Bioconductor has moved to GIT for contributed packages; the subversion logs are no longer active.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: ontoProc
Commit: 34a1b8185eed8cc999f82cae3f87de64b4cc5917
Author: Vince Carey <stvjc@channing.harvard.edu>
Date: 2019-02-17 06:19:33 -0500
Commit message:

 adding app sketch; shinyapps.io not taking R 3.6
 
Package: ontoProc
Commit: a6abaf4787998166572899e6d3e625df193bb185
Author: Vince Carey <stvjc@channing.harvard.edu>
Date: 2019-02-17 04:51:01 -0500
Commit message:

 updating README.md resources
 
Package: BridgeDbR
Commit: ab6d6146173a3b2d0d440026257b7e1ec55f8f61
Author: Egon Willighagen <egon.willighagen@gmail.com>
Date: 2019-02-17 01:36:13 +0100
Commit message:

 Added a getAttributes() method
 
Package: phyloseq
Commit: 53ee57915300808ccceb3954a0346beac07d1919
Author: Paul J. McMurdie <joey711@gmail.com>
Date: 2019-02-16 16:00:58 -0800
Commit message:

 1.27.2 resolve upstream conflict
 
Package: phyloseq
Commit: dc626c57b8151d32dcdf69aadd9238f82da74be9
Author: Paul J. McMurdie <joey711@gmail.com>
Date: 2019-02-16 15:44:50 -0800
Commit message:

 1.27.2 bugfix mt() example. Update README
 
Package: systemPipeR
Commit: dd281c565ebfc0d8a8be4baf970c2621cbff0b72
Author: tgirke <thomas.girke@ucr.edu>
Date: 2019-02-16 15:20:06 -0800
Commit message:

 fixed small bug in overLapper
 
Package: ontoProc
Commit: 331d0feb897cb75329a0cfecedbab36e682ad7a3
Author: Vince Carey <stvjc@channing.harvard.edu>
Date: 2019-02-16 17:16:07 -0500
Commit message:

 finishing vignette
 
Package: chimeraviz
Commit: 56ce1999bcb4e3888a654365434ef569f2692519
Author: Stian Lågstad <stianlagstad@users.noreply.github.com>
Date: 2019-02-16 20:09:16 +0100
Commit message:

 Merge pull request #58 from stianlagstad/improve-test-coverage

Improve test coverage 
Package: chimeraviz
Commit: 453ee4f5314832841fd52c80813ba01bfb78ee0d
Author: Stian Lågstad <stianlagstad@gmail.com>
Date: 2019-02-16 19:55:56 +0100
Commit message:

 Ignore these
 
Package: chimeraviz
Commit: ab1cac23fa581f9b3f343b885d4be8a0f2da76f0
Author: Stian Lågstad <stianlagstad@gmail.com>
Date: 2019-02-16 19:32:56 +0100
Commit message:

 Fix too long lines
 
Package: chimeraviz
Commit: 91d65042764b5896d168ace69f2f957307a992d1
Author: Stian Lågstad <stianlagstad@gmail.com>
Date: 2019-02-16 19:20:36 +0100
Commit message:

 Add tests for parameter-validations
 
Package: chimeraviz
Commit: 2f8bd96d3db7333c9688a76cbf65e76a2c352bed
Author: Stian Lågstad <stianlagstad@gmail.com>
Date: 2019-02-16 18:52:10 +0100
Commit message:

 Test .is_ylim_valid
 
Package: biosigner
Commit: 4891be95954bd234991346e30c78662212d0fb9c
Author: THEVENOT Etienne <ET207099@intra.cea.fr>
Date: 2019-02-16 19:13:03 +0100
Commit message:

 v1.11.22 minor internal corrections
 
Package: ontoProc
Commit: 125eda1ec03f87041d4a347332b14f41241c0199
Author: Vince Carey <stvjc@channing.harvard.edu>
Date: 2019-02-16 11:59:53 -0500
Commit message:

 minor changes
 
Package: ontoProc
Commit: 53056008622c248570149ee0eaf1761d2906a783
Author: Vince Carey <stvjc@channing.harvard.edu>
Date: 2019-02-16 11:24:45 -0500
Commit message:

 new material for extending an ontology, updated vignette
 
Package: BPRMeth
Commit: abc23bd3bf2540ca120ff79510e702c116eaaa7b
Author: andreaskapou <kapouranis.andreas@gmail.com>
Date: 2019-02-16 11:30:29 +0000
Commit message:

 Bump version
 
Package: BPRMeth
Commit: d6381e3c398741b8d7e82f82f14cd82c8fe9e19a
Author: andreaskapou <kapouranis.andreas@gmail.com>
Date: 2019-02-16 11:29:24 +0000
Commit message:

 Update README
 
Package: BPRMeth
Commit: ca6cfad10ce9b5b00002ec61db4989bd8a7dd840
Author: andreaskapou <kapouranis.andreas@gmail.com>
Date: 2019-02-16 11:28:15 +0000
Commit message:

 Add bioc badge
 
Package: BPRMeth
Commit: 0459f5f0e759f9bae0cec3adbc3598e01f9e5c0e
Author: andreaskapou <kapouranis.andreas@gmail.com>
Date: 2019-02-16 10:30:28 +0000
Commit message:

 Bump version
 
Package: BPRMeth
Commit: 97c03921fc903eaa56e042c7e2cf0513df60c6f7
Author: andreaskapou <kapouranis.andreas@gmail.com>
Date: 2019-02-15 23:17:27 +0000
Commit message:

 Add Zenodo link
 
Package: M3C
Commit: 5b663b307fa1ac39988ca1ab62a998aa01c04703
Author: crj32 <chris.r.john86@gmail.com>
Date: 2019-02-16 07:21:05 +0000
Commit message:

 fixed author syntax
 
Package: statTarget
Commit: dee342f8e800f6ed7ba02b305519bc7bd205f27d
Author: 13479776 <hemi.luan@gmail.com>
Date: 2019-02-16 15:12:14 +0800
Commit message:

 test
 
Package: BPRMeth
Commit: c6513e1850949fc547d4ff119b7138673ecf1921
Author: andreaskapou <kapouranis.andreas@gmail.com>
Date: 2019-02-15 23:11:00 +0000
Commit message:

 Update citation file
 
Package: dmrseq
Commit: 6e8ba0fb21458e8449bde984e662cea4ad460c8f
Author: kdkorthauer <kdkorthauer@gmail.com>
Date: 2019-02-15 18:10:44 -0500
Commit message:

 Bump version number in devel
 
Package: dmrseq
Commit: ae479b1c7669b6e0ecbf4648d2db0ce15d87a8d8
Author: kdkorthauer <kdkorthauer@gmail.com>
Date: 2019-02-15 17:51:20 -0500
Commit message:

 Merge branch 'issue-20'

Bug fix for missing columns of output with more than 3 factor groups.
Thanks to @jrhawley for pointing this out and proposing the change.
 
Package: dmrseq
Commit: 9e4ef74bdbd27cdf84628d9bb95d811f982a4529
Author: kdkorthauer <kdkorthauer@gmail.com>
Date: 2019-02-15 17:34:05 -0500
Commit message:

 Test patch to issue #20

Thanks to @jrhawley for pointing out the issue and proposing the
change.
 
Package: CRISPRseek
Commit: a6edc3664d9d7597ccffa0d4d77fe88499c3b166
Author: Julie Zhu <julie.zhu@umassmed.edu>
Date: 2019-02-15 17:15:05 -0500
Commit message:

 bump version with rXdN addition
 
Package: CRISPRseek
Commit: ce1bb7abbb06287a29f25d25f2bd2b1c3613169b
Author: Julie Zhu <julie.zhu@umassmed.edu>
Date: 2019-02-15 17:10:59 -0500
Commit message:

 bump version with rXdN addition
 
Package: CRISPRseek
Commit: fce66e4d2ea0696ce94564c4681f1c145c6deddf
Author: Julie Zhu <julie.zhu@umassmed.edu>
Date: 2019-02-15 17:08:57 -0500
Commit message:

 add rA:dN rC:dN rG:dN and rT:dN in CFDscore calculation
 
Package: seqsetvis
Commit: b396d638bff606f2328a67ad6164142ffee445d1
Author: jrboyd <jrboyd@med.uvm.edu>
Date: 2019-02-15 17:00:15 -0500
Commit message:

 v bump 1.3.4
 
Package: seqsetvis
Commit: 835c7f1cad564d89ec8caec0d497240e7957ee76
Author: jrboyd <jrboyd@med.uvm.edu>
Date: 2019-02-15 14:39:50 -0500
Commit message:

 v bump 1.3.4 improved fragLen_calcStranded() performance to avoid timeout in package CHECK.
 
Package: seqsetvis
Commit: 2593bce04f3590ba1db8626a3e0e5292da96847f
Author: jrboyd <jrboyd@med.uvm.edu>
Date: 2019-02-15 14:35:25 -0500
Commit message:

 v bump 1.3.3 docs pass CHECK
 
Package: seqsetvis
Commit: 77ce6ab1a4d942aea8372bb2a4cbbadb5a60a369
Author: jrboyd <jrboyd@med.uvm.edu>
Date: 2019-02-08 15:51:41 -0500
Commit message:

 bugfix: fetchGRanges * target_strand always missed
 
Package: seqsetvis
Commit: 44d3c6b8d6805032ef8023670f76d35b334a30ff
Author: jrboyd <jrboyd@med.uvm.edu>
Date: 2019-02-05 13:45:35 -0500
Commit message:

 added parallel processing to ssvFetch* functions.
 
Package: seqsetvis
Commit: b2e3edf5f59b9e5f8934f190980b10f5ea219a79
Author: jrboyd <jrboyd@med.uvm.edu>
Date: 2019-02-05 13:07:09 -0500
Commit message:

 updated tests for new export environment.
 
Package: seqsetvis
Commit: 0545eb1249b796a20aa61198bef1ac3d770356e8
Author: jrboyd <jrboyd@med.uvm.edu>
Date: 2019-02-05 11:05:33 -0500
Commit message:

 ssvFetchGRanges, improved functionality to match ssvFetch* (target_strand, return_data.table, win_method, anchor).
 
Package: seqsetvis
Commit: 1b1e7516ae6e7f522737fb85f29f41a4e8225951
Author: jrboyd <jrboyd@med.uvm.edu>
Date: 2019-02-05 10:13:02 -0500
Commit message:

 v bump to 1.3.1
 
Package: seqsetvis
Commit: ac690343d16e1d3739201e59483d46bb7cbe7ee8
Author: jrboyd <jrboyd@med.uvm.edu>
Date: 2019-02-05 10:10:45 -0500
Commit message:

 Merge remote-tracking branch 'upstream/master' to continue work on bioc devel.
 
Package: seqsetvis
Commit: 78a6293d624c5f1e27c4a955dc5d0d5cb9783cf5
Author: jrboyd <jrboyd@med.uvm.edu>
Date: 2019-02-05 10:09:55 -0500
Commit message:

 added ssvFetchGRanges.
added x_precision to centerAtMax.
 
Package: seqsetvis
Commit: 550e311a0f4bdaa15ee7ce8d04572f56e135302c
Author: jrboyd <jrboyd@med.uvm.edu>
Date: 2019-01-26 10:58:33 -0500
Commit message:

 Merge branch 'master' of https://github.com/jrboyd/seqsetvis

Conflicts:
	R/functions_fetch_bam.R
 
Package: seqsetvis
Commit: fca86a3411469a6487f8c78807b30d02b9324fdf
Author: jrboyd <jrboyd@med.uvm.edu>
Date: 2019-01-26 10:52:10 -0500
Commit message:

 bug fix: don't try to add sample names to empty result
 
Package: seqsetvis
Commit: 760209f19537af52d663e1f201c50059b8882769
Author: jrboyd <jrboyd@med.uvm.edu>
Date: 2019-01-26 10:52:10 -0500
Commit message:

 bug fix: don't try to add sample names to empty result
 
Package: seqsetvis
Commit: 572435ace62187ea78dc7132cce8c117fa046719
Author: jrboyd <jrboyd@med.uvm.edu>
Date: 2019-01-26 10:51:21 -0500
Commit message:

 bug fix: allow splice strategy "splice_count" in fetchBam
 
Package: seqsetvis
Commit: 085c4d10a87ae574ce1f5cb00a15761acad7f1fd
Author: jrboyd <jrboyd@med.uvm.edu>
Date: 2018-12-12 17:04:36 -0500
Commit message:

 qgr$name now used
clean up exports
 
Package: seqsetvis
Commit: 87054b8d3d67a6b4eca0f5bee6dbb2b8c7cc40d8
Author: jrboyd <jrboyd@med.uvm.edu>
Date: 2018-12-12 16:30:33 -0500
Commit message:

 docfix : fetchBam() splice_count added
 
Package: seqsetvis
Commit: 33e147b52538f87267257a388ceffd3621d09ae8
Author: jrboyd <jrboyd@med.uvm.edu>
Date: 2018-12-12 15:46:34 -0500
Commit message:

 Merge branch 'master' of https://github.com/jrboyd/seqsetvis
 
Package: seqsetvis
Commit: 074fe182e8495dbe5abd9e08191cbf39ea486bd9
Author: jrboyd <jrboyd@med.uvm.edu>
Date: 2018-12-12 15:32:06 -0500
Commit message:

 bigfix: missing id in output when qgr$id set but not names(qgr) Fixes #1
 
Package: seqsetvis
Commit: e3000e6ff4b608ee43a8ad64e3de33646e6c76b1
Author: jrboyd <jrboyd@med.uvm.edu>
Date: 2018-12-12 15:32:06 -0500
Commit message:

 bigfix: missing id in output when qgr$id set but not names(qgr)
 
Package: ELMER
Commit: 7fa711bae0b968dcb9ee8ab2f6602d9dc69ae90f
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2019-02-15 20:04:21 -0200
Commit message:

 update
 
Package: esATAC
Commit: 01b5a894617c2e71a018ccb842c6f6f22e611b48
Author: Zheng Wei <wzweizheng@qq.com>
Date: 2019-02-15 13:41:37 -0800
Commit message:

 fix bug
 
Package: esATAC
Commit: 929bffe19fa60ddebaef089a6c9d83fcf1a53643
Author: Zheng Wei <wzweizheng@qq.com>
Date: 2019-02-15 13:35:48 -0800
Commit message:

 fix bug of unexpected )
 
Package: esATAC
Commit: 0f08ed4f22b054722de574ff38fc76199b97d096
Author: Zheng Wei <wzweizheng@qq.com>
Date: 2019-01-18 12:41:25 -0800
Commit message:

 fix bug for non-hunman-and-mouse genome reference lacked of blacklist and DHS file
 
Package: chimeraviz
Commit: b554d4884fe2a3cde5d040bf83dae07ca193f883
Author: Stian Lågstad <stianlagstad@gmail.com>
Date: 2019-02-15 22:35:15 +0100
Commit message:

 Add env for password.

As the rstudio docker image requires this now.
 
Package: flowViz
Commit: 3b6fc83fb0b9ebae6c5d64ef48ee9f7ac85d9d3c
Author: Jacob Wagner <jpwagner@fredhutch.org>
Date: 2019-02-15 12:13:00 -0800
Commit message:

 bump
 
Package: flowViz
Commit: f7479d4a8b052e4ec050a53f8ae72956af8cae12
Author: Jacob Wagner <jpwagner@fredhutch.org>
Date: 2019-02-15 12:09:47 -0800
Commit message:

 More "condition has length > 1" fixes
 
Package: trackViewer
Commit: 10a3d23566671209d47260a817dc58fc263c35e6
Author: Jianhong Ou <jianhongou@Jianhongs-MBP.dhe.duke.edu>
Date: 2019-02-15 14:51:35 -0500
Commit message:

 add one-step visualization for browseTracks
 
Package: BPRMeth
Commit: 9f808c2f0d5830b6c5f56af2619c2ce16311c758
Author: andreaskapou <kapouranis.andreas@gmail.com>
Date: 2019-02-15 18:58:01 +0000
Commit message:

 Update citation
 
Package: DMRcaller
Commit: 6191d9e68dee6e0a2daedc07485bdc939e84e14e
Author: nrzabet <n.r.zabet@gen.cam.ac.uk>
Date: 2019-02-15 18:16:10 +0000
Commit message:

 bug fix
 
Package: signeR
Commit: 5b310caa1ffb5f785b5b56850c323b88be580c53
Author: Renan Valieris <renan.valieris@accamargo.org.br>
Date: 2019-02-15 13:28:12 -0200
Commit message:

 * fix prototype mismatch issue
* fix plot error: non-finite ylim when pvalue=0
 
Package: TCGAbiolinksGUI
Commit: 440fb3c3b6b042e3b882dc32da35239d17ca65e5
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2019-02-15 13:06:38 -0200
Commit message:

 Merge remote-tracking branch 'upstream/master'
 
Package: TCGAbiolinksGUI
Commit: 242736b6e987576fd9b8ccbe8e5d00480b1edc69
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2019-02-14 15:40:06 -0600
Commit message:

 elmer bug fixes
 
Package: TCGAbiolinksGUI
Commit: d677e186318656c38dcffdc7c45b20d42dde4f4a
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2019-02-14 14:34:02 -0600
Commit message:

 bug fix in elmer section
 
Package: TCGAbiolinksGUI
Commit: 782612641419af0c005b0cc4cf3c63ae2c9809fe
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2019-02-14 13:57:19 -0600
Commit message:

 bug fixes in GDC api
 
Package: TCGAbiolinksGUI
Commit: f659ed6a6b8437cc125181606fa0ccb49175f646
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2019-02-14 13:08:05 -0600
Commit message:

 Merge branch 'master' of https://github.com/BioinformaticsFMRP/TCGAbiolinksGUI
 
Package: TCGAbiolinksGUI
Commit: b93d5ae912a5eb0bfe300f21406fbe2ea443974c
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2019-02-14 13:07:49 -0600
Commit message:

 Changing from minfi to sesame
 
Package: TCGAbiolinks
Commit: 0cd9d4321c927b6386333ade82b2ce3f7ab76cbd
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2019-02-14 12:45:08 -0600
Commit message:

 Removing masking from matrix DNA methylation to SE
 
Package: TCGAbiolinks
Commit: b98e37b1729971e11349a9e6fb907f34e60049a2
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2019-02-14 12:18:57 -0600
Commit message:

 Adding IDAT prepare to vignette
 
Package: TCGAbiolinks
Commit: b5df31c3b5df9b1fef795528acc10082ba27050a
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2019-02-14 12:08:19 -0600
Commit message:

 Removing note
 
Package: TCGAbiolinks
Commit: 23f215204caa187b1bcb521efe14cb4e872eed5f
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2019-02-14 11:36:45 -0600
Commit message:

 fixing appveyor
 
Package: TCGAbiolinks
Commit: 1b1dd10ed90bba567b05ddb6266a2f251e395dec
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2019-02-14 11:34:16 -0600
Commit message:

 bug fix
 
Package: TCGAbiolinks
Commit: 5f09911d2dbe4113735bf2decb688a0927cf6f9e
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2019-02-14 11:16:29 -0600
Commit message:

 Fix Description
 
Package: TCGAbiolinks
Commit: f82a2f1dd260507e4bc7127598dc696775da012b
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2019-02-14 11:13:50 -0600
Commit message:

 updating aapveyor and namespace
 
Package: TCGAbiolinks
Commit: 0fa8abf6b45a27e9906f4ad56cf2a82bee42a9cb
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2019-02-14 11:07:36 -0600
Commit message:

 Version bump
 
Package: TCGAbiolinks
Commit: 87e1384b529f652c647846882b60e90a36554e89
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2019-02-14 11:07:08 -0600
Commit message:

 Update internal function for idat function
 
Package: TCGAbiolinks
Commit: 76e1110adb46f67f58e287c28f6caf924f03cbb5
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2019-02-14 11:06:35 -0600
Commit message:

 Adding IDAT pprepare using sesame
 
Package: ELMER
Commit: ff92ae5d865a167c1f2da63aa028c7c7943bc493
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2019-02-11 10:13:52 -0600
Commit message:

 Update README.md 
Package: AnnotationHubData
Commit: f0347494ee136f5fdecaaf60d76d3a8cb75460dd
Author: lshep <lori.shepherd@roswellpark.org>
Date: 2019-02-15 08:44:57 -0500
Commit message:

 Add loop for GTF conversion on the fly

  - ensembl started blocking consecutive hits on gtf directories which
    would cause the generation to fail.  A trycatch loop was added that if
    the access is denied (errors) it will wait 10 seconds and try again and
    completely fail after 3 attempts.
 
Package: AnnotationHubData
Commit: b7f312e1bca6d626cf918084ce873a5e7069bb6d
Author: lshep <lori.shepherd@roswellpark.org>
Date: 2019-02-14 09:59:26 -0500
Commit message:

 More clean up
 
Package: AnnotationHubData
Commit: d554b76ea998164ad4db31f5b9538393b147a4d2
Author: lshep <lori.shepherd@roswellpark.org>
Date: 2019-02-13 08:08:43 -0500
Commit message:

 tryCatch in 2bit for cleanup
 
Package: ChIPanalyser
Commit: 37fdab99738e2fb178aa73e9e6e459796ef7603f
Author: Patrick CN Martin <pm16057@essex.ac.uk>
Date: 2019-02-15 13:15:37 +0000
Commit message:

 man page mismatch
 
Package: ChIPanalyser
Commit: 5496ff9f89e44a45b0b55fb2e817276a40042db5
Author: Patrick CN Martin <pm16057@essex.ac.uk>
Date: 2019-02-15 11:30:02 +0000
Commit message:

 v1.4.1
 
Package: ChIPanalyser
Commit: 61990e15f4e5ed9c8d530c20505829242188732b
Author: Patrick CN Martin <pm16057@essex.ac.uk>
Date: 2019-02-15 11:27:58 +0000
Commit message:

 v1.5.1
 
Package: ChIPanalyser
Commit: 4b0950056dbe004d17f57ffd38fac722d5e9b99a
Author: Patrick CN Martin <pm16057@essex.ac.uk>
Date: 2019-02-15 11:08:35 +0000
Commit message:

 test
 
Package: ChIPanalyser
Commit: 79b503b069389e8dc2a31d9fb5fcb556c5303c2d
Author: Patrick CN Martin <pm16057@essex.ac.uk>
Date: 2019-02-15 11:04:43 +0000
Commit message:

 patching
 
Package: BPRMeth
Commit: 92385ad5aba25f5c4cd3a419b389b664ebe924b7
Author: andreaskapou <kapouranis.andreas@gmail.com>
Date: 2019-02-15 11:09:22 +0000
Commit message:

 Add citation
 
Package: FELLA
Commit: 3fca6aa9d7508e44cc2ede87585f4f0f78bd318c
Author: Sergi Picart <elpicart@gmail.com>
Date: 2019-02-15 09:55:59 +0100
Commit message:

 Small fixes to vignettes and citation
 
Package: cola
Commit: 20ed4888853022fe4423953db4101fd810c2b6eb
Author: Zuguang Gu <jokergoo@gmail.com>
Date: 2019-02-15 09:42:31 +0100
Commit message:

 move TEMPLATE_DIR to .onLoad()
 
Package: cola
Commit: 6d91eaf1f0df5bd7381f764bd4a068a8932d00a2
Author: Zuguang Gu <jokergoo@gmail.com>
Date: 2019-02-12 16:32:31 +0100
Commit message:

 add a new vignette
 
Package: cola
Commit: ae31cc345b5b332d7813119e82e6e7e210da33c8
Author: Zuguang Gu <jokergoo@gmail.com>
Date: 2019-02-12 12:08:27 +0100
Commit message:

 update readme
 
Package: cola
Commit: 7dff0c216abbdc9b1434d2e7c7f536bf2cb37365
Author: Zuguang Gu <jokergoo@gmail.com>
Date: 2019-02-12 12:02:04 +0100
Commit message:

 update readme
 
Package: statTarget
Commit: 2b8b4983faf4fcc7a9da7fe853a7c42218cb9e4e
Author: 13479776 <hemi.luan@gmail.com>
Date: 2019-02-15 14:09:30 +0800
Commit message:

 test
 
Package: SMAD
Commit: 3371de8ffba3d3a5cf2e91908be1ef2368742b9c
Author: zqzneptune <zqzneptune@hotmail.com>
Date: 2019-02-14 23:01:27 -0600
Commit message:

 Version Bump
 
Package: SMAD
Commit: d2ea685af14c314c5b23fd747f5e6925cc5ee804
Author: zqzneptune <zqzneptune@hotmail.com>
Date: 2019-02-14 22:52:11 -0600
Commit message:

 News
 
Package: SMAD
Commit: 734f3825434751b00202bd62e0b0e80374f132bd
Author: Qingzhou Zhang <zqzneptune@hotmail.com>
Date: 2019-02-12 23:57:59 -0600
Commit message:

 Remove CompPASSplus Hide GetPPN
 
Package: SMAD
Commit: 185d0ff799eb5a272fcfcac02487053f662954b3
Author: Qingzhou Zhang <zqzneptune@hotmail.com>
Date: 2019-02-12 23:57:19 -0600
Commit message:

 Change to BiocStyle
 
Package: SMAD
Commit: add142c8d4e49a15b0c2e414fe7e75fc57f2bdc9
Author: Qingzhou Zhang <zqzneptune@hotmail.com>
Date: 2019-02-12 23:22:33 -0600
Commit message:

 Discard CompPASSplus
 
Package: limma
Commit: 5b47facd0fddb61831a2c755c9b046f4ff3ae996
Author: Gordon Smyth <smyth@wehi.edu.au>
Date: 2019-02-15 15:42:23 +1100
Commit message:

 15 Feb 2019: limma 3.39.12

- arrayWeights() now checks for and skips over any genes with zero
  residual variances.
 
Package: COMPASS
Commit: 039c7498e7b0a957558c65cc0363fb81c24ab1d2
Author: gfinak <greg.finak@gmail.com>
Date: 2019-02-14 16:05:55 -0800
Commit message:

 fix an edge case related to previous commit
 
Package: COMPASS
Commit: 3568b47495862c84b7a72b3d3dae99b8f70b2319
Author: gfinak <greg.finak@gmail.com>
Date: 2019-02-14 15:53:33 -0800
Commit message:

 bump
 
Package: COMPASS
Commit: 0aee1e6c2319cef211f04c91317e60268e6f4416
Author: gfinak <greg.finak@gmail.com>
Date: 2019-02-14 15:50:52 -0800
Commit message:

 Merge branch 'master' into trunk
 
Package: COMPASS
Commit: dd511fb8b52f49ea4fae07eb0516357d33523559
Author: gfinak <greg.finak@gmail.com>
Date: 2019-02-14 15:48:14 -0800
Commit message:

 fix aggregation and labeling when selecting markers for the heatmap
 
Package: COMPASS
Commit: 07f49e5a7de4b762b80db68b8a94f84a8d42b75a
Author: mikejiang <wjiang2@fhcrc.org>
Date: 2019-01-08 15:28:51 -0800
Commit message:

 modify test case to work with cytolib2
 
Package: COMPASS
Commit: 4a85f1fa73108f2210838cd82c47e431e17e8ea2
Author: Greg Finak <greg.finak@gmail.com>
Date: 2018-12-13 09:59:28 -0500
Commit message:

 remove trailing whitespace in deps list 
Package: COMPASS
Commit: 373e0407287fa24b47e6bc046d62b488592a091a
Author: Greg Finak <greg.finak@gmail.com>
Date: 2018-12-13 09:58:24 -0500
Commit message:

 Update .travis.yml 
Package: COMPASS
Commit: 1f7ca90f1dc4c0df78fce6a39cdf69e3eba4ebdd
Author: Greg Finak <greg.finak@gmail.com>
Date: 2018-12-13 09:56:45 -0500
Commit message:

 Update .travis.yml 
Package: COMPASS
Commit: e03c427961e5f2cce4c7df36e5234493ad11748e
Author: Greg Finak <greg.finak@gmail.com>
Date: 2018-12-13 09:18:54 -0500
Commit message:

 Update .travis.yml 
Package: GENESIS
Commit: f7f31f3d4e2557fd3efbb7d66c6f6f159a454b39
Author: Stephanie M. Gogarten <sdmorris@uw.edu>
Date: 2019-02-13 14:23:56 -0800
Commit message:

 Merge pull request #12 from UW-GAC/admixMap

Allow SeqArray GDS files in admixMap 
Package: GENESIS
Commit: 308816bb6893aee5ec8d216c7acf4ad199e60c74
Author: Stephanie M. Gogarten <sdmorris@uw.edu>
Date: 2019-02-13 14:20:28 -0800
Commit message:

 version bump
 
Package: GENESIS
Commit: 176e209da4e1a61beacfd7c3303cae816b3978a6
Author: Stephanie M. Gogarten <sdmorris@uw.edu>
Date: 2019-02-13 14:20:15 -0800
Commit message:

 remove obsolete code
 
Package: GENESIS
Commit: 2c540c3b043cfa3ebb7a7037a08f8563a8e8682e
Author: Stephanie M. Gogarten <sdmorris@uw.edu>
Date: 2019-02-13 12:49:23 -0800
Commit message:

 update man page with SeqVarIterator option for admixMap
 
Package: GENESIS
Commit: 110b8d2c2346b0b3d311e4d9e7818b47e0675c96
Author: Stephanie M. Gogarten <sdmorris@uw.edu>
Date: 2019-02-13 12:03:05 -0800
Commit message:

 unit test compares output from two types of GDS files
 
Package: GENESIS
Commit: e24eb190b068c0f644db07f8ae0aed3d6a8d5f8f
Author: Stephanie M. Gogarten <sdmorris@uw.edu>
Date: 2019-02-13 12:02:24 -0800
Commit message:

 don't include alleles in admixMap output
 
Package: GENESIS
Commit: 09af3f4f9266069f6e7ce5ccccb51969adeb499a
Author: Stephanie M. Gogarten <sdmorris@uw.edu>
Date: 2019-02-13 11:18:45 -0800
Commit message:

 fix dimensions of frequency, set indentation
 
Package: GENESIS
Commit: 291c764e93e7fe95893e49c3b37076f366009627
Author: smgogarten <smgogarten@velasca>
Date: 2019-02-12 17:06:07 -0800
Commit message:

 use new internal function to check for identical list elements
 
Package: GENESIS
Commit: efa915de006e146e2d96deca232bb1f4998898b1
Author: smgogarten <smgogarten@velasca>
Date: 2019-02-12 17:00:27 -0800
Commit message:

 Merge branch 'master' into admixMap
 
Package: GENESIS
Commit: 5f1dd2d862fe52198fceab4a84c2e7373360ce19
Author: smgogarten <smgogarten@velasca>
Date: 2019-02-12 16:58:23 -0800
Commit message:

 bug fix: allow >2 matrices in fitNullModel

Previous fix for checking list elements identical only worked
for 2 elements in list.
 
Package: GENESIS
Commit: d51218dbb2e407dc567824b6dc4c5bc438146cbe
Author: smgogarten <smgogarten@velasca>
Date: 2019-02-12 16:52:21 -0800
Commit message:

 allow SeqVarData objects in admixMap (WIP)
 
Package: GENESIS
Commit: 3b5b0a42109457fe837a6e907bff6a12d197b2ad
Author: smgogarten <smgogarten@velasca>
Date: 2019-02-12 16:51:28 -0800
Commit message:

 move some internal code for GenotypeData objects into methods
 
Package: GENESIS
Commit: 15032d974a93754accbedfb0e0206916a64314be
Author: Stephanie M. Gogarten <sdmorris@uw.edu>
Date: 2019-01-30 14:07:25 -0800
Commit message:

 add coverage with covr
 
Package: GENESIS
Commit: ccaa42602cae64434135145eb42f799ba57e892d
Author: Stephanie M. Gogarten <sdmorris@uw.edu>
Date: 2019-01-30 10:27:09 -0800
Commit message:

 use bioc-devel for travis
 
Package: GENESIS
Commit: e13fc0df32172d44d491b651fb4012c607945f8e
Author: Stephanie M. Gogarten <sdmorris@uw.edu>
Date: 2019-01-30 10:23:31 -0800
Commit message:

 set up travis CI
 
Package: RSeqAn
Commit: 11e6bb6bcdebc6f173f70ae612f819cbcbf3b36a
Author: August Guang <august.guang@gmail.com>
Date: 2019-02-14 16:19:24 -0700
Commit message:

 Merge branch 'devel'
 
Package: RSeqAn
Commit: 76c98a7f0fee4d38ec004322a2baee3144d567ca
Author: August Guang <august.guang@gmail.com>
Date: 2019-02-12 19:52:12 -0500
Commit message:

 updated configure.sh

src/Makevars modified instead of DESCRIPTION
 
Package: RSeqAn
Commit: 7e409f4baf594cb822c2b963e08a41e1e6ffb72d
Author: August Guang <august.guang@gmail.com>
Date: 2019-02-12 19:20:52 -0500
Commit message:

 disabling wrappers for Windows
 
Package: RSeqAn
Commit: 4b4dd300edcc528e32decde7d5cbef9a47feae52
Author: august <august.guang@gmail.com>
Date: 2019-02-12 15:16:46 -0500
Commit message:

 Update README.md 
Package: RSeqAn
Commit: 3dd254d18bcd64c4efeecdbe17cd9281c700ec81
Author: august <august.guang@gmail.com>
Date: 2019-02-07 21:51:03 -0500
Commit message:

 Update paper.md 
Package: biosigner
Commit: 11436f3c5c2830266a9b50bd7ce9b51dc3a9a350
Author: THEVENOT Etienne <ET207099@intra.cea.fr>
Date: 2019-02-14 22:26:05 +0100
Commit message:

 v1.11.2Ã0 minor internal modification
 
Package: Rsamtools
Commit: d0fb5dad1b8576b956ab60964347696671d03c19
Author: Hervé Pagès <hpages@fredhutch.org>
Date: 2019-02-14 12:00:56 -0800
Commit message:

 Add 'gzindex' argument to FaFile() constructor (points to bgzip index)

Also added 'gzindex' field to FaFile objects and gzindex() getter/setter.
 
Package: recount
Commit: c95003ed394c0e9747931871b1431689f08281e2
Author: Leonardo Collado Torres <lcollado@jhsph.edu>
Date: 2019-02-14 11:52:47 -0500
Commit message:

 v1.9.2 -- add the async argument to snaptron_query() to resolve https://github.com/ChristopherWilks/snaptron/issues/11
 
Package: GenomicFeatures
Commit: 50f241ae64c568f855557c2c9fef5567054110e2
Author: vobencha <vobencha@gmail.com>
Date: 2019-02-14 08:15:26 -0800
Commit message:

 add support for mapToTranscripts() to map ranges that span introns
 
Package: GAPGOM
Commit: 1589e5eda54d1451a880b618dd07a9721a0b4fed
Author: Casper
Date: 2019-02-14 16:30:46 +0100
Commit message:

 Edited DESC: removed maintainer (already in Authors@R)
 
</div>
Package: IsoformSwitchAnalyzeR
Commit: 17f69e844c8697bf81c11b7bf5893ef3f492ffac
Author: kvittingseerup <k.vitting.seerup@gmail.com>
Date: 2019-02-14 10:22:54 +0100
Commit message:

 Vignette update
 
Package: M3C
Commit: bc24d3355ce694bbd3eacea9ba89fed83cea5ca4
Author: crj32 <chris.r.john86@gmail.com>
Date: 2019-02-14 08:15:52 +0000
Commit message:

 updated author information
 
Package: limma
Commit: 3607658415d6f8dbc133a2cb4680a5d6016206b5
Author: Gordon Smyth <smyth@wehi.edu.au>
Date: 2019-02-14 18:35:34 +1100
Commit message:

 14 Feb 2019: limma 3.39.11

- contrasts.fit() now removes any test statistics or p-values found
  in the fit object. This avoids a mis-match between coefficients and
  test statistics if eBayes() has been run on the object previously.
 
Package: limma
Commit: 7e71f5dff863952e89e69fa1996338254669da41
Author: Gordon Smyth <smyth@wehi.edu.au>
Date: 2019-02-14 18:15:49 +1100
Commit message:

 14 Feb 2019: limma 3.39.10

- arrayWeights() now chooses between the REML and original
  gene-by-gene algorithm automatically by default. REML is chosen
  when there are no prior weights or missing values and gene-by-gene
  is used otherwise.
 
Package: clusterProfiler
Commit: 76c06bb4f87ea9987c86690e83938c0f4ee16207
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2019-01-26 07:08:08 +0800
Commit message:

 optimize
 
Package: clusterProfiler
Commit: 8b0eea5cf897d6f97acb2187eb979cc4653bc6c5
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2019-01-11 23:16:52 +0800
Commit message:

 mv vignette to book
 
Package: clusterProfiler
Commit: 5e934223c100a85d1a80f64731081554ef6d68cf
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2018-12-24 15:36:31 +0800
Commit message:

 fixed R check and introduce asis in [ method
 
Package: QuasR
Commit: ed833f9d3beb69e4c7ac1df42918f4c6d14cc63f
Author: Michael Stadler <stadler.michael@gmail.com>
Date: 2019-02-14 08:05:08 +0100
Commit message:

 Merge pull request #10 from fmicompbio/rhisat2

Rhisat2 
Package: QuasR
Commit: dfc9a11a9735a1593844c8203ae406b7000081b7
Author: Charlotte Soneson <charlottesoneson@gmail.com>
Date: 2019-02-13 15:22:00 +0100
Commit message:

 Travis debug
 
Package: QuasR
Commit: ab7715205f28f29798e0e5fa87325414cf45f592
Author: Charlotte Soneson <charlottesoneson@gmail.com>
Date: 2019-02-13 14:53:18 +0100
Commit message:

 Debug travis
 
Package: QuasR
Commit: a6fab695d831bc7d9383e5b7b9ec5f3a57d457c0
Author: Charlotte Soneson <charlottesoneson@gmail.com>
Date: 2019-02-13 13:07:57 +0100
Commit message:

 Remove empty Details section
 
Package: QuasR
Commit: 0e8bab13d7acdd1c01eda611e7741e39d7b2a7ea
Author: Charlotte Soneson <charlottesoneson@gmail.com>
Date: 2019-02-13 11:40:11 +0100
Commit message:

 Add R version dependency
 
Package: QuasR
Commit: 81a4aa182cfa453939086cfabc904c3fb10515c2
Author: Charlotte Soneson <charlottesoneson@gmail.com>
Date: 2019-02-13 11:17:14 +0100
Commit message:

 Don't try to extract NH tag from unaligned reads.
 
Package: QuasR
Commit: 7b95bf42f732bf937b118c9f61b8e9920570c8b5
Author: Charlotte Soneson <charlottesoneson@gmail.com>
Date: 2019-02-13 09:04:27 +0100
Commit message:

 Consistent argument names in qProjectUpdate
 
Package: QuasR
Commit: da9da2bbdf6d468fa29307f5381c9d072e268919
Author: Charlotte Soneson <charlottesoneson@gmail.com>
Date: 2019-02-13 09:01:56 +0100
Commit message:

 Only read gene annotation if splice site file should be recreated.
 
Package: QuasR
Commit: 808227dda659d94ae6180b052efca9c92fb164d5
Author: mbstadler <stadler.michael@gmail.com>
Date: 2019-02-13 08:22:11 +0100
Commit message:

 v1.23.14 - ported filter_hisat2.c from samtools to htslib API
 
Package: QuasR
Commit: 27446b275e37a6483a3ac5521ceffb0149d2ae74
Author: Michael Stadler <stadler.michael@gmail.com>
Date: 2019-02-13 06:57:32 +0100
Commit message:

 use htslib header 
Package: QuasR
Commit: 2254d114125e63e488cd3347ba2e59aabd80b3f8
Author: Charlotte Soneson <charlottesoneson@gmail.com>
Date: 2019-02-12 21:37:39 +0100
Commit message:

 Merge branch 'master' into rhisat2
 
Package: QuasR
Commit: 02b7cb1305ea27df8307896ef49a336921e983bb
Author: Michael Stadler <stadler.michael@gmail.com>
Date: 2019-02-12 19:44:34 +0100
Commit message:

 Merge pull request #9 from hpages/master

Migrate QuasR to Rhtslib and Rsamtools 1.99.1 
Package: QuasR
Commit: f1f916bad56de6bff1e7655209f8e283c16a08e5
Author: Hervé Pagès <hpages@fredhutch.org>
Date: 2019-02-12 08:50:22 -0800
Commit message:

 Migrate QuasR to Rhtslib and Rsamtools 1.99.1
 
Package: QuasR
Commit: 1cc0debfc1289ea70f0958f78eeec785419b392a
Author: Charlotte Soneson <charlottesoneson@gmail.com>
Date: 2019-02-11 08:50:29 +0100
Commit message:

 Try to install remotes again
 
Package: QuasR
Commit: 0cd1939a9f0b81e8700c9f588b6482e45745b822
Author: Charlotte Soneson <charlottesoneson@gmail.com>
Date: 2019-02-11 07:45:52 +0100
Commit message:

 Cache packages travis
 
Package: QuasR
Commit: dc8d94dfd5afce09a63bbd1dfa4f47b96a5c6174
Author: Charlotte Soneson <charlottesoneson@gmail.com>
Date: 2019-02-10 22:04:29 +0100
Commit message:

 Use Rhisat2 from Bioconductor
 
Package: QuasR
Commit: 583134c017d028a7de935146a8a16568c1c038df
Author: Charlotte Soneson <charlottesoneson@gmail.com>
Date: 2019-02-10 17:12:05 +0100
Commit message:

 Fix test
 
Package: QuasR
Commit: 61779877554294a921e73e0de119e2bcb19e3fc3
Author: Charlotte Soneson <charlottesoneson@gmail.com>
Date: 2019-02-10 16:48:19 +0100
Commit message:

 Merge master into Rhisat2
 
Package: QuasR
Commit: 8274048e4f9420df3d71dab06a41804b15e4df09
Author: Charlotte Soneson <charlottesoneson@gmail.com>
Date: 2019-01-11 16:55:58 +0100
Commit message:

 Cosmetic changes
 
Package: QuasR
Commit: f7699b7a3cbf6308be8a2bb52a1ef1b4c407e179
Author: Charlotte Soneson <charlottesoneson@gmail.com>
Date: 2019-01-11 16:53:16 +0100
Commit message:

 Simplify align_Rhisat2
 
Package: QuasR
Commit: ef66ef7b17aa2d86840eae468d2f143b44fef5ea
Author: Charlotte Soneson <charlottesoneson@gmail.com>
Date: 2019-01-11 16:12:50 +0100
Commit message:

 Simplification (same call to Rhisat2 for spliced and unspliced alignment)
 
Package: QuasR
Commit: 1a5337d05f18aa44b3c9c57327cc05c0be0b836d
Author: Charlotte Soneson <charlottesoneson@gmail.com>
Date: 2019-01-11 16:05:20 +0100
Commit message:

 Clean up
 
Package: QuasR
Commit: 51d337ca3f79cc56216f66a2675866e14e2620e6
Author: Charlotte Soneson <charlottesoneson@gmail.com>
Date: 2019-01-11 11:50:39 +0100
Commit message:

 Add documentation for qProjectUpdate
 
Package: QuasR
Commit: a3b285b01b21c7b6b58ca72cf41df71fdd9fb53a
Author: Charlotte Soneson <charlottesoneson@gmail.com>
Date: 2019-01-11 11:44:11 +0100
Commit message:

 Add unit tests, export qProjectUpdate
 
Package: QuasR
Commit: a727a44cd29382dbf7ae26b3635636c41acf7d04
Author: Charlotte Soneson <charlottesoneson@gmail.com>
Date: 2019-01-11 08:52:57 +0100
Commit message:

 Merge pull request #7 from fmicompbio/rhisat2_maxhit

filter Rhisat2 alignments to conform with maxHits argument 
Package: QuasR
Commit: 5779fef0b468996d54dc3b9c244de8cc1eb70d0a
Author: Charlotte Soneson <charlottesoneson@gmail.com>
Date: 2019-01-10 17:20:29 +0100
Commit message:

 Fix print method for qProject class
 
Package: QuasR
Commit: 4f343cd72f281a9e8c1eabe41db9335b386f1605
Author: Charlotte Soneson <charlottesoneson@gmail.com>
Date: 2019-01-10 17:04:07 +0100
Commit message:

 Change representation to slots in qProject class definition
 
Package: QuasR
Commit: 99899f2e308925f387101f09fedd2e14139670a9
Author: Charlotte Soneson <charlottesoneson@gmail.com>
Date: 2019-01-10 17:01:45 +0100
Commit message:

 Set lib.loc to NULL if missing
 
Package: QuasR
Commit: 562400761187fee76c91ab432aea4880f53f529a
Author: Charlotte Soneson <charlottesoneson@gmail.com>
Date: 2019-01-10 11:14:36 +0100
Commit message:

 Fix unit tests for Rhisat2 alignments (with the filtering).
 
Package: QuasR
Commit: d254b6415fa93472376557fe5b5d1c32300988cb
Author: Charlotte Soneson <charlottesoneson@gmail.com>
Date: 2019-01-10 11:14:13 +0100
Commit message:

 Add maxHits argument to align_Rhisat2, call filtering function.
 
Package: QuasR
Commit: caaf08ffecbe48a4da4b4a7ead12cdac6badbaaa
Author: Charlotte Soneson <charlottesoneson@gmail.com>
Date: 2019-01-09 17:12:35 +0100
Commit message:

 Merge align_Rhisat2 and align_Rhisat2Spliced functions. Set -k to maxHits+1
 
Package: QuasR
Commit: 0dac4914fc2b3fed59206947fb94512eef4aef43
Author: mbstadler <stadler.michael@gmail.com>
Date: 2019-01-09 16:30:03 +0100
Commit message:

 symbol lookup fix
 
Package: QuasR
Commit: 400068325cb6c618c6184e8c4e67813fbe5e5538
Author: mbstadler <stadler.michael@gmail.com>
Date: 2019-01-09 14:52:35 +0100
Commit message:

 added unit test for filterHisat2
 
Package: QuasR
Commit: b17279915f9f7d5a4a55fe9c291e76d256674fb3
Author: mbstadler <stadler.michael@gmail.com>
Date: 2019-01-09 13:29:07 +0100
Commit message:

 fix flag for unmapped reads
 
Package: QuasR
Commit: 4f3397a4d4d57b03c0a140cd863d54fc01e34a44
Author: mbstadler <stadler.michael@gmail.com>
Date: 2019-01-09 09:27:57 +0100
Commit message:

 v1.23.9 : added filterHisat2()
 
Package: QuasR
Commit: 969b723269d58948eba7ab907d92aab486a11a39
Author: Charlotte Soneson <charlottesoneson@gmail.com>
Date: 2019-01-07 10:21:42 +0100
Commit message:

 Merge branch 'master' into rhisat2
 
Package: QuasR
Commit: e0a713ec6412385b66b5e68a64fa8a2e73ca6b25
Author: Charlotte Soneson <charlottesoneson@gmail.com>
Date: 2018-12-20 11:46:12 +0100
Commit message:

 Fix merge conflicts
 
Package: QuasR
Commit: b7f6df229f4ea94ad36557e44a4e7ebca7cc2e2a
Author: Charlotte Soneson <charlottesoneson@gmail.com>
Date: 2018-12-19 17:05:03 +0100
Commit message:

 Typos
 
Package: QuasR
Commit: d20f1583a1ae1194c2b7f961e7b06f5c4af11129
Author: Charlotte Soneson <charlottesoneson@gmail.com>
Date: 2018-12-19 15:38:55 +0100
Commit message:

 Merge branch 'master' into rhisat2
 
Package: QuasR
Commit: 2c283074c38fad9ba148e139bb3fc2191f548da9
Author: Charlotte Soneson <charlottesoneson@gmail.com>
Date: 2018-12-19 15:24:51 +0100
Commit message:

 Make sure that the splice site file is used if provided
 
Package: QuasR
Commit: dfc93f611801a2bb586aa6c6f6b4bd58bd64140b
Author: Charlotte Soneson <charlottesoneson@gmail.com>
Date: 2018-12-19 14:52:20 +0100
Commit message:

 Add unit tests for Rhisat2 alignments
 
Package: QuasR
Commit: bdca875a065c0680b9c7fb07d6238faeb4cf6965
Author: Charlotte Soneson <charlottesoneson@gmail.com>
Date: 2018-12-19 10:00:02 +0100
Commit message:

 Fix test failing when bam files are provided
 
Package: QuasR
Commit: b39125b28fb9e8643b45498d2399c0989580e2ce
Author: Charlotte Soneson <charlottesoneson@gmail.com>
Date: 2018-12-19 08:31:08 +0100
Commit message:

 Merge master into rhisat2
 
Package: QuasR
Commit: 8f5297c93129f23eefd2fd8bed5be120bb875e86
Author: Charlotte Soneson <charlottesoneson@gmail.com>
Date: 2018-12-17 17:35:30 +0100
Commit message:

 Add AnnotationDbi
 
Package: QuasR
Commit: 3c4e8b10e3c821a1b499f6f41b0fded6c6e63cb3
Author: Charlotte Soneson <charlottesoneson@gmail.com>
Date: 2018-12-17 17:34:58 +0100
Commit message:

 Add some documentation
 
Package: QuasR
Commit: fee5182f0579edd3b9de24acc83fdd7248bd0c83
Author: Charlotte Soneson <charlottesoneson@gmail.com>
Date: 2018-12-17 17:01:00 +0100
Commit message:

 Check whether splicesite file needs to be regenerated.
 
Package: QuasR
Commit: c14cf75a425dca586b57cabdf721670598e7ed4e
Author: Charlotte Soneson <charlottesoneson@gmail.com>
Date: 2018-12-17 16:05:46 +0100
Commit message:

 Only redo alignments if necessary
 
Package: QuasR
Commit: 51183452d4994920d3a72c2d7d73139559af115a
Author: Charlotte Soneson <charlottesoneson@gmail.com>
Date: 2018-12-17 14:02:21 +0100
Commit message:

 Add geneAnnotation to alnInfo
 
Package: QuasR
Commit: fbde83364998d713eaea83d5a75118cbfc5da47b
Author: Charlotte Soneson <charlottesoneson@gmail.com>
Date: 2018-12-17 13:58:12 +0100
Commit message:

 Create md5sum file for geneAnnotation
 
Package: QuasR
Commit: 36e19cd27a273d7d7bc262b2a21001599d1217a5
Author: Charlotte Soneson <charlottesoneson@gmail.com>
Date: 2018-12-17 13:55:51 +0100
Commit message:

 Don't check for compatible geneAnnotation if aligner is Rbowtie
 
Package: QuasR
Commit: ab281218bae38b754088c4d23f27a37f326ba9c8
Author: Charlotte Soneson <charlottesoneson@gmail.com>
Date: 2018-12-17 13:42:36 +0100
Commit message:

 Move parsing of spliced alignment parameter
 
Package: QuasR
Commit: 71a563a58c25b2a130c94d3e091e738dd4a92801
Author: Charlotte Soneson <charlottesoneson@gmail.com>
Date: 2018-12-17 13:40:56 +0100
Commit message:

 Move definition of alignment parameters to after aligner definition
 
Package: QuasR
Commit: 6061488b860f2066bde0bc8f737768e100ce41b9
Author: Charlotte Soneson <charlottesoneson@gmail.com>
Date: 2018-12-17 13:28:58 +0100
Commit message:

 Fix addition of geneAnnotation to qProject object
 
Package: QuasR
Commit: 16fde84ab223dd4c354e0762f9a43546e36336ba
Author: Charlotte Soneson <charlottesoneson@gmail.com>
Date: 2018-12-17 11:59:44 +0100
Commit message:

 Check for presence of spliceSites file
 
Package: QuasR
Commit: e0401b7546d679ae6ef0f2b169afdf14ffd8ceea
Author: Charlotte Soneson <charlottesoneson@gmail.com>
Date: 2018-12-17 11:38:21 +0100
Commit message:

 Update show
 
Package: QuasR
Commit: 9363ac9f96a63f634b1e6e7ad496865c37369653
Author: Charlotte Soneson <charlottesoneson@gmail.com>
Date: 2018-12-17 11:24:55 +0100
Commit message:

 Small fixes
 
Package: QuasR
Commit: 45dd190da437427e293eb3d77a566d86385a298a
Author: Charlotte Soneson <charlottesoneson@gmail.com>
Date: 2018-12-17 11:10:44 +0100
Commit message:

 Provided geneAnnotation now path to either gtf or sqlite file
 
Package: QuasR
Commit: e6253df4bdce2b211b59371d3e850ce31bd22840
Author: Charlotte Soneson <charlottesoneson@gmail.com>
Date: 2018-12-17 09:18:19 +0100
Commit message:

 Default txdbFile NA
 
Package: QuasR
Commit: 78bdc99f038bd418c21847e48c79a4df359aa344
Author: Charlotte Soneson <charlottesoneson@gmail.com>
Date: 2018-12-17 09:11:39 +0100
Commit message:

 default txdbFile is 'none'
 
Package: QuasR
Commit: eeeaf3999ec682462634c568fd935aa3e140aece
Author: Charlotte Soneson <charlottesoneson@gmail.com>
Date: 2018-12-17 09:07:36 +0100
Commit message:

 Merge branch 'master' into rhisat2
 
Package: QuasR
Commit: b8b11992a5ae11a4a1066560584eb15424862e0b
Author: Charlotte Soneson <charlottesoneson@gmail.com>
Date: 2018-12-17 09:07:01 +0100
Commit message:

 Add update function
 
Package: QuasR
Commit: fd5082ca2407bc074cb1f241b43680b677e740f7
Author: Charlotte Soneson <charlottesoneson@gmail.com>
Date: 2018-12-17 08:59:34 +0100
Commit message:

 Spacing
 
Package: QuasR
Commit: ae7b036399d4f097cfddbffc27e93f5cf34e75bd
Author: Charlotte Soneson <charlottesoneson@gmail.com>
Date: 2018-12-17 08:55:58 +0100
Commit message:

 Renaming
 
Package: QuasR
Commit: 16f0f39c5a4a1aa612455af2a5682ac3144361c2
Author: Charlotte Soneson <charlottesoneson@gmail.com>
Date: 2018-12-14 16:04:04 +0100
Commit message:

 Process the provided annotation
 
Package: QuasR
Commit: 6cc8a9395af1e7c5993fa916f6301e613c060567
Author: Charlotte Soneson <charlottesoneson@gmail.com>
Date: 2018-12-14 13:37:29 +0100
Commit message:

 Add spliceSiteFile slot to qProject class
 
Package: QuasR
Commit: 4e2986a574330a55552570f4ea5d76261d5f8f52
Author: Charlotte Soneson <charlottesoneson@gmail.com>
Date: 2018-12-12 15:09:14 +0100
Commit message:

 Install Rhisat2
 
Package: QuasR
Commit: ac2d4516f42e5233ee5a89cf1bae7affa1ee6a51
Author: Charlotte Soneson <charlottesoneson@gmail.com>
Date: 2018-12-12 14:53:11 +0100
Commit message:

 Merge master
 
Package: QuasR
Commit: b16351ddeafaef371db7ac120a97012ebb4184a0
Author: Charlotte Soneson <charlottesoneson@gmail.com>
Date: 2018-12-12 14:50:33 +0100
Commit message:

 hisat2-specific checks for alignment success
 
Package: QuasR
Commit: 300239555dc5400dcb7ccc3749d5b64fc1b528ff
Author: Charlotte Soneson <charlottesoneson@gmail.com>
Date: 2018-12-12 13:39:36 +0100
Commit message:

 Too early specification of proj@aligner
 
Package: QuasR
Commit: c67fe926ff9eb9e990b6a2bec8ab8fd6eb8c9dc2
Author: Charlotte Soneson <charlottesoneson@gmail.com>
Date: 2018-12-12 13:22:05 +0100
Commit message:

 Set hisat2 alignment parameters
 
Package: QuasR
Commit: f59c0758d323f9ad5fda0b013ec5879037a113a0
Author: Charlotte Soneson <charlottesoneson@gmail.com>
Date: 2018-12-11 17:32:44 +0100
Commit message:

 Add Rhisat2 as a supported aligner.
 
Package: QuasR
Commit: ce4fc79dccd7cb242e60f5e6d6aa63804379be16
Author: Charlotte Soneson <charlottesoneson@gmail.com>
Date: 2018-12-10 17:18:03 +0100
Commit message:

 Rhisat2 not supported for qMeth
 
Package: QuasR
Commit: 7cbc1cc259a92dade714caeba03d70937ae6313b
Author: Charlotte Soneson <charlottesoneson@gmail.com>
Date: 2018-12-10 15:27:42 +0100
Commit message:

 Add space
 
Package: QuasR
Commit: 036836cd8cd75e17a81493998fe346168d5d72a2
Author: Charlotte Soneson <charlottesoneson@gmail.com>
Date: 2018-12-10 10:08:37 +0100
Commit message:

 Move Rhisat2 to Imports
 
Package: QuasR
Commit: dec5465af0a664bc6304aa72c1437255927308ef
Author: Charlotte Soneson <charlottesoneson@gmail.com>
Date: 2018-12-10 09:52:31 +0100
Commit message:

 Add alignment functions for Rhisat2
 
Package: QuasR
Commit: 9f306303f3b8ec3b6c5f9451c472cfbb8506eb81
Author: Charlotte Soneson <charlottesoneson@gmail.com>
Date: 2018-12-10 09:45:53 +0100
Commit message:

 Add index building capabilities for Rhisat2
 
Package: QuasR
Commit: 715b94d1f9fbe5d37c79319f9ca7dfd0646f39cf
Author: Charlotte Soneson <charlottesoneson@gmail.com>
Date: 2018-12-10 09:42:39 +0100
Commit message:

 Add Rhisat2 to DESCRIPTION
 
Package: mogsa
Commit: 4199ff75895ffbd68c76f1f9947547aaa127141a
Author: Chen <mengchen18@gmail.com>
Date: 2019-02-13 16:12:36 +0100
Commit message:

 add bootMoa

which is used for determining the components representing significant concordant structures. Bootstrap method is used, similar to bootMbpca
 
Package: mogsa
Commit: c4937017336fa97239f899b83f2cf8ced95e18dc
Author: Chen <mengchen18@gmail.com>
Date: 2019-02-13 14:02:57 +0100
Commit message:

 moa can return raw results from svd

this can be used for bootstrap to determine the number of significant components
 
Package: mogsa
Commit: 7c5b9d27b0215ea2a397b321f7dd3880aca46705
Author: Chen <mengchen18@gmail.com>
Date: 2019-02-13 13:21:51 +0100
Commit message:

 add multiple test correction for mogsa
 
Package: mogsa
Commit: d5404fbd4ca5cb336a62aa5cb11c3e9c23398a32
Author: Chen <mengchen18@gmail.com>
Date: 2019-02-13 10:23:23 +0100
Commit message:

 fix un-matched title in vignette
 
Package: limma
Commit: a75748031c869eddb756354d803722d3467e9890
Author: Gordon Smyth <smyth@wehi.edu.au>
Date: 2019-02-14 16:56:43 +1100
Commit message:

 14 Feb 2019: limma 3.39.9

- The old function ebayes(), which was deprecated a year ago in favor
  of eBayes(), is now removed.
 
Package: limma
Commit: f60d56b3a55c4aaaeafe38fe683d02ef883b1a92
Author: Gordon Smyth <smyth@wehi.edu.au>
Date: 2019-02-14 15:50:37 +1100
Commit message:

 14 Feb 2019: limma 3.39.8

- Further simplifications and improvements to the arrayWeights() code
  when method="genebygene".

- New argument 'prior.n' for arrayWeights() to control the prior
  weight with which the array weights are squeezed towards unity.
 
Package: limma
Commit: ef25a5aded00d070c353d032d44600cee464fe2c
Author: Gordon Smyth <smyth@wehi.edu.au>
Date: 2019-02-12 17:58:04 +1100
Commit message:

 12 Feb 2019: limma 3.39.7

- The fitted() and residuals() methods for MArrayLM objects now give
  an informative error message if the object contains contrasts
  instead of the original coefficients.
 
Package: limma
Commit: c20b82c2c1cce381931b2e6be9faba87ebc8e990
Author: Gordon Smyth <smyth@wehi.edu.au>
Date: 2019-02-12 16:17:01 +1100
Commit message:

 Rename arrayWeightsSimple.R to arrayWeightsREML.R
 
Package: flowStats
Commit: fc3b201a5f12456b828cba062a02d57cb8f78f50
Author: Jacob Wagner <jpwagner@fredhutch.org>
Date: 2019-02-13 16:10:25 -0800
Commit message:

 bump
 
Package: flowCore
Commit: 4d1b76d15f28c05629e901b49d4460688992631f
Author: Jacob Wagner <jpwagner@fredhutch.org>
Date: 2019-02-13 16:09:16 -0800
Commit message:

 bump
 
Package: flowViz
Commit: 36fb5217b08b755a4c6563471a93cddd8598d906
Author: Jacob Wagner <jpwagner@fredhutch.org>
Date: 2019-02-13 16:07:58 -0800
Commit message:

 bump
 
Package: flowViz
Commit: df1ffd2d2fe7a66d1ced35ea4bef56d3b329eb96
Author: Jacob Wagner <jpwagner@fredhutch.org>
Date: 2019-02-13 15:45:59 -0800
Commit message:

 Make NA checking for list glpolygon output in densityplot more robust
 
Package: flowViz
Commit: ad0c5f3fc53337242fbeafd05ff76accb4bd64d5
Author: Jacob Wagner <jpwagner@fredhutch.org>
Date: 2019-02-13 15:15:35 -0800
Commit message:

 Fix conditionals with potential length > 1
 
Package: matter
Commit: cd238d213eb9a0161e6c53017de615a9f73496d3
Author: kuwisdelu <kuwisdelu@northeastern.edu>
Date: 2019-02-13 16:56:07 -0500
Commit message:

 minor C++ changes
 
Package: TCGAutils
Commit: 3da33100395f4a1ba5d78b6b620d580c9ec8daf9
Author: LiNk-NY <mramos09@gmail.com>
Date: 2019-02-13 16:52:12 -0500
Commit message:

 update TCGAsampleSelect documentation
 
Package: TCGAutils
Commit: e834d293ccb3bdd651983c1ce35e27b03646dec9
Author: LiNk-NY <mramos09@gmail.com>
Date: 2019-02-13 14:36:29 -0500
Commit message:

 bump version
 
Package: TCGAutils
Commit: d6481be0bf3bd60c96e60f4d5768674722b0695c
Author: LiNk-NY <mramos09@gmail.com>
Date: 2019-02-13 14:35:47 -0500
Commit message:

 update filename translation function
 
Package: flowStats
Commit: c01c7dea687aab5be28a58da984494fe1d0fe29c
Author: Jacob Wagner <jpwagner@fredhutch.org>
Date: 2019-02-12 16:34:58 -0800
Commit message:

 Update spillover_ng tests to remove unnecessary pregating
 
Package: flowCore
Commit: 4f04fd5faa48060d0074bafbb414378f561872aa
Author: Jacob Wagner <jpwagner@fredhutch.org>
Date: 2019-02-12 16:32:04 -0800
Commit message:

 Update reference compensation matrix used by flowStat tests
 
Package: macrophage
Commit: 1017205a17186bcf9d6c631bbd770f54de8354bd
Author: mikelove <michaelisaiahlove@gmail.com>
Date: 2019-02-13 13:04:55 -0500
Commit message:

 add pkg man page
 
Package: BiocCheck
Commit: 28a742b43ae6a3be24567994bcef51ebc4560643
Author: lshep <lori.shepherd@roswellpark.org>
Date: 2019-02-13 12:53:33 -0500
Commit message:

 Add existing package check to all Bioconductor repos

  - extended to check annotation, experiment, and workflows
    before was only checking CRAN and software
 
Package: biosigner
Commit: f1d0d66b7333b0a08948cc3a6f5ace4d3f789f61
Author: THEVENOT Etienne <ET207099@intra.cea.fr>
Date: 2019-02-13 16:47:08 +0100
Commit message:

 v1.11.18 minor internal modification
 
Package: biosigner
Commit: 8f13fa9652f914d43cfd2750a167ef4ade4d0c5e
Author: THEVENOT Etienne <ET207099@intra.cea.fr>
Date: 2019-02-13 16:42:09 +0100
Commit message:

 v1.11.16 optimization of ExpressionSet instance handling
 
Package: ropls
Commit: 94439c5924816131315a97d5448d49b7b6ec5e00
Author: THEVENOT Etienne <ET207099@intra.cea.fr>
Date: 2019-02-13 16:20:34 +0100
Commit message:

 v1.15.18 minor internal modification
 
Package: ropls
Commit: 426ca2b440423d5cdd0d3008d3eb731a28b35df6
Author: THEVENOT Etienne <ET207099@intra.cea.fr>
Date: 2019-02-13 16:01:29 +0100
Commit message:

 v1.15.16 optimization of pData and fData modifications; Biobase as depends
 
Package: INSPEcT
Commit: 181927a635ee58b8da67b8dca92f233e82547f2a
Author: ste-depo <ste.depo@gmail.com>
Date: 2019-02-13 15:34:55 +0100
Commit message:

 new accession to modelSelection parameters and possibility to aviod testing specific rates for variability
 
Package: Prostar
Commit: 9d0312d895c614a4a73b76d8d0e43e77310c345f
Author: Samuel Wieczorek <samuel.wieczorek@cea.fr>
Date: 2019-02-13 14:03:29 +0100
Commit message:

 bug fixed in anaDiff with Firefox
 
Package: HiCBricks
Commit: 71c500c4700f75924e7978400d13dc0e2bf172a9
Author: Koustav Pal <koustavpal1988@gmail.com>
Date: 2019-02-13 09:53:42 +0530
Commit message:

 Changed a bug in the examples.
 
Package: GAPGOM
Commit: 6b5965d35a98ca5deb3eab0d556d73842b768680
Author: Casper
Date: 2019-02-13 11:40:29 +0100
Commit message:

 Version bumped back down because off illegal version bump (oops)
 
</div>
Package: GAPGOM
Commit: e95b0aa022654c8854e33c90d7bab73bf5e37b5e
Author: Casper
Date: 2019-02-13 11:35:56 +0100
Commit message:

 Version bump, Release 1.0.0 Ready!
 
</div>
Package: statTarget
Commit: 338708954e17fdb64ef12ba86578f02e1bc298f0
Author: 13479776 <hemi.luan@gmail.com>
Date: 2019-02-13 17:44:43 +0800
Commit message:

 test
 
Package: rhdf5
Commit: f9bd2f9936333d21016d719474505f81ab532dac
Author: Mike Smith <grimbough@gmail.com>
Date: 2019-02-12 15:41:57 +0100
Commit message:

 Added some more unit tests
 
Package: rhdf5
Commit: 7c5090064eceb90a09d012fad65b4fa39de942da
Author: Mike Smith <grimbough@gmail.com>
Date: 2019-02-12 11:01:26 +0100
Commit message:

 Never use 'revert'!
 
Package: rhdf5
Commit: bcf547e2de929df24452921fab5fa7d2da858a2b
Author: Mike Smith <grimbough@gmail.com>
Date: 2019-02-12 10:18:53 +0100
Commit message:

 Version bump
 
Package: rhdf5
Commit: 10a7ab9fc92968eea8dd942de030e7535f291a83
Author: Mike Smith <grimbough@gmail.com>
Date: 2019-02-12 10:16:43 +0100
Commit message:

 Revert "More tweaks to H5Dread"

This reverts commit b6571876ab2a67b70d079811b11c0f6756604544.
 
Package: rhdf5
Commit: b6571876ab2a67b70d079811b11c0f6756604544
Author: Mike Smith <grimbough@gmail.com>
Date: 2019-02-12 10:14:22 +0100
Commit message:

 More tweaks to H5Dread
 
Package: mCSEA
Commit: 98f46727492d3fd603058131ecc93bd81694aaa3
Author: Jordi Martorell Marugán <jmartorellm@gmail.com>
Date: 2019-02-13 03:17:30 -0500
Commit message:

 fix mCSEAIntegrate
 
Package: Pigengene
Commit: 942875cec2edca9330004acfdd7bdc8f11d5ff46
Author: Habil Zare <habil_zare@yahoo.com>
Date: 2019-02-12 22:05:05 -0600
Commit message:

 Pigengene: dOrderW2
 
Package: Pigengene
Commit: 0015419ff6091ad38181d509de32a9256b1b64dd
Author: Habil Zare <habil_zare@yahoo.com>
Date: 2019-02-12 20:39:06 -0600
Commit message:

 Pigengene: dOrderW
 
Package: coseq
Commit: 51da8dc61b6e6e20da849851e964612c8d4d386f
Author: Andrea M Rau <andrea.rau@inra.fr>
Date: 2019-02-12 20:38:18 -0600
Commit message:

 Add informative error message when a subset of estimated GMM have singular covariance matrices + add generic for plot function + minor doc updates
 
Package: RSeqAn
Commit: 60cac85021d3bb5eaca6d67e13cbb76317af9b99
Author: August Guang <august.guang@gmail.com>
Date: 2019-02-07 14:59:16 -0500
Commit message:

 more description of purpose
 
Package: RSeqAn
Commit: 22a50dad24e4be1632b518e7d09417514aa2aaf1
Author: August Guang <august.guang@gmail.com>
Date: 2019-02-07 14:53:38 -0500
Commit message:

 paper draft 3
 
Package: RSeqAn
Commit: 0bb8a09290b80af573a153049e5901d9627bcbad
Author: August Guang <august.guang@gmail.com>
Date: 2019-02-06 11:00:46 -0500
Commit message:

 Merge branch 'master' of https://github.com/compbiocore/RSeqAn
 
Package: RSeqAn
Commit: 0e104be76c3f892c72f3db4057cc1c4840610c9a
Author: August Guang <august.guang@gmail.com>
Date: 2019-02-06 11:00:36 -0500
Commit message:

 updated DOIs
 
Package: RSeqAn
Commit: a7a89c3fa3c425a9a47d213d32b939554c0bc98f
Author: august <august.guang@gmail.com>
Date: 2019-02-05 13:08:50 -0500
Commit message:

 Update README.md 
Package: RSeqAn
Commit: 1a09758e1ca35e0e21780a3cf4313a5e97349ac1
Author: august <august.guang@gmail.com>
Date: 2019-02-05 13:02:01 -0500
Commit message:

 Update README.md 
Package: RSeqAn
Commit: 33577b2621ecd08f55fe29e1f7c6d1fe72bf80d9
Author: august <august.guang@gmail.com>
Date: 2019-02-05 13:01:18 -0500
Commit message:

 Update README.md 
Package: RSeqAn
Commit: aa35c057c735f3e9f40b056750a7a1499fd753b3
Author: august <august.guang@gmail.com>
Date: 2019-02-05 12:48:20 -0500
Commit message:

 Update paper.md 
Package: RSeqAn
Commit: d6b10ae09c3913b94b415e2c7037123d6d8eb423
Author: august <august.guang@gmail.com>
Date: 2019-02-05 12:44:48 -0500
Commit message:

 Update paper.md 
Package: RSeqAn
Commit: 86d801952471f1f65f8c48000a5fb7b7a2b0514a
Author: August Guang <august.guang@gmail.com>
Date: 2019-02-05 12:39:10 -0500
Commit message:

 forgot spaces in yaml
 
Package: RSeqAn
Commit: 2b7839c2aa167c9b4f0b66d151720a81dacfa22c
Author: August Guang <august.guang@gmail.com>
Date: 2019-02-05 12:10:46 -0500
Commit message:

 merging
 
Package: RSeqAn
Commit: 4baa0e33e398839ef0373602b9e8bb258ed21d3f
Author: august <august.guang@gmail.com>
Date: 2019-02-05 11:53:16 -0500
Commit message:

 Update README.md

added link to vignette as well as direct c++ code in usage 
Package: RSeqAn
Commit: 6c5882ce61918ff4e21ece0c061ee6c99e47d69a
Author: August Guang <august.guang@gmail.com>
Date: 2019-02-05 11:52:37 -0500
Commit message:

 updated date and bibliography in yaml and added direct source code in extdata
 
Package: RSeqAn
Commit: 367e5515ce3832e97daf400bac3cb812c5b746ed
Author: August Guang <august.guang@gmail.com>
Date: 2019-01-24 14:35:46 -0500
Commit message:

 updated affiliations
 
Package: RSeqAn
Commit: 5fe71b356491fb72f11ca2989f093527d1d0b8e8
Author: August Guang <august.guang@gmail.com>
Date: 2019-01-24 13:44:35 -0500
Commit message:

 fixed tables
 
Package: RSeqAn
Commit: deae809018536e4f51e4bb496e605586e004756b
Author: August Guang <august.guang@gmail.com>
Date: 2018-12-17 15:36:11 -0500
Commit message:

 Merge branch 'paper'
 
Package: RSeqAn
Commit: 4c1f7373c089b2d5842ac0c3d02bfe23ad7ee60a
Author: August Guang <august.guang@gmail.com>
Date: 2018-12-17 15:06:30 -0500
Commit message:

 finished paper and add cache to travis
 
Package: RSeqAn
Commit: b189d63e36b7487ca9ff51e549cd0c8b8d98ed10
Author: August Guang <august.guang@gmail.com>
Date: 2018-12-17 14:19:43 -0500
Commit message:

 paper is done
 
Package: RSeqAn
Commit: 978218477a2df6a79d95189a651d84eed2aca2f3
Author: August Guang <august.guang@gmail.com>
Date: 2018-12-11 14:00:03 -0500
Commit message:

 paper bibliography
 
Package: RSeqAn
Commit: e987e0a6fdcf9d98eb339aa5573201fdaf22527b
Author: August Guang <august.guang@gmail.com>
Date: 2018-12-07 17:02:25 -0500
Commit message:

 first draft of paper
 
Package: CoGAPS
Commit: f61c8836d235acb34baaaba033d71e37fa41c563
Author: Tom Sherman <tomsherman159@gmail.com>
Date: 2019-02-12 15:31:32 -0500
Commit message:

 version bump
 
Package: CoGAPS
Commit: 6a9b377b465ff3833005690efae46bfc5ff4dc11
Author: Tom Sherman <tomsherman159@gmail.com>
Date: 2019-02-12 15:29:58 -0500
Commit message:

 correctly subset gene/sample names
 
Package: MultiAssayExperiment
Commit: f1781506f1fb1178d0e1395844510ff5be38bdcf
Author: LiNk-NY <mramos09@gmail.com>
Date: 2019-02-12 17:15:22 -0500
Commit message:

 update URL and bump version
 
Package: MultiAssayExperiment
Commit: feb6d9e959b1de8273408940bb568e69604b80ba
Author: LiNk-NY <mramos09@gmail.com>
Date: 2019-02-11 18:40:38 -0500
Commit message:

 remove custom URL
 
Package: MultiAssayExperiment
Commit: b7a4dd82e48083d70e3b19403aaf2924d9430054
Author: LiNk-NY <mramos09@gmail.com>
Date: 2019-02-11 17:48:32 -0500
Commit message:

 include copy of NEWS
 
Package: MultiAssayExperiment
Commit: 19428c2a113b153855b800a99c1fd982bccaa77a
Author: LiNk-NY <mramos09@gmail.com>
Date: 2019-02-11 17:46:22 -0500
Commit message:

 update README and pkgdown.yml
 
Package: MultiAssayExperiment
Commit: 1b13d68e73c79d6141d7d4d12713b97ee671b2b9
Author: LiNk-NY <mramos09@gmail.com>
Date: 2019-02-11 17:13:23 -0500
Commit message:

 update .travis.yml file
 
Package: MultiAssayExperiment
Commit: 8377827e19428027c57d2253a41e3c5798ab00f2
Author: LiNk-NY <mramos09@gmail.com>
Date: 2019-02-11 17:07:39 -0500
Commit message:

 version bump
 
Package: MultiAssayExperiment
Commit: e4a02b2af0e04abf729dd62bc65fbd4a6e2de47b
Author: LiNk-NY <mramos09@gmail.com>
Date: 2019-02-11 17:07:00 -0500
Commit message:

 include pkgdown yml file
 
Package: MultiAssayExperiment
Commit: 1cda903cc04868d0bdbd576ddbf6f102027001de
Author: LiNk-NY <mramos09@gmail.com>
Date: 2019-02-11 17:02:35 -0500
Commit message:

 add text to NEWS.md and change inst/NEWS type
 
Package: MultiAssayExperiment
Commit: b03bb167a69a05534ab8c6fc972364dd6295cced
Author: LiNk-NY <mramos09@gmail.com>
Date: 2019-02-11 17:00:02 -0500
Commit message:

 updates to extra vignette
 
Package: MultiAssayExperiment
Commit: 7c0794a9a419e5ad076afa8d5d7ec5f5e37a158c
Author: LiNk-NY <mramos09@gmail.com>
Date: 2019-02-05 18:19:46 -0500
Commit message:

 Extend Annotated (for metadata), closes #208
 
Package: biosigner
Commit: 74867205fe115336a4be292a48403fa13fb9e1c8
Author: THEVENOT Etienne <ET207099@intra.cea.fr>
Date: 2019-02-12 22:02:41 +0100
Commit message:

 v1.11.14 minor internal modification
 
Package: ropls
Commit: f206f7c747fe477902b930ecabec1d04ed907030
Author: THEVENOT Etienne <ET207099@intra.cea.fr>
Date: 2019-02-12 21:56:31 +0100
Commit message:

 v1.15.14 minor internal modification
 
Package: bioCancer
Commit: 6afbdccf76c58a59a38faf02e7deef346aa0fec4
Author: kmezhoud
Date: 2019-02-12 21:25:45 +0100
Commit message:

 change version

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

# Conflicts:
#	DESCRIPTION
 
</div>
Package: bioCancer
Commit: 06e737f4b769349c680ce9ed879fef188d865523
Author: kmezhoud
Date: 2019-02-12 21:22:52 +0100
Commit message:

 Change the address of cgdsr: http://www.cbioportal.org/ instead http://www.cbioportal.org/public-portal/
 
</div>
Package: biosigner
Commit: 1a2ee03a3b01137b31a545b14fc5f0949861bb44
Author: THEVENOT Etienne <ET207099@intra.cea.fr>
Date: 2019-02-12 21:21:44 +0100
Commit message:

 v1.11.12 minor modification in example with ExpressionSet
 
Package: ropls
Commit: fa48d3d0c4bb56da4d3661ae49a1b76549557ac0
Author: THEVENOT Etienne <ET207099@intra.cea.fr>
Date: 2019-02-12 21:17:43 +0100
Commit message:

 v1.15.12 minor modification in examples defining ExpressionSet instances
 
Package: slingshot
Commit: 21ae598664750b787e511e55c06e3143b37ebbdb
Author: Kelly Street <kstreet@root-pcs-air.dfci.harvard.edu>
Date: 2019-02-12 14:14:30 -0500
Commit message:

 minor version bump to 1.1.2
 
Package: slingshot
Commit: a21b226177a9abbc38da531deb9852e6439f2726
Author: Kelly Street <kstreet@root-pcs-air.dfci.harvard.edu>
Date: 2019-02-12 11:41:43 -0500
Commit message:

 bug fix in getCurves: the extend = 'pc1' option was broken in a non-obvious way (if endpoints of lineages are near 0 in dimensions 2+)
 
Package: slingshot
Commit: 7aeb891d92c9dcb04678fb566bd376999a388422
Author: Kelly Street <street.kelly@gmail.com>
Date: 2019-02-12 09:23:08 -0500
Commit message:

 Merge pull request #29 from rcannood/develop

Fix travis issues 
Package: slingshot
Commit: cb6ecdec0635204ce6cc66f05d8a8c0277ebbf47
Author: Robrecht Cannoodt <rcannood@gmail.com>
Date: 2019-02-12 09:48:16 +0100
Commit message:

 remove suggested package from install 
Package: slingshot
Commit: 1243abd10583d02b2d958c8800320052dcb07cba
Author: Robrecht Cannoodt <rcannood@gmail.com>
Date: 2019-02-12 09:47:55 +0100
Commit message:

 Vignette requires more suggested packages 
Package: slingshot
Commit: e869e7e1e56c39524fe13fa5fd9faff2d61efc91
Author: Robrecht Cannoodt <rcannood@gmail.com>
Date: 2019-02-11 17:02:38 +0100
Commit message:

 attempt to get biocstyle installed
 
Package: slingshot
Commit: e085b3505d9d08846fb033228777a08fff3d3c1c
Author: Robrecht Cannoodt <rcannood@gmail.com>
Date: 2019-02-04 20:43:02 +0100
Commit message:

 install bioccheck differently 
Package: slingshot
Commit: 02f03cb2f3d552efa0f0d170ade83b18655a2b51
Author: Robrecht Cannoodt <rcannood@gmail.com>
Date: 2019-02-04 14:57:23 +0100
Commit message:

 also warm up bioc devel cache?
 
Package: slingshot
Commit: f1573e113e9554c155a0c9d6f2ffefc49e1a9b8b
Author: Robrecht Cannoodt <rcannood@gmail.com>
Date: 2019-02-04 14:56:45 +0100
Commit message:

 also install biocstyle
 
Package: slingshot
Commit: 1e7fdcb9fa59bf8b73273c5ad3441114156b31bb
Author: Robrecht Cannoodt <rcannood@gmail.com>
Date: 2019-02-01 12:48:33 +0100
Commit message:

 probably don't need these args if script is being overwritten
 
Package: slingshot
Commit: a0c34499eb4b6c8b863a1df751c0b00aafaba075
Author: Robrecht Cannoodt <rcannood@gmail.com>
Date: 2019-02-01 12:48:15 +0100
Commit message:

 override after success in prepare cache
 
Package: slingshot
Commit: 84bfa16ac4d025c2bbb125a86f8f486f6e244156
Author: Robrecht Cannoodt <rcannood@gmail.com>
Date: 2019-02-01 12:38:17 +0100
Commit message:

 third try
 
Package: slingshot
Commit: dac1b13c59d58b9007b31de238aac144bf5b2931
Author: Robrecht Cannoodt <rcannood@gmail.com>
Date: 2019-02-01 12:30:58 +0100
Commit message:

 second attempt
 
Package: slingshot
Commit: 2554725f381194ddbe61b8dcf6e34e9bf35c727d
Author: Robrecht Cannoodt <rcannood@gmail.com>
Date: 2019-02-01 12:24:56 +0100
Commit message:

 try building without init
 
Package: slingshot
Commit: c8cd4225d911fcf94b263ee092aba4c1192bb5e3
Author: Robrecht Cannoodt <rcannood@gmail.com>
Date: 2019-02-01 12:13:28 +0100
Commit message:

 solve issue with vignette not being built due to missing bib file
 
Package: slingshot
Commit: b6bb33fb9e877a4eb66eed9ecf055c09697527e3
Author: Robrecht Cannoodt <rcannood@gmail.com>
Date: 2019-02-01 12:12:43 +0100
Commit message:

 remove html
 
Package: slingshot
Commit: 8b8d23b09deb2b82d3b4848d9525d9cd99323c64
Author: Kelly Street <kstreet@root-pcs-air.dfci.harvard.edu>
Date: 2019-01-22 15:36:39 -0500
Commit message:

 undoing previous commit. Changing the header did not fix Travis' mysterious inability to see slingshot.html sitting in inst/doc/.
 
Package: slingshot
Commit: 8190a158dfea3dc3b67e67e66c62c5f686110ef5
Author: Kelly Street <kstreet@root-pcs-air.dfci.harvard.edu>
Date: 2019-01-22 14:24:54 -0500
Commit message:

 modified header of slingshot.Rmd (per suggestion on SO), rebuild vignette
 
Package: biosigner
Commit: 77a315f3670bf3cfed5c0d194bc3a5db4e9a1f3d
Author: THEVENOT Etienne <ET207099@intra.cea.fr>
Date: 2019-02-12 18:45:41 +0100
Commit message:

 v1.11.10 minor update of example
 
Package: Rsamtools
Commit: da70a1eddbd9be547e37d09e19456af695a9063a
Author: Hervé Pagès <hpages@fredhutch.org>
Date: 2019-02-12 09:19:05 -0800
Commit message:

 update migration_notes.md
 
Package: regioneR
Commit: debe68a502656f3cb49f208859d4a60fbcb6ed3b
Author: Bernat Gel <bernatgel@gmail.com>
Date: 2019-02-12 17:30:59 +0100
Commit message:

 Version Bump

 
Package: regioneR
Commit: 46021925a70ff305bac9caea83c3a3a5f96a0110
Author: Bernat Gel <bernatgel@gmail.com>
Date: 2019-02-12 17:30:19 +0100
Commit message:

 Fixed an error with non-matching seqlevels

 
Package: PrecisionTrialDrawer
Commit: e235af8054e2e3ce6f5a8f482d8c5889acc1ea20
Author: gmelloni <melloni.giorgio@gmail.com>
Date: 2019-02-12 11:15:56 -0500
Commit message:

 bug fix in cgdsr URL
 
Package: h5vc
Commit: 6de5b782cbfb0bedc3ecc5aa42ed0e4f68bf1db8
Author: Hervé Pagès <hpages@fredhutch.org>
Date: 2019-02-12 07:46:29 -0800
Commit message:

 resync with Rsmatools 1.99.1 and Rhtslib 1.15.3
 
Package: mCSEA
Commit: f4d45d3e8b0ad7388e8d7aa3718b6467fb5fe892
Author: Jordi Martorell Marugán <jmartorellm@gmail.com>
Date: 2019-02-12 10:34:34 -0500
Commit message:

 Fix a bug and update citation
 
Package: TransView
Commit: 9de15ed47dcaa4e8924c53794268cbd0308d3f45
Author: Hervé Pagès <hpages@fredhutch.org>
Date: 2019-02-12 07:27:31 -0800
Commit message:

 Compile and link C code against Rhtslib instead of Rsamtools
 
Package: podkat
Commit: a5e6ed981fbada28318a002d3ffc84ec8d1a600e
Author: Hervé Pagès <hpages@fredhutch.org>
Date: 2019-02-12 06:58:54 -0800
Commit message:

 resync with Rsmatools 1.99.1 and Rhtslib 1.15.3
 
Package: Rhtslib
Commit: 1b1510c3ebe69379c3d7139a448638b370974bf7
Author: Hervé Pagès <hpages@fredhutch.org>
Date: 2019-02-12 06:15:40 -0800
Commit message:

 Fix for Solaris

Do not build standalone executables (e.g. bgzip, tabix, etc...). They're
not needed and seem to cause problems on Solaris.
 
Package: ontoProc
Commit: 222f4ce5103bd3985ab59451ea5d3d1afb53dbf4
Author: Vince Carey <stvjc@channing.harvard.edu>
Date: 2019-02-12 08:30:21 -0500
Commit message:

 commented on substr and added sym2CellOnto in vignette
 
Package: ontoProc
Commit: 6d50c6d743cc4aba9a76e3e27176b47700c50290
Author: Vince Carey <stvjc@channing.harvard.edu>
Date: 2019-02-12 08:24:56 -0500
Commit message:

 added sym2CellOnto function
 
Package: IsoformSwitchAnalyzeR
Commit: 536d87bba2add7611538c5425e704b3fd82506e3
Author: kvittingseerup <k.vitting.seerup@gmail.com>
Date: 2019-02-12 13:43:25 +0100
Commit message:

 Documentation update - see NEWS
 
Package: IsoformSwitchAnalyzeR
Commit: 9e5821c18177ca16d7b1974350cf3c995fcdcacf
Author: kvittingseerup <k.vitting.seerup@gmail.com>
Date: 2019-02-08 16:12:28 +0100
Commit message:

 Fix ensemble import. Add IDR. See NEWs
 
Package: limma
Commit: 249e9626531b33181452dbdab345cc06a00e04c7
Author: Gordon Smyth <smyth@wehi.edu.au>
Date: 2019-02-12 16:14:24 +1100
Commit message:

 12 Feb 2019: limma 3.39.6

- Major rewrite of arrayWeights() to improve speed and stability.
  The arrayWeightsSimple() function has been removed and its
  functionality incorporated into arrayWeights(), including the
  new 'var.group' argument to simplify specification of the
  variance design matrix.
 
Package: RNAseq123
Commit: a61930120ec8b3d530655ca6ee27e22533490d2f
Author: mritchie <mritchie@wehi.edu.au>
Date: 2019-02-12 15:58:38 +1100
Commit message:

 Added package logos to vignette
 
Package: LoomExperiment
Commit: d927607842a3d8ad1eafe973920c6e458e3b31e0
Author: Daniel Van Twisk <daniel.vantwisk@roswellpark.org>
Date: 2019-02-11 23:47:42 -0500
Commit message:

 Response to Issue #2: added dgCMatrix export method and an array transposition in import
 
Package: universalmotif
Commit: 729c91f38a2e305b7cb9924305d22edab01a469c
Author: bjmt <benjmtremblay@gmail.com>
Date: 2019-02-11 23:03:41 -0500
Commit message:

 bug fix: fixed bug introduced in previous patches when running create_sequences('RNA')
 
Package: universalmotif
Commit: b2a501152308d9525bfd61f41871d03c4f5109e6
Author: bjmt <benjmtremblay@gmail.com>
Date: 2019-02-11 22:56:51 -0500
Commit message:

 version bump
 
Package: universalmotif
Commit: 42584c7112ebf294386dfcb314148dfb4d8249d9
Author: bjmt <benjmtremblay@gmail.com>
Date: 2019-02-11 22:55:05 -0500
Commit message:

 bug fix: create_sequences(alphabet=RNA) now works with difreq/trifreq
 
Package: universalmotif
Commit: 596382d4da00f1e459d596fb5b9e19b0e280439c
Author: bjmt <benjmtremblay@gmail.com>
Date: 2019-02-11 22:46:41 -0500
Commit message:

 version bump
 
Package: universalmotif
Commit: 34c006de629897b72e7cee1bb7ac15dd1d381589
Author: bjmt <benjmtremblay@gmail.com>
Date: 2019-02-11 22:44:43 -0500
Commit message:

 bug fix: create_sequences() not working properly with difreq or trifreq provided
 
Package: universalmotif
Commit: c080a44ab22fe852b2c321ce42229e11bfbb5db4
Author: bjmt <benjmtremblay@gmail.com>
Date: 2019-02-10 22:58:33 -0500
Commit message:

 more tests: compare_motifs() + convert_type()
 
Package: universalmotif
Commit: da6bc903b5a85bc803b5ffd251e7803a9692f423
Author: bjmt <benjmtremblay@gmail.com>
Date: 2019-02-10 19:58:34 -0500
Commit message:

 expanded add_multifreq() and compare_motifs() tests
 
Package: ontoProc
Commit: 4b5d024115ae32665c673ac70e03ee1792df1ce3
Author: Vince Carey <stvjc@channing.harvard.edu>
Date: 2019-02-11 22:03:50 -0500
Commit message:

 updated vignette
 
Package: ontoProc
Commit: dbc1ba84b86fa8f4011ae7d6b2fa26c6aef42049
Author: Vince Carey <stvjc@channing.harvard.edu>
Date: 2019-02-11 18:22:45 -0500
Commit message:

 ctmarks app seems stable now
 
Package: LoomExperiment
Commit: ead326346b59b987552fe58ee928efc816f785b0
Author: Daniel Van Twisk <daniel.vantwisk@roswellpark.org>
Date: 2019-02-11 18:52:49 -0500
Commit message:

 Revert R version requirement change
 
Package: GenomeInfoDb
Commit: 18c1056adb2304b0e194df31acbf061c6f6ec04b
Author: Hervé Pagès <hpages@fredhutch.org>
Date: 2019-02-11 15:06:39 -0800
Commit message:

 Fix fetchExtendedChromInfoFromUCSC("hg38")

A recent change on the UCSC side broke
fetchExtendedChromInfoFromUCSC("hg38"), the workhorse behind
Seqinfo("hg38"). See https://support.bioconductor.org/p/117808/#117831
for the details. With this fix, hg38 is still strictly mapped to
GRCh38 and not to a patched version of it (what assembly hg38 is
based on exactly has become somewhat unclear on the UCSC side).
 
Package: gmapR
Commit: 5bb21ad53d3a45549130a2a6be7252a48aae8055
Author: Michael Lawrence <michafla@gene.com>
Date: 2019-02-11 12:33:07 -0800
Commit message:

 embed samtools sources directly, since Rsamtools has moved to htslib
 
Package: ontoProc
Commit: 4f04a8c75132760fb8fd269fbaa0a2e385380dad
Author: Vince Carey <stvjc@channing.harvard.edu>
Date: 2019-02-11 15:20:09 -0500
Commit message:

 revised ctmarks app with helpText
 
Package: BiocParallel
Commit: 101436926b2c63ec7aa748b311bfb4da2f4e9927
Author: Martin Morgan <martin.morgan@roswellpark.org>
Date: 2019-02-11 12:52:51 -0500
Commit message:

 close connections in BatchtoolsParam unit tests

- requires an explicit garbage collection
 
Package: BiocParallel
Commit: 9c18d375dc5441a2e5e55fa5efb8f7183e17afbf
Author: Martin Morgan <martin.morgan@roswellpark.org>
Date: 2019-02-11 10:34:07 -0500
Commit message:

 (port) clean up Makevars
 
Package: BiocParallel
Commit: 5892fd9aeb46ab095fdc48a92b610245d908435e
Author: Martin Morgan <martin.morgan@roswellpark.org>
Date: 2019-02-11 10:33:34 -0500
Commit message:

 clean up Makevars on non-Windows
 
Package: BiocParallel
Commit: 610bf2927c3a2d69a3d7fee5de49f5a1818f6948
Author: Martin Morgan <martin.morgan@roswellpark.org>
Date: 2019-02-11 10:29:07 -0500
Commit message:

 better random number management on load

- don't create .Random.seed if not already present
 
Package: DiffBind
Commit: ef432efcc20323e61551cfa3e83aa383a328e342
Author: Gord Brown <gdbzork@gmail.com>
Date: 2019-02-11 17:19:57 +0000
Commit message:

 changes to accommodate new Rsamtools that uses Rhtslib; patch supplied by Hervé Pagès
 
Package: diffcyt
Commit: 9e46eb3139aaf950c0dd0fcd96bfed07dfcc497c
Author: Lukas Weber <lukmweber@gmail.com>
Date: 2019-02-11 16:17:02 +0100
Commit message:

 version
 
Package: diffcyt
Commit: 256e00d50a9a508d1dca8fdc5c8f55df6408fea1
Author: Lukas Weber <lukmweber@gmail.com>
Date: 2019-02-11 16:16:50 +0100
Commit message:

 fix argument
 
Package: KEGGgraph
Commit: b40b1f9571e9601563f6b55e04b3fd77a22979f4
Author: Jitao David Zhang <jitao_david.zhang@roche.com>
Date: 2019-02-11 15:53:00 +0100
Commit message:

 fix the problem of compound/unannotated nodes causing graph merge fail
 
Package: KEGGgraph
Commit: f95b569de5b53681af74556238199056d1d21d5d
Author: Jitao David Zhang <jitao_david.zhang@roche.com>
Date: 2019-02-11 15:40:16 +0100
Commit message:

 compound nodes
 
Package: diffcyt
Commit: b7bd0ce48f43cc28030dc7e7e241d84379f7e4c4
Author: Lukas Weber <lukmweber@gmail.com>
Date: 2019-02-11 15:38:05 +0100
Commit message:

 version
 
Package: diffcyt
Commit: a8e5a74492c4598a00b91d54ea8e8d0ae874efa8
Author: Lukas Weber <lukmweber@gmail.com>
Date: 2019-02-11 15:37:50 +0100
Commit message:

 topTable updates: show medians, sort columns
 
Package: RpsiXML
Commit: c725285704e966715fb65e6581632a6695c461c9
Author: Jitao David Zhang <jitao_david.zhang@roche.com>
Date: 2019-02-11 14:54:05 +0100
Commit message:

 prototype definition and slots are consistent now, thanks to the reminder sent by Lori Shepherd
 
Package: RpsiXML
Commit: 7f2e4717e4d91ff8a9d12cdbf288d3330f615113
Author: Jitao David Zhang <jitao_david.zhang@roche.com>
Date: 2019-02-11 14:45:21 +0100
Commit message:

 check works now with devtools::check()
 
Package: PhenStat
Commit: 26a907de355059dfc1e576ac5bdafcd4bbb3549b
Author: Hamed Haseli <hamedhaseli@gmail.com>
Date: 2019-02-11 13:45:46 +0000
Commit message:

 Fixed bugs
 
Package: methylKit
Commit: 21fb06ead8c9690017c7334f41fa1b37f0a4fd72
Author: alexg9010 <alex.gos90@gmail.com>
Date: 2019-02-05 10:13:38 +0100
Commit message:

 version bump & update news
 
Package: methylKit
Commit: c6e4f44d5b7b1ff2afb8fbce4fec9fc56351b0b2
Author: alexg9010 <alex.gos90@gmail.com>
Date: 2019-02-08 17:32:21 +0100
Commit message:

 headTabix: use fread.gzipped only when user wants to get more than 1e6 rows
 
Package: methylKit
Commit: ae050463de7bba235a42a1d0b0771c554d29431d
Author: alexg9010 <alex.gos90@gmail.com>
Date: 2019-02-08 11:42:41 +0100
Commit message:

 test-1-read: check if methylRawDB is same when directory is given or not, i.e. test wether directory affects object
 
Package: methylKit
Commit: edb384ba9135cec98f4290380356713b5fecede7
Author: alexg9010 <alex.gos90@gmail.com>
Date: 2019-02-07 16:58:03 +0100
Commit message:

 methylRaw: check for content in tabix file, break if not
 
Package: methylKit
Commit: 2c6fb96ddeb62b9c9fa4b2f837ba50bf2e2c6883
Author: alexg9010 <alex.gos90@gmail.com>
Date: 2019-02-07 16:53:27 +0100
Commit message:

 add some sections to methDiff.R
 
Package: methylKit
Commit: f53d5feff9d816b6b26ed368845075ff4522ede1
Author: alexg9010 <alex.gos90@gmail.com>
Date: 2019-02-07 16:52:49 +0100
Commit message:

 calculateDiffMeth: dealing with case of full model not being different from reduced model; print warning and set NaN to 1
 
Package: methylKit
Commit: 7bf960571a9088a58619f9d30f24090bda2e4776
Author: alexg9010 <alex.gos90@gmail.com>
Date: 2019-01-25 22:17:20 +0100
Commit message:

 pool: check length of treatment and number of sample is same
 
Package: methylKit
Commit: c006c8819cacfecc7f38bc1d7575d1452b91b3f6
Author: alexg9010 <alex.gos90@gmail.com>
Date: 2019-01-25 22:16:17 +0100
Commit message:

 improve validity checks for methylDB objects
 
Package: methylKit
Commit: 1dd383334d319e7efb43958901b40bb2e9eaf29d
Author: alexg9010 <alex.gos90@gmail.com>
Date: 2019-01-25 22:03:57 +0100
Commit message:

 fread.gzipped: rewrite building of shell command with system2 to mimic R.Utils::gunzip
 
Package: methylKit
Commit: 0d42408ca996c5a4b3beddcbc32645eda008cc36
Author: alexg9010 <alex.gos90@gmail.com>
Date: 2019-02-08 11:43:16 +0100
Commit message:

 add test for methylRawList Constructor
 
Package: methylKit
Commit: 7b942ee861f778bac0b42bc7cc0f5c7289b781fe
Author: alexg9010 <alex.gos90@gmail.com>
Date: 2019-02-08 11:42:41 +0100
Commit message:

 test-1-read: check if methylRawDB is same when directory is given or not, i.e. test wether directory affects object
 
Package: methylKit
Commit: e517dc4493cf0b3f5f0bf514d4d33419f55fdc01
Author: alexg9010 <alex.gos90@gmail.com>
Date: 2018-12-06 02:41:26 +0100
Commit message:

 getCorrelation: reduce code duplication and overhead by introducing S3 functions to be called by S4 methods
 
Package: methylKit
Commit: fcdc4186a7aed0e74174ceee345b0410b2639618
Author: alexg9010 <alex.gos90@gmail.com>
Date: 2019-01-18 11:33:23 +0100
Commit message:

 update NEWS and versionbump to 1.9.2
 
Package: methylKit
Commit: 9df114f793edda3b4a8a1ce9a8f621c2d98f688d
Author: alexg9010 <alex.gos90@gmail.com>
Date: 2019-01-18 11:19:56 +0100
Commit message:

 fread.gzipped: return df
 
Package: methylKit
Commit: aa6a0d122345ed31e73f226f5733da596e96ad51
Author: alexg9010 <alex.gos90@gmail.com>
Date: 2019-01-17 16:27:07 +0100
Commit message:

 headTabix: use fread.gzipped directly on the tabix file

should fix issue https://github.com/al2na/methylKit/issues/141
 
Package: methylKit
Commit: 9dc5721c58471b1c427fc838f386a47e195f1d6a
Author: alexg9010 <alex.gos90@gmail.com>
Date: 2019-01-17 12:54:19 +0100
Commit message:

 fread.gzipped: update function to check compression based on file content and allow to decompress .bgz files
 
Package: methylKit
Commit: 988113d9b4ce12c91ee0c822ffacdffb70578ab4
Author: Alexander Gosdschan <alexg9010@users.noreply.github.com>
Date: 2019-01-25 21:28:46 +0100
Commit message:

 Update README.md 
Package: methylKit
Commit: 32a32998e461efc1d1ac2ce84be121f854cbbf34
Author: Alexander Gosdschan <alexg9010@users.noreply.github.com>
Date: 2019-01-25 21:27:07 +0100
Commit message:

 Update README.md

add codecov support 
Package: methylKit
Commit: 08e237073c7363a864c8d4280be234ebbdace951
Author: Alexander Gosdschan <alexg9010@users.noreply.github.com>
Date: 2019-01-25 21:15:42 +0100
Commit message:

 Add codecov 
Package: methylKit
Commit: aef048cfe3db88100d8c0ce05758b1be78998a6c
Author: Altuna Akalin <aakalin@gmail.com>
Date: 2018-12-12 09:42:25 +0100
Commit message:

 Update README.md 
Package: INSPEcT
Commit: a1332515d77da65f574f56a2175d829f55faf692
Author: ste-depo <ste.depo@gmail.com>
Date: 2019-02-11 12:51:22 +0100
Commit message:

 modified simulated data and updated NEWS file
 
Package: TFEA.ChIP
Commit: eee012bba30b24253c1d90c9fa7c8c7fd6e695f9
Author: LauraPS1 <lpsantamaria@iib.upm.es>
Date: 2019-02-11 12:25:25 +0100
Commit message:

 Bug in preproccessInputData solved (DESeqResults to data.frame)
 
Package: KEGGgraph
Commit: 7065aaab4ce0451305cd4773f7794042334613c7
Author: Jitao David Zhang <jitao_david.zhang@roche.com>
Date: 2019-02-11 11:33:52 +0100
Commit message:

 version bump
 
Package: KEGGgraph
Commit: 56a49047dd8adafed6f4655d46e4b0e190ee5bd3
Author: Jitao David Zhang <jitao_david.zhang@roche.com>
Date: 2019-02-11 11:33:40 +0100
Commit message:

 use UTF8
 
Package: KEGGgraph
Commit: 4e9bbfd2af76906903da8e03c5bbfe4a2e18ba23
Author: Jitao David Zhang <jitao_david.zhang@roche.com>
Date: 2019-02-11 11:28:28 +0100
Commit message:

 add users who provided valuable feedback to the acknowlegement
 
Package: KEGGgraph
Commit: bb8cc73adefef084be2b43b13d0b7719d903fb07
Author: Jitao David Zhang <jitao_david.zhang@roche.com>
Date: 2019-02-11 11:28:03 +0100
Commit message:

 parseKGML2DataFrame: edgeData and KEGGedgeData can be of different length. Now the solution is to expand the shorter one. users are encouraged to report any bug
 
Package: KEGGgraph
Commit: 02e4a293c6e693b4fb93cbf819b1725d3a668f72
Author: Jitao David Zhang <jitao_david.zhang@roche.com>
Date: 2019-02-11 09:41:27 +0100
Commit message:

 add readme
 
Package: KEGGgraph
Commit: a47105cea3cd7d846b42dd2bfd77ed00a1927b48
Author: Jitao David Zhang <jitao_david.zhang@roche.com>
Date: 2019-02-11 09:34:42 +0100
Commit message:

 version bump
 
Package: KEGGgraph
Commit: f067ce26464f6db3bc6381b48f7128396c33b54b
Author: Jitao David Zhang <jitao_david.zhang@roche.com>
Date: 2019-02-11 09:32:57 +0100
Commit message:

 use devtools::check for checking
 
Package: KEGGgraph
Commit: de00d276855067783c25dd242d720e4be6d63b48
Author: Jitao David Zhang <jitao_david.zhang@roche.com>
Date: 2019-02-11 09:29:38 +0100
Commit message:

 renaming
 
Package: KEGGgraph
Commit: 580122514d3e1bff65495f5a1cbcdd9e484d3178
Author: Jitao David Zhang <jitao_david.zhang@roche.com>
Date: 2019-02-11 09:29:27 +0100
Commit message:

 import url.exists
 
Package: KEGGgraph
Commit: e74b0e8b66dcb317eda11e3cc2b179919d9434f0
Author: Jitao David Zhang <jitao_david.zhang@roche.com>
Date: 2019-02-11 09:29:17 +0100
Commit message:

 replace RUnit with testthat, add RCurl
 
Package: KEGGgraph
Commit: 1100d5e54320677aa0c91e8999faa33eca9aae41
Author: Jitao David Zhang <jitao_david.zhang@roche.com>
Date: 2019-02-11 09:28:31 +0100
Commit message:

 test existence of the URL before downloading, thanks to the suggestion of Juliane Manitz, author of the kangar00 package on CRAN
 
Package: KEGGgraph
Commit: a4dbd62458962d3095e246e420ad5d4f56b7ff2c
Author: Jitao David Zhang <jitao_david.zhang@roche.com>
Date: 2019-02-11 09:27:38 +0100
Commit message:

 use testthat instead of RUnit as the test engine
 
Package: KEGGgraph
Commit: 1c5818ed217e64e34611205198df92794df50e33
Author: Jitao David Zhang <jitao_david.zhang@roche.com>
Date: 2019-02-11 09:25:14 +0100
Commit message:

 build ignore updated for git
 
Package: KEGGgraph
Commit: 509f77ec07d89c47bd97c7c4fbfea284c2777ff5
Author: Jitao David Zhang <jitao_david.zhang@roche.com>
Date: 2019-02-11 09:20:02 +0100
Commit message:

 too long a line was truncated into shorter lines
 
Package: M3C
Commit: 2ecbf8733a4efa4c37fb59db664d5ba8b02b04fa
Author: crj32 <chris.r.john86@gmail.com>
Date: 2019-02-11 07:00:08 +0000
Commit message:

 fixed documentation
 
Package: ontoProc
Commit: c74ecd2cb5846bab57b4341c53be550141aeadc8
Author: Vince Carey <stvjc@channing.harvard.edu>
Date: 2019-02-10 22:04:54 -0500
Commit message:

 reduced size of PROonto.rda
 
Package: ontoProc
Commit: d28d927b89a6b34ea6c9cd6e0b0c1abd6a77385c
Author: Vince Carey <stvjc@channing.harvard.edu>
Date: 2019-02-10 16:37:50 -0500
Commit message:

 update with graphNEL support
 
Package: Ularcirc
Commit: 95617fc1fd63299d06b56578b6c99782a7574568
Author: David Humphreys <d.humphreys@victorchang.edu.au>
Date: 2019-02-11 13:31:17 +1100
Commit message:

 downsized TwoSzabo data set
 
Package: tximeta
Commit: fa346780b6e7f7ba28034ebb724efa3c9bb53784
Author: mikelove <michaelisaiahlove@gmail.com>
Date: 2019-02-10 20:20:49 -0500
Commit message:

 adding a try() around Seqinfo
 
Package: rgsepd
Commit: 065bc3cb2445004c51bd1e54887533702c363846
Author: Karl Stamm <karl.stamm@gmail.com>
Date: 2019-02-10 16:28:39 -0600
Commit message:

 also give the validity score during custom gene set extractprojection()
 
Package: rgsepd
Commit: ce00d529448b495a3239eaea70794a64ebf30b4a
Author: Karl Stamm <karl.stamm@gmail.com>
Date: 2019-02-10 15:53:08 -0600
Commit message:

 new feature in 1.15.12 for vstBlind
 
Package: universalmotif
Commit: 8840abc0939f82a6f7167f789aa885adefef414f
Author: bjmt <benjmtremblay@gmail.com>
Date: 2019-02-10 16:31:21 -0500
Commit message:

 v1.1.22
 
Package: universalmotif
Commit: 0869ed13a4a33c5bd0796b4187cff1f03ed46c48
Author: bjmt <benjmtremblay@gmail.com>
Date: 2019-02-10 15:55:21 -0500
Commit message:

 version bump
 
Package: universalmotif
Commit: 2ca1cd62521b3561d3c86f5b8b80abbf362d6dd9
Author: bjmt <benjmtremblay@gmail.com>
Date: 2019-02-10 15:54:57 -0500
Commit message:

 bug fix: scan_sequences() now works for motifs with pseudocount of 0
 
Package: universalmotif
Commit: 6e132e63d55dba1c99cfa24c025ddaa10e535c85
Author: bjmt <benjmtremblay@gmail.com>
Date: 2019-02-09 14:58:20 -0500
Commit message:

 fixed tests from last commit
 
Package: universalmotif
Commit: 8bfd6c8dfcc9709af229fd12a4398d1814075725
Author: bjmt <benjmtremblay@gmail.com>
Date: 2019-02-09 14:36:44 -0500
Commit message:

 updated news
 
Package: universalmotif
Commit: e2457582fa3c3837472f3ae7ca9b24e50f62f872
Author: bjmt <benjmtremblay@gmail.com>
Date: 2019-02-09 14:33:57 -0500
Commit message:

 renamed tests, added some
 
Package: universalmotif
Commit: 88bb43c3b80d896f44d05dfe9678927e0462ab7e
Author: bjmt <benjmtremblay@gmail.com>
Date: 2019-02-09 01:46:18 -0500
Commit message:

 document() changed some documentation
 
Package: universalmotif
Commit: 590f67f9c12a8beb6bbb347f63e6401181013ec5
Author: bjmt <benjmtremblay@gmail.com>
Date: 2019-02-09 01:31:30 -0500
Commit message:

 added spell check test
 
Package: biosigner
Commit: e860c09745541094fd09b6c9b026781cdc73ec78
Author: THEVENOT Etienne <ET207099@intra.cea.fr>
Date: 2019-02-10 19:23:42 +0100
Commit message:

 v1.11.8 minor vignette update
 
Package: biosigner
Commit: 29399fcc4995e4e2e0b0403867c71a4ca3a1d906
Author: THEVENOT Etienne <ET207099@intra.cea.fr>
Date: 2019-02-10 18:45:01 +0100
Commit message:

 v1.11.4 error message when using a character now fixed
 
Package: ropls
Commit: 08d531cb8878cd63a31cf73463902b571ed7fa13
Author: THEVENOT Etienne <ET207099@intra.cea.fr>
Date: 2019-02-10 18:17:46 +0100
Commit message:

 testthat directory and eset slot in opls class
 
Package: biosigner
Commit: dd9e12cdc1e7bd6ec61f1b8105549cc50b0349f4
Author: THEVENOT Etienne <ET207099@intra.cea.fr>
Date: 2019-02-10 17:55:29 +0100
Commit message:

 v1.11.2 getEset method
 
Package: Prostar
Commit: 621e8cdd9310e87a6ad675bee8fa208e8d8fe47c
Author: Samuel Wieczorek <samuel.wieczorek@cea.fr>
Date: 2019-02-10 06:04:26 +0100
Commit message:

 1.15.11 : add sum as aggregation function
 
Package: ropls
Commit: 71dce294e1d7d89acc243ca336d3cc678a1f3401
Author: THEVENOT Etienne <ET207099@intra.cea.fr>
Date: 2019-02-09 20:42:53 +0100
Commit message:

 v1.15.8 BiocCheck OK
 
Package: ropls
Commit: 6822f6ced096dc35fed8eb69dfa5ba09c14cb6d6
Author: THEVENOT Etienne <ET207099@intra.cea.fr>
Date: 2019-02-09 20:12:51 +0100
Commit message:

 v1.15.8; opls-eset: scores, loadings, VIP, etc. in pData and fData from getEset; parPaletteVc argument in plot-opls
 
Package: Rsamtools
Commit: 1da383535335396d65f77fa338e74cd80ce84844
Author: Hervé Pagès <hpages@fredhutch.org>
Date: 2019-02-09 10:48:10 -0800
Commit message:

 oops, forgot closing curly bracket
 
Package: Rsamtools
Commit: 62f46111498c3914fc418b48f903387f4d91d143
Author: Hervé Pagès <hpages@fredhutch.org>
Date: 2019-02-09 10:41:30 -0800
Commit message:

 Remove knet_win32_init()/knet_win32_destroy() calls on Windows
 
Package: Rsamtools
Commit: 8ac1df19057e9f99b94fe74f5b839a4c0795f017
Author: Hervé Pagès <hpages@fredhutch.org>
Date: 2019-02-09 10:37:55 -0800
Commit message:

 Disable applyPileups() examples and a few more of its tests
 
Package: Prostar
Commit: 8208b936a93e78e995ba081f71be9760b4c2d730
Author: Samuel Wieczorek <samuel.wieczorek@cea.fr>
Date: 2019-02-09 08:21:12 +0100
Commit message:

 new version 1.15.10 to fix a bug in agregation stats
 
Package: DAPAR
Commit: 32b9518270a6fd4120b30fbb7c762b560195741d
Author: Samuel Wieczorek <samuel.wieczorek@cea.fr>
Date: 2019-02-09 07:48:14 +0100
Commit message:

 version 1.15.9, fix bug in agregationStats
 
Package: universalmotif
Commit: e0697a8616a0e41a09bc3fd12ce2cffe76b494b6
Author: bjmt <benjmtremblay@gmail.com>
Date: 2019-02-09 01:15:42 -0500
Commit message:

 minor change: fixed spelling mistakes + added lang field to desc
 
Package: TCC
Commit: e3a874b4467a7ddf95191df52f68f57592d99613
Author: jqsun <wukong@bi.a.u-tokyo.ac.jp>
Date: 2019-02-09 09:53:40 +0900
Commit message:

 fixed merge conflict.
 
Package: TCC
Commit: 1763a9ee638421d83885c7018335e7e5b730a82d
Author: jqsun <wukong@bi.a.u-tokyo.ac.jp>
Date: 2019-02-09 09:51:24 +0900
Commit message:

 changed the function of filterLowCountGenes.
 
Package: CoGAPS
Commit: 1ad444f38734ff65f6ec8e0bd5602485c0b3f1bb
Author: Tom Sherman <tomsherman159@gmail.com>
Date: 2019-02-08 15:17:29 -0500
Commit message:

 version bump
 
Package: CoGAPS
Commit: 974be59fbcf1138adea1db442ee7591c639f7b86
Author: Tom Sherman <tomsherman159@gmail.com>
Date: 2019-02-08 15:08:59 -0500
Commit message:

 fixed windows build issues
 
Package: CoGAPS
Commit: ce62fc6166ea2778c74ddacdfdceca6ff085a52f
Author: Tom Sherman <tomsherman159@gmail.com>
Date: 2019-02-08 10:21:19 -0500
Commit message:

 Merge branch 'master' of github.com:FertigLab/CoGAPS
 
Package: CoGAPS
Commit: 6f43b8ba45511c4e474afdd4f4676c55f3737bce
Author: Tom Sherman <tomsherman159@gmail.com>
Date: 2019-02-08 10:21:15 -0500
Commit message:

 missing documentation
 
Package: CoGAPS
Commit: bf751d4f4d47a37c67ee8278dc6d6e800e4e3b7f
Author: Tom Sherman <tomsherman159@gmail.com>
Date: 2019-02-07 17:02:02 -0500
Commit message:

 fix downloads link 
Package: CoGAPS
Commit: 55e4cd1fa8d6bdf918e3d9450ef22c4717771389
Author: Tom Sherman <tomsherman159@gmail.com>
Date: 2019-02-07 16:58:23 -0500
Commit message:

 add link to travis in status button 
Package: CoGAPS
Commit: 46e763be0f5b3515af35660cd2cfe66791182673
Author: Tom Sherman <tomsherman159@gmail.com>
Date: 2019-02-07 16:57:36 -0500
Commit message:

 fix embedded travis status 
Package: CoGAPS
Commit: c048fef8e0032918951c335ec3e4b6275a91ba9d
Author: Tom Sherman <tomsherman159@gmail.com>
Date: 2019-02-07 16:55:04 -0500
Commit message:

 embed travis status in readme 
Package: CoGAPS
Commit: 42342c1e947bac7db26ddb080d1db220ad01d3b4
Author: Tom Sherman <tomsherman159@gmail.com>
Date: 2019-02-07 16:48:59 -0500
Commit message:

 bump version
 
Package: CoGAPS
Commit: bc8d66d9e66c379d3a37b07ef92baac8068547e2
Author: Tom Sherman <tomsherman159@gmail.com>
Date: 2019-02-07 16:47:44 -0500
Commit message:

 fix comment
 
Package: CoGAPS
Commit: 7252bff2abf366ae5c8eccc20f5b26f742fc90ed
Author: Tom Sherman <tomsherman159@gmail.com>
Date: 2019-02-07 16:40:40 -0500
Commit message:

 fix up merge errors; remove incomplete hdf5 code
 
Package: CoGAPS
Commit: 17550909d7c0588d1c3f1f88e8756f0fba81e8dd
Author: Tom Sherman <tomsherman159@gmail.com>
Date: 2019-02-07 16:34:56 -0500
Commit message:

 merge
 
Package: CoGAPS
Commit: 63ac85f148a5cb9de36419dfcb6b77e6b5335a85
Author: Tom Sherman <tomsherman159@gmail.com>
Date: 2019-02-04 18:03:18 -0500
Commit message:

 version bump
 
Package: CoGAPS
Commit: 4ca2061e64ab25b9baef382bc8766650ec74b503
Author: Tom Sherman <tomsherman159@gmail.com>
Date: 2019-02-04 18:03:08 -0500
Commit message:

 add test to check that 'none' gets converted to NULL when passed for distributed
 
Package: CoGAPS
Commit: d50d528b23d06ad4bb14bf6aae628c280e516860
Author: Tom Sherman <tomsherman159@gmail.com>
Date: 2019-02-04 18:02:33 -0500
Commit message:

 properly set distributed to NULL in initialize method
 
Package: CoGAPS
Commit: d40e808bb3bc2efc66ef2be5d4025652622d0181
Author: Tom Sherman <tomsherman159@gmail.com>
Date: 2019-02-04 18:02:05 -0500
Commit message:

 extra paranthesis
 
Package: CoGAPS
Commit: 14db68e07f6c9901e833cf02c9ebb427a436f6c2
Author: Tom Sherman <tomsherman159@gmail.com>
Date: 2019-02-04 17:53:53 -0500
Commit message:

 don't check file extension if data is not a file path
 
Package: CoGAPS
Commit: e3b7bab603097aab874e41448c312631ae8d3b33
Author: Tom Sherman <tomsherman159@gmail.com>
Date: 2019-02-04 17:34:40 -0500
Commit message:

 allow 'none' for distributed method
 
Package: CoGAPS
Commit: 70c436209e9d5436dd41270caf425b2ac82df054
Author: Tom Sherman <tomsherman159@gmail.com>
Date: 2019-01-31 16:42:58 -0500
Commit message:

 version bump
 
Package: CoGAPS
Commit: 844bb0021c4cabbf0bc08fdb9a36f81654875793
Author: Tom Sherman <tomsherman159@gmail.com>
Date: 2019-01-31 16:41:38 -0500
Commit message:

 ignore build files
 
Package: CoGAPS
Commit: f21bbff0575612eb8169082d793f164fb34d1113
Author: Tom Sherman <tomsherman159@gmail.com>
Date: 2019-01-31 16:22:03 -0500
Commit message:

 allow for RDS files to be passed in
 
Package: CoGAPS
Commit: b2de8302c0967e57a482997c5074d395599f536f
Author: Tom Sherman <tomsherman159@gmail.com>
Date: 2019-01-29 15:09:05 -0500
Commit message:

 added check for params@distributed
 
Package: CoGAPS
Commit: 4daa5452c0e4cfa3150d1fbd0eee9061b5274ea7
Author: Tom Sherman <tomsherman159@gmail.com>
Date: 2019-01-09 13:25:20 -0500
Commit message:

 added blank Hdf5Parser class
 
Package: CoGAPS
Commit: c8c9b60599420844d43cee258358d9c408eecbba
Author: Tom Sherman <tomsherman159@gmail.com>
Date: 2019-01-08 17:16:52 -0500
Commit message:

 implemented policy based design for sparse/dense storage in the GibbsSampler
 
Package: CoGAPS
Commit: 3711db62cf61644c28c1f03d11ee4614473cf339
Author: Tom Sherman <tomsherman159@gmail.com>
Date: 2019-01-08 10:10:46 -0500
Commit message:

 link against Rhdf5 library
 
Package: TCGAutils
Commit: c4a7058cb796220f8c528ea6f70a30a636a67425
Author: LiNk-NY <mramos09@gmail.com>
Date: 2019-02-08 14:33:32 -0500
Commit message:

 replace names with patientID
 
Package: TCGAutils
Commit: c2be9e1a2d10af4be4ecc47676d7d5f3c16daeb5
Author: LiNk-NY <mramos09@gmail.com>
Date: 2019-02-08 14:21:59 -0500
Commit message:

 TCGAsampleSelect works with vector of sample codes
 
Package: TCGAutils
Commit: 184258f421079b4368ed222403ebee28ed76cc95
Author: LiNk-NY <mramos09@gmail.com>
Date: 2019-02-08 13:30:40 -0500
Commit message:

 Merge remote-tracking branch 'origin/dev'
 
Package: TCGAutils
Commit: 1956312572b9ad9b5c3ad90e09ecbce38e390ee3
Author: LiNk-NY <mramos09@gmail.com>
Date: 2019-01-23 19:20:13 -0500
Commit message:

 add package argument to data calls
 
Package: curatedTCGAData
Commit: 403f034bc7aa4cc4f9c56b77cceb7ebfd534abf1
Author: LiNk-NY <mramos09@gmail.com>
Date: 2019-02-08 15:30:45 -0500
Commit message:

 version bump
 
Package: curatedTCGAData
Commit: 5b05a9144897695a3f0a48be9d96e924ab8719c4
Author: LiNk-NY <mramos09@gmail.com>
Date: 2019-02-08 15:29:14 -0500
Commit message:

 update table of data type descriptions
 
Package: curatedTCGAData
Commit: b1397d2ef8208f74fb2523a47b3dcb5a90bf7fe3
Author: Levi Waldron <lwaldron.research@gmail.com>
Date: 2019-02-04 16:23:53 -0500
Commit message:

 Update README.md 
Package: curatedTCGAData
Commit: 4232c51fd1a1ae76c1b134d9e4ccc397f5352e78
Author: Levi Waldron <lwaldron.research@gmail.com>
Date: 2019-02-04 16:21:36 -0500
Commit message:

 Update README.md 
Package: universalmotif
Commit: 45ba701a48ae8f7cbd039f0e6b0501be39995033
Author: bjmt <benjmtremblay@gmail.com>
Date: 2019-02-08 15:35:39 -0500
Commit message:

 minor change: increased character param security + bug fix: method documentation for motif_tree()
 
Package: pathview
Commit: bae55496707d43bc7dd8ff98a8dc5532c9dbff5f
Author: Weijun Luo <luo_weijun@yahoo.com>
Date: 2019-02-08 15:12:01 -0500
Commit message:

 version 1.23.3-2
 
Package: simpleSingleCell
Commit: a703b06e5aab9218970c77dd6fc31d33da5cc4fc
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2019-02-08 17:59:01 +0000
Commit message:

 Consistent naming of RDS output files.
 
Package: simpleSingleCell
Commit: bf4341b135e21180f107ef7583547b63f2204fb4
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2019-02-08 17:58:15 +0000
Commit message:

 Use tempdir() to avoid polluting the working dir.
 
Package: LoomExperiment
Commit: d881996e05859e4bfdbd1bbd5bacad5d098f2431
Author: Daniel Van Twisk <daniel.vantwisk@roswellpark.org>
Date: 2019-02-08 12:51:39 -0500
Commit message:

 Response to Issue #3: Prioritze rowData over empty Granges objects
 
Package: LoomExperiment
Commit: d0ebb6da0b3baa56d74165d24e9c76b47c9feb0c
Author: Daniel Van Twisk <daniel.vantwisk@roswellpark.org>
Date: 2019-02-08 12:50:43 -0500
Commit message:

 Merge branch 'master' of git.bioconductor.org:packages/LoomExperiment
 
Package: LoomExperiment
Commit: 23899d0a13839fc0c689a6913fb401c46c154347
Author: Daniel Van Twisk <daniel.vantwisk@roswellpark.org>
Date: 2018-11-14 11:46:47 -0500
Commit message:

 Added cbind to LoomGraphs documentation
 
Package: simpleSingleCell
Commit: d857fb9bccb8af5dbb8a355e9c61fa602004ad32
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2019-02-08 17:43:24 +0000
Commit message:

 Reorganized text in sections and comments.
Mentioned how to get per-gene corrected values.
 
Package: simpleSingleCell
Commit: 56a8e2ec90680b64f7ee1398ece1344b48962603
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2019-02-08 11:23:36 +0000
Commit message:

 Bumped version number, date.
 
Package: simpleSingleCell
Commit: 88ca4ab02465e21642caed219f09c3b375c7afca
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2019-02-08 11:23:02 +0000
Commit message:

 Made heatmap of log-fold changes for the brain data.
 
Package: simpleSingleCell
Commit: b43b57a25b7974699713a9f5975fda66057ccedb
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2019-02-07 10:08:55 +0000
Commit message:

 Forgot to add references.
 
Package: simpleSingleCell
Commit: fab8ef2d1b80c8d7deefa19f1114e3c25411503d
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2019-02-07 10:07:55 +0000
Commit message:

 Added paragraph about experimental strategies.
 
Package: simpleSingleCell
Commit: 87fb31e2ecaca29dcc1d5a9274e2738f2822703d
Author: Aaron Lun <aaron.lun@cruk.cam.ac.uk>
Date: 2019-02-07 09:59:42 +0000
Commit message:

 Reorganized text, elaborated on the doublet score interpretation.
 
Package: IntEREst
Commit: 0f408441df7390687e460fd5c7aefc4fe58662bb
Author: Ali Oghabian <oghabian@introni.biocenter.helsinki.fi>
Date: 2019-02-08 18:40:42 +0200
Commit message:

 Support for qnamePrefixEnd and qnameSuffixStart params in interest().
 
Package: universalmotif
Commit: 0c9939595f1de06be7cec33923cadc646e33b8f2
Author: bjmt <benjmtremblay@gmail.com>
Date: 2019-02-08 12:04:00 -0500
Commit message:

 new feature: motif_peaks()
 
Package: universalmotif
Commit: df4412aa10d2901b441708a51ebbfc1bbecefe74
Author: bjmt <benjmtremblay@gmail.com>
Date: 2019-02-08 12:02:19 -0500
Commit message:

 motif_peaks() work nearing final state, ready to merge
 
Package: universalmotif
Commit: 62bdad701022a797b1841d5fecd5a9553e574388
Author: bjmt <benjmtremblay@gmail.com>
Date: 2019-02-02 01:03:52 -0500
Commit message:

 cleaned up code
 
Package: universalmotif
Commit: 0c55a57c59f68257cead397c417da7f70cd3693c
Author: bjmt <benjmtremblay@gmail.com>
Date: 2019-02-02 00:29:35 -0500
Commit message:

 cpp code for linbin and peakfinder functions
 
Package: universalmotif
Commit: 7d9bd101a784a697b2d48d4bbf8214b30f4031ee
Author: bjmt <benjmtremblay@gmail.com>
Date: 2019-02-01 18:17:36 -0500
Commit message:

 Merge branch 'master' into experimental
 
Package: universalmotif
Commit: 688a1ab5f01c482ab9564a7af2d223f9203ba3cb
Author: bjmt <benjmtremblay@gmail.com>
Date: 2019-02-01 18:11:32 -0500
Commit message:

 motif_peaks() R code all done
 
Package: universalmotif
Commit: c9b538db0bc0e3f9cff7f274a33fe1fb3863162a
Author: bjmt <benjmtremblay@gmail.com>
Date: 2019-02-01 17:43:50 -0500
Commit message:

 documentation first draft
 
Package: universalmotif
Commit: 170e50623bedc3b6e6dad360b9c3c0c7006ea1b1
Author: bjmt <benjmtremblay@gmail.com>
Date: 2019-02-01 14:44:06 -0500
Commit message:

 now exporting motif_peaks
 
Package: universalmotif
Commit: 7b2e8835991e00ce5cb020987b15c97d7e1b288b
Author: bjmt <benjmtremblay@gmail.com>
Date: 2019-02-01 14:26:42 -0500
Commit message:

 Merge branch 'master' into experimental
 
Package: universalmotif
Commit: b4a72a43db7d6e6b7fc2ab07dcf805250eb4bb11
Author: bjmt <benjmtremblay@gmail.com>
Date: 2019-02-01 12:07:55 -0500
Commit message:

 motif_peaks() has matured a bit
 
Package: universalmotif
Commit: d79cb7d2aa6c01a40348eabeb34966faccc61bb8
Author: bjmt <benjmtremblay@gmail.com>
Date: 2019-01-30 17:10:26 -0500
Commit message:

 initial motif_peaks() function created
 
Package: universalmotif
Commit: 6aeba0f1b25a4fdc76ef1312a0aff3407443f9f7
Author: bjmt <benjmtremblay@gmail.com>
Date: 2019-01-30 17:10:00 -0500
Commit message:

 initial motif_peaks() function created
 
Package: universalmotif
Commit: 3a706b58070aece05f3956b4feb1dfd5782245d1
Author: bjmt <benjmtremblay@gmail.com>
Date: 2019-01-29 14:16:14 -0500
Commit message:

 basic implementation for finding significant motif peaks in sequence data
 
Package: universalmotif
Commit: 147abee010defd0cbe8f762b04bdee4b2963feff
Author: bjmt <benjmtremblay@gmail.com>
Date: 2019-01-27 15:12:32 -0500
Commit message:

 added create_cluster()
 
Package: universalmotif
Commit: 0dd4f7bf950659fce98e083836dab51e25fd9fb4
Author: bjmt <benjmtremblay@gmail.com>
Date: 2019-01-26 17:10:37 -0500
Commit message:

 basic cluster framework set up
 
Package: universalmotif
Commit: 8b84d32a6dcd3f1fd1dfb4d5f5e04d0ef7ce0ddc
Author: bjmt <benjmtremblay@gmail.com>
Date: 2019-01-26 12:25:29 -0500
Commit message:

 init experimental branch
 
Package: universalmotif
Commit: 8eea14570e28ac9dc599c73203d1b66d2651caaf
Author: bjmt <benjmtremblay@gmail.com>
Date: 2019-01-12 10:26:25 -0500
Commit message:

 update .Rbuildignore
 
Package: INSPEcT
Commit: 0404031a968d017d714578c1b86baf45372f5283
Author: ste-depo <ste.depo@gmail.com>
Date: 2019-02-08 17:21:00 +0100
Commit message:

 added RNAdynamics vignette
 
Package: rhdf5
Commit: c692f6cb9a73e9a0551eedbd040ff6c61ded6fc1
Author: Mike Smith <grimbough@gmail.com>
Date: 2019-02-08 17:00:26 +0100
Commit message:

 More ENUM fixes
 
Package: rhdf5
Commit: a554b7bba5d111117a1b5b534619485385745e06
Author: Mike Smith <grimbough@gmail.com>
Date: 2019-02-08 16:34:27 +0100
Commit message:

 Merge branch 'master' of github.com:grimbough/rhdf5
 
Package: rhdf5
Commit: 9ef7688dc87debbf6c6de9ad2279d2ea2bf0951e
Author: Mike Smith <grimbough@gmail.com>
Date: 2019-02-08 16:34:04 +0100
Commit message:

 Fix bug introduced in read ENUM/factor
 
Package: rhdf5
Commit: a2bd49bfc4c72cfe1038d6fa6b62f2397ebbe5ea
Author: Mike Smith <grimbough@gmail.com>
Date: 2019-02-07 15:12:38 +0100
Commit message:

 Skip test creating large vectors on Travis
 
Package: BiocParallel
Commit: 5b810ed55cd15af3b2eec72fd900f54527ec6930
Author: Martin Morgan <martin.morgan@roswellpark.org>
Date: 2019-02-08 09:12:40 -0500
Commit message:

 (port) configure file to add -lrt linking
 
Package: BiocParallel
Commit: 7f7a54c47f4949b600b9fd568289a519496bc4d4
Author: Martin Morgan <martin.morgan@roswellpark.org>
Date: 2019-02-08 09:10:39 -0500
Commit message:

 version bump and configure script

- closes #93 closes #94
 
Package: BiocParallel
Commit: 9f1f3da78d44543aea0088119f9877cf9d289010
Author: Tom Callaway <spot@fedoraproject.org>
Date: 2019-02-07 11:31:27 -0500
Commit message:

 add configure.ac, src/Makevars.in to check librt for shm_open and link to it if needed
 
Package: ORFik
Commit: 8bc02c3a2b3afbc036e6013ee8dbca1c54b21808
Author: Håkon Tjeldnes <hauken_heyken@hotmail.com>
Date: 2019-02-08 14:11:04 +0100
Commit message:

 added new features, more tests and documentation (#70)

* added new features, more tests and documentation

* fixed space

* made docs more clear and spaces
 
Package: ORFik
Commit: 624fe649f3be6852dc86559104c540a5083cef6d
Author: Håkon Tjeldnes <hauken_heyken@hotmail.com>
Date: 2019-02-01 10:56:41 +0100
Commit message:

 docfixes and fix to kozaksequenceScore (#69)

 
Package: ORFik
Commit: 5e203ac81ed4ea450231e762bb2f58d633edb114
Author: Håkon Tjeldnes <hauken_heyken@hotmail.com>
Date: 2019-01-25 16:11:30 +0100
Commit message:

 small securityfix for windowPerGroup (#68)

* small securityfix for windowPerGroup

* small fix for merge
 
Package: Rsamtools
Commit: e7b06e71a94c3348614b7a9a058b543b831d6870
Author: Hervé Pagès <hpages@fredhutch.org>
Date: 2019-02-07 19:14:15 -0800
Commit message:

 remove one migration leftover
 
Package: VariantAnnotation
Commit: 528c2939a6bfc98386af0bade38979cf490d505b
Author: Hervé Pagès <hpages@fredhutch.org>
Date: 2019-02-07 17:17:01 -0800
Commit message:

 fix invalid VCF files
 
Package: VariantAnnotation
Commit: 53393b13fffaa8159acf6b30e16ab2ece57e1348
Author: Hervé Pagès <hpages@fredhutch.org>
Date: 2019-02-07 16:49:34 -0800
Commit message:

 Migrate to Rhtslib (htslib 1.7) and to Rsamtools 1.99.0
 
Package: VariantAnnotation
Commit: 72c7e3db68335e7abeeb43daacd49146595b0729
Author: Hervé Pagès <hpages@fredhutch.org>
Date: 2019-02-07 16:40:32 -0800
Commit message:

 minor tweak to src/Makevars[.win] files
 

</div> </div>

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: