Bioconductor has moved to GIT for contributed packages; the subversion logs are no longer active.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

GIT Logs

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

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

Package: Rsubread
Commit: a15f162f41827e360f7c26ee8bc909ca9cf857be
Author: Yang Liao <dbpzdbpz@gmail.com>
Date: 2019-01-19 14:30:58 +1100
Commit message:

 Change the wrapper to avoid stack running out
 
Package: Rsubread
Commit: 53e1082bf31fbdbc6fc776bccab8e239f9a4c21d
Author: Yang Liao <dbpzdbpz@gmail.com>
Date: 2019-01-19 14:15:03 +1100
Commit message:

 Recovered wrong C file
 
Package: Rsubread
Commit: bce28364f9fd4422380cc298bae68ce3998ff972
Author: Yang LIAO <liao@wehi.edu.au>
Date: 2019-01-18 20:02:54 -0500
Commit message:

 removed warning messages from rand(), srand() and R_CStackLimit
 
Package: chipseq
Commit: 06ea67a5ba169b45305ffc8c8934c9c55c609c93
Author: Michael Lawrence <michafla@gene.com>
Date: 2019-01-18 14:19:42 -0800
Commit message:

 vignette updates
 
Package: VariantAnnotation
Commit: 7cd73d96b0db76c709420829345998289e89edfa
Author: vobencha <vobencha@gmail.com>
Date: 2019-01-18 13:42:35 -0800
Commit message:

 Re-enable code chunks that were disabled in commits
3e4ed9abbf094ae4608b8a6e688f44ebb27d6de0 and
b6a6c1cb47e2a1f783fc6105840c0e19512e1fd9
 
Package: BiocPkgTools
Commit: d676b5fc77dc143212909b1a76f9cc29d9da4fb7
Author: Sean Davis <seandavi@gmail.com>
Date: 2019-01-18 16:38:46 -0500
Commit message:

 version bump
 
Package: BiocPkgTools
Commit: 3328bcf08d0332b70dd070005eacb441353af5c6
Author: Sean Davis <seandavi@gmail.com>
Date: 2019-01-18 16:37:16 -0500
Commit message:

 New pkg doi code with new EZID API through datacite

Just note that this is irrelevant for normal
users.
 
Package: BiocPkgTools
Commit: f93fa01bd8a44a3298216105d31ab87bb43a6d5d
Author: Sean Davis <seandavi@gmail.com>
Date: 2019-01-18 13:49:07 -0500
Commit message:

 Merge branch 'master' into RELEASE_3_8
 
Package: BiocPkgTools
Commit: ee8307a03417db7ff4f79b5f1af3e31f7c758710
Author: Sean Davis <seandavi@gmail.com>
Date: 2018-12-10 21:24:08 -0500
Commit message:

 version bump
 
Package: BiocPkgTools
Commit: ccd39fc6ecf13ee41cad6ff5f85d3374a8cc7c50
Author: Shians <registertonysu@gmail.com>
Date: 2018-12-11 10:32:43 +1100
Commit message:

 Fixed installation instructions and package home line
 
Package: VariantAnnotation
Commit: dc791121caeaca10cfd855f2ce6b10017ccdbbff
Author: vobencha <vobencha@gmail.com>
Date: 2019-01-18 12:56:54 -0800
Commit message:

 Fix bug in buffer reallocation when a record fills the buffer exactly

See https://github.com/Bioconductor/VariantAnnotation/issues/19 for
details
 
Package: rTANDEM
Commit: 5092692904064a6391d787b4a7a1d4bb084600fd
Author: Frederic-bioinfo <frederic.bioinfo@gmail.com>
Date: 2019-01-18 15:51:06 -0500
Commit message:

 Fix comparison between pointer and integer (pValue=='\0')
 
Package: VariantAnnotation
Commit: b6a6c1cb47e2a1f783fc6105840c0e19512e1fd9
Author: vobencha <vobencha@gmail.com>
Date: 2019-01-18 12:43:33 -0800
Commit message:

 Silence man page example while we investigate C stack usage
 
Package: RegParallel
Commit: 3d7f3a86324404a94dca522b408c067f7b9ddc22
Author: Kevin Blighe <kblighe@CLINICALBIO.dlink.com>
Date: 2019-01-18 17:41:44 -0200
Commit message:

 Tidy blocksize error msg
 
Package: RegParallel
Commit: fc03e69f7dcc74690980b870f9ccfb3892c6d63f
Author: Kevin Blighe <kblighe@CLINICALBIO.dlink.com>
Date: 2018-11-01 09:36:59 -0300
Commit message:

 Update vignette
 
Package: RegParallel
Commit: 5c0a5ffc3ae2d64978e89a202acde24594afbf8c
Author: Kevin Blighe <kblighe@CLINICALBIO.dlink.com>
Date: 2018-11-01 08:24:36 -0300
Commit message:

 Update 1.3.0
 
Package: RegParallel
Commit: 87990f916a88eab9a30d2bead24a47f784db2cfc
Author: Kevin Blighe <kblighe@CLINICALBIO.dlink.com>
Date: 2018-11-01 08:19:19 -0300
Commit message:

 Update to 1.2.0
 
Package: EnhancedVolcano
Commit: a6bfd55c8286a3ca9e4b097489736092c02b38e6
Author: Kevin Blighe <kblighe@CLINICALBIO.dlink.com>
Date: 2019-01-17 23:07:02 -0200
Commit message:

 v1.1.2
 
Package: EnhancedVolcano
Commit: 4366a2809fa2997516f4eebe032522ab943490ed
Author: Kevin Blighe <kblighe@CLINICALBIO.dlink.com>
Date: 2019-01-17 22:45:11 -0200
Commit message:

 Change DrawConnectors to drawConnectors
 
Package: EnhancedVolcano
Commit: 1e920ca3c2ec3b47901e0e5797360968b1b90a18
Author: Kevin Blighe <kblighe@CLINICALBIO.dlink.com>
Date: 2018-12-02 21:27:32 -0200
Commit message:

 Minor doc edit
 
Package: BiocPkgTools
Commit: 4df9f3e33a9ddd6267f1d53cc68893916e05f689
Author: Sean Davis <seandavi@gmail.com>
Date: 2019-01-18 13:47:14 -0500
Commit message:

 Merge branch 'master' of github.com:seandavi/BiocPkgTools
 
Package: BiocPkgTools
Commit: 63f8ff8aa95e3cb57eb6e9ee81948aefb5ded5ee
Author: Sean Davis <seandavi@gmail.com>
Date: 2019-01-18 13:46:37 -0500
Commit message:

 Fixes #26

With Bioc 3.9, there are 4 builders, not 3,
so the html scraping code was broken.
 
Package: BiocPkgTools
Commit: 6458de9b1f2dc558f4971ba550a21d004a48ce21
Author: Sean Davis <seandavi@gmail.com>
Date: 2018-12-16 23:13:56 -0500
Commit message:

 Merge pull request #24 from Shians/master

Added new filter "None", set as default 
Package: BiocPkgTools
Commit: 07e48e65cb5192bf17a841a39957b5e17c75f842
Author: Shians <registertonysu@gmail.com>
Date: 2018-12-17 14:26:29 +1100
Commit message:

 Added new filter "None", set as default
 
Package: phenopath
Commit: de6847c0b0095fc244694fcc4ca32f7c039311c0
Author: Kieran Campbell <kieranrcampbell@gmail.com>
Date: 2019-01-18 10:38:22 -0800
Commit message:

 Bump version number to trigger bioc rebuild
 
Package: phenopath
Commit: d1729d0994115bc0605430fbb86852195fc1d64d
Author: Kieran Campbell <kieranrcampbell@gmail.com>
Date: 2019-01-18 10:37:24 -0800
Commit message:

 Change to as_tibble
 
Package: phenopath
Commit: c1dc8731e1e75a6477f8aebcb458fd57403f6d89
Author: Kieran Campbell <kieranrcampbell@gmail.com>
Date: 2019-01-18 10:32:18 -0800
Commit message:

 Merge remote-tracking branch 'upstream/master'
 
Package: phenopath
Commit: e749b5cfe98e13176e1d38a26bba6db587dfd7d7
Author: Kieran Campbell <kieranrcampbell@gmail.com>
Date: 2019-01-18 10:14:26 -0800
Commit message:

 Update vignette to fix bioconductor build error
 
Package: DMRcaller
Commit: 3a940b840c42aa88b1d2c3ccc927849ce384926d
Author: nrzabet <n.r.zabet@gen.cam.ac.uk>
Date: 2019-01-18 17:54:23 +0000
Commit message:

 bug fix
 
Package: ndexr
Commit: 766306940eb4636895177c5377e441ef6486f261
Author: Florian Auer <florian.auer@informatik.uni-augsburg.de>
Date: 2019-01-18 17:30:15 +0100
Commit message:

 api change for metadata (removed test 1.3); update email after move to AUG;
 
Package: ndexr
Commit: 942fccf9192a65b6b54c8e1321a4f672f2261e66
Author: Florian Auer <auerf@misit003.informatik.uni-augsburg.de>
Date: 2019-01-08 11:09:31 +0100
Commit message:

 Update contact info
 
Package: QuasR
Commit: 7fbd7dffc3122960fad5694381a8051ccecce46d
Author: mbstadler <stadler.michael@gmail.com>
Date: 2019-01-18 17:13:05 +0100
Commit message:

 bump version
 
Package: QuasR
Commit: 8fe88025874ff789558fbf8cb0bdc8ac9a005d6e
Author: mbstadler <stadler.michael@gmail.com>
Date: 2019-01-18 16:39:15 +0100
Commit message:

 fix multi-element conditionals in qProfile
 
Package: BiocSklearn
Commit: 9728135747fe50668325725f669a0a563fb35827
Author: Vince Carey <stvjc@channing.harvard.edu>
Date: 2019-01-18 10:21:05 -0500
Commit message:

 removing large HDF5 file that prevents update
 
Package: BiocSklearn
Commit: 848a98e9355fe0aa75a6a12ea9a4ceac97cc8d29
Author: Vince Carey <stvjc@channing.harvard.edu>
Date: 2019-01-18 10:07:27 -0500
Commit message:

 updated the serialized SummarizedExperiment for compliance
 
Package: INSPEcT
Commit: b32bab017cf9abb29dc4e1ad5adce8a02745df63
Author: ste-depo <ste.depo@gmail.com>
Date: 2019-01-18 15:43:51 +0100
Commit message:

 version bumbing
 
Package: INSPEcT
Commit: d2f699bb946a104e259467321ff26ab2da41df4b
Author: ste-depo <ste.depo@gmail.com>
Date: 2019-01-18 15:42:31 +0100
Commit message:

 fixed a bug in the model minimization in RNAdynamics app and in the comparison between two steady-states when one of the two prior rates was either 0 or NA
 
Package: amplican
Commit: 160fb95f8b0161272dde30b6ff80ad7fd84def39
Author: JokingHero <kornellabun@gmail.com>
Date: 2019-01-18 15:16:54 +0100
Commit message:

 now IndexHopping is Conservative
 
Package: NestLink
Commit: 7869b9245fa7271f0cd5fbe4b6b86b0977a24f66
Author: Christian Panse <cp@fgcz.ethz.ch>
Date: 2019-01-18 14:03:07 +0100
Commit message:

 spell check by Lucy
 
Package: amplican
Commit: afb3fe249b01aaf0f6188519ae7892ddf747aced
Author: JokingHero <kornellabun@gmail.com>
Date: 2019-01-18 12:57:40 +0100
Commit message:

 version++
 
Package: amplican
Commit: db6a3ef8f382e835071ce15fd0a22c51b6a387d3
Author: JokingHero <kornellabun@gmail.com>
Date: 2019-01-18 12:56:57 +0100
Commit message:

 fix function name in FAQ
 
Package: scran
Commit: e833e85233c95cb65d0e0d863b5c58a53b53ff26
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2019-01-18 10:52:56 +0000
Commit message:

 Removed package reference in links.
Bumped package version, date.
 
Package: NestLink
Commit: 3e007888f06d73a864c13e1b5c995051bdd039ff
Author: Christian Panse <cp@fgcz.ethz.ch>
Date: 2019-01-18 08:39:22 +0100
Commit message:

 cosmetics
 
Package: Rsubread
Commit: 0b19c59987cd686c2b610eb55452f21328ddf5b2
Author: Gordon Smyth <smyth@wehi.edu.au>
Date: 2019-01-18 18:13:26 +1100
Commit message:

 Add Rsubread bioRxiv paper to align, featureCounts and buildindex Rd pages.
 
Package: Rsubread
Commit: 4c774d543b97fe6de76e1aa5cbe62db4ef7d3899
Author: Gordon Smyth <smyth@wehi.edu.au>
Date: 2019-01-18 17:47:32 +1100
Commit message:

 Remove createAnnotationFile() and write.Rsubread(). Edit package Description.
 
Package: QuasR
Commit: 739fea93a2f10b24994aaad26bd33930c379cbb2
Author: mbstadler <stadler.michael@gmail.com>
Date: 2019-01-17 18:16:31 +0100
Commit message:

 consistently use 4-space identation
 
Package: QuasR
Commit: 217695758c35360f86a4ae9704706e99df4cb519
Author: mbstadler <stadler.michael@gmail.com>
Date: 2019-01-17 17:49:13 +0100
Commit message:

 untrack .gitignore
 
Package: QuasR
Commit: ba0f7953c0327d2adf711f8b3c1f048d0675d6fd
Author: mbstadler <stadler.michael@gmail.com>
Date: 2019-01-17 17:47:30 +0100
Commit message:

 v1.23.9: fix scaling in if condition in qExportWig

Merge branch 'master' of github.com:fmicompbio/QuasR

Conflicts:
	DESCRIPTION
	R/qExportWig.R
 
Package: QuasR
Commit: 7adedbae012e8cb4545ee24a24818159b95e5f3f
Author: mbstadler <stadler.michael@gmail.com>
Date: 2019-01-17 17:39:23 +0100
Commit message:

 v1.23.8: fix if condition
 
Package: Rsubread
Commit: fb2cc475ee6b84ce499d5416b7f8ae6a49824aad
Author: Gordon Smyth <smyth@wehi.edu.au>
Date: 2019-01-18 16:24:44 +1100
Commit message:

 Delete extra space
 
Package: Rsubread
Commit: dd5889588c4a0e49c1160f758604d19f0051bb46
Author: Yang LIAO <liao@wehi.edu.au>
Date: 2019-01-17 23:48:23 -0500
Commit message:

 changed opotion names for simReads()
 
Package: Rsubread
Commit: 7414676145b622d873fdfa0a11f6ee7ca1be5c80
Author: Gordon Smyth <smyth@wehi.edu.au>
Date: 2019-01-18 15:29:37 +1100
Commit message:

 Use tabular format for Value section. Remove reference.
 
Package: S4Vectors
Commit: 39bd2363b55a0f18ea65ef9011a823151d708e76
Author: larman <michafla@gene.com>
Date: 2019-01-17 16:01:27 -0800
Commit message:

 return to calling callNextMethod() in union,Hits,Hits()
 
Package: GENESIS
Commit: 20362677ec11c4226cf6146d33268413007b69ba
Author: Stephanie M. Gogarten <sdmorris@uw.edu>
Date: 2019-01-17 15:05:33 -0800
Commit message:

 bug fix for named covariance matrix list
 
Package: GENESIS
Commit: 64c42738571c7d8338ef57b1de651736b9089022
Author: Stephanie M. Gogarten <sdmorris@uw.edu>
Date: 2019-01-17 15:05:11 -0800
Commit message:

 fix unit test with new function name for Gtilde
 
Package: GENESIS
Commit: c68f859341ae3b51190312c668e946ce4fc2014a
Author: Stephanie M. Gogarten <sdmorris@uw.edu>
Date: 2019-01-17 15:04:40 -0800
Commit message:

 unit test reflects bug fix
 
Package: GENESIS
Commit: 1f81813af2d7d18b528278cf9832011e2d741a2b
Author: Matt <mconomos@uw.edu>
Date: 2019-01-17 13:59:47 -0800
Commit message:

 fixed bug in workingY for logistic regression case
 
Package: GENESIS
Commit: 6214fe5a41a2ac63955156c93e36eb79baed5853
Author: smgogarten <smgogarten@velasca>
Date: 2019-01-17 12:49:51 -0800
Commit message:

 version bump
 
Package: GENESIS
Commit: 47fceb48ec015200e2fecabbd9d90655ad22d6c9
Author: Stephanie M. Gogarten <sdmorris@uw.edu>
Date: 2019-01-17 12:32:05 -0800
Commit message:

 Merge pull request #6 from UW-GAC/dosage

add option to read dosage from DS field instead of genotypes 
Package: GENESIS
Commit: b8d3deb122b36a4042cd0b8f0676f1416c6a8399
Author: Stephanie M. Gogarten <sdmorris@uw.edu>
Date: 2019-01-17 12:30:04 -0800
Commit message:

 Merge branch 'master' into dosage 
Package: GENESIS
Commit: 0b7cf5a69156ad88f7451fc4a7be663576df67a4
Author: Matt Conomos <mconomos@uw.edu>
Date: 2019-01-16 16:11:25 -0800
Commit message:

 Merge pull request #8 from UW-GAC/gtilde

Gtilde 
Package: GENESIS
Commit: 5040a163aef70f2ae51153cf05647a6d4e3ae3dd
Author: Matt <mconomos@uw.edu>
Date: 2019-01-16 16:08:34 -0800
Commit message:

 missed one thing to comment out
 
Package: GENESIS
Commit: 520a1532ebccd30efcd04e62c786c912285e8a67
Author: Matt <mconomos@uw.edu>
Date: 2019-01-16 16:05:21 -0800
Commit message:

 temporarily remove fastSKAT and fastSMMAT functionality to merge Gtilde into master
 
Package: GENESIS
Commit: b8ef53ee976658ff8b55d5cc24df82f0ef691d3a
Author: Matt <mconomos@uw.edu>
Date: 2019-01-03 16:59:03 -0800
Commit message:

 updated assocTestAggregate for fastSKAT and fastSMMAT
 
Package: GENESIS
Commit: e4c62d5b0517d7ed4a3e6e69ad54c9ab1661b53a
Author: Matt <mconomos@uw.edu>
Date: 2019-01-03 16:00:41 -0800
Commit message:

 wip
 
Package: GENESIS
Commit: 8ddafd3ec01542e796177775d4acc8ab0603b341
Author: Matt <mconomos@uw.edu>
Date: 2019-01-03 14:33:22 -0800
Commit message:

 wip: adding in support for fastSMMAT and rewriting fastSKAT
 
Package: GENESIS
Commit: cede5d7f4fe68b0ada760fdabf6b4f1edda29b60
Author: Matt <mconomos@uw.edu>
Date: 2019-01-02 11:32:59 -0800
Commit message:

 wrote calcGtilde to use QR decomposition; changed notation of Xtilde to Gtilde
 
Package: GENESIS
Commit: a07d18f197cc4bea7981cdcd0ed8dd1a89889e62
Author: smgogarten <smgogarten@velasca>
Date: 2018-12-05 10:36:02 -0500
Commit message:

 add option to read dosage from DS field instead of genotypes
 
Package: BrowserViz
Commit: 12a26ef3f4a2a3d557fb4db382c9e80fb075cf38
Author: paul-shannon <paul.thurmond.shannon@gmail.com>
Date: 2019-01-17 12:47:26 -0800
Commit message:

 merge
 
Package: BrowserViz
Commit: 2720ebd72c4e6a096d5c5ebe89dd265c202ba818
Author: paul-shannon <paul.thurmond.shannon@gmail.com>
Date: 2019-01-17 12:46:48 -0800
Commit message:

 added standard runTests() function, prepare for package rewrite
 
Package: SeqVarTools
Commit: 47d2a858153a5442ddcbc0f2a7fc091093a8cb76
Author: smgogarten <smgogarten@velasca>
Date: 2019-01-17 12:22:04 -0800
Commit message:

 version bump
 
Package: SeqVarTools
Commit: a61afe99f4c61235d602f40a3df43bc799389406
Author: Stephanie M. Gogarten <sdmorris@uw.edu>
Date: 2019-01-17 12:18:17 -0800
Commit message:

 Merge pull request #1 from smgogarten/dosage

add method to read dosage from DS field 
Package: SeqVarTools
Commit: 1c0772443bb5f8836432592c626c451bb70983e0
Author: smgogarten <smgogarten@velasca>
Date: 2018-12-05 10:34:19 -0500
Commit message:

 add method to read dosage from DS field
 
Package: scater
Commit: 4d99380471a03e15aa1a97d203631894bad9d4f1
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2019-01-17 16:30:13 +0000
Commit message:

 Fixes #79 in isOutlier (log=TRUE with per-batch thresholds).
Added tests for per-batch threshold reporting.
 
Package: Rbowtie
Commit: 90c89177e211cb7924a78405af05aa9778309ae7
Author: mbstadler <stadler.michael@gmail.com>
Date: 2019-01-17 16:56:54 +0100
Commit message:

 add README
 
Package: Rbowtie
Commit: 77039fec6dde2b9486623f69b7833440c3b13362
Author: mbstadler <stadler.michael@gmail.com>
Date: 2019-01-17 16:25:02 +0100
Commit message:

 add travis
 
Package: Rbowtie
Commit: 379bccf6a822b0d874dd656ab91a23b8bc53abe7
Author: mbstadler <stadler.michael@gmail.com>
Date: 2019-01-17 16:11:45 +0100
Commit message:

 v.1.23.1 : expand paths before shQuote (e.g. to support paths containing ~)
 
Package: msPurity
Commit: 166e189d8aef7b532e3fd86a6ad7ae707dbb0f35
Author: Thomas N Lawson <thomas.nigel.lawson@gmail.com>
Date: 2019-01-17 11:52:30 +0000
Commit message:

 update test for spectral matching (too time consuming) (#26)

 
Package: scran
Commit: f13c376129773920b2925ba25315fbb429f089dd
Author: Aaron Lun <infinite.monkeys.with.keyboards@gmail.com>
Date: 2019-01-17 09:38:11 +0000
Commit message:

 Remove explicit R dependency.
 
Package: beachmat
Commit: cbed28935009652a6176a45ebc6a4f692ae51ade
Author: Aaron Lun <infinite.monkeys.with.keyboards@gmail.com>
Date: 2019-01-17 09:58:45 +0000
Commit message:

 Removed explicit R dependency from all DESCRIPTIONs.
Bumped date in internal DESCRIPTIONs.
 
Package: SingleCellExperiment
Commit: 786d118b1ece7bc21d1efa90f3c10663397c1218
Author: Aaron Lun <infinite.monkeys.with.keyboards@gmail.com>
Date: 2019-01-17 09:40:42 +0000
Commit message:

 Removed explicit R dependency.
 
Package: DropletUtils
Commit: aba4c7848fbea9c48a625d4bea6c0a517cbf52b1
Author: Aaron Lun <infinite.monkeys.with.keyboards@gmail.com>
Date: 2019-01-17 09:39:08 +0000
Commit message:

 Remove explicit R dependency, Depends on BiocParallel.
 
Package: singleCellTK
Commit: 6bc8dae08c5ab7639f31fc90f48b3c989585b8ce
Author: David Jenkins <d.jenkins0@gmail.com>
Date: 2019-01-16 23:37:32 -0500
Commit message:

 Version bump after cleaning
 
Package: singleCellTK
Commit: eaa86d32cdea459daca012fcf14705549a68a47e
Author: David Jenkins <d.jenkins0@gmail.com>
Date: 2019-01-16 23:27:58 -0500
Commit message:

 Merge branch 'master' of github.com:compbiomed/singleCellTK
 
Package: singleCellTK
Commit: e53ba94e1ec5a296d8923ad7215946639ffd17bd
Author: David Jenkins <d.jenkins0@gmail.com>
Date: 2019-01-16 22:51:11 -0500
Commit message:

 Merge branch 'mmkhan19-master'
 
Package: singleCellTK
Commit: 02d99071d265c7d5fc3315e1a69555302f24572d
Author: David Jenkins <d.jenkins0@gmail.com>
Date: 2019-01-16 22:51:11 -0500
Commit message:

 Merge branch 'mmkhan19-master'


Former-commit-id: e53ba94e1ec5a296d8923ad7215946639ffd17bd 
Package: singleCellTK
Commit: a41424633acc613ade4371d1aad967f068baf0b2
Author: David Jenkins <d.jenkins0@gmail.com>
Date: 2019-01-16 22:49:58 -0500
Commit message:

 Make theme configurable
 
Package: singleCellTK
Commit: 815a10f4b057f6b6a3dbd6d58a6f77b485549889
Author: David Jenkins <d.jenkins0@gmail.com>
Date: 2019-01-16 22:49:58 -0500
Commit message:

 Make theme configurable


Former-commit-id: a41424633acc613ade4371d1aad967f068baf0b2 
Package: singleCellTK
Commit: f21c50f937558891db0d54c35168dcd77ffe6c2c
Author: Mohammed Muzamil Khan <mmkhan@bu.edu>
Date: 2019-01-16 16:59:42 -0500
Commit message:

 resolved issue #177 - stop reactivity of tabsetpanel in enrichR tab.
 
Package: singleCellTK
Commit: 0c8fa44c4b31fa670ae7dfc123ae7f53e27102d8
Author: Mohammed Muzamil Khan <mmkhan@bu.edu>
Date: 2019-01-16 16:59:42 -0500
Commit message:

 resolved issue #177 - stop reactivity of tabsetpanel in enrichR tab.


Former-commit-id: f21c50f937558891db0d54c35168dcd77ffe6c2c 
Package: singleCellTK
Commit: 2a902149c826bb0754230725827366fd0286ea27
Author: Mohammed Muzamil Khan <mmkhan@bu.edu>
Date: 2019-01-15 17:47:11 -0500
Commit message:

 new UI, increased the range of visGenes to 25, restructured visplot code, no condition for barplot, version bump
 
Package: singleCellTK
Commit: 83266d73a6d3b2be30ad95601ceed78df3f542d1
Author: Mohammed Muzamil Khan <mmkhan@bu.edu>
Date: 2019-01-15 17:47:11 -0500
Commit message:

 new UI, increased the range of visGenes to 25, restructured visplot code, no condition for barplot, version bump


Former-commit-id: 2a902149c826bb0754230725827366fd0286ea27 
Package: singleCellTK
Commit: 8b1ebf032f37f7986de501f43f6848364f6e28cd
Author: Mohammed Muzamil Khan <mmkhan@bu.edu>
Date: 2019-01-09 20:13:10 -0500
Commit message:

 changed stop() to shinyalert() to maintain consistency for diffexSavedResults(), changed myValues and dList to diffExValues and diffExList respectively and restructured code for saving the results when an alert is encountered
 
Package: singleCellTK
Commit: 0760f139e8c2968e29d23a0361a21cf2899a5d16
Author: Mohammed Muzamil Khan <mmkhan@bu.edu>
Date: 2019-01-09 20:13:10 -0500
Commit message:

 changed stop() to shinyalert() to maintain consistency for diffexSavedResults(), changed myValues and dList to diffExValues and diffExList respectively and restructured code for saving the results when an alert is encountered


Former-commit-id: 8b1ebf032f37f7986de501f43f6848364f6e28cd 
Package: singleCellTK
Commit: cf2921685aaad58290d6ca735b80279cf8d07da3
Author: Mohammed Muzamil Khan <mmkhan@bu.edu>
Date: 2019-01-09 16:45:46 -0500
Commit message:

 help notes in enrichR and diffex tab, fixed the issue in saving diffex results with a unique name, version bump
 
Package: singleCellTK
Commit: 3338fe22b3e16f373b113ba8fd6a9dc97bf1c694
Author: Mohammed Muzamil Khan <mmkhan@bu.edu>
Date: 2019-01-09 16:45:46 -0500
Commit message:

 help notes in enrichR and diffex tab, fixed the issue in saving diffex results with a unique name, version bump


Former-commit-id: cf2921685aaad58290d6ca735b80279cf8d07da3 
Package: singleCellTK
Commit: 9e1f988703133132e5f7f2949f2f29edbad3d07a
Author: Mohammed Muzamil Khan <mmkhan@bu.edu>
Date: 2018-11-04 18:15:43 -0500
Commit message:

 version bump
 
Package: singleCellTK
Commit: cb1c026f1456b1b73ad2a0e4a44dbef3dbbd542f
Author: Mohammed Muzamil Khan <mmkhan@bu.edu>
Date: 2018-11-04 18:15:43 -0500
Commit message:

 version bump


Former-commit-id: 9e1f988703133132e5f7f2949f2f29edbad3d07a 
Package: singleCellTK
Commit: cb11f9d431b7acc2c3913f71fa1822843ba884d3
Author: Mohammed Muzamil Khan <mmkhan@bu.edu>
Date: 2018-11-04 18:14:41 -0500
Commit message:

 updated bioconductor packages and resolved the dataframe error, ordered padj columns, removed unncessary code from loadsavedresults(), added  code for exact match of loading similar names of saved results
 
Package: singleCellTK
Commit: 400cf51e40574a667fde8f3864ec9fbd55b05bdd
Author: Mohammed Muzamil Khan <mmkhan@bu.edu>
Date: 2018-11-04 18:14:41 -0500
Commit message:

 updated bioconductor packages and resolved the dataframe error, ordered padj columns, removed unncessary code from loadsavedresults(), added  code for exact match of loading similar names of saved results


Former-commit-id: cb11f9d431b7acc2c3913f71fa1822843ba884d3 
Package: mixOmics
Commit: ca0303f06040dfca5b2dc90b0c915245ea41289d
Author: frohart <florian.rohart@gmail.com>
Date: 2019-01-17 13:19:51 +1000
Commit message:

 faster scaling function
 
Package: mixOmics
Commit: 77298d2a2998fdb818b415b3ee9e923dc679c266
Author: frohart <florian.rohart@gmail.com>
Date: 2019-01-10 18:54:40 +1000
Commit message:

 replace 1: by seq_len()
 
Package: mixOmics
Commit: 3d6de68f5aed4d1b174e54d3607383bd329ddb6b
Author: frohart <florian.rohart@gmail.com>
Date: 2019-01-10 15:35:39 +1000
Commit message:

 replace 1: by seq_len()
 
Package: mixOmics
Commit: edaa9fe9a23e3c981158e476c85488456853fbc1
Author: frohart <florian.rohart@gmail.com>
Date: 2019-01-10 14:47:31 +1000
Commit message:

 faster scaling function
 
Package: SWATH2stats
Commit: 36dde94f94505eb9d87d5d7a92c48a483104151e
Author: Peter Blattmann <blattmann@imsb.biol.ethz.ch>
Date: 2019-01-16 23:44:15 +0100
Commit message:

 v1.13.3 move PECA to enhance in Description
 
Package: TFutils
Commit: 5089ea987f9df06aa87eccadb824ba9eb0c5a46b
Author: Vince Carey <stvjc@channing.harvard.edu>
Date: 2019-01-16 15:29:11 -0500
Commit message:

 ready for submission to f1000
 
Package: VariantAnnotation
Commit: 3e4ed9abbf094ae4608b8a6e688f44ebb27d6de0
Author: vobencha <vobencha@gmail.com>
Date: 2019-01-16 10:47:24 -0800
Commit message:

 Silence filterVcf vignette code chunk while we investigate C stack usage
 
Package: DaMiRseq
Commit: 85e0e7369ede9b8db78ba4b2a6604cd4e0b882d2
Author: BioinfoMonzino <mattia.chiesa@cardiologicomonzino.it>
Date: 2019-01-16 15:35:40 +0100
Commit message:

 bug fixed v1.7.3
 
Package: MAST
Commit: 5b6270ccf8f686def014156d49dfe2f38c69f0a3
Author: Andrew McDavid <amcdavid@fhcrc.org>
Date: 2019-01-16 08:19:48 -0500
Commit message:

 Merge branch 'master' of github.com:RGLab/MAST
 
Package: MAST
Commit: af1792df51b425c5ca324dfe7bdc4a2a006700ac
Author: Andrew McDavid <amcdavid@fhcrc.org>
Date: 2019-01-16 08:19:20 -0500
Commit message:

 fix mismatch in BayesGLMLike prototype vs representation
 
Package: MAST
Commit: 99866917f97d10d494d0a3821164d548ed2a6736
Author: Andrew McDavid <andrew.n.mcdavid@gmail.com>
Date: 2018-11-30 16:40:02 -0500
Commit message:

 Merge pull request #104 from seaaan/patch-1

minor typos 
Package: MAST
Commit: 1eb4662b045561272d163fdf9e048ec7d3d40626
Author: Sean Hughes <seaaan@gmail.com>
Date: 2018-11-30 12:44:55 -0800
Commit message:

 minor typos 
Package: amplican
Commit: ff3c460b6c82cf9374ac2142c2c2caf28bf87afe
Author: JokingHero <kornellabun@gmail.com>
Date: 2019-01-16 13:54:15 +0100
Commit message:

 index hopping improbability cases covered
 
Package: NestLink
Commit: 75fbe3c8fb436c6ae7f70fbfdcd1ebcf31b184a9
Author: Christian Panse <cp@fgcz.ethz.ch>
Date: 2019-01-16 09:49:47 +0100
Commit message:

 corrected emails
changed maintainer email to cp@fgcz.ethz.ch
 
Package: ClassifyR
Commit: 4bd325207913e9af69f8a2778e99dc838bff6937
Author: Dario Strbenac <dstr7320@uni.sydney.edu.au>
Date: 2019-01-16 15:03:34 +1100
Commit message:

 Remove all references to formerly used mnlogit package which provies a multinomial logistic regression implementation. Functions using it were removed in a previous version.
 
Package: beachmat
Commit: 3f40b1269bd5eed3667779fe552ad1237ea8cb49
Author: Aaron Lun <infinite.monkeys.with.keyboards@gmail.com>
Date: 2019-01-16 03:39:34 +0000
Commit message:

 Fixed remaining (un)signed integer comparison warnings.
 
Package: beachmat
Commit: 26edf02d9c5b3dc81131b625ee6c4d35563e0301
Author: Aaron Lun <infinite.monkeys.with.keyboards@gmail.com>
Date: 2019-01-16 00:46:47 +0000
Commit message:

 Minor clean-up of vignette comments, bumped version and date.
 
Package: beachmat
Commit: 7cee611f2e2b67414ea16f8df296df79c8302d69
Author: Aaron Lun <infinite.monkeys.with.keyboards@gmail.com>
Date: 2019-01-16 00:27:09 +0000
Commit message:

 Renamed delayed_matrix to delayed_reader for consistency.
 
Package: simpleSingleCell
Commit: 70e10014c3d4ebf52056faa5dfe0317b7c93c626
Author: Aaron Lun <infinite.monkeys.with.keyboards@gmail.com>
Date: 2019-01-16 00:07:41 +0000
Commit message:

 Switch to math mode when writing 'p-values'.
 
Package: simpleSingleCell
Commit: 87b43953e27669dae139fed6b239640f8dac3728
Author: Aaron Lun <infinite.monkeys.with.keyboards@gmail.com>
Date: 2019-01-16 00:05:02 +0000
Commit message:

 Mentioned use of largest niters in emptyDrops.
 
Package: RaggedExperiment
Commit: af4e842e768ac928618dd40b88858f0bbe914abd
Author: LiNk-NY <mramos09@gmail.com>
Date: 2019-01-15 16:55:27 -0500
Commit message:

 add rowRanges<- method
 
Package: graphite
Commit: 3cef65ffd66006430a24078ea8b855e947531628
Author: Gabriele Sales <gbrsales@gmail.com>
Date: 2019-01-15 21:47:30 +0100
Commit message:

 Discard automatically invalid pathway data files
 
Package: HDCytoData
Commit: 5da91293a8df6c5a9bf7be8635f860ae2d5940cc
Author: Lukas Weber <lukmweber@gmail.com>
Date: 2019-01-15 21:48:29 +0100
Commit message:

 version
 
Package: HDCytoData
Commit: 3a4c5b846a5213d33026affee98f1e5b51cda9ef
Author: Lukas Weber <lukmweber@gmail.com>
Date: 2019-01-15 21:48:18 +0100
Commit message:

 fix UTF encoding issue (long hyphens)
 
Package: HDCytoData
Commit: 1afb9e5e0c6627bda806ac6fb0503668940fddea
Author: Lukas Weber <lukmweber@gmail.com>
Date: 2019-01-15 20:51:21 +0100
Commit message:

 version
 
Package: HDCytoData
Commit: 345598245ae7965014af325855d2ed001bb8bd3f
Author: Lukas Weber <lukmweber@gmail.com>
Date: 2019-01-15 20:51:04 +0100
Commit message:

 update ExperimentHub IDs in vignette
 
Package: SeqArray
Commit: 7810338996e51e5d00875993e60a8d65e27c988c
Author: Xiuwen Zheng <zhengxwen@gmail.com>
Date: 2019-01-15 13:41:59 -0600
Commit message:

 seqMerge() merges GDS files without genotypes
 
Package: HDCytoData
Commit: f93e4970919e61107f1f9e925106ce28fcd2568d
Author: Lukas Weber <lukmweber@gmail.com>
Date: 2019-01-15 20:23:16 +0100
Commit message:

 version
 
Package: HDCytoData
Commit: c70df657564d4fdfcb422e858c8d30934ce6d4d2
Author: Lukas Weber <lukmweber@gmail.com>
Date: 2019-01-15 20:22:58 +0100
Commit message:

 vignette: fix affiliations
 
Package: AnnotationHubData
Commit: bd63665df355fc246ed858e9cee193601d446157
Author: lshep <lori.shepherd@roswellpark.org>
Date: 2019-01-15 12:56:06 -0500
Commit message:

 Add requested SourceType FCS in validation

  - reportedly widely used as the standard filetype for both flow cytometry and mass cytometry
 
Package: msPurity
Commit: 15bf36407d85985d8941ccdf659847aabf3a2966
Author: tomnl <thomas.nigel.lawson@gmail.com>
Date: 2019-01-15 17:19:27 +0000
Commit message:

 Merge branch 'master' of https://github.com/computational-metabolomics/msPurity
 
Package: msPurity
Commit: 8f24a3af946e2dac5e78b4c11c1afbccff49d8df
Author: tomnl <thomas.nigel.lawson@gmail.com>
Date: 2019-01-15 17:19:15 +0000
Commit message:

 version bump
 
Package: msPurity
Commit: 8f2f2b82e5b61dfb4c988f06b458bd3648893287
Author: Thomas N Lawson <thomas.nigel.lawson@gmail.com>
Date: 2019-01-15 17:17:57 +0000
Commit message:

 Spectral matching bugfix (#25)

* sm bug fix (collate and polarity)

* add catch for overfiltering library
 
Package: BiocCheck
Commit: f0d516a13f04a79a5c4455a5528d868424713f8d
Author: lshep <lori.shepherd@roswellpark.org>
Date: 2019-01-15 11:47:45 -0500
Commit message:

 Fix output of system2 grep call
 
Package: brainImageR
Commit: e6046d0c00122875a9f1101a39f213e8bf459835
Author: Sara Linker <sara.linker@gmail.com>
Date: 2019-01-15 08:38:49 -0800
Commit message:

 version bump
 
Package: brainImageR
Commit: 9a6f093f837c8a35541e0db35d28eea82c2ea583
Author: Sara Linker <sara.linker@gmail.com>
Date: 2019-01-15 08:36:12 -0800
Commit message:

 big fix: adult dup row name and adult inverted fig legend
 
Package: brainImageR
Commit: d1057e8b847900dec74e3e209410834ce2bd66f6
Author: Sara Linker <sara.linker@gmail.com>
Date: 2019-01-15 07:51:29 -0800
Commit message:

 Merge branch 'master' of github.com:saralinker/brainImageR
 
Package: brainImageR
Commit: a0accfc84053d1a760b49245f3ab7ceee3c9abe8
Author: Sara <saralinker@users.noreply.github.com>
Date: 2019-01-14 08:38:35 -0800
Commit message:

 Update README.md 
Package: brainImageR
Commit: 52c1da6024b6fe40a2bf2ec8386fd5126a122bec
Author: Sara <saralinker@users.noreply.github.com>
Date: 2018-08-30 06:07:29 -0700
Commit message:

 Update brainImageR.Rmd 
Package: brainImageR
Commit: b655b8d1c540f6b255ea77500dfe2035dba4b5a4
Author: Sara <saralinker@users.noreply.github.com>
Date: 2018-08-30 06:07:02 -0700
Commit message:

 Update brainImageR.Rmd 
Package: brainImageR
Commit: 0f1c0641d5f393c3d7e5aaec3c324567cbce5d7c
Author: Sara <saralinker@users.noreply.github.com>
Date: 2018-08-30 06:01:05 -0700
Commit message:

 Update brainImageR.Rmd 
Package: brainImageR
Commit: f51e4e9790f57683347f69fe4e8a79af6df4e967
Author: Sara <saralinker@users.noreply.github.com>
Date: 2018-08-30 05:45:46 -0700
Commit message:

 Update README.md 
Package: brainImageR
Commit: 94dc77c6d801bb1cc527436aa820b278047b0d8f
Author: Sara <saralinker@users.noreply.github.com>
Date: 2018-08-30 05:45:30 -0700
Commit message:

 Update README.md 
Package: tximeta
Commit: a0e343a17b3435dbd965892132f609840a8a96bb
Author: mikelove <michaelisaiahlove@gmail.com>
Date: 2019-01-15 10:59:04 -0500
Commit message:

 add M20
 
Package: HDCytoData
Commit: b4d5953efded3367f65b90e41b2504fb4276c53c
Author: Lukas Weber <lukmweber@gmail.com>
Date: 2019-01-14 20:42:02 +0100
Commit message:

 version
 
Package: HDCytoData
Commit: 3db1f58bd6bcd167db93cd76e08249840aaca602
Author: Lukas Weber <lukmweber@gmail.com>
Date: 2019-01-14 20:41:54 +0100
Commit message:

 update NEWS
 
Package: HDCytoData
Commit: 80a3192235d10e3f534381b92cbf53777a4296af
Author: Lukas Weber <lukmweber@gmail.com>
Date: 2019-01-14 20:41:37 +0100
Commit message:

 add Krieg_Anti_PD_1 dataset, update Bodenmiller_BCR_XL flowSet object
 
Package: HDCytoData
Commit: b05ca3e31feb46062a5951182fe0e79e948644c9
Author: Lukas Weber <lukmweber@gmail.com>
Date: 2019-01-14 17:13:53 +0100
Commit message:

 update Bodenmiller_BCR_XL dataset; update description slots in flowSets
 
Package: HDCytoData
Commit: db8233d86ab08d53c896e606cac6c44bd22a3216
Author: Lukas Weber <lukmweber@gmail.com>
Date: 2019-01-11 20:42:01 +0100
Commit message:

 add Nilsson_rare and Mosmann_rare datasets
 
Package: HDCytoData
Commit: 9a58baa34e728a5f9c7b3840afda55403b88c052
Author: Lukas Weber <lukmweber@gmail.com>
Date: 2019-01-10 17:03:15 +0100
Commit message:

 clean up
 
Package: HDCytoData
Commit: 5601cc2366074fcca1f7d23cf4f8f37c0596812e
Author: Lukas Weber <lukmweber@gmail.com>
Date: 2019-01-10 16:28:52 +0100
Commit message:

 add Samusik_01 and Samusik_all datasets
 
Package: SWATH2stats
Commit: 0769cd20b6fe308eb59ab3fd03b71f39e7e6a8ab
Author: Peter Blattmann <blattmann@imsb.biol.ethz.ch>
Date: 2019-01-15 13:47:21 +0100
Commit message:

 v1.13.2 make that PECA chunk in vignette is not evaluated to prevent build errors
 
Package: simpleSingleCell
Commit: d7cd3d6b0b1a6a62823c64273511281f8200ea46
Author: Aaron Lun <infinite.monkeys.with.keyboards@gmail.com>
Date: 2019-01-15 12:44:10 +0000
Commit message:

 Merge remote-tracking branch 'upstream/master'
 
Package: simpleSingleCell
Commit: 81f709c666e2a72e7f689043dd450f60107e3df7
Author: Aaron Lun <infinite.monkeys.with.keyboards@gmail.com>
Date: 2019-01-15 12:42:23 +0000
Commit message:

 Updated expected platelet cluster for emptyDrops RNG changes.
 
Package: TVTB
Commit: de4dfb2f81f9ebf2d7c61d7885cd92ba91d425b2
Author: Kevin Rue-Albrecht <kevinrue67@gmail.com>
Date: 2019-01-15 11:59:58 +0000
Commit message:

 Merge pull request #1 from kevinrue/test

Fix for R-devel update 
Package: TVTB
Commit: 8f26e624103266027458542ba93bfe7261baffe5
Author: Kevin Rue-Albrecht <kevinrue67@gmail.com>
Date: 2019-01-15 10:49:10 +0000
Commit message:

 version bump and date
 
Package: TVTB
Commit: aadcf1e2515887546c32abecb29deab5628e566d
Author: Kevin Rue-Albrecht <kevinrue67@gmail.com>
Date: 2019-01-15 10:38:49 +0000
Commit message:

 update Travis YAML from iSEE
 
Package: TVTB
Commit: 3302f33da74db44d473b57ed5e19d584270e1b7b
Author: Kevin Rue-Albrecht <kevinrue67@gmail.com>
Date: 2019-01-15 10:24:28 +0000
Commit message:

 declare prototype for all slots
 
Package: DropletUtils
Commit: f2f1cbf92c2f994e80ccf620ff9bb7a39b5db3d0
Author: Aaron Lun <infinite.monkeys.with.keyboards@gmail.com>
Date: 2019-01-15 11:04:36 +0000
Commit message:

 Simplified PCG32 seeding with integer inputs,
at the cost of not seeding across the full state space.
 
Package: scran
Commit: 4d91c593f013c31ab1615802ce65ef5f47201bd3
Author: Aaron Lun <infinite.monkeys.with.keyboards@gmail.com>
Date: 2019-01-15 10:41:57 +0000
Commit message:

 Fixed seeding in shuffle tests, extended sanity checks.
 
Package: scran
Commit: d7f280e3f1e2aedde76899f4c0190f14466cfb7a
Author: Aaron Lun <infinite.monkeys.with.keyboards@gmail.com>
Date: 2019-01-15 10:18:28 +0000
Commit message:

 Simplified PCG32 seeding to use integer inputs,
at the cost of not seeding across the full state space.
 
Package: scran
Commit: 65b89093492e6fe5f4728e7f8996ce6b3381f04e
Author: Aaron Lun <infinite.monkeys.with.keyboards@gmail.com>
Date: 2019-01-13 03:16:25 +0000
Commit message:

 Added casts to avoid signed/unsigned comparisons.
 
Package: fgsea
Commit: f59e90354f7c4df5d2169065e73d167bb9328168
Author: Alexey Sergushichev <alsergbox@gmail.com>
Date: 2019-01-15 13:29:02 +0300
Commit message:

 version bump
 
Package: fgsea
Commit: a3540dddd0eba19ae06fcbbd564162535fa30670
Author: Alexey Sergushichev <alsergbox@gmail.com>
Date: 2019-01-15 12:43:48 +0300
Commit message:

 Merge branch 'vdsukhov-master'
 
Package: fgsea
Commit: 6edee4e42173cafd0132d792f4635d756f58f7e1
Author: Vladimir Sukhov <vdsukhov@ya.ru>
Date: 2019-01-15 01:01:36 +0300
Commit message:

 Refactoring and bug fixes in fgseaMultilevel
 
Package: fgsea
Commit: f9fc66d2ffecf2941b1c66494a1c055aec5ac1d3
Author: Alexey Sergushichev <alsergbox@gmail.com>
Date: 2019-01-11 11:50:34 +0300
Commit message:

 Update LICENCE 
Package: fgsea
Commit: 53f5f2a7bad3549deef69c1992cb6b76b0588dfd
Author: Alexey Sergushichev <alsergbox@gmail.com>
Date: 2018-11-16 21:22:38 +0300
Commit message:

 Merge branch 'vdsukhov-fgseaMultilevel'
 
Package: fgsea
Commit: ca711425951ea439cf5ecd7da42c9ae8cbb87b5a
Author: Alexey Sergushichev <alsergbox@gmail.com>
Date: 2018-11-16 21:22:12 +0300
Commit message:

 description update
 
Package: fgsea
Commit: 1b00fb8e11354a5f34f92aa0151bfa78bf5d9dad
Author: Vladimir Sukhov <vdsukhov@ya.ru>
Date: 2018-11-16 18:52:24 +0300
Commit message:

 Implemented new features based on adaptive multilevel splitting Monte Carlo approach
 
Package: ensembldb
Commit: 46c8eaa3c2dd1d42e502ce5431bb9cd32b616ca1
Author: jotsetung <johannes.rainer@gmail.com>
Date: 2019-01-15 10:28:04 +0100
Commit message:

 Fix wrong slot naming in classes extending AnnotationFilter
 
Package: ensembldb
Commit: 3db600da448e6f520f99fb15e801903cb29befa1
Author: jotsetung <johannes.rainer@gmail.com>
Date: 2018-12-07 14:34:15 +0100
Commit message:

 Convert roxygen documentation for Filter classes to md
 
Package: ensembldb
Commit: 70232af6c6f934d07b9eda3567495acb24ba485f
Author: jotsetung <johannes.rainer@gmail.com>
Date: 2018-12-07 11:56:24 +0100
Commit message:

 Modify perl script to include transcript and gene versions

- Modify the perl script to extract the gene and transcript IDs with version
  from Ensembl (issue #89).
- Add columns tx_id_version and gene_id_version to the transcript and gene
  database tables.
 
Package: INSPEcT
Commit: f8965fe86e336cd0da3e025e4e50c27a9a851b21
Author: ste-depo <ste.depo@gmail.com>
Date: 2019-01-15 10:24:26 +0100
Commit message:

 removed .DS_Store file
 
Package: INSPEcT
Commit: 91f494e99ba1c6551e17d15ae7c4d4bc947f64e9
Author: ste-depo <ste.depo@gmail.com>
Date: 2019-01-15 10:22:20 +0100
Commit message:

 fixed loading of default file in shiny apps
 
Package: INSPEcT
Commit: fe9f7d01028e470d749c1ec32f2687557d3a678b
Author: ste-depo <ste.depo@gmail.com>
Date: 2018-12-24 10:33:30 +0100
Commit message:

 version 1.12.1
 
Package: statTarget
Commit: 8334a64e84eb92cafb1ef7d7ecccafb3c7af3992
Author: 13479776 <hemi.luan@gmail.com>
Date: 2019-01-15 16:18:46 +0800
Commit message:

 pathway
 
Package: statTarget
Commit: 03b738ea65b691cf2717c501ab3cda966df26489
Author: 13479776 <hemi.luan@gmail.com>
Date: 2019-01-15 16:18:08 +0800
Commit message:

 pathway
 
Package: bsseq
Commit: c93310e9d33da5ed1bf0373013170668cc8c7ba2
Author: Peter Hickey <peter.hickey@gmail.com>
Date: 2019-01-15 16:58:24 +1100
Commit message:

 Bump minimum beachmat version on advice of Aaron
 
Package: bsseq
Commit: bb84a98edd5978382778f92658dc3cdadc240acf
Author: Peter Hickey <peter.hickey@gmail.com>
Date: 2019-01-15 16:55:22 +1100
Commit message:

 Merge remote-tracking branch 'upstream/master'
 
Package: bsseq
Commit: 0f038250d18b3e8f7c1d70c0f52a3d865b667cb6
Author: Peter Hickey <peter.hickey@gmail.com>
Date: 2018-10-31 07:40:12 +1100
Commit message:

 Merge remote-tracking branch 'bioc/master'
 
Package: bsseq
Commit: fb5b6ff840b301b0fbb9f2ed13ef9d731cd867f5
Author: Kasper Daniel Hansen <kasperdanielhansen@gmail.com>
Date: 2018-10-29 22:51:14 -0400
Commit message:

 added BatchJobs to Suggests
 
Package: scater
Commit: 632a29b35cc77a1034b3d602ae69dbb7f4d9ad07
Author: Aaron Lun <infinite.monkeys.with.keyboards@gmail.com>
Date: 2019-01-15 02:36:40 +0000
Commit message:

 Version bump for beachmat update.
 
Package: DropletUtils
Commit: 9b0c4cc107546d81c5c3d4dd9c6c8dd67735ee5c
Author: Aaron Lun <infinite.monkeys.with.keyboards@gmail.com>
Date: 2019-01-15 02:20:20 +0000
Commit message:

 Bumped version number for beachmat update.
 
Package: supraHex
Commit: 505cec5601b7fbacd601ffd8e6c720ca2c1ccca8
Author: Hai Fang <hfang.shanghai@gmail.com>
Date: 2019-01-13 23:04:16 +0000
Commit message:

 Update to the version 1.21.1
 
Package: supraHex
Commit: a2b974780ec83702e30ded1f98c8d6f122862401
Author: Hai Fang <hfang.shanghai@gmail.com>
Date: 2019-01-11 23:31:24 +0000
Commit message:

 Update to the version 1.21.2
 
Package: supraHex
Commit: 6537de5547fb2a538112538ed97a159a5e0fab61
Author: Hai Fang <hfang.shanghai@gmail.com>
Date: 2019-01-10 12:32:05 +0000
Commit message:

 Update to the version 1.21.2
 
Package: NestLink
Commit: 4f0c2658a0f64c22023d9e884b5340e102601d90
Author: Christian Panse <cp@fgcz.ethz.ch>
Date: 2019-01-14 22:26:08 +0100
Commit message:

 ORCID cosmetics
 
Package: Rsamtools
Commit: 8295faea342360c89d13a8c1912fb7b87a98705b
Author: Martin Morgan <martin.morgan@roswellpark.org>
Date: 2019-01-14 16:08:31 -0500
Commit message:

 use R_NilValue SEXP rather than NULL in Rf_MakeExternalPtr()
 
Package: TimeSeriesExperiment
Commit: b7936a23fd3c705e826f73126f3df44100694d48
Author: Lan Huong Nguyen <nlhuong90@gmail.com>
Date: 2019-01-14 12:54:30 -0800
Commit message:

 bump up the devel version
 
Package: TimeSeriesExperiment
Commit: f27f5d390e685f4b9b990717316c65c0db36d6f4
Author: Lan Huong Nguyen <nlhuong90@gmail.com>
Date: 2019-01-14 01:06:49 -0800
Commit message:

 fix cluster naming and plots
 
Package: TimeSeriesExperiment
Commit: db8a989d0762fc805189a24ec14389cd305d15c4
Author: Lan Huong Nguyen <nlhuong90@gmail.com>
Date: 2019-01-13 16:39:27 -0800
Commit message:

 fix plot scales for facet_wrapping
 
Package: ggcyto
Commit: e733739f51494ea49580e6cb7d22c34eb8ad9e10
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-01-14 12:29:02 -0800
Commit message:

 bump
 
Package: ggcyto
Commit: 1c2fe68e00a7880bef228a3dd08836e91733347b
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-01-14 12:18:24 -0800
Commit message:

 revalidate figs for test cases. #43
 
Package: ggcyto
Commit: 770764f7cd10c78065eca2bd7f6108ca57824ede
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-01-14 11:58:10 -0800
Commit message:

 add test case. #43
 
Package: ggcyto
Commit: 989114037a387455bf4144ad39987eb9cace791b
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-01-14 11:57:29 -0800
Commit message:

 fix the geom_gate dispatching error. #43
 
Package: ggcyto
Commit: cd44d9d8073a66e74ef4e889c275e667667a551d
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-01-14 12:23:58 -0800
Commit message:

 bump
 
Package: ggcyto
Commit: 2bd7bcd4c2ad62afe510de36c31d093e50196c2e
Author: Kayla-Morrell <kayla.morrell@roswellpark.org>
Date: 2019-01-04 13:34:31 -0500
Commit message:

 Add ImmunoOncology biocViews term
 
Package: ggcyto
Commit: c884db09f375d5156cc647322cc40044d88b1bf3
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-01-14 12:18:24 -0800
Commit message:

 revalidate figs for test cases. #43
 
Package: ggcyto
Commit: 850d444ffac07e92d317a17b0be3935abb91c589
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-01-14 11:58:10 -0800
Commit message:

 add test case. #43
 
Package: ggcyto
Commit: c70d3ae111573088217893ff56dbbf4a86d275bc
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-01-14 11:57:29 -0800
Commit message:

 fix the geom_gate dispatching error. #43
 
Package: debrowser
Commit: 29e5529e60a1831fb40ea6a8ef4cb0e36877963c
Author: Alper Kucukural <alper.kucukural@umassmed.edu>
Date: 2019-01-14 15:15:20 -0500
Commit message:

 json load fix
 
Package: debrowser
Commit: 350e731e3f2667c17ceef62954827e155dae7114
Author: Alper Kucukural <alper.kucukural@umassmed.edu>
Date: 2019-01-14 13:46:40 -0500
Commit message:

 version fix
 
Package: debrowser
Commit: 45e5cb1be9b7d7f7374657c631a36cfa1bc77f18
Author: Alper Kucukural <alper.kucukural@umassmed.edu>
Date: 2019-01-14 13:44:39 -0500
Commit message:

 load debrowser added into .initial
 
Package: debrowser
Commit: c2a8ae339f8c9916beedfa3dd6b81d5f25351177
Author: Alper Kucukural <alper.kucukural@umassmed.edu>
Date: 2019-01-14 12:02:59 -0500
Commit message:

 Merge branch 'RELEASE_3_8' of git.bioconductor.org:packages/debrowser into RELEASE_3_8
 
Package: debrowser
Commit: e2e5caade42e42b15fed831aa13484b932573f48
Author: Alper Kucukural <alper.kucukural@umassmed.edu>
Date: 2019-01-14 12:02:13 -0500
Commit message:

 Shiny-server compatibility
 
Package: debrowser
Commit: 334cc6ffb8e98a5904f1f04320c60bc0ac83140c
Author: Alper Kucukural <alper.kucukural@umassmed.edu>
Date: 2019-01-13 20:10:31 -0500
Commit message:

 Merge branch 'master' into RELEASE_3_8
 
Package: debrowser
Commit: 9d6540808cd14f8a763c00b05396aca9cc2e7928
Author: Alper Kucukural <alper.kucukural@umassmed.edu>
Date: 2019-01-13 19:47:17 -0500
Commit message:

 version increase
 
Package: debrowser
Commit: 0e04117ebb584fedd9b9254bac3c6deb8e095abe
Author: Alper Kucukural <alper.kucukural@umassmed.edu>
Date: 2019-01-13 19:46:41 -0500
Commit message:

 Merge branch 'master' into RELEASE_3_8
 
Package: debrowser
Commit: 5a0415debb66bc69c33445032613279ee4a1277a
Author: Alper Kucukural <alper.kucukural@umassmed.edu>
Date: 2019-01-06 16:36:45 -0500
Commit message:

 Merge branch 'master' into RELEASE_3_8
 
Package: debrowser
Commit: 5f03b2805782181e107370da83b1113678535dfc
Author: Alper Kucukural <alper.kucukural@umassmed.edu>
Date: 2019-01-06 16:32:57 -0500
Commit message:

 Citation added to the documentation
 
Package: ggbio
Commit: b04a9840cf5c0bd0514db2536f2e610bbd364727
Author: Michael Lawrence <michafla@gene.com>
Date: 2019-01-14 09:42:45 -0800
Commit message:

 fix prototype slot name
 
Package: mdp
Commit: 1a53a0d1d3ea128111aec5f807565720aedec564
Author: André Nicolau <anicolau85@gmail.com>
Date: 2019-01-14 15:01:58 -0200
Commit message:

 Some alterations
 
Package: mdp
Commit: 0d411e215ad15732bcdcf7f0009f0f84ad6d359b
Author: Andre Nicolau <anicolau85@gmail.com>
Date: 2019-01-10 15:32:54 -0200
Commit message:

 Change plot title font size for barplot
 
Package: mdp
Commit: 81aec6175bb4e4cc0de392e7bae4fdb2bccf7a0b
Author: Andre Nicolau <anicolau85@gmail.com>
Date: 2019-01-10 15:13:55 -0200
Commit message:

 Change legend title font size for barplot
 
Package: mdp
Commit: 2563df14de14faabe7428ed3f8a9a51e6a79935a
Author: Andre Nicolau <anicolau85@gmail.com>
Date: 2019-01-10 15:10:57 -0200
Commit message:

 Change font size for boxplot
 
Package: mdp
Commit: 8bf11545b4dd380ced722c47e29d946b9ce8f06b
Author: Andre Nicolau <anicolau85@gmail.com>
Date: 2019-01-10 15:08:55 -0200
Commit message:

 Change font size for boxplot
 
Package: mdp
Commit: f0ebf9a837b22ceaeda0f2610dc27d463846a6a7
Author: Andre Nicolau <anicolau85@gmail.com>
Date: 2019-01-10 13:33:37 -0200
Commit message:

 Change font size for barplot
 
Package: mdp
Commit: af791a50e27a04251d38bcdd4c8ca727e01d2396
Author: Andre Nicolau <anicolau85@gmail.com>
Date: 2019-01-09 19:23:58 -0200
Commit message:

 Change palette color
 
Package: debrowser
Commit: f241b96e388bfec970dd96bd75e18c68284abbe0
Author: Alper Kucukural <alper.kucukural@umassmed.edu>
Date: 2019-01-14 12:00:50 -0500
Commit message:

 shiny-server compatiblity
 
Package: ExperimentHub
Commit: 6c27e272c72e95831d744715d208f4393f9cef0c
Author: lshep <lori.shepherd@roswellpark.org>
Date: 2019-01-14 10:17:01 -0500
Commit message:

 version bump for levi's change to vignette
 
Package: ExperimentHub
Commit: 8c4a0928872759f71e1d9684f2d148be9382baf5
Author: lshep <lori.shepherd@roswellpark.org>
Date: 2019-01-14 10:16:29 -0500
Commit message:

 Merge branch 'lwaldron-patch-1'
 
Package: ExperimentHub
Commit: 5e6a7d7711d76184ba72929181202d7d11ec78a5
Author: Levi Waldron <lwaldron.research@gmail.com>
Date: 2019-01-13 17:41:04 +0100
Commit message:

 put head() around unique(eh$dataprovider)

The pages of output currently make the vignette look bad (https://bioconductor.org/packages/release/bioc/vignettes/ExperimentHub/inst/doc/ExperimentHub.html#experimenthub-objects) 
Package: beachmat
Commit: 88bb2f4909518500d3e0f919264cefa850d4921a
Author: Aaron Lun <infinite.monkeys.with.keyboards@gmail.com>
Date: 2019-01-14 13:32:18 +0000
Commit message:

 Bumped version, date; updated NEWS.
 
Package: beachmat
Commit: 835c8bf403fa3e43bf0deb3b900a558747e02058
Author: Aaron Lun <infinite.monkeys.with.keyboards@gmail.com>
Date: 2019-01-14 12:59:18 +0000
Commit message:

 Streamlined simple LIN output class.
 
Package: beachmat
Commit: 3f54fa40f3d0b8a4d3794f78bf6dfd04c955c0e9
Author: Aaron Lun <infinite.monkeys.with.keyboards@gmail.com>
Date: 2019-01-14 12:57:02 +0000
Commit message:

 Streamlined throw of stringstream'd error message.
 
Package: beachmat
Commit: 3082bb700bf5e9cdd7a3a706be9285412280f91b
Author: Aaron Lun <infinite.monkeys.with.keyboards@gmail.com>
Date: 2019-01-14 12:54:08 +0000
Commit message:

 Avoid promiscuous includes, removed extraneous header files.
 
Package: beachmat
Commit: 85af14adbd4aa3d5ed03591a2105a74d30525294
Author: Aaron Lun <infinite.monkeys.with.keyboards@gmail.com>
Date: 2019-01-14 12:29:14 +0000
Commit message:

 Fix bug in external_reader DL.
 
Package: beachmat
Commit: 2e70142fa06a5c0575c3a9c9966da7f3e3651a87
Author: Aaron Lun <infinite.monkeys.with.keyboards@gmail.com>
Date: 2019-01-14 00:39:07 +0000
Commit message:

 Define external_ptr class to avoid rule-of-5'ing external_reader classes.
 
Package: beachmat
Commit: 155b430d707cc4d39b9ffd2ea0f054d33ad59b95
Author: Aaron Lun <infinite.monkeys.with.keyboards@gmail.com>
Date: 2019-01-13 15:00:52 +0000
Commit message:

 Updated instructions for external linkage.
 
Package: beachmat
Commit: f9a005871b1e18c38bb154e62f848086e1be9ff2
Author: Aaron Lun <infinite.monkeys.with.keyboards@gmail.com>
Date: 2019-01-13 14:49:42 +0000
Commit message:

 Updated test code for new external API.
 
Package: beachmat
Commit: d014bef067b1d2d5ddc9efb7353c0e439309fdda
Author: Aaron Lun <infinite.monkeys.with.keyboards@gmail.com>
Date: 2019-01-13 11:49:49 +0000
Commit message:

 Fix memory leak in external_reader copy assignment.
 
Package: beachmat
Commit: a4e76f6f099dfa6399e502a628eab09911b830d8
Author: Aaron Lun <infinite.monkeys.with.keyboards@gmail.com>
Date: 2019-01-13 11:48:08 +0000
Commit message:

 Switch external reader API to use pointers to Rcpp classes.
 
Package: BEclear
Commit: 065e95ad5b850c82f55331f2080129d7f983eeee
Author: David Rasp <david.j.rasp@gmail.com>
Date: 2019-01-14 13:39:45 +0100
Commit message:

 version bump
 
Package: BEclear
Commit: a3ec30c1a001fa215232a427a3af2bd7c68b3fbd
Author: David Rasp <david.j.rasp@gmail.com>
Date: 2019-01-14 13:38:04 +0100
Commit message:

 serial execution of the method is now the default
 
Package: BEclear
Commit: fc67a7316458eceefe47c521d4fc874309d35709
Author: David Rasp <david.j.rasp@gmail.com>
Date: 2019-01-14 13:17:59 +0100
Commit message:

 change regarding the text formatting
 
Package: BEclear
Commit: 6c263093246f11a418939437f8b4e00c97859a31
Author: David Rasp <david.j.rasp@gmail.com>
Date: 2019-01-14 13:07:59 +0100
Commit message:

 update to README
 
Package: BEclear
Commit: d73bec8b1dac7fe01c01ae1d72d24a4e2e48e089
Author: David Rasp <david.j.rasp@gmail.com>
Date: 2019-01-11 15:22:00 +0100
Commit message:

 Update issue templates 
Package: ORFik
Commit: 56956d7c7598b0d3f06a5cd1701c9f5286035e9c
Author: Håkon Tjeldnes <hauken_heyken@hotmail.com>
Date: 2019-01-14 12:20:22 +0100
Commit message:

 Hotfix2 jan19 (#67)

* reimplemenation of pmapFromTranscripts in c++

* added the tests

* fixed some docs
 
Package: msPurity
Commit: 6db47a399e71f9884b63f77132f7ba9413276327
Author: tomnl <thomas.nigel.lawson@gmail.com>
Date: 2019-01-14 10:14:05 +0000
Commit message:

 merge description
 
Package: msPurity
Commit: 382b32b0c9c077ede0a9e2f6671036d6b85815c9
Author: Thomas N Lawson <thomas.nigel.lawson@gmail.com>
Date: 2018-12-19 13:28:19 +0000
Commit message:

 Spectral matching rt filter and new match factor algorithm implementation (#24)

* test and print clean up

* added RT and match factor spectral matching approach
 
Package: msPurity
Commit: 5b0a6c5c187a859e898c143407b46fceee23bab1
Author: Thomas N Lawson <thomas.nigel.lawson@gmail.com>
Date: 2018-12-11 14:27:00 +0000
Commit message:

 Average Inter fix for Galaxy  (#22)

* av fix for inter

* Update appveyor

* update appveyor

* update appveyor

* delete appveyor

* Removed appveyor badge

* update readme
 
Package: msPurity
Commit: 5924b5faba8a97e414af11fd84436510693f8558
Author: Thomas N Lawson <thomas.nigel.lawson@gmail.com>
Date: 2018-12-06 08:12:29 +0000
Commit message:

 version bump 
Package: msPurity
Commit: 73d0d98e347d7525fb1c605da8ac728d4b98babe
Author: Ralf Weber <RJMW@users.noreply.github.com>
Date: 2018-12-06 08:09:53 +0000
Commit message:

 Split averaging functions (#21)

 
Package: msPurity
Commit: 6f5f922b0276902a4b933ed48f35c6b83d190661
Author: tomnl <thomas.nigel.lawson@gmail.com>
Date: 2018-12-05 11:18:48 +0000
Commit message:

 use adduct split with metadata (skip when metadata not available)
 
Package: DOSE
Commit: b626f2ae4a4b25af6934d983fd0c11dfc6761a42
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2019-01-14 16:29:58 +0800
Commit message:

 update setReadable
 
Package: ggtree
Commit: e72823b4d76a8a01f6191a1e0bca1c529cbf78e3
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2019-01-14 14:41:18 +0800
Commit message:

 update citation
 
Package: ggtree
Commit: cb272bfc6eaf888aa18642a1343044be234af8ae
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2019-01-14 14:38:08 +0800
Commit message:

 update citation
 
Package: ggtree
Commit: 2b9d5e9df3c50bdc0588087fbdc87e7974f30ab0
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2019-01-14 10:40:45 +0800
Commit message:

 bug fixed of theme_tree2(),
see also #218
 
Package: DOSE
Commit: cb3daaf08005f98657603f829ebbd80284c24dfa
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2019-01-14 13:54:31 +0800
Commit message:

 bug fixed
 
Package: Rsubread
Commit: b7f029dcd6167b2374036fd568fb87060d2194f8
Author: Yang Liao <dbpzdbpz@gmail.com>
Date: 2019-01-14 16:09:07 +1100
Commit message:

 Changed screen output from simReads()
 
Package: Rsubread
Commit: c2a4fb4df3aa315d9bc09b9bb7c8286c5ffa2e0f
Author: Yang Liao <dbpzdbpz@gmail.com>
Date: 2019-01-14 14:51:29 +1100
Commit message:

 Changed screen output in simReads()
 
Package: Rsubread
Commit: e906c5f7d0704adf30d8b983f1da7e6d8a7b756f
Author: Yang Liao <dbpzdbpz@gmail.com>
Date: 2019-01-14 14:48:53 +1100
Commit message:

 Change the option name for simReads(): TPM => expression.levels
 
Package: Rsubread
Commit: f4f635bb2b1fef334a6d3434319abadc051c1307
Author: Yang Liao <dbpzdbpz@gmail.com>
Date: 2019-01-14 14:37:26 +1100
Commit message:

 1) The sum of the expression levels can be any value (non zero, not negative). Not necessarily 1,000,000. (ie, can be TPM or not TPM)
2) In the returned data.frame from scanFasta(), the "Duplicated" column has the same meaning of duplicated() in R; "Unique" means if a sequence is very unique in the Fasta.
 
Package: debrowser
Commit: bfdc45847bdbb6f1baae7a35e773f275eada0402
Author: Alper Kucukural <alper.kucukural@umassmed.edu>
Date: 2019-01-13 20:09:33 -0500
Commit message:

 package name made lowercase
 
Package: debrowser
Commit: 760308a1f9d4b0c4db649b548fb2d4960178bfdc
Author: Alper Kucukural <alper.kucukural@umassmed.edu>
Date: 2019-01-13 19:48:28 -0500
Commit message:

 version increase
 
Package: debrowser
Commit: f74a195b0b6ea1d86f26dd677f84213ad3c9910a
Author: Alper Kucukural <alper.kucukural@umassmed.edu>
Date: 2019-01-13 19:45:51 -0500
Commit message:

 DT table fix while running with runApp("R")
 
Package: TCGAutils
Commit: 5875801e898562c5b9710b4c564c97523c313b3a
Author: LiNk-NY <mramos09@gmail.com>
Date: 2019-01-10 15:47:09 -0500
Commit message:

 fix vignette error
 
Package: PureCN
Commit: aa4c865b93e05f4958f9c60602790dbd07afe6da
Author: lima1 <mriester@gmx.de>
Date: 2019-01-12 17:42:34 -0500
Commit message:

 Minor documentation fixes.
 
Package: PureCN
Commit: bf482df0b6ffa1911d83ea47a3535d5a7070931f
Author: lima1 <mriester@gmx.de>
Date: 2019-01-12 16:06:25 -0500
Commit message:

 Minor documentation fixes.
 
Package: BioCor
Commit: e8187f6763a443459fde84622ea6beaaf6f48af1
Author: Lluís Revilla <lluis.revilla@gmail.com>
Date: 2019-01-13 14:35:12 +0100
Commit message:

 Do not build Travis in Windows

It is not supported
 
Package: BioCor
Commit: 4ae9169b8cfdea328c0ec5bf1d0274f03e92403e
Author: Lluís Revilla <lluis.revilla@gmail.com>
Date: 2019-01-13 14:30:43 +0100
Commit message:

 Test pathStim with a GeneSetCollection
 
Package: BioCor
Commit: cdab8b60f1869416c2f8059e6ace529b3cbffe10
Author: Lluís Revilla <lluis.revilla@gmail.com>
Date: 2019-01-13 14:28:08 +0100
Commit message:

 Add test with GSC

I don't know how are they loaded
 
Package: BioCor
Commit: a65e500d2f1bb4f342cea30e424a13f864340586
Author: Lluís Revilla <lluis.revilla@gmail.com>
Date: 2019-01-13 14:20:03 +0100
Commit message:

 Improve coherence between using list and GeneSetCollections
 
Package: BioCor
Commit: 6069942c1e8358e1fcbca432a69af2e2311ee088
Author: Lluís Revilla <lluis.revilla@gmail.com>
Date: 2019-01-13 01:15:45 +0100
Commit message:

 Correct mistake on linking the vignettes
 
Package: BioCor
Commit: 1d7f553cb3bc528caf05b833fd249dc673752360
Author: Lluís Revilla <lluis.revilla@gmail.com>
Date: 2019-01-12 17:39:09 +0100
Commit message:

 Add links between vignettes
 
Package: BioCor
Commit: 025d399f24c4620a02fbf5076fac4f994a6a5f90
Author: Lluís Revilla <lluis.revilla@gmail.com>
Date: 2019-01-12 17:32:45 +0100
Commit message:

 Merge branch 'master' of github.com:llrs/BioCor
 
Package: BioCor
Commit: 88899b8f4313a806180dd1b5e39bbb987c775008
Author: Lluís Revilla <lluis.revilla@gmail.com>
Date: 2019-01-12 17:32:27 +0100
Commit message:

 Update Description to Roxygen 6.1.1
 
Package: BioCor
Commit: 9b7984c88f480d0e0e25921b2f344f0313e81c69
Author: Lluís Revilla <lluis.revilla@gmail.com>
Date: 2019-01-12 17:32:04 +0100
Commit message:

 Simplifies correctly the gsc (Closes #17 )
 
Package: BioCor
Commit: 3b44a317b8f37333fb14739f3eed19d53bf04da8
Author: Lluís Revilla <lluis.revilla@gmail.com>
Date: 2019-01-12 17:16:11 +0100
Commit message:

 Closes #17 by checking if is NULL
 
Package: BioCor
Commit: 3c8bd7819552a45722854174e75b0cf113170795
Author: Lluís Revilla <lluis.revilla@gmail.com>
Date: 2019-01-12 16:35:14 +0100
Commit message:

 Update to make it easier to read
 
Package: BioCor
Commit: 50f00db71ec4eb912d88dad6235c0a0ca623e6f9
Author: Lluís <llrs@users.noreply.github.com>
Date: 2018-10-31 12:54:22 +0100
Commit message:

 Change links to the appveyor 
Package: TFutils
Commit: da58d603e6211f9afa42891b7197f73a5e82c167
Author: Vince Carey <stvjc@channing.harvard.edu>
Date: 2019-01-13 06:08:58 -0500
Commit message:

 updated markdown preparatory to submission to f1000
 
Package: beachmat
Commit: 356e8df291fdb3f6f034ce61d3318f9955837a0b
Author: Aaron Lun <infinite.monkeys.with.keyboards@gmail.com>
Date: 2019-01-13 07:44:30 +0000
Commit message:

 Minor fixes to OMP section.
 
Package: beachmat
Commit: aab9ed122e409bbdc8b630e4228789ede47006db
Author: Aaron Lun <infinite.monkeys.with.keyboards@gmail.com>
Date: 2019-01-13 07:22:04 +0000
Commit message:

 Remove check for now-impossible HDF5 seed error.
 
Package: beachmat
Commit: 017463208af5900f42c25cd0b553500228e34e80
Author: Aaron Lun <infinite.monkeys.with.keyboards@gmail.com>
Date: 2019-01-13 07:21:30 +0000
Commit message:

 Fix attribute storage bug with logical HDF5 output.
 
Package: beachmat
Commit: ce0351a8be516bf6e38a73e5ddca0ffa1455bd91
Author: Aaron Lun <infinite.monkeys.with.keyboards@gmail.com>
Date: 2019-01-13 04:19:35 +0000
Commit message:

 Bumped version number, date; updated R dependency.
 
Package: beachmat
Commit: 41b3fa4cf8c5ea74a632f1f03a174fcdb0cc86b1
Author: Aaron Lun <infinite.monkeys.with.keyboards@gmail.com>
Date: 2019-01-13 04:19:00 +0000
Commit message:

 Generalized applications of cloning, commented on HDF5 thread-unsafeness.
 
Package: beachmat
Commit: 584d44079089b242ee9632117e5ffe5f5a5bde30
Author: Aaron Lun <infinite.monkeys.with.keyboards@gmail.com>
Date: 2019-01-13 03:26:14 +0000
Commit message:

 Explicit casting for signed/unsigned comparisons.
 
Package: scran
Commit: 6dcd5e441fc9b2da43f1821bff21c1056693130d
Author: Aaron Lun <infinite.monkeys.with.keyboards@gmail.com>
Date: 2019-01-13 01:54:53 +0000
Commit message:

 Gave up (again) on cyclone win32 failures!
 
Package: GenoGAM
Commit: 0b32fd0d0e0aca11a8f5fd86a6da55d88d5be6c4
Author: Juri <georg.stricker@gmx.net>
Date: 2019-01-12 11:58:40 +0100
Commit message:

 fixed Collate field
 
Package: consensusDE
Commit: a256bc2db79ac9165889bec4f7c79af157a089fc
Author: Ashley J. Waardenberg <a.waardenberg@gmail.com>
Date: 2019-01-12 19:47:36 +1000
Commit message:

 bump version number
 
Package: consensusDE
Commit: 1d02328ec4ec63fdf99a8f0e213ac922e32652fb
Author: Ashley J. Waardenberg <a.waardenberg@gmail.com>
Date: 2019-01-12 19:43:23 +1000
Commit message:

 version bump
 
Package: consensusDE
Commit: ab63e023117a1e233e773437a61951ddc25bf341
Author: Ashley J. Waardenberg <a.waardenberg@gmail.com>
Date: 2019-01-12 19:38:22 +1000
Commit message:

 fix rank sum
add p_max to merged tables
 
Package: consensusDE
Commit: e5cf940de9050408f106000070fcd89606913f5d
Author: Ashley J. Waardenberg <a.waardenberg@gmail.com>
Date: 2019-01-09 16:23:04 +1000
Commit message:

 bump version number
 
Package: consensusDE
Commit: e72ab7c9a03f6909cf413cf52e54e8e46ef8c9b7
Author: Ashley J. Waardenberg <a.waardenberg@gmail.com>
Date: 2019-01-09 16:22:35 +1000
Commit message:

 version bump

Merge branch 'master' into RELEASE_3_8

# Conflicts:
#	DESCRIPTION
#	NEWS
 
Package: consensusDE
Commit: 67daa6ca2060cc20bbc95a2c1c146ec5cc394e22
Author: Ashley J. Waardenberg <a.waardenberg@gmail.com>
Date: 2019-01-09 13:06:41 +1000
Commit message:

 bump version number
 
Package: consensusDE
Commit: 2603163b3f48f789973a23cafe392ffb82d32477
Author: Ashley J. Waardenberg <a.waardenberg@gmail.com>
Date: 2019-01-09 13:06:11 +1000
Commit message:

 bug fixes

Merge branch 'master' into RELEASE_3_8

# Conflicts:
#	DESCRIPTION
#	NEWS
#	R/build_summarized.R
 
Package: consensusDE
Commit: 0ddc9eae58e2471b11bdb29350a3e25c1f589926
Author: Ashley J. Waardenberg <a.waardenberg@gmail.com>
Date: 2019-01-07 12:35:06 +1000
Commit message:

 bump version number
 
Package: consensusDE
Commit: 833c781975865146e641f450b9aa7cecb2c87a60
Author: Ashley J. Waardenberg <a.waardenberg@gmail.com>
Date: 2019-01-07 12:34:02 +1000
Commit message:

 fixing gtf from path bug
 
Package: CATALYST
Commit: e184fd3116ff7d90f0732cbb28bb434d0a63ecc9
Author: HelenaLC <helena@crowells.eu>
Date: 2019-01-12 09:00:38 +0100
Commit message:

 bug fix- diffcyt changed 'marker' to 'marker_id' in results
 
Package: universalmotif
Commit: d2bd7c6c64892960842424bb521aa7cbe58544a3
Author: bjmt <benjmtremblay@gmail.com>
Date: 2019-01-12 01:54:32 -0500
Commit message:

 devel 1.1.12
 
Package: universalmotif
Commit: e0bd92f8aa0c1ce4d352850a0157a043101278cc
Author: bjmt <benjmtremblay@gmail.com>
Date: 2019-01-12 01:53:11 -0500
Commit message:

 Bug fix: motif_tree() now works with dist objects without throwing an error
 
Package: universalmotif
Commit: 189f56bddfe3dc6798f7684284674d336554f0c9
Author: bjmt <benjmtremblay@gmail.com>
Date: 2019-01-12 01:38:42 -0500
Commit message:

 Bug fix: motif_pvalue() no longer throws an error for motif_pvalue(..., pvalue=0)
 
Package: universalmotif
Commit: 6e2fcf4fd116ad24e60c916277e492421bb12f18
Author: bjmt <benjmtremblay@gmail.com>
Date: 2019-01-11 22:56:42 -0500
Commit message:

 devel 1.1.11
 
Package: universalmotif
Commit: 639905a07ed10188ac1ca8cec0d611bf041dd315
Author: bjmt <benjmtremblay@gmail.com>
Date: 2019-01-11 22:55:36 -0500
Commit message:

 Bug fix: compare_motifs() min.mean.ic example in Advanced usage vignette now makes more sense
 
Package: universalmotif
Commit: 1e5762fa85503428ac7c86277019920162081207
Author: bjmt <benjmtremblay@gmail.com>
Date: 2019-01-11 22:19:41 -0500
Commit message:

 changed description formatting
 
Package: chipseqDB
Commit: d5ac065e96b3425410af400f49f6653de7c263c4
Author: Aaron Lun <infinite.monkeys.with.keyboards@gmail.com>
Date: 2019-01-12 03:20:35 +0000
Commit message:

 Tidied up DESCRIPTION.
 
Package: chipseqDB
Commit: 78fd2924e91cf96f9a32b61e9095fc16a8773972
Author: Aaron Lun <infinite.monkeys.with.keyboards@gmail.com>
Date: 2019-01-12 01:29:11 +0000
Commit message:

 Cleaned up DESCRIPTION, bumped version to trigger rebuild.
 
Package: rtracklayer
Commit: 7af7260f1a1733341b54cd09b09f504af39cf6bd
Author: Michael Lawrence <michafla@gene.com>
Date: 2019-01-11 14:30:00 -0800
Commit message:

 more connection management refactoring
 
Package: rtracklayer
Commit: 571e8b3c87d795354e069627b6a48386937f4260
Author: Michael Lawrence <michafla@gene.com>
Date: 2019-01-10 14:51:17 -0800
Commit message:

 initial attempt to manage connections without using the GC
 
Package: universalmotif
Commit: 2acc98f2baeb2d15c1d218dc48fb0280f77e0d11
Author: bjmt <benjmtremblay@gmail.com>
Date: 2019-01-11 15:56:03 -0500
Commit message:

 devel 1.1.10
 
Package: universalmotif
Commit: 8b54c4b00c9aa66daffb845009b73d8907b5ec35
Author: bjmt <benjmtremblay@gmail.com>
Date: 2019-01-11 15:55:12 -0500
Commit message:

 Bug fix: more strangely behaving MotifDb code addressed in Advanced usage vignette
 
Package: S4Vectors
Commit: e3157433c47d384d634d3b73b7bd612f68d11b72
Author: Michael Lawrence <michafla@gene.com>
Date: 2019-01-11 09:55:27 -0800
Commit message:

 need to call the original S4 generics
 
Package: S4Vectors
Commit: 5aea39ccb5cd64eb8421e8f772698dfad3c59767
Author: Michael Lawrence <michafla@gene.com>
Date: 2019-01-11 09:38:40 -0800
Commit message:

 setop dispatch is now S3 => S4
 
Package: chipseqDB
Commit: 2227eb40621baecfab1ac4191d5de66a0cac5791
Author: Aaron Lun <infinite.monkeys.with.keyboards@gmail.com>
Date: 2019-01-11 15:43:41 +0000
Commit message:

 Minor rewording around CBP MDS plot.
 
Package: chipseqDB
Commit: ebecde8da2e2a7de4359576d034bb16dea2569eb
Author: Aaron Lun <infinite.monkeys.with.keyboards@gmail.com>
Date: 2019-01-11 15:31:17 +0000
Commit message:

 Bugfix to H3K9ac workflow.
 
Package: ChIPseeker
Commit: 013b26d9ace15d4f827eb3645f3d8f1dc1881913
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2019-01-11 11:18:28 +0800
Commit message:

 Merge pull request #92 from daniel-wells/master

uncomment targetFiles <- NULL 
Package: ChIPseeker
Commit: 0c299c5b73521123cb66e18a4c970247f55cdae7
Author: daniel-wells <daniel-wells@users.noreply.github.com>
Date: 2019-01-07 14:29:27 +0000
Commit message:

 uncomment targetFiles <- NULL

otherwise if statement on line 164 fails
 
Package: ggtree
Commit: a0cd85ce1c818275faf14757a4ade0f7f5629acd
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2019-01-11 19:16:48 +0800
Commit message:

 mv rescale_tree to treeio
 
Package: ggtree
Commit: ce5f23d29f74b052d0b9edbccfd049994f693c7b
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2019-01-10 21:23:53 +0800
Commit message:

 update readme
 
Package: treeio
Commit: 93d22007dd7aacfe38327e75e3336d27a7d1e880
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2019-01-11 23:15:36 +0800
Commit message:

 update news
 
Package: treeio
Commit: d8040522121e7b08e457bf2d45dc4f49227bbd46
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2019-01-11 19:17:14 +0800
Commit message:

 rescale_tree from ggtree
 
Package: chipseqDBData
Commit: 9bcb3e60d40c2f027eb1f40ec875f65134108cf0
Author: Aaron Lun <infinite.monkeys.with.keyboards@gmail.com>
Date: 2019-01-11 14:44:33 +0000
Commit message:

 Bumped version, date.
 
Package: chipseqDBData
Commit: a5b895764df36aa9d03c1421b17c54f1d749ed92
Author: LTLA <aaron.lun@cruk.cam.ac.uk>
Date: 2019-01-11 14:40:13 +0000
Commit message:

 Standardized alignment for NF-YA and H3k4me3 datasets.
 
Package: chipseqDBData
Commit: 7bd7b56f77042c2f0f860a72b05de82f1ff92fb8
Author: LTLA <aaron.lun@cruk.cam.ac.uk>
Date: 2019-01-11 01:42:38 +0000
Commit message:

 Added unique=TRUE for all align() steps with long reads.
 
Package: chipseqDBData
Commit: c0b4b23c2c18268f12013a7c58e4a9aef83fe9f8
Author: LTLA <aaron.lun@cruk.cam.ac.uk>
Date: 2019-01-10 07:09:31 +0000
Commit message:

 Fix to H3K9ac alignment script for better downstream results.
 
Package: AssessORF
Commit: 4c50e8f2beb79bb9def582992c039d9dba9de738
Author: Deepank Korandla <deepankrk@gmail.com>
Date: 2019-01-11 09:39:16 -0500
Commit message:

 Update to how conserved starts and conserved stops are utilized in AssessGenes; Removed weighted score; Made clarifications to the man pages; Minor edits to the vignette
 
Package: BEclear
Commit: f0c6bce024b5037106e4b14337f853273c1fd2a2
Author: David Rasp <david.j.rasp@gmail.com>
Date: 2019-01-11 14:57:10 +0100
Commit message:

 no file output set to default and supression of warning about ties in ks.test
 
Package: deco
Commit: f8067b409da096df9b6d6781e73ac97771c393ad
Author: fjcamlab <fjcamlab@gmail.com>
Date: 2019-01-11 13:36:42 +0000
Commit message:

 deco
 
Package: BEclear
Commit: d13edff5a899f716adaae9ff08eb733cbd414f3e
Author: David Rasp <david.j.rasp@gmail.com>
Date: 2019-01-11 14:29:35 +0100
Commit message:

 version bump
 
Package: BEclear
Commit: 5a243ce8d2d3a107ca3ef9cc1623d18ed4ea3e11
Author: David Rasp <david.j.rasp@gmail.com>
Date: 2019-01-11 14:15:43 +0100
Commit message:

 Merge pull request #17 from David-J-R/add-license-1

Create LICENSE 
Package: BEclear
Commit: 380e4aa095852efa9432a4551fbc3c731615e3ee
Author: David Rasp <david.j.rasp@gmail.com>
Date: 2019-01-11 14:15:14 +0100
Commit message:

 Create LICENSE 
Package: BEclear
Commit: a42c55f0c437526f54d73c8798acfc4c89323e98
Author: David Rasp <david.j.rasp@gmail.com>
Date: 2019-01-11 14:07:17 +0100
Commit message:

 update to README and DESCRIPTION
 
Package: BEclear
Commit: 90ae1a008e06c3ff9e9f7cce91ad40756b3c53d9
Author: David Rasp <david.j.rasp@gmail.com>
Date: 2019-01-11 13:52:50 +0100
Commit message:

 Update to the README
 
Package: BEclear
Commit: 412bfa2efb5423794062c118539cae27ed3c2ca1
Author: David Rasp <david.j.rasp@gmail.com>
Date: 2019-01-11 13:43:37 +0100
Commit message:

 Update to the README
 
Package: BEclear
Commit: e9ea06a73efb1e331aaf2c854e000d1b4c9c418b
Author: David Rasp <david.j.rasp@gmail.com>
Date: 2019-01-11 13:28:48 +0100
Commit message:

 small update
 
Package: BEclear
Commit: 0b2b49802c2f051ebe00c664ffa4998c63c5dc72
Author: David Rasp <david.j.rasp@gmail.com>
Date: 2019-01-11 13:19:21 +0100
Commit message:

 small update
 
Package: BEclear
Commit: 10b1c47ae629e345df72b13d24c3bab5d1dcafaa
Author: David Rasp <david.j.rasp@gmail.com>
Date: 2019-01-11 13:10:44 +0100
Commit message:

 small update
 
Package: BEclear
Commit: 14c58e463f78e25284f4965c9f64c15551f0dc51
Author: David Rasp <david.j.rasp@gmail.com>
Date: 2019-01-11 12:56:27 +0100
Commit message:

 performance improvment, addition of .travis.yml
 
Package: CATALYST
Commit: a9f59366069665d09dda66d7849b22a9081ff2b1
Author: HelenaLC <helena@crowells.eu>
Date: 2019-01-11 12:08:00 +0100
Commit message:

 resolve merge & bump version
 
Package: CATALYST
Commit: 278b99eeba3a16b7c8ccdde780347a3492d97526
Author: HelenaLC <helena@crowells.eu>
Date: 2019-01-11 12:06:57 +0100
Commit message:

 update dox
 
Package: CATALYST
Commit: 4d9eb97e8ef4ec6fd5bf3c8014f0abdf0764b601
Author: HelenaLC <helena@crowells.eu>
Date: 2019-01-11 12:06:52 +0100
Commit message:

 add dplyr::arrange to imports
 
Package: CATALYST
Commit: 1fcf233e2bdb138a132beaa0f2ec16e372bdb7a4
Author: HelenaLC <helena@crowells.eu>
Date: 2019-01-11 12:06:32 +0100
Commit message:

 simplify computation of cluster frequencies
 
Package: CATALYST
Commit: 3bae165bc704c209cd04f506e694fab4d50d05a5
Author: HelenaLC <helena@crowells.eu>
Date: 2019-01-11 12:06:10 +0100
Commit message:

 replace class() with is()
 
Package: CATALYST
Commit: 971a196472465023d0b962b0213d33fecbdb5ebe
Author: HelenaLC <helena@crowells.eu>
Date: 2019-01-11 12:05:49 +0100
Commit message:

 restructure daFrame class for different signatures
 
Package: CATALYST
Commit: f5c0d67965393b731cc0c26e31f68bf477e5ce7b
Author: HelenaLC <helena@crowells.eu>
Date: 2019-01-11 12:05:15 +0100
Commit message:

 replace re with daf in example
 
Package: CATALYST
Commit: fde8174a5ff377af7e852b4e94c213cb16a062bf
Author: HelenaLC <helena@crowells.eu>
Date: 2019-01-11 12:05:08 +0100
Commit message:

 replace re with daf in example
 
Package: CATALYST
Commit: d45a3f642162f4f9646beb96527d9f2488251d0f
Author: HelenaLC <helena@crowells.eu>
Date: 2019-01-11 12:04:44 +0100
Commit message:

 add FlowCytometry to biocViews
 
Package: BEclear
Commit: 67face368b0cb20bd767997f652e7a2530eb44d8
Author: David Rasp <david.j.rasp@gmail.com>
Date: 2019-01-11 10:30:48 +0100
Commit message:

 small change to the vignette
 
Package: BEclear
Commit: 2d234c475d2756960be98c0c5518002f6b13ba78
Author: David Rasp <david.j.rasp@gmail.com>
Date: 2019-01-11 10:22:47 +0100
Commit message:

 fix at the tests
 
Package: M3C
Commit: 07f30f694eb1da5e370d6cca204ec6d57cbcfe18
Author: crj32 <chris.r.john86@gmail.com>
Date: 2019-01-11 08:54:15 +0000
Commit message:

 adjusted description file and readme
 
Package: Rsubread
Commit: 87d9ca22e5dd6d30e02ee08f20b08e7e40d40a9d
Author: Gordon Smyth <smyth@wehi.edu.au>
Date: 2019-01-11 19:11:32 +1100
Commit message:

 Correct spelling of "Occurrence"
 
Package: Rsubread
Commit: f220af1aabf4cd266b604036b43c22ac316b87f8
Author: Gordon Smyth <smyth@wehi.edu.au>
Date: 2019-01-11 18:45:38 +1100
Commit message:

 Fix typos.
 
Package: ImmuneSpaceR
Commit: e239a442ac1c596f9d40fcb79eb5b6b24563e3fc
Author: ImmuneSpace <immunespace@gmail.com>
Date: 2019-01-11 04:07:40 +0000
Commit message:

 Bump version
 
Package: ImmuneSpaceR
Commit: 0ddf6875ee657bf50340c32bf552a53306d83c17
Author: J. Kim <jkim2345@fredhutch.org>
Date: 2019-01-10 15:50:01 -0800
Commit message:

 Merge branch 'dev'
 
Package: ImmuneSpaceR
Commit: 075e3e9da09cad29fa64d22eda45172e4e94d194
Author: J. Kim <jkim2345@fredhutch.org>
Date: 2019-01-10 13:23:22 -0800
Commit message:

 Rebuild pkgdown site
 
Package: ImmuneSpaceR
Commit: 363e757524237e987220bc98fcdf252518942444
Author: J. Kim <jkim2345@fredhutch.org>
Date: 2019-01-10 13:23:13 -0800
Commit message:

 Bump version
 
Package: ImmuneSpaceR
Commit: 54c19238becd1150fbf6dcd06e60e9a4f8aaf640
Author: J. Kim <jkim2345@fredhutch.org>
Date: 2019-01-10 13:18:10 -0800
Commit message:

 Disable participant group tests for non readonly users
 
Package: chipseqDB
Commit: a9e8bb2aa055ff0ab9905fe3092c92884703c991
Author: Aaron Lun <infinite.monkeys.with.keyboards@gmail.com>
Date: 2019-01-11 01:58:50 +0000
Commit message:

 Updated expected regions in H3K9ac workflow for new BAM files.
 
Package: PureCN
Commit: 484faecfa580bda6d7310ad41fdec2a3e3981adb
Author: Markus Riester <markus.riester@novartis.com>
Date: 2019-01-09 23:19:27 -0500
Commit message:

 Fix for failed test in previous commit.
 
Package: PureCN
Commit: 7e3f1b1fe6282771a9fe4f3519a80065709c8ab8
Author: Markus Riester <markus.riester@novartis.com>
Date: 2019-01-09 22:27:54 -0500
Commit message:

 First attempt in improving the CCF estimates (#66)
 
Package: AssessORFData
Commit: 75e4a28913c92c3f5b9461185bf9839c0fd8d322
Author: Deepank Korandla <deepankrk@gmail.com>
Date: 2019-01-10 15:39:27 -0500
Commit message:

 Pushing data for AssessORF v1.1.5
 
Package: Biobase
Commit: 528dca2c41f05c6cba3248f98467e804fc79c7d2
Author: Michael Lawrence <michafla@gene.com>
Date: 2019-01-10 12:26:44 -0800
Commit message:

 export as.data.frame.ExpressionSet()
 
Package: AssessORFData
Commit: 80374ed62ba387db763d6c66f5239e5a6284ed91
Author: Deepank Korandla <deepankrk@gmail.com>
Date: 2019-01-10 14:48:35 -0500
Commit message:

 Removing all data objects
 
Package: DESeq2
Commit: 25dce70bd5a13ae7f8f0dd038da1e767516130f3
Author: mikelove <michaelisaiahlove@gmail.com>
Date: 2019-01-10 13:55:54 -0500
Commit message:

 add new normal message
 
Package: enrichplot
Commit: 89bfa8435df8645070c087937d034afe764624d4
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2019-01-10 23:03:52 +0800
Commit message:

 update dotplot
 
Package: enrichplot
Commit: 551ba91fdca4785d99488bba74253555277ab724
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2019-01-10 22:55:08 +0800
Commit message:

 update vignette
 
Package: enrichplot
Commit: ef50b2848ff54e703d09185ab4cf1b2c8b0e1bae
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2019-01-07 11:36:10 +0800
Commit message:

 update docs
 
Package: DOSE
Commit: dde7b2afb039119d402c669f324c987f2d14da4e
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2019-01-10 23:15:21 +0800
Commit message:

 update vignettes
 
Package: qvalue
Commit: f15d3849236fc8a1758696ee59f42d36fc579625
Author: Andrew Bass <ajbass@princeton.edu>
Date: 2019-01-10 09:28:39 -0500
Commit message:

 update author listing
 
Package: ggtree
Commit: b6760093755cb83bac6ce00ff5f8ac12b96b42d7
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2019-01-10 21:18:05 +0800
Commit message:

 new MRCA methods
 
Package: treeio
Commit: 2cf6b614fe3e9ecc1fa7b55ff2c71eddb494202d
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2019-01-10 21:17:23 +0800
Commit message:

 MRCA methods
 
Package: treeio
Commit: af2e1ac1b0039e30a902709b6df2c5d1886fd909
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2019-01-10 21:07:55 +0800
Commit message:

 treedata-book
 
Package: treeio
Commit: 6415bc37b80c688889139e6a3fea6bd9edba1f47
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2019-01-08 23:00:33 +0800
Commit message:

 Merge pull request #16 from heavywatal/fix-rd-width

Remove rd warning by separating the line 
Package: treeio
Commit: fb632654658bf09cee3b93965bfaae898b3061fa
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2019-01-08 22:59:32 +0800
Commit message:

 Merge pull request #14 from heavywatal/explicit-dependency

Add Biostrings and phangorn to "Suggests" 
Package: treeio
Commit: c51fe3f81da421159380d9e34498b548b7e30a52
Author: Watal M. Iwasaki <heavywatal@users.noreply.github.com>
Date: 2019-01-07 19:34:18 +0900
Commit message:

 Remove rd warning by separating the line
 
Package: treeio
Commit: 06714cc909774f0de97c506184f6351971963a99
Author: Watal M. Iwasaki <heavywatal@users.noreply.github.com>
Date: 2019-01-07 16:57:33 +0900
Commit message:

 Add Biostrings and phangorn to "Suggests"

As a result, rvcheck can be removed from "Imports".
 
Package: diffcyt
Commit: 370862dc5154fc6dea6f79976fc47a0b389d4231
Author: Lukas Weber <lukmweber@gmail.com>
Date: 2019-01-10 13:03:53 +0100
Commit message:

 version
 
Package: diffcyt
Commit: 42601deee0463e6ae6a0cc922212e8a6510deab7
Author: Lukas Weber <lukmweber@gmail.com>
Date: 2019-01-10 13:03:40 +0100
Commit message:

 update NEWS
 
Package: diffcyt
Commit: 888a28878c1453c4feafe52b449e3414df5d8580
Author: Lukas Weber <lukmweber@gmail.com>
Date: 2019-01-10 12:55:45 +0100
Commit message:

 version
 
Package: diffcyt
Commit: 6ecd13f21451c97a70c3645f9aa615e90ec461ec
Author: Lukas Weber <lukmweber@gmail.com>
Date: 2019-01-10 12:54:09 +0100
Commit message:

 documentation
 
Package: diffcyt
Commit: 9e5d3350d63c0cfba970e1d60d960a5ca12e459b
Author: Lukas Weber <lukmweber@gmail.com>
Date: 2019-01-10 12:51:45 +0100
Commit message:

 add alias function 'topClusters' for backward compatibility
 
Package: diffcyt
Commit: 96fcf85c851c47f27511238f7a726a2303012634
Author: Lukas Weber <lukmweber@gmail.com>
Date: 2019-01-10 11:28:22 +0100
Commit message:

 topTable: add option to order by other columns
 
Package: ggtree
Commit: 9c4b3c86d42e5c733452638c646e0388b44bf141
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2019-01-10 18:30:26 +0800
Commit message:

 update docs
 
Package: ggtree
Commit: c69c6bd71d8305622503c881e41b15d8ebcd1379
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2019-01-10 18:16:43 +0800
Commit message:

 ggtree book
 
Package: ggtree
Commit: 3bc5befac996168eba98fda2734c2c89699ac134
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2019-01-09 15:25:04 +0800
Commit message:

 update readme
 
Package: ggtree
Commit: 6d0b84518f128d8828fc720937703d065e4a1012
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2019-01-03 15:04:31 +0800
Commit message:

 Update README.Rmd 
Package: ggtree
Commit: e45b2f26d12a50eaa3358182deb1e3e702452136
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2018-12-28 18:06:53 +0800
Commit message:

 update docs
 
Package: EDASeq
Commit: a82a57095ed882d315ae9463e4663d5cc346ada0
Author: Davide Risso <risso.davide@gmail.com>
Date: 2019-01-10 10:12:55 +0100
Commit message:

 Fix warnings
 
Package: EDASeq
Commit: 83248aff4b530d7432f24db9fe6bfb38ae4e7975
Author: Davide Risso <risso.davide@gmail.com>
Date: 2019-01-08 17:07:38 +0100
Commit message:

 Speed-up length and gcc
 
Package: EDASeq
Commit: 09d376cad4abf55c96ad047db8209e44b137f230
Author: Davide Risso <risso.davide@gmail.com>
Date: 2019-01-08 16:59:34 +0100
Commit message:

 Address #3: faster length and gcc computation
 
Package: universalmotif
Commit: f5e5f1e6c96b51cc0d7d731c3158dd0f5ea8f060
Author: bjmt <benjmtremblay@gmail.com>
Date: 2019-01-09 23:50:25 -0500
Commit message:

 devel 1.1.9
 
Package: universalmotif
Commit: 66237f2b8ba973c15d1da5df75364c52db5f5069
Author: bjmt <benjmtremblay@gmail.com>
Date: 2019-01-09 23:49:33 -0500
Commit message:

 Bug fix: shuffle_motifs() produces shuffled motifs of proper length
 
Package: scran
Commit: 5ae462e9b4035741902d361acaaf7bb196920a5b
Author: Aaron Lun <infinite.monkeys.with.keyboards@gmail.com>
Date: 2019-01-10 04:10:20 +0000
Commit message:

 Bumped version number, date.
 
Package: scran
Commit: ff226e0b65b1b07e437edb1a4ec3714e2593911a
Author: Aaron Lun <infinite.monkeys.with.keyboards@gmail.com>
Date: 2019-01-10 04:02:25 +0000
Commit message:

 Restore short cut in cyclone C++ code.
Minor cleanup to cyclone test.
 
Package: scran
Commit: c33a4af2791339761c27b50a138ba83887139874
Author: Aaron Lun <infinite.monkeys.with.keyboards@gmail.com>
Date: 2019-01-09 05:34:45 +0000
Commit message:

 Avoid promiscuous includes in C++ code.
 
Package: scran
Commit: 693a9bfb4c6e0ab6e755d91e3478b4aa0e1733ed
Author: Aaron Lun <infinite.monkeys.with.keyboards@gmail.com>
Date: 2019-01-08 12:46:48 +0000
Commit message:

 Updated test code for stream choice in C++ code.
 
Package: scran
Commit: 4a84c1db6e17ffca8c5c58d9c7b1da4370ca3422
Author: Aaron Lun <infinite.monkeys.with.keyboards@gmail.com>
Date: 2019-01-08 12:45:59 +0000
Commit message:

 Added stream option to all calls to PRNG-containing C++ code.
 
Package: scran
Commit: bd28c2ce2b2bd0bbfc009f00a7384381b087a0c2
Author: Aaron Lun <infinite.monkeys.with.keyboards@gmail.com>
Date: 2019-01-08 12:27:54 +0000
Commit message:

 Switched all C++ PRNGs to use dqrng's pcg32 implementation.
Avoid issues with MT seeding, non-independent streams.
 
Package: mixOmics
Commit: 672950e0bf0b574efa77c1913670e0dabc6f183a
Author: frohart <florian.rohart@gmail.com>
Date: 2019-01-10 11:28:35 +1000
Commit message:

 lhei with col.sideColors for CIM()
 
Package: universalmotif
Commit: 976786288286f6c61751a05892606488f9315649
Author: bjmt <benjmtremblay@gmail.com>
Date: 2019-01-09 18:16:29 -0500
Commit message:

 devel 1.1.8
 
Package: universalmotif
Commit: b7486811cb2a55145455f88648c948808754fd8a
Author: bjmt <benjmtremblay@gmail.com>
Date: 2019-01-09 18:15:32 -0500
Commit message:

 Bug fix: trying to prevent R CMD BUILD from changing the behaviour of vignette examples using MotifDb
 
Package: universalmotif
Commit: c5f43fc8360dc94f9d43e902706bf080f0f5ee8c
Author: bjmt <benjmtremblay@gmail.com>
Date: 2019-01-09 17:55:39 -0500
Commit message:

 devel 1.1.7
 
Package: universalmotif
Commit: fb6e3ee2ff1fddba596b8cb543ea301564030e37
Author: bjmt <benjmtremblay@gmail.com>
Date: 2019-01-09 17:54:01 -0500
Commit message:

 Bug fix: merge_motifs will not show repeat families, organisms, and show method will not show altname as name
 
Package: DESeq2
Commit: 2716ab3e7070c64ec47a12eba27d2e1d44869057
Author: mikelove <michaelisaiahlove@gmail.com>
Date: 2019-01-09 15:33:46 -0500
Commit message:

 man page update
 
Package: scmeth
Commit: b7cfe0ff8967c89c87c679456f79f777282b3e39
Author: Divyagash <sdivyagash@yahoo.com>
Date: 2019-01-09 15:08:41 -0500
Commit message:

 Added back the repMask function
 
Package: GenoGAM
Commit: b74d761c5753bb100906d1b853676ecb6c4dcee9
Author: Juri <georg.stricker@gmx.net>
Date: 2019-01-09 20:19:08 +0100
Commit message:

 deleted redundant files due to faulty merge
 
Package: SCnorm
Commit: 98b58016d1d1370274f2e7267976cddc8ab22f63
Author: rhondabacher <rhonda.bacher@gmail.com>
Date: 2019-01-09 13:21:42 -0500
Commit message:

 update vignette
 
Package: SCnorm
Commit: 74776ea4cc4815b1cbe223929d7eb68db3b808ce
Author: rhondabacher <rhonda.bacher@gmail.com>
Date: 2019-01-09 13:11:34 -0500
Commit message:

 allow separate norm then scaling
 
Package: SCnorm
Commit: 50a45884b21b2f2859338028c1186513178a28ae
Author: rhondabacher <rhonda.bacher@gmail.com>
Date: 2018-12-18 11:29:46 -0500
Commit message:

 change readme to .md
 
Package: SCnorm
Commit: fe641cd84c138d5aba163f52fea3058ef6adbf34
Author: rhondabacher <rhonda.bacher@gmail.com>
Date: 2018-12-18 11:28:06 -0500
Commit message:

 fix Conditions error; add function imports
 
Package: SCnorm
Commit: ff0986059f9ab38d135d87a96404a54c16cc79cd
Author: rhondabacher <rhonda.bacher@gmail.com>
Date: 2018-12-11 11:40:17 -0500
Commit message:

 add ImmunoOncology to biocviews
 
Package: SCnorm
Commit: ef28dc1015e3d3fe1b40beb70ca2e64a3d655da1
Author: rhondabacher <rhonda.bacher@gmail.com>
Date: 2018-12-10 14:29:34 -0500
Commit message:

 fix compatability of results() function
 
Package: curatedTCGAData
Commit: 182fafba48e9e64830beb7fa1cc631d4de3e02ef
Author: LiNk-NY <mramos09@gmail.com>
Date: 2019-01-09 12:55:25 -0500
Commit message:

 bug fix: use 'assay001' name in H5 file, fix list names
 
Package: curatedTCGAData
Commit: 9cc95490654c2401a358331887926605bd891afa
Author: LiNk-NY <mramos09@gmail.com>
Date: 2019-01-08 13:53:52 -0500
Commit message:

 update metadata file and format make_metadata
 
Package: curatedTCGAData
Commit: 24766e86f88dc55e70d8445e64f1961e7eb5c051
Author: LiNk-NY <mramos09@gmail.com>
Date: 2019-01-08 13:32:10 -0500
Commit message:

 minor change: lowercase s in Homo sapiens
 
Package: curatedTCGAData
Commit: 33fc64f75fb3cfb8db77346cc4054b8cfa1a5524
Author: LiNk-NY <mramos09@gmail.com>
Date: 2019-01-03 17:05:28 -0500
Commit message:

 update Maintainer fields
 
Package: curatedTCGAData
Commit: 55ed711d81e427e3ca89e4e35e3987188402a239
Author: LiNk-NY <mramos09@gmail.com>
Date: 2019-01-02 14:55:52 -0500
Commit message:

 update helpers to use EHub, update vignette, and qualify imported functions
 
Package: curatedTCGAData
Commit: 5bb294c52941b09068c27a5573c682f44293b268
Author: LiNk-NY <mramos09@gmail.com>
Date: 2018-12-28 17:08:05 -0500
Commit message:

 Merge branch 'dev' of github.com:waldronlab/curatedTCGAdata into dev
 
Package: curatedTCGAData
Commit: 750b9461d10f2cd27453ea35d46b6d5372c576e3
Author: LiNk-NY <mramos09@gmail.com>
Date: 2018-12-28 17:07:51 -0500
Commit message:

 wip vignette changes
 
Package: curatedTCGAData
Commit: d55fc629a77026f3f3c79396e547c95b5b604618
Author: LiNk-NY <mramos09@gmail.com>
Date: 2018-12-25 23:10:48 -0500
Commit message:

 Merge branch 'dev' of github.com:waldronlab/curatedTCGAData into dev
 
Package: curatedTCGAData
Commit: 3af3efacc1cdde1217796d5eb2059e8cf5c5cc2f
Author: LiNk-NY <mramos09@gmail.com>
Date: 2018-12-25 23:10:30 -0500
Commit message:

 update curatedTCGAData to support methylation
 
Package: curatedTCGAData
Commit: 5b2e1261ed7512bf39f5b8eab86ff1464013f2ea
Author: LiNk-NY <mramos09@gmail.com>
Date: 2018-12-21 16:44:14 -0500
Commit message:

 update bits2rd call
 
Package: curatedTCGAData
Commit: 6ba326b532d9322b0f4368c6d27e2ef1b4880b74
Author: LiNk-NY <mramos09@gmail.com>
Date: 2018-12-21 14:01:34 -0500
Commit message:

 update fileMatches result from index
 
Package: curatedTCGAData
Commit: d5e3a6ab300b63aaa3e093610c653acbfa59abbc
Author: LiNk-NY <mramos09@gmail.com>
Date: 2018-12-20 19:06:34 -0500
Commit message:

 wip: combine and match diseaseCode and assays inputs
 
Package: curatedTCGAData
Commit: d18dd607e0b411e97c1afc24e5401a2aaf8b4fe9
Author: LiNk-NY <mramos09@gmail.com>
Date: 2018-12-20 15:40:20 -0500
Commit message:

 update metadata.csv file
 
Package: curatedTCGAData
Commit: b6e223e49b526a4b7aa95482952aa661a3a72553
Author: LiNk-NY <mramos09@gmail.com>
Date: 2018-12-20 15:37:31 -0500
Commit message:

 update getMetadata function adapt to Methyl datasets
 
Package: curatedTCGAData
Commit: 12aa678ff95bd2595fc9ff6ee37be2c630b5b528
Author: LiNk-NY <mramos09@gmail.com>
Date: 2018-12-20 15:16:02 -0500
Commit message:

 update Description in DESCRIPTION
 
Package: curatedTCGAData
Commit: 9e373317b611bb9581738d9a035989d2b4583593
Author: LiNk-NY <mramos09@gmail.com>
Date: 2018-12-18 17:36:08 -0500
Commit message:

 wip: metadata.csv generation helpers
 
Package: curatedTCGAData
Commit: 9c0c4b64077e4899df13525a2512cbe5f924d7ca
Author: LiNk-NY <mramos09@gmail.com>
Date: 2018-12-17 16:44:54 -0500
Commit message:

 update docs with updated data
 
Package: curatedTCGAData
Commit: bbf38fdeed2a33a22d1efc38e8e987c27354422a
Author: LiNk-NY <mramos09@gmail.com>
Date: 2018-12-17 16:44:35 -0500
Commit message:

 set width for docs
 
Package: curatedTCGAData
Commit: a4de9196ff7889fda7cfeb633e144e20acd0c58b
Author: LiNk-NY <mramos09@gmail.com>
Date: 2018-12-17 15:17:07 -0500
Commit message:

 support new methylation files in documentation function

- use metadata table as unified object name and location resource
- add helper for accessing parts of metadata table
- use lapply method for loading and obtaining metadata for data resources
- document methylation datasets last
 
Package: curatedTCGAData
Commit: 9b8e4370bd4dac81e67b9515a8ad07b39a23f5c4
Author: LiNk-NY <mramos09@gmail.com>
Date: 2018-12-17 14:55:24 -0500
Commit message:

 set default manDir for make_documentation
 
Package: curatedTCGAData
Commit: 1e3d08540fb3c0223adc45c342602de906a813b0
Author: LiNk-NY <mramos09@gmail.com>
Date: 2018-12-13 11:44:48 -0500
Commit message:

 include REPO var if missing
 
Package: curatedTCGAData
Commit: e501605ab0bffcea7338bfca81fd10fb2ab2a1d7
Author: LiNk-NY <mramos09@gmail.com>
Date: 2018-12-11 13:58:58 -0500
Commit message:

 update loadMethyl to HDF5Array 1.11.7
 
Package: curatedTCGAData
Commit: ce5d3f07d567547db25b46bb68b5edbfa91d0ad9
Author: LiNk-NY <mramos09@gmail.com>
Date: 2018-12-09 17:29:33 -0500
Commit message:

 update bits2rd.R script
 
Package: curatedTCGAData
Commit: 16a33cc03d4aed4c9503477bf4f7d4320811c12a
Author: LiNk-NY <mramos09@gmail.com>
Date: 2018-12-09 17:24:54 -0500
Commit message:

 Merge branch 'dev' of github.com:waldronlab/curatedTCGAdata into dev
 
Package: curatedTCGAData
Commit: af801de1a7fa7d5734cc2fd896799e7fc616298d
Author: LiNk-NY <mramos09@gmail.com>
Date: 2018-12-09 17:16:32 -0500
Commit message:

 update makeMetaDocs script
 
Package: curatedTCGAData
Commit: bb634f99b681c0cad4d28dbcb984fcf489289201
Author: LiNk-NY <mramos09@gmail.com>
Date: 2018-10-11 17:48:12 -0400
Commit message:

 minor changes for methylation files
 
Package: Rhtslib
Commit: 43db581ea4d2fbfa88266029a2eee3cafcbd3c44
Author: Hervé Pagès <hpages@fredhutch.org>
Date: 2019-01-09 08:56:23 -0800
Commit message:

 Merge remote-tracking branch 'origin/master'
 
Package: Rhtslib
Commit: c02d76d52d4c0f0db9dd7069e4a10c58400215ae
Author: Hervé Pagès <hpages@fredhutch.org>
Date: 2019-01-09 08:54:58 -0800
Commit message:

 Merge remote-tracking branch 'upstream/master'
 
Package: Rhtslib
Commit: 3a559a4a4ccc9de341465803d09a20e1ce104e25
Author: Nitesh Turaga <nitesh.turaga@gmail.com>
Date: 2018-10-30 14:24:59 -0400
Commit message:

 Merge remote-tracking branch 'upstream/master'
 
Package: Rhtslib
Commit: c6d658f9ada1b6be7d195020683a0d52e79813ba
Author: Hervé Pagès <hpages@fredhutch.org>
Date: 2018-10-05 04:10:11 -0700
Commit message:

 Include textutils_internal.h and hts_internal.h from htslib-1.7
 
Package: ChIPpeakAnno
Commit: e73cf8a73c047d5a9edd62c374701295222eaa51
Author: Jianhong Ou <jianhongou@Jianhongs-MBP.dhe.duke.edu>
Date: 2019-01-09 11:12:36 -0500
Commit message:

 fix the bug in annotatePeakInBatch which can not accept bindingType parameter.
 
Package: VariantAnnotation
Commit: 54ca8c69ec4ef0d3aed9919e861f1968eb166e55
Author: vobencha <vobencha@gmail.com>
Date: 2019-01-09 07:41:23 -0800
Commit message:

 Revert commit 605c06b46df283c4f56dc28b80f11f56c5da30bf

The change was made in response to 4094 byte records and buffer
reallocation: https://github.com/Bioconductor/VariantAnnotation/issues/19.
The implementation didn't handle all cases and will be reworked.
 
Package: netSmooth
Commit: 8f955c0815e3f71d70c1c1e1652bc471c87df271
Author: jona <yablee@gmail.com>
Date: 2019-01-09 15:28:06 +0100
Commit message:

 Merge remote-tracking branch 'upstream/master'
 
Package: netSmooth
Commit: f24ab17c129462bc5760f46f50d622217ef99fc3
Author: vobencha <vobencha@gmail.com>
Date: 2018-10-30 11:54:39 -0400
Commit message:

 bump x.y.z versions to odd y after creation of RELEASE_3_8 branch
 
Package: netSmooth
Commit: 218bde17fc150de53df7d5cec88d2e499ee2b4b5
Author: vobencha <vobencha@gmail.com>
Date: 2018-10-30 11:42:09 -0400
Commit message:

 bump x.y.z versions to even y prior to creation of RELEASE_3_8 branch
 
Package: netSmooth
Commit: cfa8c18d68a3aa59364ffff679c39eeb47fe8a88
Author: LiNk-NY <mramos09@gmail.com>
Date: 2018-08-30 13:53:16 -0400
Commit message:

 replace BiocInstaller biocLite mentions with BiocManager
 
Package: netSmooth
Commit: 348894e9f7a8d9c9a30909c41dc21d1690e70a7c
Author: jona <yablee@gmail.com>
Date: 2019-01-09 15:18:06 +0100
Commit message:

 fix global name note
 
Package: netSmooth
Commit: 72a2d75b57bd26ad40811338218c8ccab04ea9a6
Author: Jona <jonathanronen@users.noreply.github.com>
Date: 2018-10-31 16:54:05 +0100
Commit message:

 Merge pull request #12 from nagoli104/hdf5_support

HDF5 support (#9), UMAP for for dimensionality reduction (#10) 
Package: netSmooth
Commit: 08344be7dfaf5b4c31043fd28ff79e60049da36e
Author: nagoli <nagoli@tornado06.campus.fu-berlin.de>
Date: 2018-10-22 14:48:01 +0200
Commit message:

 added tests for DelayedMatrix, updated NAMESPACE with roxygen2, adjusted documentation
 
Package: netSmooth
Commit: 15e8e5862b4860e9db90ce2a55bc7248c1d9c924
Author: Oliver Nagel <oliver.nagel@fu-berlin.de>
Date: 2018-10-18 22:38:58 +0200
Commit message:

 filehandling, fixed bug in scoreSmoothing function
 
Package: netSmooth
Commit: 5072b545a2e93822793f404880143ac34ddf8f67
Author: Oliver Nagel <oliver.nagel@fu-berlin.de>
Date: 2018-10-17 20:07:16 +0200
Commit message:

 added filepath as variable to let the user decide where the output file is suppossed to be saved for the delayedmatrix input
 
Package: netSmooth
Commit: 28a0bcb1bb093f9aea4cfbbd029f77562f16b321
Author: Oliver Nagel <oliver.nagel@fu-berlin.de>
Date: 2018-10-16 13:52:32 +0200
Commit message:

 deletion of temp smoothed file after recombination added
 
Package: netSmooth
Commit: 0979baa2c200e1e47159541b648cc2001e6b815b
Author: Oliver Nagel <oliver.nagel@fu-berlin.de>
Date: 2018-10-11 17:53:48 +0200
Commit message:

 added chunk.size as input parameter do how many columns are smoothed simultaniously when using DelayedMatrix as input for the count data
 
Package: netSmooth
Commit: 96d1cf807bdb3f25cd52fd4cbe4854ea9e0f0436
Author: Oliver Nagel <oliver.nagel@fu-berlin.de>
Date: 2018-10-10 15:53:01 +0200
Commit message:

 added support for DelayedMatrices with dimnames slot
 
Package: netSmooth
Commit: 9162a3a67e079fc66c75fc01efe3ecb8d231766c
Author: Oliver Nagel <oliver.nagel@fu-berlin.de>
Date: 2018-09-04 13:46:07 +0200
Commit message:

 changed r version from release to bioc-devel in travis.yml
 
Package: netSmooth
Commit: 205d6146bc6c67cc2f8eef5aeeda2ad9632e7f59
Author: Oliver Nagel <oliver.nagel@fu-berlin.de>
Date: 2018-09-03 21:20:00 +0200
Commit message:

 added umap for dim reduction and clustering, renamed combineMany parameter to makeConsensus in clusterExperimentWorkflow, updated documentation accordingly
 
Package: mCSEA
Commit: e7e0dc26aca886ad7b8ee523184f6bc1912bb3d9
Author: Jordi Martorell Marugán <jmartorellm@gmail.com>
Date: 2019-01-09 09:11:42 -0500
Commit message:

 Update vignette
 
Package: Uniquorn
Commit: 9be36924a46f25b5075378726a42149dc12439dd
Author: RaikOtto <fubioinf@gmail.com>
Date: 2019-01-09 14:53:37 +0100
Commit message:

 update to fix data.table
 
Package: chipseqDB
Commit: 117b4465630b5d16e1644f49e485666aa655c967
Author: Aaron Lun <infinite.monkeys.with.keyboards@gmail.com>
Date: 2019-01-09 10:19:56 +0000
Commit message:

 Merge remote-tracking branch 'upstream/master'
 
Package: chipseqDB
Commit: ac5553c175c6accc345e2447ca20c46b330effc6
Author: Aaron Lun <infinite.monkeys.with.keyboards@gmail.com>
Date: 2019-01-09 09:56:21 +0000
Commit message:

 Bumped version number, date.
 
Package: chipseqDB
Commit: 35bbcfcef9a6defab4439add83e82a3af3abacf1
Author: Aaron Lun <infinite.monkeys.with.keyboards@gmail.com>
Date: 2019-01-09 09:56:06 +0000
Commit message:

 Bugfixes for the CBP workflow.
 
Package: chipseqDB
Commit: 6e37aa4b7c323d18e208a3796fc37181a9752809
Author: Aaron Lun <infinite.monkeys.with.keyboards@gmail.com>
Date: 2019-01-09 07:12:02 +0000
Commit message:

 Bugfixes for the H3K9ac workflow, updated expected results.
 
Package: consensusDE
Commit: c909a7a007ee1be1527f4a1428ff875c762b995a
Author: Ashley J. Waardenberg <a.waardenberg@gmail.com>
Date: 2019-01-09 16:18:57 +1000
Commit message:

 update
 
Package: consensusDE
Commit: d10c849e89f48d428d6fbce92f8303de3a7a8391
Author: Ashley J. Waardenberg <a.waardenberg@gmail.com>
Date: 2019-01-09 16:18:42 +1000
Commit message:

 fix slot error for ensembl_annotate
 
Package: consensusDE
Commit: 87d91ad6592b9274b1237d670654a574a3f293de
Author: Ashley J. Waardenberg <a.waardenberg@gmail.com>
Date: 2019-01-09 16:18:01 +1000
Commit message:

 Update NEWS file
 
Package: consensusDE
Commit: 53acb2c2de491ad9413a8f3b2159d6636d948288
Author: Ashley J. Waardenberg <a.waardenberg@gmail.com>
Date: 2019-01-09 16:17:48 +1000
Commit message:

 update to NAMESPACE
 
Package: mixOmics
Commit: 6c145e95cfa8605a41d2317e395b4c3e6318e37c
Author: frohart <florian.rohart@gmail.com>
Date: 2019-01-09 16:01:59 +1000
Commit message:

 replace 1: by seq_len( in plotVar
 
Package: mixOmics
Commit: d0631dc372ffab54712167c1b561adb434bed96c
Author: frohart <florian.rohart@gmail.com>
Date: 2019-01-09 15:40:56 +1000
Commit message:

 customization of plotVar legend
 
Package: mixOmics
Commit: 665041f36eee196394b42db770e6a8d5468d7cf3
Author: frohart <florian.rohart@gmail.com>
Date: 2019-01-09 14:55:58 +1000
Commit message:

 replace 1:x by seq_len(x)
 
Package: mixOmics
Commit: f2d66488e4abd0c7f612aa14874b67641cd15be9
Author: frohart <florian.rohart@gmail.com>
Date: 2019-01-09 14:17:42 +1000
Commit message:

 add plot.tune.rcc function
 
Package: mixOmics
Commit: 6b1226e3e7574db3b793be3d9c540bb76aa48079
Author: frohart <florian.rohart@gmail.com>
Date: 2019-01-09 14:17:22 +1000
Commit message:

 add plot.tune.rcc function
 
Package: mixOmics
Commit: ad3211d8e04526af039356f1b2f542faf34649bc
Author: frohart <florian.rohart@gmail.com>
Date: 2019-01-09 14:09:56 +1000
Commit message:

 reset par at the end of image.tune.rcc issue#7
 
Package: mixOmics
Commit: d7c3fec949bf47dc14c118b69b9656c6bbc12355
Author: frohart <florian.rohart@gmail.com>
Date: 2019-01-09 14:02:01 +1000
Commit message:

 comment out cat(results) in tune.rcc
 
Package: mixOmics
Commit: 6ac785171587cdc6d6d4b36a1776d54290a987c9
Author: frohart <florian.rohart@gmail.com>
Date: 2019-01-09 11:42:39 +1000
Commit message:

 merge RELEASE_3_8 into master
 
Package: mixOmics
Commit: 1a80849e7f3fcb65031783995e933f3363fab32d
Author: Kim-Anh Le Cao <kimanh.lecao@unimelb.edu.au>
Date: 2018-12-11 15:52:59 +1100
Commit message:

 Merge branch 'master' of https://github.com/mixOmicsTeam/mixOmics
 
Package: mixOmics
Commit: 65c0f5a8e5e085d674355a19ece64bb2975acc77
Author: Kim-Anh Le Cao <kimanh.lecao@unimelb.edu.au>
Date: 2018-12-11 15:52:30 +1100
Commit message:

 biocViews tag
 
Package: mixOmics
Commit: 5c29fcde63f3144ad3d990e8ac01631707511c6c
Author: mixOmicsTeam <39628589+mixOmicsTeam@users.noreply.github.com>
Date: 2018-12-11 15:48:05 +1100
Commit message:

 Update README.md 
Package: mixOmics
Commit: 35db250eee99f70433ebb070ae1341b78f0a4887
Author: mixOmicsTeam <39628589+mixOmicsTeam@users.noreply.github.com>
Date: 2018-12-11 15:47:51 +1100
Commit message:

 Update README.md 
Package: mixOmics
Commit: b330c1dca11a7dbe72f246ff9a77d2dc51c26442
Author: mixOmicsTeam <39628589+mixOmicsTeam@users.noreply.github.com>
Date: 2018-12-11 15:47:34 +1100
Commit message:

 Update README.md 
Package: scater
Commit: 22196a8592f32a01c6892c41bcd020d519ae4496
Author: Aaron Lun <infinite.monkeys.with.keyboards@gmail.com>
Date: 2019-01-09 03:22:33 +0000
Commit message:

 Bumped version, corrected date.
 
Package: scater
Commit: 47a5908211bf9f410ee74c7de1fef5132332fb87
Author: Aaron Lun <infinite.monkeys.with.keyboards@gmail.com>
Date: 2019-01-09 03:21:54 +0000
Commit message:

 Merge remote-tracking branch 'upstream/master'
 
Package: scater
Commit: 60fb8ef568e4f08a34bbaa00452c64fda84821f9
Author: Aaron Lun <infinite.monkeys.with.keyboards@gmail.com>
Date: 2019-01-09 03:16:11 +0000
Commit message:

 Avoid promiscuous includes in C++ code.
 
Package: TCGAbiolinks
Commit: 57e7b0d0383ec4453878c578e4f621ae2f205abe
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2019-01-08 21:09:22 -0600
Commit message:

 Fix description
 
Package: diffHic
Commit: 94ad794f683ff7915320465105049edb30de4eca
Author: Aaron Lun <infinite.monkeys.with.keyboards@gmail.com>
Date: 2019-01-09 03:05:47 +0000
Commit message:

 Bugfix for capping stats in prunePairs.
 
Package: ELMER
Commit: ffa0afde1b791ead3cb2b8fcd516001fded0f6af
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2019-01-08 21:02:54 -0600
Commit message:

 Removing devtools
 
Package: consensusDE
Commit: a79eac0a513205e6f516638a7b991e91ef37e337
Author: Ashley J. Waardenberg <a.waardenberg@gmail.com>
Date: 2019-01-09 12:58:52 +1000
Commit message:

 remove ensembl_annotate option for T/F
update vignette
 
Package: consensusDE
Commit: 14b7e3a2ab91c4df93f7ad8ee68a86b76f138274
Author: Ashley J. Waardenberg <a.waardenberg@gmail.com>
Date: 2019-01-09 12:43:04 +1000
Commit message:

 add force_build parameter to buildSummarized
update vignette
change tx_db to annotations for multi_de_pairs
update examples
add error checking for sample numbers
 
Package: consensusDE
Commit: 6a034cf71394e1f2a65c532823ea0d6c76a198bc
Author: Ashley J. Waardenberg <a.waardenberg@gmail.com>
Date: 2019-01-08 16:01:58 +1000
Commit message:

 bug fix - colors
 
Package: consensusDE
Commit: 1777dc6fe785cf0923253fea7fc03a7e57561432
Author: Ashley J. Waardenberg <a.waardenberg@gmail.com>
Date: 2019-01-08 13:16:36 +1000
Commit message:

 update missing dependency
 
Package: consensusDE
Commit: 985723cbb464a3ac113b707eb7a09e0383ccf12a
Author: Ashley J. Waardenberg <a.waardenberg@gmail.com>
Date: 2019-01-08 12:49:50 +1000
Commit message:

 update error for filter
 
Package: consensusDE
Commit: 4c4a7a7f929f9ce3a8e6b19c73379943cecc3fec
Author: Ashley J. Waardenberg <a.waardenberg@gmail.com>
Date: 2019-01-08 11:28:52 +1000
Commit message:

 update counts
version bump
 
Package: TCGAbiolinks
Commit: 85d4e78b58ea56a8b94a24142fce0bf518f6a3ba
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2019-01-08 20:56:48 -0600
Commit message:

 improving man
 
Package: ELMER
Commit: 75e96509c75d6c5dc071795c23e227966d86902e
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2019-01-08 20:31:34 -0600
Commit message:

 Remove :::
 
Package: diffHic
Commit: e02e0dba7b2b549be0c513eb9c5237739e342f65
Author: Aaron Lun <infinite.monkeys.with.keyboards@gmail.com>
Date: 2019-01-09 01:32:35 +0000
Commit message:

 Avoid integer overflow when computing whole-of-sample statistics.
 
Package: ELMER
Commit: 8c203cc587eec98134fcea2c8e94ee44a4ab6ddd
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2019-01-08 19:22:38 -0600
Commit message:

 remove warning
 
Package: TCGAbiolinks
Commit: e7e085c07afec2bace12dbe290bef993e179348f
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2019-01-08 19:16:16 -0600
Commit message:

 remmoving warning
 
Package: TCGAbiolinks
Commit: ab28a07fb99bde5a25e952ab05ed0d032f7164ba
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2019-01-08 18:49:15 -0600
Commit message:

 Exporting functions used in ELMER
 
Package: TENxBrainData
Commit: 7cd239630dec061a6b0061b2ebc79dff57bdc3e7
Author: Martin Morgan <martin.morgan@roswellpark.org>
Date: 2019-01-08 18:37:35 -0500
Commit message:

 Merge remote-tracking branch 'origin/master'

- includes fixes pushed to github only
 
Package: TENxBrainData
Commit: 36670c90cebd9fca86a117c43003a3d2710641f0
Author: Aaron Lun <alun@wehi.edu.au>
Date: 2018-10-09 16:49:07 +0100
Commit message:

 Removed old email.
 
Package: TENxBrainData
Commit: 489058e7156c4ff95fee1d8a113b1bf544971b20
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2018-09-24 09:12:51 +0100
Commit message:

 Added missing doc alias for 20k function.
 
Package: PureCN
Commit: 4010268a8b4cd784fa2fb139b06ceef0eeb472b8
Author: Markus Riester <markus.riester@novartis.com>
Date: 2019-01-08 10:48:06 -0500
Commit message:

 Fix crash when coverage contains no off-target reads, but off-target regions were defined; version bump
 
Package: PureCN
Commit: c2a14bdecc346f5e751c4d7c7901b148c4ae777c
Author: lima1 <mriester@gmx.de>
Date: 2019-01-06 12:05:08 -0500
Commit message:

 Minor documentation edits.
 
Package: BiocCheck
Commit: a00e4fb12b29726354b7bd1db2ca8f2ba1a60b44
Author: Martin Morgan <martin.morgan@roswellpark.org>
Date: 2019-01-08 17:34:30 -0500
Commit message:

 don't change working directory on interactive unit tests
 
Package: TCGAbiolinks
Commit: 2806f566c9fd0c3ee5c1815babdfdf5b72f03bf1
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2019-01-08 12:21:29 -0600
Commit message:

 Add gistic example
 
Package: dagLogo
Commit: b0416523e343caa234aeea21b9667b03eb30853e
Author: Jianhong Ou <jianhongou@Jianhongs-MBP.dhe.duke.edu>
Date: 2019-01-08 13:14:26 -0500
Commit message:

 add function cleanPeptides
 
Package: DelayedArray
Commit: e01b66f6242419b8421a2bd63e3f821cfe0eac62
Author: Hervé Pagès <hpages@fredhutch.org>
Date: 2019-01-08 09:22:34 -0800
Commit message:

 Split code and doc of RleArraySeed and RleArray classes
 
Package: HDF5Array
Commit: 7fa9ca4a894bb88a5ed25db4ed14124f2f2fcc33
Author: Hervé Pagès <hpages@fredhutch.org>
Date: 2019-01-08 09:18:45 -0800
Commit message:

 light cosmetic
 

Source Code & Build Reports »

Source code is stored in Git.

Software packages are built and checked nightly. Build reports:

 

Development Version »

Bioconductor packages under development:

Developer Resources: