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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: singscore
Commit: 97d6eb2d20f68b942a641ee0930350ef9865b2c6
Author: Ruqian Lyu <xiaoru.best@gmail.com>
Date: 2019-03-23 14:40:22 +1100
Commit message:

 - fix example errors
 
Package: universalmotif
Commit: 1c7c00590ef32b9edea6177ccdb0098ef7c3e8d7
Author: bjmt <benjmtremblay@gmail.com>
Date: 2019-03-22 22:17:03 -0400
Commit message:

 code refactoring
 
Package: NBSplice
Commit: bb665f81d93d290a62ac057e723cb17c8971b8ee
Author: gabycleta <merino.gabriela33@gmail.com>
Date: 2019-03-22 21:49:56 -0300
Commit message:

 updating NBTest function
 
Package: IRanges
Commit: f6eb2f0fea626149cf566aecf10c062d84b84018
Author: Michael Lawrence <lawremi@gmail.com>
Date: 2019-02-14 17:30:08 -0800
Commit message:

 Merge pull request #7 from FelixErnst/Issue-#6

fixed removed rownames upon replacing in a SplitDataFrameList 
Package: IRanges
Commit: 44048b63e1cc3fbe05e5553696f4fd7727b6f977
Author: Felix Ernst <felix.ernst@ulb.ac.be>
Date: 2019-02-14 13:23:55 +0100
Commit message:

 added test for fix of Issue #6
 
Package: IRanges
Commit: 0f00ab95f4f68262fef57bce1e472a83b5a26ae4
Author: Felix Ernst <felix.ernst@ulb.ac.be>
Date: 2019-02-14 13:08:22 +0100
Commit message:

 fixed removed rownames upon replacing in a SplitDataFrameList
 
Package: Rsamtools
Commit: 9354dc820167640ab442993bafd942801e3b43cd
Author: Hervé Pagès <hpages@fredhutch.org>
Date: 2019-03-22 15:11:56 -0700
Commit message:

 update migration_notes.md
 
Package: chimeraviz
Commit: b75a767e4e1ca83235d3c3d79fe693a892d57ac5
Author: Stian Lågstad <stianlagstad@users.noreply.github.com>
Date: 2019-03-22 22:33:56 +0100
Commit message:

 Merge pull request #64 from stianlagstad/plot_fusion_without_bamfile_or_bedfile

Allow plot_fusion without coverage. 
Package: chimeraviz
Commit: 0f76e6b079b0958da47f4737d7c06abbea41c460
Author: Stian Lågstad <stianlagstad@gmail.com>
Date: 2019-03-22 22:23:05 +0100
Commit message:

 Update version and news
 
Package: chimeraviz
Commit: e10d68919a6ff8b56e0e310b1f6160f46d5fda66
Author: Stian Lågstad <stianlagstad@gmail.com>
Date: 2019-03-22 21:44:29 +0100
Commit message:

 Allow plot_fusion without coverage.

+ fix linter issues
 
Package: SeqArray
Commit: 257b6ac27bb04ce89e9ee7bc72d9a59ec605110f
Author: Xiuwen Zheng <zhengxwen@gmail.com>
Date: 2019-03-22 16:26:06 -0500
Commit message:

 updates
 
Package: SeqArray
Commit: 576810c51bd4858affc05d79f4a631e7e8f64c85
Author: Xiuwen Zheng <zhengxwen@gmail.com>
Date: 2019-03-12 15:16:24 -0500
Commit message:

 update internal .IsForking()
 
Package: rgsepd
Commit: 7ed2a00e71e9dcb0d71db2a653de0e70d17bfc32
Author: Karl Stamm <karl.stamm@gmail.com>
Date: 2019-03-22 16:01:56 -0500
Commit message:

 adding references and versions.
 
Package: rgsepd
Commit: 78e9f89922ed7d12ef58e414a9195cb8b1c4d047
Author: Karl Stamm <karl.stamm@gmail.com>
Date: 2019-03-22 15:51:48 -0500
Commit message:

 dont worry about the vignettes folder
 
Package: seqbias
Commit: 30d6f83816896711eddb7d440e650b07bce82b9b
Author: Daniel C. Jones <dcjones@cs.washington.edu>
Date: 2019-03-22 13:05:41 -0700
Commit message:

 Update for Rhtslib compatibility. (Patch by Hervé Pagès)
 
Package: RaggedExperiment
Commit: 2ee0afba6006fb9ec4816229990929c603ce5c22
Author: LiNk-NY <mramos09@gmail.com>
Date: 2019-03-22 14:30:28 -0400
Commit message:

 update weightedmean fx
 
Package: GAPGOM
Commit: a7ee37e1a08f56b2b7bf2dd3b7a7c2d6f7287224
Author: Berghopper <Casper98@protonmail.com>
Date: 2019-03-22 18:53:59 +0100
Commit message:

 Added error message if gene id is not present in expression set (for main prediction algorithm and scoring)
 
Package: universalmotif
Commit: f686140ed58803828722aeff35cb88d55b66a672
Author: bjmt <benjmtremblay@gmail.com>
Date: 2019-03-22 13:14:52 -0400
Commit message:

 T-->TRUE in R/read_meme.R
 
Package: universalmotif
Commit: d00184c6ca92de02999348a73a75c23f802ddd76
Author: bjmt <benjmtremblay@gmail.com>
Date: 2019-03-20 21:49:23 -0400
Commit message:

 appveyor.yml v10
 
Package: universalmotif
Commit: cd11ed3ee025dda0ea19da801bdc932a5a9ee8cb
Author: bjmt <benjmtremblay@gmail.com>
Date: 2019-03-20 21:49:06 -0400
Commit message:

 removed TFBSTools:::schneider_correction call from tsts
 
Package: universalmotif
Commit: b4ec3d2c4f84c7771121a25ecab49fe240a0d1d2
Author: bjmt <benjmtremblay@gmail.com>
Date: 2019-03-20 21:39:30 -0400
Commit message:

 appveyor.yml v9
 
Package: universalmotif
Commit: 5c3b2529b621851c17aebfbbfa8baaea47143a02
Author: bjmt <benjmtremblay@gmail.com>
Date: 2019-03-20 21:38:49 -0400
Commit message:

 appveyor.yml v8
 
Package: NADfinder
Commit: 2cf769212c7049274d84d9657eade65570a61384
Author: Julie Zhu <julie.zhu@umassmed.edu>
Date: 2019-03-22 12:39:49 -0400
Commit message:

 fixed rbamtools dependency
 
Package: BiocPkgTools
Commit: ddde9b2b47df1a58273852b8c35772650311bf5a
Author: Sean Davis <seandavi@gmail.com>
Date: 2019-03-22 12:30:32 -0400
Commit message:

 Fix some issues with biocPkgList and biocDownloadStats
 
Package: RBGL
Commit: 0272416c0170951fde5854aad270b4c1684f53ff
Author: Samuela Pollack <spollack@jimmy.harvard.edu>
Date: 2019-03-22 11:28:39 -0400
Commit message:

 Removing obsolete Windows config file
 
Package: RBGL
Commit: 77a9073a62ca4a4f44168c23c6c776e90a7f3b25
Author: Ubuntu <ubuntu@ip-172-31-87-253.ec2.internal>
Date: 2019-03-22 15:02:44 +0000
Commit message:

 Modifications to .Rd and .Rnw to remove warnings during check
 
Package: RBGL
Commit: f13711cda070f62a6eeeab38505d7af4ad64ec33
Author: Ubuntu <ubuntu@ip-172-31-87-253.ec2.internal>
Date: 2019-03-22 13:22:54 +0000
Commit message:

 Updated configure file for hidden source file
 
Package: RBGL
Commit: d61ed70bd17ad1fe720de7ceaad3347226dac05c
Author: Ubuntu <ubuntu@ip-172-31-87-253.ec2.internal>
Date: 2019-03-13 20:19:58 +0000
Commit message:

 Temporarily removed function which prevents compilation with LLVM C++ library
 
Package: RBGL
Commit: 8f152f5654a721c237ecd0c5bb288c9a060b4a5d
Author: Samuela Pollack <sampoll@users.noreply.github.com>
Date: 2019-02-20 14:23:23 -0500
Commit message:

 Removed uncalled macro from configure.ac and updated cleanup script
 
Package: RBGL
Commit: 1d76c84a2340f0b05948e0e0e64c51f5b2941e67
Author: Samuela Pollack <spollack@jimmy.harvard.edu>
Date: 2019-02-12 18:55:20 -0500
Commit message:

 Fixed error in error message
 
Package: RBGL
Commit: 36172184a1ee2451bd2d7a383149394413a9f801
Author: Samuela Pollack <spollack@jimmy.harvard.edu>
Date: 2019-02-12 16:45:34 -0500
Commit message:

 Modify Makevars.in to substitute kludge for 'abort'
 
Package: RBGL
Commit: 592221a47c8220dce8d88f54bc29d2b5509d6e78
Author: Samuela Pollack <spollack@jimmy.harvard.edu>
Date: 2019-02-12 16:22:05 -0500
Commit message:

 Adding M4 macro to check for presence of BH package
 
Package: RBGL
Commit: 6411dd0bba4fb3e2735f004245cd1bc5691cc735
Author: Samuela Pollack <spollack@jimmy.harvard.edu>
Date: 2019-02-12 16:20:09 -0500
Commit message:

 Kludge to eliminate warning from boost call to 'abort'
 
Package: RBGL
Commit: bb43c5231f5668eedec381eb8769d0cdcc2b5929
Author: Samuela Pollack <spollack@jimmy.harvard.edu>
Date: 2018-12-19 06:09:33 -0500
Commit message:

 Removed unused tarball and build product configure script
 
Package: RBGL
Commit: 64ef807504dd429a86027c5599b543faa2c388ac
Author: Samuela Pollack <spollack@jimmy.harvard.edu>
Date: 2018-12-19 06:08:17 -0500
Commit message:

 Link to headers in installed package CRAN BH
 
Package: karyoploteR
Commit: 252de448519919b1471a89d6f3d08b8628b433a4
Author: Bernat Gel <bernatgel@gmail.com>
Date: 2019-03-22 16:11:49 +0100
Commit message:

 Version Bump

 
Package: karyoploteR
Commit: f5c0da6b6a0f1ce0d16ab640a229f09881d93d34
Author: Bernat Gel <bernatgel@gmail.com>
Date: 2019-03-22 16:11:37 +0100
Commit message:

 Added a missing return

 
Package: BiocCheck
Commit: bf1db66a2dfc58e43993dfeb5d258620aa066062
Author: lshep <lori.shepherd@roswellpark.org>
Date: 2019-03-22 10:11:47 -0400
Commit message:

 Fixes #48

   - Update biocViews but not BiocCheck for the md location.
   - implemented with tests.
 
Package: Prostar
Commit: 8ad0978333c6c6e638db9c79d64e3a979eb59f7f
Author: Samuel Wieczorek <samuel.wieczorek@cea.fr>
Date: 2019-03-22 14:59:31 +0100
Commit message:

 add numerical filtering
 
Package: DAPAR
Commit: be8420bd7d2f060112e070228d3b004b71b42745
Author: Samuel Wieczorek <samuel.wieczorek@cea.fr>
Date: 2019-03-22 14:42:51 +0100
Commit message:

 version 1.15.12 : add numerical filtering addon
 
Package: DAPAR
Commit: 4c84c26105eef5b4ab4f5ee0a347aa880be29118
Author: Samuel Wieczorek <samuel.wieczorek@cea.fr>
Date: 2019-03-22 14:33:26 +0100
Commit message:

 add detailed infos after aggregation
 
Package: fishpond
Commit: c0f5b761f566d35467e2f643c1627c06330ca047
Author: mikelove <michaelisaiahlove@gmail.com>
Date: 2019-03-22 08:23:43 -0400
Commit message:

 clean up check note, importFrom less
 
Package: MACPET
Commit: d9224266e2f7e4b2d852c001b710440f3b3675ce
Author: IoannisVardaxis <ioannis.vardaxis@ntnu.no>
Date: 2019-03-22 13:08:28 +0100
Commit message:

 version
 
Package: MACPET
Commit: eba09bb77d02e29c0521a6e1f02a53036284f2a4
Author: IoannisVardaxis <ioannis.vardaxis@ntnu.no>
Date: 2019-03-22 13:07:02 +0100
Commit message:

 changes
 
Package: MACPET
Commit: a478cfbc823ec6f92ab0fcb0f3d9188e704f145f
Author: IoannisVardaxis <ioannis.vardaxis@ntnu.no>
Date: 2019-03-22 13:06:51 +0100
Commit message:

 updates

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

# Conflicts:
#	DESCRIPTION
 
Package: MACPET
Commit: c77894d948d3b95dd67e60e834ecf76141b15267
Author: IoannisVardaxis <ioannis.vardaxis@ntnu.no>
Date: 2019-03-22 12:57:28 +0100
Commit message:

 date
 
Package: MACPET
Commit: cc5bbf6c58ea4a89531f2be1aa5171bdabffdc32
Author: IoannisVardaxis <ioannis.vardaxis@ntnu.no>
Date: 2019-03-22 12:53:08 +0100
Commit message:

 date
 
Package: MACPET
Commit: 7581d8c9f8f031bfd7e9a5714ce615430f399bf4
Author: IoannisVardaxis <ioannis.vardaxis@ntnu.no>
Date: 2019-03-20 23:02:12 +0100
Commit message:

 version
 
Package: MACPET
Commit: 8782d43d0f5669713a9f7a549906a075e0ea70d6
Author: IoannisVardaxis <ioannis.vardaxis@ntnu.no>
Date: 2019-03-20 21:59:23 +0100
Commit message:

 version update as well as packages update
 
Package: BASiCS
Commit: 2010d3e54e822c0c3084d963eb37d31be95aeb4e
Author: catavallejos <cata.vallejos.m@gmail.com>
Date: 2019-03-22 10:16:25 +0000
Commit message:

 version 1.5.7: (2019-03-22)
- Added default value for 'BatchInfo' within 'BASiCS_MCMC'
 
Package: DAPAR
Commit: 48520e49672258f91ceba2877c27f0ad9ea0a5e9
Author: Samuel Wieczorek <samuel.wieczorek@cea.fr>
Date: 2019-03-22 10:04:11 +0100
Commit message:

 version 1.15.12 : add numerical filtering
 
Package: karyoploteR
Commit: 4fb0b1ae49b697b03d22a2cc79d39ed47b5699e0
Author: Bernat Gel <bernatgel@gmail.com>
Date: 2019-03-22 09:22:45 +0100
Commit message:

 Version Bump

 
Package: karyoploteR
Commit: 2141927b48c5a52e61a6abee7f8f201fa10596a1
Author: Bernat Gel <bernatgel@gmail.com>
Date: 2019-03-21 15:41:57 +0100
Commit message:

 Removed a logical comparison longer than 1

 
Package: karyoploteR
Commit: fbdeec1d630dc84df30467117c873c00dd37d412
Author: Bernat Gel <bernatgel@gmail.com>
Date: 2019-03-21 15:19:03 +0100
Commit message:

 Added documentation to mergeTranscripts

 
Package: FamAgg
Commit: 5e2079b81e3e9139a3b7805c21177e8f79beb801
Author: jotsetung <johannes.rainer@gmail.com>
Date: 2019-03-22 07:34:38 +0100
Commit message:

 Fix bug in buildPed, prune = TRUE resulting in missing parents

- Fix a bug in buildPed with prune = TRUE that resulted in either a missing
  mother or father for some complicated pedigrees.
 
Package: esATAC
Commit: 2143dc4261c98a3871a73d8cdb651aed6f8968ab
Author: Zheng Wei <wzweizheng@qq.com>
Date: 2019-03-21 22:05:17 -0700
Commit message:

 version bump
 
Package: esATAC
Commit: e2def944f7e23d1cc2f2ee04f55b45cc7f02fb50
Author: Zheng Wei <wzweizheng@qq.com>
Date: 2019-03-21 22:01:29 -0700
Commit message:

 remove import genome
 
Package: curatedOvarianData
Commit: cb694eef85d0370b46fe741485aaa78ac5c8a10d
Author: LiNk-NY <mramos09@gmail.com>
Date: 2019-03-21 19:19:39 -0400
Commit message:

 add Rbuildignore
 
Package: curatedOvarianData
Commit: 9397fcf763eb3c81995159b0c81e9bee2438e8a6
Author: LiNk-NY <mramos09@gmail.com>
Date: 2019-03-21 12:05:43 -0400
Commit message:

 version bump
 
Package: curatedOvarianData
Commit: 1ddf9fac48b6bc821ca2777f046fd2751433c39f
Author: LiNk-NY <mramos09@gmail.com>
Date: 2019-03-19 16:17:46 -0400
Commit message:

 Merge remote-tracking branch 'upstream/master'
 
Package: curatedOvarianData
Commit: 3b2e9b05b7ce650142b581fe47d5fd7a8765fb98
Author: LiNk-NY <mramos09@gmail.com>
Date: 2019-03-15 18:38:38 -0400
Commit message:

 devel version bump
 
Package: curatedOvarianData
Commit: 041848b0af82520effeb771a8a27697258857949
Author: LiNk-NY <mramos09@gmail.com>
Date: 2019-03-15 18:38:18 -0400
Commit message:

 bug fix in vignette
 
Package: curatedOvarianData
Commit: 34afe2fae55b3f4d1e9154fc9c3bb2a150331ef1
Author: Levi Waldron <lwaldron.research@gmail.com>
Date: 2017-09-05 16:45:12 -0400
Commit message:

 Add README.md
 
Package: curatedOvarianData
Commit: c73b8658519569e3254fd2f57c2bf7e860708cfb
Author: Levi Waldron <lwaldron.research@gmail.com>
Date: 2017-09-05 16:33:05 -0400
Commit message:

 Commit lfs files
 
Package: curatedOvarianData
Commit: 714e7151fe0f0de7e3431b1dc5e24cd8ba03930f
Author: Levi Waldron <lwaldron.research@gmail.com>
Date: 2017-09-05 16:13:34 -0400
Commit message:

 Enable LFS.
 
Package: Rsubread
Commit: e2289ef1f33cbdd145221212a854209f487121ba
Author: Yang Liao <dbpzdbpz@gmail.com>
Date: 2019-03-22 08:56:36 +1100
Commit message:

 suppressed warning message in scanFasta() called by simReads()
 
Package: GAPGOM
Commit: 49709d76d912119c5e318ce270b7e7d49c2bee47
Author: Berghopper <Casper98@protonmail.com>
Date: 2019-03-21 21:34:44 +0100
Commit message:

 Progress bar edit and unecessary code removal
 
Package: flowWorkspace
Commit: 4a1d577cddb632578215138944920a97a23dba88
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-03-21 12:40:25 -0700
Commit message:

 merge trunk
 
Package: flowWorkspace
Commit: 235091fd2d5e2dad1d062adb3fa845a1310d2a21
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-03-20 11:53:41 -0700
Commit message:

 deprecate some api
 
Package: flowWorkspace
Commit: 17c7ea505f93c29db7fe9626858ce8e4b10e24e9
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-03-20 11:19:34 -0700
Commit message:

 update vignette
 
Package: flowWorkspace
Commit: d8073ec0a5d3ad801c52466d4d9e53305687c5b4
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-03-20 11:15:25 -0700
Commit message:

 run roxygen
 
Package: flowWorkspace
Commit: e369c20f1c25c3369b13fe627cee83994ea5ec5b
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-03-20 10:57:39 -0700
Commit message:

 rm dep on xml
 
Package: flowWorkspace
Commit: 3bb89312057dfae7c29d22d80946678f4f5388fe
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-03-19 15:50:10 -0700
Commit message:

 rm flowjo parsing code
 
Package: flowWorkspace
Commit: da0b379646fc237fe00a499e6170c5a9cb2ff79f
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-03-18 13:58:11 -0700
Commit message:

 include Rcpp header after cytolib to avoid masking pb macro defs by R
 
Package: flowWorkspace
Commit: 6d7ad84794333b19986bfb279430332536f08d6d
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-03-08 14:38:55 -0800
Commit message:

 fix test-copyNode
 
Package: flowWorkspace
Commit: edc1992621f84bf75fb0e5074aa964ef74b95db0
Author: Greg Finak <greg.finak@gmail.com>
Date: 2019-03-08 09:11:17 -0800
Commit message:

 Update .travis.yml 
Package: flowWorkspace
Commit: 6bfa44ec1748bc867e719e8fb9fa48f18ce40484
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-03-07 12:27:34 -0800
Commit message:

 eliminate the path generation for allNodes #280
 
Package: flowWorkspace
Commit: 0770f91e7686eb9dea44588916ad8271ac1ca0a9
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-03-06 16:17:48 -0800
Commit message:

 parallel getPopStats #280
 
Package: flowWorkspace
Commit: aeba84ed2f5aee88ff553f3d3e1ff443f18b7b3e
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-03-06 14:23:33 -0800
Commit message:

 set path='full' by default for getPopStats #280
 
Package: flowWorkspace
Commit: 5bbf96d0bb3623d5020e6c252f27731e9fea506f
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-03-06 12:43:05 -0800
Commit message:

 switch from vector to deque for efficient gate path handling. #280
 
Package: flowWorkspace
Commit: d228870944abc18fc2e4db959cc71cb7a78eb6f5
Author: Jacob Wagner <jpwagner@fredhutch.org>
Date: 2019-03-06 12:36:09 -0800
Commit message:

 Update travis.yml
 
Package: flowWorkspace
Commit: 28df5dab2e9d9176ac3e4952798e844144bdeaef
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-03-05 15:42:42 -0800
Commit message:

 speed up get_leaf_node
 
Package: flowWorkspace
Commit: b1f7bee2d2eb33ba1518dbba2dda159fd96e95ed
Author: Jacob Wagner <jpwagner@fredhutch.org>
Date: 2019-03-04 11:24:59 -0800
Commit message:

 Make parseWorkspace guid format and warnings match cytoset branch
 
Package: flowWorkspace
Commit: 107dbdc9a8615dfb8d0f86082123c3b62713aae7
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-03-01 14:46:38 -0800
Commit message:

 add get_leaf_node
 
Package: flowWorkspace
Commit: 0b89cdeff3044fb052b3263fb1033d0b9b328605
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-03-20 15:36:44 -0700
Commit message:

 bump
 
Package: flowWorkspace
Commit: 61000b61304b6bc06b98cd082e893047d8c0d8ac
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-03-20 11:53:41 -0700
Commit message:

 deprecate some api
 
Package: flowWorkspace
Commit: ee416078d69a34aa852d9bb6b3219ec9b20dcd04
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-03-20 11:19:34 -0700
Commit message:

 update vignette
 
Package: flowWorkspace
Commit: e2f30233d55602e502255bee4abc80052f83ce57
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-03-20 11:15:25 -0700
Commit message:

 run roxygen
 
Package: flowWorkspace
Commit: 31f28ad8a7ccf1fefdca03634633d75fe7882051
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-03-20 10:57:39 -0700
Commit message:

 rm dep on xml
 
Package: flowWorkspace
Commit: f818cf2a876f1aa36057bd0ff864d763d33507cb
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-03-19 15:50:10 -0700
Commit message:

 rm flowjo parsing code
 
Package: flowWorkspace
Commit: 7c594ebd32c56f849f41ca75df7c8accf0ae4839
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-03-18 13:58:11 -0700
Commit message:

 include Rcpp header after cytolib to avoid masking pb macro defs by R
 
Package: flowWorkspace
Commit: 3508f0224e8b0b2380c384749384b4ebc82a0cc7
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-03-08 14:38:55 -0800
Commit message:

 fix test-copyNode
 
Package: flowWorkspace
Commit: 6ac3f7417bbd65983537fcd0f5fe1cefbab5684c
Author: Greg Finak <greg.finak@gmail.com>
Date: 2019-03-08 09:11:17 -0800
Commit message:

 Update .travis.yml 
Package: flowWorkspace
Commit: 759edea7b755074920d07bb9b0a7f96dadddb380
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-03-07 12:27:34 -0800
Commit message:

 eliminate the path generation for allNodes #280
 
Package: flowWorkspace
Commit: 7b8b4e72aa18d21fc647964a4338a43ba753f5c1
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-03-06 16:17:48 -0800
Commit message:

 parallel getPopStats #280
 
Package: flowWorkspace
Commit: 3946ddc17bbe2e92faf4efae8c47fbdb947db9f1
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-03-06 14:23:33 -0800
Commit message:

 set path='full' by default for getPopStats #280
 
Package: flowWorkspace
Commit: 74810dd202c9620ce5d796224370a8a9a9cfa6c2
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-03-06 12:43:05 -0800
Commit message:

 switch from vector to deque for efficient gate path handling. #280
 
Package: flowWorkspace
Commit: 14e0d1bc4b444c9cb97a2566123958e580ef59fa
Author: Jacob Wagner <jpwagner@fredhutch.org>
Date: 2019-03-06 12:36:09 -0800
Commit message:

 Update travis.yml
 
Package: flowWorkspace
Commit: d22b2373dbcf4bf3b70e667ccd8728d37c93ca97
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-03-05 15:42:42 -0800
Commit message:

 speed up get_leaf_node
 
Package: flowWorkspace
Commit: bc16846781f4e0135e9a1dce9b50606e977618b8
Author: Jacob Wagner <jpwagner@fredhutch.org>
Date: 2019-03-04 11:24:59 -0800
Commit message:

 Make parseWorkspace guid format and warnings match cytoset branch
 
Package: flowWorkspace
Commit: 7a23335124e524266422bccd7156835018fb024f
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-03-01 14:47:11 -0800
Commit message:

 bump
 
Package: flowWorkspace
Commit: 620b808d40b2da447f273181eeb1ed0084438fd3
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-03-01 14:46:38 -0800
Commit message:

 add get_leaf_node
 
Package: flowWorkspace
Commit: 8e9d4cbc2f5b555405facfe4a1558947e8680b0c
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-02-22 16:52:43 -0800
Commit message:

 bump
 
Package: flowWorkspace
Commit: 607aa63b04696cc212120515afec417c9d108607
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-02-22 16:52:34 -0800
Commit message:

 fix typo
 
Package: flowWorkspace
Commit: 8e3107d3ce3fe741da8b402d9cd194075110ff31
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-02-22 16:50:43 -0800
Commit message:

 Merge branch 'trunk' of github.com:RGLab/flowWorkspace into trunk
 
Package: flowWorkspace
Commit: 795bc95b740f81afbfcc93fabca758c05b83a04d
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-02-22 16:40:37 -0800
Commit message:

 change getTransformations/getCompensationMatrices to S3
 
Package: flowWorkspace
Commit: 5347c17e8c8b04d3e17991ae4f85d225a875823d
Author: Jacob Wagner <jpwagner@fredhutch.org>
Date: 2019-02-22 14:39:19 -0800
Commit message:

 Rename use.sampleID to additional.sampleID and add doc
 
Package: flowWorkspace
Commit: 624fb936e166ee23e2b15795754ac4c1f9c8de4b
Author: Jacob Wagner <jpwagner@fredhutch.org>
Date: 2019-02-21 17:21:43 -0800
Commit message:

 Add use.sampleID option for guid in parseWorkspace
 
Package: flowWorkspace
Commit: 072ddc665463b65dc55a3e7a960c1a2357a2a895
Author: Jacob Wagner <jpwagner@fredhutch.org>
Date: 2019-02-20 16:48:55 -0800
Commit message:

 Improve copyNode recursion
 
Package: flowWorkspace
Commit: d9498ea538878b7fdb55c0ee7a9f50e435e2a7b9
Author: Jacob Wagner <jpwagner@fredhutch.org>
Date: 2019-02-20 14:51:01 -0800
Commit message:

 Add copyNode
 
Package: flowWorkspace
Commit: ac28f5c06e2225549ec5c6cb143e761fa436800e
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-02-20 11:50:47 -0800
Commit message:

 roxygenize getFullNodePath
 
Package: flowWorkspace
Commit: 24ef6a3f9c11eb01d7bb887e6dd52b285a2f8aab
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-02-20 11:43:49 -0800
Commit message:

 expose getNodePath c++ API to R
 
Package: flowWorkspace
Commit: 0041d2126465e732d7e837e8d8cd4c20d666d7c7
Author: Jacob Wagner <jpwagner@fredhutch.org>
Date: 2019-02-14 16:50:28 -0800
Commit message:

 bump
 
Package: flowWorkspace
Commit: 9a00ef88872cadaa452707b6f00766bd1fb5691e
Author: Jacob Wagner <jpwagner@fredhutch.org>
Date: 2019-02-14 16:46:46 -0800
Commit message:

 Fix repeated filename printing...
 
Package: flowWorkspace
Commit: 92ba0302ab06d2d348ed1c8ad441908989237a74
Author: Jacob Wagner <jpwagner@fredhutch.org>
Date: 2019-02-14 16:20:00 -0800
Commit message:

 Make parseWorkspace throw error for duplicated FCS in workspace
 
Package: flowWorkspace
Commit: 0bb0f58d5e0f993828689e0952393c4c1df89dbd
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-02-12 12:03:50 -0800
Commit message:

 bump
 
Package: flowWorkspace
Commit: f5bb13c068fc4807c7020703dd1cc0556cadf111
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-02-12 11:30:16 -0800
Commit message:

 Merge branch 'trunk' of github.com:RGLab/flowWorkspace into trunk
 
Package: flowWorkspace
Commit: 583492a7049b0327d7bca88d2199a7a4fdc21a24
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-02-12 11:26:43 -0800
Commit message:

 generate guid for GatingSetList within identifier getter
 
Package: flowWorkspace
Commit: 9bf6795919ad551d9749837c7ebd2a286f27f910
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-02-12 10:51:16 -0800
Commit message:

 overload identifier method and avoid direct access to guid slot
 
Package: flowWorkspace
Commit: ec32ac747580d15d321989baff4f3bf60b7a05fe
Author: Jacob Wagner <jpwagner@fredhutch.org>
Date: 2019-02-08 14:05:08 -0800
Commit message:

 Fix bug to allow parseWorkspace to handle duplicate FCS in workspace XML
 
Package: flowWorkspace
Commit: c8c17ea9ef72b37ea32a14c0f0c9b19b02b56140
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-02-07 14:40:02 -0800
Commit message:

 merge conflicts
 
Package: flowWorkspace
Commit: 2a795622c9aea8c0bcaeb02942a0ec0edbd00ce2
Author: Kayla-Morrell <kayla.morrell@roswellpark.org>
Date: 2019-01-04 13:33:20 -0500
Commit message:

 Add ImmunoOncology biocViews term
 
Package: flowWorkspace
Commit: 8dde2ef28983fecd9545ccbdcc3f18fd4dd3659e
Author: Jacob Wagner <jpwagner@fredhutch.org>
Date: 2019-02-04 14:27:20 -0800
Commit message:

 Add guid slot to GatingSetList
 
Package: flowWorkspace
Commit: 709e4a687b8b98e5ed307bb34f87b87a6b82aab7
Author: Jacob Wagner <jpwagner@fredhutch.org>
Date: 2019-01-29 10:55:16 -0800
Commit message:

 Add docs for transform_gate methods
 
Package: flowWorkspace
Commit: 75b396ed73e94b0806212eafaa882b6927a1b328
Author: Jacob Wagner <jpwagner@fredhutch.org>
Date: 2019-01-25 17:10:36 -0800
Commit message:

 Add methods for transforming gates from nodes in GatingHierachy/GatingSet
 
Package: CytoML
Commit: 0c9a0ab2037a59412b2c1a21153cd4778893c99b
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-03-21 12:28:36 -0700
Commit message:

 Merge branch 'trunk' into devel
 
Package: CytoML
Commit: ed32c4529bb99234a8ddc33703fefb5408a0ccca
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-03-21 12:07:47 -0700
Commit message:

 rerun roxgyen
 
Package: CytoML
Commit: c6f08b595a56afaa026ebbf851bb6e954d72b7f5
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-03-20 15:39:17 -0700
Commit message:

 fix doc
 
Package: CytoML
Commit: 2e93976b74e5770886affa8a7fb19b4c64cd9754
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-03-20 15:37:18 -0700
Commit message:

 bump
 
Package: CytoML
Commit: ba5b464463746cfb83e465cd4cbdbe3610643f16
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-03-20 13:06:07 -0700
Commit message:

 adapt flowJo parser
 
Package: CytoML
Commit: f34de6924e10f13de46c098810b3e8330ef19068
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-03-20 11:22:31 -0700
Commit message:

 add flowJo parser from flowWorkspace
 
Package: fishpond
Commit: 6fd3a6b2b88970fff8762058e725b5771241ccb5
Author: mikelove <michaelisaiahlove@gmail.com>
Date: 2019-03-21 15:25:14 -0400
Commit message:

 removing lower quantile approach
 
Package: cytolib
Commit: 6766faf8f25e6f91f8636b12ace8c8b02d632580
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-03-21 12:21:37 -0700
Commit message:

 merge trunk
 
Package: cytolib
Commit: 5371b52e954a4e361a0157328a9714684be0a09c
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-03-21 12:19:51 -0700
Commit message:

 bump
 
Package: cytolib
Commit: 86587755c692a0460768f62e71512f6f0ccb6b34
Author: Kayla-Morrell <kayla.morrell@roswellpark.org>
Date: 2019-01-04 13:27:46 -0500
Commit message:

 Add ImmunoOncology biocViews term
 
Package: cytolib
Commit: 09f2df74e652bb49ed18780702d3f834038757e2
Author: vobencha <vobencha@gmail.com>
Date: 2018-10-30 11:54:38 -0400
Commit message:

 bump x.y.z versions to odd y after creation of RELEASE_3_8 branch
 
Package: cytolib
Commit: 8aebcd995920488fd897259594309ee1da1efed4
Author: vobencha <vobencha@gmail.com>
Date: 2018-10-30 11:42:06 -0400
Commit message:

 bump x.y.z versions to even y prior to creation of RELEASE_3_8 branch
 
Package: cytolib
Commit: f0540930ccc86c9c2a397152b225d99f24a3b27a
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-03-07 12:28:59 -0800
Commit message:

 optimize getNodePath by caching searching routes
 
Package: cytolib
Commit: 5cab210dbaf1f007ad3bebac5c3c0ba97102e55c
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-03-07 11:16:16 -0800
Commit message:

 rename getPopPaths to getNodePaths and move the logic into and call getNodePath API
 
Package: cytolib
Commit: e8a58c62dd6e7977c27afcd37d1d4650c3523e9f
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-03-06 12:44:21 -0800
Commit message:

 bump
 
Package: cytolib
Commit: 6c3a8360916aa7dd27d22f03c7839fae1f9a530f
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-03-06 12:39:16 -0800
Commit message:

 call queryByPath instead of getNodeId to avoid exception overhead for getPopPaths. RGLab/flowWorkspace#280
 
Package: GAPGOM
Commit: 14cf60dc1dc934dd8da67498b12ed873b2a1dfde
Author: Berghopper <Casper98@protonmail.com>
Date: 2019-03-21 18:39:23 +0100
Commit message:

 Fixed some output messages
 
Package: sevenbridges
Commit: d3c7b4ab79d3c0e6932718045d40587268e2a29a
Author: Nan Xiao <road2stat@gmail.com>
Date: 2019-03-21 13:35:49 -0400
Commit message:

 v1.13.5 release
 
Package: maftools
Commit: 2bf1668d8decef24be70ae890b694557da93429b
Author: PoisonAlien <anandmt3@gmail.com>
Date: 2019-03-21 16:13:55 +0100
Commit message:

 move to base graphics
 
Package: maftools
Commit: 895e3614bc49251a68d2dd33bc2966e288650a14
Author: PoisonAlien <anandmt3@gmail.com>
Date: 2019-03-21 10:22:14 +0100
Commit message:

 update docs, and vectorized code #266 #267
 
Package: maftools
Commit: aa1838097a3efb83baf85c7e012dfac83c2b65a6
Author: PoisonAlien <anandmt3@gmail.com>
Date: 2019-03-08 13:38:47 +0100
Commit message:

 fix
 
Package: maftools
Commit: 408eaa7b2a903a3049ff10b651934aa63471ff6a
Author: PoisonAlien <anandmt3@gmail.com>
Date: 2019-03-08 13:34:01 +0100
Commit message:

 add axis lims and segment size options
 
Package: maftools
Commit: d02e81b1f2422fa385788fc02f47f0f2f1c160ac
Author: PoisonAlien <anandmt3@gmail.com>
Date: 2019-03-07 16:21:37 +0100
Commit message:

 pretty x-axis for lp-plot
 
Package: maftools
Commit: 11e9d9c84c9c5726b56f3d69963425f49e639bf3
Author: PoisonAlien <anandmt3@gmail.com>
Date: 2019-03-07 16:08:59 +0100
Commit message:

 Address #255
 
Package: maftools
Commit: 266737a8b27481a6f6c9dde718e14e3d4df4b10c
Author: PoisonAlien <anandmt3@gmail.com>
Date: 2019-03-06 10:05:48 +0100
Commit message:

 Address #261
 
Package: maftools
Commit: 0ba842de8945747635c585f7983007558f091c13
Author: PoisonAlien <anandmt3@gmail.com>
Date: 2019-02-27 13:33:35 +0100
Commit message:

 address #256
 
Package: maftools
Commit: 32ecdd8d73799adc3d7a4437fced3200ed2768db
Author: PoisonAlien <anandmt3@gmail.com>
Date: 2019-02-26 16:16:25 +0100
Commit message:

 update NEWS
 
Package: maftools
Commit: 7010de00b108fced04adb6caee17ea5502504be5
Author: PoisonAlien <anandmt3@gmail.com>
Date: 2019-02-26 16:15:06 +0100
Commit message:

 Address #254
 
Package: maftools
Commit: 0e48dea9db1821377a63e72d669688f13a47a54f
Author: PoisonAlien <anandmt3@gmail.com>
Date: 2019-02-25 18:01:25 +0100
Commit message:

 Fix #253
 
Package: maftools
Commit: a980ae645edada978dcf0e64f20d5f774fdc2e97
Author: PoisonAlien <anandmt3@gmail.com>
Date: 2019-02-22 18:18:24 +0100
Commit message:

 update news
 
Package: maftools
Commit: 2040d9ebeb0cabdd910bfb771055326e7e963e96
Author: PoisonAlien <anandmt3@gmail.com>
Date: 2019-02-22 18:17:23 +0100
Commit message:

 address #249
 
Package: maftools
Commit: ff19c026b180243a17de3297fc282d4aa391a994
Author: Anand Mayakonda <anandmt3@gmail.com>
Date: 2019-02-22 09:50:14 +0100
Commit message:

 Merge pull request #251 from JohnMCMa/master

Implement showMutationRate argument in lollipopPlot 
Package: maftools
Commit: 8739f2f4cb0fe67bafa86415c8876c099b547617
Author: John Ma <JohnMCMa@users.noreply.github.com>
Date: 2019-02-21 14:55:25 -0600
Commit message:

 Implement showMutationRate argument in lollipopPlot

`lollipopPlot` has a `showMutationRate` argument, which is declared not never explained nor implemented in any way. I perceive this argument to control whether the somatic mutation rate is displayed as part of the title, and implemented it accordingly.

This commit sets the plot title, saved as the variable `cbioSubtitle`, to be `geneID` as default; somatic mutation rate is appended to the title if `showMutationRate=TRUE`.
 
Package: maftools
Commit: 4f9a742c8a3d64a28e33e16e1fa5d5aafcb1a4e0
Author: PoisonAlien <anandmt3@gmail.com>
Date: 2019-02-20 18:25:29 +0100
Commit message:

 update news
 
Package: maftools
Commit: caca926887c1c38860a2b538fcccbe7b37874d01
Author: PoisonAlien <anandmt3@gmail.com>
Date: 2019-02-20 18:25:14 +0100
Commit message:

 address #247 and #225
 
Package: maftools
Commit: c3ea2d569c5e0aad8a40b2be04108199fbe5d347
Author: PoisonAlien <anandmt3@gmail.com>
Date: 2019-02-13 11:48:27 +0100
Commit message:

 address variable name coflicts
 
Package: maftools
Commit: 4f4259b56e57f731b4fde53de60adfd163f432b5
Author: Anand Mayakonda <anandmt3@gmail.com>
Date: 2019-02-13 10:54:47 +0100
Commit message:

 Merge pull request #243 from mattdowle/master

recycle rep to pass data.table 1.12.2 
Package: maftools
Commit: b4e9c3af865837abd850bb5b51bb079cd2be510b
Author: PoisonAlien <anandmt3@gmail.com>
Date: 2019-02-13 10:52:32 +0100
Commit message:

 address #241 #244
 
Package: maftools
Commit: f26e20b501421184bf193098d1010abaa3d02537
Author: mattdowle <mattjdowle@gmail.com>
Date: 2019-02-12 23:02:57 -0800
Commit message:

 recycle rep to pass data.table 1.12.2
 
Package: maftools
Commit: 74b1c1788c3568fadaf2e17fde2b78fd79c5197c
Author: PoisonAlien <anandmt3@gmail.com>
Date: 2019-02-12 18:06:06 +0100
Commit message:

 Address #241 and #242
 
Package: maftools
Commit: c4adbe84c3ab94915b8d27c847c8baa2bcc56568
Author: PoisonAlien <anandmt3@gmail.com>
Date: 2019-02-12 13:28:28 +0100
Commit message:

 Address #240
 
Package: maftools
Commit: 73b56a1867c7d6020d422359c086400274df0f5a
Author: PoisonAlien <anandmt3@gmail.com>
Date: 2019-02-02 16:18:02 +0100
Commit message:

 base graphics
 
Package: maftools
Commit: 767fbfd91d732fb7cdf4dd58f125c4ef4c211f7b
Author: PoisonAlien <anandmt3@gmail.com>
Date: 2019-02-02 11:14:32 +0100
Commit message:

 update news
 
Package: maftools
Commit: e2696f65398676b7869f51936f2b2c13d28b50c8
Author: PoisonAlien <anandmt3@gmail.com>
Date: 2019-02-02 11:12:30 +0100
Commit message:

 Change default value for mafObj to TRUE
 
Package: maftools
Commit: 7635042adaaf83ee642a13204d557326102611e3
Author: PoisonAlien <anandmt3@gmail.com>
Date: 2019-01-28 13:41:21 +0100
Commit message:

 address #207
 
Package: maftools
Commit: 1e684e5ce4dfe1546a0e2f47609d9201ea11cbde
Author: PoisonAlien <anandmt3@gmail.com>
Date: 2019-01-16 16:43:56 +0100
Commit message:

 address #214
 
Package: GAPGOM
Commit: 053c29dda7dc1672d35288474d72a19f2d5e7125
Author: Berghopper <Casper98@protonmail.com>
Date: 2019-03-21 16:07:23 +0100
Commit message:

 Fixed some error catching
 
Package: GAPGOM
Commit: 416770b75c14dfbe24727bd0a727041d5b618922
Author: Berghopper <Casper98@protonmail.com>
Date: 2019-03-21 15:28:54 +0100
Commit message:

 Added lots of performance improvements, also fixed rezvans improvement (disjunctive common ancestors were not being calculated).
 
Package: Prostar
Commit: 6f52fa5c8b0e5b5acc04579d37ed4a4b8b6951c3
Author: Samuel Wieczorek <samuel.wieczorek@cea.fr>
Date: 2019-03-21 15:09:30 +0100
Commit message:

 Add modulePlots
 
Package: Prostar
Commit: 5856e7a036e4d3013bfebef5aa9b374ae213ac8c
Author: Samuel Wieczorek <samuel.wieczorek@cea.fr>
Date: 2019-03-21 15:08:38 +0100
Commit message:

 Add modulePlots
 
Package: S4Vectors
Commit: ad6d0aa703a5633c559c07cce13c75127f67d67e
Author: Michael Lawrence <michafla@gene.com>
Date: 2019-03-21 06:49:09 -0700
Commit message:

 factor out an extractCOLS() from [,DataFrame
 
Package: VariantAnnotation
Commit: 802d25f20f23b287bdabf005a34f0e1a9dda385e
Author: vobencha <vobencha@gmail.com>
Date: 2019-03-21 05:10:51 -0700
Commit message:

 Forgot to add .gitignore in last commit
 
Package: VariantAnnotation
Commit: ac2f40857c1d712f99f12c0af063fb0db69eede5
Author: vobencha <vobencha@gmail.com>
Date: 2019-03-21 05:07:01 -0700
Commit message:

 Reapply commit 58ffe2c5838b156ffde69b914d74b075e2088efd:

This patch from lcougnaud DID NOT break VariantAnnotation on Windows.
The cause of the breakage is still being investigated.
 
Package: CATALYST
Commit: fcba366174cd7eba57bd92c83ee3d8c2aeaccf23
Author: HelenaLC <helena@crowells.eu>
Date: 2019-03-21 12:35:10 +0100
Commit message:

 fix dox
 
Package: BaalChIP
Commit: ad3ee38bfdfd8426c7c03f91f93c636b11707cb9
Author: Ines de Santiago <inesdesantiago@gmail.com>
Date: 2019-03-21 11:18:15 +0000
Commit message:

 changed version
 
Package: CATALYST
Commit: c431f66a187f20cb96c7d76ddba00acb9f913ba5
Author: HelenaLC <helena@crowells.eu>
Date: 2019-03-21 12:16:52 +0100
Commit message:

 bug fix in daFrame-constructor
 
Package: Rsubread
Commit: 68f40eeae09aeaaea51b359dc20a7ff3753f3363
Author: Yang Liao <dbpzdbpz@gmail.com>
Date: 2019-03-21 16:11:30 +1100
Commit message:

 Add many checks to parameters
 
Package: Rsubread
Commit: e155000c14bbf9162bfe2773c0b307730d8acfca
Author: Yang Liao <dbpzdbpz@gmail.com>
Date: 2019-03-21 16:06:37 +1100
Commit message:

 Fixed a typo in error message
 
Package: scruff
Commit: 0ab26ca562e8396c2808502a151765d551ed8d6f
Author: zhewa <314100793@qq.com>
Date: 2019-03-20 21:57:25 -0400
Commit message:

 remove refGenome dependency. version bump
 
Package: scruff
Commit: 0fb0ec42201799e1d54fc8f300192f4ba9a84c3c
Author: zhewa <314100793@qq.com>
Date: 2019-03-19 21:42:54 -0400
Commit message:

 hide Rsubread messages if verbose == FALSE in alignRsubread
 
Package: scruff
Commit: 05615589ab97b58351d97965e2671a8cc7e4365f
Author: Zhe Wang <314100793@qq.com>
Date: 2019-02-04 12:05:14 -0500
Commit message:

 Merge pull request #107 from zhewa/master

Update bug reports URL to Bioconductor 
Package: universalmotif
Commit: dd5cb1caa9ac24163b76301d699e7e3eb68ce167
Author: bjmt <benjmtremblay@gmail.com>
Date: 2019-03-20 21:37:37 -0400
Commit message:

 fixed test using && instead of &
 
Package: universalmotif
Commit: b791f2e9838c52347f857b89a5379bf4828e77d7
Author: bjmt <benjmtremblay@gmail.com>
Date: 2019-03-20 21:35:07 -0400
Commit message:

 appveyor.yml v7
 
Package: universalmotif
Commit: f9a98ebbe79c28af32f89de2966ac07a6d43b914
Author: bjmt <benjmtremblay@gmail.com>
Date: 2019-03-20 21:34:35 -0400
Commit message:

 appveyor.yml v6
 
Package: universalmotif
Commit: 8c6ab2fe5f9657bf559a821bcf02c66ff9b2d0f1
Author: bjmt <benjmtremblay@gmail.com>
Date: 2019-03-20 21:31:22 -0400
Commit message:

 appveyor.yml now install TFBSTools v6
 
Package: universalmotif
Commit: d60b72d0a6ee3e97ae46f4b2d9f9057e79398b14
Author: bjmt <benjmtremblay@gmail.com>
Date: 2019-03-20 21:30:42 -0400
Commit message:

 appveyor.yml now install TFBSTools v5
 
Package: universalmotif
Commit: 3fd223eea60315b7509b843aa5757870eae44777
Author: bjmt <benjmtremblay@gmail.com>
Date: 2019-03-20 21:25:37 -0400
Commit message:

 appveyor.yml now install TFBSTools v4
 
Package: universalmotif
Commit: 79d98dc3635717880078a4cc495219974532386e
Author: bjmt <benjmtremblay@gmail.com>
Date: 2019-03-20 21:24:42 -0400
Commit message:

 appveyor.yml now install TFBSTools v3
 
Package: universalmotif
Commit: 1be04bed05bf34ccd6f621c5e3d62c42ac890915
Author: bjmt <benjmtremblay@gmail.com>
Date: 2019-03-20 21:22:54 -0400
Commit message:

 appveyor.yml now install TFBSTools v2
 
Package: universalmotif
Commit: 09e8d199504cdf8c5bff034a9e61655e4c942386
Author: bjmt <benjmtremblay@gmail.com>
Date: 2019-03-20 21:21:22 -0400
Commit message:

 appveyor.yml now install TFBSTools
 
Package: singscore
Commit: cc0226b103e00a591102eb5104d35c2a8fee25c6
Author: bhuvad <bhuva.d@wehi.edu.au>
Date: 2019-03-21 12:34:37 +1100
Commit message:

 version bump and update github io page
 
Package: universalmotif
Commit: 1626ca8a35990ed02bb0c438f9b78c6be1ca336f
Author: bjmt <benjmtremblay@gmail.com>
Date: 2019-03-20 21:18:22 -0400
Commit message:

 cpp code changes, .travis.yml changes
 
Package: Rsubread
Commit: a42632d4dbda1bedda464b4d6a7afdc4fe28f8ec
Author: Yang Liao <dbpzdbpz@gmail.com>
Date: 2019-03-21 11:44:09 +1100
Commit message:

 Changed type of expression.levels from data.frame to vector
 
Package: S4Vectors
Commit: aea0f90b7dd96193f4b629313b9312e442962098
Author: Michael Lawrence <michafla@gene.com>
Date: 2019-03-20 17:00:42 -0700
Commit message:

 export replaceCOLS()
 
Package: S4Vectors
Commit: 05b878f3d47d0654208f111efc9695360b0ac318
Author: Michael Lawrence <michafla@gene.com>
Date: 2019-03-20 16:49:42 -0700
Commit message:

 refactor [<-,DataFrame; expect breakage

also no longer unifies element types in as(x, "SimpleList")
 
Package: BASiCS
Commit: a9c067fea63f07b0a0a02c18ffe4a2bbecab9c7f
Author: catavallejos <cata.vallejos.m@gmail.com>
Date: 2019-03-20 23:42:03 +0000
Commit message:

 Merge branch 'RELEASE_3_8'

version 1.5.6: (2019-03-20) - merge from RELEASE_3_8 branch
- Bug fix when not providing BatchInfo as factor
- Extra check if batch names contain spaces
- Added line breaks after individual error messages
- Bug fix that corrects for the number of factors in BatchInfo vector
- Small bug fix in 'test_mcmc_arguments.R'
 
Package: BASiCS
Commit: ed6a8d008d8d0644cce19c74030dd3dddc7a4b6c
Author: catavallejos <cata.vallejos.m@gmail.com>
Date: 2019-03-20 15:06:08 +0000
Commit message:

 version 1.4.6: (2019-03-20)
- Same as 1.4.5 but with minor additional fix.
 
Package: BASiCS
Commit: 2f9e6bb893770773199f3bb06fd56aa7125198ed
Author: catavallejos <cata.vallejos.m@gmail.com>
Date: 2019-03-20 15:04:58 +0000
Commit message:

 version 1.4.5: (2019-03-20)
- Small bug fix in 'test_mcmc_arguments.R'
 
Package: BASiCS
Commit: f5482df6f756795e3998faa0ca51063f2d1f96cb
Author: catavallejos <cata.vallejos.m@gmail.com>
Date: 2019-03-20 13:51:19 +0000
Commit message:

 updated RoxygenNote in DESCRIPTION
 
Package: BASiCS
Commit: 89dd095b108609271ac13cbfd82ee8015ba17055
Author: catavallejos <cata.vallejos.m@gmail.com>
Date: 2019-03-20 13:50:01 +0000
Commit message:

 Minor commit
 
Package: BASiCS
Commit: 5fb0aabb86df267abb68f659c818231305dad6e1
Author: Nils Eling <nils.eling@gmx.de>
Date: 2019-03-17 18:05:55 +0100
Commit message:

 version 1.4.4: (2019-03-17)
 
Package: BASiCS
Commit: 57539ea0bac07319161dc0561d6656230ffeebbd
Author: Nils Eling <nils.eling@gmx.de>
Date: 2019-03-15 10:43:10 +0100
Commit message:

 version 1.4.3 (2019-03-15)
 
Package: BASiCS
Commit: 63f84dd8cd9b4cc46ebbc584c7cd5925eaf1d451
Author: Nils Eling <nils.eling@gmx.de>
Date: 2019-03-15 10:03:07 +0100
Commit message:

 version 1.4.2: (2019-03-15)
 
Package: BASiCS
Commit: 772e23d8b515a36be1ff195d5601a82938444afb
Author: Kayla-Morrell <kayla.morrell@roswellpark.org>
Date: 2019-01-04 13:03:46 -0500
Commit message:

 Add ImmunoOncology biocViews term
 
Package: celaref
Commit: 68af72eb4c4ba4f6ca5e3508111cc01bb2189fe5
Author: Sarah Williams <sarah.williams1@monash.edu>
Date: 2019-03-21 10:40:07 +1100
Commit message:

 version bump
 
Package: TCGAutils
Commit: b7ad024245e600e6d964c33060590b3468281b6d
Author: LiNk-NY <mramos09@gmail.com>
Date: 2019-03-20 18:48:01 -0400
Commit message:

 bug fix: use BiocGenerics::relist
 
Package: TCGAutils
Commit: e1afc9f979fb9f1a4bbe7df5cb226bbd387723e4
Author: LiNk-NY <mramos09@gmail.com>
Date: 2019-03-20 17:56:21 -0400
Commit message:

 further enhancements
 
Package: TCGAutils
Commit: d36b062309689c6b38cdc4cd68e96490b6e54733
Author: LiNk-NY <mramos09@gmail.com>
Date: 2019-03-20 17:36:15 -0400
Commit message:

 re-use helper functions, expand functionality
 
Package: TCGAutils
Commit: 4ecfacf93def99bb9f976f578bdfcd7f66a2311e
Author: LiNk-NY <mramos09@gmail.com>
Date: 2019-03-20 13:44:31 -0400
Commit message:

 update docs
 
Package: TCGAutils
Commit: b7466853e062073d54e2d73aa82264a11d9f44cd
Author: LiNk-NY <mramos09@gmail.com>
Date: 2019-03-20 13:19:18 -0400
Commit message:

 splitAssays clean up and add exclusive argument
 
Package: MultiAssayExperiment
Commit: cdd5a4f425ecabcc562702f87dbe59b08147a0c7
Author: LiNk-NY <mramos09@gmail.com>
Date: 2019-03-20 10:30:31 -0400
Commit message:

 fix if condition > 1 in isEmpty
 
Package: mpra
Commit: 6073b78cb62fda14fba7e39dff3bbba17288bfcf
Author: Leslie Myint <leslie.myint@gmail.com>
Date: 2019-03-20 15:13:03 -0500
Commit message:

 Fix non-ASCII character
 
Package: variancePartition
Commit: 9b09895fb069479525e810f3be9027558b986f8d
Author: GabrielHoffman <gabrielhoffman@typhon.local>
Date: 2019-03-20 14:51:09 -0400
Commit message:

 v1.13.6
 
Package: rgsepd
Commit: 9b7051f61092427306c27241a1f1a21a7e36cd93
Author: Karl Stamm <karl.stamm@gmail.com>
Date: 2019-03-20 13:15:15 -0500
Commit message:

 version bump to prod bioc to see new CITATION file
 
Package: rgsepd
Commit: 95245c82e46ae8cfb7b4eb16d333edb306e697f4
Author: Karl Stamm <karl.stamm@gmail.com>
Date: 2019-03-20 13:01:14 -0500
Commit message:

 new file
 
Package: fgsea
Commit: 2305b384a106306791cb36d1bcb52cca5eda63b4
Author: Alexey Sergushichev <alsergbox@gmail.com>
Date: 2019-03-20 17:58:20 +0300
Commit message:

 version bump
 
Package: fgsea
Commit: e6272f73aa3747eeb36699af727b7aec526de6c8
Author: Vladimir Sukhov <vdsukhov@ya.ru>
Date: 2019-03-19 18:22:38 +0300
Commit message:

 Added a couple tests to increase coverage
 
Package: fgsea
Commit: acde494a70a55c44898612591345798fabbc9ea9
Author: Vladimir Sukhov <vdsukhov@ya.ru>
Date: 2019-03-19 17:39:48 +0300
Commit message:

 One test modified
 
Package: fgsea
Commit: 73ed9bc95e9352920b7869d198d25b237999b984
Author: Vladimir Sukhov <vdsukhov@ya.ru>
Date: 2019-03-19 17:08:10 +0300
Commit message:

 Added tests for fgseaMultilevel
 
Package: fgsea
Commit: cdd99aa9f9c3a21312a2158be2e39d5c3f04db01
Author: Vladimir Sukhov <vdsukhov@ya.ru>
Date: 2019-02-12 18:28:41 +0300
Commit message:

 Code refactoring
 
Package: GAPGOM
Commit: 83590a57265ce3cf9563c40fcfe0fdde87c222e8
Author: Berghopper <Casper98@protonmail.com>
Date: 2019-03-20 16:43:50 +0100
Commit message:

 Finished fixing code for checks, subrelease ready
 
Package: GAPGOM
Commit: 161a32c04357d965a51e891b074b2ba4fb765ccc
Author: Berghopper <Casper98@protonmail.com>
Date: 2019-03-20 15:12:16 +0100
Commit message:

 Almost finished touching up, running checks and fixing tests...
 
Package: GAPGOM
Commit: 22759a97a8d47c95a0775c95b1aacc8f0516e916
Author: Berghopper <Casper98@protonmail.com>
Date: 2019-03-19 23:34:39 +0100
Commit message:

 Edited some logic, touched up algorithms a bit more, added documentation...
 
Package: GAPGOM
Commit: d8b4e07010339384aff94d2dbe139cf9b1b9ef39
Author: Berghopper <Casper98@protonmail.com>
Date: 2019-03-19 14:10:49 +0100
Commit message:

 Added Rezvans new improvement and reformatted slightly
 
Package: karyoploteR
Commit: 753ff3c8943324628903c261f4e587bc8205b6c2
Author: Bernat Gel <bernatgel@gmail.com>
Date: 2019-03-20 16:22:15 +0100
Commit message:

 Updated doc

 
Package: karyoploteR
Commit: 04af6db2ed02a2805735900449f985973437d905
Author: Bernat Gel <bernatgel@gmail.com>
Date: 2019-03-20 16:15:56 +0100
Commit message:

 Fixed bug in kpAddCytobandsAsLine with plot.type!=1

 
Package: karyoploteR
Commit: b8f5ee723b426e5744d64471e99088899cdcb2e1
Author: Bernat Gel <bernatgel@gmail.com>
Date: 2019-03-20 08:31:19 +0100
Commit message:

 Merge remote-tracking branch 'github/master'

 
Package: karyoploteR
Commit: 0e3db2c954eb101ba1e739f7a219d442e63894d3
Author: Bernat Gel <bernatgel@gmail.com>
Date: 2019-03-01 00:29:16 +0100
Commit message:

 documentes a coupld of points

 
Package: karyoploteR
Commit: 093e3d0916db6241918a781110dc73700933ad33
Author: Bernat Gel <bernatgel@gmail.com>
Date: 2019-02-25 16:04:20 +0100
Commit message:

 Version bump

 
Package: karyoploteR
Commit: 753b058f193c0b7a2c50ee7a67a95ca921e1cc46
Author: Bernat Gel <bernatgel@gmail.com>
Date: 2019-02-25 16:02:45 +0100
Commit message:

 Merge branch 'RevampGenes' 
Package: karyoploteR
Commit: 7eb060a42a38115f0cf555c3157ad06c53bb816a
Author: Bernat Gel <bernatgel@gmail.com>
Date: 2019-02-25 15:57:35 +0100
Commit message:

 Improved gene label positioning in kpPlotGenes.

And added and fixed a number of related functions and examples 
Package: karyoploteR
Commit: 4c8ef565e68c4031acfb43bdc2799852e04ac414
Author: Bernat Gel <bernatgel@gmail.com>
Date: 2019-02-25 14:49:12 +0100
Commit message:

 Added improved gene name selection

 
Package: karyoploteR
Commit: e89fa3a6ecd18292eae44ca629d91c9a690a8804
Author: Bernat Gel <bernatgel@gmail.com>
Date: 2019-02-25 14:41:19 +0100
Commit message:

 Added getTextSize utility function. Created text.R file

 
Package: karyoploteR
Commit: f4fbdbd1df3ff3c1ef02b0ea895e5718b69cf756
Author: Bernat Gel <bernatgel@gmail.com>
Date: 2019-02-25 11:25:51 +0100
Commit message:

 Added mergeTranscripts function

 
Package: karyoploteR
Commit: 0d093130ea6b679fc60098e9cf4172454decf9df
Author: Bernat Gel <bernatgel@gmail.com>
Date: 2019-02-22 14:06:57 +0100
Commit message:

 Version bump

 
Package: karyoploteR
Commit: 1cf812d6c794253912811b258c56a53c766004e5
Author: Bernat Gel <bernatgel@gmail.com>
Date: 2019-02-22 14:06:10 +0100
Commit message:

 Created a package wide structure to hold color schemas and color info

Created a package wide structure to hold color schemas and color info and adapted getCytobandColors and getVariantsColors. Adapted the two functions to use the colors from the package-wide structure 
Package: karyoploteR
Commit: 827733e5868805d65c2470e7e4dff01c35859a15
Author: Bernat Gel <bernatgel@gmail.com>
Date: 2019-02-22 12:43:23 +0100
Commit message:

 Fixed a few problems with the new genes functions

 
Package: karyoploteR
Commit: 921abb4b40d530ac66cc0d0a312f320d0b8bbfe3
Author: Bernat Gel <bernatgel@gmail.com>
Date: 2019-02-22 00:33:53 +0100
Commit message:

 Added addGeneNames to add the symbols to the GenesData object

 
Package: karyoploteR
Commit: 9ececd524a76a3e3a500e515d2b80f252cf92801
Author: Bernat Gel <bernatgel@gmail.com>
Date: 2019-02-21 23:31:31 +0100
Commit message:

 Added the class "GenesData" to the object returned by the creator

 
Package: karyoploteR
Commit: cbe7f1a8dc0f2725a7395484ace34791e15c91a2
Author: Bernat Gel <bernatgel@gmail.com>
Date: 2019-02-21 23:30:24 +0100
Commit message:

 Added metadata to GenesData object when created from TxDb

 
Package: karyoploteR
Commit: 17281a1c3e531595e8b59a01093491108931a205
Author: Bernat Gel <bernatgel@gmail.com>
Date: 2019-02-21 23:15:02 +0100
Commit message:

 Move functions dealing with GenesData to genes.R

 
Package: karyoploteR
Commit: efe1cdb89961e9e068440351df6ed497d63f5ced
Author: Bernat Gel <bernatgel@gmail.com>
Date: 2019-02-21 23:09:09 +0100
Commit message:

 Added a couple of TODOs

 
Package: karyoploteR
Commit: 27ca38cf7b9bb7c519fb2c77cd23fe9e741b5763
Author: Bernat Gel <bernatgel@gmail.com>
Date: 2019-02-21 22:54:27 +0100
Commit message:

 Set add.transcripts.names to FALSE by default

 
Package: karyoploteR
Commit: ae903f54b1bb0f2ceee98be4c3b7728510bdcd26
Author: Bernat Gel <bernatgel@gmail.com>
Date: 2019-01-31 09:19:46 +0100
Commit message:

 Added a section to README.md with examples

 
Package: karyoploteR
Commit: c3feaed97b6a87ba5b90e79a4bcc630cff5c178c
Author: Bernat Gel <bernatgel@gmail.com>
Date: 2019-01-30 08:24:11 +0100
Commit message:

 Version bump

 
Package: karyoploteR
Commit: bcf2f97c781376d0e90713b6ba565d48322488c2
Author: Bernat Gel <bernatgel@gmail.com>
Date: 2019-01-30 08:24:00 +0100
Commit message:

 Changed cut.last.tile.in.chrom to TRUE in kpPlotDensity

To ensure all windows (except the last in the chromosome) have the same length. In response to https://github.com/bernatgel/karyoploteR/issues/30 
Package: karyoploteR
Commit: 5d7a146d0aea5883b75091c76b62fd443446fbb6
Author: Bernat Gel <bernatgel@gmail.com>
Date: 2019-01-23 09:52:35 +0100
Commit message:

 Version bump

 
Package: karyoploteR
Commit: efe7b66174559ac51f3229b068da2e6c8fb607bf
Author: Bernat Gel <bernatgel@gmail.com>
Date: 2019-01-23 09:52:24 +0100
Commit message:

 Added colByRegion function

 
Package: BaalChIP
Commit: 7cebb7bceb90edf5be7403bf6f983cf926eb7ef0
Author: Ines de Santiago <inesdesantiago@gmail.com>
Date: 2019-03-20 14:54:49 +0000
Commit message:

 fixed pileup function was updated and gives slightly different results that were maing uniTests fail
 
Package: BaalChIP
Commit: 3a65105de06633490ea6a6e79518e5eba377e2be
Author: Ines de Santiago <inesdesantiago@gmail.com>
Date: 2019-03-20 14:50:36 +0000
Commit message:

 changes in readme
 
Package: BaalChIP
Commit: 3a2ec53bb58b71614c377e16f07673ed1373e55e
Author: Ines de Santiago <inesdesantiago@gmail.com>
Date: 2019-03-20 14:49:50 +0000
Commit message:

 changes in readme
 
Package: BaalChIP
Commit: e2134bd52f0b7c3d4d56e07371fa987fa48811d0
Author: Ines de Santiago <inesdesantiago@gmail.com>
Date: 2018-05-29 08:56:42 +0100
Commit message:

 python code
 
Package: BaalChIP
Commit: 903c5dfe8245459653d33c211a40dfc0d360f1ae
Author: Ines de Santiago <inesdesantiago@gmail.com>
Date: 2018-05-29 08:56:08 +0100
Commit message:

 first commit
 
Package: TCGAutils
Commit: 45c8cacccc14200721695fe4ab25cc4e398d29b2
Author: LiNk-NY <mramos09@gmail.com>
Date: 2019-03-19 18:34:58 -0400
Commit message:

 add trimColData function, update examples, include pkgs in Suggests
 
Package: MultiAssayExperiment
Commit: 105d4e9a0660f2055cccb819b3c4e122808c48c0
Author: LiNk-NY <mramos09@gmail.com>
Date: 2019-03-19 15:16:59 -0400
Commit message:

 bug fix: include object that inherit from List
 
Package: MultiAssayExperiment
Commit: 66f3a7f6a75ebfd9eaa1b9bd0d376e883dc9b36d
Author: LiNk-NY <mramos09@gmail.com>
Date: 2019-03-18 19:04:01 -0400
Commit message:

 bug fix: c method when named list provided
 
Package: MultiAssayExperiment
Commit: 9a6717152ea18c6c5547435c1f6051a11a762fb3
Author: LiNk-NY <mramos09@gmail.com>
Date: 2019-02-14 13:20:31 -0500
Commit message:

 update travis.yml
 
Package: MultiAssayExperiment
Commit: de2295afb2b66dce78d419f084c6a5e1c3dc67ce
Author: LiNk-NY <mramos09@gmail.com>
Date: 2019-02-12 17:29:25 -0500
Commit message:

 remove _pkgdown.yml from devel ver.
 
Package: TCGAbiolinks
Commit: b99acace01817512d73fea983739a21f8eab0fba
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2019-03-20 11:09:58 -0300
Commit message:

 version bump
 
Package: TCGAbiolinks
Commit: 9cc27d9d86e9241838b1ef22e57ada516fa6306b
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2019-03-20 11:08:18 -0300
Commit message:

 Preparing multiple GISTIC files #304
 
Package: TCGAbiolinks
Commit: 965e9b171511d5402e1d0efbc192b82b6dbfd0db
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2019-03-20 10:56:15 -0300
Commit message:

 Changing from patinet ID to  sample ID #304
 
Package: FamAgg
Commit: c641feb049f58c0fa3983c5f2a1ef631a55ae46c
Author: jotsetung <johannes.rainer@gmail.com>
Date: 2019-03-20 13:47:27 +0100
Commit message:

 Fix buildPed and pedigree<-

- Fix bugs in buildPed and pedigree<- for some special cases.
 
Package: FamAgg
Commit: 4d1bcec2013ace0f137a06f025fd1f850373626e
Author: Johannes Rainer <jotsetung@users.noreply.github.com>
Date: 2019-03-19 11:25:51 +0100
Commit message:

 Merge pull request #17 from EuracBiomedicalResearch/haplopainter_bug

Haplopainter bug 
Package: FamAgg
Commit: d68d882d299d4c2d758916634deb66fdb9a7bf64
Author: Chris X. Weichenberger <christian.weichenberger@eurac.edu>
Date: 2019-03-19 10:32:53 +0100
Commit message:

 Merge branch 'master' into haplopainter_bug
 
Package: FamAgg
Commit: be038423852c627fae9ca905b943570264f4db0f
Author: Chris X. Weichenberger <christian.weichenberger@eurac.edu>
Date: 2019-03-05 17:26:31 +0100
Commit message:

 Fix haplopainter pedigree file generation problem.

In very rare cases it may happen that during a pruning step a father or
mother ID is deleted (set to NA), whereas the other remains non-NA,
causing any plotting method to report an error. Fixed by this commit.
 
Package: FamAgg
Commit: 9ab4e855956d5e33ecd2a364884cbabda6788808
Author: Chris X. Weichenberger <christian.weichenberger@eurac.edu>
Date: 2019-03-05 17:23:56 +0100
Commit message:

 Re-introduce "-family" parameter for haplopainter.

This option has been removed during a refactoring process (issue #16).
However, it's a mandatory parameter in the haplopainter command line, causing
an error message when calling the haplopainter Perl script.
 
Package: microbiome
Commit: c49b6f42102cfc5274b8668fe5f91bc468f5cc07
Author: Leo Lahti <leo.lahti@iki.fi>
Date: 2019-03-19 15:52:03 +0200
Commit message:

 Merge pull request #109 from aa-m-sa/master

pseudocount added after compositionality in CLR 
Package: microbiome
Commit: 45eedd4f05d55fe2959c3c25e0fb7acca6ccfa70
Author: Aaro Salosensaari <aaro.salosensaari@iki.fi>
Date: 2019-03-19 15:21:38 +0200
Commit message:

 pseudocount added after compositionality in CLR

when making a CLR tranformation, transform to compositional before
adding the small v/2 pseudocount to ensure that the prior induced by the
pseudocount is constant across varying library sizes.
 
Package: microbiome
Commit: c76553c71ed81752f163a28ab33b94cfa5bdaaf0
Author: antagomir <leo.lahti@iki.fi>
Date: 2019-02-13 09:57:01 +0200
Commit message:

 man
 
Package: microbiome
Commit: 78a1818bb81e18a1cf00a18aecd6351114073857
Author: antagomir <leo.lahti@iki.fi>
Date: 2019-02-13 09:18:28 +0200
Commit message:

 ok
 
Package: microbiome
Commit: 51e0c70ec7bce2a452638135a03b4fc45c0ee6b6
Author: antagomir <leo.lahti@iki.fi>
Date: 2019-02-13 00:31:34 +0200
Commit message:

 update
 
Package: microbiome
Commit: 48abbdad952847000c411d8369440630bec41386
Author: antagomir <leo.lahti@iki.fi>
Date: 2019-02-13 00:23:40 +0200
Commit message:

 sync
 
Package: microbiome
Commit: db93d7a2dda19314c25956730051e0f5b79b68e7
Author: Leo <leo.lahti@iki.fi>
Date: 2019-01-25 11:16:08 +0200
Commit message:

 CITATION info updated
 
Package: microbiome
Commit: 8c682e958a4b75d79e819e3a483f0fb8080d46b9
Author: antagomir <leo.lahti@iki.fi>
Date: 2018-11-30 22:34:20 +0200
Commit message:

 ok
 
Package: deco
Commit: 32b99d0c1ea690e722f5de9887fcb4ba71be86f6
Author: fjcamlab <fjcamlab@gmail.com>
Date: 2019-03-20 12:19:59 +0000
Commit message:

 deco
 
Package: deco
Commit: 74a61a11fa2126d355345dacae8d1915ae9594d3
Author: Francisco J Campos-Laborie <39339795+fjcamlab@users.noreply.github.com>
Date: 2019-03-18 14:51:28 +0000
Commit message:

 Update README.md 
Package: deco
Commit: e7c0910fcdedbdf98b9dbc18ef622d690a4cbbe1
Author: Francisco J Campos-Laborie <39339795+fjcamlab@users.noreply.github.com>
Date: 2019-03-18 14:50:40 +0000
Commit message:

 Update README.md 
Package: deco
Commit: aa94d5578c504e0900ae54976ca284491fcfe441
Author: Francisco J Campos-Laborie <39339795+fjcamlab@users.noreply.github.com>
Date: 2019-03-18 14:50:03 +0000
Commit message:

 Update README.md 
Package: deco
Commit: 62754c03f0f2dfbacdc71be12b5c3fc7689b663d
Author: Francisco J Campos-Laborie <39339795+fjcamlab@users.noreply.github.com>
Date: 2019-03-18 14:49:06 +0000
Commit message:

 Update README.md 
Package: QuasR
Commit: 8d300b4f5c644fa0446214441476464623c5039d
Author: mbstadler <stadler.michael@gmail.com>
Date: 2019-03-20 11:26:38 +0100
Commit message:

 v1.23.17 qQCReport updates
 
Package: QuasR
Commit: 7e1e6785ad9b2497df2d37222d9aef64c1e6e4fc
Author: Michael Stadler <stadler.michael@gmail.com>
Date: 2019-03-20 11:22:21 +0100
Commit message:

 Merge pull request #13 from fmicompbio/fixpar

Fixpar 
Package: QuasR
Commit: d0751c7f3b004e880445132422cce0c41a04d6ae
Author: Charlotte Soneson <charlottesoneson@gmail.com>
Date: 2019-03-19 18:15:38 +0100
Commit message:

 Fix usage section qQCReport
 
Package: QuasR
Commit: 14666fea5c2d15e98c9737008677880d5711fdee
Author: Charlotte Soneson <charlottesoneson@gmail.com>
Date: 2019-03-19 18:11:27 +0100
Commit message:

 Fix usage section qQCReport
 
Package: QuasR
Commit: cdd10d53ccf0b2802b304ec18bb1a5082645d999
Author: Charlotte Soneson <charlottesoneson@gmail.com>
Date: 2019-03-19 17:25:46 +0100
Commit message:

 Fix qQCReport docs
 
Package: QuasR
Commit: f37e98e8cf5c0daf501e9cce1c9da7293087ec65
Author: Charlotte Soneson <charlottesoneson@gmail.com>
Date: 2019-03-19 17:23:25 +0100
Commit message:

 Merge branch 'master' into fixpar
 
Package: QuasR
Commit: 7eb385b5ccae55aa1561c08f12ccbfa759c68943
Author: Charlotte Soneson <charlottesoneson@gmail.com>
Date: 2019-03-19 17:22:46 +0100
Commit message:

 Merge pull request #11 from hrhotz/patch-1

Update qQCReport.Rd 
Package: QuasR
Commit: 790605b9b26baaa822cb369211aee98245fb5b1b
Author: Michael Stadler <stadler.michael@gmail.com>
Date: 2019-03-19 15:57:23 +0100
Commit message:

 inactivate appveyor cache (fails updating package glue) 
Package: QuasR
Commit: a91e71de6a89adea57986de85772d8ea7155df72
Author: Michael Stadler <stadler.michael@gmail.com>
Date: 2019-03-19 15:18:12 +0100
Commit message:

 re-enable appveyor cache 
Package: QuasR
Commit: 6c11911fb746336a557851b048b44ad92a9fb469
Author: Hans-Rudolf Hotz <hrhotz@users.noreply.github.com>
Date: 2019-03-19 15:07:17 +0100
Commit message:

 Update qQCReport.Rd 
Package: QuasR
Commit: 54150e6a926cf18287b9141fc17f475aaa1004c6
Author: Michael Stadler <stadler.michael@gmail.com>
Date: 2019-03-19 15:01:18 +0100
Commit message:

 delete appveyor cache 
Package: QuasR
Commit: cf5eab9f6d7a94788a06fc99d057489b49264423
Author: Charlotte Soneson <charlottesoneson@gmail.com>
Date: 2019-03-19 14:58:03 +0100
Commit message:

 Merge branch 'master' into fixpar
 
Package: QuasR
Commit: c099e87785c6417541ae429f6ed36961508cd076
Author: Charlotte Soneson <charlottesoneson@gmail.com>
Date: 2019-03-19 14:57:40 +0100
Commit message:

 Fix subplot sizes for mapping/uniqueness plots to work with a single sample
 
Package: QuasR
Commit: e7b5d3b240ab75df357b82d7b6a44c439049f97d
Author: Hans-Rudolf Hotz <hrhotz@users.noreply.github.com>
Date: 2019-03-19 14:47:23 +0100
Commit message:

 Update qQCReport.Rd 
Package: QuasR
Commit: f49252ba891754032aafdc255d243edc9a87c380
Author: Hans-Rudolf Hotz <hrhotz@users.noreply.github.com>
Date: 2019-03-06 11:07:54 +0100
Commit message:

 Update qQCReport.Rd

This is a quick fix following the question on the BioC mailing list (https://support.bioconductor.org/p/118580/). It is still not correct, e.g. what happens when you generate a qProject with bam files which do not contain the quality.....

Hence, it is rather work in progress and should not be merged yet, but might trigger a discussion. 
Package: Rsubread
Commit: 03b20e8b86670de8a6633097af3ce5013dd54d47
Author: Gordon Smyth <smyth@wehi.edu.au>
Date: 2019-03-20 19:23:54 +1100
Commit message:

 .simFragments now passed n.fragments to simReads.
 
Package: Rsubread
Commit: 170d285c1ac5dbe90e25bf0a98cfe28925537379
Author: Gordon Smyth <smyth@wehi.edu.au>
Date: 2019-03-20 19:03:33 +1100
Commit message:

 Allow the df of expression.values to have fewer rows than the transcript file.
 
Package: Rsubread
Commit: d54e7a24b31420281327241dcf2ccac37e3a3483
Author: Gordon Smyth <smyth@wehi.edu.au>
Date: 2019-03-20 18:42:04 +1100
Commit message:

 Edits to simReads.Rd
 
Package: CATALYST
Commit: 84ae05d761af79692569a9cb99c49d57fa0f55f2
Author: HelenaLC <helena@crowells.eu>
Date: 2019-03-20 08:21:42 +0100
Commit message:

 fix documentation link to S4Vectors::DataFrame
 
Package: CATALYST
Commit: 7ae0422b04e07d095a96b7e8d28d27ad59eda3a4
Author: HelenaLC <helena@crowells.eu>
Date: 2019-03-19 14:21:29 +0100
Commit message:

 bug fix in plotSpillmat with custom_isotope_list
 
Package: Rsubread
Commit: 53ef5160207b21be7a35aa25a894821ac070745f
Author: Gordon Smyth <smyth@wehi.edu.au>
Date: 2019-03-20 17:55:44 +1100
Commit message:

 - Update simReads.Rd to match code.
- Make simFragments and fix_simReads non-exported functions.
 
Package: Rsubread
Commit: 59f0d739bd863088f8852d3cd77ece553a5080f7
Author: Gordon Smyth <smyth@wehi.edu.au>
Date: 2019-03-20 17:35:34 +1100
Commit message:

 Remove deprecated arg 'low.transcripts'
 
Package: Rsubread
Commit: 35bfff6c45f04a3d6b5d3f5808725d3588340a25
Author: Gordon Smyth <smyth@wehi.edu.au>
Date: 2019-03-20 17:26:05 +1100
Commit message:

 - library.size instead of out.sample.size.
- make defaults for fragment size distn in simReads agree with simFragments.
 
Package: Rsubread
Commit: 2b1c3fa8f2fb770ade130974acbc0dd7a3ee160c
Author: Gordon Smyth <smyth@wehi.edu.au>
Date: 2019-03-20 16:45:04 +1100
Commit message:

 Remove deprecated arguments from simReads
 
Package: Rsubread
Commit: 09b3778167579b7e36ae3edb869d4e64ce8937e5
Author: Gordon Smyth <smyth@wehi.edu.au>
Date: 2019-03-20 16:36:10 +1100
Commit message:

 Fix spelling of "Occurrence"
 
Package: singscore
Commit: 392ef98f02a33e015d52aa0358f22ab6da3ec18d
Author: bhuvad <bhuva.d@wehi.edu.au>
Date: 2019-03-20 15:47:14 +1100
Commit message:

 changed maintainer. changed order of authors
 
Package: singscore
Commit: 627e6c4b930a74b48dfb7a76dc8cc8c23c04c352
Author: bhuvad <bhuva.d@wehi.edu.au>
Date: 2019-03-20 15:29:23 +1100
Commit message:

 updated news, version bump for changes
 
Package: singscore
Commit: ac6c45eff223a1ada0dfcc536d8fdfbdf0752d1e
Author: bhuvad <bhuva.d@wehi.edu.au>
Date: 2019-03-20 15:11:18 +1100
Commit message:

 merged with changes on bioconductor
 
Package: singscore
Commit: e3988f91f7f40acc74208ba736e309c6f9c06156
Author: bhuvad <bhuva.d@wehi.edu.au>
Date: 2019-03-20 14:54:29 +1100
Commit message:

 Correct version for sync with bioconductor
 
Package: singscore
Commit: 8e1b554fb367ffba60fdc1b178e9af7f4ea9ac08
Author: bhuvad <bhuva.d@wehi.edu.au>
Date: 2019-03-13 13:30:42 +1100
Commit message:

 updated github readme page. updated package site. updated style for the vignette (BiocStyle)
 
Package: singscore
Commit: d1bbb111b6b1cd0c62c932010bd9b6addb544495
Author: Dharmesh Bhuva <bhuva.d@wehi.edu.au>
Date: 2019-03-13 12:56:44 +1100
Commit message:

 Merge pull request #13 from DavisLaboratory/issue_7

Issue 7 
Package: singscore
Commit: 920188ffc41b2acae2099cd5092752d7f39c2e7f
Author: bhuvad <bhuva.d@wehi.edu.au>
Date: 2019-03-13 12:55:55 +1100
Commit message:

 Addressed comments from BiocCheck and R CMD Check
 
Package: singscore
Commit: c608b74def8d775305e66ed6a7353870750d5e28
Author: bhuvad <bhuva.d@wehi.edu.au>
Date: 2019-03-13 12:38:34 +1100
Commit message:

 singscore now supports scoring of multiple signatures. Code restructured to achieve this and reduce code redundancy. Changed signature of simple score from ANY to matrix for rankData param.
 
Package: singscore
Commit: ca3de5cf79123472b4ed946e1918750020a19f5c
Author: bhuvad <bhuva.d@wehi.edu.au>
Date: 2019-03-08 12:10:53 +1100
Commit message:

 changed order of plots in plotDispersion to Total,Up,Down
 
Package: singscore
Commit: 7c7857dbdc1e0671c4a00dd3b02abb52573526b5
Author: bhuvad <bhuva.d@wehi.edu.au>
Date: 2019-03-08 11:11:18 +1100
Commit message:

 fixed issue with checking annotations that was throwing warnings for character annotations
 
Package: singscore
Commit: 4d6856a62296b09a67dbf559665a5477633d0c72
Author: bhuvad <bhuva.d@wehi.edu.au>
Date: 2019-03-08 11:02:35 +1100
Commit message:

 free scales in the plotDispersion facet
 
Package: singscore
Commit: 9a8725f54980dedfbec2ba93ae066492e5129557
Author: bhuvad <bhuva.d@wehi.edu.au>
Date: 2019-03-08 10:48:42 +1100
Commit message:

 updated the NEWS file
 
Package: singscore
Commit: 876a255384ea50bccd061eff408aebb09d3dd6e7
Author: bhuvad <bhuva.d@wehi.edu.au>
Date: 2019-03-08 10:44:32 +1100
Commit message:

 TotalDispersion is the mean of independent dispersions, not the sum. Since dispersion is the median absolute deviation, we use mean, which is close enough to the median for all genes. It is not the best estimate but a good enough approximation
 
Package: singscore
Commit: 8badfbf098fd7f9c61dd5cff0df5db9bd3c5e6cd
Author: bhuvad <bhuva.d@wehi.edu.au>
Date: 2019-03-07 19:19:23 +1100
Commit message:

 plot title size increased
 
Package: singscore
Commit: 36190680a116072f4f3069b6da01483fde74e154
Author: bhuvad <bhuva.d@wehi.edu.au>
Date: 2019-02-28 19:27:48 +1100
Commit message:

 multiSingscore implemented and works. Need to build generics for it
 
Package: singscore
Commit: 022d6dd41f189b0a44a86c72455ec9c9bd38d14d
Author: bhuvad <bhuva.d@wehi.edu.au>
Date: 2019-02-28 15:54:30 +1100
Commit message:

 remove old code
 
Package: singscore
Commit: 476e74b96d9d1a30ec8308c4bd7be7c90ac69cce
Author: bhuvad <bhuva.d@wehi.edu.au>
Date: 2019-02-28 15:43:31 +1100
Commit message:

 correct bugs in tests that used internal functions. Replaced old implementation completely with the new one
 
Package: singscore
Commit: 761c440762286c0832d387a0d307ac5b3f2c00e8
Author: bhuvad <bhuva.d@wehi.edu.au>
Date: 2019-02-28 15:25:37 +1100
Commit message:

 new structure for scoring functions implemented. Modular structure will ease integration of scoring function that scores multiple signatures
 
Package: singscore
Commit: e4871dd4e78954bdfc0e0a05d4308541b9fce6fd
Author: bhuvad <bhuva.d@wehi.edu.au>
Date: 2019-02-28 10:46:22 +1100
Commit message:

 removed gene checks and warnings from plotRankDensity
 
Package: singscore
Commit: 0159cf976bc6995e3fa7ae9dd20719b590d31d81
Author: bhuvad <bhuva.d@wehi.edu.au>
Date: 2019-02-28 10:19:58 +1100
Commit message:

 Merge branch 'master' of github.com:DavisLaboratory/singscore

Changed colours of the plotRankDensity to be colour-blind friendly
 
Package: singscore
Commit: 663b5a4b8c9203aaedd964830349d70310408768
Author: bhuvad <bhuva.d@wehi.edu.au>
Date: 2019-02-28 10:19:27 +1100
Commit message:

 changed colour palette of plotRankDensity to a colour-blind friendlt palette
 
Package: singscore
Commit: 1b5a79cf95228312150c64a82d22a358e3209356
Author: Dharmesh Bhuva <bhuva.d@wehi.edu.au>
Date: 2019-02-27 23:36:42 +1100
Commit message:

 Merge pull request #12 from DavisLaboratory/issue_9

automatically select the number of bins as sqrt(num_obs) 
Package: singscore
Commit: 00d9678c69b1a476b09a52c59052499d4d6ac719
Author: bhuvad <bhuva.d@wehi.edu.au>
Date: 2019-02-27 23:35:20 +1100
Commit message:

 automatically select the number of bins as sqrt(num_obs)
 
Package: singscore
Commit: b091915c09b74465309a1411db326126a83baa98
Author: Dharmesh Bhuva <bhuva.d@wehi.edu.au>
Date: 2019-02-27 23:28:03 +1100
Commit message:

 Merge pull request #11 from DavisLaboratory/issue_10

Issue 10 
Package: singscore
Commit: cd067a27fe014de92ab2aca2670fca363769abc6
Author: bhuvad <bhuva.d@wehi.edu.au>
Date: 2019-02-27 23:26:00 +1100
Commit message:

 version bump
 
Package: singscore
Commit: dfef900d8e57f43d7659d652eabc247c5395beeb
Author: bhuvad <bhuva.d@wehi.edu.au>
Date: 2019-02-27 23:21:58 +1100
Commit message:

 updated citation and re-built site
 
Package: singscore
Commit: fdee798e6a46474ab1762a0bfd0f1918e3d16814
Author: bhuvad <bhuva.d@wehi.edu.au>
Date: 2019-02-27 22:41:14 +1100
Commit message:

 projectScoreLandscape now allows the enhaced range of annotations for interactive plots too.
 
Package: singscore
Commit: 261ad68e9653170acef64af0ae60059624ef2b13
Author: bhuvad <bhuva.d@wehi.edu.au>
Date: 2019-02-27 21:27:00 +1100
Commit message:

 numeric, factor and column of data.frames can now be used as annotations for static plots. Plot style updated. Need to extend functionality to interactive plots.
 
Package: singscore
Commit: c5618921535b7d7af0264e1c28bd5907f544406d
Author: Dharmesh Bhuva <bhuva.d@wehi.edu.au>
Date: 2019-02-27 17:03:08 +1100
Commit message:

 updated style for plotScoreLandscape
 
Package: singscore
Commit: 160b93cafd0280aaf5b0da4fa6ba60befe8c074b
Author: Dharmesh Bhuva <bhuva.d@wehi.edu.au>
Date: 2019-02-27 16:45:01 +1100
Commit message:

 plotDispersion can now deal with different forms of annotations incl. factors, numerics and columns appended to the score data.frame
 
Package: singscore
Commit: 675c0fdaf14cb7d2499245b20a0a10fcc855ec7d
Author: bhuvad <bhuva.d@wehi.edu.au>
Date: 2018-10-15 10:00:45 +1100
Commit message:

 changed location of the logo
 
Package: singscore
Commit: c8141b1913d42f0f6a7990c4329af38143f861a9
Author: bhuvad <bhuva.d@wehi.edu.au>
Date: 2018-10-09 21:18:35 +1100
Commit message:

 update website
 
Package: singscore
Commit: 5071ac0b250e73a701aa211c810173e86cde54fb
Author: bhuvad <bhuva.d@wehi.edu.au>
Date: 2018-10-09 21:16:47 +1100
Commit message:

 bump up version
 
Package: singscore
Commit: 811ea44763cab197d45fec05b20ae8405c5e895b
Author: bhuvad <bhuva.d@wehi.edu.au>
Date: 2018-10-09 21:14:08 +1100
Commit message:

 modify NEWS.md to comply with website format
 
Package: singscore
Commit: a0326810ddf2c144b5f09d9ba9f162bb02126bab
Author: bhuvad <bhuva.d@wehi.edu.au>
Date: 2018-10-09 21:01:22 +1100
Commit message:

 create a website for the package
 
Package: singscore
Commit: b564ca76e6b0fa8efd04e05fbb29a28e8dadb599
Author: bhuvad <bhuva.d@wehi.edu.au>
Date: 2018-10-09 20:25:08 +1100
Commit message:

 added a git ignore
 
Package: celaref
Commit: 98b001a86319a24b6bce78b05bbdab7efe0639fc
Author: Sarah Williams <sarah.williams1@monash.edu>
Date: 2019-03-20 11:20:41 +1100
Commit message:

 merged github and bioconductor versionsx
 
Package: celaref
Commit: 6ba3cbaf3e3e4689fe29f72f025857d7872cd006
Author: Sarah Williams <sarah.williams@biointeractive.novalocal>
Date: 2019-03-19 16:34:47 +1100
Commit message:

 fix unit test filename
 
Package: celaref
Commit: e07bcd82ba6732df9e897e4820d63148cb6231a6
Author: Sarah Williams <sarah.williams1@monash.edu>
Date: 2019-03-18 16:01:01 +1100
Commit message:

 Actual fix for singleCellAssay coercion/as bug? A few unit tests
 
Package: celaref
Commit: 5a4eb8fc39ee525437c9cafa8582dc91b7541ec3
Author: Sarah Williams <sarah.williams1@monash.edu>
Date: 2019-02-05 17:33:15 +1100
Commit message:

 loading helper function tests
 
Package: celaref
Commit: 035e32deabe93d787e360bbadf3868683238cbbb
Author: Sarah Williams <sarah.williams1@monash.edu>
Date: 2019-01-16 11:08:55 +1100
Commit message:

 fix - import 'as' coercion method from MAST internally (no need for library(MAST) in sparse matrix branch)
 
Package: celaref
Commit: 76eb16f5b7c3ebd9c40d9355f4e6271ac875c741
Author: Sarah Williams <sarah.williams1@monash.edu>
Date: 2018-12-17 14:18:00 +1100
Commit message:

 don't coerce to dense matrix when calcing pofgenes
 
Package: celaref
Commit: 6dbe5808f4c4129e1b7c11632126859a04597696
Author: Sarah Williams <sarah.williams1@monash.edu>
Date: 2018-12-12 14:32:45 +1100
Commit message:

 sparse matrix support
 
Package: celaref
Commit: 728d8064c9df2e1f8ee698e2ae5dc59982b14c91
Author: Sarah Williams <sarah.williams1@monash.edu>
Date: 2018-12-09 20:36:41 +1100
Commit message:

 tidied rankmetrics options
 
Package: celaref
Commit: 62c1a8a56ede6a1bf28b18cb5e54d89766338b07
Author: Sarah Williams <sarah.williams1@monash.edu>
Date: 2018-11-26 17:03:21 +1100
Commit message:

 make_ref_similarity_names now also accepts rankmetrics
 
Package: celaref
Commit: 04df819f0d8cae77546b01341eccc6d0ae00d591
Author: Sarah Williams <sarah.williams1@monash.edu>
Date: 2018-11-26 15:54:26 +1100
Commit message:

 Added new rankmetrics for evalation, and n parameter.
 
Package: celaref
Commit: da65fb01cb488fd1d3e82c37582e375b360df434
Author: Sarah Williams <sarah.williams1@monash.edu>
Date: 2018-11-25 14:27:46 +1100
Commit message:

 convert coldata/rowdata to data.frame
 
Package: Rsubread
Commit: a8a67eac20a16995254783510735eec68895cc37
Author: Gordon Smyth <smyth@wehi.edu.au>
Date: 2019-03-20 11:13:21 +1100
Commit message:

 Add dgamma and rmultinom to NAMESPACE imports
 
Package: Rsubread
Commit: e2fd744d5169542bfb384e899e587efa7512850e
Author: Yang Liao <dbpzdbpz@gmail.com>
Date: 2019-03-20 10:42:22 +1100
Commit message:

 Added 100M read limit
 
Package: Rsubread
Commit: 0776ab0d317a53eaff63e51467d8b3518627ded3
Author: Yang Liao <dbpzdbpz@gmail.com>
Date: 2019-03-20 10:33:51 +1100
Commit message:

 Fix a bug
 
Package: Rsubread
Commit: d0684cb351169d1f4d1fb5b5eb7b6211590e7e74
Author: Yang LIAO <liao@wehi.edu.au>
Date: 2019-03-19 19:08:18 -0400
Commit message:

 Return data frame from simReads
 
Package: Rsubread
Commit: 5c5bba49db5aa368b8de168a4a86c2f5460b2a42
Author: Yang Liao <dbpzdbpz@gmail.com>
Date: 2019-03-20 10:02:45 +1100
Commit message:

 Anonynous input matrix
 
Package: Rsubread
Commit: 02867ec05740601262111df5d0c8dac165bad5de
Author: Yang Liao <dbpzdbpz@gmail.com>
Date: 2019-03-20 09:36:46 +1100
Commit message:

 Bumped version number
 
Package: GenoGAM
Commit: c2e559544a5cb874cba39addd5f3625dea3bae9e
Author: Juri <georg.stricker@gmx.net>
Date: 2019-03-19 23:01:09 +0100
Commit message:

 fixing bug in computing the score in broadPeaks function with HDF5 backend
 
Package: Rsubread
Commit: 54e9d530ec17c726b663d8af7a0f0b96a12e6af8
Author: Yang Liao <dbpzdbpz@gmail.com>
Date: 2019-03-20 08:59:34 +1100
Commit message:

 Bug fix
 
Package: Rsubread
Commit: 5007fac7d9fa56ed7ac44582a5898638b75c59ff
Author: Yang Liao <dbpzdbpz@gmail.com>
Date: 2019-03-20 08:55:21 +1100
Commit message:

 Minor changes
 
Package: universalmotif
Commit: 5ef26a0793f1d1dd5d0e2b9c1052c2bb1476834a
Author: bjmt <benjmtremblay@gmail.com>
Date: 2019-03-19 14:55:40 -0400
Commit message:

 using Rprintf instead of Rcout in print_pb
 
Package: ggbio
Commit: a36c7b4029bb25a287e3dfe282000d09a627236d
Author: Michael Lawrence <michafla@gene.com>
Date: 2019-03-19 10:36:35 -0700
Commit message:

 version bump
 
Package: gwascat
Commit: 9941882f4ec7842c6545fb8475aa3bb508a63196
Author: Vince Carey <stvjc@channing.harvard.edu>
Date: 2019-03-19 13:34:25 -0400
Commit message:

 fix prob with gwascat-package.Rd
 
Package: VariantAnnotation
Commit: 310c3b09c8386c2ccc48c75558ec5eb59e138974
Author: vobencha <vobencha@gmail.com>
Date: 2019-03-19 10:28:03 -0700
Commit message:

 Improve bug fix in commit 167fcdfcf3077be16db54cd6ce8590a77ca391e8

- Document why fix is necessary with new mapToTranscripts() behavior
- Implement fix for predictCoding(). The last commit only addressed
  locateVarants().
 
Package: variants
Commit: 7f5f17fd07add8a5a38f2d9b11cd93b3890789e2
Author: vobencha <vobencha@gmail.com>
Date: 2019-03-19 10:25:42 -0700
Commit message:

 Minor update in how header metadata is displayed
 
Package: NADfinder
Commit: a42e88999fe667766158240d21085ddfbc5bb12b
Author: Julie Zhu <julie.zhu@umassmed.edu>
Date: 2019-03-19 13:05:20 -0400
Commit message:

 removed rbamtools dependency
 
Package: variancePartition
Commit: a42a3c6d87b902883f0c8ea44b63499c53c7ef9a
Author: GabrielHoffman <gabrielhoffman@typhon.wireless.mountsinai.org>
Date: 2019-03-19 12:31:38 -0400
Commit message:

 v1.13.5
 
Package: gwascat
Commit: 6bd1ac137ed71c8d102ea63071fa39414cc7ab40
Author: Vince Carey <stvjc@channing.harvard.edu>
Date: 2019-03-19 12:21:42 -0400
Commit message:

 reducing dependencies and imports
 
Package: BiocCheck
Commit: e5ee4fbd924d66d31bb21f087b2f40cafca0a606
Author: lshep <lori.shepherd@roswellpark.org>
Date: 2019-03-19 12:07:56 -0400
Commit message:

 Revert check for Authors@R vs Author/Maintainer

  - remove unit test
 
Package: BiocCheck
Commit: 78f5cd0b6622d964a16f69a3539caa673db9e358
Author: lshep <lori.shepherd@roswellpark.org>
Date: 2019-03-19 11:53:31 -0400
Commit message:

 Rethink check for Authors@R vs Author/Maintainer

  - the check worked fine on open directories
  - when R does R CMD build, and then that tar is untarred, the additional Author and Maintainer fields where added based on Author@R so the check is always positive resulting in false positives
 
Package: qrqc
Commit: 5c584bb2ee6a27d68e5ae7717fb46d8509692214
Author: Vince Buffalo <vsbuffaloAAAAAA@gmail.com>
Date: 2019-03-19 08:45:09 -0700
Commit message:

 Merge of the Bioconductor version, keeping their updates over mine
 
Package: qrqc
Commit: 10f7d213c561fb3261235bad92336799fcce7b32
Author: Vince Buffalo <vsbuffalo@gmail.com>
Date: 2012-11-28 01:35:27 -0800
Commit message:

 cleaned up memory setting; should be every so slightly faster
 
Package: qrqc
Commit: 7c4c773797e6148bf8efbdc5a95c7962165804d6
Author: Vince Buffalo <vsbuffalo@gmail.com>
Date: 2012-07-04 14:32:35 -0700
Commit message:

 initial move to knitr for report generation
 
Package: qrqc
Commit: 53ab3381c715dbd5afdff4055a8547e47b3c3d81
Author: Vince Buffalo <vsbuffalo@gmail.com>
Date: 2012-06-27 13:45:46 -0700
Commit message:

 Merge branch 'master' of github.com:vsbuffalo/qrqc
 
Package: qrqc
Commit: 4be0be1314fa534bd41d2abcbb6f8eed4e16e89a
Author: Vince Buffalo <vsbuffalo@gmail.com>
Date: 2012-06-27 01:26:56 -0700
Commit message:

 version bump
 
Package: qrqc
Commit: ae53b66269851993315556dca78ff0b92cc22cff
Author: Vince Buffalo <vsbuffalo@gmail.com>
Date: 2012-06-27 01:25:19 -0700
Commit message:

 fixed bug with ggplot and basePlot
 
Package: qrqc
Commit: 0fae820f3e91b357c72873a422cb09341425792f
Author: Vince Buffalo <vsbuffalo@gmail.com>
Date: 2012-04-17 12:18:26 -0700
Commit message:

 version bump
 
Package: qrqc
Commit: 493b76bd4883c75fefee86008e961969e81cfdaa
Author: Vince Buffalo <vsbuffalo@gmail.com>
Date: 2012-04-17 12:14:04 -0700
Commit message:

 fixed typo in show methods
 
Package: qrqc
Commit: f94bac65f1e13ab5c9a7cd5cec0bc2faf1fb1738
Author: Vince Buffalo <vsbuffalo@gmail.com>
Date: 2012-03-19 16:32:29 -0700
Commit message:

 fixed minor issue
 
Package: qrqc
Commit: f8ef833b270198594bc515e354d36210b9fe0bc6
Author: Vince Buffalo <vsbuffalo@gmail.com>
Date: 2012-03-19 13:58:40 -0700
Commit message:

 fixed doc issues
 
Package: qrqc
Commit: bbfe398a4ba2d6d40fdb255299c33ae742350f57
Author: Vince Buffalo <vsbuffalo@gmail.com>
Date: 2012-03-06 11:46:28 -0800
Commit message:

 major (simple) restructuring to remove wrapper directory, for bioc git-svn compat
 
Package: qrqc
Commit: 2fd9e25b6b13dde83eace00b73e0b321357a3bd4
Author: Vince Buffalo <vsbuffalo@ucdavis.edu>
Date: 2012-03-05 18:22:08 -0800
Commit message:

 minor changes to avoid linux build warnings
 
Package: qrqc
Commit: 38da8694cc31669ac2c981ceb7f9473b96936b70
Author: Vince Buffalo <vsbuffalo@gmail.com>
Date: 2012-03-05 09:48:00 -0800
Commit message:

 changed quality range checking
 
Package: qrqc
Commit: d73732f2189334a1aa12aa30b4a7b1486f0b8905
Author: Vince Buffalo <vsbuffalo@gmail.com>
Date: 2012-03-03 13:26:49 -0800
Commit message:

 few documention changes
 
Package: qrqc
Commit: 13dc580a78e085bdc2db7e5db32d62a5a3cb9c77
Author: Vince Buffalo <vsbuffalo@gmail.com>
Date: 2012-03-03 13:13:30 -0800
Commit message:

 vignette corrections, version bump
 
Package: qrqc
Commit: e4b65a3d788e125fe6eb9c128a9e32ed8d81e73c
Author: Vince Buffalo <vsbuffalo@gmail.com>
Date: 2012-03-03 12:36:23 -0800
Commit message:

 added k-mer doc
 
Package: qrqc
Commit: 37742e211e7a8bfc94e6730f23493e32e8f2b180
Author: Vince Buffalo <vsbuffalo@gmail.com>
Date: 2012-03-02 18:34:12 -0800
Commit message:

 fixed ugly code in calcKL - what the hell was that?
 
Package: qrqc
Commit: 4ef9c24f147179448b708830a036b3eef3b9b3b4
Author: Vince Buffalo <vsbuffalo@gmail.com>
Date: 2012-03-02 18:13:41 -0800
Commit message:

 added doc on new KL methods
 
Package: qrqc
Commit: 3d1cb8b5ccb94a31e392bde25e7014c80082037f
Author: Vince Buffalo <vsbuffalo@gmail.com>
Date: 2012-03-02 17:32:28 -0800
Commit message:

 packaged contam file, added kmerKLPlot doc draft, minor changes
 
Package: qrqc
Commit: f01ccb57b0d5bae56969f8d8892e8044b75bb53b
Author: Vince Buffalo <vsbuffalo@gmail.com>
Date: 2012-02-29 21:57:29 -0800
Commit message:

 changes made to kmer handing, info theo approaches
 
Package: qrqc
Commit: 50138a38e5f2ac9f55e12e492dcf3cc30b92c6e8
Author: Vince Buffalo <vsbuffalo@gmail.com>
Date: 2012-02-26 18:14:20 -0800
Commit message:

 fixed memory leak with k-mer handling
 
Package: qrqc
Commit: b8ad8417aa0d6528a1bdcaf837810e2249874a8c
Author: Vince Buffalo <vsbuffalo@gmail.com>
Date: 2012-02-26 06:01:19 -0800
Commit message:

 fixed bug with k-mer handling (stopping before end)
 
Package: qrqc
Commit: 7b7f35c56419cb352c1623cdd3f9cb5bd3966068
Author: Vince Buffalo <vsbuffalo@gmail.com>
Date: 2012-02-24 00:44:01 -0800
Commit message:

 added more comments
 
Package: qrqc
Commit: 578599b615a9b1c5600dca0f0686b011994f5552
Author: Vince Buffalo <vsbuffalo@gmail.com>
Date: 2012-02-23 18:09:52 -0800
Commit message:

 added positional k-mer hashing, plots, accessors
 
Package: qrqc
Commit: bcb2341166e1a51de2e0e8b42a9d8af33cdb3ec1
Author: Vince Buffalo <vsbuffalo@gmail.com>
Date: 2012-02-23 16:00:27 -0800
Commit message:

 intial go at k-mer hashing, non-positional
 
Package: qrqc
Commit: 91b3ef2beded0e02de14b3be64b863342cfe0bec
Author: Vince Buffalo <vsbuffalo@gmail.com>
Date: 2012-02-20 17:55:45 -0800
Commit message:

 removed phred quality, added blurb about qualities in readseqfile
 
Package: qrqc
Commit: facd6c2184bdff228010cb765665fef84ac08a53
Author: Vince Buffalo <vsbuffalo@gmail.com>
Date: 2012-02-20 17:40:26 -0800
Commit message:

 added changes to news
 
Package: qrqc
Commit: 6a6297dff5bf25189501d04998a10507994dd123
Author: Vince Buffalo <vsbuffalo@gmail.com>
Date: 2012-02-20 17:17:13 -0800
Commit message:

 new vignette
 
Package: qrqc
Commit: fa7f1d4331cdf3fc33b0096d3666254eca0f31f6
Author: Vince Buffalo <vsbuffalo@gmail.com>
Date: 2012-02-20 13:37:25 -0800
Commit message:

 fixed import issues, fixed issues which led to examples not working
 
Package: qrqc
Commit: ff7a6750f40d0d3b9fcdbdf94950d1baa6033317
Author: Vince Buffalo <vsbuffalo@gmail.com>
Date: 2012-02-20 02:01:52 -0800
Commit message:

 fixed some build issues with doc
 
Package: qrqc
Commit: 8087564dc0df6d08a327527b5af07713dc40f2bb
Author: Vince Buffalo <vsbuffalo@gmail.com>
Date: 2012-02-19 20:33:59 -0800
Commit message:

 added more docs
 
Package: qrqc
Commit: 6ddaa523c1206d8802846ec16bd7d0aa5b7fdab7
Author: Vince Buffalo <vsbuffalo@gmail.com>
Date: 2012-02-19 19:51:22 -0800
Commit message:

 additions to readme, added more ggplot2 fun doc
 
Package: qrqc
Commit: 7ef8abd1ade33b3741e45b918c7cd2f00a5e8c20
Author: Vince Buffalo <vsbuffalo@gmail.com>
Date: 2012-02-19 13:29:25 -0800
Commit message:

 getBase and getQual accesor doc added, also added new color functions
 
Package: qrqc
Commit: 18895c2cbb0f57e8d8b94639fd543a3f3e3e8a6e
Author: Vince Buffalo <vsbuffalo@gmail.com>
Date: 2012-02-19 12:38:26 -0800
Commit message:

 added doc templates, some new doc
 
Package: qrqc
Commit: 35038488a330a345f17266eb0769684140d2590c
Author: Vince Buffalo <vsbuffalo@gmail.com>
Date: 2012-02-19 11:42:33 -0800
Commit message:

 fixed color issues, added drop for getBase
 
Package: qrqc
Commit: 09ef453e1f0d9de0529f51f0242f3593881f9518
Author: Vince Buffalo <vsbuffalo@gmail.com>
Date: 2012-02-19 03:59:26 -0800
Commit message:

 readme/description changes, minor plot additions
 
Package: qrqc
Commit: 8ffd36abde30705649d39082d3e178e47abd48ad
Author: Vince Buffalo <vsbuffalo@gmail.com>
Date: 2012-02-19 02:50:55 -0800
Commit message:

 more ggplot2 based graphics additions
 
Package: qrqc
Commit: 78fd1aa4f1934a524ad9578567e97e9c4ea4b3db
Author: Vince Buffalo <vsbuffalo@gmail.com>
Date: 2012-02-19 01:08:50 -0800
Commit message:

 added geom bar for basePlot
 
Package: qrqc
Commit: e9f303c1c28b1c078c85a877bc7e444866e6e249
Author: Vince Buffalo <vsbuffalo@gmail.com>
Date: 2012-02-19 00:22:07 -0800
Commit message:

 more plotting functions added
 
Package: qrqc
Commit: c1d206afa89c4af276d213d6bdf2985150d4be37
Author: Vince Buffalo <vsbuffalo@gmail.com>
Date: 2012-02-18 23:18:01 -0800
Commit message:

 added new ggplot-based plotting functions
 
Package: qrqc
Commit: 20da4dbde86949b71c31869c62aaf739ed9c564c
Author: Vince Buffalo <vsbuffalo@gmail.com>
Date: 2011-05-24 12:52:14 -0700
Commit message:

 slight mod to Makefile to clean check dir
 
Package: qrqc
Commit: cba0e813d0c4423a29b009bd74650a5f85140fe6
Author: Vince Buffalo <vsbuffalo@ucdavis.edu>
Date: 2011-05-24 12:14:32 -0700
Commit message:

 fixed issue in io.c with phred quality, added GNU-style change log
 
Package: qrqc
Commit: 2a0f6258b6f5e28c4b66662fe4d4f39dd5ea22d4
Author: Vince Buffalo <vsbuffalo@ucdavis.edu>
Date: 2011-05-23 11:46:39 -0700
Commit message:

 changed windows makevars for bioc compliance
 
Package: qrqc
Commit: d0adc8c8f51d0ff59f752d1eed6064c81fc39760
Author: Vince Buffalo <vsbuffalo@ucdavis.edu>
Date: 2011-05-23 11:41:56 -0700
Commit message:

 small bug fixes - removed called to browser(), error in Sanger/Phred quality schemes
 
Package: qrqc
Commit: 3f4444a509605fec5ae1cf7d3f8f6511d86badb2
Author: Vince Buffalo <vsbuffalo@gmail.com>
Date: 2011-05-02 16:27:42 -0700
Commit message:

 added test-trimmed.fastq
 
Package: qrqc
Commit: 7094659677b536b12bd2cbfe7a7cb8b1860d6358
Author: Vince Buffalo <vsbuffalo@gmail.com>
Date: 2011-04-11 12:55:40 -0700
Commit message:

 version bump
 
Package: qrqc
Commit: afb5501ad12467fd5c0c0d2a72a63b98120bba0c
Author: Vince Buffalo <vsbuffalo@gmail.com>
Date: 2011-04-11 12:34:45 -0700
Commit message:

 fixed bug with plotSeqLengths, added new example to vignette
 
Package: qrqc
Commit: ea270b580d3cda2b262eb5433e93260c6b2385bd
Author: Vince Buffalo <vsbuffalo@gmail.com>
Date: 2011-04-09 22:14:23 -0700
Commit message:

 version bump
 
Package: qrqc
Commit: 5dd38f5ad9b4c02be77f26d42c71d637b7d58775
Author: Vince Buffalo <vsbuffalo@ucdavis.edu>
Date: 2011-04-09 22:02:27 -0700
Commit message:

 fixed minor issues in doc and vignette
 
Package: qrqc
Commit: f7df4065b17b500173e457b7e9c7b25d2451c588
Author: Vince Buffalo <vsbuffalo@gmail.com>
Date: 2011-03-30 15:27:14 -0700
Commit message:

 fixed issue
 
Package: qrqc
Commit: fc8e3962fe30e8bceab00e4a1f77e17ee91f3cb0
Author: Vince Buffalo <vsbuffalo@gmail.com>
Date: 2011-03-29 16:13:13 -0700
Commit message:

 version bump
 
Package: qrqc
Commit: 727f9c564a748924129de17693cf0ee87f61b7d2
Author: Vince Buffalo <vsbuffalo@gmail.com>
Date: 2011-03-29 16:11:10 -0700
Commit message:

 fixed Makefile, doc aliases, and Makevars
 
Package: qrqc
Commit: d550da07af32c631cf23a15bf7dc56f7e92129b7
Author: Vince Buffalo <vsbuffalo@gmail.com>
Date: 2011-03-26 12:20:51 -0700
Commit message:

 fixed documentation issues and inconsistencies
 
Package: qrqc
Commit: 994e57003cadfcdd92e55485e39213bff52ce5c8
Author: Vince Buffalo <vsbuffalo@gmail.com>
Date: 2011-03-25 13:01:04 -0700
Commit message:

 removed RColorBrewer Dependency
 
Package: qrqc
Commit: a28b61832c9ec2a373c41df89346f2a3ea8540d4
Author: Vince Buffalo <vsbuffalo@gmail.com>
Date: 2011-03-22 15:16:35 -0700
Commit message:

 whipped out TODO - these are all done
 
Package: qrqc
Commit: 530798afcece896e34412e672a18a652049c5ae3
Author: Vince Buffalo <vsbuffalo@gmail.com>
Date: 2011-03-22 15:12:27 -0700
Commit message:

 version bump
 
Package: qrqc
Commit: d581c8a1a5626e688d7d1c61d43b5b6208069427
Author: Vince Buffalo <vsbuffalo@gmail.com>
Date: 2011-03-22 15:09:13 -0700
Commit message:

 fixed mans, added khash/kseq depends via Rsamtools
 
Package: qrqc
Commit: 53d53b7c9aa00b194a192ad8e072f14fc1d0f9e2
Author: Vince Buffalo <vsbuffalo@gmail.com>
Date: 2011-03-22 13:26:09 -0700
Commit message:

 fixed report output directory, added legend
 
Package: qrqc
Commit: 76eace471cd309e4054b6c0021f0220f3e4cf566
Author: Vince Buffalo <vsbuffalo@gmail.com>
Date: 2011-03-21 22:20:24 -0700
Commit message:

 added better report writing, fixed many issues for bioc compatability
 
Package: qrqc
Commit: 2d4a07a73e04795960ee0dde7703c88f8e0a1d7b
Author: Vince Buffalo <vsbuffalo@gmail.com>
Date: 2011-03-21 14:26:33 -0700
Commit message:

 added Makevars for windows
 
Package: qrqc
Commit: c8fee8e2bf883e66807cfadb98a15c362d43d790
Author: Vince Buffalo <vsbuffalo@gmail.com>
Date: 2011-03-21 14:24:05 -0700
Commit message:

 fixed issues with plotQual window and functionality with few values
 
Package: qrqc
Commit: 4fe73501a8a9c446596ed72e81334585bd76ad86
Author: Vince Buffalo <vsbuffalo@gmail.com>
Date: 2010-12-20 16:08:05 -0800
Commit message:

 version bump for last change
 
Package: qrqc
Commit: 831543952972dee8d59d39824400918c58d66270
Author: Vince Buffalo <vsbuffalo@gmail.com>
Date: 2010-12-16 17:04:52 -0800
Commit message:

 added extern to summarize_file
 
Package: qrqc
Commit: e049f5c9bdf028aaec16354a4520e27f79421997
Author: Vince Buffalo <vsbuffalo@gmail.com>
Date: 2010-12-10 02:03:49 -0800
Commit message:

 version bump for last change to gzreadclone
 
Package: qrqc
Commit: 684f909336db88dc0fa47a5942e37abe9f0e3aec
Author: Vince Buffalo <vsbuffalo@gmail.com>
Date: 2010-12-10 02:01:02 -0800
Commit message:

 changed type of c in gzreadclone to char
 
Package: qrqc
Commit: c3951e03cd1d1381a5051824340a2eab3579004d
Author: Vince Buffalo <vsbuffalo@gmail.com>
Date: 2010-12-10 01:22:25 -0800
Commit message:

 version bump, fixed s4 method documentation, added NEWS
 
Package: qrqc
Commit: 05b94bb7a2240007887e3831455297c3a38475b1
Author: Vince Buffalo <vsbuffalo@gmail.com>
Date: 2010-12-10 00:11:26 -0800
Commit message:

 added initializations for qual (not always used) vars, to prevent warnings on Windows sytems
 
Package: qrqc
Commit: 266c0085cfa9b82e83386118068f0b5460155109
Author: Vince Buffalo <vsbuffalo@gmail.com>
Date: 2010-12-09 23:57:22 -0800
Commit message:

 to resolve windows portability (no zlib.h), KSEQ_INIT is given clone function when _WIN32 defined
 
Package: qrqc
Commit: 20046748d548f0eb5f545baeee1469c6b6dac79d
Author: Vince Buffalo <vsbuffalo@ucdavis.edu>
Date: 2010-12-09 19:38:00 -0800
Commit message:

 added makeReport documentation
 
Package: qrqc
Commit: 7b73f036219be52975ce673178a4a1e56b9407ff
Author: Vince Buffalo <vsbuffalo@ucdavis.edu>
Date: 2010-12-09 19:26:21 -0800
Commit message:

 minor change to gitignore to ignore tex auto directories
 
Package: qrqc
Commit: 9c6d429245eb702b954a355c6efd7d79733030fc
Author: Vince Buffalo <vsbuffalo@ucdavis.edu>
Date: 2010-12-09 19:23:13 -0800
Commit message:

 added optional filename to makeReport, fixed vignette
 
Package: qrqc
Commit: 6d38f94b93b7166975c8aed85bfae8be2f9a218f
Author: Vince Buffalo <vsbuffalo@ucdavis.edu>
Date: 2010-12-09 19:09:14 -0800
Commit message:

 added vignette draft
 
Package: qrqc
Commit: 1662df99a05ee416fe5e03a2911a490cd1ffd4f5
Author: Vince Buffalo <vsbuffalo@ucdavis.edu>
Date: 2010-12-09 17:56:35 -0800
Commit message:

 added frequent sequences to HTML report
 
Package: qrqc
Commit: 0d4956d04852dbc624661adaa619a4a6e349afb3
Author: Vince Buffalo <vsbuffalo@ucdavis.edu>
Date: 2010-12-09 15:02:13 -0800
Commit message:

 new methods for FASTA and FASTQ files
 
Package: qrqc
Commit: 4975d67f172b43bd9e7e4ccfe1ce749f27dcaa23
Author: Vince Buffalo <vsbuffalo@ucdavis.edu>
Date: 2010-12-09 13:05:59 -0800
Commit message:

 initial methods for report generation and template
 
Package: qrqc
Commit: 4d56be207e3892fe120e213eea9421162b1db3bb
Author: Vince Buffalo <vsbuffalo@ucdavis.edu>
Date: 2010-12-08 17:34:29 -0800
Commit message:

 moved more functions to utils.R, added more test functions
 
Package: qrqc
Commit: 49db166dce3bbe6504666031c21e410ec7e04845
Author: Vince Buffalo <vsbuffalo@ucdavis.edu>
Date: 2010-12-08 17:19:37 -0800
Commit message:

 seperate doc added for FASTQSummary and FASTASummary classes
 
Package: qrqc
Commit: 06b3d0f6e2828adc590884a9487dff540bffc989
Author: Vince Buffalo <vsbuffalo@ucdavis.edu>
Date: 2010-12-08 16:58:14 -0800
Commit message:

 moved methods and generics to own files to follow Bioconductor package guidelines, wrote generic wrappers around all plotting functions, fixed offset-by-1 issue with plotQuals
 
Package: qrqc
Commit: 25669988913baaddbdf643f84d890474b1e71f1c
Author: Vince Buffalo <vsbuffalo@ucdavis.edu>
Date: 2010-12-08 15:03:58 -0800
Commit message:

 removed generic Makefile template information
 
Package: qrqc
Commit: 421ebb9b843dbf2c98eb1f21f788e9f2277ebecf
Author: Vince Buffalo <vsbuffalo@ucdavis.edu>
Date: 2010-12-08 15:02:46 -0800
Commit message:

 added man page for SequenceSummary class
 
Package: qrqc
Commit: 3b55f52795ede92930277f8a8feb0d1dc1193f58
Author: Vince Buffalo <vsbuffalo@ucdavis.edu>
Date: 2010-12-08 14:02:52 -0800
Commit message:

 seperated classes and methods, added new man pages for plotting functions, added functions to NAMESPACE
 
Package: qrqc
Commit: 4f9f3ea0faf8ba5d0ccd803f5be4262214966465
Author: Vince Buffalo <vsbuffalo@ucdavis.edu>
Date: 2010-12-08 12:25:44 -0800
Commit message:

 added man page for readSeqFile
 
Package: qrqc
Commit: d33eac3f68913a35867c2855256b6a9773da97b8
Author: Vince Buffalo <vsbuffalo@ucdavis.edu>
Date: 2010-12-07 18:11:34 -0800
Commit message:

 added set.seed for reproducible MC graphics
 
Package: qrqc
Commit: ecbeffebc8d6d158ec919708356604055dff3c4b
Author: Vince Buffalo <vsbuffalo@ucdavis.edu>
Date: 2010-12-07 18:03:37 -0800
Commit message:

 fixed bug with plotSeqLengths
 
Package: qrqc
Commit: 36b6f6ce937cfec56aba44c99c76b9b56b58d340
Author: Vince Buffalo <vsbuffalo@ucdavis.edu>
Date: 2010-12-07 17:05:52 -0800
Commit message:

 added test for default case of meanFromBins
 
Package: qrqc
Commit: 45699d0faab2031a75bfc041bbb32c827c93ebb8
Author: Vince Buffalo <vsbuffalo@ucdavis.edu>
Date: 2010-12-07 16:36:18 -0800
Commit message:

 added basic unit testing of some functions
 
Package: qrqc
Commit: 93c1f3d9ffcb6ce23388de528a798997ea73d4b4
Author: Vince Buffalo <vsbuffalo@ucdavis.edu>
Date: 2010-12-07 13:44:54 -0800
Commit message:

 fixed issue with plotBaseProp, added more output to S4 show method
 
Package: qrqc
Commit: 6b379c28ee643631331db8520f6bd53fab1b51a6
Author: Vince Buffalo <vsbuffalo@ucdavis.edu>
Date: 2010-12-06 18:43:24 -0800
Commit message:

 initial show method outlined
 
Package: qrqc
Commit: 477954ec7df3acff9690bd885b0c16a23cffeb16
Author: Vince Buffalo <vsbuffalo@ucdavis.edu>
Date: 2010-12-06 18:06:16 -0800
Commit message:

 fixed incorrect commit with scan.R having changes main.R should have
 
Package: qrqc
Commit: 96d0ab11fd6c274e721c595270ed98e2faee6a66
Author: Vince Buffalo <vsbuffalo@ucdavis.edu>
Date: 2010-12-06 18:03:38 -0800
Commit message:

 Initial outline of S4 system, plus moving graphics functions to graphics.R

- New items in TODO
- Renamed scan.R to main.R
 
Package: qrqc
Commit: e155c7c5cc970cb0f90cbe21bdaf7d8882f12994
Author: Vince Buffalo <vsbuffalo@ucdavis.edu>
Date: 2010-12-06 15:43:03 -0800
Commit message:

 added comments to io.c file
 
Package: qrqc
Commit: 5fe600ea03fed8adb329bda1c8be557a879473ca
Author: Vince Buffalo <vsbuffalo@ucdavis.edu>
Date: 2010-12-06 12:00:19 -0800
Commit message:

 version bump; namespace added, and description edited
 
Package: qrqc
Commit: 9124350e381d1f1a7ff1f638854535441496ad2a
Author: Vince Buffalo <vsbuffalo@ucdavis.edu>
Date: 2010-12-06 11:45:02 -0800
Commit message:

 fixed issue with PROTECT stack imbalance, and qual plot uses 0.1 and 0.9 quantiles
 
Package: qrqc
Commit: 6d439fa36b54f2b8c9ee09f5d666f546d7a94401
Author: Vince Buffalo <vsbuffalo@ucdavis.edu>
Date: 2010-12-06 11:29:50 -0800
Commit message:

 finished plot with histogram and proper labels
 
Package: qrqc
Commit: 4724b1005c543aa0d6e1167800c4c6022f8953e1
Author: Vince Buffalo <vsbuffalo@gmail.com>
Date: 2010-12-06 00:50:49 -0800
Commit message:

 early histogram/qual plot
 
Package: qrqc
Commit: d439e984c507226dec9e6a75b3bb26967190c12e
Author: Vince Buffalo <vsbuffalo@gmail.com>
Date: 2010-12-05 12:01:39 -0800
Commit message:

 refactored, fixed seq.length issue
 
Package: qrqc
Commit: a1a58f2022f18241c66c78dc6f11783c06bcc6da
Author: Vince Buffalo <vsbuffalo@gmail.com>
Date: 2010-12-04 23:29:09 -0800
Commit message:

 using kseq length instead of strlen
 
Package: qrqc
Commit: c3c60203fc54b9d62aa6e5c9c015fe787b872041
Author: Vince Buffalo <vsbuffalo@gmail.com>
Date: 2010-12-03 13:07:00 -0800
Commit message:

 working refactor around kseq.h sequence reading library
 
Package: qrqc
Commit: 2077a950e6da7874838608477677613440808cd1
Author: Vince Buffalo <vsbuffalo@ucdavis.edu>
Date: 2010-11-30 19:25:43 -0800
Commit message:

 commented out buffer overflow in seq_lengths handling
 
Package: qrqc
Commit: 08bd706c26bed432560fad56c909171bd9d4898e
Author: Vince Buffalo <vsbuffalo@ucdavis.edu>
Date: 2010-11-30 14:24:16 -0800
Commit message:

 minor grammar change to DESCRIPTION
 
Package: qrqc
Commit: c1d8fbfad5544a8598f06401ea7bfddc07579ab1
Author: Vince Buffalo <vsbuffalo@gmail.com>
Date: 2010-11-30 12:48:02 -0800
Commit message:

 new gitignore entries, base-specific freq plots, Makefile, and namespace added
 
Package: qrqc
Commit: 79bd08ee952a3fda7c226432c745a0dccfb5d48c
Author: Vince Buffalo <vsbuffalo@gmail.com>
Date: 2010-11-30 12:01:37 -0800
Commit message:

 added more function documentation
 
Package: qrqc
Commit: 8de7e2f573fe719d3584bd1d76c5a224f1c5c9b5
Author: Vince Buffalo <vsbuffalo@gmail.com>
Date: 2010-11-30 11:49:33 -0800
Commit message:

 sequence length plus reformatting to clean up code style a bit
 
Package: qrqc
Commit: cd26e402627a4f0b32eeb9594dce042c8af6adf1
Author: Vince Buffalo <vsbuffalo@ucdavis.edu>
Date: 2010-11-29 17:50:07 -0800
Commit message:

 added sequence length statistics
 
Package: qrqc
Commit: 06db6f69979b3d32faabe4d26e2481e452d0dd74
Author: Vince Buffalo <vsbuffalo@ucdavis.edu>
Date: 2010-11-29 16:42:32 -0800
Commit message:

 switched to base graphics
 
Package: qrqc
Commit: ea71a1583ba4331f659b3a9024e167971117409d
Author: Vince Buffalo <vsbuffalo@ucdavis.edu>
Date: 2010-11-29 15:30:27 -0800
Commit message:

 cleaner mean plotting character
 
Package: qrqc
Commit: 56e3fb29a00811dcefa43d35157045908a19d739
Author: Vince Buffalo <vsbuffalo@ucdavis.edu>
Date: 2010-11-29 15:22:30 -0800
Commit message:

 early version of qualMClowess
 
Package: qrqc
Commit: e1bbcf22be0a85a78f704649319a4560ab512d1b
Author: Vince Buffalo <vsbuffalo@ucdavis.edu>
Date: 2010-11-29 13:27:25 -0800
Commit message:

 improved empirical quantile handling
 
Package: qrqc
Commit: b17f71680c6f8a4ef97df497dd5fb3515cd37239
Author: Vince Buffalo <vsbuffalo@ucdavis.edu>
Date: 2010-11-28 23:03:07 -0800
Commit message:

 adding more interesting test sequences
 
Package: qrqc
Commit: 5e060226f6a989da78ab8d41836d1e8e00f76621
Author: Vince Buffalo <vsbuffalo@ucdavis.edu>
Date: 2010-11-28 21:55:45 -0800
Commit message:

 added test data file
 
Package: qrqc
Commit: e2e1b1ba2fd80c57817ae6ca53f98ebb84b6c62a
Author: Vince Buffalo <vsbuffalo@gmail.com>
Date: 2010-11-28 19:57:52 -0800
Commit message:

 restructuring directory
 
Package: qrqc
Commit: 8f71f86298b8ef6233ef9bcb4ab4032f16618a7f
Author: Vince Buffalo <vsbuffalo@ucdavis.edu>
Date: 2010-11-28 11:49:23 -0800
Commit message:

 changed protect to PROTECT, removed unused function
 
Package: qrqc
Commit: 182383f67e79a8430adef678b53642172c80e165
Author: Vince Buffalo <vsbuffalo@ucdavis.edu>
Date: 2010-11-28 11:37:18 -0800
Commit message:

 renamed getline to get_line to solve issue with function name clash on Linux systems
 
Package: qrqc
Commit: 2d94923483e52ad51d6c5a099120590572f0ab8f
Author: Vince Buffalo <vsbuffalo@ucdavis.edu>
Date: 2010-11-27 01:42:49 -0800
Commit message:

 fixing misnamed variable, again
 
Package: qrqc
Commit: a15fc5a103aa7cf0e72a649829b36e380a1cca9c
Author: Vince Buffalo <vsbuffalo@ucdavis.edu>
Date: 2010-11-27 01:39:30 -0800
Commit message:

 fixing misnamed variable
 
Package: qrqc
Commit: 5a451f7b59b9893e152f3277b0c0199284750f6f
Author: Vince Buffalo <vsbuffalo@ucdavis.edu>
Date: 2010-11-27 01:31:45 -0800
Commit message:

 basic quantile function from binned data, and qual linerange plots
 
Package: qrqc
Commit: f590f89eb7636a42a8f84e77c3b36c7e249f9ae9
Author: Vince Buffalo <vsbuffalo@ucdavis.edu>
Date: 2010-11-26 23:16:24 -0800
Commit message:

 data mungning, basic base freq and prop plots added
 
Package: qrqc
Commit: f9d4c70a401071b6ef43abcbfd0688da67fc80d1
Author: Vince Buffalo <vsbuffalo@ucdavis.edu>
Date: 2010-11-26 21:27:57 -0800
Commit message:

 fixed issue with lack of strdup, which lead to improper sequence names
 
Package: qrqc
Commit: 10cecec87eef011009babd0cb52e04e38d92d7e1
Author: Vince Buffalo <vsbuffalo@ucdavis.edu>
Date: 2010-11-26 20:05:13 -0800
Commit message:

 increased default hash size
 
Package: qrqc
Commit: d9e9ea1df66028cdc8594c543d15034b6fc1af5e
Author: Vince Buffalo <vsbuffalo@ucdavis.edu>
Date: 2010-11-26 20:04:31 -0800
Commit message:

 changed output verbosity level to be based on nblocks
 
Package: qrqc
Commit: 51a218346d6b094ec1fb29516bc28e56f13503c2
Author: Vince Buffalo <vsbuffalo@ucdavis.edu>
Date: 2010-11-26 19:59:37 -0800
Commit message:

 nblock count was incorrect - fixed
 
Package: qrqc
Commit: 9fda34cdb71f55cd7723634fc98ca5435f6dbff6
Author: Vince Buffalo <vsbuffalo@ucdavis.edu>
Date: 2010-11-26 19:55:27 -0800
Commit message:

 unique count was incorrect - fixed
 
Package: qrqc
Commit: 47e8b114faa737a3273e43879b322214b718ac17
Author: Vince Buffalo <vsbuffalo@ucdavis.edu>
Date: 2010-11-26 19:53:25 -0800
Commit message:

 better verbosity - now includes num unique seqs
 
Package: qrqc
Commit: b09cf2848bab510846b673f3dff06da08bcde0b4
Author: Vince Buffalo <vsbuffalo@ucdavis.edu>
Date: 2010-11-26 19:51:24 -0800
Commit message:

 try higher initial hash size
 
Package: qrqc
Commit: e38f18b2ceff604ed135c289b34655a4b6c7705d
Author: Vince Buffalo <vsbuffalo@ucdavis.edu>
Date: 2010-11-26 19:13:06 -0800
Commit message:

 removed void statement, fixed memory leak
 

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