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GIT Logs

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

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Package: TrajectoryGeometry
Commit: eab6045dc6804e5f712446bea2f938d94e45b2c3
Author: AnnaLaddach <annaladdach@gmail.com>
Date: 2020-11-26 10:15:30 +0000
Commit message:

 R version dependency changed
 
Package: ceRNAnetsim
Commit: e1ddfb39c64f712f70f4a060fb76f779fe6a0a7f
Author: selcenari <selcenarii@gmail.com>
Date: 2020-11-26 11:17:09 +0300
Commit message:

 DESCRIPTION
 
Package: ceRNAnetsim
Commit: 4ddd9985a7d14a8102132b6babf0cabf2dc34545
Author: selcenari <selcenarii@gmail.com>
Date: 2020-11-26 11:02:07 +0300
Commit message:

 version check
 
Package: ceRNAnetsim
Commit: 0f0db69ad4fcd4518be15166156c66a23a43652d
Author: selcenari <selcenarii@gmail.com>
Date: 2020-11-25 15:08:40 +0300
Commit message:

 test to solve Illegal version bump
 
Package: ceRNAnetsim
Commit: 116e6f7060efffe4ade911dd4490f81dd51f7535
Author: selcenari <selcenarii@gmail.com>
Date: 2020-11-25 15:03:08 +0300
Commit message:

 version issue
 
Package: ceRNAnetsim
Commit: db798e115060028b03711974883ffd53764328ab
Author: selcenari <selcenarii@gmail.com>
Date: 2020-11-25 14:49:34 +0300
Commit message:

 description error
 
Package: casper
Commit: 25e48f6b93a23dfc935b3cca9b2e0895323ecf4f
Author: davidrusi <rosselldavid@gmail.com>
Date: 2020-11-26 09:32:53 +0100
Commit message:

 bumped version number
 
Package: miRSM
Commit: 1c19d4da297bc2f2977dc2cfff689aacef67ac62
Author: zhangjunpeng411 <zhangjunpeng_411@yahoo.com>
Date: 2020-11-26 16:02:53 +0800
Commit message:

 Update
 
Package: miRSM
Commit: 5fa0f031c69f2d803aead3c6adc58a7590f6c14f
Author: zhangjunpeng411 <zhangjunpeng_411@yahoo.com>
Date: 2020-11-15 08:23:25 +0800
Commit message:

 Update
 
Package: csaw
Commit: 04c8109c832da385b923124845fcfbdc59836260
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2020-11-26 00:01:47 -0800
Commit message:

 Got rid of invalid links.
 
Package: csaw
Commit: 3d15672de27daba35d357f80996bb3b62ffc776a
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2020-11-25 23:49:30 -0800
Commit message:

 Redirect users to the book for documentation.
 
Package: csaw
Commit: 58343f09e4c6d6f86ae2c130f4e639119152b59c
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2020-11-09 13:16:05 -0800
Commit message:

 Moved AnnotationDbi, GenomicFeatures to Suggests.
 
Package: chipseqDB
Commit: 38462bb57a15a6cb6823d3affa1912396fe84563
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2020-11-25 23:50:05 -0800
Commit message:

 Redirect to the csawBook.
 
Package: csawUsersGuide
Commit: 8dd056e6b333bd107cabb2ef4282bca7b2b81ab0
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2020-11-25 23:26:22 -0800
Commit message:

 Purged content, added redirection to the new csawBook.
 
Package: scran
Commit: 7ba644f0d7a503a48114acda8beede27934ae5ad
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2020-11-25 22:33:44 -0800
Commit message:

 Cut out a lot of redundant C++ code.
 
Package: basilisk
Commit: 917422249c59de49cc5f207b2c13145e01e16adc
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2020-11-25 21:53:30 -0800
Commit message:

 Mention some legal stuff about ToS.
 
Package: basilisk.utils
Commit: 09d5eadd7a2ac8ed4364ff4418917fb5deba2adc
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2020-11-25 21:42:44 -0800
Commit message:

 Simplified the installer caching behavior.
 
Package: batchelor
Commit: 7860135933718afe095986a830aa1cebc8a8a623
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2020-11-25 21:02:40 -0800
Commit message:

 Improved the error message for checkBatchConsistency.
Closes #22.
 
Package: Rsubread
Commit: 113a96059b3a74e157e3f9be9dd18d63b4577170
Author: Yang Liao <liao_y@svr2672.licr.unimelb.edu.au>
Date: 2020-11-26 16:01:32 +1100
Commit message:

 nearly finished parallel gzip and bam sorting.
 
Package: spatialHeatmap
Commit: e4a268da92d3dd24a04ceccfc1f86af0278e509d
Author: jianhaizhang <jzhan067@ucr.edu>
Date: 2020-11-25 20:42:47 -0800
Commit message:

 Small change.
 
Package: spatialHeatmap
Commit: 7dec30667c949f4afbf69725b1dc5af7451e54ed
Author: jianhaizhang <jzhan067@ucr.edu>
Date: 2020-11-25 20:23:45 -0800
Commit message:

 Bump version.
 
Package: spatialHeatmap
Commit: 1ca68ee7f828bc3cc82de48928eb9a95b2638e00
Author: jianhaizhang <jzhan067@ucr.edu>
Date: 2020-11-25 20:22:32 -0800
Commit message:

 Break long text in help files to avoid overflowing.
 
Package: spatialHeatmap
Commit: cf064f616574c7f2c775d05a027982d0bfe70a9a
Author: jianhaizhang <jzhan067@ucr.edu>
Date: 2020-11-25 19:57:46 -0800
Commit message:

 Use new naming scheme for aSVG files: _[view]_shm.svg.
 </pre>
    </div>
  
    
Package: BUSpaRse
Commit: a05bf453eaaa4598b6667d4433d96680d89582fd
Author: Lambda Moses <dlu2@caltech.edu>
Date: 2020-11-25 19:51:56 -0800
Commit message:

 useMart deals with Ensembl archives differently from useEnsembl
 
Package: BUSpaRse
Commit: e699478bebdc47512745c097b4ea3c5f7fcaabfe
Author: Lambda Moses <dlu2@caltech.edu>
Date: 2020-11-25 19:23:52 -0800
Commit message:

 In Bioconductor devel, biomaRt::useEnsembl no longer works with ensemblgenomes.org. So I switched to useMart.
 
Package: scClassify
Commit: 059a3b7421b899ed6747115102b3b718781413b6
Author: yingxinlin <yingxinlindsay@gmail.com>
Date: 2020-11-25 19:26:12 +1100
Commit message:

 fix predict_scClassify
 
Package: scClassify
Commit: bb0aa39897c9ae2fc237eeed65b17e8bf8f049fc
Author: YingxinLin <yingxinlindsay@gmail.com>
Date: 2020-11-25 19:17:07 +1100
Commit message:

 Merge remote-tracking branch 'upstream/master'
 
Package: scClassify
Commit: 751a14e81e40be3b668f7fcd2ca4c25dec1d4c58
Author: yingxinlin <yingxinlindsay@gmail.com>
Date: 2020-09-30 20:04:06 +1000
Commit message:

 fix feature selection
 
Package: scClassify
Commit: f46ef43c4c86572b1573f9b1147e12a03c2d4ab2
Author: yingxinlin <yingxinlindsay@gmail.com>
Date: 2020-04-22 22:55:42 +1000
Commit message:

 edit travis
 
Package: easyRNASeq
Commit: 22c6ff4e318e43ec66d3318652609bdfbad0e7c8
Author: nicolasDelhomme <nicolas.delhomme@slu.se>
Date: 2020-11-25 23:49:06 +0100
Commit message:

 Removed DESeq as a dependency
Removed defunct functions
Additional warning about RPKM usage
 
Package: regutools
Commit: 5330c34d08d1c6d2b3259429cdff9ca67f48fac3
Author: Leonardo Collado Torres <lcolladotor@gmail.com>
Date: 2020-11-25 15:12:53 -0500
Commit message:

 v1.3.1 -- merge with Bioc's git. b36cba5 should have been v1.3.1.
 
Package: regutools
Commit: b36cba52f8c7bf412b60a003e4b8038b6aad610e
Author: Leonardo Collado Torres <lcolladotor@gmail.com>
Date: 2020-11-25 15:08:23 -0500
Commit message:

 v1.1.4 -- switch to the latest biocthis GHA workflow. Update URL to resolve https://github.com/ComunidadBioInfo/regutools/issues/33
 
Package: microbiome
Commit: d2ecbeb0218bb98d6e27d7d763239f8e0d702d71
Author: Leo <leo.lahti@iki.fi>
Date: 2020-11-25 22:05:42 +0200
Commit message:

 vignette fixed
 
Package: microbiome
Commit: 359eacebd6aa9a9275ad6f3a1031e847bc1b2b2b
Author: Leo <leo.lahti@iki.fi>
Date: 2020-11-25 21:49:52 +0200
Commit message:

 Merge remote-tracking branch 'upstream/master'
 
Package: microbiome
Commit: 146eafc63a9885f8c6add489dcff4c1639f9a308
Author: Leo <leo.lahti@iki.fi>
Date: 2020-11-25 21:49:39 +0200
Commit message:

 sync
 
Package: mtbls2
Commit: 967fb7f024e733021f3fce7ec325115370b55965
Author: Steffen Neumann <sneumann@ipb-halle.de>
Date: 2020-11-25 20:40:58 +0100
Commit message:

 disable parallel processing (again).
 
Package: preciseTADhub
Commit: ab31195d9a2a53278a134bb4b0529041af7055c3
Author: stilianoudakis <stilianoudasc@mymail.vcu.edu>
Date: 2020-11-25 14:40:40 -0500
Commit message:

 version bump
 
Package: preciseTADhub
Commit: 66ce837c53402b73f93cbc207149658f70509478
Author: stilianoudakis <stilianoudasc@mymail.vcu.edu>
Date: 2020-11-25 14:23:29 -0500
Commit message:

 removed \dontrun
 
Package: DelayedArray
Commit: c94885374489d8386bb01e2659b981477b556a0b
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2020-11-25 11:13:21 -0800
Commit message:

 Fix small issue in dim() setter
 
Package: TFutils
Commit: efcc8a604328c0f18f52b4e3313a2da6d4be0103
Author: Vince Carey <stvjc@channing.harvard.edu>
Date: 2020-11-25 13:53:40 -0500
Commit message:

 change cre setting so vjc is maintainer
 
Package: TFutils
Commit: 33b71d64444abd671f75f44548d1a2ba24080b92
Author: Vince Carey <stvjc@channing.harvard.edu>
Date: 2020-11-25 13:52:46 -0500
Commit message:

 fix problem with importing factor from base
 
Package: scAlign
Commit: 3f7b57a01d921339dc4033e7a65bf97df2574623
Author: UCDNJJ <njjohansen@ucdavis.edu>
Date: 2020-11-25 10:46:55 -0800
Commit message:

 tf2_3
 
Package: scAlign
Commit: a41d126e1e0b6ac2c08630f0f0caf7e4289bfa44
Author: UCDNJJ <njjohansen@ucdavis.edu>
Date: 2020-11-25 10:21:23 -0800
Commit message:

 tf2_2
 
Package: GEOfastq
Commit: 4dba465a62987fe41da38ab102225514fcb9c4df
Author: Alex Pickering <alexvpickering@gmail.com>
Date: 2020-11-25 10:30:22 -0800
Commit message:

 address review comments
 
Package: casper
Commit: 5100b5b43010f16f0f78065194d8e9eeae874626
Author: davidrusi <rosselldavid@gmail.com>
Date: 2020-11-25 18:26:29 +0100
Commit message:

 Fixed version number and date
 
Package: PROPER
Commit: 8e84ead795ce189cf70903f94694e64a98d2fcbe
Author: hwu30 <hwu30@Haos-MacBook-Pro-16.local>
Date: 2020-11-25 12:19:01 -0500
Commit message:

 Remove DESeq from DE method
 
Package: scDblFinder
Commit: 27c799f91f58c42e194f7ec73f610cde8da4a18b
Author: plger <pl.germain@gmail.com>
Date: 2020-11-19 13:11:05 +0100
Commit message:

 Merge branch 'master' of github.com:plger/scDblFinder
 
Package: scDblFinder
Commit: ed19e1f6c5ac85eecbdae4e06bf84c283a828eab
Author: plger <pl.germain@gmail.com>
Date: 2020-11-19 13:10:54 +0100
Commit message:

 version bump
 
Package: scDblFinder
Commit: 3c0f9a4bb4f69dbc1a9af089282cccd825c406c6
Author: Pierre-Luc <pl.germain@gmail.com>
Date: 2020-11-19 13:10:37 +0100
Commit message:

 added temp extra install 
Package: scDblFinder
Commit: 9f8f08f64eeecfea6e4741a63cc3da83e0d59b9f
Author: plger <pl.germain@gmail.com>
Date: 2020-11-19 09:53:48 +0100
Commit message:

 added :: dependencies to suggest
 
Package: scDblFinder
Commit: 9ff13f7210d078870fb2e38883cb1a072771cab1
Author: plger <pl.germain@gmail.com>
Date: 2020-11-19 09:17:35 +0100
Commit message:

 Merge branch 'master' of github.com:plger/scDblFinder
 
Package: scDblFinder
Commit: f71970bc009367b94bdd9dcd06228bf268a29570
Author: plger <pl.germain@gmail.com>
Date: 2020-11-19 09:17:22 +0100
Commit message:

 fixed wrong container
 
Package: scDblFinder
Commit: 92f589cf1b7bc09e9978e8776531fb1ae4f6892b
Author: Pierre-Luc <pl.germain@gmail.com>
Date: 2020-11-19 09:08:07 +0100
Commit message:

 Merge pull request #29 from LTLA/master

Refer to the right internal function in tests. 
Package: scDblFinder
Commit: 5ef6ddd189fed2f50f2647996fb308e1b137b9ee
Author: plger <pl.germain@gmail.com>
Date: 2020-11-19 09:06:43 +0100
Commit message:

 updated the workflow to use image with dependencies
 
Package: scDblFinder
Commit: d48e431d80f65bc557bd3452e5b31288051c7932
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2020-11-18 20:52:36 -0800
Commit message:

 Removed unnecessary argument from docs.
 
Package: scDblFinder
Commit: 792a521346dd227c8a170ea3be48dc3862fd1eaa
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2020-11-18 20:34:33 -0800
Commit message:

 Refer to the right internal function in tests.
 
Package: scDblFinder
Commit: 4d835404749dc4329c1e78c88473210d9a3e1e71
Author: Pierre-Luc Germain <pl.germain@gmail.com>
Date: 2020-10-29 12:08:22 +0100
Commit message:

 Merge remote-tracking branch 'upstream/master'
 
Package: scDblFinder
Commit: 16d9952965c88a16083edc0610279b77e6f3dddd
Author: Pierre-Luc Germain <pl.germain@gmail.com>
Date: 2020-10-29 12:07:22 +0100
Commit message:

 version bump
 
Package: scDblFinder
Commit: 41d747da7cda98802d6813143c2dec6a279c8990
Author: Pierre-Luc Germain <pl.germain@gmail.com>
Date: 2020-10-29 11:54:59 +0100
Commit message:

 Merge branch 'master' of github.com:plger/scDblFinder
 
Package: scDblFinder
Commit: 27294cc4fde28d1ee4c809b1fbc9daade7e5e3b5
Author: Pierre-Luc Germain <pl.germain@gmail.com>
Date: 2020-10-29 11:54:45 +0100
Commit message:

 Merge branch 'RELEASE_3_12'
 
Package: scDblFinder
Commit: d710d5b7ed89e874253071b17da0e1c0f7d130d1
Author: Pierre-Luc <pl.germain@gmail.com>
Date: 2020-10-28 10:54:40 +0100
Commit message:

 Update README.md 
Package: scDblFinder
Commit: 98a344193971acc4af7e709a8f2d09648e38a134
Author: Pierre-Luc Germain <pl.germain@gmail.com>
Date: 2020-10-27 16:54:03 +0100
Commit message:

 version bump
 
Package: scDblFinder
Commit: 59152d8cdc5efca400a05756fa8eb87b4fafcc0e
Author: Pierre-Luc Germain <pl.germain@gmail.com>
Date: 2020-10-27 16:53:46 +0100
Commit message:

 updated documentation
 
Package: scDblFinder
Commit: c3f5c0244e7e7876ce8e0dbed810a781b082ad65
Author: Pierre-Luc Germain <pl.germain@gmail.com>
Date: 2020-10-27 16:53:34 +0100
Commit message:

 changed clustering to pass BNPARAM and BPPARAM
 
Package: scDblFinder
Commit: 469ed74e05eddf6421929a4aeab2e1c5d901e819
Author: Pierre-Luc Germain <pl.germain@gmail.com>
Date: 2020-10-27 16:53:01 +0100
Commit message:

 changed clustering to pass BNPARAM and BPPARAM
 
Package: vulcan
Commit: 671bcde1083a01087494d94f63d70ed7abeb0acc
Author: Federico Manuel Giorgi <federico.giorgi@unibo.it>
Date: 2020-11-25 18:17:35 +0100
Commit message:

 Updated to DESeq2
 
Package: vulcan
Commit: 26c71c124a7ce6bb47bb539cf14624114bb4141a
Author: Federico Manuel Giorgi <federico.giorgi@unibo.it>
Date: 2020-11-25 18:16:23 +0100
Commit message:

 Updated to DESeq2
 
Package: vulcan
Commit: 712b4ffa75d54fd7a26d7bd3d92ac80199b022e8
Author: Federico Manuel Giorgi <federico.giorgi@unibo.it>
Date: 2020-11-25 17:43:21 +0100
Commit message:

 Updated to DESeq2
 
Package: PROPER
Commit: 8803260229687571568174a884ba1f2d0dcb914f
Author: hwu30 <hwu30@Haos-MacBook-Pro-16.local>
Date: 2020-11-25 12:10:15 -0500
Commit message:

 Remove DESeq from DE method
 
Package: PROPER
Commit: 7f0ef08c8e6762294c1eb079b8da6bf53bba4998
Author: hwu30 <hwu30@Haos-MacBook-Pro-16.local>
Date: 2020-11-25 12:09:36 -0500
Commit message:

 Merge branch 'master' of git.bioconductor.org:packages/PROPER
 
Package: PROPER
Commit: d5124bc6c72b3f330875cdfd26158087cffacbd7
Author: hwu30 <hwu30@Haos-MacBook-Pro-16.local>
Date: 2020-11-25 12:09:12 -0500
Commit message:

 Remove DESeq from DE method
 
Package: DEsubs
Commit: 8bff392a2f0bb21e7f9f73f4915aaa901eff6d89
Author: Panos Balomenos <balomenos@upatras.gr>
Date: 2020-11-25 18:59:35 +0200
Commit message:

 Removed support for DESeq
 
Package: yaqcaffy
Commit: aba97fddaa46e24eb4c5d64157eeb15b01e59ea7
Author: Laurent Gatto <laurent.gatto@uclouvain.be>
Date: 2020-11-25 17:52:11 +0100
Commit message:

 udpate maintainer email
 
Package: PhyloProfile
Commit: 53e58de7037e212f16c6aaa42582ed6d06a8980f
Author: trvinh <trvinh@gmail.com>
Date: 2020-11-25 17:12:39 +0100
Commit message:

 Plot background for NA orthologs
 
Package: tRanslatome
Commit: 4ee27ef14687fe3fc95a891b60f3bd4dc790d28a
Author: erik.dassi@gmail.com <erikdassi@users.noreply.github.com>
Date: 2020-11-25 16:50:17 +0100
Commit message:

 change to DESeq2
 
Package: tRanslatome
Commit: e820b69c29b0a6ce33accc90684ec83222525a65
Author: erik.dassi@gmail.com <erikdassi@users.noreply.github.com>
Date: 2020-11-25 16:48:58 +0100
Commit message:

 change to DESeq2
 
Package: Spectra
Commit: d4927cc63467280596d5c8f3f70ca3aa888689c7
Author: Johannes Rainer <5506112+jorainer@users.noreply.github.com>
Date: 2020-11-25 15:58:02 +0100
Commit message:

 Merge pull request #166 from rformassspectrometry/jomain

Add support for arbitrary parameters in filterIntensity (issue #164) 
Package: Spectra
Commit: 616d6fd9052055becf92ab23fcf2b577ada62864
Author: jorainer <johannes.rainer@gmail.com>
Date: 2020-11-25 15:26:05 +0100
Commit message:

 ci: fix tar call
 
Package: Spectra
Commit: 7e6037eb9dc020a80fe580d49979f50a68455942
Author: jorainer <johannes.rainer@gmail.com>
Date: 2020-11-25 15:21:14 +0100
Commit message:

 tests: remove obsolete lines
 
Package: Spectra
Commit: 5c24ec7fe2d9950d1712660e3e2a41d1c00d906c
Author: jorainer <johannes.rainer@gmail.com>
Date: 2020-11-25 15:18:49 +0100
Commit message:

 ci: fix netcdf archive extraction
 
Package: Spectra
Commit: 55556b79860fecc9f1f8adf3bf53f46f32ebf8e2
Author: jorainer <johannes.rainer@gmail.com>
Date: 2020-11-25 14:56:20 +0100
Commit message:

 ci: fix download and install of netcdf on macos
 
Package: Spectra
Commit: 29f084be4e0d1f23ac026943ab69270b5282fe8f
Author: jorainer <johannes.rainer@gmail.com>
Date: 2020-11-25 14:42:22 +0100
Commit message:

 ci: install pre-build netcdf from mac.r-project.org
 
Package: Spectra
Commit: 2233ffd0a518ba073365b6dac8fb09b2ead2c1b4
Author: jorainer <johannes.rainer@gmail.com>
Date: 2020-11-25 13:18:07 +0100
Commit message:

 refactor: support passing arguments in filterIntensity

- Support passing of parameters to filter function in `filterIntensity` (issue
  #164).
 
Package: Spectra
Commit: c19d0527ea0317526a0d3d4592a8b8b1bd1f8786
Author: jorainer <johannes.rainer@gmail.com>
Date: 2020-11-24 20:03:59 +0100
Commit message:

 ci: disable installation of netcdf on macOS
 
Package: Spectra
Commit: c7c2f7f4e825324b9347878031cb7d7ccc9ac77b
Author: jorainer <johannes.rainer@gmail.com>
Date: 2020-11-24 19:13:29 +0100
Commit message:

 ci: add installation of netcdf on macOS
 
Package: Spectra
Commit: 24f14975ee74e19edfb9d482b8f88da15c111721
Author: Johannes Rainer <5506112+jorainer@users.noreply.github.com>
Date: 2020-11-24 18:46:12 +0100
Commit message:

 Merge pull request #165 from rformassspectrometry/jomain

Merge directly as this affects only CI 
Package: Spectra
Commit: 6494abacdd8c8e1ab3bcb9a25835c669b0cab4bf
Author: jorainer <johannes.rainer@gmail.com>
Date: 2020-11-24 17:47:03 +0100
Commit message:

 ci: force manual install of some packages
 
Package: Spectra
Commit: 5c9fa820bec583de87825ae9c02be87098e1c8fa
Author: jorainer <johannes.rainer@gmail.com>
Date: 2020-11-24 16:34:53 +0100
Commit message:

 fix: fix error message
 
Package: Spectra
Commit: cdc165af0fe293218837d89caae867d34e717065
Author: jorainer <johannes.rainer@gmail.com>
Date: 2020-11-24 16:34:10 +0100
Commit message:

 ci: force manual install of packages
 
Package: Spectra
Commit: ddc962a74e0fb5cb9decf3e093eced460fa6899d
Author: jorainer <johannes.rainer@gmail.com>
Date: 2020-11-24 16:02:52 +0100
Commit message:

 ci: disable vdiffr tests
 
Package: Spectra
Commit: 937c474267e84fae12cd526c95094a74cbaf37db
Author: jorainer <johannes.rainer@gmail.com>
Date: 2020-11-24 15:38:03 +0100
Commit message:

 ci: update/replace GH with recent biocthis
 
Package: Spectra
Commit: e9125e9bfd2e8002e34fa02c840985f23a3b29e5
Author: jorainer <johannes.rainer@gmail.com>
Date: 2020-11-20 08:48:23 +0100
Commit message:

 ci: set environment variable CI=true
 
Package: Spectra
Commit: f4786d07a712becfb7a9af5989196c188d9efa2a
Author: jorainer <johannes.rainer@gmail.com>
Date: 2020-11-20 08:10:24 +0100
Commit message:

 bump version
 
Package: TrajectoryGeometry
Commit: 706ea7c4ac1e56fd2096989a355c68de42c0489a
Author: AnnaLaddach <annaladdach@gmail.com>
Date: 2020-11-25 14:56:58 +0000
Commit message:

 traj2Data documented
 
Package: cmapR
Commit: e7d1faeddae406da6295fbbe2c21cbbf10678845
Author: Ted Natoli <ted.e.natoli@gmail.com>
Date: 2020-11-25 09:09:45 -0500
Commit message:

 resolving merge conflicts
 
Package: cmapR
Commit: 700e9419a313179ab50fcb6ad34b7c1ce12d487d
Author: Ted Natoli <ted.e.natoli@gmail.com>
Date: 2020-11-25 08:43:40 -0500
Commit message:

 Merge branch 'master' of https://github.com/cmap/cmapR
 
Package: cmapR
Commit: de3fdba439a30d13873ffac8359d3eea76ee2acc
Author: Ted Natoli <ted.e.natoli@gmail.com>
Date: 2020-11-24 17:56:41 -0500
Commit message:

 updating date
 
Package: cmapR
Commit: 379f2483f962c56fc9e17231d4ab3029ee699fe5
Author: Ted Natoli <ted.e.natoli@gmail.com>
Date: 2020-11-24 10:25:20 -0500
Commit message:

 Merge pull request #61 from nuno-agostinho/patch-1

Fix tutorial's installation instructions 
Package: cmapR
Commit: 3192d341da9e6fce5237cb40056e42c6780b39f7
Author: Ted Natoli <ted.e.natoli@gmail.com>
Date: 2020-11-24 10:25:08 -0500
Commit message:

 Merge branch 'master' into patch-1 
Package: cmapR
Commit: 82aa4c861228b06ba0c66b8006768558d94997a5
Author: Ted Natoli <ted.e.natoli@gmail.com>
Date: 2020-11-23 11:58:22 -0500
Commit message:

 removing dependency on prada and replacing with flowCore
 
Package: cmapR
Commit: 68bf698869d9dcda9d772399cf5ac87e773f1890
Author: Ted Natoli <ted.e.natoli@gmail.com>
Date: 2020-11-23 11:52:27 -0500
Commit message:

 Update tutorial.Rmd
 
Package: cmapR
Commit: 5a724269adb8d19ffc8842d27cfb07d08200ee1b
Author: Ted Natoli <ted.e.natoli@gmail.com>
Date: 2020-11-23 11:52:22 -0500
Commit message:

 updating docs
 
Package: cmapR
Commit: bf8607969725fe66f5b34df8c4f5296c28268017
Author: Nuno Agostinho <nunodanielagostinho@gmail.com>
Date: 2020-08-14 01:15:05 +0100
Commit message:

 Fix tutorial's installation instructions 
Package: cmapR
Commit: b804d22b701021487591f810045869b98477e089
Author: Ted Natoli <ted.e.natoli@gmail.com>
Date: 2020-07-08 14:13:11 -0400
Commit message:

 Delete cmapR_tutorial.ipynb

superseded by vignette 
Package: cmapR
Commit: 44b25832fb2558a511959952e46d9ba8394add3b
Author: Ted Natoli <ted.e.natoli@gmail.com>
Date: 2020-05-08 10:29:06 -0400
Commit message:

 Update README.md

update after acceptance into Bioconductor 
Package: cmapR
Commit: 93714b7f11ca4adbfb98554084d4c2951ef284a7
Author: Ted Natoli <ted.e.natoli@gmail.com>
Date: 2020-04-22 09:25:43 -0400
Commit message:

 fixing bug in writing GCT version 1.2

closes issue #55
 
Package: cmapR
Commit: d9671a44189dd1756f97b97fa1b9b50696eab94c
Author: Ted Natoli <ted.e.natoli@gmail.com>
Date: 2020-04-01 13:44:44 -0400
Commit message:

 Update DESCRIPTION
 
Package: cmapR
Commit: 28cc36b4aa7c811277fecec97fc81773ba3b4e30
Author: Ted Natoli <ted.e.natoli@gmail.com>
Date: 2020-04-01 12:57:54 -0400
Commit message:

 Merge pull request #54 from cmap/bioc

Update utils.R 
Package: cmapR
Commit: 19025916962dbea019480240bd0c87d7825dd706
Author: Ted Natoli <ted.e.natoli@gmail.com>
Date: 2020-03-26 15:07:53 -0400
Commit message:

 Update utils.R
 
Package: metaseqR2
Commit: aad1316f438572c1ba91826a0733fbddd88d3008
Author: Panagiotis Moulos <moulos@fleming.gr>
Date: 2020-11-25 16:10:07 +0200
Commit message:

 Removed DESeq namespace from scvBiasCorrectionFits.rda
 
Package: glmGamPoi
Commit: 89aac9d45befbacbd9f97225277e634ba3c5bd22
Author: const-ae <artjom31415@googlemail.com>
Date: 2020-11-25 14:52:03 +0100
Commit message:

 Bump version and update NEWS
 
Package: glmGamPoi
Commit: d6aeb2753cd5155fc6967b2abe4e046262a6bc0d
Author: const-ae <artjom31415@googlemail.com>
Date: 2020-11-25 14:50:35 +0100
Commit message:

 Update man page for loc_median_fit
 
Package: glmGamPoi
Commit: 0deacb3e00310c3956780264d33b0dbf8e2084b2
Author: const-ae <artjom31415@googlemail.com>
Date: 2020-11-25 14:50:21 +0100
Commit message:

 Return offset_matrix from glm_gp
 
Package: glmGamPoi
Commit: 14c7c450d52be25da877d34284a70ed2f71ed1b5
Author: const-ae <artjom31415@googlemail.com>
Date: 2020-11-25 14:44:22 +0100
Commit message:

 Handle HDF5Matrix offset
 
Package: ceRNAnetsim
Commit: 8f35b59d784b862896b322e19311f5c793d6e9dd
Author: selcenari <selcenarii@gmail.com>
Date: 2020-11-25 14:45:54 +0300
Commit message:

 solving conflict

Merge remote-tracking branch 'upstream/RELEASE_3_12'

# Conflicts:
#	R/vis_graph.R
 
Package: ceRNAnetsim
Commit: 9a345a814367a0a6e30dc3bf11a71a89014cfe60
Author: selcenari <selcenarii@gmail.com>
Date: 2020-11-25 14:25:09 +0300
Commit message:

 Update version bump
 
Package: ceRNAnetsim
Commit: a067406550917891925d9b70a26cfc0216e7e7bf
Author: selcenari <selcenarii@gmail.com>
Date: 2020-11-25 14:21:30 +0300
Commit message:

 fixed bug
 
Package: scAlign
Commit: ab840d5c6ad83d32c0794522f6ec283344385299
Author: UCDNJJ <njjohansen@ucdavis.edu>
Date: 2020-11-25 03:11:08 -0800
Commit message:

 tf2
 
Package: ceRNAnetsim
Commit: 5678cd8ca3e9323a9f0354aa72d8d91cdecb7efe
Author: selcenari <selcenarii@gmail.com>
Date: 2020-11-25 12:47:54 +0300
Commit message:

 merging bioconductor upstream
 
Package: ceRNAnetsim
Commit: 03c1def76ac6eed76992c78ffde5c47b8efd130f
Author: selcenari <32389240+selcenari@users.noreply.github.com>
Date: 2020-11-24 18:40:21 +0300
Commit message:

 solved typing problems 
Package: ceRNAnetsim
Commit: 3a4f8d15cf9b9c6d0649e15ddf8fcb8061b9555c
Author: selcenari <32389240+selcenari@users.noreply.github.com>
Date: 2020-11-24 18:39:46 +0300
Commit message:

 typing fixed 
Package: ceRNAnetsim
Commit: ea89928a4ad047082b3270ab6b578af8f9b41245
Author: selcenari <32389240+selcenari@users.noreply.github.com>
Date: 2020-11-24 18:38:30 +0300
Commit message:

 bioconductor version update 
Package: ceRNAnetsim
Commit: 1a152c83f387292e44a4feb11b5fb3f6f186a7e4
Author: selcenari <32389240+selcenari@users.noreply.github.com>
Date: 2020-11-23 21:42:50 +0300
Commit message:

 layout problem solving 
Package: ceRNAnetsim
Commit: a84fa67cb0407c09666da1780fa082e6a8358c5f
Author: selcenari <32389240+selcenari@users.noreply.github.com>
Date: 2020-11-23 12:19:20 +0300
Commit message:

 Update .travis.yml 
Package: ceRNAnetsim
Commit: aec1a9937803fa1d73bdf2f00cb4610b836635da
Author: selcenari <32389240+selcenari@users.noreply.github.com>
Date: 2020-11-23 11:50:26 +0300
Commit message:

 Update .travis.yml 
Package: ceRNAnetsim
Commit: 9b7dbb33dc561420112ed1d36d6c7a7b33ad0dac
Author: selcenari <32389240+selcenari@users.noreply.github.com>
Date: 2020-11-22 21:11:30 +0300
Commit message:

 test for solving ggraph error 
Package: ceRNAnetsim
Commit: 03831705ab3ceb0a7677f9cf36b6328935a1b52a
Author: selcenari <32389240+selcenari@users.noreply.github.com>
Date: 2020-11-19 14:58:01 +0300
Commit message:

 solved wrong typing 
Package: ceRNAnetsim
Commit: fe8237b9946613493a831e86b1862fb65dffdd26
Author: selcenari <32389240+selcenari@users.noreply.github.com>
Date: 2020-11-19 14:03:39 +0300
Commit message:

 graph is layout now!!??  thomasp85/ggraph#208 
Package: ceRNAnetsim
Commit: 7f7b39f5eda115a16d601375f34ed2eb50a74357
Author: selcenari <32389240+selcenari@users.noreply.github.com>
Date: 2019-11-28 22:35:55 +0300
Commit message:

 solution forgetten pipe 
Package: ceRNAnetsim
Commit: 1c4bfa8db5e71ae957c4a0ed610f94be1377f36f
Author: selcenari <32389240+selcenari@users.noreply.github.com>
Date: 2019-11-28 22:28:20 +0300
Commit message:

 fixed bug because of removing all nodes 
Package: EnMCB
Commit: 6433a883fc8d7a52c16991d7560027b23c735db3
Author: 于昕 MacBook pro <yuxin@yuxindeMacBook-Pro.local>
Date: 2020-11-25 16:43:00 +0800
Commit message:

 ensemble bug fix
 
Package: MOFA2
Commit: baef973a129f9ad59a43250bb0c73eeb5413062c
Author: bv2 <britta.velten@gmail.com>
Date: 2020-11-25 08:35:06 +0100
Commit message:

 updated NEWS
 
Package: MOFA2
Commit: 8e08ee51bd926afc283e41a283ef396852a3cf30
Author: Ricard Argelaguet <ricard.argelaguet@gmail.com>
Date: 2020-11-24 17:59:39 +0100
Commit message:

 Merge pull request #58 from bioFAM/main-dev

Bring the latest fixes to the base branch 
Package: MOFA2
Commit: 22b839510f335db91e00de07d5eab1762314855b
Author: Ricard Argelaguet <ricard.argelaguet@gmail.com>
Date: 2020-11-24 17:59:24 +0100
Commit message:

 Merge pull request #55 from bioFAM/mefisto

Mefisto 
Package: MOFA2
Commit: 998b497c7ea782208317be200dbca0ec29debbdf
Author: Danila Bredikhin <danila.bredikhin@embl.de>
Date: 2020-11-24 16:54:38 +0100
Commit message:

 Merge branch 'master' into main-dev
 
Package: MOFA2
Commit: 49abe6ee6f4e971678d24fd9d3982d266e5b51df
Author: Danila Bredikhin <danila.bredikhin@embl.de>
Date: 2020-11-24 13:53:14 +0100
Commit message:

 Add basilisk dependency to the Dockerfile
 
Package: MOFA2
Commit: 946836f15fac9c2da44545e1bb5e24fcf26bcbc2
Author: bv2 <britta.velten@gmail.com>
Date: 2020-11-24 10:17:20 +0100
Commit message:

 Merge branch 'master' into mefisto
 
Package: MOFA2
Commit: fd5895cd5b6e78a2156cf81d06e5a40fbec1eef4
Author: bv2 <britta.velten@gmail.com>
Date: 2020-11-16 13:32:27 +0100
Commit message:

 updated doc to clarify MEFISTO usage
 
Package: MOFA2
Commit: 1aeebfc0bc7adecfbc380f9bc8e3997d402a491d
Author: bv2 <britta.velten@gmail.com>
Date: 2020-11-16 09:55:12 +0100
Commit message:

 added dtw dependency for basilisk
 
Package: MOFA2
Commit: a1bb4d7f6c0e26f8ab883b961f9df3a48b180600
Author: rargelaguet <ricard.argelaguet@gmail.com>
Date: 2020-11-16 09:53:11 +0100
Commit message:

 minor update in plot_factors
 
Package: MOFA2
Commit: 3d191a10a244934cf69c521f56472fd06d1f9348
Author: bv2 <britta.velten@gmail.com>
Date: 2020-11-16 09:50:15 +0100
Commit message:

 added missing requirments for mefisto
 
Package: MOFA2
Commit: 797e7bccb2ffc0de7554df9c3735a70633c003b6
Author: bv2 <britta.velten@gmail.com>
Date: 2020-11-13 11:41:29 +0100
Commit message:

 minor change for spatial factor plot
 
Package: MOFA2
Commit: 246ff8823b1eacf2ae469af56f3281a8a6abb1f0
Author: Danila Bredikhin <danila.bredikhin@embl.de>
Date: 2020-11-11 20:18:05 +0100
Commit message:

 Add some basic tests for the Python interface
 
Package: MOFA2
Commit: 0e7608c26130ad6dea1b38597dc9549e9624fac0
Author: Danila Bredikhin <danila.bredikhin@embl.de>
Date: 2020-11-11 20:14:52 +0100
Commit message:

 Fix AnnData interface for multi-group MOFA
 
Package: MOFA2
Commit: e65202daaf13b1615eb78f0e209683bb21024581
Author: bv2 <britta.velten@gmail.com>
Date: 2020-11-11 09:26:08 +0100
Commit message:

 minor change
 
Package: MOFA2
Commit: 17bac9767f8729840d9d9939d6614940d83c5918
Author: bv2 <britta.velten@gmail.com>
Date: 2020-11-11 08:13:04 +0100
Commit message:

 moved dtw import to respective function
 
Package: MOFA2
Commit: f84fb5d236ca054459e68276a019f858a0dc971b
Author: bv2 <britta.velten@gmail.com>
Date: 2020-11-10 16:53:04 +0100
Commit message:

 disabled warning on N per group for MEFISTO
 
Package: MOFA2
Commit: 4cebc602a320f8db12148d6badbb2298eeb6502b
Author: bv2 <britta.velten@gmail.com>
Date: 2020-11-10 13:51:01 +0100
Commit message:

 enable passing covariates as string
 
Package: MOFA2
Commit: c62766f5768bc22607bc49580b2d26eacad99cf7
Author: bv2 <britta.velten@gmail.com>
Date: 2020-11-09 13:57:23 +0100
Commit message:

 minor fix in interpolation and added more examples
 
Package: MOFA2
Commit: fc62a9f3964b2e5d6541f7aabff4dcf17c834aa6
Author: bv2 <britta.velten@gmail.com>
Date: 2020-11-09 13:57:02 +0100
Commit message:

 merged master into mefisto
 
Package: MOFA2
Commit: a69ce3b246abec669c3eec2cecac96346e818ac8
Author: bv2 <britta.velten@gmail.com>
Date: 2020-11-09 12:32:59 +0100
Commit message:

 changed n_inducing option to frac_inducing
 
Package: MOFA2
Commit: 9ebddf372d561d5c79e1ac6f29d06e27c88e7786
Author: bv2 <britta.velten@gmail.com>
Date: 2020-11-09 10:28:21 +0100
Commit message:

 added warning on sparseGP
 
Package: MOFA2
Commit: 106764c68ad461d6d555f871979236df07153da1
Author: bv2 <britta.velten@gmail.com>
Date: 2020-11-09 10:24:11 +0100
Commit message:

 disabled warning of N per group for MEFISTO and minor changes
 
Package: MOFA2
Commit: e7dbacfe5269135b4d7ad35b5dcda139e9ad6af6
Author: Danila Bredikhin <danila.bredikhin@embl.de>
Date: 2020-11-04 03:20:49 +0100
Commit message:

 Fix Saving metadata with Unicode characters
 
Package: MOFA2
Commit: 87c882218d195a142f5caa1012ddc2dcf57f8266
Author: Danila Bredikhin <danila.bredikhin@embl.de>
Date: 2020-11-04 03:20:21 +0100
Commit message:

 Merge branch 'master' into main-dev
 
Package: MOFA2
Commit: 2583551e49aa8aca559152ff74202640533b6fdf
Author: rargelaguet <ricard.argelaguet@gmail.com>
Date: 2020-11-03 12:01:22 +0100
Commit message:

 fix order of groups in plot_data_overview
 
Package: MOFA2
Commit: 9ee70e08d4258c6c0280a61e6db16b52a9a48212
Author: bv2 <britta.velten@gmail.com>
Date: 2020-10-29 13:43:38 +0100
Commit message:

 minor changes
 
Package: MOFA2
Commit: 2a75af8da2887c2574b482e94910e9e4e9a194b9
Author: bv2 <britta.velten@gmail.com>
Date: 2020-10-28 16:56:13 +0100
Commit message:

 minor changes
 
Package: MOFA2
Commit: 919ed739f30d48a7170024ff6392d5ee4e6b674f
Author: bv2 <britta.velten@gmail.com>
Date: 2020-10-28 11:31:54 +0100
Commit message:

 minor fix
 
Package: MOFA2
Commit: e5a19168e8df3c72afea471d72c949764369e9d0
Author: bv2 <britta.velten@gmail.com>
Date: 2020-10-23 13:35:15 +0200
Commit message:

 disable model_groups for G=1
 
Package: MOFA2
Commit: 6b643219fd2d7ecf0f896cadd268bd96fe5c2235
Author: bv2 <britta.velten@gmail.com>
Date: 2020-10-23 13:34:33 +0200
Commit message:

 minor changes
 
Package: MOFA2
Commit: 176e791f4ec8c82dece20fd91b6675fbf3ec5ab0
Author: bv2 <britta.velten@gmail.com>
Date: 2020-10-23 11:07:14 +0200
Commit message:

 added interpolation option to smooth_opts
 
Package: MOFA2
Commit: fa9ff38b2bf03a305e177a8f1be052fa4653d733
Author: bv2 <britta.velten@gmail.com>
Date: 2020-10-22 17:51:44 +0200
Commit message:

 nicer plots and better documentation
 
Package: MOFA2
Commit: 2f7f774ed9ba07d7bf561088525f77921bdc1945
Author: bv2 <britta.velten@gmail.com>
Date: 2020-10-22 17:44:40 +0200
Commit message:

 nicer plots and better documentation
 
Package: MOFA2
Commit: d2184dd383514e197c735953f5af99493d4e0b80
Author: bv2 <britta.velten@gmail.com>
Date: 2020-10-21 16:12:38 +0200
Commit message:

 added interpolation to vignette
 
Package: MOFA2
Commit: a6ed7a1c871a773532e22905b08823afe22e79b5
Author: bv2 <britta.velten@gmail.com>
Date: 2020-10-21 15:59:14 +0200
Commit message:

 fixed minor bug
 
Package: MOFA2
Commit: f8c70a87965fff9a8ee3003a6b7f245857a65fba
Author: bv2 <britta.velten@gmail.com>
Date: 2020-10-21 15:45:44 +0200
Commit message:

 implemented interpolation in R
 
Package: MOFA2
Commit: 542936a9777a2181d47eec7bba6880e8813cf2ca
Author: bv2 <britta.velten@gmail.com>
Date: 2020-10-21 07:55:04 +0200
Commit message:

 added test model
 
Package: MOFA2
Commit: 665d126862a7c3118cba4a58fff469119421abd3
Author: bv2 <britta.velten@gmail.com>
Date: 2020-10-20 17:18:47 +0200
Commit message:

 updated documentation
 
Package: MOFA2
Commit: 9f91229d1c380a29911c44234c74af73b1be934e
Author: bv2 <britta.velten@gmail.com>
Date: 2020-10-20 17:13:08 +0200
Commit message:

 drafted experimental interpolation functions in R
 
Package: MOFA2
Commit: 8fe4d75621ccf5c86f234e1f0c323a927cc71506
Author: bv2 <britta.velten@gmail.com>
Date: 2020-10-20 15:57:06 +0200
Commit message:

 added some more documentation and examples to mefisto parts
 
Package: MOFA2
Commit: 3e2515f7dba02a08b44eb07bae95b169a3284bcc
Author: bv2 <britta.velten@gmail.com>
Date: 2020-10-20 15:23:19 +0200
Commit message:

 minor changes
 
Package: MOFA2
Commit: 0ed4b89c5bb11d223584459abc30ce6ec91caafd
Author: bv2 <britta.velten@gmail.com>
Date: 2020-10-20 14:29:51 +0200
Commit message:

 minor changes
 
Package: MOFA2
Commit: edaea1ed46c038690b9f7cce6189fd6f31f2b8be
Author: bv2 <britta.velten@gmail.com>
Date: 2020-10-20 13:09:17 +0200
Commit message:

 fixed minor bug
 
Package: MOFA2
Commit: b2ef021f2d0d6f2404643753c2cb7e2d9b4b3576
Author: bv2 <britta.velten@gmail.com>
Date: 2020-10-20 11:52:05 +0200
Commit message:

 less stringent warnings
 
Package: MOFA2
Commit: f2e6c79c0145028f39b5a72a2357fae1988bffe9
Author: bv2 <britta.velten@gmail.com>
Date: 2020-10-20 11:51:33 +0200
Commit message:

 added warping option to plot_factors_vs_cov
 
Package: MOFA2
Commit: 5bc843b0e1cefba16cf9203272a05fbdc8c9f48f
Author: bv2 <britta.velten@gmail.com>
Date: 2020-10-20 11:21:27 +0200
Commit message:

 fixed minor bug
 
Package: MOFA2
Commit: ca772093f9136ce4a589790ddaa1deaa8fd29a1b
Author: bv2 <britta.velten@gmail.com>
Date: 2020-10-20 11:15:56 +0200
Commit message:

 enable covariate passing as dataframe in create_mofa, debugged set_covariates
 
Package: MOFA2
Commit: 8b72d5b2b54c1ae79fe92a4cceac811d81d2c9b5
Author: bv2 <britta.velten@gmail.com>
Date: 2020-10-20 10:25:54 +0200
Commit message:

 fixed plotting factors vs cov (2d) and updated simulation vignettes
 
Package: MOFA2
Commit: e990058c3875e00159e3ca488d2ef215d44b422b
Author: bv2 <britta.velten@gmail.com>
Date: 2020-10-20 09:29:12 +0200
Commit message:

 fixed plot_factors_vs_covariate
 
Package: MOFA2
Commit: f2eb120e611097844a75fc9444411be122453fcb
Author: bv2 <britta.velten@gmail.com>
Date: 2020-10-20 09:10:54 +0200
Commit message:

 removed images
 
Package: MOFA2
Commit: b6ce143def88c9f662dfeec5f35458b83ebbe969
Author: bv2 <britta.velten@gmail.com>
Date: 2020-10-20 09:04:58 +0200
Commit message:

 moved vignettes and removed empty MOFA2 R folder
 
Package: MOFA2
Commit: 0884993c25145dd5fe6864240fdc0dd6e3a61ea6
Author: bv2 <britta.velten@gmail.com>
Date: 2020-10-20 08:48:35 +0200
Commit message:

 Merge branch 'master' into mefisto
 
Package: MOFA2
Commit: 764c80fb6a5a3623f11e3496ef832c7ca78f7fac
Author: bv2 <britta.velten@gmail.com>
Date: 2020-10-16 11:00:17 +0200
Commit message:

 fixed minor bud in set_covariates
 
Package: MOFA2
Commit: 234cd69cc8a0efb3e838a5d01bcae7d6916beca7
Author: bv2 <britta.velten@gmail.com>
Date: 2020-10-16 10:16:58 +0200
Commit message:

 fixed bug introduces in restructuring
 
Package: MOFA2
Commit: 44caac995599cd4b4b501e91d7207585026d85b8
Author: Danila Bredikhin <danila.bredikhin@embl.de>
Date: 2020-10-14 15:48:09 +0200
Commit message:

 Add textshaping package dependencies to the Dockerfile
 
Package: MOFA2
Commit: f353ab4a004a31d93b812c5db77a80ab68d1b232
Author: bv2 <britta.velten@gmail.com>
Date: 2020-10-14 14:35:45 +0200
Commit message:

 enable multi-group sparse inference
 
Package: MOFA2
Commit: 27d37f48366aa1fd9bafe418b707f1ac75b769f1
Author: bv2 <britta.velten@gmail.com>
Date: 2020-10-14 14:34:47 +0200
Commit message:

 adapted simulation setup for sharedness
 
Package: MOFA2
Commit: c753b59ea2cf57d5473f32fcadbc06b7f7ef95e1
Author: bv2 <britta.velten@gmail.com>
Date: 2020-10-13 15:02:59 +0200
Commit message:

 fixed bug
 
Package: MOFA2
Commit: 611c3422d443dc4d4da6628f1649545b947ac76b
Author: bv2 <britta.velten@gmail.com>
Date: 2020-10-13 14:14:06 +0200
Commit message:

 fixed saving for normal (non-smooth) MOFA models
 
Package: MOFA2
Commit: 87a7a76eb44b31015dcfdb05b21fdd8759576d8c
Author: bv2 <britta.velten@gmail.com>
Date: 2020-10-13 11:05:20 +0200
Commit message:

 added missing groups argument
 
Package: MOFA2
Commit: 789400f0194e554310c6ca7fbd02d6a39ec26db3
Author: bv2 <britta.velten@gmail.com>
Date: 2020-10-13 11:03:09 +0200
Commit message:

 added missing group argument
 
Package: MOFA2
Commit: 9a9ffad7cde1669de555c5d3600febbdc10bd42a
Author: bv2 <britta.velten@gmail.com>
Date: 2020-10-13 10:58:07 +0200
Commit message:

 merging
 
Package: MOFA2
Commit: 4986794e5eead07a3b9ef2de64a22af5e0de8517
Author: rargelaguet <ricard.argelaguet@gmail.com>
Date: 2020-10-12 10:15:44 +0200
Commit message:

 reformat plot_factor_vs_cov
 
Package: MOFA2
Commit: 36a32594edf98642ca10980e0956dd57cce23fb8
Author: rargelaguet <ricard.argelaguet@gmail.com>
Date: 2020-10-11 20:53:48 +0200
Commit message:

 remove lineplot
 
Package: MOFA2
Commit: 533a847746ad151572763803cb5fad6f4d45038c
Author: rargelaguet <ricard.argelaguet@gmail.com>
Date: 2020-10-11 20:41:21 +0200
Commit message:

 add groups attribute to Y nodes. Also reformat groups option in init_model
 
Package: MOFA2
Commit: 29d6f6bf2d5e1ada8472e9fefd62b757fe4520ac
Author: rargelaguet <ricard.argelaguet@gmail.com>
Date: 2020-10-11 19:06:45 +0200
Commit message:

 update R packages. Move all covariates functions to mefisto.R
 
Package: MOFA2
Commit: fac8add57d9f41048e27cd07305b24a2afaacd69
Author: rargelaguet <ricard.argelaguet@gmail.com>
Date: 2020-10-09 15:47:12 +0200
Commit message:

 remove covariates from create_mofa
 
Package: MOFA2
Commit: b026f11d9185db88469f3ca6f1fd974a1149357a
Author: rargelaguet <ricard.argelaguet@gmail.com>
Date: 2020-10-09 15:44:16 +0200
Commit message:

 Merge branch 'code_reformat' of https://github.com/bv2/MOFA2 into code_reformat
 
Package: MOFA2
Commit: ecdff2e9637f2b5354a1fcedbf6baddd16737f9c
Author: rargelaguet <ricard.argelaguet@gmail.com>
Date: 2020-10-09 15:44:13 +0200
Commit message:

 modifying entry_point.py
 
Package: MOFA2
Commit: 229591d19e2f7df41592d53da62aac6264fcdacc
Author: bv2 <britta.velten@gmail.com>
Date: 2020-10-09 15:32:55 +0200
Commit message:

 adapted vignettes to new covariate passing
 
Package: MOFA2
Commit: 027bca5260dfbb22868029d7dbd7cbc8a7c80178
Author: bv2 <britta.velten@gmail.com>
Date: 2020-10-09 15:18:56 +0200
Commit message:

 added documentation to set_covariates and exporting
 
Package: MOFA2
Commit: 872d1d1f64ec8b3e8538ec43bffcc3f3e54a1a9a
Author: bv2 <britta.velten@gmail.com>
Date: 2020-10-09 14:35:31 +0200
Commit message:

 added doc to smooth options and nicer warning for sparse + align
 
Package: MOFA2
Commit: d91fe21934fdd704dac85c3be42bc0f357825270
Author: rargelaguet <ricard.argelaguet@gmail.com>
Date: 2020-10-09 14:00:25 +0200
Commit message:

 fix errors when saving and loading the model
 
Package: MOFA2
Commit: 581322bd1dd19e1b64fde0284a076237e98e5c47
Author: rargelaguet <ricard.argelaguet@gmail.com>
Date: 2020-10-09 12:47:53 +0200
Commit message:

 Merge branch 'SMOFA' into code_reformat
 
Package: MOFA2
Commit: 7d4f7b1e4b71785e4c367de31247732334fdd14b
Author: rargelaguet <ricard.argelaguet@gmail.com>
Date: 2020-10-09 12:45:33 +0200
Commit message:

 fix conflicts entry_point
 
Package: MOFA2
Commit: baaf87049b7c8ca3df7bdd6af632596ffe968c69
Author: rargelaguet <ricard.argelaguet@gmail.com>
Date: 2020-10-09 12:43:27 +0200
Commit message:

 both R and Python are now functional, berfore merging with SMOFA branch
 
Package: MOFA2
Commit: 6c4d99138ccd3b099f9459199119aca39da4b1f1
Author: bv2 <britta.velten@gmail.com>
Date: 2020-10-09 10:14:31 +0200
Commit message:

 fixed noise level in simulations
 
Package: MOFA2
Commit: 41c04296fcf0f900161dd00c84245f7a3d39e910
Author: bv2 <britta.velten@gmail.com>
Date: 2020-10-08 08:53:13 +0200
Commit message:

 minor fix
 
Package: MOFA2
Commit: e09d9b7dfebce7c266e0f2c0b2c8668ff1f6fade
Author: bv2 <britta.velten@gmail.com>
Date: 2020-10-07 15:50:29 +0200
Commit message:

 added some documentation and move inducing point selection to gp_utils
 
Package: MOFA2
Commit: 9c920eb064fd68156ef2e45324fcc801ce6fe198
Author: bv2 <britta.velten@gmail.com>
Date: 2020-10-07 13:30:21 +0200
Commit message:

 added plotting functions for GP hyperparameters and minor fix
 
Package: MOFA2
Commit: 6d43a26489d576cd9ce06cc08713b8aeb04bafd3
Author: rargelaguet <ricard.argelaguet@gmail.com>
Date: 2020-10-07 12:34:07 +0200
Commit message:

 remove Y_ELBO_TauTrick in entry_point
 
Package: MOFA2
Commit: f3137372b11d63fac2f3b2964bae14d34b66948b
Author: bv2 <britta.velten@gmail.com>
Date: 2020-10-06 14:50:57 +0200
Commit message:

 removed torch dependencies
 
Package: MOFA2
Commit: ea0b260262755a1e109471c0aad9d554f375ca4e
Author: bv2 <britta.velten@gmail.com>
Date: 2020-10-06 14:45:32 +0200
Commit message:

 removed sigma_const option, enabled no model_groups and warping, fixed dimension of Sigma terms in sparse node
 
Package: MOFA2
Commit: 14005779ca9e47a36522597a0b4a68fd41ae5c71
Author: rargelaguet <ricard.argelaguet@gmail.com>
Date: 2020-10-06 13:32:19 +0200
Commit message:

 modularise Sigma code
 
Package: MOFA2
Commit: f40acc690a40fbb5a866c3baa0914292c95dba7f
Author: bv2 <britta.velten@gmail.com>
Date: 2020-10-05 18:26:47 +0200
Commit message:

 fixed minor bugs
 
Package: MOFA2
Commit: 226984309ddcfdddb271cd08b7cd86dfe384f4d7
Author: bv2 <britta.velten@gmail.com>
Date: 2020-10-05 18:19:57 +0200
Commit message:

 introduce bas class for Sigma to avoid reinits of Kc
 
Package: MOFA2
Commit: f450e8c7d2e63e03393661e941e8131f3a75a296
Author: bv2 <britta.velten@gmail.com>
Date: 2020-10-05 18:15:21 +0200
Commit message:

 modularized Sigma node
 
Package: MOFA2
Commit: d83a469caf46fa8bf54a0b40313386034c5f6a75
Author: bv2 <britta.velten@gmail.com>
Date: 2020-10-05 16:38:00 +0200
Commit message:

 Merge branch 'SMOFA' into code_reformat
 
Package: MOFA2
Commit: c707e4a48edb7d00318d76150d6691310f288d25
Author: bv2 <britta.velten@gmail.com>
Date: 2020-10-05 16:15:22 +0200
Commit message:

 refactored gradient calc
 
Package: MOFA2
Commit: 9a0ae07276dd4755b14739f4ab1bfe4de57ff150
Author: rargelaguet <ricard.argelaguet@gmail.com>
Date: 2020-10-05 15:53:52 +0200
Commit message:

 remove univariate smooth factor options
 
Package: MOFA2
Commit: 56159e5c95c71ed4ce952fcd20ae9257c38d82d1
Author: rargelaguet <ricard.argelaguet@gmail.com>
Date: 2020-10-05 15:37:32 +0200
Commit message:

 merge with master, R code
 
Package: MOFA2
Commit: d6e2f38897b9dc0d568095fb1cf3671e9bdbab79
Author: rargelaguet <ricard.argelaguet@gmail.com>
Date: 2020-10-05 15:35:23 +0200
Commit message:

 merge with master and reformat python code
 
Package: MOFA2
Commit: 4740d8ae792d151cf7e6f05678c7f632760f07ed
Author: bv2 <britta.velten@gmail.com>
Date: 2020-10-02 17:12:10 +0200
Commit message:

 fixed bug in gradient calc with kronecker
 
Package: MOFA2
Commit: 610e478119faffd84321205626b1d36165c69c4c
Author: bv2 <britta.velten@gmail.com>
Date: 2020-10-02 15:51:10 +0200
Commit message:

 Merge branch 'SMOFA' into dev_speedups
 
Package: MOFA2
Commit: 6df7f90f8f3da5e192112befeecbe60122ca6753
Author: bv2 <britta.velten@gmail.com>
Date: 2020-10-02 15:51:05 +0200
Commit message:

 minor change in checks
 
Package: MOFA2
Commit: 12592661d3e42dfcbacb1de2cc521132e9eb5420
Author: bv2 <britta.velten@gmail.com>
Date: 2020-10-02 11:57:18 +0200
Commit message:

 added html vignettes for temp. and spatial data
 
Package: MOFA2
Commit: 1178d75280a2d256fcfa13199a5b6eb856450e24
Author: bv2 <britta.velten@gmail.com>
Date: 2020-10-02 11:56:55 +0200
Commit message:

 cleaned SMOFA stuff and updated vignettes for temp. and spatial data
 
Package: MOFA2
Commit: 6df11baa2619114cf2eb50a7eb2bf70a0489352b
Author: bv2 <britta.velten@gmail.com>
Date: 2020-10-02 11:27:17 +0200
Commit message:

 removed unused training option and nodes
 
Package: MOFA2
Commit: a31a8037b017ca47cb2bc4d70a942070f53db086
Author: bv2 <britta.velten@gmail.com>
Date: 2020-10-02 11:22:56 +0200
Commit message:

 removed unused training option
 
Package: MOFA2
Commit: e5291eaa72d5a22bc1bd51c77fc6088675dbda83
Author: bv2 <britta.velten@gmail.com>
Date: 2020-10-02 08:35:48 +0200
Commit message:

 minor fix and restructuring
 
Package: MOFA2
Commit: 0534330273cdaaa2fea2e0213bbc2ab6aebe8bf5
Author: bv2 <britta.velten@gmail.com>
Date: 2020-09-30 14:54:28 +0200
Commit message:

 adapted gradients for sparse GPs
 
Package: MOFA2
Commit: 7732afae9633a775d0cd3237f5d942827e612d96
Author: bv2 <britta.velten@gmail.com>
Date: 2020-09-30 14:36:40 +0200
Commit message:

 fixed bugs in gradients (sign, unscaled G)
 
Package: MOFA2
Commit: 49b1989da4fdf7d92dbed1be18ea99c5e9644956
Author: bv2 <britta.velten@gmail.com>
Date: 2020-09-30 14:22:16 +0200
Commit message:

 cleaned graident functions, disabled gpytorch node
 
Package: MOFA2
Commit: 990d7f0bc1aea39655ca2c5a5094768e153e150d
Author: bv2 <britta.velten@gmail.com>
Date: 2020-09-30 12:37:34 +0200
Commit message:

 corrected gradients
 
Package: MOFA2
Commit: 7d91d708da5d3780350f2400155cea5e877c4b82
Author: bv2 <britta.velten@gmail.com>
Date: 2020-09-30 09:38:23 +0200
Commit message:

 added parameter constraints
 
Package: MOFA2
Commit: 1b8b83093cfdbcef1e17b31cc272a6e8992f7b31
Author: bv2 <britta.velten@gmail.com>
Date: 2020-09-30 09:07:01 +0200
Commit message:

 fidex minor bugs
 
Package: MOFA2
Commit: a07df10d7fd2531b9f53ff09bd8881bf8b5cf0f4
Author: bv2 <britta.velten@gmail.com>
Date: 2020-09-29 16:57:27 +0200
Commit message:

 fixed parameter type (list -> array) and zeta to 1-zeta
 
Package: MOFA2
Commit: 1ac090b3dd14dea78fd678cf6708b79a6645f005
Author: bv2 <britta.velten@gmail.com>
Date: 2020-09-29 14:26:17 +0200
Commit message:

 added standard MultiTaskModel as alternative
 
Package: MOFA2
Commit: 0eab9b783cee960048d0a745263099beb7af831c
Author: bv2 <britta.velten@gmail.com>
Date: 2020-09-29 13:39:30 +0200
Commit message:

 added draft of gpytorch equivalent
 
Package: MOFA2
Commit: bf50330c13e7e69701b60199c6794c0399626335
Author: bv2 <britta.velten@gmail.com>
Date: 2020-09-29 09:54:52 +0200
Commit message:

 Merge branch 'MEFISTO' into dev_speedups
 
Package: MOFA2
Commit: c5607068225febf096133dd194a1fe62d63dc424
Author: bv2 <britta.velten@gmail.com>
Date: 2020-09-29 09:20:33 +0200
Commit message:

 updated figure for MEFISTO
 
Package: MOFA2
Commit: 03a710b0a42a90234c4e59a3b6cbe141cc2b0102
Author: bv2 <britta.velten@gmail.com>
Date: 2020-09-29 09:19:27 +0200
Commit message:

 updated README for MEFISTO
 
Package: MOFA2
Commit: 4e71affff07a733a0f2831179555540d58c15b83
Author: bv2 <britta.velten@gmail.com>
Date: 2020-09-29 08:34:47 +0200
Commit message:

 testing speedups in optimizaiton using gradients or torch
 
Package: MOFA2
Commit: 4633711d70ce1ea5006686e87376c9eec6c26ee8
Author: bv2 <britta.velten@gmail.com>
Date: 2020-09-26 11:26:44 +0200
Commit message:

 fixed ordering of groups in R2
 
Package: MOFA2
Commit: 8f65144e966905d365e7c439d5c84dadb356b292
Author: bv2 <britta.velten@gmail.com>
Date: 2020-09-23 15:23:30 +0200
Commit message:

 fixed minor bug in loading trainstats
 
Package: MOFA2
Commit: 636d2986516cb935735dfe077f8d18c10e0dc2ee
Author: bv2 <britta.velten@gmail.com>
Date: 2020-09-21 14:25:59 +0200
Commit message:

 minor changes
 
Package: MOFA2
Commit: a67cbe4f72c20cfbcb3bcdb9dc0a64d06c86b8a9
Author: bv2 <britta.velten@gmail.com>
Date: 2020-09-15 09:49:12 +0200
Commit message:

 minor changes
 
Package: MOFA2
Commit: bf881605ca6dd51afffb97d92fa3b97f72fb9804
Author: bv2 <britta.velten@gmail.com>
Date: 2020-09-15 09:48:45 +0200
Commit message:

 avoid storing Kmat when storin spectral decomposition
 
Package: MOFA2
Commit: 2b0c2f218a6787a71381e29bb44a83a87c0d4437
Author: bv2 <britta.velten@gmail.com>
Date: 2020-09-09 10:14:46 +0200
Commit message:

 added some more options to  extract interpolated factors
 
Package: MOFA2
Commit: 8c05bf7edbf84118afc19d14b13bbf5d8a4f9b2e
Author: bv2 <britta.velten@gmail.com>
Date: 2020-09-08 14:44:37 +0200
Commit message:

 updated doc
 
Package: MOFA2
Commit: e79bb0212bcefbad0fad011e91f1c86b89c8c74e
Author: bv2 <britta.velten@gmail.com>
Date: 2020-09-08 14:44:12 +0200
Commit message:

 added interpolation functionalities and option to not center groups
 
Package: MOFA2
Commit: 0e84f5f3d48de2d5112dd7e99b79033ca300447f
Author: bv2 <britta.velten@gmail.com>
Date: 2020-09-03 12:14:34 +0200
Commit message:

 minor changes
 
Package: MOFA2
Commit: e64e1deceadfb5c315631ccf0ffc1cde9b657fb8
Author: bv2 <britta.velten@gmail.com>
Date: 2020-09-02 16:42:00 +0200
Commit message:

 only diagonal group structure for zero s or ls
 
Package: MOFA2
Commit: e6443a9296e4ffebf68fb3eab0acb01bf11f38f8
Author: bv2 <britta.velten@gmail.com>
Date: 2020-09-02 16:40:42 +0200
Commit message:

 fixed inducing points selection
 
Package: MOFA2
Commit: 31e47150a22780ca2df32dc760e1ed03750faae5
Author: bv2 <britta.velten@gmail.com>
Date: 2020-09-02 14:06:13 +0200
Commit message:

 fixed minor bug in selection of inducing points
 
Package: MOFA2
Commit: 94cfd7f34a3a3640a85d60e3639c6c3daf794415
Author: bv2 <britta.velten@gmail.com>
Date: 2020-09-02 13:56:50 +0200
Commit message:

 drafted sparse GP in conjunction with groups
 
Package: MOFA2
Commit: 77bd822c373309f63c2685f024566d0360bf0430
Author: bv2 <britta.velten@gmail.com>
Date: 2020-09-02 13:20:55 +0200
Commit message:

 added cases for non-identifiable hyperparameters
 
Package: MOFA2
Commit: e084d0b1da21d90b728870869df51d3b196007df
Author: bv2 <britta.velten@gmail.com>
Date: 2020-09-02 12:53:17 +0200
Commit message:

 fixed bug in simulation for ls=0
 
Package: MOFA2
Commit: 81e26ec61edb75995986631a2acd9ec868ff0476
Author: bv2 <britta.velten@gmail.com>
Date: 2020-09-02 12:44:24 +0200
Commit message:

 minor changes
 
Package: MOFA2
Commit: 6bb20f0ebc0826670453d300a70a572b88d11d84
Author: bv2 <britta.velten@gmail.com>
Date: 2020-09-02 11:30:41 +0200
Commit message:

 enabled warping in conjunction with model_groups
 
Package: MOFA2
Commit: 9e04cd76ae9c2bfea86050672062f917b3e82b34
Author: bv2 <britta.velten@gmail.com>
Date: 2020-09-02 11:12:38 +0200
Commit message:

 fixed minor bugs and avoid unnecessary (repetitive) updates
 
Package: MOFA2
Commit: 4607dd452fb0e0890da8c3f5a5cd9ce6f94c64f6
Author: bv2 <britta.velten@gmail.com>
Date: 2020-09-02 09:57:34 +0200
Commit message:

 setting negative R2 (missing views) to 0
 
Package: MOFA2
Commit: d42da9956e494634d7e9ae6c874acfedf8e3c99c
Author: bv2 <britta.velten@gmail.com>
Date: 2020-09-01 16:39:59 +0200
Commit message:

 added documentation for new R function
 
Package: MOFA2
Commit: 7d7e8df904978832580d53fa19f1faa1e24a2b54
Author: bv2 <britta.velten@gmail.com>
Date: 2020-09-01 16:24:15 +0200
Commit message:

 added support for non-Kronecker sample structure
 
Package: MOFA2
Commit: b997cfa5c1454373075aea2ee2f3a1c6ccc70fb4
Author: bv2 <britta.velten@gmail.com>
Date: 2020-09-01 16:23:27 +0200
Commit message:

 added group names to KG matrix
 
Package: MOFA2
Commit: 0ab5c8edad49356bbf72a0e4ca16ac86d79fcd53
Author: bv2 <britta.velten@gmail.com>
Date: 2020-09-01 11:43:47 +0200
Commit message:

 added predict function for extra/interpolation of Z
 
Package: MOFA2
Commit: 4f34255d9077a22d07461a2b4c9b74408fccf709
Author: bv2 <britta.velten@gmail.com>
Date: 2020-08-31 17:15:53 +0200
Commit message:

 added Kg of 1s if no group modelling
 
Package: MOFA2
Commit: a1a7d6e6a82b355fabf7d7a84ec04637fa17a2fe
Author: bv2 <britta.velten@gmail.com>
Date: 2020-08-31 16:59:19 +0200
Commit message:

 variable rank of Kg, passing Kg to save and fixing parameters for ls0
 
Package: MOFA2
Commit: 844bcc8469a4493d5d0e58c5f1d2d7b714d6936b
Author: bv2 <britta.velten@gmail.com>
Date: 2020-08-31 16:54:15 +0200
Commit message:

 scaling Kg to correlation matrix
 
Package: MOFA2
Commit: 14bb6690405465f75e09441e452e4f226edebbd8
Author: bv2 <britta.velten@gmail.com>
Date: 2020-08-31 16:52:17 +0200
Commit message:

 use 0/1 for Kg in simulations
 
Package: MOFA2
Commit: f013a65137ecd05ee1a3109841d50bacad142b8a
Author: bv2 <britta.velten@gmail.com>
Date: 2020-08-31 16:51:37 +0200
Commit message:

 saving GP hyperparameters at end of training
 
Package: MOFA2
Commit: 59e84edb4d73737cbfa47c67c969363beca54b4c
Author: bv2 <britta.velten@gmail.com>
Date: 2020-08-31 16:50:09 +0200
Commit message:

 passed GP hyperparameters to R
 
Package: MOFA2
Commit: 87a9e6ef516c6b9d214bdc9d15b374b137134b6e
Author: bv2 <britta.velten@gmail.com>
Date: 2020-08-31 11:47:15 +0200
Commit message:

 renamed Sigma node
 
Package: MOFA2
Commit: f2d2bf52a6ecceb02df4d551a8aa2865e776db9c
Author: bv2 <britta.velten@gmail.com>
Date: 2020-08-31 11:37:46 +0200
Commit message:

 minor change
 
Package: MOFA2
Commit: 17d8ab4aa13d672aca5adc02fbd91dbf80ff489f
Author: bv2 <britta.velten@gmail.com>
Date: 2020-08-31 11:34:43 +0200
Commit message:

 replaced old Sigma node
 
Package: MOFA2
Commit: 77b06115bf8d9b30eadb41d3455f4f90f63fcae8
Author: bv2 <britta.velten@gmail.com>
Date: 2020-08-31 11:33:59 +0200
Commit message:

 replaced old Sigma node
 
Package: MOFA2
Commit: d2198894f78aa33c0cebea1887bf8e66d2b9e4f6
Author: bv2 <britta.velten@gmail.com>
Date: 2020-08-31 11:25:26 +0200
Commit message:

 fixed bug in inducing point grid
 
Package: MOFA2
Commit: 6961f9927126f0a8aafbb52ef0a0f67cb2fb411c
Author: bv2 <britta.velten@gmail.com>
Date: 2020-08-31 11:07:10 +0200
Commit message:

 fixed bug in new Sigma node with sparse GPs
 
Package: MOFA2
Commit: 7943d92edeadb7ce29426a2e0e8774d05624c5e9
Author: bv2 <britta.velten@gmail.com>
Date: 2020-08-28 11:39:10 +0200
Commit message:

 generalized kronSigma node to use for all models, cleaned up (Alpha-suff, kernel functions)
 
Package: MOFA2
Commit: 7eab0d5eb07f7c5c83a24d63a5840e2d98ff8dc5
Author: bv2 <britta.velten@gmail.com>
Date: 2020-08-28 10:50:19 +0200
Commit message:

 improved doc + names
 
Package: MOFA2
Commit: 4d70171b6808e56dc19b1a88626570ebf2dfb66f
Author: bv2 <britta.velten@gmail.com>
Date: 2020-08-28 10:49:16 +0200
Commit message:

 uncluttered training/model options and stats
 
Package: MOFA2
Commit: 482049a38883c1488cbf9b557717cfadfe7e5881
Author: bv2 <britta.velten@gmail.com>
Date: 2020-08-27 14:54:23 +0200
Commit message:

 set option to add non-constant digaonal in group kernel
 
Package: MOFA2
Commit: b19a8b1da714f7623720dbda957af65f3b419ae3
Author: bv2 <britta.velten@gmail.com>
Date: 2020-08-27 10:43:39 +0200
Commit message:

 fixed bugs in marginal covariance (pytorch) and bounds (kronSigma)
 
Package: MOFA2
Commit: f71c8c7ead02f8ad4fe3b383e83ad8a81bfdcc05
Author: bv2 <britta.velten@gmail.com>
Date: 2020-08-26 16:58:30 +0200
Commit message:

 fixed bug in Sigma calculation (order of kron)
 
Package: MOFA2
Commit: 1149935f2659f204edfa934fd10b79f7d0af0e7c
Author: bv2 <britta.velten@gmail.com>
Date: 2020-08-26 14:28:11 +0200
Commit message:

 added experimental gpytorch Sigma node
 
Package: MOFA2
Commit: 42dcdc4672f658c7af1093640e46f3bd338e3709
Author: bv2 <britta.velten@gmail.com>
Date: 2020-08-25 14:38:19 +0200
Commit message:

 added group structure draft, fixed bug in det in ELBO_Z and removed univ_Znode option
 
Package: MOFA2
Commit: fa8136be44021700ee36a75fdb29b87de2acf4e4
Author: bv2 <britta.velten@gmail.com>
Date: 2020-08-21 09:46:56 +0200
Commit message:

 added hyperparameter opt options, disentangling scale and ls
 
Package: MOFA2
Commit: c9579e8eedac70342b8763d8673fa1e70be83c9d
Author: bv2 <britta.velten@gmail.com>
Date: 2020-08-19 09:07:10 +0200
Commit message:

 removed NA row from scales and lscales if maxiter is reached
 
Package: MOFA2
Commit: c4b765033d0ad119979d77400e4773e4cdb2f553
Author: bv2 <britta.velten@gmail.com>
Date: 2020-08-14 08:34:40 +0200
Commit message:

 minor change
 
Package: MOFA2
Commit: df7c0feffd3f833d2972d3b5152f43ac9a8521b4
Author: bv2 <britta.velten@gmail.com>
Date: 2020-08-13 11:15:30 +0200
Commit message:

 added names and subsetting for scales
 
Package: MOFA2
Commit: 383dcd1290c26228c004ff6f07a7148c89751818
Author: bv2 <britta.velten@gmail.com>
Date: 2020-08-13 08:49:21 +0200
Commit message:

 made masking of outliers in imputation optional
 
Package: MOFA2
Commit: 89485a2dd1b146736f1c0b4a94c56f244b383a86
Author: bv2 <britta.velten@gmail.com>
Date: 2020-08-12 12:30:41 +0200
Commit message:

 changed zeta init
 
Package: MOFA2
Commit: 7b22c07b4ce48d09553f81f57c73ebc27bf271ed
Author: bv2 <britta.velten@gmail.com>
Date: 2020-08-11 14:03:51 +0200
Commit message:

 minor changes to vignette
 
Package: MOFA2
Commit: 839149e3b602233293665c2f61b15642b905d327
Author: bv2 <britta.velten@gmail.com>
Date: 2020-08-11 10:30:12 +0200
Commit message:

 adapted simulation to multiple groups and varying scales
 
Package: MOFA2
Commit: 4e9642a6ab5fa3e03097fda073aa2ad8e495df4e
Author: bv2 <britta.velten@gmail.com>
Date: 2020-08-10 13:51:57 +0200
Commit message:

 use consistent defaults in python and R
 
Package: MOFA2
Commit: 930d4a004cf72f117573933f1108897605e6be56
Author: bv2 <britta.velten@gmail.com>
Date: 2020-08-10 13:42:09 +0200
Commit message:

 changed defaults to warping + opt in same step
 
Package: MOFA2
Commit: 2e27e1427b7d9ebb49c232014ba0ba79b67f51f2
Author: bv2 <britta.velten@gmail.com>
Date: 2020-08-10 12:48:44 +0200
Commit message:

 fixed bugs in alignment
 
Package: MOFA2
Commit: a9c88f54605c2831f051f0c2885ebaa416de2c44
Author: bv2 <britta.velten@gmail.com>
Date: 2020-08-10 11:28:57 +0200
Commit message:

 fixed bugs in sparse Sigma version and removed 0 lengthscale
 
Package: MOFA2
Commit: b4fc88473af28a3e175d888cef17befad4a92ca1
Author: bv2 <britta.velten@gmail.com>
Date: 2020-08-07 15:31:38 +0200
Commit message:

 passed opt_freq as paramater
 
Package: MOFA2
Commit: 7d19da61594a4dcbec8deb16c40a067d6fe445a1
Author: bv2 <britta.velten@gmail.com>
Date: 2020-08-07 15:14:46 +0200
Commit message:

 removed smooth_all option, added scale to train_stats
 
Package: MOFA2
Commit: d898e604bd64c5d5e47e4a042f4b4cdfb1c768e4
Author: bv2 <britta.velten@gmail.com>
Date: 2020-08-07 14:37:34 +0200
Commit message:

 added optimization of zeta using optimize
 
Package: MOFA2
Commit: 293c1f573b2b1e35a0064747dc180758cb38e1a0
Author: bv2 <britta.velten@gmail.com>
Date: 2020-08-07 14:32:20 +0200
Commit message:

 reduced default number of grid points
 
Package: MOFA2
Commit: fc4ec369ad6c76ed7c0e89d2f0859ada08df961a
Author: bv2 <britta.velten@gmail.com>
Date: 2020-07-17 11:49:27 +0200
Commit message:

 fixed bug in dropping factor
 
Package: MOFA2
Commit: 7629ef95e25816074e1e7501a8cc4d74d9817b48
Author: bv2 <britta.velten@gmail.com>
Date: 2020-07-17 11:36:32 +0200
Commit message:

 added sanity check on reference group
 
Package: MOFA2
Commit: ad52c3115b5b2b4f1ef5c84b40d9314b94bd648b
Author: bv2 <britta.velten@gmail.com>
Date: 2020-07-17 11:27:00 +0200
Commit message:

 added opt_freq parameter for Sigma and cleaned TODOs
 
Package: MOFA2
Commit: 84713af15f10f29ca8aeb21c1d50453941790f77
Author: bv2 <britta.velten@gmail.com>
Date: 2020-07-17 09:42:29 +0200
Commit message:

 added optimization of scale parameter
 
Package: MOFA2
Commit: e684d094af2b3f9b102718c9acebc944e5f3037f
Author: bv2 <britta.velten@gmail.com>
Date: 2020-07-14 13:15:10 +0200
Commit message:

 fixed lineplot vs cov for multiple samples at same value
 
Package: MOFA2
Commit: 5b5e87874b78a740b304091226ad4cb2e43d659b
Author: bv2 <britta.velten@gmail.com>
Date: 2020-07-14 11:29:07 +0200
Commit message:

 fixed minor bugs in alignment
 
Package: MOFA2
Commit: 055645da720941db042203f2af0eb798a7eb28e9
Author: bv2 <britta.velten@gmail.com>
Date: 2020-07-14 09:33:57 +0200
Commit message:

 passed options for partial alignment
 
Package: MOFA2
Commit: c2e5fa7bf9e50b84ae7664ea8d37feba027a79cd
Author: bv2 <britta.velten@gmail.com>
Date: 2020-07-14 09:14:40 +0200
Commit message:

 fixed order of samples and allow partial mapping in alignment
 
Package: MOFA2
Commit: c261caf5a3e0b7bb265423cdb0b789d665b6f224
Author: bv2 <britta.velten@gmail.com>
Date: 2020-07-11 09:05:13 +0200
Commit message:

 fixed bug in loading sample_cov from df
 
Package: MOFA2
Commit: 13f5c0538583449a8197c50b77b69cbba3a5a5b5
Author: bv2 <britta.velten@gmail.com>
Date: 2020-07-10 10:52:01 +0200
Commit message:

 implemented two warping strategies (dtw, linear)
 
Package: MOFA2
Commit: f4ad918d03045b165ea151cf4f6d7bd0790ab34e
Author: bv2 <britta.velten@gmail.com>
Date: 2020-07-10 10:50:51 +0200
Commit message:

 updated doc
 
Package: MOFA2
Commit: b9f431547e844abc2a27f40ac46b7bd6aa3fea08
Author: bv2 <britta.velten@gmail.com>
Date: 2020-07-10 10:45:00 +0200
Commit message:

 fixed colours in plot_data_overview
 
Package: MOFA2
Commit: 8c4e6112e6b9bb5be979d53613acd8ace3ecef91
Author: bv2 <britta.velten@gmail.com>
Date: 2020-07-06 17:39:31 +0200
Commit message:

 minor changes
 
Package: MOFA2
Commit: 77655da12bea701607fa9d75cac4f3cefae25146
Author: bv2 <britta.velten@gmail.com>
Date: 2020-07-06 10:52:27 +0200
Commit message:

 deactivated ARD Z for GP
 
Package: MOFA2
Commit: 219cbd0f08b2e8e3387feb53549d9f096890b7b1
Author: bv2 <britta.velten@gmail.com>
Date: 2020-07-02 17:52:00 +0200
Commit message:

 updated documentation
 
Package: MOFA2
Commit: 18e7d3c6d31535b5688641d0615451e13d6b9e56
Author: bv2 <britta.velten@gmail.com>
Date: 2020-07-02 15:56:01 +0200
Commit message:

 added data_vs_cov scatter plot function and fixed imputation option for data scatters
 
Package: MOFA2
Commit: 7ed4954235d0e8aedebe4954ae3f6ce5a39d7722
Author: bv2 <britta.velten@gmail.com>
Date: 2020-07-02 11:24:18 +0200
Commit message:

 implemented ARD_Z and weights for GP nodes
 
Package: MOFA2
Commit: e9e4397f5c6e1c5b4525d1691577c121c6bdf37b
Author: bv2 <britta.velten@gmail.com>
Date: 2020-06-30 17:14:44 +0200
Commit message:

 enabled smooth_all option
 
Package: MOFA2
Commit: 68a4c71cdeea9d84e553cd973ca5d04636b4205c
Author: bv2 <britta.velten@gmail.com>
Date: 2020-06-30 17:14:30 +0200
Commit message:

 fixed get_data for missing groups
 
Package: MOFA2
Commit: aa0b145dd082b4eeeea82b53110fdbe052b20f51
Author: bv2 <britta.velten@gmail.com>
Date: 2020-06-30 14:13:37 +0200
Commit message:

 minor fix
 
Package: MOFA2
Commit: 09cf45cec0e997c8d751856a57c1df4249374fc5
Author: bv2 <britta.velten@gmail.com>
Date: 2020-06-30 13:11:11 +0200
Commit message:

 fixed sorting and R2 calc for missing groups and no ARD_Z
 
Package: MOFA2
Commit: ebe4dce5836c6521f9a0737bba084a3f7f75d1ab
Author: bv2 <britta.velten@gmail.com>
Date: 2020-06-30 09:48:05 +0200
Commit message:

 fixed passing covariate as data.frame columns
 
Package: MOFA2
Commit: 087ab0a16234901121f24c890351197257a9b039
Author: bv2 <britta.velten@gmail.com>
Date: 2020-06-30 09:34:19 +0200
Commit message:

 renamed covariate argument in create_mofa
 
Package: MOFA2
Commit: 24d8352170cf71566d33230c84004740438bee60
Author: bv2 <britta.velten@gmail.com>
Date: 2020-06-30 09:13:28 +0200
Commit message:

 added covariates to data overview plot
 
Package: MOFA2
Commit: ab740915aea291cb244cc298caf720f6a9ca51c0
Author: bv2 <britta.velten@gmail.com>
Date: 2020-06-29 18:11:18 +0200
Commit message:

 fixed bug when dropping factors
 
Package: MOFA2
Commit: 43b8758e3d9e04811b4bb3e2b2aeb87c28491179
Author: bv2 <britta.velten@gmail.com>
Date: 2020-06-29 17:52:23 +0200
Commit message:

 fixed SMOFAvignettes
 
Package: MOFA2
Commit: 09f3cd82994e2cf3db922e3f03c9b98614757cfb
Author: bv2 <britta.velten@gmail.com>
Date: 2020-06-29 15:09:48 +0200
Commit message:

 fixed covariate passing and running MOFA from R
 
Package: MOFA2
Commit: b2ce11c86e868e5169346eabeae85ad4af5cdae6
Author: bv2 <britta.velten@gmail.com>
Date: 2020-06-26 14:49:06 +0200
Commit message:

 fixed module names
 
Package: MOFA2
Commit: 4c0e7a47e20a31ff0d11c10817bda1c6c894ceee
Author: bv2 <britta.velten@gmail.com>
Date: 2020-06-26 10:57:05 +0200
Commit message:

 added message  when using sample_cov for loom and anndata
 
Package: MOFA2
Commit: ea59c9e36481dae59c84cda45eda70c92ce1c723
Author: bv2 <britta.velten@gmail.com>
Date: 2020-06-26 10:14:08 +0200
Commit message:

 debugged passing covariates as dataframe
 
Package: MOFA2
Commit: 9c38a3cf1930318c6f65e07f88cb42c9dbc857f5
Author: bv2 <britta.velten@gmail.com>
Date: 2020-06-25 11:17:00 +0200
Commit message:

 debugged python module for use with matrix lists
 
Package: MOFA2
Commit: 1bb4d55799f013e33b478eeb7a585d9717adb98f
Author: bv2 <britta.velten@gmail.com>
Date: 2020-06-25 09:36:44 +0200
Commit message:

 made factor prior options mutually exclusive
 
Package: MOFA2
Commit: 1175bb4f45d7d26823ef864ef4585c1c4ff8efa1
Author: bv2 <britta.velten@gmail.com>
Date: 2020-06-25 09:27:24 +0200
Commit message:

 adapted template scripts for R to SMOFA
 
Package: MOFA2
Commit: 956f2e4d29abf1eaa2a5150734ebc9090e49326f
Author: bv2 <britta.velten@gmail.com>
Date: 2020-06-25 09:10:39 +0200
Commit message:

 removed old template script
 
Package: MOFA2
Commit: 083241d5c2ed19a5261d9391fcd0082146468db8
Author: bv2 <britta.velten@gmail.com>
Date: 2020-06-25 09:10:05 +0200
Commit message:

 fixed minor bugs and merged python template_script
 
Package: MOFA2
Commit: 46f29b34b75a461df3d022d39e11f9b8c5a39fdf
Author: bv2 <britta.velten@gmail.com>
Date: 2020-06-23 15:26:46 +0200
Commit message:

 fixed bugs from merge and updated documentation
 
Package: MOFA2
Commit: cfc920b9cf4bb7855c9ce2eb0d26f3dc38e5fa1a
Author: bv2 <britta.velten@gmail.com>
Date: 2020-06-23 15:16:40 +0200
Commit message:

 extended R part to SMOFA - missing files
 
Package: MOFA2
Commit: 47103d82f7361274213b61553e369f88db07496a
Author: bv2 <britta.velten@gmail.com>
Date: 2020-06-23 14:22:37 +0200
Commit message:

 added template and simulation scripts for SMOFA
 
Package: MOFA2
Commit: 3ee95c7f7e4f8a978c8413a56ec5e1b1c709726c
Author: bv2 <britta.velten@gmail.com>
Date: 2020-06-23 14:20:12 +0200
Commit message:

 adapted entrypoint for SMOFA
 
Package: MOFA2
Commit: 105fa291c3d00987e2d60b56263a43ab0dbc1cec
Author: bv2 <britta.velten@gmail.com>
Date: 2020-06-23 14:04:22 +0200
Commit message:

 added new nodes for SMOFA
 
Package: MOFA2
Commit: 96bbd2f3337b301f9dffb71a60a0f92aaac25b0a
Author: bv2 <britta.velten@gmail.com>
Date: 2020-06-23 14:03:39 +0200
Commit message:

 extended mofapy2 core to SMOFA
 
Package: MOFA2
Commit: a467fe5e1e573f9157521f5d44af15f2f2a6aca3
Author: bv2 <britta.velten@gmail.com>
Date: 2020-06-23 13:42:00 +0200
Commit message:

 extended build_model to SMOFA
 
Package: MOFA2
Commit: d7af8f779c0a43c46aa5589d5a0fe6baeb8204b8
Author: bv2 <britta.velten@gmail.com>
Date: 2020-06-23 11:00:35 +0200
Commit message:

 adapted package sidestuff  to include SMOFA
 
Package: MOFA2
Commit: e3bf863fbae29ee23c746ac081658e0b5cb397a8
Author: bv2 <britta.velten@gmail.com>
Date: 2020-06-23 10:40:50 +0200
Commit message:

 integrated SMOFA into MOFA - R part
 
Package: GDCRNATools
Commit: 27e91b82b79a9267e9448d4d6a1515822e99cd8c
Author: Ruidong Li <rli012@ucr.edu>
Date: 2020-11-24 23:27:44 -0800
Commit message:

 version bump
 
Package: GDCRNATools
Commit: 214cc5d7ce8706feb1bbaa162ed099c6a9ac9be6
Author: Ruidong Li <rli012@ucr.edu>
Date: 2020-11-24 23:26:19 -0800
Commit message:

 gdc-client v1.6.0
 
Package: GDCRNATools
Commit: 43ddf6525cde78f6d4fc2bdecba930320a3a1d7f
Author: Ruidong Li <rli012@pelican.ib.hpcc.ucr.edu>
Date: 2020-11-24 23:10:18 -0800
Commit message:

 Merge remote-tracking branch 'upstream/master'
 
Package: GDCRNATools
Commit: dae8968829b36e5aa6b7a58af637b15d072c8a61
Author: Jialab-UCR <jialab.ucr@gmail.com>
Date: 2020-01-29 12:06:34 -0800
Commit message:

 1.3 to 1.4
 
Package: Rsubread
Commit: 46dcfecbbda45b4dcc93ec35c67e8350e7747e84
Author: Yang Liao <liao_y@svr2672.licr.unimelb.edu.au>
Date: 2020-11-25 15:35:06 +1100
Commit message:

 just minor changes.
 
Package: Rsubread
Commit: d416dc8982b07abb5e7836e8955389162e80075f
Author: Yang Liao <liao_y@svr2672.licr.unimelb.edu.au>
Date: 2020-11-25 14:52:19 +1100
Commit message:

 start writting BAM and FASTQ
 
Package: preprocessCore
Commit: 6b016db3871f58b9fd21b72d02f423181fc6236f
Author: Ben Bolstad <bmb@bmbolstad.com>
Date: 2020-11-24 08:02:23 -0800
Commit message:

 disable use of __pthread_get_minstack   which is non public symbol   (this may be a temporary fix)
 
Package: MethylSeqData
Commit: c1b25727efb672562682aba3db4664d38e410861
Author: Peter Hickey <peter.hickey@gmail.com>
Date: 2020-11-25 11:59:48 +1100
Commit message:

 Correct data in vignette
 
Package: epihet
Commit: eb4c259224015d97a357c95350fc4e5bdc851cb5
Author: Xiaowen Chen <chenx@helix.(none)>
Date: 2020-11-24 19:12:51 -0500
Commit message:

 Fixed conflicts in version change
 
Package: epihet
Commit: 553ed095b10e1dd6e1fa987334dd2ca2a5254dc4
Author: xiaowen chen <30912295+xiaowenchenjax@users.noreply.github.com>
Date: 2020-11-24 19:10:17 -0500
Commit message:

 Update DESCRIPTION 
Package: epihet
Commit: c3e3a65056ea9fddd1e032fdb63c178039a8e92a
Author: xiaowen chen <30912295+xiaowenchenjax@users.noreply.github.com>
Date: 2020-11-24 18:57:17 -0500
Commit message:

 Update DESCRIPTION 
Package: epihet
Commit: e5d37880c162d153175dc9f9ea7c96f5994fb927
Author: xiaowen chen <30912295+xiaowenchenjax@users.noreply.github.com>
Date: 2020-11-24 18:52:42 -0500
Commit message:

 Update DESCRIPTION 
Package: epihet
Commit: a33c45a323669ba4720b3887bcd76a9f9453f1e5
Author: xiaowen chen <30912295+xiaowenchenjax@users.noreply.github.com>
Date: 2020-11-24 11:14:06 -0500
Commit message:

 Update epihet.Rnw 
Package: epihet
Commit: b0c6a74f4bb56f093b8049dabb86aa87559e3ed9
Author: xiaowen chen <30912295+xiaowenchenjax@users.noreply.github.com>
Date: 2020-11-24 10:51:09 -0500
Commit message:

 Update epiPathway.Rd 
Package: epihet
Commit: 54534edc40203d11eab2eba446ee968731976ea6
Author: xiaowen chen <30912295+xiaowenchenjax@users.noreply.github.com>
Date: 2020-11-24 10:45:56 -0500
Commit message:

 Update epiPathway.Rd 
Package: epihet
Commit: fb20b8173e9bd77c25d3b59892e2134537203f8b
Author: xiaowen chen <30912295+xiaowenchenjax@users.noreply.github.com>
Date: 2020-11-24 10:39:34 -0500
Commit message:

 Update epiPathway.R 
Package: flowGraph
Commit: a84c37449d7f154710b928931c3e0b9b81bcf62a
Author: aya43@sfu.ca <aya43@sfu.ca>
Date: 2020-11-24 16:00:23 -0800
Commit message:

 R version bump
 
Package: rcellminer
Commit: 6e9266a10c911256467a6878795395039544e9c0
Author: Elloumi <elloumif@nci-02048674-ml.nih.gov>
Date: 2020-11-24 18:15:38 -0500
Commit message:

 merge origin and upstream for master branch
 
Package: rcellminer
Commit: 684148d616eed47da6f0e82b6c02c77aedf86705
Author: Elloumi <elloumif@nci-02048674-ml.nih.gov>
Date: 2020-11-24 18:09:09 -0500
Commit message:

 new version number matching bioconductor
 
Package: rcellminer
Commit: aa92d58eabcc3ce1d132ed889b0ae2c14414dfab
Author: Elloumi <elloumif@nci-02048674-ml.nih.gov>
Date: 2020-10-02 14:29:59 -0400
Commit message:

 Removed 3 shiny apps
 
Package: rcellminer
Commit: c3b62c01a77d4d49ae45f5175518e28d2e717e9e
Author: Elloumi <elloumif@nci-02048674-ml.nih.gov>
Date: 2020-09-02 17:07:44 -0400
Commit message:

 Merge branch 'nojdk'
 
Package: rcellminer
Commit: b2a816205fbc19e61e1b2b4b553a7b0972d60af4
Author: Elloumi <elloumif@nci-02048674-ml.nih.gov>
Date: 2020-08-25 09:42:28 -0400
Commit message:

 updated MOA keys
 
Package: flowGraph
Commit: 6c2f3a2b82e346f2c31301dc312c75e5d6ddc55f
Author: aya43@sfu.ca <aya43@sfu.ca>
Date: 2020-11-24 15:14:00 -0800
Commit message:

 R version bump
 
Package: flowGraph
Commit: 032368c7f2297df7986abe592b38137f8d956d0f
Author: aya43@sfu.ca <aya43@sfu.ca>
Date: 2020-11-24 15:10:46 -0800
Commit message:

 R version bump
 
Package: flowGraph
Commit: b266bc767dead381484ec686cc4975e3a74ad773
Author: aya43@sfu.ca <aya43@sfu.ca>
Date: 2020-11-24 14:35:45 -0800
Commit message:

 R version bump
 
Package: flowGraph
Commit: 41f6e2af20e4958b8381a4044c37d5c555b40d7f
Author: aya43@sfu.ca <aya43@sfu.ca>
Date: 2020-11-24 14:17:55 -0800
Commit message:

 R version bump
 
Package: rSWeeP
Commit: 965d5f139b009f2d375d6d652c87148027ef0b1b
Author: DanrleyRF <danrleyrf@gmail.com>
Date: 2020-11-24 17:50:37 -0300
Commit message:

 Update version bump
 
Package: rSWeeP
Commit: b1c1f71a083311128ba494d5e7949e90155bf8cd
Author: DanrleyRF <danrleyrf@gmail.com>
Date: 2020-11-24 17:45:31 -0300
Commit message:

 Update version bump
 
Package: rSWeeP
Commit: 56347384a28b2d1aa71504ca0f32caa07f457894
Author: DanrleyRF <danrleyrf@gmail.com>
Date: 2020-11-24 17:34:24 -0300
Commit message:

 Version bump
 
Package: rSWeeP
Commit: 888953082f363cad6f7384fde15d656d7c021f05
Author: DanrleyRF <danrleyrf@gmail.com>
Date: 2020-11-24 17:33:11 -0300
Commit message:

 Bug fix
 
Package: flowGraph
Commit: 768f16bd29ae0aab2b650db25fcf8eb23e1e7af6
Author: aya43@sfu.ca <aya43@sfu.ca>
Date: 2020-11-24 12:30:49 -0800
Commit message:

 update notes
 
Package: preciseTAD
Commit: 8ca9dd519adabc6fb03037b647113838212c81bf
Author: stilianoudakis <stilianoudasc@mymail.vcu.edu>
Date: 2020-11-24 15:23:44 -0500
Commit message:

 version bump
 
Package: preciseTAD
Commit: b5f2e1857df47c1c45a1947448622c1c2f06fcc3
Author: stilianoudakis <stilianoudasc@mymail.vcu.edu>
Date: 2020-11-24 15:00:41 -0500
Commit message:

 added column names
 
Package: DelayedArray
Commit: f1279e072d94793add8ba65f281def5a967a4406
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2020-11-24 12:20:16 -0800
Commit message:

 cbind()/rbind() no longer coerce supplied objects to type of 1st object
 
Package: Gviz
Commit: c5aa4ed665a4d0b5a71fe0653e9684c2f327178e
Author: Robert Ivánek <robert.ivanek@unibas.ch>
Date: 2020-11-23 11:29:16 +0100
Commit message:

 version bump
 
Package: Gviz
Commit: bfe10e3f6c5c10ba4fdead33984e5e0503afeb5e
Author: Robert Ivánek <robert.ivanek@unibas.ch>
Date: 2020-11-23 11:25:39 +0100
Commit message:

 Clean-up after defunct
 
Package: Gviz
Commit: c63bb8de3ccbdfec44e9407275ce5f23a6fadf97
Author: Robert Ivánek <robert.ivanek@unibas.ch>
Date: 2020-11-20 23:58:38 +0100
Commit message:

 Deprecated -> Defunct
 
Package: DelayedArray
Commit: 8623979c85fff8be8721845981ba1673d6b8ff83
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2020-11-24 10:25:50 -0800
Commit message:

 Make sure subsetting of a DelayedArray object always propagates the
names/dimnames, even when drop=TRUE and the result has only 1 dimension

This addresses https://github.com/Bioconductor/DelayedArray/issues/78.
 
Package: HPAanalyze
Commit: 9ae741a80b03c58dccfe941a2d09ccce83e31e42
Author: Anh Tran <trannhatanh89@gmail.com>
Date: 2020-11-24 11:50:29 -0600
Commit message:

 Update the built-in dataset to v20

 
Package: HPAanalyze
Commit: e785b3d9b30bd36740250ae803430a9f68116f53
Author: Anh Tran <trannhatanh89@gmail.com>
Date: 2020-11-24 11:42:27 -0600
Commit message:

 Fix error where rna_tissue_concensus.tsv could not be found

 
Package: phosphonormalizer
Commit: 996a802ad03e7c22c061522cdcc91bb3b6d5bd96
Author: sohrab.saraei <sohrab.saraei@blueprintgenetics.com>
Date: 2020-11-24 19:13:24 +0200
Commit message:

 phosphonormalizer: version bump
 
Package: phosphonormalizer
Commit: 020afc9edead1bf372c79baadbf24ab29a2d25cd
Author: sohrab.saraei <sohrab.saraei@blueprintgenetics.com>
Date: 2020-11-24 19:08:58 +0200
Commit message:

 RELEASE_3_12: phosphonormalizer version bump
 
Package: phosphonormalizer
Commit: d246d440aeb908759a47693c5aa09d0261bfa488
Author: sohrab.saraei <sohrab.saraei@blueprintgenetics.com>
Date: 2020-11-24 18:42:43 +0200
Commit message:

 RELEASE_3_12: phosphonormalizer: maintainer email updated
 
Package: phosphonormalizer
Commit: 9e477386f18d3f5d9723a9b66cf503634f0d982c
Author: sohrab.saraei <sohrab.saraei@blueprintgenetics.com>
Date: 2020-11-23 15:33:10 +0200
Commit message:

 RELEASE_3_12: addressing the problem with condition
 
Package: preciseTADhub
Commit: 0e9265d5d456460c0fc2fdaf0382f54495bd50c0
Author: stilianoudakis <stilianoudasc@mymail.vcu.edu>
Date: 2020-11-24 12:09:47 -0500
Commit message:

 version bump
 
Package: preciseTADhub
Commit: afed93a2fc695bd05abd86e59e8399e78bf592fd
Author: stilianoudakis <stilianoudasc@mymail.vcu.edu>
Date: 2020-11-24 12:09:11 -0500
Commit message:

 fixed errors in vignette from readEH function
 
Package: preciseTADhub
Commit: 818e7da725249b57f54c6f602afce1eb7923f35d
Author: stilianoudakis <stilianoudasc@mymail.vcu.edu>
Date: 2020-11-24 10:56:14 -0500
Commit message:

 added wrapper function to R folder, fixed biocviews, version bump
 
Package: easyreporting
Commit: b16b1cef6c25e6511fd8d7ae49e80725d76d2399
Author: Dario <dario.righelli@gmail.com>
Date: 2020-11-24 16:37:47 +0100
Commit message:

 bumping version
 
Package: easyreporting
Commit: d69ff8b932d6b36b156ea4cdd8e868f466192f9b
Author: Dario <dario.righelli@gmail.com>
Date: 2020-11-24 16:36:20 +0100
Commit message:

 some fixing
 
Package: densvis
Commit: bdf1edb28dec65367fa2a10aad4d9f6de2ac51fd
Author: Alan O'Callaghan <alan.ocallaghan@outlook.com>
Date: 2020-11-24 13:54:20 +0000
Commit message:

 Merge branch 'master' of git.bioconductor.org:packages/densvis
 
Package: densvis
Commit: ef0ad3cd654dd8d18d7d17779ce1bb44da22986c
Author: Alan O'Callaghan <alan.ocallaghan@outlook.com>
Date: 2020-11-24 13:53:31 +0000
Commit message:

 Merge branch 'RELEASE_3_12'
 
Package: densvis
Commit: 4de114e312efc725955c94d42cf25eb93effb5ed
Author: Alan O'Callaghan <alan.ocallaghan@outlook.com>
Date: 2020-11-24 13:52:55 +0000
Commit message:

 v1.0.4; Correct labels in vignette
 
Package: densvis
Commit: 124978e24bec4bd955b7a519465fcc3c1d3096b5
Author: Alan O'Callaghan <alan.ocallaghan@outlook.com>
Date: 2020-11-20 20:19:00 +0000
Commit message:

 Version 1.00.3; densmap 0.2.2 on pypi
 
Package: densvis
Commit: e3d319bebc92f7793df636e0e0897986898dd048
Author: Alan O'Callaghan <alan.ocallaghan@outlook.com>
Date: 2020-11-20 19:52:48 +0000
Commit message:

 Bump densmap version
 
Package: densvis
Commit: 15831626401357381f224485709641c5933ecfdb
Author: Alan O'Callaghan <alan.ocallaghan@outlook.com>
Date: 2020-11-19 03:32:19 +0000
Commit message:

 Bugfix relating to errant parallelisation
 
Package: densvis
Commit: e8993d0bc2183cfa081c07c7deb7d35b70427a78
Author: Alan O'Callaghan <alan.ocallaghan@outlook.com>
Date: 2020-11-19 03:32:19 +0000
Commit message:

 Bugfix relating to errant parallelisation
 
Package: densvis
Commit: 561852a84405cb4eeb474cc174697fe0e7935ece
Author: Alan O'Callaghan <alan.ocallaghan@outlook.com>
Date: 2020-10-28 20:59:48 +0000
Commit message:

 Uneven version in devel
 
Package: densvis
Commit: db1997b56ecc5fafcd577bf03ae7b5447ba63ab7
Author: Alan O'Callaghan <alan.ocallaghan@outlook.com>
Date: 2020-10-28 20:58:25 +0000
Commit message:

 Correct citation and license information
 
Package: epiNEM
Commit: c952711e8e29e6843e6bb18e1d3ef43adc8d2c86
Author: mpirkl <martin.pirkl@bsse.ethz.ch>
Date: 2020-11-24 14:08:01 +0100
Commit message:

 fixed colorkey=NULL
 
Package: easyreporting
Commit: 7f2dbec2ab4657eb8f93e2d8393d7e5ef1e48aef
Author: Dario <dario.righelli@gmail.com>
Date: 2020-11-24 11:31:50 +0100
Commit message:

 ignore file
 
Package: easyreporting
Commit: ec7d278485cccf9dd6265588242996f90620c459
Author: Dario <dario.righelli@gmail.com>
Date: 2020-11-24 11:31:22 +0100
Commit message:

 adding volcano shiny app
 
Package: DelayedMatrixStats
Commit: f2a05aea8fd61c8c120e0cbfec5fbc3286299c81
Author: Peter Hickey <peter.hickey@gmail.com>
Date: 2020-11-24 20:52:51 +1100
Commit message:

 Merge pull request #69 from hpages/master

Fix 2 issues with how the 'center' argument is handled 
Package: DelayedMatrixStats
Commit: 84f344cbc84da5b54dde5f2a97227be90425a410
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2020-11-23 21:58:27 -0800
Commit message:

 Fix 2 issues with how the 'center' argument is handled

See https://github.com/PeteHaitch/DelayedMatrixStats/issues/68 for
the details.
 
Package: BiocStyle
Commit: 42e9365b9d46c4e62b9be53fb6438ad9c69370de
Author: Mike Smith <grimbough@gmail.com>
Date: 2020-11-24 10:50:38 +0100
Commit message:

 Add NEWS entry
 
Package: BiocStyle
Commit: c47acf3546252039e4eb327abe8f09258ab08fe1
Author: Mike Smith <grimbough@gmail.com>
Date: 2020-11-24 10:33:21 +0100
Commit message:

 Merge pull request #84 from grimbough/out-width

Patch issue with out.width for smallfigure and widefigure environments 
Package: BiocStyle
Commit: 40c40043e783fbf656827750d1a09e4abfec9214
Author: Mike Smith <grimbough@gmail.com>
Date: 2020-11-24 10:23:37 +0100
Commit message:

 remove commented out code
 
Package: BiocStyle
Commit: f8ec81f1bd1c2c33f97f3f40a04319fbf7432c57
Author: Mike Smith <grimbough@gmail.com>
Date: 2020-11-23 14:25:35 +0100
Commit message:

 Remove out.width argument committed by mistake
 
Package: BiocStyle
Commit: b3e36d002aac1adcba2be3a0d57a8d460c05922f
Author: Mike Smith <grimbough@gmail.com>
Date: 2020-11-23 14:18:15 +0100
Commit message:

 Patch issue with out.width for smallfigure and widefigure environments
 
Package: scran
Commit: 84954b7b9bd07a63486bbfcace491390dea75c28
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2020-11-23 23:41:51 -0800
Commit message:

 Deprecated combinePValues in favor of metapod::combineParallelPValues.
Updated tests.
 
Package: scran
Commit: 868f286c6384295507352904608af2076206ef60
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2020-11-08 00:36:05 -0800
Commit message:

 Catch warnings in pairwise* tests, minor streamlining.
 
Package: metapod
Commit: f2d71c7d693bf7e25ed8a67e775549d8475f4eef
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2020-11-24 00:48:54 -0800
Commit message:

 Throw error from non-finite weights.
 
Package: metapod
Commit: d06b6a537f231d1cf322025f959957a255a3aec1
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2020-11-24 00:23:56 -0800
Commit message:

 Bugfixes for correct Stouffer edge cases when log.p=TRUE.
 
Package: metapod
Commit: f6d9a98721ec98371bd32d1e879e0ebbf2851c9f
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2020-11-23 23:16:53 -0800
Commit message:

 Cleaned up documentation on wrappers.
 
Package: beachmat
Commit: 67dc7df4974c84a00053eef3f0132dfb8b89b940
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2020-11-23 21:49:03 -0800
Commit message:

 More efficient fallback for blockApply when DA is pristine.
Updated tests for more thorough checks.
 
Package: Rsubread
Commit: 805c98279416ec90b94f3f5538a3fa2bdc2c8889
Author: Yang LIAO <yang.liao@onjcri.org.au>
Date: 2020-11-24 17:06:25 +1100
Commit message:

 Parallel gzip
 
Package: Rsubread
Commit: 7220ee3ed80d2180d6ddfdec3f0e5e98ca448216
Author: Yang Liao <liao_y@svr2672.licr.unimelb.edu.au>
Date: 2020-11-24 15:49:12 +1100
Commit message:

 added comments to the junction-read assignment
 
Package: Rsubread
Commit: 360566014b3ecfa3cb54d0f3cb3d72e82e4eabbd
Author: Yang Liao <liao_y@svr2672.licr.unimelb.edu.au>
Date: 2020-11-24 15:16:04 +1100
Commit message:

 Moved junction read counting after basic read filters.
 
Package: Rsubread
Commit: 29a443da089fe45b1b7fb8d63b0f72f593466137
Author: Yang Liao <liao_y@svr2672.licr.unimelb.edu.au>
Date: 2020-11-24 14:37:58 +1100
Commit message:

 added parallel bam sorting
 
Package: EnrichmentBrowser
Commit: 8a666da69e0d842c14959d2c57b0eed537223d39
Author: lgeistlinger <ludwig.geistlinger@bio.ifi.lmu.de>
Date: 2020-11-23 18:44:02 -0500
Commit message:

 getGenesets: sync with msigdbr updates
 
Package: flowAI
Commit: f91149db132db2c9f243c4de7594461eab042583
Author: Gianni <mongianni1@gmail.com>
Date: 2020-11-23 23:36:11 +0100
Commit message:

 anomaly detection zeros
 
Package: SQLDataFrame
Commit: 0a90071a41afd81824d4da0ebeaff02dc72bf378
Author: Qian Liu <qliu7@buffalo.edu>
Date: 2020-11-23 17:16:19 -0500
Commit message:

 fixing mysql and bigrquery code in vignette
 
Package: diffcoexp
Commit: 2fed67b6aa0865010750664d4c8e3eca63bc661a
Author: Wenbin Wei <wenbinwei@da-bsc-44.home>
Date: 2020-11-23 16:17:32 +0000
Commit message:

 Updated maintainer's email address.
 
Package: diffcoexp
Commit: 563ddc806420b104e19b02e99dd067d4e4a85f20
Author: Wenbin Wei <wenbinwei@da-bsc-44.home>
Date: 2020-11-23 13:07:45 +0000
Commit message:

 Merge remote-tracking branch 'upstream/master'
 
Package: diffcoexp
Commit: 4ea9774972c3923b6307c65fa68aeef27d1db332
Author: wenbinwei <W.Wei@sheffield.ac.uk>
Date: 2019-05-15 14:39:13 +0100
Commit message:

 Updated version number.
 
Package: diffcoexp
Commit: 982d1821a77024dfec5e59f0cd8ca5d4204a2cf6
Author: Wenbin Wei <W.Wei@sheffield.ac.uk>
Date: 2019-05-15 13:34:25 +0100
Commit message:

 Merge pull request #2 from dktanwar/master

updated diffcor function to resolve an error 
Package: diffcoexp
Commit: bb822e40a810d4c9008e8bdc0e814dfe8264193b
Author: Deepak Tanwar <dktanwar@hotmail.com>
Date: 2019-05-15 08:50:48 +0200
Commit message:

 updated diffcor function to resolve an error
 
Package: dittoSeq
Commit: 07dfcaae85f1189c4dc0ec3f98ca010084490016
Author: dtm2451 <Daniel.Bunis@ucsf.edu>
Date: 2020-11-23 10:20:13 -0800
Commit message:

 Version Bump & NEWS Update
 
Package: dittoSeq
Commit: 5515d8bb36c2cd59d2b253ae8b50ded8b6464e80
Author: Daniel Bunis <daniel.bunis@ucsf.edu>
Date: 2020-11-23 10:16:47 -0800
Commit message:

 Bug Fix: keep `split.by` factor level order when used with `do.label` (#66)

 
Package: PharmacoGx
Commit: eeee68a021549bdfab23e85cdf57c15ae54a52cc
Author: ChristopherEeles <christopher.eeles@outlook.com>
Date: 2020-11-23 13:16:15 -0500
Commit message:

 Fix: type in downloadPertSig docs; version bump for Bioc push
 
Package: PharmacoGx
Commit: 26c3cbc22b6aab1bedfde61f6f2ba0539455e03c
Author: ChristopherEeles <christopher.eeles@outlook.com>
Date: 2020-11-23 13:13:50 -0500
Commit message:

 Add: NAMESPACE and man/
 
Package: PharmacoGx
Commit: 874e2d2f4e14022e6efa7715a54af2e45e9fe812
Author: ChristopherEeles <christopher.eeles@outlook.com>
Date: 2020-11-23 13:13:29 -0500
Commit message:

 Fix: downloadPertSig was failing due to download timeout, now temporarily changing timeout inside the function
 
Package: preciseTADhub
Commit: fc6c30e89d5db21cbc65bc1a2462dd9e1fb84743
Author: stilianoudakis <stilianoudasc@mymail.vcu.edu>
Date: 2020-11-23 12:51:09 -0500
Commit message:

 removed .Rproj, version bump
 
Package: preciseTADhub
Commit: c3edbe951e8e962c1e125145c63208abcee13a9a
Author: stilianoudakis <stilianoudasc@mymail.vcu.edu>
Date: 2020-11-23 12:49:31 -0500
Commit message:

 took out experimenthub from biocviews
 
Package: preciseTADhub
Commit: 640e9a6788af3d72b4e3b468b68afe28b5773093
Author: stilianoudakis <stilianoudasc@mymail.vcu.edu>
Date: 2020-11-23 12:18:28 -0500
Commit message:

 changed R version; version bump; edits to vignette
 
Package: PharmacoGx
Commit: b589c15c1b9f7c150711354da80bad2b35512d5c
Author: ChristopherEeles <christopher.eeles@outlook.com>
Date: 2020-11-23 12:17:14 -0500
Commit message:

 Update: downloadPertSig now uses the `PSet Name` column, the same as downloadPSet
 
Package: PharmacoGx
Commit: eb8e088b2a86ece326dda64053529da97af29c02
Author: ChristopherEeles <christopher.eeles@outlook.com>
Date: 2020-11-23 12:14:36 -0500
Commit message:

 Fix: Version bump for Bioc
 
Package: scuttle
Commit: 1ede46df3c54441900af998664e2863588b85c4a
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2020-11-23 09:00:57 -0800
Commit message:

 Proper support for Vectors in colData during aggregation.
 
Package: KnowSeq
Commit: cadaa0a30fc32958b8741a7b54d0253507baaa55
Author: casedUgr <cased@ugr.es>
Date: 2020-11-23 18:06:12 +0100
Commit message:

 Fixing bugs
 
Package: KEGGREST
Commit: a51655535b71c2cc3eae14c888fcbc02b71ff560
Author: Martin Morgan <Martin.Morgan@RoswellPark.org>
Date: 2020-11-23 12:04:39 -0500
Commit message:

 version bump
 
Package: KEGGREST
Commit: fd9970ea9df117d625257b8c6351cf85098cfbc1
Author: Martin Morgan <Martin.Morgan@RoswellPark.org>
Date: 2020-11-23 12:01:02 -0500
Commit message:

 version bump, acknowledgement, updated Title / Description

- Thanks Jeremy Vokening! closing #4
 
Package: KEGGREST
Commit: bfd08a1d1d5fd86cabaf27403b947e2d4d5295a6
Author: Martin Morgan <Martin.Morgan@RoswellPark.org>
Date: 2020-11-23 12:00:10 -0500
Commit message:

 minor tweaks

- mention offending function, and don't capitalize start, in error message
- avoid attaching httr in unit tests
 
Package: KEGGREST
Commit: d8d399c99bc74cd06621738e2e8bc9571c191fed
Author: jvolkening <jdv@base2bio.com>
Date: 2020-11-22 23:35:37 -0600
Commit message:

 use POST to fetch color maps
 
Package: SynExtend
Commit: 27d45d3cc420f0637017605001785d426cf220a0
Author: Cooley <npc19@Wrightlab-mnb-1.local>
Date: 2020-11-23 11:49:28 -0500
Commit message:

 fixed incorrect iterator
 
Package: multiHiCcompare
Commit: 5b1e6a576c64d3213caa91001ab4481d447f0bb1
Author: Mikhail Dozmorov <mikhail.dozmorov@gmail.com>
Date: 2020-11-23 11:14:18 -0500
Commit message:

 Ignore pkgdown
 
Package: multiHiCcompare
Commit: 63833565e906f525d3af050603644cd0d6ce3547
Author: Mikhail Dozmorov <mikhail.dozmorov@gmail.com>
Date: 2020-11-23 11:14:00 -0500
Commit message:

 Version 2.0.0 major update, see NEWS
 
Package: multiHiCcompare
Commit: bf9218bf42ee59d81649fde24eee7a5af33465cd
Author: Mikhail Dozmorov <mikhail.dozmorov@gmail.com>
Date: 2020-11-22 15:34:23 -0500
Commit message:

 Make filtering global and remove alpha parameter
 
Package: multiHiCcompare
Commit: a2fdae9f4a8f490358c0c9bc04d8e0e7afcf1eac
Author: Mikhail Dozmorov <mikhail.dozmorov@gmail.com>
Date: 2020-11-22 15:26:02 -0500
Commit message:

 Yaml adjustment
 
Package: multiHiCcompare
Commit: 0b80b5b14e932265485ecaef4136b35c82ec9943
Author: Mikhail Dozmorov <mikhail.dozmorov@gmail.com>
Date: 2020-11-22 15:20:25 -0500
Commit message:

 Merge branch 'master' of git.bioconductor.org:packages/multiHiCcompare
 
Package: multiHiCcompare
Commit: 41d4d5030f1d4d1c736830a6a9e47d1a8b4ce1f7
Author: Mikhail Dozmorov <mikhail.dozmorov@gmail.com>
Date: 2020-08-28 13:38:45 -0400
Commit message:

 Add Lifecycle stable badge
 
Package: multiHiCcompare
Commit: 2699f6f0e59e8b92c7389d3b5d51850a9cfb6125
Author: Mikhail Dozmorov <mikhail.dozmorov@gmail.com>
Date: 2020-08-28 13:38:00 -0400
Commit message:

 Add BioC badge
 
Package: VarCon
Commit: 99f44e040df67e6419309cc0ab70e8fc9c99d54c
Author: caggtaagtat <Johannes@web.de>
Date: 2020-11-23 17:11:35 +0100
Commit message:

 removed quotes from file
 
Package: CNVgears
Commit: a31d32885a4b66077a9d454d110082b1a260fa9b
Author: Simone Montalbano <simone.montalbano@protonmail.com>
Date: 2020-11-23 16:58:51 +0100
Commit message:

 version bump
 
Package: CNVgears
Commit: 72a4ccd7fdbf9dbb9041b3ca0920458e49ae75bb
Author: Simone Montalbano <simone.montalbano@protonmail.com>
Date: 2020-11-23 16:58:29 +0100
Commit message:

 several minor fixes
 
Package: VarCon
Commit: d1bcc605f9bd0b05d4562f536a147fded454b568
Author: caggtaagtat <Johannes@web.de>
Date: 2020-11-23 16:46:09 +0100
Commit message:

 FALSE instead of F
 
Package: CNVgears
Commit: f89059a7c8c604adbb328ad91e26c52fb9b39ec6
Author: Simone Montalbano <simone.montalbano@protonmail.com>
Date: 2020-11-23 16:35:45 +0100
Commit message:

 version bump
 
Package: CNVgears
Commit: 648395e9e26f4079a13ba6a80d995ad16694fb68
Author: Simone Montalbano <simone.montalbano@protonmail.com>
Date: 2020-11-23 16:33:51 +0100
Commit message:

 expanded man pages of the example data
 
Package: CNVgears
Commit: b6a927b8f82fb9ede10d14fd2de55776ff4a0052
Author: Simone Montalbano <simone.montalbano@protonmail.com>
Date: 2020-11-23 16:25:52 +0100
Commit message:

 changed vingette file name
 
Package: CNVgears
Commit: 23a2f4b11209bbeb767b2f66455b53bb4aa07ca4
Author: Simone Montalbano <simone.montalbano@protonmail.com>
Date: 2020-11-23 16:24:42 +0100
Commit message:

 updated DESCRIPTION
 
Package: CNVgears
Commit: 7b2821742f17748c2dc798659e0068e04fe7315f
Author: Simone Montalbano <simone.montalbano@protonmail.com>
Date: 2020-11-23 11:51:07 +0100
Commit message:

 updated vignette
 
Package: CNVgears
Commit: dbd91a4a81cf71610358e97d5bd274e63cfa4add
Author: Simone Montalbano <simone.montalbano@protonmail.com>
Date: 2020-11-23 11:50:55 +0100
Commit message:

 improved a warning
 
Package: CNVgears
Commit: 1737d593e05965267d3bed54f84818fca4c1573f
Author: Simone Montalbano <simone.montalbano@protonmail.com>
Date: 2020-11-23 11:10:05 +0100
Commit message:

 changed cat() to message()
 
Package: CNVgears
Commit: d4636b85f898e48f8909cc3cfeecfd9fefe6ef51
Author: Simone Montalbano <simone.montalbano@protonmail.com>
Date: 2020-11-20 16:12:56 +0100
Commit message:

 updated vignette
 
Package: CNVgears
Commit: d6611593b59aaf3808b63391df4b57190146b008
Author: Simone Montalbano <simone.montalbano@protonmail.com>
Date: 2020-10-28 10:54:28 +0100
Commit message:

 update
 
Package: CNVgears
Commit: 755dfc1a104b27992ebfcd10d3941877ce4dce6e
Author: Simone Montalbano <simone.montalbano@protonmail.com>
Date: 2020-10-28 10:47:52 +0100
Commit message:

 version bump
 
Package: CNVgears
Commit: 1aa937496f8ef471f86f68f14a4e925bfa3e14d1
Author: Simone Montalbano <simone.montalbano@protonmail.com>
Date: 2020-10-22 15:20:13 +0200
Commit message:

 cnmops conversion was not complete
 
Package: VarCon
Commit: 0c4ddd44de216c14fb261e803422cf80aed46ec4
Author: caggtaagtat <Johannes@web.de>
Date: 2020-11-23 16:28:33 +0100
Commit message:

 version
 
Package: VarCon
Commit: e243544afb3184a549e7aac34ad5cad0849d3320
Author: caggtaagtat <Johannes@web.de>
Date: 2020-11-23 16:26:49 +0100
Commit message:

 temp file
 
Package: CoGAPS
Commit: e448a5906fba3203ef6ec9b0f71796ac9549ae0b
Author: lothm2014 <lothm2014@yahoo.com>
Date: 2020-11-23 07:49:16 -0500
Commit message:

 Fixed merge conflict
 
Package: CoGAPS
Commit: 898e0728fb732e7b91a82138a41384e2cff5f1f7
Author: lothm2014 <lothm2014@yahoo.com>
Date: 2020-11-23 07:43:57 -0500
Commit message:

 Updated version on README
 
Package: CoGAPS
Commit: 04046b9dba14207fad3f7ea5c32e8e89e2f3522f
Author: lothm2014 <lothm2014@yahoo.com>
Date: 2020-11-23 07:42:06 -0500
Commit message:

 Updated version on bh updates
 
Package: CoGAPS
Commit: ffe8aca25ae33e7b2bdfeb4ae347ab1e5097587e
Author: ejfertig <ejfertig@jhmi.edu>
Date: 2020-10-29 15:07:11 -0400
Commit message:

 upped version of description
 
Package: CoGAPS
Commit: c7bfef9db6d4672c09c10d53462407f0d8309734
Author: ejfertig <ejfertig@jhmi.edu>
Date: 2020-10-29 15:01:56 -0400
Commit message:

 added BH dependency
 
Package: CoGAPS
Commit: f34ce7ea3adae95f608d6c5751ac80624da3774f
Author: ejfertig <ejfertig@jhmi.edu>
Date: 2020-10-29 14:53:48 -0400
Commit message:

 remove manual inclusion of boost
 
Package: VarCon
Commit: 9142641093b862272097be0390012473b237c301
Author: caggtaagtat <Johannes@web.de>
Date: 2020-11-23 12:55:44 +0100
Commit message:

 des
 
Package: VarCon
Commit: 1ef1651775e15c6904c20915c59890e20d538cfe
Author: caggtaagtat <Johannes@web.de>
Date: 2020-11-23 12:47:47 +0100
Commit message:

 add example transcript table
 
Package: VarCon
Commit: 5594dbc4a0ca13f1f9bf1b7ee668e43642bbd006
Author: caggtaagtat <Johannes@web.de>
Date: 2020-11-23 12:41:20 +0100
Commit message:

 work on reviewers remarks
 
Package: AnVIL
Commit: 09bf387494153be29912acc91f1e7dbab9d63645
Author: Martin Morgan <Martin.Morgan@RoswellPark.org>
Date: 2020-11-23 05:54:05 -0500
Commit message:

 version bump and documentation tweaks
 
Package: AnVIL
Commit: d31e5feab21f8a02fd0c634d628f7986b01f3498
Author: Sehyun Oh <shbrief@gmail.com>
Date: 2020-11-22 23:26:13 -0500
Commit message:

 Include the submission status information for avworkflow_jobs
 
Package: AnVIL
Commit: 308c12ad8ee7fd6729e8eceab5937d4f47503f1a
Author: Martin Morgan <Martin.Morgan@RoswellPark.org>
Date: 2020-11-23 05:30:55 -0500
Commit message:

 add avnotebooks_*()
 
Package: DEScan2
Commit: fd11c2ac39cdec89bb14752f7f7bc1d4ef4a9b50
Author: Dario <dario.righelli@gmail.com>
Date: 2020-11-23 09:12:30 +0100
Commit message:

 fixed filepath in countFinalRegions
 
Package: MicrobiotaProcess
Commit: 6a538fc118192637aef75ce9f52c502dc8b75272
Author: xiangpin <xshuangbin@163.com>
Date: 2020-11-23 15:38:42 +0800
Commit message:

 update news and bump version
 
Package: MicrobiotaProcess
Commit: d37c0555fdfa3b9cc73d1dab801c82b4f2b577eb
Author: xiangpin <xshuangbin@163.com>
Date: 2020-11-23 15:38:14 +0800
Commit message:

 add as.treedata
 
Package: ReactomeContentService4R
Commit: 9791277ea662d2092724027404c146f43fa0a746
Author: chilampoon <clpoon807@gmail.com>
Date: 2020-11-23 12:08:04 +0800
Commit message:

 Correct license format & bump version
 
Package: ReactomeContentService4R
Commit: 3ed7275d7c80aa1fa9f4f2843f440f232bb5a22c
Author: chilampoon <clpoon807@gmail.com>
Date: 2020-11-23 12:07:36 +0800
Commit message:

 Add .onLoad()
 
Package: proActiv
Commit: c5b35139b1feb27d0aaf6d1a337e2a46320c37d8
Author: Joseph Lee <joseph.lee@u.nus.edu>
Date: 2020-11-23 10:57:03 +0800
Commit message:

 Merge remote-tracking branch 'upstream/master'
 
Package: proActiv
Commit: dd632f4ccda9b535ecb7566afb2d4aaac1ebf1ba
Author: Joseph Lee <joseph.lee@u.nus.edu>
Date: 2020-11-23 10:54:21 +0800
Commit message:

 update vignette
 
Package: proActiv
Commit: 07d9fe0ff809d10a9fb4f2c27c3cf8a018afd60d
Author: Joseph Lee <joseph.lee@u.nus.edu>
Date: 2020-11-23 10:53:47 +0800
Commit message:

 updated README
 
Package: proActiv
Commit: 9e4b065e503f12dcf5d07882cd51845d854c21d6
Author: Joseph Lee <joseph.lee@u.nus.edu>
Date: 2020-11-23 10:53:16 +0800
Commit message:

 update NEWS
 
Package: CellaRepertorium
Commit: ddcab247d898281bc59928bb483058ac9fa49c81
Author: Andrew McDavid <andrew.n.mcdavid@gmail.com>
Date: 2020-11-22 16:24:05 -0500
Commit message:

 bump
 
Package: CellaRepertorium
Commit: b23e97bd7d2248feb619499d941f8e38ac2adc24
Author: Andrew McDavid <andrew.n.mcdavid@gmail.com>
Date: 2020-11-22 16:23:14 -0500
Commit message:

 more care for pairing in cells with no contigs
 
Package: CellaRepertorium
Commit: dd80804245472fdaa39d74fcf2b0b5e0a3891f64
Author: Andrew McDavid <andrew.n.mcdavid@gmail.com>
Date: 2020-11-05 17:32:06 -0500
Commit message:

 Fixes #6
 
Package: flowAI
Commit: c1f740b9ae80aca7f1cf509f84a0dec31ac99df6
Author: Gianni <mongianni1@gmail.com>
Date: 2020-11-22 22:10:43 +0100
Commit message:

 add out of range check
 
Package: SpectralTAD
Commit: 69032f749cab1669e1aa2e0d3e6835315024c01d
Author: Mikhail Dozmorov <mikhail.dozmorov@gmail.com>
Date: 2020-11-22 15:11:19 -0500
Commit message:

 Version bump
 

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