
Author: katharinazirngibl <76971380+katharinazirngibl@users.noreply.github.com>
Date: 2021-06-08 11:03:17 +0200
Commit message:

 Merge pull request #11 from saezlab/vapply_to_sapply

reverted vapply to sapply 
Package: cosmosR
Commit: 910968a345e3a319b26ec027985aa6bc0984e88c
Author: adugourd <adugourd@ukaachen.de>
Date: 2021-06-07 15:45:09 +0200
Commit message:

 reverted vapply to sapply
 
Package: QFeatures
Commit: c2b3296dfe20b56bb537a1aed401e128197a2b4a
Author: Laurent Gatto <laurent.gatto@uclouvain.be>
Date: 2021-06-22 13:51:18 +0200
Commit message:

 fix missing rowData<-,QFeatures,ANYwarning entry
 
Package: QFeatures
Commit: 7759c5b6975e820ba8fb7c69037c3fa5146d27bf
Author: Laurent Gatto <laurent.gatto@gmail.com>
Date: 2021-06-22 13:11:03 +0200
Commit message:

 Merge pull request #134 from cvanderaa/master

Improved functionality for rowData manipulation 
Package: QFeatures
Commit: 2148cf8ab6936715b19806f8e2fff38ad2e6e40f
Author: Christophe Vanderaa <vanderaa.christophe@gmail.com>
Date: 2021-06-14 14:23:48 +0200
Commit message:

 build: updated NEWS and version bump
 
Package: QFeatures
Commit: fdde2b4589a3d444363dfe938f4d812d5cd3a3c8
Author: Christophe Vanderaa <vanderaa.christophe@gmail.com>
Date: 2021-06-14 14:23:11 +0200
Commit message:

 docs: improved vignette based on PR#134 review
 
Package: QFeatures
Commit: 12e6b3060abf87a904f2cda43bc1108ceec038e7
Author: Christophe Vanderaa <vanderaa.christophe@gmail.com>
Date: 2021-06-14 07:54:57 +0200
Commit message:

 Merge branch 'master' of https://github.com/rformassspectrometry/QFeatures
 
Package: QFeatures
Commit: 92679b6bafe0466a58b16789a29f7c9c3d5dec3c
Author: lgatto <laurent.gatto@gmail.com>
Date: 2021-06-13 09:43:01 +0200
Commit message:

 Update NEWS file to reflect new version
 
Package: QFeatures
Commit: aa72fc35635685d6ba2bf782315bca69b1b8b25d
Author: Christophe Vanderaa <vanderaa.christophe@gmail.com>
Date: 2021-06-12 01:00:01 +0200
Commit message:

 docs: removed obsolete documentation section
 
Package: QFeatures
Commit: bb2f3deb55332e020b1364b0d6d79dc864f9e8d4
Author: Christophe Vanderaa <vanderaa.christophe@gmail.com>
Date: 2021-06-11 16:07:36 +0200
Commit message:

 refactor: renamed getRowData and setRowData to rbindRowData and rowData<-
 
Package: QFeatures
Commit: cdcbbc131fbfe82fa0cf589e084d7bafe63dd017
Author: Christophe Vanderaa <vanderaa.christophe@gmail.com>
Date: 2021-06-11 10:29:36 +0200
Commit message:

 refactor: removed obsolete functions
 
Package: QFeatures
Commit: 85fec87ce7ca99756a8569fd2dcd85fb11fa0143
Author: Christophe Vanderaa <vanderaa.christophe@gmail.com>
Date: 2021-06-02 18:42:33 +0200
Commit message:

 style: fixed some typos
 
Package: QFeatures
Commit: ed3bbd4976badf56b21b683ae26b900d3056a973
Author: Christophe Vanderaa <vanderaa.christophe@gmail.com>
Date: 2021-06-02 18:25:47 +0200
Commit message:

 Fixed merge
 
Package: QFeatures
Commit: 2bd2fe98977060d3a79bbef690e80dd9b12a5678
Author: Christophe Vanderaa <vanderaa.christophe@gmail.com>
Date: 2021-06-02 18:23:08 +0200
Commit message:

 docs: added a new section 'Accessors' to vignette
 
Package: QFeatures
Commit: cb3619122c5f1d369d581fd212ac2e64261be27e
Author: Christophe Vanderaa <vanderaa.christophe@gmail.com>
Date: 2021-06-02 18:22:38 +0200
Commit message:

 test+docs: included unit tests and documentation for getRowData and setRowData
 
Package: QFeatures
Commit: 877fa24efa52670f444b43a93beb00ba4e0e7ed0
Author: Christophe Vanderaa <vanderaa.christophe@gmail.com>
Date: 2021-06-02 18:21:46 +0200
Commit message:

 feat: added getRowData and setRowData functions
 
Package: bioCancer
Commit: 33a3a7ae5ce7550d196f93bf5d75f4cc76cb37cc
Author: kmezhoud <kmezhoud@gmail.com>
Date: 2021-06-22 10:55:18 +0100
Commit message:

 rm AnnotationFuncs dependency
 
Package: zellkonverter
Commit: 8a4f8557790f41605b70e974b36fe6f26fbff9bc
Author: Luke Zappia <lazappi@users.noreply.github.com>
Date: 2021-06-22 10:03:15 +0200
Commit message:

 Merge branch 'RELEASE_3_13'

* RELEASE_3_13:
  Fix bug in converting dgRMatrix sparse matrices
 
Package: zellkonverter
Commit: a3c4f3128d0c8dc19f2568bf5444f92a49c23f1f
Author: Luke Zappia <lazappi@users.noreply.github.com>
Date: 2021-06-22 10:00:09 +0200
Commit message:

 Fix bug in converting dgRMatrix sparse matrices

Need to convert to CSparseMatrix rather than dgCMatrix

Fixes #55
 
Package: MOGAMUN
Commit: b278a67a0c5dde5683bde4bb2683bcce6315978d
Author: Elva Novoa <elvanov@hotmail.com>
Date: 2021-06-22 09:33:19 +0200
Commit message:

 Fixed bug in mutation that seldomly produced individuals of invalid sizes
 
Package: fishpond
Commit: 2d515026191766ea8f71c0b85a7b68941627cc59
Author: mikelove <michaelisaiahlove@gmail.com>
Date: 2021-06-22 09:14:22 +0200
Commit message:

 fix bib
 
Package: airpart
Commit: 017489b19cdcb31cd79ef27b65dc74258046f57d
Author: Wancen <42752661+Wancen@users.noreply.github.com>
Date: 2021-06-22 01:40:45 -0400
Commit message:

 fix rank deficient
 
Package: airpart
Commit: e664af3cdf921dfee9eb5bb5a19e848ac52140c0
Author: mikelove <michaelisaiahlove@gmail.com>
Date: 2021-06-21 17:34:33 +0200
Commit message:

 fixing more counts -> assays
 
Package: airpart
Commit: 09a6d42d84efa7fa3f7719819c4ed49438d20c10
Author: mikelove <michaelisaiahlove@gmail.com>
Date: 2021-06-21 17:31:07 +0200
Commit message:

 another one
 
Package: airpart
Commit: 75fbcd4e3edf00ddabe7007259f18afdc010d0ba
Author: mikelove <michaelisaiahlove@gmail.com>
Date: 2021-06-21 17:27:22 +0200
Commit message:

 use assay instead of counts
 
Package: FLAMES
Commit: 63adced6cefa9c0803c1ee1cb0a8360f8c97ec65
Author: Oliver Voogd <olivervoogd@gmail.com>
Date: 2021-06-22 15:00:23 +1000
Commit message:

 preprint reference added
 
Package: R453Plus1Toolbox
Commit: 04496600082fd82cbe8305f10d9171924be4c640
Author: huklein
Date: 2021-06-21 23:41:06 -0400
Commit message:

 Added the option plot to complexity.entropy() to suppress plotting of the histogram.
 
</div>
Package: NeuCA
Commit: 80dcff6f4efdda90ffc9187f2eaeae462aa2d568
Author: Hao Harry Feng <fenghaoea@gmail.com>
Date: 2021-06-21 22:33:05 -0400
Commit message:

 version bump
 
Package: NeuCA
Commit: 9c1655ac9e6644b5d82c15582d147d676b526b1a
Author: Hao Harry Feng <fenghaoea@gmail.com>
Date: 2021-06-21 22:31:48 -0400
Commit message:

 T/F replaced with TRUE/FALSE
 
Package: NeuCA
Commit: e5942ed6b65710035a3dc0053d1ed24aaa7951e7
Author: Hao Harry Feng <fenghaoea@gmail.com>
Date: 2021-06-18 17:02:37 -0400
Commit message:

 model size description added
 
Package: NeuCA
Commit: 792c5801bfe2d89c74db4d970f16770ed392d207
Author: Hao Harry Feng <fenghaoea@gmail.com>
Date: 2021-06-18 13:31:45 -0400
Commit message:

 version bump
 
Package: Dino
Commit: effd323247dbd0fcb647e766d29e1b46db961606
Author: brown46 <brown46@brown46.local>
Date: 2021-06-21 13:18:26 -0500
Commit message:

 Bug fix for small input data
 
Package: Dino
Commit: c9b2c535d26ba8b8611d57390373932173722c43
Author: brown46 <brown46@brown46.local>
Date: 2021-06-03 09:17:53 -0500
Commit message:

 Readme update; upload to Zenodo
 
Package: rhdf5client
Commit: 5b8e6d9781524494b7167fa6c9afa4d64da7c590
Author: vjcitn <stvjc@channing.harvard.edu>
Date: 2021-06-21 17:33:16 -0400
Commit message:

 change test folders to /shared/bioconductor
 
Package: AnVIL
Commit: 6d5d0f97fb4583b7231f567ad7397e372a492417
Author: Martin Morgan <Martin.Morgan@RoswellPark.org>
Date: 2021-06-21 17:05:22 -0400
Commit message:

 Merge branch 'RELEASE_3_13'
 
Package: AnVIL
Commit: d4bcc97e8a5986b440317c0652f95261633bc3f4
Author: Martin Morgan <Martin.Morgan@RoswellPark.org>
Date: 2021-06-21 17:03:53 -0400
Commit message:

 bug fix: only install() packages on known Bioconductor docker images
 
Package: BiocPkgTools
Commit: 6a0dfdd125a82b700703b299c3489e21fbc02892
Author: LiNk-NY <marcel.ramosperez@roswellpark.org>
Date: 2021-06-21 17:56:40 +0000
Commit message:

 version bump 1.11.4
 
Package: BiocPkgTools
Commit: 270fdf192ae2ce37983372913c7355405464f82e
Author: LiNk-NY <marcel.ramosperez@roswellpark.org>
Date: 2021-06-21 17:56:18 +0000
Commit message:

 convert to numeric version from input
 
Package: bioCancer
Commit: ba681a1c9888b3c46d7a0f57f9d389bd1f708391
Author: kmezhoud <kmezhoud@gmail.com>
Date: 2021-06-21 20:24:10 +0100
Commit message:

 sync version

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

# Conflicts:
#	DESCRIPTION
 
Package: bioCancer
Commit: 61c6481dad48682c1757f271210805839d5d88a9
Author: kmezhoud <kmezhoud@gmail.com>
Date: 2021-06-21 20:23:16 +0100
Commit message:

 pupup version
 
Package: bioCancer
Commit: 9a55692cfc001e93f3080d7c9048f809f89bca67
Author: kmezhoud <kmezhoud@gmail.com>
Date: 2021-06-21 19:53:33 +0100
Commit message:

 pupup RoxygenNote
 
Package: GWAS.BAYES
Commit: 989df9d7df85b81fc5a57e1d93b9d656ce210554
Author: Lori Shepherd <lori.shepherd@roswellpark.org>
Date: 2021-06-21 12:59:42 -0400
Commit message:

 deprecate

 - unresponsive
 
Package: gramm4R
Commit: 99b83c55ec5e822ec8689f3713031ca245ac28db
Author: Lori Shepherd <lori.shepherd@roswellpark.org>
Date: 2021-06-21 12:58:52 -0400
Commit message:

 deprecate

 - unrepsonisve
 
Package: ENVISIONQuery
Commit: a6b23c752fbc70778af334b8e47d0079c7fd9ff6
Author: Lori Shepherd <lori.shepherd@roswellpark.org>
Date: 2021-06-21 12:58:05 -0400
Commit message:

 deprecate

 - unresponsive
 
Package: ENCODExplorer
Commit: 4714b1200dd20e675bb5319e3ae4bf56fc704119
Author: Lori Shepherd <lori.shepherd@roswellpark.org>
Date: 2021-06-21 12:56:33 -0400
Commit message:

 deprecate

 - unresponsive
 
Package: MouseFM
Commit: 99c51e85230a30252a659970c0b14bd86ba6ecdc
Author: Lori Shepherd <lori.shepherd@roswellpark.org>
Date: 2021-06-21 12:55:44 -0400
Commit message:

 deprecate

 --unresponsive
 
Package: destiny
Commit: 124f17a40221928e3ad7d1e70c0ba4f0e11b6f51
Author: Lori Shepherd <lori.shepherd@roswellpark.org>
Date: 2021-06-21 12:54:54 -0400
Commit message:

 deprecate

 - unresposnive
 
Package: KEGGprofile
Commit: 57cda91cd1b58e6afd90172c9adfc0c53aae016e
Author: Lori Shepherd <lori.shepherd@roswellpark.org>
Date: 2021-06-21 11:37:30 -0400
Commit message:

 deprecate

 -- unresponsive
 
Package: MetaGxPancreas
Commit: fc6a75fb408e5c35bf98c2defa6fa8f207ba771d
Author: ChristopherEeles <christopher.eeles@outlook.com>
Date: 2021-06-21 11:09:05 -0400
Commit message:

 Changed maintainer and version bump for BioC build
 
Package: GeneAnswers
Commit: 187eb87695d5433e6ae33eadb6c4eb69b8a59155
Author: Lori Shepherd <lori.shepherd@roswellpark.org>
Date: 2021-06-21 11:00:38 -0400
Commit message:

 deprecate

 - unresponsive maintainer
 
Package: SwimR
Commit: f1a07b287f197d6197559c927b05405abb0225ca
Author: Lori Shepherd <lori.shepherd@roswellpark.org>
Date: 2021-06-21 10:54:11 -0400
Commit message:

 deprecate

 - unresponsive maintainer
 
Package: SRGnet
Commit: 7df3262b9a1f4ee7ca473f9ee7c06919f6020605
Author: Lori Shepherd <lori.shepherd@roswellpark.org>
Date: 2021-06-21 10:53:19 -0400
Commit message:

 deprecate

 - unresponsive maintainer
 
Package: BrainStars
Commit: 370ad7d4fd575eb03eea52d238bf863d98783294
Author: Lori Shepherd <lori.shepherd@roswellpark.org>
Date: 2021-06-21 10:39:16 -0400
Commit message:

 deprecate

 -- unresponsive maintainer
 
Package: AlpsNMR
Commit: b6042ed964e49d47018847a92026ee568ad194ed
Author: Lori Shepherd <lori.shepherd@roswellpark.org>
Date: 2021-06-21 10:38:10 -0400
Commit message:

 deprecate

 -- maintainer unresponsive
 
Package: ALPS
Commit: 6f38b5dead1e464ac9d038248907ffc2931017e5
Author: Lori Shepherd <lori.shepherd@roswellpark.org>
Date: 2021-06-21 10:37:10 -0400
Commit message:

 Merge branch 'master' of git.bioconductor.org:packages/ALPS
 
Package: ALPS
Commit: e1c02738f2a4b4d2a15aa1a802375211b0d0f8ea
Author: Lori Shepherd <lori.shepherd@roswellpark.org>
Date: 2021-06-21 10:36:14 -0400
Commit message:

 Deprecate

 -- maintainer unresponsive
 
Package: affyPara
Commit: c98e8b1bfab0ed221768e75400511213c41c2e56
Author: Lori Shepherd <lori.shepherd@roswellpark.org>
Date: 2021-06-21 10:35:09 -0400
Commit message:

 Deprecated

  - maintainer unresponsive
 
Package: MSstatsTMTPTM
Commit: f38d8e3d5e16beff523df00ec2f42b40c1c009ee
Author: Lori Shepherd <lori.shepherd@roswellpark.org>
Date: 2021-06-21 10:29:31 -0400
Commit message:

 User requested deprecation
 
Package: airpart
Commit: acc6492a4634739e957571006266f9260f93185a
Author: Wancen <42752661+Wancen@users.noreply.github.com>
Date: 2021-06-21 09:38:51 -0400
Commit message:

 deal col>12 and offset dimension
 
Package: hca
Commit: b18949237fea31df876e36e443883781f553c120
Author: MRMcD <49954418+reed-mcdaniel-716@users.noreply.github.com>
Date: 2021-06-16 09:13:53 -0400
Commit message:

 Merge pull request #19 from Bioconductor/1.1.2_changes

1.1.2 changes 
Package: hca
Commit: 611bf7fe57cd1e8e1ddffea5667d44f5f3328fe6
Author: Maya Reed McDaniel <maya.mcdaniel@roswellpark.org>
Date: 2021-06-15 13:54:56 -0400
Commit message:

 update NEWS.md
 
Package: hca
Commit: 27a1c7f4ce3c2497520c9cf151d8236f2a3fb001
Author: Maya Reed McDaniel <maya.mcdaniel@roswellpark.org>
Date: 2021-06-15 13:48:59 -0400
Commit message:

 increment devel version
 
Package: hca
Commit: 572a610427335c42fc761968f09700ec524d3706
Author: Maya Reed McDaniel <maya.mcdaniel@roswellpark.org>
Date: 2021-06-15 13:37:49 -0400
Commit message:

 fix file download efficiency
 
Package: scanMiR
Commit: b2c1b7fbf1437c131a55bdcdf91527e2c4064cb1
Author: fridoling <fridoling@hotmail.com>
Date: 2021-06-21 11:43:16 +0000
Commit message:

 bump version number
 
Package: scanMiR
Commit: f3ae6ffd8be505e2ae0eaddc57cc2f306c73fba0
Author: plger <pl.germain@gmail.com>
Date: 2021-06-21 09:35:42 +0200
Commit message:

 fixed undocumented param
 
Package: scanMiR
Commit: a352d4574086114c70743dfc01533223857996f4
Author: Pierre-Luc <pl.germain@gmail.com>
Date: 2021-06-19 18:51:42 +0200
Commit message:

 added auto build and check 
Package: scanMiR
Commit: 29da4bdee01ff9edf7b4f461585e76a440a951ee
Author: Pierre-Luc <pl.germain@gmail.com>
Date: 2021-06-19 18:27:30 +0200
Commit message:

 replaced wrong || 
Package: scanMiR
Commit: 64398640f1aa9efa02f88534359d9856a3022565
Author: Pierre-Luc <pl.germain@gmail.com>
Date: 2021-06-19 10:49:13 +0200
Commit message:

 missing parenthesis 
Package: scanMiR
Commit: a8d9ba86556e4c1e29d7e377022413a3b38c68cb
Author: Pierre-Luc <pl.germain@gmail.com>
Date: 2021-06-19 10:36:18 +0200
Commit message:

 fixed missing quote 
Package: scanMiR
Commit: c4ff65900a59bb34ecf0e28a5b2cd1876d284de5
Author: Pierre-Luc <pl.germain@gmail.com>
Date: 2021-06-19 09:57:07 +0200
Commit message:

 Create Dockerfile 
Package: scanMiR
Commit: 617a4cdf1e1fac4ba26da6a411945f32dfd260ff
Author: fridoling <fridoling@hotmail.com>
Date: 2021-06-18 15:10:07 +0000
Commit message:

 fixed missing miRNA column
 
Package: scanMiR
Commit: d0d4b56ee2c38da7ac640d3cc330727e87562342
Author: plger <pl.germain@gmail.com>
Date: 2021-06-17 19:53:13 +0000
Commit message:

 fixed viewTargetAlignment bug on very close matches
 
Package: scanMiR
Commit: 485dfc29071477021ad1233fefb20840fa2f988b
Author: plger <pl.germain@gmail.com>
Date: 2021-06-17 15:47:42 +0200
Commit message:

 added RleList import
 
Package: scanMiR
Commit: ac2ad5e014e0d0faee59db047a1353072685abc3
Author: fridoling <fridoling@hotmail.com>
Date: 2021-06-17 12:28:23 +0000
Commit message:

 fix bug about tx_info.length
 
Package: ramr
Commit: 2037baa3e90f3a5e837ba8763f8641dc204ad76f
Author: Oleksii.Nikolaienko <oleksii.nikolaienko@uib.no>
Date: 2021-06-21 13:35:50 +0200
Commit message:

 version bump
 
Package: ramr
Commit: a9f921f9c89761ca1b0ae47de4fa2b829da8f8a6
Author: Oleksii.Nikolaienko <oleksii.nikolaienko@uib.no>
Date: 2021-06-21 13:34:37 +0200
Commit message:

 merge
 
Package: ramr
Commit: 731bd8fa87cb2cb90e30c0919b339a5afd043d32
Author: Oleksii.Nikolaienko <oleksii.nikolaienko@uib.no>
Date: 2021-05-31 13:34:05 +0200
Commit message:

 dataset -> data set
 
Package: ramr
Commit: d6808d5fc8faa1fcefc289bd210dcb0a103403c1
Author: Oleksii.Nikolaienko <oleksii.nikolaienko@uib.no>
Date: 2021-05-31 13:23:10 +0200
Commit message:

 fast epimutate
 
Package: ramr
Commit: 1da480315f9fd1f052df8b689182c70a8b8f9e6e
Author: Oleksii.Nikolaienko <oleksii.nikolaienko@uib.no>
Date: 2021-05-31 11:12:44 +0200
Commit message:

 p-value correction by ncol
 
Package: ramr
Commit: 1a902dcf5e513bd3df3cc3ba6ce584a94c2d6818
Author: Oleksii.Nikolaienko <oleksii.nikolaienko@uib.no>
Date: 2021-05-28 19:35:33 +0200
Commit message:

 docs updated, typos fixed, version bump
 
Package: ramr
Commit: f3df943666dbf3817fc3ddbc31bb90c805bb684a
Author: Oleksii.Nikolaienko <oleksii.nikolaienko@uib.no>
Date: 2021-05-28 19:34:56 +0200
Commit message:

 docs updated, typos fixed, version bump
 
Package: ramr
Commit: 274f379de00a708d164515bdb3504ba9fe19a4e7
Author: Oleksii.Nikolaienko <oleksii.nikolaienko@uib.no>
Date: 2021-05-28 19:21:41 +0200
Commit message:

 docs updated, typos fixed
 
Package: ramr
Commit: 404584be9ce16bc9529d615dc5557a4839f81fa6
Author: Oleksii.Nikolaienko <oleksii.nikolaienko@uib.no>
Date: 2021-05-28 19:19:30 +0200
Commit message:

 docs updated, typos fixed
 
Package: ramr
Commit: 6f89f309e930bdd0aa68c31648f929395fb2530e
Author: Oleksii.Nikolaienko <oleksii.nikolaienko@uib.no>
Date: 2021-05-28 19:19:06 +0200
Commit message:

 docs updated
 
Package: ramr
Commit: 577a62029cba8d3ae1c7ee581dec8964497296bf
Author: Oleksii.Nikolaienko <oleksii.nikolaienko@uib.no>
Date: 2021-05-28 19:18:22 +0200
Commit message:

 ramr.ranges -> amr.ranges
 
Package: ramr
Commit: e7a2b441863b244ffab794616c12e59d319f4886
Author: Oleksii.Nikolaienko <oleksii.nikolaienko@uib.no>
Date: 2021-05-28 16:12:21 +0200
Commit message:

 verbose for slow functions
 
Package: ramr
Commit: b2f87e7b471b3e3e733570b144dab1a72d03758e
Author: Oleksii.Nikolaienko <oleksii.nikolaienko@uib.no>
Date: 2021-05-28 15:56:49 +0200
Commit message:

 verbose for slow functions
 
Package: ramr
Commit: d95494abfe3fe754590138a22484414bc396f69d
Author: Oleksii.Nikolaienko <oleksii.nikolaienko@uib.no>
Date: 2021-05-28 15:32:45 +0200
Commit message:

 data.samples==NULL covered
 
Package: ramr
Commit: 39ca030553423e64c60ad48fc68e888f5862ee51
Author: Oleksii.Nikolaienko <oleksii.nikolaienko@uib.no>
Date: 2021-05-28 15:23:44 +0200
Commit message:

 docs updated
 
Package: ramr
Commit: a6e8cdb6223070f5de3e7ad31736fc36846a2ac6
Author: Oleksii.Nikolaienko <oleksii.nikolaienko@uib.no>
Date: 2021-05-28 15:10:56 +0200
Commit message:

 reproducibility by %dorng%
 
Package: ramr
Commit: b0ab0fa559537f1c219de7a94f6821111d9a8282
Author: Oleksii.Nikolaienko <oleksii.nikolaienko@uib.no>
Date: 2021-05-28 15:10:33 +0200
Commit message:

 reproducibility by %dorng%
 
Package: ramr
Commit: b12aa7f0eb7d4085facb01bfb3844dd50cf56fbe
Author: Oleksii.Nikolaienko <oleksii.nikolaienko@uib.no>
Date: 2021-05-28 13:26:03 +0200
Commit message:

 docs updated, tests optimized
 
Package: ramr
Commit: cc79843d57d7005b5175c02271e4a43ed096d7bf
Author: Oleksii.Nikolaienko <oleksii.nikolaienko@uib.no>
Date: 2021-05-28 12:54:09 +0200
Commit message:

 docs updated
 
Package: ramr
Commit: 17a0acd577eb8b638842ca2e1b20749520a6ea9b
Author: Oleksii.Nikolaienko <oleksii.nikolaienko@uib.no>
Date: 2021-05-28 12:49:07 +0200
Commit message:

 new default for data.samples
 
Package: ramr
Commit: 41f95700bf305942dacfbd586ecce95a024460e2
Author: Oleksii.Nikolaienko <oleksii.nikolaienko@uib.no>
Date: 2021-05-28 12:13:15 +0200
Commit message:

 updated with simulate* methods
 
Package: ramr
Commit: aed6ab76e6db7fc4ce96465850a9a9b353253d53
Author: Oleksii.Nikolaienko <oleksii.nikolaienko@uib.no>
Date: 2021-05-28 11:27:03 +0200
Commit message:

 updated with simulate* methods
 
Package: ramr
Commit: 97fad03d9188322bdeb86516fbbf02186e0c69b2
Author: Oleksii.Nikolaienko <oleksii.nikolaienko@uib.no>
Date: 2021-05-28 10:42:31 +0200
Commit message:

 new default for data.samples
 
Package: ramr
Commit: e41503890847f73120d8ce3629df0d0a7b01fc68
Author: Oleksii.Nikolaienko <oleksii.nikolaienko@uib.no>
Date: 2021-05-28 10:38:40 +0200
Commit message:

 simulation methods ready
 
Package: ramr
Commit: 318fcbf6e0bdfa6fb346efc3dbd9cc425d258af7
Author: Oleksii.Nikolaienko <oleksii.nikolaienko@uib.no>
Date: 2021-05-28 10:38:10 +0200
Commit message:

 docs updated
 
Package: ramr
Commit: 8af7b4c1b49c976c2198e40488cd965fbcef7de6
Author: Oleksii.Nikolaienko <oleksii.nikolaienko@uib.no>
Date: 2021-05-28 10:37:34 +0200
Commit message:

 new default for data.samples
 
Package: ramr
Commit: 74aa2c816ac14b2b6b3d5497cf00c3dc6a687a57
Author: Oleksii.Nikolaienko <oleksii.nikolaienko@uib.no>
Date: 2021-05-27 15:11:13 +0200
Commit message:

 simulateData method code, unit tests
 
Package: ramr
Commit: 46da673fce599e925f7b4d28d9c6f91811100bda
Author: Oleksii.Nikolaienko <oleksii.nikolaienko@uib.no>
Date: 2021-05-27 15:10:22 +0200
Commit message:

 simulateAMR takes dbeta==NA
 
Package: ramr
Commit: 4d802413315943f86569a689179b5d7ef91f6ad7
Author: Oleksii.Nikolaienko <oleksii.nikolaienko@uib.no>
Date: 2021-05-27 14:05:45 +0200
Commit message:

 simulateAMR documented and tested
 
Package: ramr
Commit: 0e23b42dd954d04874acc9114494f24f4c758ad3
Author: Oleksii.Nikolaienko <oleksii.nikolaienko@uib.no>
Date: 2021-05-26 17:30:47 +0200
Commit message:

 simulateAMR added
 
Package: ramr
Commit: 89cefb0b2fb7009a9719007cf1bed1b167764c34
Author: Oleksii.Nikolaienko <oleksii.nikolaienko@uib.no>
Date: 2021-05-26 17:30:11 +0200
Commit message:

 @seealso updated
 
Package: ramr
Commit: 4c0dbe4dcde823db4c0ad9a8196d940b05a719ca
Author: Oleksii.Nikolaienko <oleksii.nikolaienko@uib.no>
Date: 2021-05-26 16:24:58 +0200
Commit message:

 verbose defaults, fixed typos
 
Package: ramr
Commit: 887ddbb23268a35cb315b6a03e977dccee9e18c9
Author: Oleksii.Nikolaienko <oleksii.nikolaienko@uib.no>
Date: 2021-05-26 16:23:05 +0200
Commit message:

 verbose defaults
 
Package: ramr
Commit: 51cc9d5a2422c6bd89794cc143f7c64280edb1df
Author: Oleksii.Nikolaienko <oleksii.nikolaienko@uib.no>
Date: 2021-05-26 12:25:30 +0200
Commit message:

 cleaner Import, fixed typos
 
Package: ramr
Commit: ed4ba41e956fefb44d3175bb5a16f05b69856c27
Author: Oleksii.Nikolaienko <oleksii.nikolaienko@uib.no>
Date: 2021-05-26 10:26:23 +0200
Commit message:

 cleaner Import
 
Package: ramr
Commit: 9ec97f66c454f2cb4cd8755f88a0eb9a3ef833e4
Author: Oleksii.Nikolaienko <oleksii.nikolaienko@uib.no>
Date: 2021-05-21 09:59:37 +0200
Commit message:

 fixed links
 
Package: ramr
Commit: 4848743cb319e5ca0315d0c7bd50fb862955e301
Author: Oleksii.Nikolaienko <oleksii.nikolaienko@uib.no>
Date: 2021-05-21 08:53:11 +0200
Commit message:

 released at bioc
 
Package: ramr
Commit: 273fad2d0f7b6bfc9be8d817a3e8017e7caf6363
Author: Oleksii.Nikolaienko <oleksii.nikolaienko@uib.no>
Date: 2021-05-21 08:39:43 +0200
Commit message:

 released at bioc
 
Package: COTAN
Commit: 51f98b71b76c7e5dd70fefc699127deac467eb21
Author: seriph78 <s.galfre@gmail.com>
Date: 2021-06-21 11:19:40 +0200
Commit message:

 Forget again to change the version.
 
Package: COTAN
Commit: f35eb13f189c05fe0034f9d8d417a6fdf44325d0
Author: seriph78 <s.galfre@gmail.com>
Date: 2021-06-21 10:50:35 +0200
Commit message:

 Wrongly left COTAN.Rcheck from the previous check.
 
Package: COTAN
Commit: dabf4893cc6c9f521e5d1dcddc64e207701bc45e
Author: seriph78 <s.galfre@gmail.com>
Date: 2021-06-21 10:08:14 +0200
Commit message:

 Forgotten to change the version number.
 
Package: ggtree
Commit: 7b03d4c1c4cfd72820c5ba5d03079c90aa1a80ae
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2021-06-21 10:21:27 +0800
Commit message:

 bump version up
 
Package: ggtree
Commit: b7a8e27aaca23ea8565fb5a155db2ed1347beae1
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2021-06-11 17:02:22 +0800
Commit message:

 update docs
 
Package: ggtree
Commit: 58495f5d43cce18566a700b900aa955a4c9797fc
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2021-06-11 17:00:22 +0800
Commit message:

 Merge pull request #414 from xiangpin/Unrooted_branch

add branch.x and branch.y for unrooted layout 
Package: ggtree
Commit: c6c351a60bec9a581cb3a239ab39eb3770c61fc2
Author: xiangpin <xshuangbin@163.com>
Date: 2021-06-11 16:26:56 +0800
Commit message:

 fix vector logical check
 
Package: ggtree
Commit: 64fcaa9ed7ef474c2187523ceb54df8dc4a9c61b
Author: xiangpin <xshuangbin@163.com>
Date: 2021-06-11 16:26:23 +0800
Commit message:

 branch.x and branch.y for branch label of unrooted layout
 
Package: ggtree
Commit: 765d04e9b93725b7a3761a97ef8e568037d1b434
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2021-06-04 15:24:02 +0800
Commit message:

 update docs
 
Package: ggtree
Commit: 4ed362e0805ffd604c6f3869ac0d57d149bc3ab1
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2021-06-04 15:23:22 +0800
Commit message:

 Merge pull request #411 from xiangpin/geom_range

optimizing geom_range to support the mapping of color, size. 
Package: ggtree
Commit: d15cabb181764ec9c6a8e3551a7afb3b553b5efc
Author: xiangpin <xshuangbin@163.com>
Date: 2021-06-03 15:53:09 +0800
Commit message:

 Merge remote-tracking branch 'upstream/master' into geom_range
 
Package: ggtree
Commit: 960e999fcb83b07bcfde87a4ad04d1849ff37e6d
Author: xiangpin <xshuangbin@163.com>
Date: 2021-06-03 15:29:25 +0800
Commit message:

 geom_range supports aes mapping
 
Package: DOSE
Commit: 8b75f8a1df455fe381c8323d01a572522734e734
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2021-06-21 10:19:40 +0800
Commit message:

 bump version up
 
Package: DOSE
Commit: 52613be3ae58a5ac381ee0f9fd7b9e04e09926f1
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2021-06-21 10:18:59 +0800
Commit message:

 Merge pull request #50 from huerqiang/master

fix a bug 
Package: DOSE
Commit: a71ca021d1336810f35a005a6684cbdeedc555c2
Author: huerqiang <13766876214@163.com>
Date: 2021-06-19 12:53:04 +0800
Commit message:

 fix a bug
 
Package: VAExprs
Commit: e2899ddd20388d2f6ddd724522785f7db44c2aed
Author: dongminjung <dongminjung@Dongmins-MacBook-Pro.local>
Date: 2021-06-21 10:58:00 +0900
Commit message:

 update
 
Package: COTAN
Commit: b4530c977c4bbe3b0699f18afae613af553ced54
Author: seriph78 <s.galfre@gmail.com>
Date: 2021-06-20 21:08:11 +0200
Commit message:

 Previous error in saving test files.
They should be saved with saveRDS instead of save function (with the option compress='xz').
Now the tests pass. We also had to re-save the data in /data with the same compression.
We also cleaned the data.R file. The names for the datasets are now the same as the saved files (in the data folder).
Because of this, we had to change the corresponding names in the examples and in the tests.
 
Package: COTAN
Commit: 70c9b2244bb581b761749467b8b1575e921b09f5
Author: seriph78 <s.galfre@gmail.com>
Date: 2021-06-20 16:53:08 +0200
Commit message:

 Previous version gave WARNING
“checking data for ASCII and uncompressed saves”.
It should be solved re-saving all test files with save([file],file="[name].RDS", compress='xz')
 
Package: hpar
Commit: 4fb49bda0aea81d76b8ebfb521a5829c1d1413f5
Author: Laurent Gatto <laurent.gatto@uclouvain.be>
Date: 2021-06-20 15:23:20 +0200
Commit message:

 bump version
 
Package: hpar
Commit: 196798416b1b9d494db89271c14a137d1e06a558
Author: Laurent Gatto <laurent.gatto@gmail.com>
Date: 2021-06-20 15:19:00 +0200
Commit message:

 Merge pull request #9 from ManonMartin/master

debugged action R-CMD-check-bioc 
Package: hpar
Commit: c9671c32a09a4d763b2c23072a6883b3c0a897b8
Author: Manon Martin <manon.martin@uclouvain.be>
Date: 2021-06-17 10:30:32 +0200
Commit message:

 added rmarkdown in Suggest
 
Package: hpar
Commit: 4376aa7dc379479c7cfbf62bb939ebf257a434e8
Author: Manon Martin <ManonMartin@users.noreply.github.com>
Date: 2021-06-17 10:02:00 +0200
Commit message:

 Merge branch 'lgatto:master' into master
 
Package: hpar
Commit: 4e7586a15380c53c38b0e9ff6300a954d9dac327
Author: Manon Martin <ManonMartin@users.noreply.github.com>
Date: 2021-06-17 09:44:43 +0200
Commit message:

 Update test-gh-actions.yml 
Package: hpar
Commit: 61a36610e69ff52bfd389437b3cac4b6d66e07ee
Author: Laurent Gatto <laurent.gatto@gmail.com>
Date: 2021-03-08 12:41:38 +0100
Commit message:

 run action on ubuntu only 
Package: hpar
Commit: d44c1ed0b4b44b5a5c794a0de474f243f1d34326
Author: Laurent Gatto <laurent.gatto@gmail.com>
Date: 2021-03-08 11:46:11 +0100
Commit message:

 Merge pull request #8 from ManonMartin/master

added the GHA to test for HPA version 
Package: hpar
Commit: d17c0ccc15ef6e516d04e1da44d925a7dd60bbc4
Author: Manon Martin <manon.martin@uclouvain.be>
Date: 2021-03-08 10:46:32 +0100
Commit message:

 updated HPA version
 
Package: hpar
Commit: 6397b875c5f8041d569fde0e8633cbc11eee20c4
Author: Manon Martin <manon.martin@uclouvain.be>
Date: 2021-02-12 16:15:58 +0100
Commit message:

 debug bioc cmd check
 
Package: hpar
Commit: ad671bd80fed491f4b1603d0d39ec5ae2cc4d174
Author: Manon Martin <manon.martin@uclouvain.be>
Date: 2021-02-12 16:03:28 +0100
Commit message:

 debug bioc cmd check
 
Package: hpar
Commit: f5fb052ac15515cdd3a3fbfd3812f8169d1b0e72
Author: Manon Martin <manon.martin@uclouvain.be>
Date: 2021-02-12 15:30:06 +0100
Commit message:

 added the GHA test for HPA version
 
Package: hpar
Commit: 61984528d232807b1e11c4596704b013636e294b
Author: Laurent Gatto <laurent.gatto@uclouvain.be>
Date: 2020-12-17 14:16:23 +0100
Commit message:

 new newHpaVersion() function
 
Package: hpar
Commit: ba575358f0b0f28036417f92b426ff5099b537b4
Author: Laurent Gatto <laurent.gatto@uclouvain.be>
Date: 2020-12-16 15:10:14 +0100
Commit message:

 feat: function to get version from hpa website
 
Package: VAExprs
Commit: 4eff54d02ed124bec7c5c5bdd84cd759c1bbee0b
Author: dongminjung <dongminjung@Dongmins-MacBook-Pro.local>
Date: 2021-06-20 13:21:33 +0900
Commit message:

 update
 
Package: annaffy
Commit: a9d40d7e53d5c73f9a26a026a85de8510aa24a4c
Author: Colin Smith <colin@colinsmith.org>
Date: 2021-06-19 21:05:19 -0400
Commit message:

 Bump version number
 
Package: annaffy
Commit: 432a240b389a4f48ba12a30af49b2657c5d87719
Author: Colin Smith <colin@colinsmith.org>
Date: 2021-06-19 21:03:31 -0400
Commit message:

 Remove UniGene class from NAMESPACE
 
Package: packFinder
Commit: 6338cdab3491a442d4beaf64ed75daed53973dd0
Author: Jack Gisby <jackgisby@gmail.com>
Date: 2021-06-19 13:30:04 +0100
Commit message:

 Bump version for citation and description changes
 
Package: packFinder
Commit: ea41e5c3020fb7d7f65b7d1d8b7eebe3da0af89f
Author: Jack Gisby <jackgisby@gmail.com>
Date: 2021-06-19 13:28:04 +0100
Commit message:

 Fix description conflict
 
Package: packFinder
Commit: c68f9aac1cc504d687ac64b0dc0cde79c327afdc
Author: Jack Gisby <jackgisby@gmail.com>
Date: 2021-06-19 13:13:10 +0100
Commit message:

 Fix citation
 
Package: packFinder
Commit: f9aade96d6ecefe0827d637c52954b86d2e35175
Author: Jack Gisby <jackgisby@gmail.com>
Date: 2021-06-19 13:08:09 +0100
Commit message:

 Bump version number to update package
 
Package: packFinder
Commit: 903776d9f51f01687ba5ed799a5f0584f3db314c
Author: Jack Gisby <jackgisby@gmail.com>
Date: 2021-06-19 12:51:10 +0100
Commit message:

 Add biorxiv citation
 
Package: packFinder
Commit: ca7b06e1e6c077424799659b43b796251bfb44e4
Author: Jack Gisby <jackgisby@gmail.com>
Date: 2021-06-19 12:43:26 +0100
Commit message:

 Add ORCID to authors
 
Package: packFinder
Commit: f10989a038575d772d004c7b1f6e04391e4c6cc6
Author: Jack Gisby <jackgisby@gmail.com>
Date: 2021-06-19 12:40:07 +0100
Commit message:

 Update version
 
Package: muscat
Commit: 78a1d52ab4f6b83ca2a997af996f71ba1a3d3c98
Author: HelenaLC <helena@crowells.eu>
Date: 2021-06-19 09:35:23 +0200
Commit message:

 version bump
 
Package: muscat
Commit: 4c9ac38c0ee9a8355590c59d11dfc9b464746d19
Author: HelenaLC <helena@crowells.eu>
Date: 2021-06-19 09:32:47 +0200
Commit message:

 add unit test for single cluster est/sim
 
Package: muscat
Commit: 05e45badafd2eb7cb3d35cafbf91000b1471be7d
Author: HelenaLC <helena@crowells.eu>
Date: 2021-06-19 09:32:28 +0200
Commit message:

 bug fix: single cluster est/sim works again
 
Package: muscat
Commit: face2431d54185aa94bf7c87a897c98ee3f86b2c
Author: HelenaLC <helena@crowells.eu>
Date: 2021-06-19 09:32:03 +0200
Commit message:

 rmv lazy data; add statmod to suggests; version bump
 
Package: PWMEnrich
Commit: 96da45daede3a666280c983b28e7b81c8e65cf38
Author: Diego Diez <diego10ruiz@gmail.com>
Date: 2021-06-19 06:32:14 +0000
Commit message:

 Version bump.
 
Package: rTRM
Commit: 3023691547a8d3521b74c004d45de35e63d6f73c
Author: Diego Diez <diego10ruiz@gmail.com>
Date: 2021-06-19 05:20:53 +0000
Commit message:

 Version bump.
 
Package: rTRM
Commit: 4aa506bf45134690daeddb9eb9a4b951fe719379
Author: Diego Diez <diego10ruiz@gmail.com>
Date: 2021-06-19 05:20:30 +0000
Commit message:

 Add vignette references to bibtex file.
 
Package: rTRM
Commit: 94c332dbe66ef594f67e970297f7054af9cbff3c
Author: Diego Diez <diego10ruiz@gmail.com>
Date: 2021-06-19 05:20:07 +0000
Commit message:

 Update .gitignore.
 
Package: rTRM
Commit: 176a2e84b934c8b639eb1d1866467453876f488c
Author: Diego Diez <diego10ruiz@gmail.com>
Date: 2021-06-19 03:38:36 +0000
Commit message:

 Version bump.
 
Package: rTRM
Commit: a27fae0235df6c50b624de34ec18496ca64b4393
Author: Diego Diez <diego10ruiz@gmail.com>
Date: 2021-06-19 01:47:26 +0000
Commit message:

 Use HTML vignette.
 
Package: rTRM
Commit: c07f9d8341e009f8373e356554c800c686c1a933
Author: Diego Diez <diego10ruiz@gmail.com>
Date: 2021-06-19 01:47:09 +0000
Commit message:

 Adjust title case.
 
Package: rTRM
Commit: e679065b86427486650e897ffaac2616bc95970f
Author: Diego Diez <diego10ruiz@gmail.com>
Date: 2021-06-19 01:46:06 +0000
Commit message:

 Fix checking object class.
 
Package: PDATK
Commit: cfa69f2600bb14e948779a400891aacd9b832c92
Author: Christopher Eeles <44755307+ChristopherEeles@users.noreply.github.com>
Date: 2021-06-18 19:41:26 -0400
Commit message:

 Merge pull request #8 from bhklab/development

Fix: accidentally left 1000 repeasts for model training in the vignette 
Package: PDATK
Commit: e17dac099bba8d647c200fed95b7821a724f1f3f
Author: ChristopherEeles <christopher.eeles@outlook.com>
Date: 2021-06-18 19:23:59 -0400
Commit message:

 Fix: accidentally left 1000 repeasts for model training in the vignette
 
Package: DEsubs
Commit: fe35de3b3abbbd976607d1305d0ae672b8f620a4
Author: Panos Balomenos <balomenos@upatras.gr>
Date: 2021-06-19 02:34:29 +0300
Commit message:

 Resolve rmarkdown dependency issue
 
Package: FLAMES
Commit: 64e19141a4399252fe8c2bdb2e7107fc18774fa8
Author: Oliver Voogd <olivervoogd@gmail.com>
Date: 2021-06-19 09:23:35 +1000
Commit message:

 vignette single cell example
 
Package: PDATK
Commit: 4f1b539ceb086d65088e3191d97c658adbf770b2
Author: Christopher Eeles <44755307+ChristopherEeles@users.noreply.github.com>
Date: 2021-06-18 18:54:44 -0400
Commit message:

 Merge pull request #6 from bhklab/development

Fix: converted groupBy columns to factors in forestPlot,ModelComparison-method 
Package: PDATK
Commit: 2d7806e1fab315f30e4344b21266154a297bc33a
Author: ChristopherEeles <christopher.eeles@outlook.com>
Date: 2021-06-18 18:37:53 -0400
Commit message:

 Fix: disabled error check for factor columns in survival_time
* Support has been added for attepting a coercion, then erroring only if it fails to yield the expected types
* Modified the event_occurred error test to check for the new error message
 
Package: PDATK
Commit: 8147742e9074b2579bf42f3bd56cbd55d478c232
Author: ChristopherEeles <christopher.eeles@outlook.com>
Date: 2021-06-18 10:53:31 -0400
Commit message:

 Update: forestPlot for ModelComparsion object now orders facets correctly
 
Package: PDATK
Commit: 2c999b090f4903fd5635ad7360fc8e47ab25b443
Author: ChristopherEeles <christopher.eeles@outlook.com>
Date: 2021-06-17 14:21:17 -0400
Commit message:

 Fix: CohortList no longer drops mDataType
* Also added factor handling to SurvivalExperiment for surival_time and event_occurred columns
* Verison bump for BioC
 
Package: PDATK
Commit: 11c67467d3018f914b68f2ea713205ab7f1d7da2
Author: ChristopherEeles <christopher.eeles@outlook.com>
Date: 2021-06-17 12:46:57 -0400
Commit message:

 Update: add local_data folder to .gitignore
 
Package: clusterExperiment
Commit: 85fefb4dce3bd0e80a8edca03934fe6f9e5d447f
Author: Elizabeth Purdom <epurdom@stat.berkeley.edu>
Date: 2021-06-18 15:00:54 -0700
Commit message:

 bump up version
 
Package: clusterExperiment
Commit: 33d33e0fe8ad7014a2d03f04ecf2a5e66915e5c5
Author: Elizabeth Purdom <epurdom@stat.berkeley.edu>
Date: 2021-06-18 15:00:06 -0700
Commit message:

 Merge branch 'master' of git.bioconductor.org:packages/clusterExperiment
 
Package: clusterExperiment
Commit: d8855ec4bfa11451f37b208e9cad6c9e4b0e9a3a
Author: Elizabeth Purdom <epurdom@stat.berkeley.edu>
Date: 2021-06-18 15:00:02 -0700
Commit message:

 fix error in DESCRIPTION because of rmarkdown dependency
 
Package: PWMEnrich
Commit: a86991b5f3fcd3899e86d72c994c579089db0a41
Author: Diego Diez <diego10ruiz@gmail.com>
Date: 2021-06-18 21:37:04 +0000
Commit message:

 Move grid package to Imports.
 
Package: PWMEnrich
Commit: ee2ea713a941883c4663fc34ea8e190cb8a2d7b1
Author: Diego Diez <diego10ruiz@gmail.com>
Date: 2021-06-18 21:36:52 +0000
Commit message:

 Explicitly import grid dependencies to avoid conflict bewtween grid::pattern and Biostrings::pattern.
 
Package: cBioPortalData
Commit: 7fb9c1a58a585f52aae25e386ea616296b15efa9
Author: LiNk-NY <mramos09@gmail.com>
Date: 2021-06-18 15:49:53 -0400
Commit message:

 fix file locations in errors vignette
 
Package: cBioPortalData
Commit: e62ee6e1e465d9706ae6dc31d359d0c6f5943427
Author: LiNK-NY <mramos09@gmail.com>
Date: 2021-06-18 14:05:32 -0400
Commit message:

 bump version 2.5.7
 
Package: cBioPortalData
Commit: 6da2317b1aa45493e5fe4f787619e45f6608628e
Author: LiNK-NY <mramos09@gmail.com>
Date: 2021-06-18 14:02:36 -0400
Commit message:

 major updates
 
Package: cBioPortalData
Commit: 8e80f4e3c6a80a67faf7badbdd6bb3cb375afa67
Author: LiNK-NY <mramos09@gmail.com>
Date: 2021-06-16 15:58:25 -0400
Commit message:

 update API protocol from website
 
Package: cBioPortalData
Commit: a5a7e254c08bc990e68dc2da32ce9fed1dc7d2de
Author: LiNk-NY <mramos09@gmail.com>
Date: 2021-06-16 12:23:42 -0400
Commit message:

 update studiesTable list
 
Package: cBioPortalData
Commit: f3946266c1a0c78c7d9adeb3edf58a01ae480da1
Author: LiNk-NY <mramos09@gmail.com>
Date: 2021-06-16 12:23:25 -0400
Commit message:

 remove extra output from error vignette
 
Package: scry
Commit: d1c3144bb4e7bc37ed9177a63fee8dd783c6a90c
Author: Stephanie Hicks <stephaniechicks@gmail.com>
Date: 2021-06-18 13:02:13 -0400
Commit message:

 added markdown to Suggests to resolve changes in knitr
 
Package: bodymapRat
Commit: 4e3e1aca1d7d5f614568465f89e60a1bd636fc2c
Author: Stephanie Hicks <stephaniechicks@gmail.com>
Date: 2021-06-18 13:26:51 -0400
Commit message:

 added rmarkdown to Suggests to resolve changes in knitr
 
Package: benchmarkfdrData2019
Commit: 4c4b21cdca5a0d2451867330911c4f6e92a9b830
Author: Stephanie Hicks <stephaniechicks@gmail.com>
Date: 2021-06-18 13:18:54 -0400
Commit message:

 added rmarkdown to Suggests to resolve changes in knitr
 
Package: methylCC
Commit: 57bf100e2fea1e7c752f36b4253db01a1e9431c7
Author: Stephanie Hicks <stephaniechicks@gmail.com>
Date: 2021-06-18 12:53:37 -0400
Commit message:

 add rmarkdown to Suggests in DESCRIPTION per changes in knitr
 
Package: mzR
Commit: 60bf78693cfe3c50a861bb10b17c576ce81433af
Author: Laurent Gatto <laurent.gatto@uclouvain.be>
Date: 2021-06-18 18:37:31 +0200
Commit message:

 misc + version update
 
Package: mzR
Commit: d1bfdcc6dd02ec034f870d433845174ad1c9adf9
Author: Laurent Gatto <laurent.gatto@uclouvain.be>
Date: 2021-06-18 17:35:44 +0200
Commit message:

 Merge pull request #248 from vjcitn/vince_M1_file

needed on M1 mac 
Package: mzR
Commit: dbc53ee30fa01e14ce028921d270bd3ca644683f
Author: Vince Carey <stvjc@channing.harvard.edu>
Date: 2021-06-18 09:41:18 -0400
Commit message:

 needed on M1 mac 
Package: quantro
Commit: da23fd1b970d5618917c6e6469aa923a3c5150a7
Author: Stephanie Hicks <stephaniechicks@gmail.com>
Date: 2021-06-18 12:36:32 -0400
Commit message:

 added reference to vignette; added rmarkdown to Suggests
 
Package: csdR
Commit: 7388eacc31587147a080122e3f6f02ca33d9cac0
Author: Jakob Peder Pettersen <jakobpeder.pettersen@gmail.com>
Date: 2021-06-18 15:01:39 +0200
Commit message:

 Included an install section in the vignette in addtion to breaking long
lines.
 
Package: kebabs
Commit: 3331cffed1c12eac6e82f3ca1a60b21b06d31a6f
Author: UBodenhofer <ulrich@quomatic.ai>
Date: 2021-06-18 14:50:36 +0200
Commit message:

 fix in evaluatePrediction(); version number bumped to 1.27.1
 
Package: csdR
Commit: d545409c3b2e5fcf4b8f6d96ab50d1a736a0e045
Author: Jakob Peder Pettersen <jakobpeder.pettersen@gmail.com>
Date: 2021-06-18 11:22:18 +0200
Commit message:

 Minor changes to satisfy the automated checking processes.
The greatest change was to remove lazyData.
 
Package: procoil
Commit: b4e400f681f1fa00563da24e0d3559d68affc4ec
Author: UBodenhofer <ulrich@quomatic.ai>
Date: 2021-06-18 11:47:27 +0200
Commit message:

 fix of plot() method; version number bumped to 2.21.1
 
Package: EDASeq
Commit: 48d19be93c781992ac57741a5c6fe2024a4f2b93
Author: Davide Risso <risso.davide@gmail.com>
Date: 2021-06-18 10:51:51 +0200
Commit message:

 Bump version
 
Package: EDASeq
Commit: 41d596b0085863092e38bcab510fdb6bed39b15c
Author: Davide Risso <risso.davide@gmail.com>
Date: 2021-06-18 10:51:19 +0200
Commit message:

 Add rmarkdown in Suggests:
 
Package: missMethyl
Commit: 20dc68d2db5a9860b1947b1034538ca408f6d66e
Author: JovMaksimovic <jovana.maksimovic@petermac.org>
Date: 2021-06-18 17:40:41 +1000
Commit message:

 Bug fix: fixed issue with annotation subsetting in goregion and added code to make sure query regions are using UCSC style chr names
 
Package: DelayedTensor
Commit: 009455091932a6d0a9084e384c76a607657d256e
Author: kokitsuyuzaki <k.t.the-answer@hotmail.co.jp>
Date: 2021-06-18 15:57:32 +0900
Commit message:

 v-0.99.7
 
Package: MOFA2
Commit: 15ec4be60b6d47478465664d39caa8df3b77ba61
Author: bv2 <britta.velten@gmail.com>
Date: 2021-06-18 08:29:13 +0200
Commit message:

 added dtw-python dependency for basilisk
 
Package: DelayedTensor
Commit: d8067703e5306dcb1d174135f295aabe5853d961
Author: kokitsuyuzaki <k.t.the-answer@hotmail.co.jp>
Date: 2021-06-18 15:30:21 +0900
Commit message:

 v-0.99.6
 
Package: DelayedTensor
Commit: 43a2f0adb1aac4215911be37bc24952942b7ed0b
Author: kokitsuyuzaki <k.t.the-answer@hotmail.co.jp>
Date: 2021-06-18 15:14:33 +0900
Commit message:

 v-0.99.5
 
Package: DelayedTensor
Commit: fa072f0c682ce67ec7f37ca71eb692ad46ebc04c
Author: kokitsuyuzaki <k.t.the-answer@hotmail.co.jp>
Date: 2021-06-18 14:40:11 +0900
Commit message:

 v-0.99.4
 
Package: DelayedTensor
Commit: 8f8faea66ba33ed83ac41e7f2b2c15b877d69598
Author: kokitsuyuzaki <k.t.the-answer@hotmail.co.jp>
Date: 2021-06-18 14:14:45 +0900
Commit message:

 v-0.99.3
 
Package: DelayedTensor
Commit: dd91e1770866675e48c5d8afd8bf5ce082ef33e2
Author: kokitsuyuzaki <k.t.the-answer@hotmail.co.jp>
Date: 2021-06-18 13:45:46 +0900
Commit message:

 v-0.99.2
 
Package: sesame
Commit: 6482ce7ab6be8e21b41a4ce58d18f03f13db65ea
Author: Wanding Zhou <zhouwanding@gmail.com>
Date: 2021-06-17 16:47:48 -0400
Commit message:

 bump to 1.11.5
 
Package: sesame
Commit: 748213426f8d7d9b269c4d97468129ddd38557cc
Author: Wanding Zhou <zhouwanding@gmail.com>
Date: 2021-06-17 16:47:21 -0400
Commit message:

 multiple fix to examples and vignettes
 
Package: sesame
Commit: 0b9594d3cf22513840f1e0ef3642fd99c207ec99
Author: Wanding Zhou <zhouwanding@gmail.com>
Date: 2021-06-16 10:26:00 -0400
Commit message:

 fix control probe loading issue for mouse array
 
Package: sesame
Commit: 4a621563a6631859a9ef506f154ade382ad5eb9f
Author: Wanding Zhou <zhouwanding@gmail.com>
Date: 2021-06-10 17:31:29 -0400
Commit message:

 minor, message omitted
 
Package: sesame
Commit: a254a2b1861660501bc2857a27ba9c91a8f5f24e
Author: Wanding Zhou <zhouwanding@gmail.com>
Date: 2021-06-10 16:41:12 -0400
Commit message:

 DMR fix
 
Package: sesame
Commit: 853adf162d8d9b47a3135da4f9ba2b77189eefc2
Author: Wanding Zhou <zhouwanding@gmail.com>
Date: 2021-06-10 13:44:46 -0400
Commit message:

 default assembly
 
Package: sesame
Commit: 12a04ba9c8ea225f787536d130205f4dfb3a63d6
Author: Wanding Zhou <zhouwanding@gmail.com>
Date: 2021-06-10 13:33:34 -0400
Commit message:

 removed DMLShrinkage and reformatted DMR input
 
Package: sesame
Commit: d9fb8336c446831d96f60d970d6305efa6260963
Author: Wanding Zhou <zhouwanding@gmail.com>
Date: 2021-06-10 09:06:00 -0400
Commit message:

 added attachManifest
 
Package: sesame
Commit: cc73ecff6c15805d579a8df4db267599fc2ae9ed
Author: Wanding Zhou <zhouwanding@gmail.com>
Date: 2021-06-09 17:14:41 -0400
Commit message:

 fix to DML level cleaning
 
Package: Rsubread
Commit: de5faec313a1e2ae5b5b8034b12126a854918822
Author: Yang Liao <yang.liao@onjcri.org.au>
Date: 2021-06-18 06:00:23 +1000
Commit message:

 updated the users guide
 
Package: tximeta
Commit: ed11df507c131a4c105d6ca0ac2707ddd80c7fe8
Author: mikelove <michaelisaiahlove@gmail.com>
Date: 2021-06-17 20:50:37 +0200
Commit message:

 fix citation
 
Package: categoryCompare
Commit: 1da4bb20ea35fdd82d7c2b4ff1d7f64cdaed268b
Author: rmflight <r.flight79@gmail.com>
Date: 2021-06-17 14:46:47 -0400
Commit message:

 fixing recent issue with soft dependency of rmarkdown in knitr. Version bump to rebuild.
 
Package: AnnotationHub
Commit: a75ecbd22c96b64396d3808997e5d0f6bdf3ccd2
Author: Lori Shepherd <lori.shepherd@roswellpark.org>
Date: 2021-06-17 14:34:36 -0400
Commit message:

 Update .updateEntry

  If a duplicate resources is found in the cache it no longer ERRORs. Instead if
  the duplicate resource is not the resource requested, it is ignored.  If the
  duplicate resources is request, a warning is given and the first entry found
  in the cache is used.
 
Package: STexampleData
Commit: 0d73f53422895236afcc6d62aba6cbb7d98458ea
Author: Lukas Weber <lukas.weber.edu@gmail.com>
Date: 2021-06-17 14:03:45 -0400
Commit message:

 version
 
Package: STexampleData
Commit: 57f5210bbfece9e0149309985de1c28eab482899
Author: Lukas Weber <lukas.weber.edu@gmail.com>
Date: 2021-06-17 14:03:33 -0400
Commit message:

 add rmarkdown to Suggests
 
Package: GSAR
Commit: 1065a6735c10e253072605dec677f1316b6b3048
Author: yrahmatallah <yrahmatallah@uams.edu>
Date: 2021-06-17 12:53:34 -0500
Commit message:

 commit1_17June2021
 
Package: ToxicoGx
Commit: f77f3633fd0bdbb60c81314031d758f6ed95cd5f
Author: Christopher Eeles <44755307+ChristopherEeles@users.noreply.github.com>
Date: 2021-06-17 13:09:17 -0400
Commit message:

 Merge pull request #4 from bhklab/development

computeLimmaDiffExpr bug fix 
Package: ToxicoGx
Commit: f6fe3c018d2a1514a06614b0f9e7ea7459f097b1
Author: ChristopherEeles <christopher.eeles@outlook.com>
Date: 2021-06-17 12:31:13 -0400
Commit message:

 Fix: bug in computeLimmaDiffExpr
* The protocolData of a SummarizedExperiment is not subset in subsetTo (nor should it be)
* Added a workaround where I delete it in the function for now
* Ultimate solution will be to remove protocol data in ORCESTRA
 
Package: ToxicoGx
Commit: d9ecd5e0baa29ef8adbf6552ce33453e1397c88f
Author: ChristopherEeles <christopher.eeles@outlook.com>
Date: 2021-06-02 21:45:27 -0400
Commit message:

 Fix: shrank test data size to prevent > 5.0 Mb ERROR
 
Package: ToxicoGx
Commit: 3ec26168e192dbe12fa68f23e4eb2b8bd8baad97
Author: ChristopherEeles <christopher.eeles@outlook.com>
Date: 2021-06-02 15:39:07 -0400
Commit message:

 Merge branch 'master' of github.com:bhklab/ToxicoGx
 
Package: ToxicoGx
Commit: 5e696b360f9d020bee834f6510b6c7f9e275959d
Author: ChristopherEeles <christopher.eeles@outlook.com>
Date: 2021-06-02 15:38:02 -0400
Commit message:

 Fix: removed GHA for Windows and macOS since workflows are broken
* Updated the GHA badge in README.md
 
Package: ToxicoGx
Commit: ac0d20fb4e502cd8e3ab1794250ee1f5619ff9ba
Author: ChristopherEeles <christopher.eeles@outlook.com>
Date: 2021-06-02 15:38:02 -0400
Commit message:

 Fix: removed GHA for Windows and macOS single workflows are broken
* Updated the GHA badge in README.md
 
Package: ToxicoGx
Commit: ef0bdef5d12990889224d77c55b57ad645f77841
Author: ChristopherEeles <christopher.eeles@outlook.com>
Date: 2021-06-02 15:26:09 -0400
Commit message:

 Testing `biocthis` GHA workflow
 
Package: Rsamtools
Commit: 151a388fd7160c12907387cd18538d5f20946e27
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2021-06-17 09:30:27 -0700
Commit message:

 update NEWS
 
Package: escape
Commit: 1570626bceed4b1a4186bb41dc188d906c71a60d
Author: Nick <nicholas-borcherding@uiowa.edu>
Date: 2021-06-17 11:12:28 -0500
Commit message:

 Merge remote-tracking branch 'upstream/master'
 
Package: escape
Commit: 3d7a95d3d3e90fe3801f327efb616f5cc1f53cb4
Author: Nick <nicholas-borcherding@uiowa.edu>
Date: 2021-06-17 09:53:02 -0500
Commit message:

 Aligning versions

Making sure versions are aligned with the current bioconductor releases
fixing build issues with sce conversion
prepping for expanding functions - yeah I said it, not just check out the dev branch
 
Package: Rsamtools
Commit: 2b0a778d751a66d375568764e09ee69cbf7fc4c5
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2021-06-17 08:40:03 -0700
Commit message:

 Deprecate applyPileups() in favor of pileup()
 
Package: EWCE
Commit: 6379a47dc8ce067150da6bd81f571a7d5f422f7e
Author: Al-Murphy <alanmurph94@hotmail.com>
Date: 2021-06-17 15:25:21 +0100
Commit message:

 bug fix: my bug fix
 
Package: ternarynet
Commit: 0e3b7cfd3c8c5296a41fe915ca18edc18f96afc5
Author: mccallm <mccallm@gmail.com>
Date: 2021-06-17 10:08:59 -0400
Commit message:

 Start to reintroduce malloc
 
Package: ternarynet
Commit: 6666576944900ded31b89af771ad279c07131e17
Author: mccallm <mccallm@gmail.com>
Date: 2021-06-17 10:05:44 -0400
Commit message:

 Start to reintroduce malloc
 
Package: restfulSEData
Commit: 0267b0dceffc107e99a64441a425cb2c5e3a50b6
Author: Lori Shepherd <lori.shepherd@roswellpark.org>
Date: 2021-06-17 07:53:41 -0400
Commit message:

 Add rmarkdown to Suggests

       - changes in knitr require explicit declaration
 
Package: GSE62944
Commit: 5e38eef3e67209b6dda3de6c8154b557791fc1d1
Author: Lori Shepherd <lori.shepherd@roswellpark.org>
Date: 2021-06-17 07:52:41 -0400
Commit message:

 Add rmarkdown to Suggests

       - changes in knitr require explicit declaration
 
Package: TENxBrainData
Commit: a0a79ee872e04e01ee8ac850aa1c74942e29dd04
Author: Lori Shepherd <lori.shepherd@roswellpark.org>
Date: 2021-06-17 07:50:05 -0400
Commit message:

 Add rmarkdown to Suggests

   - changes in knitr require explicit declaration
 
Package: fishpond
Commit: d532e1578851bcf0c8de6f41cdd1fb853eb4899d
Author: mikelove <michaelisaiahlove@gmail.com>
Date: 2021-06-17 12:47:30 +0200
Commit message:

 update cite
 
Package: scanMiR
Commit: ba2ccd9e7e2a5534f3ec2b745a6f1cab1de76d28
Author: fridoling <fridoling@hotmail.com>
Date: 2021-06-17 09:42:10 +0000
Commit message:

 bump version number
 
Package: scanMiR
Commit: 404e394b924d47667e81bc09dea46ba119a772e2
Author: Pierre-Luc <pl.germain@gmail.com>
Date: 2021-06-12 08:58:29 +0200
Commit message:

 added link to scanmirapp 
Package: scanMiR
Commit: 5d671e1027ec1066315ca0d680bf39ce45c08887
Author: plger <pl.germain@gmail.com>
Date: 2021-06-07 07:37:34 +0000
Commit message:

 changed aggregateSites counts to integers
 
Package: scanMiR
Commit: cfccdbf53267c2475bbef60f119820a972626da0
Author: plger <pl.germain@gmail.com>
Date: 2021-06-04 17:40:37 +0000
Commit message:

 fixed misreported slicing and bug in unlist Rle
 
Package: scanMiR
Commit: ed62a1d87dd2ad18fec72b424755a676626bba08
Author: plger <pl.germain@gmail.com>
Date: 2021-06-04 11:49:46 +0000
Commit message:

 sped up re-scan (no overlap check)
 
Package: scanMiR
Commit: 4f04cf45a6c32a923d39fbdd6b4bbe244d3271c1
Author: plger <pl.germain@gmail.com>
Date: 2021-06-04 11:49:41 +0000
Commit message:

 removed final gc
 
Package: scanMiR
Commit: a2a817d1855ea08337e146156177ed545af9cfe8
Author: plger <pl.germain@gmail.com>
Date: 2021-06-04 11:37:30 +0000
Commit message:

 balanced bulge difference and added option to remove singletons
 
Package: scanMiR
Commit: 7a78ccf85bafb817c9fc1fe8af3e8a2bfced7f91
Author: plger <pl.germain@gmail.com>
Date: 2021-06-04 11:36:46 +0000
Commit message:

 changed merging of Rle fields
 
Package: scanMiR
Commit: 683c47ff275766b9ef8aebb12b16a39032528999
Author: plger <pl.germain@gmail.com>
Date: 2021-06-02 13:29:42 +0000
Commit message:

 added 9-11 slicing rule
 
Package: scanMiR
Commit: 3e39b6c820e8791ecbeee8b72b200ca7ebbde7ef
Author: plger <pl.germain@gmail.com>
Date: 2021-06-02 13:29:19 +0000
Commit message:

 fixed wobble display, changed sequence display to RNA
 
Package: scanMiR
Commit: b7688c785221381ba33cbabcec40dfca50dbe23f
Author: plger <pl.germain@gmail.com>
Date: 2021-06-01 16:50:19 +0000
Commit message:

 fixed wobble display in viewTargetAlignment
 
Package: scanMiR
Commit: fbd07d8943399f29b64cedf2616e132a96289159
Author: plger <pl.germain@gmail.com>
Date: 2021-06-01 15:34:11 +0000
Commit message:

 relaxed TDMD end binding rule
 
Package: scanMiR
Commit: 88616dc10ad06574394b3329e02e1a7a14c3ab52
Author: plger <pl.germain@gmail.com>
Date: 2021-05-31 17:47:39 +0000
Commit message:

 updated doc
 
Package: scanMiR
Commit: 6be9dcab4770a2ae6b481b800ed38741cbfc036f
Author: Pierre-Luc <pl.germain@gmail.com>
Date: 2021-05-31 19:46:27 +0200
Commit message:

 added get8merRange 
Package: scanMiR
Commit: 6ffe71aa4fdeefd485ff4352ee432f9446a0971e
Author: plger <pl.germain@gmail.com>
Date: 2021-05-31 11:50:38 +0200
Commit message:

 kept g-bulged
 
Package: scanMiR
Commit: 84231cec808e89f9c4cf9fddd9419f28146b1726
Author: plger <pl.germain@gmail.com>
Date: 2021-05-31 11:48:37 +0200
Commit message:

 simplified TDMD rule
 
Package: scanMiR
Commit: 1c7e74cf7f287e4ae1eb6f63af5c6477b4750352
Author: plger <pl.germain@gmail.com>
Date: 2021-05-31 11:46:27 +0200
Commit message:

 update slicing rules
 
Package: xcms
Commit: fb7308946d66aefc0a4cab5792eca1721193d3da
Author: Steffen Neumann <sneumann@ipb-halle.de>
Date: 2021-06-17 11:07:57 +0200
Commit message:

 Merge branch 'jomain'
 
Package: xcms
Commit: 7ab273070407f3f5ce74cc42bccb99e55545533f
Author: jorainer <johannes.rainer@gmail.com>
Date: 2021-06-16 11:03:11 +0200
Commit message:

 fix: replace |> with %>%
 
Package: xcms
Commit: e114b1c09397b8336710a8022f1b60799eb71802
Author: jorainer <johannes.rainer@gmail.com>
Date: 2021-06-16 08:27:29 +0200
Commit message:

 fix: fix LC-MS/MS vignette and unit tests (issue #564)
 
Package: xcms
Commit: 77f2bb6aa79181bb1372007bd47c1b370a6c541c
Author: jorainer <johannes.rainer@gmail.com>
Date: 2021-06-16 08:26:09 +0200
Commit message:

 Merge branch 'master' into jomain
 
Package: xcms
Commit: 15f1682772475eae7d18b4728dcf1d2edf4e4fd5
Author: Steffen Neumann <sneumann@ipb-halle.de>
Date: 2021-06-14 14:59:51 +0200
Commit message:

 Revert "Bump BioC test environment to 3.15"

This reverts commit 5c4cae7330ef5d74883d056636acf9e96c22f097
which was obviously the wrong approach.
 
Package: xcms
Commit: 5c4cae7330ef5d74883d056636acf9e96c22f097
Author: Steffen Neumann <sneumann@ipb-halle.de>
Date: 2021-06-14 13:52:45 +0200
Commit message:

 Bump BioC test environment to 3.15
 
Package: xcms
Commit: 7bca0a026d683a5e4cba6f487de33d9ceefac43c
Author: jorainer <johannes.rainer@gmail.com>
Date: 2021-05-21 08:53:06 +0200
Commit message:

 Merge branch 'master' into jomain
 
Package: xcms
Commit: 742ad47aa701e9a109b41ec44f5123e646e37caf
Author: jorainer <johannes.rainer@gmail.com>
Date: 2021-04-06 13:04:29 +0200
Commit message:

 refactor: use inherits instead of class
 
Package: MOGAMUN
Commit: e68703e257099226c8bfc23ef01f1070ee1bc5e0
Author: Elva Novoa <elvanov@hotmail.com>
Date: 2021-06-17 11:06:47 +0200
Commit message:

 Removed blank line to fix broken DESCRIPTION file
 
Package: PhyloProfile
Commit: e94b26990eebca9c4d4cf7494d6eaf52bc20726d
Author: trvinh <trvinh@gmail.com>
Date: 2021-06-17 10:09:01 +0200
Commit message:

 modify warning msg for links
 
Package: geneplast.data
Commit: 29c7ecfc500edfff4c73a1c15f7644fac64f83fa
Author: Leonardo RS Campos <leofields@gmail.com>
Date: 2021-06-17 09:00:59 +0200
Commit message:

 Minor adjusts in metadata. Version bump.
 
Package: IHW
Commit: 82911b1edcb9d80903e25d4cc632738fc74cb377
Author: Nikos Ignatiadis <nikos.ignatiadis01@gmail.com>
Date: 2021-06-16 17:25:13 -0700
Commit message:

 update readme
 
Package: IHW
Commit: ea7f593e61777b7e5b5d439432d7ceec579a69e2
Author: Nikos Ignatiadis <nikos.ignatiadis01@gmail.com>
Date: 2021-06-16 17:15:57 -0700
Commit message:

 remove censoring option (that was never functional)
 
Package: Rsubread
Commit: 1c37ce971a49af499f152875326b3387aa917cdb
Author: Yang Liao <liao_y@svr2672.licr.unimelb.edu.au>
Date: 2021-06-17 08:45:23 +1000
Commit message:

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

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

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

 fixed the bug of multiple boolean values in "if"
 
Package: kebabs
Commit: e237f264f3ca238e4f4f2b15462f3b4e6d2b7945
Author: UBodenhofer <ulrich@quomatic.ai>
Date: 2021-06-16 22:25:06 +0200
Commit message:

 minor fix in C++ code; fix in kebabsDemo(); version number bumped to 1.27.1
 
Package: restfulSE
Commit: 4ab5d63da57ae7d7ba320ee93539cdfd667540d2
Author: Shweta Gopal <sgopal@sgopal-mbp19.local>
Date: 2021-06-16 13:52:54 -0500
Commit message:

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

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

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

 Merge remote-tracking branch 'upstream/master'
 
Package: scRepertoire
Commit: e637b42dbfb343d345a45f107fd2f87751da5945
Author: Nick <nicholas-borcherding@uiowa.edu>
Date: 2021-06-16 09:31:31 -0500
Commit message:

 Update Coding Practice

Yeah that's right, just formating based on devtools and bioccheck to commit to bioconductor, not particularly sexy
 
Package: scRepertoire
Commit: 9e54abcdc15cb5940fa224c3724ceeab3100dc2e
Author: Nick <nicholas-borcherding@uiowa.edu>
Date: 2021-06-04 09:57:01 -0500
Commit message:

 v1.2.1
 
Package: scRepertoire
Commit: 78de0b824583a96411e3fa3be0734a95a01f1eeb
Author: theHumanBorch <ncborch@gmail.com>
Date: 2021-06-03 12:07:30 -0500
Commit message:

 Update utils.R

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

 Update seuratFunctions.R

added labels to alluvialClonotype per many suggestions 
Package: scRepertoire
Commit: 1e382785fb45dd1a488053fcc7429b89a8571098
Author: theHumanBorch <ncborch@gmail.com>
Date: 2021-05-25 12:30:47 -0500
Commit message:

 Fix grabMeta()

Added conditional assessment of colnames in meta data 
Package: scRepertoire
Commit: 65dcf3ae08ed97a7bac625670c7f717083914bac
Author: theHumanBorch <ncborch@gmail.com>
Date: 2021-05-25 07:49:59 -0500
Commit message:

 Update clusterTCR.R

Add group variable, reflect new annotation 
Package: scRepertoire
Commit: 4b16f0fc8018d46adddde56ce4bd2b9e6bcd7cac
Author: theHumanBorch <ncborch@gmail.com>
Date: 2021-05-20 09:35:51 -0500
Commit message:

 Update README.md

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

 Update viz.R

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

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

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

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

 CombineTCR() fix

Fixing combineTCR() and filterMulti parameters
 
Package: scRepertoire
Commit: c515e7f9c62fd20dd6a20450fb4111a6b2058f9d
Author: Nick <nicholas-borcherding@uiowa.edu>
Date: 2021-05-09 07:38:47 -0500
Commit message:

 CombineTCR() issue

Issue with situation in which given two contigs of a barcode - one is assumed TCRA and the other is assumed TCRB
 
Package: scRepertoire
Commit: 251ef773822d8ff72e0fb21c73a4b93b18735ad0
Author: Nick <nicholas-borcherding@uiowa.edu>
Date: 2021-05-07 06:01:39 -0500
Commit message:

 adding else

combineBCR and clusterTCR add else to generate mean edit distance by length of the two cdr3 sequence lengths
 
Package: scRepertoire
Commit: d5965eb185e73019d5e2c88d3631fe15ca1ce4b5
Author: Nick <nicholas-borcherding@uiowa.edu>
Date: 2021-04-26 08:22:19 -0500
Commit message:

 Update utils.R

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

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

 Update utils.R

Refined parseBCR to ensure all light chains are properly recorded
 
Package: scRepertoire
Commit: 50b10c39ad88804625eeaac7133c28e13ef62b44
Author: Nick <nicholas-borcherding@uiowa.edu>
Date: 2021-04-09 12:49:26 -0500
Commit message:

 Update clusterTCR.R

Removing V genes
Fixed issue with multiple chains
 
Package: scRepertoire
Commit: e2d079a3dd5f2b45f9fd104d247f50989c25e798
Author: Nick <nicholas-borcherding@uiowa.edu>
Date: 2021-04-09 08:58:19 -0500
Commit message:

 Update clusterTCR.R

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

 Update clusterTCR.R

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

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

 v1.0.3 Commit
 
Package: scRepertoire
Commit: 5b2886bf7b5cccbddde21b0bda3cf53611a1c82f
Author: Nick <nicholas-borcherding@uiowa.edu>
Date: 2021-04-08 12:10:06 -0500
Commit message:

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

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

 Merge remote-tracking branch 'origin/RELEASE_3_12'

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

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

 Merge pull request #70 from ncborcherding/master

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

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

 Update diversity.R

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

 update annotation

Added update to function annotation for ocupiedscRepertoire and overlay

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

 Update seuratFunctions.R

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

 clonalOverlay() function

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

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

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

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

 Merge branch 'dev' of https://github.com/ncborcherding/scRepertoire into dev
 
Package: scRepertoire
Commit: 7a99c9d51724e000c3735c9e49c47ffab9464ed5
Author: theHumanBorch <ncborch@gmail.com>
Date: 2021-02-25 15:36:33 -0600
Commit message:

 Merge pull request #61 from ncborcherding/refine

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

 Merge branch 'dev' of https://github.com/ncborcherding/scRepertoire into dev
 
Package: scRepertoire
Commit: 07e3d4f81eb47bd70d73a0138d6947cc4dd392b7
Author: theHumanBorch <ncborch@gmail.com>
Date: 2021-02-25 15:05:54 -0600
Commit message:

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

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

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

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

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

 Update clusterTCR.R

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

 Create clusterTCR.R

Use to cluster TCR chains by edit distance.
 
Package: scRepertoire
Commit: 0b37efda63a9d49560f632c362c9525ff822599f
Author: Nick <nicholas-borcherding@uiowa.edu>
Date: 2021-02-07 14:16:37 -0600
Commit message:

 Fix LVcompare

Was not outputing the LD - clusters by edit distance for use downstream in combineBCR.
 
Package: scRepertoire
Commit: c65e8a8be462cc4bccf0b2184e0742e18256f154
Author: theHumanBorch <ncborch@gmail.com>
Date: 2021-02-01 08:26:17 -0600
Commit message:

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

 Update utils.R

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

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

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

 adding da truth

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

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

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

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

 Updating calling of BCR clonotypes

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

In addition updated the NEWS, DESCRIPTION and startrac.R to reflect updates or edits in examples.
 
Package: scRepertoire
Commit: 2a6192dcb0dadb61e520e3a4c2c996f6a72f8b6c
Author: theHumanBorch <nicholas-borcherding@uiowa.edu>
Date: 2020-09-21 06:50:20 -0500
Commit message:

 Update utils.R

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

 Update utils.R

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

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

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

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

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

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

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

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

 Merge pull request #14 from scfurl/master

Support for Monocle3

Had to update the DESCRIPTION to include monocle3 into dependencies. Will test the contributions this week. 
Package: scRepertoire
Commit: 6af25ad1a8237670f5a4f53daa04a7b549cdcc3e
Author: theHumanBorch <nicholas-borcherding@uiowa.edu>
Date: 2020-06-04 18:37:29 -0500
Commit message:

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

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

 add monocle3 support (3)
 
Package: scRepertoire
Commit: 82d11131ae782ec228b58b72ee7a58a925525218
Author: scfurl <sfurlan@uw.edu>
Date: 2020-06-04 10:54:54 -0700
Commit message:

 add support monocle3 (2)
 
Package: scRepertoire
Commit: 71e89f50beab8695b2a8f6441f89cd11f8436c1f
Author: scfurl <sfurlan@uw.edu>
Date: 2020-06-04 10:24:55 -0700
Commit message:

 add support monocle3 (1)
 
Package: BiocStyle
Commit: 62f4772d00483ecae39d36eceb73fb10a6f011e1
Author: Mike Smith <grimbough@gmail.com>
Date: 2021-06-16 14:55:20 +0200
Commit message:

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

 Switch to fixed pattern matching to try and address #88
 
Package: podkat
Commit: 17c976bc91883651c34a634bdceab5ea9bc4d45c
Author: UBodenhofer <ulrich@quomatic.ai>
Date: 2021-06-16 15:03:02 +0200
Commit message:

 Adapted namespace imports to account for changes in BiocGenerics; version number bumped to 1.25.1
 
Package: MsBackendMgf
Commit: 91bdf29192f03ef1d51d76d0d7d0f00c81056921
Author: Johannes Rainer <5506112+jorainer@users.noreply.github.com>
Date: 2021-06-16 12:43:39 +0200
Commit message:

 Merge pull request #17 from rformassspectrometry/jomaster

Fixes CHARGE export/import and adds support to export without TITLE 
Package: MsBackendMgf
Commit: c400d1fdf5b21aa58faed150a8934bb9bc69ccad
Author: jorainer <johannes.rainer@gmail.com>
Date: 2021-06-16 11:22:47 +0200
Commit message:

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

 feat: add parameter exportTitle to the export function (issue #14)
 
Package: MsBackendMgf
Commit: ed0f5f066a324ecdb6f2352b8fe7114fbc124cf1
Author: jorainer <johannes.rainer@gmail.com>
Date: 2021-06-16 11:00:27 +0200
Commit message:

 feat: export/import CHARGE in correct format (issue #16)
 
Package: SpidermiR
Commit: 552bf6582fb73100f3cd4306491f9d0c4df6d1f7
Author: claudia.cava <claudia.cava@ibfm.cnr.it>
Date: 2021-06-16 12:19:40 +0200
Commit message:

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

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

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

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

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

 'biocthis' version 1.3.1 generated GHA
 
Package: sitePath
Commit: badb572bd1a630aa549132a77644d27cce2bc20d
Author: Chengyang Ji <chengyang.ji12@alumni.xjtlu.edu.cn>
Date: 2021-06-16 05:11:56 +0000
Commit message:

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

 Add test cases for 'plotMutSites' function; Minor code reformat
 
Package: sitePath
Commit: 8794877215c5724022fc7056967415d7f4bc355f
Author: Chengyang Ji <chengyang.ji12@alumni.xjtlu.edu.cn>
Date: 2021-06-11 09:31:56 +0000
Commit message:

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

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

 Not scaling of 'minEffectiveSize' for lineages
 
Package: sitePath
Commit: 25d7aa318a2d02a580078a952b78289251259bd1
Author: Chengyang Ji <chengyang.ji12@alumni.xjtlu.edu.cn>
Date: 2021-05-22 08:48:05 +0000
Commit message:

 The first 'stable' path as default 'lineagePath'
 
Package: sitePath
Commit: 22526524a0a6aaf778b714dec7f2930794fd4782
Author: Chengyang Ji <chengyang.ji12@alumni.xjtlu.edu.cn>
Date: 2021-05-22 06:43:02 +0000
Commit message:

 Add 'usedSites' argument to 'setSiteNumbering' function
 
Package: GENESIS
Commit: b47ffba769561555c565d67a26baada2c41467d0
Author: Stephanie M. Gogarten <sdmorris@uw.edu>
Date: 2021-06-15 22:30:18 -0700
Commit message:

 move checks on family to method instead of internal function

Adding the two.stage argument introduced a bug where if 'family'
was not a character string, fitNullModel would fail.
One of the family checks requires the two.stage argument, which
is not passed to the internal .fitNullModel function. Move these
checks to the data.frame method instead (in the form of another
internal function). The internal function now assumes that
'family' is in the form of a function all (e.g., 'gaussian()'),
so modify unit tests accordingly.
 
Package: GENESIS
Commit: 0440a7a2b30908d20fe13246f24e2c9ad113d156
Author: Stephanie M. Gogarten <sdmorris@uw.edu>
Date: 2021-06-02 11:39:07 -0700
Commit message:

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

 bug fix: allow MatrixGenotypeReader in pcrelate

GenotypeData objects created with MatrixGenotypeReader would fail
since there was no readGeno method defined. Fix this by adding a
method.
 
Package: metapone
Commit: 5997bd66d9eb35ada8ed0063ddaff0c223c788e6
Author: Tianwei Yu <tianwei.yu@outlook.com>
Date: 2021-06-16 12:33:31 +0800
Commit message:

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

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

 0.99.1
 
Package: metapone
Commit: 7d231f9b36de4ca3d762db3f31f28dece99cd0dd
Author: Tianwei Yu <tianwei.yu@outlook.com>
Date: 2021-06-16 11:28:44 +0800
Commit message:

 Merge remote-tracking branch 'origin/main'
 
Package: metapone
Commit: 2010a6042a665f6fdce4cd96fcbd19b003599d6d
Author: Tianwei Yu <tianwei.yu@outlook.com>
Date: 2021-06-16 11:18:30 +0800
Commit message:

 update 0.99.1
 
Package: metapone
Commit: a4e34862292ed7edc671cae23fd5764998357cb3
Author: tianwei-yu <65949207+tianwei-yu@users.noreply.github.com>
Date: 2021-06-16 11:16:48 +0800
Commit message:

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

 Fix issue #141
 
Package: RCy3
Commit: ad4d3375581396edf0db71c48bf5719251c0dec1
Author: Yihang Xin <yihang.xin@gladstone.ucsf.edu>
Date: 2021-06-15 17:07:27 -0700
Commit message:

 Fix issue #141
 
Package: RCy3
Commit: 8269b0508b31d51c71ce2c54efc46347b662eee8
Author: Yihang Xin <yihang.xin@gladstone.ucsf.edu>
Date: 2021-06-15 17:06:47 -0700
Commit message:

 Fix issue #141
 
Package: RCy3
Commit: f699eb673e3a441f2fea94681945d0306f48443b
Author: Yihang Xin <yihang.xin@gladstone.ucsf.edu>
Date: 2021-06-15 00:14:14 -0700
Commit message:

 Fix issue #141
 
Package: OmnipathR
Commit: 38757b463ab27a8b56d4b7be07c420abcb6877c4
Author: Türei Dénes <turei.denes@gmail.com>
Date: 2021-06-15 14:29:06 +0200
Commit message:

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

 logfile is disabled if the `omnipath.logfile` config option is `"none"`
 
Package: OmnipathR
Commit: e32fcf36e6747fc8fb4eb41a0beadc61027a8baa
Author: Türei Dénes <turei.denes@gmail.com>
Date: 2021-06-15 02:18:28 +0200
Commit message:

 config options can be overridden by env variables
 
Package: OmnipathR
Commit: 641ef68a2054c31da55d3e4fd6478dfdea04db16
Author: Türei Dénes <turei.denes@gmail.com>
Date: 2021-06-15 02:18:02 +0200
Commit message:

 misc: `as_type` - convert variable to the type of another
 
Package: OmnipathR
Commit: 9fab07f5e6220072add5c2184141daf52d94324b
Author: Türei Dénes <turei.denes@gmail.com>
Date: 2021-06-15 01:47:30 +0200
Commit message:

 logging: `logdir` option & disable logfile if the `logfile` option is `none`
 
Package: OmnipathR
Commit: 4b9b6d912aa31fbde30db4c3db809e2035985e6e
Author: Türei Dénes <turei.denes@gmail.com>
Date: 2021-06-14 02:03:42 +0200
Commit message:

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

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

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

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

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

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

 v3.1.1
 
Package: OmnipathR
Commit: 5c1c79a18a19079c99ac8fd1451a3cf716c32b5a
Author: Türei Dénes <turei.denes@gmail.com>
Date: 2021-05-30 01:44:09 +0200
Commit message:

 fixed issue in `ontology_db_transformations` which caused critical performance loss in ontology tree lookups
 
Package: OmnipathR
Commit: a8e74e177c11e9e2d234b59b904e79d5f03d6f5d
Author: Türei Dénes <turei.denes@gmail.com>
Date: 2021-05-29 22:35:10 +0200
Commit message:

 go annotations: using comment character instead of skip
 
Package: cBioPortalData
Commit: ffbc402b4dc4a774448b3a37b2080cb8d6a0ec2d
Author: LiNk-NY <mramos09@gmail.com>
Date: 2021-06-15 11:16:41 -0400
Commit message:

 version bump 2.5.6
 
Package: cBioPortalData
Commit: 3f2d7b5bc330660e5fa3a208a049fd6453b57536
Author: LiNk-NY <mramos09@gmail.com>
Date: 2021-06-15 11:09:36 -0400
Commit message:

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

 version bump 2.5.5
 
Package: cBioPortalData
Commit: 961b7739166c3e9a45a0a0b415c37c9c279f0859
Author: LiNk-NY <mramos09@gmail.com>
Date: 2021-06-15 10:51:34 -0400
Commit message:

 encapsulate single args in lists for @Bioconductor/AnVIL#37
 
Package: synergyfinder
Commit: 069fa11849f8618c9b59e135358c069e90c11b7b
Author: Shuyu <shuyu.zheng@helsinki.fi>
Date: 2021-06-15 17:05:53 +0300
Commit message:

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

 Update version number to 3.0.8 to start the rebuild
 
Package: synergyfinder
Commit: 97dfcc39ee6487dee32dabb4d98ebbbab55b37ef
Author: Shuyu <shuyu.zheng@helsinki.fi>
Date: 2021-06-15 17:02:39 +0300
Commit message:

 If there is only one concentration combination is replicated in a block, extract whole block into the response_statistic table
 
Package: synergyfinder
Commit: 90867967eceb9b625ba19b288a01557b02604283
Author: Shuyu <shuyu.zheng@helsinki.fi>
Date: 2021-06-15 16:59:43 +0300
Commit message:

 Fix bug: The CalculateRI can't fit dose-response curve if all the response values are exactly same.
 
Package: synergyfinder
Commit: 5ae2728619b887a02ad543d184070fc6501625c9
Author: Shuyu <shuyu.zheng@helsinki.fi>
Date: 2021-06-11 19:32:21 +0300
Commit message:

 update version number to 3.0.7
 
Package: synergyfinder
Commit: 9bcc0106015b4e6f10374e210dc2a7e2629a5d9b
Author: Shuyu <shuyu.zheng@helsinki.fi>
Date: 2021-06-04 17:44:17 +0300
Commit message:

 update version number to 3.0.6 to initiate rebuild
 
Package: MSstatsConvert
Commit: e979538cfbf27b9d6f6ed4f4b02a0bb2dea1efb2
Author: mstaniak <mtst@mstaniak.pl>
Date: 2021-06-15 12:52:35 +0000
Commit message:

 updated from: Version 1.3.0 to: Version 1.3.1
 
Package: MSstatsConvert
Commit: bd918d2510a673d5975f62f447f21d0a3a6b70a3
Author: mstaniak <mtst@mstaniak.pl>
Date: 2021-06-15 12:51:15 +0000
Commit message:

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

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

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

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

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

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

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

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

 bug fix: wrapperWPM without any special wells not possible
 
Package: wpm
Commit: ec90b7c6337aaf5254f0fc706ff7ace775e8fa3c
Author: HelBor <borges.helene.sophie@gmail.com>
Date: 2021-06-15 13:32:59 +0200
Commit message:

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

 version 2.1.3
 
Package: TreeSummarizedExperiment
Commit: edd0ba5f29a11858c2328f8b73a6b55a07d16724
Author: fionarhuang <ruizhuRH@gmail.com>
Date: 2021-06-15 12:24:46 +0200
Commit message:

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

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

 rename a file (version 2.1.2)
 
Package: TreeSummarizedExperiment
Commit: 04c1387a876d8d1cff716e354ad36319773460b6
Author: fionarhuang <ruizhuRH@gmail.com>
Date: 2021-06-15 11:10:56 +0200
Commit message:

 version 2.1.1
 
Package: TreeSummarizedExperiment
Commit: 33072578553ac23fde0ca2e7fa375a7d3d1bf7bf
Author: fionarhuang <ruizhuRH@gmail.com>
Date: 2021-06-13 19:06:26 +0200
Commit message:

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

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

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

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

 set 'knitr::opts_chunk(error=TRUE)' in vignette to get useful error msg; version bump to 1.1.8
 
Package: signatureSearch
Commit: 6c193ae73064ef865123205f53fffee823e6a841
Author: Yuzhu Duan <yduan004@ucr.edu>
Date: 2021-06-14 18:05:15 -0700
Commit message:

 deal with corrupt cache; jump to 1.7.2
 
Package: signatureSearch
Commit: 36a02212fafcb6c09e176da43045f61cbdc7af3c
Author: Yuzhu Duan <yduan004@ucr.edu>
Date: 2021-05-20 21:04:40 -0700
Commit message:

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

 Merge pull request #5 from bhklab/development

Fix: bug in validateModel,ClinicalModel,SurvivalExperiment-method 
Package: PDATK
Commit: 43a670aefb006e6b61984a991fc969dc4e1c63f8
Author: ChristopherEeles <christopher.eeles@outlook.com>
Date: 2021-06-14 16:05:11 -0400
Commit message:

 Fix: forgot to import setDF in validateModel fix
 
Package: PDATK
Commit: 01961c1653ebc97f8d0ca5364aef106c14e25759
Author: ChristopherEeles <christopher.eeles@outlook.com>
Date: 2021-06-14 15:22:37 -0400
Commit message:

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

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

 Fix: Update GHA to fix PR merge conflict 
Package: PDATK
Commit: f11eee7e68ee7fde72b73d21086f5aa3ba1b8707
Author: ChristopherEeles <christopher.eeles@outlook.com>
Date: 2021-06-14 15:13:45 -0400
Commit message:

 Fix: updated GHA workflow to most recent working version
 
Package: PDATK
Commit: a7bf307ec913e6a9cec7ecd71f7287d8b246502c
Author: ChristopherEeles <christopher.eeles@outlook.com>
Date: 2021-06-14 15:09:47 -0400
Commit message:

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

 Fix: bug in validateModel for ClinicalModel class was taking log of lower and upper for concordance index and AUC
* Resulted in negative values for upper and lower and forest plots with confidence intervals where the estimate is outside the CI
* Fixed to only log the upper and lower for log D index in validateModel,ClinicalModel,SurvivalExperiment-method
 
Package: PDATK
Commit: fd9525f458cfeaf4fcc6637f54e5cf7728877421
Author: Christopher Eeles <44755307+ChristopherEeles@users.noreply.github.com>
Date: 2021-06-01 18:51:08 -0400
Commit message:

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

 Revert to GHA without BiocCheck 
Package: PDATK
Commit: caa11fccde989fb3f76d3fd63b1590f7b7bca9d6
Author: Christopher Eeles <44755307+ChristopherEeles@users.noreply.github.com>
Date: 2021-06-01 16:21:33 -0400
Commit message:

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

 warn if colour duplicated between rows and columns
 
Package: scater
Commit: 092703b2bd3dca6d97ca85b5dbe887a661388281
Author: Alan O'Callaghan <alan.ocallaghan@outlook.com>
Date: 2021-05-25 21:25:16 +0100
Commit message:

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

 v1.21.2, add row color arguments to plotHeatmap, #147
 
Package: scater
Commit: 72cc85f54cb0aefc6924336b0a1bb987bd69c74d
Author: Alan O'Callaghan <alan.ocallaghan@outlook.com>
Date: 2021-05-24 18:28:58 +0100
Commit message:

 v1.21.1; correct check for BiocParallel params #148
 
Package: MSstatsTMT
Commit: 63c1ec3f08bf17dd0fc32242983393a511730ca5
Author: Ting Huang <huang.tin@husky.neu.edu>
Date: 2021-06-14 15:10:42 -0400
Commit message:

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

 Fixed bug in mutation that caused (in very particular cases) individuals to reach bigger sizes than allowed.
 
Package: FEVV
Commit: e5879abd5f9bbd1d3d7ea62a7f66b402ed7d3701
Author: Isar Nassiri <isar.nassiri@oncology.ox.ac.uk>
Date: 2021-06-14 19:47:48 +0100
Commit message:

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

 Merge remote-tracking branch 'origin/main'
 
Package: FEVV
Commit: 3ea69f4995ed99617eec9e8cc45363c8fc40aa8c
Author: isarnassiri <isar.nassiri@oncology.ox.ac.uk>
Date: 2021-06-14 19:45:01 +0100
Commit message:

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

 Merge remote-tracking branch 'origin/main'

git add FEVV/R/FEVV.R
git add FEVV/man/
git commit -m "Fixed conflicts in version change"
git push upstream master
 
Package: FEVV
Commit: 383713b1c1f8389d8b232ed457eb8598a5533703
Author: isarnassiri <isar.nassiri@oncology.ox.ac.uk>
Date: 2021-06-14 19:02:18 +0100
Commit message:

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

 Merge remote-tracking branch 'origin/main'

git add FEVV/R/FEVV.R
git add FEVV/man/
git commit -m "Fixed conflicts in version change"
git push upstream mastere commit.
 
Package: FEVV
Commit: adb46c4083f0d0a102fbd55ffe988f5db0b93117
Author: isarnassiri <isar.nassiri@oncology.ox.ac.uk>
Date: 2021-06-14 18:12:20 +0100
Commit message:

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

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

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

 Merge remote-tracking branch 'origin/main'

git add FEVV/R/FEVV.R
git commit -m "Fixed conflicts in version change"Q
 
Package: FEVV
Commit: 5d2596d88bac34ef9c5e7dc49df9a980d3662c28
Author: isarnassiri <isar.nassiri@oncology.ox.ac.uk>
Date: 2021-06-14 15:38:28 +0100
Commit message:

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

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

 T3:wq
Merge remote-tracking branch 'origin/main'
 
Package: FEVV
Commit: 4045bf022e936850b5d7da4365c6e6b34da639f9
Author: isarnassiri <isar.nassiri@oncology.ox.ac.uk>
Date: 2021-06-14 15:06:22 +0100
Commit message:

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

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

 Revidesemote-tracking branch 'origin/main'
 
Package: FEVV
Commit: c634a59c4108e1c1db9a87e2b181b820274bd7ee
Author: isarnassiri <isar.nassiri@oncology.ox.ac.uk>
Date: 2021-06-14 14:41:20 +0100
Commit message:

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

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

 test merge remote-tracking branch 'origin/main'
 
Package: FEVV
Commit: 1aa4904eca0f99992c594247e665639fc9eef461
Author: isarnassiri <isar.nassiri@oncology.ox.ac.uk>
Date: 2021-06-14 12:50:25 +0100
Commit message:

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

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

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

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

 update conf to be compatible with bioconductor
 
Package: BgeeDB
Commit: c82da02ba6db6c5430a345039a770217233a7a4c
Author: Julien <julien.wollbrett@gmail.com>
Date: 2021-06-11 13:12:33 +0200
Commit message:

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

 allow to filter on full length for topanat analysis
 
Package: BgeeDB
Commit: 49b963fcb1d239166268366b38c67378e0b4cddc
Author: Julien <julien.wollbrett@gmail.com>
Date: 2021-06-11 10:24:19 +0200
Commit message:

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

 solve bug of filtering on sex, strain, celtype for releases before Bgee 15.0
 
Package: BgeeDB
Commit: 244913e88fa3b49d65243c003e333089fe4b3dd2
Author: Julien <julien.wollbrett@gmail.com>
Date: 2021-06-11 09:26:01 +0200
Commit message:

 solve bugs for release before 15.0
 

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