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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: scFeatures
Commit: 4ca6bc88abab158f8556e46fdb26680b955d2187
Author: Yue Cao <yuec@maths.usyd.edu.au>
Date: 2022-12-06 12:48:58 +1100
Commit message:

 Revert "stupid change"

This reverts commit 53c230d41fe9cd70a69686098a9f2ebf2f665e9c.
 
Package: scFeatures
Commit: 53c230d41fe9cd70a69686098a9f2ebf2f665e9c
Author: Nicholas Robertson <nickrrrr@gmail.com>
Date: 2022-12-06 12:47:05 +1100
Commit message:

 stupid change
 
Package: scFeatures
Commit: 7651a03653cff99e59e50e377124b734356b034c
Author: Nick <nickrrrr@gmail.com>
Date: 2022-12-06 12:03:20 +1100
Commit message:

 start fixing output report
 
Package: scFeatures
Commit: fb0084f999d9284f348ef55d3848f9e0645fcc12
Author: Nick <nickrrrr@gmail.com>
Date: 2022-12-06 11:49:58 +1100
Commit message:

 remove inline
 
Package: scFeatures
Commit: 16199291cbc473fc669a8dc76ca168c01e2ea056
Author: Nick <nickrrrr@gmail.com>
Date: 2022-12-06 11:43:21 +1100
Commit message:

 remove RhpcBLASctl
 
Package: scFeatures
Commit: db4b899e3ae028cfa430d201e9460e58b5b03770
Author: Nick <nickrrrr@gmail.com>
Date: 2022-12-06 11:40:19 +1100
Commit message:

 re-add ClassifyR
 
Package: scFeatures
Commit: 823a2fb81cbb340a8d64da051abd20c69f11257f
Author: Nick <nickrrrr@gmail.com>
Date: 2022-12-06 11:39:12 +1100
Commit message:

 use `BiocStyle`
 
Package: scFeatures
Commit: 3e9c6caea50f8614518894ebbdac3ef10a6dc09a
Author: Nick <nickrrrr@gmail.com>
Date: 2022-12-06 10:31:07 +1100
Commit message:

 downsample scrnaseq data
 
Package: scFeatures
Commit: f8776d3f1caa516e513eecec293ed6d18cc3b0c9
Author: Nick <nickrrrr@gmail.com>
Date: 2022-12-06 09:40:07 +1100
Commit message:

 Merge branch 'master' of github.com:SydneyBioX/scFeatures
 
Package: scFeatures
Commit: 02ffbb1d7fb7896c5506ee6515d37bb13fe3e48e
Author: Nick <nickrrrr@gmail.com>
Date: 2022-12-06 09:39:28 +1100
Commit message:

 add review comment from Pete
 
Package: Voyager
Commit: 4589718b4afe4c87bb96fe730cab9b831d113887
Author: Lambda Moses <dlu2@caltech.edu>
Date: 2022-12-05 17:19:18 -0800
Commit message:

 version bump
 
Package: Voyager
Commit: ca613478dc023b3355b08b38ff61bd715fa58e52
Author: Lambda Moses <dlu2@caltech.edu>
Date: 2022-12-05 17:11:16 -0800
Commit message:

 Merge from main

Merge branch 'main' into devel
 
Package: Voyager
Commit: e581995c0fa6c66f15c3b8d9040103a37026cd66
Author: Lambda Moses <dlu2@caltech.edu>
Date: 2022-12-05 17:10:48 -0800
Commit message:

 Problem with show_symbol when rowData only has one column
 
Package: Voyager
Commit: 85b251f9e3459496f944152bf0cc934d440f4a74
Author: Lambda Moses <dlu2@caltech.edu>
Date: 2022-12-03 22:47:41 -0800
Commit message:

 Use ditto_colors to fill in plotColDataHistogram
 
Package: Voyager
Commit: 6bbe5de3c5b045a7c3cedec395b70631f812850b
Author: Lambda Moses <dlu2@caltech.edu>
Date: 2022-12-03 22:47:11 -0800
Commit message:

 plotGeometry
 
Package: Voyager
Commit: 6a77d46ba13346da8bc8822f9e0fa8eee8c0c8d5
Author: Lambda Moses <dlu2@caltech.edu>
Date: 2022-12-03 21:04:29 -0800
Commit message:

 Merge from main

Merge branch 'main' into devel
 
Package: Voyager
Commit: b4d133901b23f24e0e517e7a59ad6104701a14b1
Author: Lambda Moses <dlu2@caltech.edu>
Date: 2022-12-03 21:04:07 -0800
Commit message:

 Plot cell density bin2D for multiple samples. Also changed defaults from sample_id = NULL to sample_id = "all"
 
Package: Voyager
Commit: 1a7f29769cc8fd17be69673052a3596a8fe5e90e
Author: Lambda Moses <dlu2@caltech.edu>
Date: 2022-12-03 14:50:36 -0800
Commit message:

 Use setup-bioc action
 
Package: Voyager
Commit: 87cd55b3de432f0ab8ac4a2369459b4dfa561c13
Author: Lambda Moses <dlu2@caltech.edu>
Date: 2022-12-03 14:32:18 -0800
Commit message:

 Install Bioc version 3.16 for codecov
 
Package: Voyager
Commit: 193a76328f1c575e4c2c1978995f4553f0fec5fc
Author: Lambda Moses <dlu2@caltech.edu>
Date: 2022-12-03 13:59:27 -0800
Commit message:

 Force codecov to use current version of ExperimentHub
 
Package: Voyager
Commit: 1a973cf802fcada9c3c8973515b47008d4155d8f
Author: Lambda Moses <dlu2@caltech.edu>
Date: 2022-12-02 22:51:14 -0800
Commit message:

 Merge from main

Merge branch 'main' into devel

# Conflicts:
#	DESCRIPTION
 
Package: Voyager
Commit: bdea8e260046164779a8f9b1a7868efb9d4fb531
Author: Lambda Moses <dlu2@caltech.edu>
Date: 2022-12-02 22:49:26 -0800
Commit message:

 version bump and news
 
Package: Voyager
Commit: d643149c9ceb236af272e656c52758d65b825353
Author: Lambda Moses <dlu2@caltech.edu>
Date: 2022-12-02 22:47:17 -0800
Commit message:

 Delete pkgdown_dev. Use fork instead
 
Package: Voyager
Commit: ca472608150c31bb7eb0f36bdbad33b49a6d0653
Author: Lambda Moses <dlu2@caltech.edu>
Date: 2022-12-02 22:43:07 -0800
Commit message:

 Already in devel, but really should be in main
 
Package: Voyager
Commit: 37bed4bf9138ed3a8ddf38adce810f83d6f8b1a0
Author: Lambda Moses <dlu2@caltech.edu>
Date: 2022-12-02 22:37:33 -0800
Commit message:

 Also add facet_by to plotColDataHistogram. And rename the argument from sfe to sce since these plotting functions are non-spatial.
 
Package: Voyager
Commit: 92a30801c2629ba895c70a42a6028707e12a1178
Author: Lambda Moses <dlu2@caltech.edu>
Date: 2022-12-02 22:16:35 -0800
Commit message:

 Remove pkgdown_dev
 
Package: Voyager
Commit: c32d20f0601e6c2e44cd0f9b63e47d93f5a8b907
Author: Lambda Moses <dlu2@caltech.edu>
Date: 2022-12-02 22:08:38 -0800
Commit message:

 Added facet_by to plotColDataBin2D, such as to plot different samples in different facets.
 
Package: Voyager
Commit: 49685adcdef25158aad102017297c51b8178d779
Author: Lambda Moses <dlu2@caltech.edu>
Date: 2022-12-02 21:11:07 -0800
Commit message:

 Fix error when "symbol" column is absent from rowData
 
Package: Voyager
Commit: c485efdf457fe55aa9eb4044e14729d73c0aeaf7
Author: Lambda Moses <dlu2@caltech.edu>
Date: 2022-12-01 21:42:56 -0800
Commit message:

 Merge from main

Merge branch 'main' into devel

# Conflicts:
#	DESCRIPTION
 
Package: Voyager
Commit: 400057f800804d0d701ac7694dd8ef455d7023d3
Author: Lambda Moses <dlu2@caltech.edu>
Date: 2022-12-01 20:54:54 -0800
Commit message:

 Make that new unit test for multiple features as well as multiple samples
 
Package: Voyager
Commit: 6dd406b83e414b4544545969da8016470342805d
Author: Lambda Moses <dlu2@caltech.edu>
Date: 2022-12-01 19:59:54 -0800
Commit message:

 New unit test for localResults and multiple samples
 
Package: Voyager
Commit: 93c8e27f43adfac54e31f47dad1593f6e249f31b
Author: Lambda Moses <dlu2@caltech.edu>
Date: 2022-12-01 17:09:01 -0800
Commit message:

 Try new pkgdown_dev workflow for development version of website
 
Package: Voyager
Commit: 68354e1c74adcdb3db6bc9b2c86c842f9b35b9ba
Author: Lambda Moses <dlu2@caltech.edu>
Date: 2022-11-30 23:13:12 -0800
Commit message:

 Merge branch 'main' of github.com:pachterlab/voyager
 
Package: Voyager
Commit: f9bc22a45264fad7ec49076a26ea9eda9c45cb23
Author: Lambda Moses <dlu2@caltech.edu>
Date: 2022-11-30 23:12:44 -0800
Commit message:

 Temporarily comment out hexbin unit tests until ggplot2 team fixes that bug
 
Package: Voyager
Commit: 43d821c6666912ce54ec8485fd3e8394b8296985
Author: Lambda Moses <dlu2@caltech.edu>
Date: 2022-11-30 23:12:25 -0800
Commit message:

 Removed aes_string, which is deprecated.
 
Package: Voyager
Commit: b3311670ebeb65e0863333e3525398cd3b960e7a
Author: Lambda Moses <dlu2@caltech.edu>
Date: 2022-11-21 09:54:41 -0800
Commit message:

 New snapshots for new version of ggplot
 
Package: Voyager
Commit: f0778b2c247804add2cc2c1ae2561fdab2aea5f8
Author: Lambda Moses <dlu2@caltech.edu>
Date: 2022-11-18 15:59:37 -0800
Commit message:

 Merge branch 'RELEASE_3_16' of git.bioconductor.org:packages/Voyager
 
Package: Voyager
Commit: 152f3ce7ad1613f858aa3466a176dacc26962130
Author: Lambda Moses <dlu2@caltech.edu>
Date: 2022-11-16 20:58:41 -0800
Commit message:

 Merge branch 'main' of github.com:pachterlab/voyager
 
Package: Voyager
Commit: 02b13bbaf57c733bdf747722a7eea98a592291f5
Author: Lambda Moses <dlu2@caltech.edu>
Date: 2022-11-16 20:44:40 -0800
Commit message:

 Fixed bug in show_symbol in moranPlot
 
Package: Voyager
Commit: b1f2a0a7f6457893ae2dd4e17f5b8577ef0cea8b
Author: Lambda Moses <dlu2@caltech.edu>
Date: 2022-11-07 15:51:33 -0800
Commit message:

 Merged from main

Merge branch 'main' into RELEASE_3_16
 
Package: Voyager
Commit: d67bd7be05fb889b204985a4d85d7b973e0fd3aa
Author: Lambda Moses <dlu2@caltech.edu>
Date: 2022-11-07 15:48:45 -0800
Commit message:

 Version bump for bug fix
 
Package: Voyager
Commit: 3e4c55c8e2335a3db16526c42677eee3fa5bd64f
Author: Lambda Moses <dlu2@caltech.edu>
Date: 2022-11-02 17:44:42 -0700
Commit message:

 Suggest dbscan

Merge branch 'main' into RELEASE_3_16
 
Package: Voyager
Commit: 449ad8baa70a325db6764ec6c2eb79b99feb6d40
Author: Lambda Moses <dlu2@caltech.edu>
Date: 2022-11-02 16:01:07 -0700
Commit message:

 Merged from main

Merge branch 'main' into RELEASE_3_16
 
Package: Voyager
Commit: 3c5483413131c043321aef457cf27635e45f8f8a
Author: Lambda Moses <dlu2@caltech.edu>
Date: 2022-11-01 20:49:13 -0700
Commit message:

 Forgot orcid

Merge branch 'main' into RELEASE_3_16

# Conflicts:
#	DESCRIPTION
 
Package: Voyager
Commit: b8ab6746df680d882e5cefd509f3c84da4abbd6d
Author: Lambda Moses <dlu2@caltech.edu>
Date: 2022-11-01 20:43:47 -0700
Commit message:

 Added Kayla
 
Package: cfDNAPro
Commit: f90c93616c143138dd2edcb747dfe3a7bca10f70
Author: haichao <wanghaichao2014@gmail.com>
Date: 2022-12-05 22:34:15 +0000
Commit message:

 remove a typo

 
Package: cfDNAPro
Commit: f3df096b23a4e8fb7332f0267fbe6304116728a1
Author: haichao <wanghaichao2014@gmail.com>
Date: 2022-12-05 22:32:39 +0000
Commit message:

 Merge remote-tracking branch 'origin/master'

 
Package: cfDNAPro
Commit: d9e740840f12991fc2e19ad4f57cba1bb1b24480
Author: haichao <wanghaichao2014@gmail.com>
Date: 2022-12-05 22:32:25 +0000
Commit message:

 move BSgenome from 'suggests' to 'Imports'

and added hg38-NCBI  
Package: cfDNAPro
Commit: 2ebd2f402ee5528354e561c7dafe1cef0a0330f7
Author: haichaowang <wanghaichao2014@gmail.com>
Date: 2022-12-05 21:30:32 +0000
Commit message:

 Update README.md 
Package: cfDNAPro
Commit: 11b7800a625d9e26c98af9354a328ed5d0bd39d8
Author: haichao <wanghaichao2014@gmail.com>
Date: 2022-12-05 21:27:38 +0000
Commit message:

 Merge remote-tracking branch 'origin/master'

 
Package: cfDNAPro
Commit: 95bf72fb5d6609b19cdea584dc942ece01f8aee4
Author: haichaowang <wanghaichao2014@gmail.com>
Date: 2022-12-05 21:26:31 +0000
Commit message:

 upload logo with transparent background 
Package: cfDNAPro
Commit: 44ea58ac5b7e58bb55df6db7d31c52c1dfec6a15
Author: haichaowang <wanghaichao2014@gmail.com>
Date: 2022-12-05 21:25:56 +0000
Commit message:

 Delete logo.png 
Package: cfDNAPro
Commit: b24b2a5ec04adc8bf70f654af2a48822d95cb103
Author: haichao <wanghaichao2014@gmail.com>
Date: 2022-12-03 12:49:53 +0000
Commit message:

 Merge remote-tracking branch 'origin/master'

 
Package: cfDNAPro
Commit: 114f9db230e6c0a2d9e843c53fd29cfa1deca2d0
Author: haichaowang <wanghaichao2014@gmail.com>
Date: 2022-12-03 12:49:09 +0000
Commit message:

 Update README.md 
Package: cfDNAPro
Commit: 986b19ec98fd7d3ad2e3b987493f46ba4bdbd705
Author: haichaowang <wanghaichao2014@gmail.com>
Date: 2022-12-03 12:48:37 +0000
Commit message:

 Update README.md 
Package: cfDNAPro
Commit: 8059fb86fcf007e715d5460c4972761d41d1b725
Author: haichaowang <wanghaichao2014@gmail.com>
Date: 2022-12-02 21:31:24 +0000
Commit message:

 Update README.md 
Package: cfDNAPro
Commit: 07fa8c886d2df304ab2e4bf2f776d0276e123340
Author: haichaowang <wanghaichao2014@gmail.com>
Date: 2022-12-02 21:30:37 +0000
Commit message:

 Update README.md 
Package: cfDNAPro
Commit: 50d090e0503c02fe981e41f48957f4fc7562c48e
Author: haichaowang <wanghaichao2014@gmail.com>
Date: 2022-12-02 21:28:52 +0000
Commit message:

 Update README.md 
Package: cfDNAPro
Commit: 076b2a600e0783b417541088f529ddd35413b018
Author: haichaowang <wanghaichao2014@gmail.com>
Date: 2022-12-02 21:24:26 +0000
Commit message:

 Update README.md 
Package: cfDNAPro
Commit: 4686af0bd359e7b3fdfc74bd65bd1b8efa5454b0
Author: haichaowang <wanghaichao2014@gmail.com>
Date: 2022-12-02 21:21:56 +0000
Commit message:

 update version number 
Package: cfDNAPro
Commit: 9f332d08cdb0042d129f6124aef1da7a36b6767c
Author: haichao <wanghaichao2014@gmail.com>
Date: 2022-12-02 20:13:19 +0000
Commit message:

 Merge remote-tracking branch 'origin/master'

 
Package: cfDNAPro
Commit: 4b6b41c8bd025937f8de09d6044caedaa49d4175
Author: haichaowang <wanghaichao2014@gmail.com>
Date: 2022-12-02 20:09:47 +0000
Commit message:

 Update README.md 
Package: cfDNAPro
Commit: 305ef83651a52c3ed9c33f6d2fcc00a4b593ceb8
Author: haichaowang <wanghaichao2014@gmail.com>
Date: 2022-12-02 20:08:43 +0000
Commit message:

 added hit badge 
Package: cfDNAPro
Commit: 64afe68aa0524438cf28a385b5fef4f22099c7d8
Author: haichaowang <wanghaichao2014@gmail.com>
Date: 2022-12-02 16:41:08 +0000
Commit message:

 added download stats to Readme 
Package: cfDNAPro
Commit: 5a60dcb12ebfa5ac3d825924387cbaaf5eb4ecf8
Author: haichao <wanghaichao2014@gmail.com>
Date: 2022-11-29 17:34:13 +0000
Commit message:

 draft CNV and motif functions 

 
Package: S4Vectors
Commit: 78f8e38ecef0f41fb4cc900033e3d89cde3fb836
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2022-12-05 10:33:46 -0800
Commit message:

 Small tweak to default_extractROWS()

Do not use 'drop=FALSE' when subsetting 'x' in 'default_extractROWS(x, i)'
when 'x' has no dimensions (i.e. when 'dim(x)' is NULL). This ensures that
extractROWS() works on S3 objects that inherit from an atomic type but
break on 'x[i, drop=FALSE]'. See:
    https://support.bioconductor.org/p/9148139/#9148195
and
    https://github.com/tidyverse/haven/issues/698
 
Package: katdetectr
Commit: 5203eb8bc34b069b9506f3cdc328356f46ba0bb8
Author: Daan Hazelaar <daanhazelaar@gmail.com>
Date: 2022-12-05 18:02:32 +0100
Commit message:

 implement hg38 reference genome and user specified reference genome
 
Package: katdetectr
Commit: 27dfdfc0e8ff795522e4ab877aa502b4b43d35f0
Author: Daan Hazelaar <daanhazelaar@gmail.com>
Date: 2022-11-02 10:22:09 +0100
Commit message:

 update IMD cutoff function and search method
 
Package: katdetectr
Commit: a70093d0d738a77368a38d7357a7803a21f1a1f7
Author: Daan Hazelaar <daanhazelaar@gmail.com>
Date: 2022-11-02 09:54:36 +0100
Commit message:

 added option for custom function for IMD cutoff value. And allow user to specifiy search method
 
Package: katdetectr
Commit: 67dacdf9120b24ec5614a216b35447c25cd20c1d
Author: Daan Hazelaar <daanhazelaar@gmail.com>
Date: 2022-10-17 09:43:41 +0200
Commit message:

 bug fix in performChangepointAnalysis
 
Package: katdetectr
Commit: dfe79ac4b1dc2ce884062fef97cfbf0c2220a419
Author: Daan Hazelaar <daanhazelaar@gmail.com>
Date: 2022-10-14 13:32:59 +0200
Commit message:

 rebase
 
Package: msa
Commit: 398d017d95aad258b63e42b2d66dc84256fdb64b
Author: UBod <ulrich@bodenhofer.com>
Date: 2022-12-05 12:55:56 +0100
Commit message:

 Update of gc; version number bumped to 1.31.1
 
Package: msa
Commit: 2407cb93f3c786cb68c6703bb87bfda14d4d9813
Author: UBod <ulrich@bodenhofer.com>
Date: 2022-12-05 12:43:12 +0100
Commit message:

 Update of gc
 
Package: msa
Commit: 79494b5f80da91798e1064f2e68da1d852981ee4
Author: UBod <ulrich@bodenhofer.com>
Date: 2022-12-02 12:06:59 +0100
Commit message:

 update of gc; version number bumped to 1.31.1
 
Package: scFeatures
Commit: 80034c0ec37c206d63a08198e22dda351126b805
Author: Nicholas Robertson <nickrrrr@gmail.com>
Date: 2022-12-05 14:06:24 +1100
Commit message:

 remove large file
 
Package: scFeatures
Commit: 75ee626710e420fadc74667f669ee8a4d3867ad0
Author: Nicholas Robertson <nickrrrr@gmail.com>
Date: 2022-12-05 13:32:15 +1100
Commit message:

 ignore docs
 
Package: scFeatures
Commit: 70f2368548e0de7d6a31bf6d1dc6a839b6c3e04e
Author: Nicholas Robertson <nickrrrr@gmail.com>
Date: 2022-12-05 13:26:00 +1100
Commit message:

 add web page
 
Package: scFeatures
Commit: 8f211a4f97d5e0a3306f32e48fc035ea28e0094b
Author: Nick <nickrrrr@gmail.com>
Date: 2022-11-28 15:15:19 +1100
Commit message:

 bump version
 
Package: scFeatures
Commit: 9de0d8bdfe164120b415b2f80e4a7f08fcf94c37
Author: Nick <nickrrrr@gmail.com>
Date: 2022-11-28 15:14:54 +1100
Commit message:

 remove ensembldb::select from namespace
 
Package: scFeatures
Commit: a40fddce4b7b7a7a1d1d23a3873f6325a70154a2
Author: Nick <nickrrrr@gmail.com>
Date: 2022-11-28 14:56:38 +1100
Commit message:

 FIX CHECK ERRORS
 
Package: scFeatures
Commit: 0eb998750787154d38afe825e755c6e0468fcd27
Author: Nicholas Robertson <nickrrrr@gmail.com>
Date: 2022-11-23 16:10:25 +1100
Commit message:

 new benchmark
 
Package: scFeatures
Commit: 209e7ca667232ec53b0516edae50c691bb9b0603
Author: Nicholas Robertson <nickrrrr@gmail.com>
Date: 2022-11-23 15:55:54 +1100
Commit message:

 move dev functions so that they are loaded round 2
 
Package: scFeatures
Commit: 7c711cf2cf1d69e3c4bdcca6c036882047d3f2b2
Author: Nicholas Robertson <nickrrrr@gmail.com>
Date: 2022-11-23 15:52:17 +1100
Commit message:

 move dev functions so that they are loaded
 
Package: scFeatures
Commit: 709f075578bf01b1823dc39fe1d5617472c3f888
Author: Nicholas Robertson <nickrrrr@gmail.com>
Date: 2022-11-23 15:48:28 +1100
Commit message:

 run styler
 
Package: scFeatures
Commit: 0c41ba6077af3df463e325d6cc138ead5ab0d9c4
Author: Nicholas Robertson <nickrrrr@gmail.com>
Date: 2022-11-23 11:57:11 +1100
Commit message:

 add refactoring code
 
Package: SPIAT
Commit: c18187503c98d633fae8e621d2bb5f4dc5c1f9bc
Author: fuerzhou <yuzhou0610@gmail.com>
Date: 2022-12-05 14:11:36 +1100
Commit message:

 Updated the version in CITATION
 
Package: SPIAT
Commit: d8faaa116cfa012dd3760e846b6752aeff898262
Author: fuerzhou <yuzhou0610@gmail.com>
Date: 2022-12-05 13:59:04 +1100
Commit message:

 Version bump in dev branch.
 
Package: SPIAT
Commit: 5299dc2f42c8746adf1ecb53d5e1edce7688f87d
Author: fuerzhou <yuzhou0610@gmail.com>
Date: 2022-12-05 13:56:38 +1100
Commit message:

 Updated README
 
Package: SPIAT
Commit: 8f403c8edb178e982014b3d89d145cd26a3995d5
Author: fuerzhou <yuzhou0610@gmail.com>
Date: 2022-12-05 13:01:23 +1100
Commit message:

 Improved the documentation of data formatting with "general" option.
 
Package: SPIAT
Commit: add1f515c7ba502aa97ad23d9ea460a920209b54
Author: fuerzhou <yuzhou0610@gmail.com>
Date: 2022-12-05 12:35:48 +1100
Commit message:

 Try organsing the vignettes into categories
 
Package: SPIAT
Commit: aee43ff9edfbe37276c4ceed5d803d625babb2fd
Author: fuerzhou <yuzhou0610@gmail.com>
Date: 2022-12-05 12:19:58 +1100
Commit message:

 Updated vignette (the overview jpg)
 
Package: SPIAT
Commit: 1de7034b849465fe520598e35a6ba684d69969f4
Author: fuerzhou <yuzhou0610@gmail.com>
Date: 2022-12-02 17:23:30 +1100
Commit message:

 Add links to other vignettes to all vignettes
 
Package: SPIAT
Commit: 25412f81fc6f31c936ab482d69d5ad98b8d01a60
Author: fuerzhou <yuzhou0610@gmail.com>
Date: 2022-12-02 16:50:23 +1100
Commit message:

 Updated all vignettes.
 
Package: SPIAT
Commit: 5c5d5e4465b408dd6e46ddd105bc64b4826bd343
Author: fuerzhou <yuzhou0610@gmail.com>
Date: 2022-12-02 16:23:46 +1100
Commit message:

 Try splitting the vignettes and adding links.
 
Package: SPIAT
Commit: ee3c78b764c74ad05695b1680ed49927e42e1f80
Author: fuerzhou <yuzhou0610@gmail.com>
Date: 2022-12-01 15:12:58 +1100
Commit message:

 Updated citation to current version.
 
Package: SPIAT
Commit: 39b3480792493aac088d2c47c17f30a392489f45
Author: fuerzhou <yuzhou0610@gmail.com>
Date: 2022-12-01 15:12:38 +1100
Commit message:

 Amended pkgdown to v2; deleted other workflows.
 
Package: SPIAT
Commit: 0b230b26c0b162ac8a20775852a1675cfeafd64e
Author: fuerzhou <yuzhou0610@gmail.com>
Date: 2022-12-01 15:06:21 +1100
Commit message:

 Try adding another vignette
 
Package: SPIAT
Commit: 3d9fbe82cec06868e3d8ea706f7fdbbd5bd3da21
Author: fuerzhou <yuzhou0610@gmail.com>
Date: 2022-12-01 15:05:45 +1100
Commit message:

 fix colData bug
 
Package: enrichplot
Commit: d367cea2ba9163492e5f28c71c4206b5fb24f783
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2022-12-05 09:50:24 +0800
Commit message:

 bump version
 
Package: enrichplot
Commit: 2dcdf98c8cee349b1f481c21d35b9a1fe38f51d3
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2022-12-05 09:42:57 +0800
Commit message:

 Merge pull request #216 from huerqiang/cnetplot

fix `cnetplot()` for `node_label` parameter is flipped 
Package: enrichplot
Commit: a7386f47e7a59c3e2dcf25405c459ad6646f62d5
Author: huerqiang <13766876214@163.com>
Date: 2022-12-04 20:03:00 +0800
Commit message:

 fix `cnetplot()` for `node_label` parameter is flipped
 
Package: enrichplot
Commit: a33af5e46486abcf54f74eaeb5e9b1c63c0f3597
Author: Erqiang Hu <13766876214@163.com>
Date: 2022-11-18 17:27:39 +0800
Commit message:

 Merge pull request #40 from YuLab-SMU/master

merge from yulab to me 
Package: enrichplot
Commit: 91d78170ca3b59c7956cb9db84b68df333cd1bcf
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2022-11-18 10:56:09 +0800
Commit message:

 bug fixed
 
Package: enrichplot
Commit: afd5c0b85b28b22774180d6f6e1da100286cc0b2
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2022-11-18 09:11:55 +0800
Commit message:

 Merge pull request #208 from huerqiang/master

enable `dotplot()` and `autofacet()` for `gseaResultList` object 
Package: enrichplot
Commit: 93076c4faa9600991c915dbbff82a4dfddea84ae
Author: Erqiang Hu <13766876214@163.com>
Date: 2022-11-15 04:45:01 +0800
Commit message:

 Merge pull request #39 from YuLab-SMU/master

merge 
Package: enrichplot
Commit: f9fe6f7e9150ab97def30aedb3ecf72dbb0ea25e
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2022-11-02 10:57:59 +0800
Commit message:

 update bioc version
 
Package: enrichplot
Commit: b1f74758c237b27d454d3953db7a53f906ff438c
Author: huerqiang <13766876214@163.com>
Date: 2022-10-30 07:11:58 +0800
Commit message:

 enable `dotplot()` and `autofacet()` for `gseaResultList` object
 
Package: enrichplot
Commit: 41fcde707001e94ed0ad342578b8603edde1e23c
Author: Erqiang Hu <13766876214@163.com>
Date: 2022-10-30 00:15:22 +0800
Commit message:

 Merge pull request #38 from YuLab-SMU/master

merge from yulab to me 
Package: MSstatsShiny
Commit: a84e27dfef698b82db194a46128415428db760be
Author: Devon Kohler <35807256+devonjkohler@users.noreply.github.com>
Date: 2022-12-04 10:10:08 -0500
Commit message:

 Update DESCRIPTION 
Package: MSstatsShiny
Commit: a11233b8ba515606ff5ad2911e4856d6093b16d4
Author: Devon Kohler <35807256+devonjkohler@users.noreply.github.com>
Date: 2022-12-04 10:10:01 -0500
Commit message:

 Fix version 
Package: MSstatsShiny
Commit: 68780137fa817281399790a8bb147ea619c4fe1d
Author: Devon Kohler <35807256+devonjkohler@users.noreply.github.com>
Date: 2022-12-04 10:09:17 -0500
Commit message:

 Merge pull request #43 from Vitek-Lab/develop

minor bug fixes to code creation 
Package: MSstatsShiny
Commit: eb80cc46f9cc4912b4b06d75db0cce9852148cb1
Author: devonjkohler <devonjkohler@gmail.com>
Date: 2022-12-04 10:08:33 -0500
Commit message:

 minor bug fixes to code creation
 
Package: SpatialFeatureExperiment
Commit: a8fe82b800d14f99f4b5c0267d2083e5c5fe6eec
Author: Lambda Moses <dlu2@caltech.edu>
Date: 2022-12-03 21:07:46 -0800
Commit message:

 Merge from main

Merge branch 'main' into devel
 
Package: SpatialFeatureExperiment
Commit: 0546e3b91c660edb7a6f32b66150afca295a9928
Author: Lambda Moses <dlu2@caltech.edu>
Date: 2022-12-03 21:06:49 -0800
Commit message:

 Removed longlat argument, when this info in encoded in the sf dataframe itself
 
Package: SpatialFeatureExperiment
Commit: 131e6001c7f052813b5dbafbad3a1eced2208c4f
Author: Lambda Moses <dlu2@caltech.edu>
Date: 2022-12-03 20:34:21 -0800
Commit message:

 Merge from main

Merge branch 'main' into devel

# Conflicts:
#	DESCRIPTION
 
Package: SpatialFeatureExperiment
Commit: bf5f997d5f2e37a734e6c2bcc70d84bea5bf3417
Author: Lambda Moses <dlu2@caltech.edu>
Date: 2022-12-03 20:32:53 -0800
Commit message:

 Use setup-bioc action
 
Package: SpatialFeatureExperiment
Commit: 34ebb187313dce8bba9a9fe4953770632880aea8
Author: Lambda Moses <dlu2@caltech.edu>
Date: 2022-12-03 20:30:25 -0800
Commit message:

 Rownames woes, and do test for rownames in unit tests
 
Package: SpatialFeatureExperiment
Commit: 91fff9b93338b1dd818c55bb6e16db2fa44fbf02
Author: Lambda Moses <dlu2@caltech.edu>
Date: 2022-12-03 20:02:03 -0800
Commit message:

 Merge from upstream

Merge branch 'master' of git.bioconductor.org:packages/SpatialFeatureExperiment into devel

# Conflicts:
#	DESCRIPTION
 
Package: SpatialFeatureExperiment
Commit: fc4d8b2cff1136f4d45a9c0a7baf1f5e1a3634fb
Author: Lambda Moses <dlu2@caltech.edu>
Date: 2022-12-03 20:00:25 -0800
Commit message:

 Version bump devel branch for bug fix
 
Package: SpatialFeatureExperiment
Commit: cd604949f80ac3fbc5b2004e7bd7ad5725b18bd3
Author: Lambda Moses <dlu2@caltech.edu>
Date: 2022-12-03 19:57:30 -0800
Commit message:

 Version bump and news

Merge remote-tracking branch 'upstream/RELEASE_3_16'
 
Package: SpatialFeatureExperiment
Commit: b2eb819f51c7fa0567e1cb3ae1f3aea1feaa0a2e
Author: Lambda Moses <dlu2@caltech.edu>
Date: 2022-12-03 19:55:19 -0800
Commit message:

 Correctly move spatialCoords in removeEmptySpace
 
Package: ggcyto
Commit: cf68fa6109dfe6e81fa4b641e520e124702f0810
Author: mikejiang <mike@ozette.ai>
Date: 2022-12-03 17:22:06 -0800
Commit message:

 bump
 
Package: ggcyto
Commit: 6a870c4f3758df7f02ee1d22cbd09b8c2c4ade6c
Author: mikejiang <mike@ozette.ai>
Date: 2022-12-03 17:21:02 -0800
Commit message:

 use flowjo_biexp_trans in scale_x_logicle to avoid DidNotConverge error #88
 
Package: ggcyto
Commit: 49178df327b5b1adc94b9c5746158b936dedcdbc
Author: mikejiang <mike@ozette.ai>
Date: 2022-12-03 17:06:35 -0800
Commit message:

 Revert "rm scale_x_logicle from vignette because it is broken in ggplot"

This reverts commit 1eb811787accc0ed3416139557fb532b65b49acc.
 
Package: basilisk.utils
Commit: 411502fabdca972bb10b4f12115b9f7bd5b05c5d
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2022-12-04 08:52:26 +1100
Commit message:

 Merge branch 'master' of git.bioconductor.org:packages/basilisk.utils
 
Package: basilisk.utils
Commit: d482c974826dc5251ffbf9b065d6bd141529e6c9
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2022-12-04 08:51:07 +1100
Commit message:

 Do not attempt to establish a socket connection if activation fails.
 
Package: S4Vectors
Commit: cdcb2a4d402beb8d8a711e88278259e173332d79
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2022-12-03 12:11:44 -0800
Commit message:

 Adapt test_Rle_runq_integer() to a change in R-devel's quantile()

The (undocumented) change in the behavior of quantile() has to do with
the class of the returned object when the input is an integer vector:

- In R < 4.3:
   > x <- sample(99, 20)
   > sapply(1:9, function(type) class(quantile(x, type=type)))
   [1] "integer" "numeric" "integer" "integer" "numeric" "numeric" "numeric"
   [8] "numeric" "numeric"

- In R >= 4.3:
   > sapply(1:9, function(type) class(quantile(x, type=type)))
   [1] "numeric" "numeric" "numeric" "numeric" "numeric" "numeric" "numeric"
   [8] "numeric" "numeric"

So in R >= 4.3, the returned class is always numeric, whatever the input or
quantile algorithm specified via the 'type' argument.

This change broke the tests in test_Rle_runq_integer(). This commit adapts
the tests to make them work again with the new behavior of quantile().
 
Package: nullranges
Commit: d54c18de9039e68bbd3b00188b57c7a565eb9d3e
Author: mikelove <michaelisaiahlove@gmail.com>
Date: 2022-12-03 10:58:51 -0500
Commit message:

 version bump
 
Package: nullranges
Commit: 2f8be24d577ddb1cfbb88bd13b2f0c0371d13086
Author: mikelove <michaelisaiahlove@gmail.com>
Date: 2022-12-03 10:41:14 -0500
Commit message:

 add instructions for r2u
 
Package: SMAD
Commit: 63136ba8838771c8e50b7a6d5f91a24a4d8e75df
Author: Qingzhou Zhang <5545472+zqzneptune@users.noreply.github.com>
Date: 2022-12-01 09:29:13 -0500
Commit message:

 Correct again
 
Package: SMAD
Commit: ea5feb0a0249f2fe732806e266e16bb745c64f08
Author: Qingzhou Zhang <5545472+zqzneptune@users.noreply.github.com>
Date: 2022-11-29 22:52:53 -0500
Commit message:

 Corect version bump to comply Bioc policy
 
Package: SMAD
Commit: 32827acc75ccf614553491e828159d342035fc51
Author: Qingzhou Zhang <5545472+zqzneptune@users.noreply.github.com>
Date: 2022-11-27 23:53:33 -0500
Commit message:

 Description
 
Package: SMAD
Commit: 59ba03c95a29f94e01da63d4eff3678db62dce82
Author: Qingzhou Zhang <5545472+zqzneptune@users.noreply.github.com>
Date: 2022-11-27 23:29:24 -0500
Commit message:

 Merge branch 'master' into RELEASE_3_16
 
Package: SMAD
Commit: 4d5f66e57ffd31cd90225d59796ba2b4c3e2727d
Author: Qingzhou Zhang <5545472+zqzneptune@users.noreply.github.com>
Date: 2022-11-27 23:26:10 -0500
Commit message:

 Merge branch 'RELEASE_3_16' of git.bioconductor.org:packages/SMAD into RELEASE_3_16
 
Package: SMAD
Commit: 833b6079377ec1c3495b59e386037fa335ca665d
Author: Qingzhou Zhang <5545472+zqzneptune@users.noreply.github.com>
Date: 2022-11-27 23:25:14 -0500
Commit message:

 version bump
 
Package: SMAD
Commit: 989bd14a70464d41fb4e1918682eb23b128a805b
Author: Qingzhou Zhang <5545472+zqzneptune@users.noreply.github.com>
Date: 2022-11-27 23:23:55 -0500
Commit message:

 version bump
 
Package: SMAD
Commit: 9f5281fcedf9995ded99c6d6c20884d589b22711
Author: Qingzhou Zhang <zqzneptune@gmail.com>
Date: 2022-11-27 12:35:38 -0500
Commit message:

 version bump
 
Package: SMAD
Commit: b6bd9574634d01c64de1862a397c05ab8f90b3f6
Author: Qingzhou Zhang <zhang40q@MBP-zqz.local>
Date: 2022-11-27 07:22:47 -0500
Commit message:

 Merge branch 'master' into RELEASE_3_16
Fix WD
 
Package: SMAD
Commit: da3da683ec6381457448113600e2ad3c4fa495c7
Author: Qingzhou Zhang <zhang40q@MBP-zqz.local>
Date: 2022-11-27 07:17:49 -0500
Commit message:

 Minor
 
Package: gdsfmt
Commit: c859ed1392bdea30a6c4c42b7787b2dec9bcae16
Author: Xiuwen Zheng <zhengxwen@gmail.com>
Date: 2022-12-02 18:38:49 -0600
Commit message:

 update xz-5.2.9
 
Package: TraRe
Commit: dc420afec8b5adce75961a78bba2b8c753f27d1c
Author: ubioinformat <jdelafuentec@unav.es>
Date: 2022-12-02 17:56:24 -0500
Commit message:

 changed to version 1.7.1
 
Package: TraRe
Commit: fd516da6db4bf3167a5bae00ecdc9c9cc7e1b8a6
Author: ubioinformat <jdelafuentec@unav.es>
Date: 2022-12-02 17:53:59 -0500
Commit message:

  version 1.8.0
 
Package: TraRe
Commit: cba3ac32cdb715a96f4ea5e0f748fca4a6bb4713
Author: ubioinformat <jdelafuentec@unav.es>
Date: 2022-12-02 17:50:19 -0500
Commit message:

 .C() functions implemented
 
Package: TraRe
Commit: 645bfed252f122c60c35142438ff3b1a895ba1c9
Author: ubioinformat <jdelafuentec@unav.es>
Date: 2022-12-02 17:22:03 -0500
Commit message:

 export not included
 
Package: TraRe
Commit: 429876cc7bd314c53bc59ba678631aaf1fd80495
Author: ubioinformat <jdelafuentec@unav.es>
Date: 2022-12-02 16:31:26 -0500
Commit message:

 dynamic managing c files
 
Package: TraRe
Commit: 10fe6edf84c3c876d9ca670c1d238d0f7d91a856
Author: ubioinformat <jdelafuentec@unav.es>
Date: 2022-12-02 13:40:45 -0500
Commit message:

 C dependencies included in vbsr.R
 
Package: IntOMICS
Commit: 3f3e2ab414923443127310f93137d3aaf2d3a69c
Author: anna-pacinkova <ana.pacinkova@gmail.com>
Date: 2022-12-02 23:24:16 +0100
Commit message:

 num mod lower
 
Package: IntOMICS
Commit: 18847b76064b6c14c36109647030f8c22bafe464
Author: anna-pacinkova <ana.pacinkova@gmail.com>
Date: 2022-12-02 23:04:22 +0100
Commit message:

 omics_to_list bask
 
Package: IntOMICS
Commit: 24c45d0dbddf6a7edaea05f363626b35a59a91a9
Author: anna-pacinkova <ana.pacinkova@gmail.com>
Date: 2022-12-02 21:14:20 +0100
Commit message:

 num samples corr
 
Package: IntOMICS
Commit: d5018903bce7f81275c2b3915481755cc7a8bfb7
Author: anna-pacinkova <ana.pacinkova@gmail.com>
Date: 2022-12-02 21:01:34 +0100
Commit message:

 omics_p removed
 
Package: IntOMICS
Commit: 79c979ecdeab3c30e1152b738bad160bd478f45a
Author: anna-pacinkova <ana.pacinkova@gmail.com>
Date: 2022-12-02 20:57:29 +0100
Commit message:

 Matched to Multi
 
Package: LEA
Commit: ae4871780cc471a981ec6bb7e3d7e9f43b8f96d7
Author: francois <francois@timc-bcm-42p.home>
Date: 2022-12-02 20:51:24 +0100
Commit message:

 minor fix genetic gap d=1
 
Package: IntOMICS
Commit: ad169637739545672b860467552d56625b0bd433
Author: anna-pacinkova <ana.pacinkova@gmail.com>
Date: 2022-12-02 19:39:26 +0100
Commit message:

 version update
 
Package: IntOMICS
Commit: d173d0c4abb5932b5f3f4994e05c1312bf35b24e
Author: anna-pacinkova <ana.pacinkova@gmail.com>
Date: 2022-12-02 19:35:49 +0100
Commit message:

 MatchedAssayExp omics changed
 
Package: Rsubread
Commit: 736a37e71675c0cc7586e23f05500855b1af7415
Author: Yang Liao <liao_y@svr2672.licr.unimelb.edu.au>
Date: 2022-12-03 05:25:08 +1100
Commit message:

 removed log messages
 
Package: Rsubread
Commit: 6edb04623c146ca48253bc96620a2d844180ff65
Author: Yang Liao <liao_y@svr2672.licr.unimelb.edu.au>
Date: 2022-12-03 05:23:57 +1100
Commit message:

 fixed a bug in cellCounts that does not init vote numbers when no index bucket is found.
 
Package: SynExtend
Commit: d83bbcd0a2a8dc63ee3a2f49dc59d8f17875c71f
Author: Nicholas Cooley <39340402+npcooley@users.noreply.github.com>
Date: 2022-12-02 09:49:09 -0500
Commit message:

 Merge pull request #31 from ahl27/master

fix: bugfixes and features for `ShuffleC` 
Package: SynExtend
Commit: 5683962d32a51579fb99d46106da4eba9793c80a
Author: ahl27 <ahl27@pitt.edu>
Date: 2022-12-02 09:23:37 -0500
Commit message:

 fix: update news and description
 
Package: SynExtend
Commit: 2f8e562d240c801c2414e2265e89ed14fe9d7f46
Author: Aidan Lakshman <ahl27@pitt.edu>
Date: 2022-12-02 09:20:05 -0500
Commit message:

 Merge branch 'npcooley:master' into master
 
Package: SynExtend
Commit: 8d83e6f5314599dc7d235ca04024e8933022dd40
Author: Aidan Lakshman <ahl27@pitt.edu>
Date: 2022-12-02 09:19:54 -0500
Commit message:

 sampling with replacement and bugfix to support R set.seed reproducibility (#11)

 
Package: SynExtend
Commit: b11c7eda251e408878137e1d4435a9de77495509
Author: Nicholas Cooley <39340402+npcooley@users.noreply.github.com>
Date: 2022-12-01 17:33:09 -0500
Commit message:

 Merge pull request #30 from ahl27/master

TreeDistance, RNG, CorrGL, Refactor 
Package: SynExtend
Commit: 9c1638737987100c6ba557b3b0f58d0bc76aa453
Author: ahl27 <ahl27@pitt.edu>
Date: 2022-12-01 17:05:35 -0500
Commit message:

 fix: adds argument to select out length of sampling, should speed up subsamples
 
Package: SynExtend
Commit: 0fad4a66712f7e7c0c4511a161f4efac6d1d8ca0
Author: Aidan Lakshman <ahl27@pitt.edu>
Date: 2022-12-01 16:54:23 -0500
Commit message:

 feat: C Replacement for `sample`, bootstrapping for `GainLoss` (#10)

* added bootstrapping for gainloss method

* adds bootstrap test, adds new shuffle function with R accessor 
Package: SynExtend
Commit: 5c563153e46bdcf07532f814e597f5831060bdd6
Author: Aidan Lakshman <ahl27@pitt.edu>
Date: 2022-11-29 11:40:27 -0500
Commit message:

 fix: Code refactor (#9)

* refactored code to consolidate identical blocks of code from various predictors

* fixing some bugs etc. from rcmdcheck 
Package: SynExtend
Commit: f41acccd719546323fecde7beda56c0f1eb79b3b
Author: Aidan Lakshman <ahl27@pitt.edu>
Date: 2022-11-28 16:22:15 -0500
Commit message:

 fix: remove old code, adjust random projection length (#8)

minor bugfixes 
Package: SynExtend
Commit: 86ab5f5e6421a0891d3e69fda70ef8006bfbf2dd
Author: Aidan Lakshman <ahl27@pitt.edu>
Date: 2022-11-28 13:20:25 -0500
Commit message:

 fix: Pearson Correlation for HammingGL (#7)

* HammingGL now CorrGL, uses pearson's r weighted by p-value
* Minor complication of commit history due to mistake, not a problem and will not be replicated in the future 
Package: SynExtend
Commit: 3a7d1f293beb44cdb181854fb9f8948f878ace71
Author: Aidan Lakshman <ahl27@pitt.edu>
Date: 2022-11-28 11:27:37 -0500
Commit message:

 feat: RNG, Random Projection for MirrorTree (#6)

* adds `TreeDistance` predictor for ProtWeaver, various other optimzations and bugfixes

* fixing rcmdcheck/BiocCheck warnings

* fixing some internal RNG stuff, updates news and description

* removes test function

* fixing rcmdcheck errors 
Package: SynExtend
Commit: 997dea0b722bd06736a73224eda31dcccd5aa73d
Author: Aidan Lakshman <ahl27@pitt.edu>
Date: 2022-11-09 20:57:55 -0500
Commit message:

 feat: TreeDistance ProtWeaver Predictor

* adds `TreeDistance` predictor for ProtWeaver, various other optimzations and bugfixes

* fixing rcmdcheck/BiocCheck warnings 
Package: IntOMICS
Commit: a10750ec5b50a8fc8cd57b21cdd093c3435efddc
Author: anna-pacinkova <ana.pacinkova@gmail.com>
Date: 2022-12-02 17:31:55 +0100
Commit message:

 version update
 
Package: sechm
Commit: d876195f65b6d0eb12c403fb06537758da182c0e
Author: plger <pl.germain@gmail.com>
Date: 2022-12-02 17:02:55 +0100
Commit message:

 Merge branch 'master' of github.com:plger/sechm
 
Package: sechm
Commit: 12906855ceaf198a90aea3c5a838fdb8cc2b8562
Author: plger <pl.germain@gmail.com>
Date: 2022-12-02 17:02:33 +0100
Commit message:

 fixed missing import
 
Package: sechm
Commit: 5dbff0cc10ec65964a9fa2d36b422158432a408c
Author: Pierre-Luc <pl.germain@gmail.com>
Date: 2022-12-02 16:41:52 +0100
Commit message:

 version bump 
Package: sechm
Commit: 8fbf7708c0fd374ac26104d78cb5adb51bdd0b63
Author: Pierre-Luc <pl.germain@gmail.com>
Date: 2022-12-02 14:21:19 +0100
Commit message:

 Rename check to check.yaml 
Package: sechm
Commit: 817718d0308b5bc573909a72a9d0fa203a7b474b
Author: Pierre-Luc <pl.germain@gmail.com>
Date: 2022-12-02 14:20:58 +0100
Commit message:

 Create check 
Package: IntOMICS
Commit: b38c7b3652dab4655486ad4935fb3aa60d3e08cd
Author: anna-pacinkova <ana.pacinkova@gmail.com>
Date: 2022-12-02 16:50:08 +0100
Commit message:

 testthat
 
Package: IntOMICS
Commit: 99629bfaa1822b67a724dc7d7f199c1fd6a3d15e
Author: anna-pacinkova <ana.pacinkova@gmail.com>
Date: 2022-12-02 15:03:47 +0100
Commit message:

 rhd5
 
Package: mitch
Commit: d90c3fa6514fb4632c35309cc2d86674ec85efca
Author: markziemann <mark.ziemann@gmail.com>
Date: 2022-12-03 00:10:16 +1100
Commit message:

 removed warning from kable in the loop
 
Package: IntOMICS
Commit: b7f84f933232b46c4306c31838d0eafc12f7e791
Author: anna-pacinkova <ana.pacinkova@gmail.com>
Date: 2022-12-02 13:57:19 +0100
Commit message:

 example updated
 
Package: IntOMICS
Commit: 03c3cba9f299c2477def4dc487af74d402faf496
Author: anna-pacinkova <ana.pacinkova@gmail.com>
Date: 2022-12-02 13:21:06 +0100
Commit message:

 examples
 
Package: HiContactsData
Commit: a7ebf8974365e879546f8c97ba0cd5d1343c6476
Author: js2264 <jacquesserizay@gmail.com>
Date: 2022-12-02 13:30:18 +0100
Commit message:

 bump to 1.1.7
 
Package: epiNEM
Commit: 59cec5725f46cfe87039468bf565fcc224e58412
Author: mpirkl <martinpirkl@yahoo.de>
Date: 2022-12-02 12:35:19 +0100
Commit message:

 Merge commit '5804d63a18e68c21a9e1ca00d09b1992dd268be5'
 
Package: epiNEM
Commit: 0b4f6e5653b0bfd128616b8034e03c4fe4a67388
Author: mpirkl <martinpirkl@yahoo.de>
Date: 2022-12-02 12:18:23 +0100
Commit message:

 Merge remote-tracking branch 'upstream/master'
 
Package: epiNEM
Commit: 75493b82d9cbf4625f53e93069510364c16120f4
Author: J Wokaty <jennifer.wokaty@sph.cuny.edu>
Date: 2022-11-01 11:15:18 -0400
Commit message:

 bump x.y.z version to odd y following creation of RELEASE_3_16 branch
 
Package: epiNEM
Commit: 029c928134171f6c3aac0c60e5cc48305d011a92
Author: J Wokaty <jennifer.wokaty@sph.cuny.edu>
Date: 2022-11-01 11:15:18 -0400
Commit message:

 bump x.y.z version to even y prior to creation of RELEASE_3_16 branch
 
Package: epiNEM
Commit: 5804d63a18e68c21a9e1ca00d09b1992dd268be5
Author: mpirkl <martinpirkl@yahoo.de>
Date: 2022-12-02 12:18:23 +0100
Commit message:

 Merge remote-tracking branch 'upstream/master'
 
Package: epiNEM
Commit: 8290f7811beccbcdf8296916670c1166e6a1c330
Author: mpirkl <martinpirkl@yahoo.de>
Date: 2022-12-02 11:08:18 +0100
Commit message:

 code cleaning
 
Package: epiNEM
Commit: dbc80019a8dfb757a519420b6bae412a2dddde3d
Author: mpirkl <martinpirkl@yahoo.de>
Date: 2022-12-02 11:06:06 +0100
Commit message:

 fixed two clustering bugs
 
Package: mitch
Commit: 7adb4c735ae09a18707cee328da73a2ad4d2b317
Author: markziemann <mark.ziemann@gmail.com>
Date: 2022-12-02 21:25:21 +1100
Commit message:

 bump version
 
Package: mitch
Commit: f64160374ff86b539f7cdfa84bef790aa90c023f
Author: markziemann <mark.ziemann@gmail.com>
Date: 2022-12-02 21:24:30 +1100
Commit message:

 DESCRIPTION
 
Package: mitch
Commit: 2c35441323d7c9cac398ae1c422fed791ea89d18
Author: markziemann <mark.ziemann@gmail.com>
Date: 2022-12-02 21:23:02 +1100
Commit message:

 Merge remote-tracking branch 'upstream/master'
 
Package: mitch
Commit: 60c246d35de9aeb006bc8c2551e07156f69f558a
Author: markziemann <mark.ziemann@gmail.com>
Date: 2022-12-02 21:22:52 +1100
Commit message:

 better charts with kableExtra
 
Package: mitch
Commit: 927e1da3f7c46af4a8dce3438fa2c91d0ddece46
Author: markziemann <mark.ziemann@gmail.com>
Date: 2022-02-22 14:22:14 +1100
Commit message:

 fix issue with ss_long header values in ggplots for report and plots
 
Package: nempi
Commit: b74a3dc0cd80a488982ab21b428b566639452ed0
Author: mpirkl <martinpirkl@yahoo.de>
Date: 2022-12-02 11:17:12 +0100
Commit message:

 Merge remote-tracking branch 'upstream/master'
 
Package: bnem
Commit: c3803aed935580896a366509fdfc18550e9c7671
Author: mpirkl <martinpirkl@yahoo.de>
Date: 2022-12-02 11:16:11 +0100
Commit message:

 Merge remote-tracking branch 'upstream/master'
 
Package: MungeSumstats
Commit: dfb082fae2633e1559495ef5ece96921e0eb03f7
Author: Al-Murphy <alanmurph94@hotmail.com>
Date: 2022-12-02 09:19:04 +0000
Commit message:

 GHA update
 
Package: IntOMICS
Commit: 923114bce540457b597dc27b1a5c9c85876523f2
Author: anna-pacinkova <ana.pacinkova@gmail.com>
Date: 2022-12-02 09:28:45 +0100
Commit message:

 timeout crorr interactive
 
Package: spatialHeatmap
Commit: 78d2fdf65110719dbd82720e664cedbf6a3046ad
Author: jianhaizhang <jzhan067@ucr.edu>
Date: 2022-12-02 00:01:15 -0800
Commit message:

 Fixed errors in SVG feature extraction and detect_cluster.R, which arose in Bioc Devel.
 
Package: spatialHeatmap
Commit: 60c87e206e6d744bb8615cc0a18151e576287654
Author: jianhaizhang <jzhan067@ucr.edu>
Date: 2022-11-28 13:28:06 -0800
Commit message:

 Added "requireNamespace" for packages in Imports in ui.R.
 
Package: spatialHeatmap
Commit: c9d1581d27ecdcd35ab94d8f0949466b0b283556
Author: jianhaizhang <jzhan067@ucr.edu>
Date: 2022-11-20 03:32:12 -0800
Commit message:

 Fixed a bug in col_bar.R
 
Package: bambu
Commit: 0f6195251bb2198a93993527131d3ae54ebbc4b5
Author: Chen Ying <chen_ying@gis.a-star.edu.sg>
Date: 2022-12-02 15:52:55 +0800
Commit message:

 update version number
 
Package: bambu
Commit: fee6e3dcbe7b90517902b1e0a6852ac574ff8d0d
Author: Chen Ying <chen_ying@gis.a-star.edu.sg>
Date: 2022-12-02 15:48:33 +0800
Commit message:

 Merge branch 'RELEASE_3_16' into master 
Package: bambu
Commit: 1e672d96d60e1bf6e0ae81129fe797641b58e65b
Author: Chen Ying <chen_ying@gis.a-star.edu.sg>
Date: 2022-12-02 15:12:19 +0800
Commit message:

 Merge pull request #334 from GoekeLab/windows_genome_bug

Windows genome bug 
Package: bambu
Commit: 618b8d768f77516961dcb79c36f65b9e95d82b17
Author: Andre <andre_sim@gis.a-star.edu.sg>
Date: 2022-12-01 17:23:30 +0800
Commit message:

 update github installation documentation

 
Package: bambu
Commit: b1e118c87b6710457e96d28832ae44ba39557ff9
Author: Andre <andre_sim@gis.a-star.edu.sg>
Date: 2022-12-01 17:23:13 +0800
Commit message:

 Remove windows specific genome load in

 
Package: bambu
Commit: 2ef650d571cb4b2c5905d4e40935e4b72f3b53f6
Author: Chen Ying <chen_ying@gis.a-star.edu.sg>
Date: 2022-11-17 11:57:38 +0800
Commit message:

 update RELEASE version number
 
Package: bambu
Commit: f2863d7bd63e5644c681979a50b159a5e7bc86d6
Author: Chen Ying <chen_ying@gis.a-star.edu.sg>
Date: 2022-11-17 11:57:25 +0800
Commit message:

 edit version number
 
Package: bambu
Commit: 9064e21d405a202b6991b00860c173ff4c4df666
Author: Chen Ying <chen_ying@gis.a-star.edu.sg>
Date: 2022-11-17 11:55:24 +0800
Commit message:

 bug fix: update citation
 
Package: bambu
Commit: ec4d3173462a50c6f720bd0b60858447f7513534
Author: Chen Ying <chen_ying@gis.a-star.edu.sg>
Date: 2022-11-17 11:46:03 +0800
Commit message:

 update RELEASE version number
 
Package: bambu
Commit: f8c44c33d8b0a7f3e969522aebace482a7d10ca3
Author: Chen Ying <chen_ying@gis.a-star.edu.sg>
Date: 2022-11-04 15:19:19 +0800
Commit message:

 update RELEASE version number
 
Package: bambu
Commit: 480821653e1ca623ad5c955994e1e3f21329d38a
Author: Chen Ying <chen_ying@gis.a-star.edu.sg>
Date: 2022-11-04 15:19:00 +0800
Commit message:

 update install github
 
Package: bambu
Commit: 03ccfff870e048f9977df3523ff014f2049f965c
Author: Chen Ying <chen_ying@gis.a-star.edu.sg>
Date: 2022-11-04 10:18:21 +0800
Commit message:

 update version number
 
Package: bambu
Commit: b0927d579ea5ff92518fa8f2ab5a6b290cfda51c
Author: Chen Ying <chen_ying@gis.a-star.edu.sg>
Date: 2022-11-04 10:16:30 +0800
Commit message:

 fix bug when readclass exists in multiple genes in the same estimation group
 
Package: bambu
Commit: b8ce8be69e0c9015760c14898750248d753ea7ff
Author: Chen Ying <chen_ying@gis.a-star.edu.sg>
Date: 2022-11-04 15:01:04 +0800
Commit message:

 update version number
 
Package: bambu
Commit: b833566f74c2243dbf86c0ea5c75c6fa8d2b01f1
Author: Chen Ying <chen_ying@gis.a-star.edu.sg>
Date: 2022-11-04 15:01:04 +0800
Commit message:

 revert back
 
Package: bambu
Commit: 786e2b14a80015871b79201f34984baffce1490d
Author: Chen Ying <chen_ying@gis.a-star.edu.sg>
Date: 2022-11-04 15:01:04 +0800
Commit message:

 update version number
 
Package: CNVfilteR
Commit: 3806805e85dc66791ac8fbdd99ebd63826d12547
Author: j <jpuntomarcos@gmail.com>
Date: 2022-12-02 08:27:17 +0200
Commit message:

 Version bump
 
Package: CNVfilteR
Commit: 9f9f39c0bd58cdeb0d5af9b911f75af0df9faca6
Author: j <jpuntomarcos@gmail.com>
Date: 2022-12-02 08:26:43 +0200
Commit message:

 NEWS updated
 
Package: CNVfilteR
Commit: db3a2e748bb173dd6a89aa08fe9f6ae5a58f2297
Author: j <jpuntomarcos@gmail.com>
Date: 2022-12-02 08:23:17 +0200
Commit message:

 Added limitation: CNVfilteR does not support mutiallelic sites
 
Package: CNVfilteR
Commit: 6c54c89f3fb416f0a76b25c86c5b09e08b5bb5e8
Author: j <jpuntomarcos@gmail.com>
Date: 2022-12-02 08:13:15 +0200
Commit message:

 Minor change: show explicitly that genome is an option in loadVCFs()
 
Package: PhosR
Commit: c63dd903904364477549028514fa119b369a8635
Author: Taiyun (Mac2017) <taiyun.kim91@gmail.com>
Date: 2022-12-02 16:11:26 +1100
Commit message:

 bug fixes
 
Package: PhosR
Commit: 3aecc0d175084db6d3453020623cdcff5a3c7ec5
Author: Taiyun (Mac2017) <taiyun.kim91@gmail.com>
Date: 2022-12-02 10:57:07 +1100
Commit message:

 bug fixes and updates: kinaseSubstrateScore utilises different species
 
Package: PhosR
Commit: d2cb6f91590fcd6047d2eaf1c5817a751006215b
Author: Carissa Chen <carissachen97@gmail.com>
Date: 2022-05-12 10:20:03 +1000
Commit message:

 add filepath option
 
Package: PhosR
Commit: 8dd429a429dfa411adf77177e5e5d0c4d6fa163a
Author: Carissa Chen <carissachen97@gmail.com>
Date: 2022-05-11 16:33:57 +1000
Commit message:

 add filepath option
 
Package: PhosR
Commit: 16e8847000177e84206fef01265ff6162f69158c
Author: Hani Jieun Kim <hani.kim127@gmail.com>
Date: 2022-05-04 16:17:34 +1000
Commit message:

 add NA error
 
Package: PhosR
Commit: 85e8ca7bc94b97c5107502ee7b84423c6fc929e2
Author: Taiyun (Mac2017) <taiyun.kim91@gmail.com>
Date: 2022-05-01 15:24:47 +1000
Commit message:

 Merging commits
 
Package: PhosR
Commit: af8c6a191a2fd723aad29eb8b95cd953533c457e
Author: Taiyun (Mac2017) <taiyun.kim91@gmail.com>
Date: 2022-05-01 14:55:56 +1000
Commit message:

 Allowed motif list of other species for KinaseSubstrateScore function, minor bug fixes, Updates on documentations
 
Package: PhosR
Commit: c1f7771cdc1b678faee2d21e435b5635632cd633
Author: Carissa Chen <carissachen97@gmail.com>
Date: 2022-04-27 20:03:30 +1000
Commit message:

 import functions
 
Package: PhosR
Commit: f161e5f3fbdd8091abf3426695dc79ef87b3f245
Author: Carissa Chen <carissachen97@gmail.com>
Date: 2022-04-27 18:07:57 +1000
Commit message:

 bug fix with package
 
Package: PhosR
Commit: 7a6a2848cde2847e3702d10952ab3e2b1f58a8a9
Author: Carissa Chen <carissachen97@gmail.com>
Date: 2022-04-27 17:22:52 +1000
Commit message:

 import package
 
Package: PhosR
Commit: 8e32e0a8fa8959c2d414ee86fa7e035db77020c6
Author: Carissa Chen <carissachen97@gmail.com>
Date: 2022-04-27 16:14:12 +1000
Commit message:

 Updated DESCRIPTION
 
Package: PhosR
Commit: cc784df179b51b59915cc5295d7cc05acc8ef27a
Author: Carissa Chen <carissachen97@gmail.com>
Date: 2022-04-27 14:52:10 +1000
Commit message:

 Added plotting parameters in kinaseSubstrateHeatmap function
 
Package: speckle
Commit: ad873d361e3b7d026c52e9326758b4b499521cf8
Author: bphipson <12027703+bphipson@users.noreply.github.com>
Date: 2022-12-02 09:57:32 +1100
Commit message:

 bump version number
 
Package: MSstatsShiny
Commit: 66f75f11cdf507e6b2ed9022621ee38a957360c8
Author: Devon Kohler <35807256+devonjkohler@users.noreply.github.com>
Date: 2022-12-01 16:11:21 -0500
Commit message:

 Update DESCRIPTION 
Package: MSstatsShiny
Commit: b0d4a5cf06ed55285d95276125639f5d36ae75aa
Author: Devon Kohler <35807256+devonjkohler@users.noreply.github.com>
Date: 2022-12-01 16:11:01 -0500
Commit message:

 Merge branch 'RELEASE_3_16' into main 
Package: MSstatsShiny
Commit: d727300e1a17378f2095bbfbd0974bc7df59214a
Author: Devon Kohler <35807256+devonjkohler@users.noreply.github.com>
Date: 2022-12-01 16:10:06 -0500
Commit message:

 Merge pull request #41 from Vitek-Lab/develop

minor bug fixes 
Package: MSstatsShiny
Commit: 1bedbc4510faf9990abc507554f4fd7dced9beea
Author: Devon Kohler <35807256+devonjkohler@users.noreply.github.com>
Date: 2022-12-01 16:09:57 -0500
Commit message:

 Merge branch 'main' into develop 
Package: MSstatsShiny
Commit: 723030e3787bb4d62761dc085d44a08de59ae9c4
Author: devonjkohler <devonjkohler@gmail.com>
Date: 2022-12-01 16:09:08 -0500
Commit message:

 minor bug fixes
 
Package: MSstatsShiny
Commit: 0cf4f58baf1a9f5118cbf8088f493131396c8cd7
Author: devonjkohler <devonjkohler@gmail.com>
Date: 2022-11-21 08:56:28 -0500
Commit message:

 fixed vignette bug
 
Package: MSstatsShiny
Commit: 47ebcca9b6816c545183ed485799e7e6694f1cb9
Author: Devon Kohler <35807256+devonjkohler@users.noreply.github.com>
Date: 2022-11-19 09:51:52 -0500
Commit message:

 Update DESCRIPTION 
Package: MSstatsShiny
Commit: 0e4956fce1d349b1952ba8391095fa1627bb0d85
Author: Devon Kohler <35807256+devonjkohler@users.noreply.github.com>
Date: 2022-11-19 09:51:32 -0500
Commit message:

 Merge pull request #40 from Vitek-Lab/main

merge release with bug fix 
Package: mixOmics
Commit: 500e8791cb997885e12ef21ed73a518f1b652160
Author: Kim-Anh Lê Cao <mixomicsdeveloper@gmail.com>
Date: 2022-12-02 07:46:42 +1100
Commit message:

 Merge branch 'master' of github.com:mixOmicsTeam/mixOmics
 
Package: mixOmics
Commit: 13e58046785bebc60dff94f9f621fed40146b56a
Author: Max-Bladen <mbladen19@gmail.com>
Date: 2022-11-28 09:22:54 +1100
Commit message:

 Updated authors

docs: added my name to author list and updated maintainer
 
Package: mixOmics
Commit: 7427868e87e2c17572226f0b5c6ae319571544db
Author: Max Bladen <60872845+Max-Bladen@users.noreply.github.com>
Date: 2022-11-23 09:50:32 +1100
Commit message:

 Fix for Issue #270 (#271)

fix: changed the depreciated `size` parameter to `linewidth` and changed `aes_string()` to `aes()`

fix: additional `aes_string()` call changed to `aes()`

fix: changing `aes_string()` to `aes()` introduced error. Adjusted `geom_path` calls so X and Y vectors are appropriately set

refactor: removed some commented lines

tests: added test for `plotIndiv.mint.plsda()` with `ellipse = TRUE` 
Package: Pigengene
Commit: 3e220ed9c16f54bb530a3cc951f20d632e4bbdd5
Author: Sogand Sajedi <ssajedi@atlassian.com>
Date: 2022-12-01 13:40:48 -0600
Commit message:

 Sogand added symbol to the pw table. v- 1.25.4
 
Package: LEA
Commit: 794f1626c4bd2a525d68026632652af7ea6942ab
Author: francois <francois@timc-bcm-42p.home>
Date: 2022-12-01 20:27:12 +0100
Commit message:

 fix FCONE
 
Package: LEA
Commit: 163fcf11de8aa4bf5546a75b2309af67aa98c611
Author: francois <francois@timc-bcm-42p.home>
Date: 2022-12-01 20:20:23 +0100
Commit message:

 fix sylvester.c FCONE
 
Package: ArrayExpressHTS
Commit: c9590d2fc5b3d18a708dbc94aeefd80e5c44df36
Author: lshep <lori.shepherd@roswellpark.org>
Date: 2022-12-01 14:06:42 -0500
Commit message:

 Deprecation

 - unresponsive
 
Package: BiocParallel
Commit: fd7bec02cb41decf7cda649d11fb95d823dc33c4
Author: Martin Morgan <Martin.Morgan@RoswellPark.org>
Date: 2022-12-01 13:45:22 -0500
Commit message:

 Merge branch 'C++-configure'
 
Package: BiocParallel
Commit: b04cf1f3dc5dd7ee6ac3be05832293fadcf03ad4
Author: Martin Morgan <Martin.Morgan@RoswellPark.org>
Date: 2022-11-26 07:40:35 -0500
Commit message:

 update configure.ac to use C++

- test for sys/mman.h
- use AC_SEARCH_LIBS() to add -lrt if necessary, instead of
  AC_CHECK_LIB(), as recommended by
  https://www.gnu.org/software/autoconf/manual/autoconf-2.67/html_node/Libraries.html
- updates #93, updates #94
 
Package: BiocParallel
Commit: 06e87f92f2fc90c712aecf7248eb0d153f23c836
Author: Martin Morgan <Martin.Morgan@RoswellPark.org>
Date: 2022-11-23 11:16:56 -0500
Commit message:

 Merge branch 'issue-235-3.16' into RELEASE_3_16
 
Package: BiocParallel
Commit: d59f4aae838cf0b2f6850e3ed01ad4897e9aa7ef
Author: Martin Morgan <Martin.Morgan@RoswellPark.org>
Date: 2022-11-23 10:43:13 -0500
Commit message:

 version bump and NEWS entry
 
Package: BiocParallel
Commit: 6802b862af8e185ce4fb95f15a6ae3457c6de2ef
Author: Martin Morgan <Martin.Morgan@RoswellPark.org>
Date: 2022-11-23 10:37:29 -0500
Commit message:

 add unit test for issue #235
 
Package: BiocParallel
Commit: 8b99ff71fef2633a1409dc1a5e4155d47e5aad40
Author: Jiefei-Wang <szwjf08@gmail.com>
Date: 2022-11-22 17:06:11 -0600
Commit message:

 Fix issue 234

- Recover the replaced variables in the global environment after the worker finishes its job
 
Package: BiocParallel
Commit: 6c85dbad596a74a6d3022173a4a11c6b81a4a2c2
Author: Martin Morgan <Martin.Morgan@RoswellPark.org>
Date: 2022-11-07 09:05:33 -0500
Commit message:

 version bump
 
Package: BiocParallel
Commit: 4a0c2ae642a94e0b134f19b31ac87da9ec877c40
Author: Martin Morgan <Martin.Morgan@RoswellPark.org>
Date: 2022-11-07 09:05:04 -0500
Commit message:

 use IS_BIOC_BUILD_MACHINE instead of BBS_HOME
 
Package: spbtest3
Commit: 25590dd0089d0cc3ec10909112ca1c340979b286
Author: lshep <lori.shepherd@roswellpark.org>
Date: 2022-12-01 12:02:51 -0500
Commit message:

 Take down test time

  - needed to trigger timeout/warning on windows but wanted to test quickly mac
 
Package: Pigengene
Commit: 6c89208bf1aa51e8c9cce9438f882327567f330b
Author: Habil Zare <zare@uthscsa.edu>
Date: 2022-12-01 10:21:17 -0600
Commit message:

 Habil: Version 1.23.4
 
Package: Pigengene
Commit: 1739d9313f6dab105f284bafefc3dc0f0b8f5f02
Author: Habil Zare <zare@uthscsa.edu>
Date: 2022-12-01 10:20:14 -0600
Commit message:

 Habil: Version 1.23.4
 
Package: AUCell
Commit: 6b2ee7c875b5f62f35d06ae3a0424efc1e3e56d4
Author: Sara Aibar <sara.aibar@kuleuven.be>
Date: 2022-12-01 16:41:36 +0100
Commit message:

 Add Matrix dependency
 
Package: MultiAssayExperiment
Commit: 1c143a2d09644bfb9ebd9ef9e0b9db4ea2ce0209
Author: LiNk-NY <marcel.ramosperez@roswellpark.org>
Date: 2022-12-01 10:36:50 -0500
Commit message:

 version bump 1.25.3
 
Package: MultiAssayExperiment
Commit: ce228434ec0e39579342093e9541cdae71d588a0
Author: LiNk-NY <marcel.ramosperez@roswellpark.org>
Date: 2022-12-01 10:36:46 -0500
Commit message:

 update news entries for earlier versions
 
Package: MultiAssayExperiment
Commit: 2e02c7bca153590c42a2069b2a8d6df6eb66d0c0
Author: LiNk-NY <marcel.ramosperez@roswellpark.org>
Date: 2022-11-30 22:56:57 +0000
Commit message:

 version bump 1.25.2
 
Package: MultiAssayExperiment
Commit: cae049e654c0015e6799650414a15e0cfa24cf92
Author: LiNk-NY <marcel.ramosperez@roswellpark.org>
Date: 2022-11-30 22:56:51 +0000
Commit message:

 update NEWS
 
Package: MultiAssayExperiment
Commit: 53ff70a813253918b3cff0f39d67f6f5338b0732
Author: LiNk-NY <marcel.ramosperez@roswellpark.org>
Date: 2022-11-30 22:45:44 +0000
Commit message:

 include names with single bracket replacement
 
Package: MultiAssayExperiment
Commit: 5b7e8c78da21316b5a41047a69571360cafde630
Author: LiNk-NY <marcel.ramosperez@roswellpark.org>
Date: 2022-11-29 19:58:35 +0000
Commit message:

 ignore build_site products and caches
 
Package: MultiAssayExperiment
Commit: 01438d4745e684d313aed71c74299be1bf9ebfb0
Author: LiNk-NY <marcel.ramosperez@roswellpark.org>
Date: 2022-11-29 19:58:22 +0000
Commit message:

 use jammy to conincide with devel image
 
Package: RcisTarget
Commit: 33623d40f1ad4b4c21f510d570183328cf06eafe
Author: Sara Aibar <sara.aibar@kuleuven.be>
Date: 2022-12-01 16:36:14 +0100
Commit message:

 version bump
 
Package: RcisTarget
Commit: 8c0481bba5709de7a0654e74868cb9e5bba52ca9
Author: Sara Aibar <sara.aibar@kuleuven.be>
Date: 2022-12-01 16:30:00 +0100
Commit message:

 update examples
 
Package: PhyloProfile
Commit: 933ee2e1e0810cf7c4904a2bfe664020ca746e7e
Author: trvinh <trvinh@gmail.com>
Date: 2022-12-01 16:12:58 +0100
Commit message:

 option for uploading sorted taxon list
 
Package: hipathia
Commit: f4adf0010fb62fda06333a7f83d6861f6bd767bf
Author: Marta R. Hidalgo <marta.hidalgo@outlook.es>
Date: 2022-12-01 14:02:29 +0100
Commit message:

 roxygenize new version
 
Package: hipathia
Commit: 721f54d8e1d44d8fcfc591d2d160985bb9c85db7
Author: Marta R. Hidalgo <marta.hidalgo@outlook.es>
Date: 2022-11-29 17:20:29 +0100
Commit message:

 adding package guide v3.0
 
Package: ISAnalytics
Commit: 9af855b99600c50443ce080c5ca523a872571b89
Author: Giulia Pais <giuliapais1@gmail.com>
Date: 2022-12-01 13:41:17 +0100
Commit message:

 updated readme status badges
 
Package: ISAnalytics
Commit: a8f78779b2f48a10cc08da25837a6f8df3607c92
Author: Giulia Pais <giuliapais1@gmail.com>
Date: 2022-12-01 11:33:24 +0100
Commit message:

 [U] Update to 1.9.1
 
Package: ISAnalytics
Commit: 837e29e50a378920815c2079a71a7ef1d21b01fa
Author: Giulia Pais <giuliapais1@gmail.com>
Date: 2022-12-01 10:17:25 +0100
Commit message:

 [U] Added bonferroni correction in gene_frequency_fisher
 
Package: ISAnalytics
Commit: 9b7eb4ae9424bb082fb8273adabc14a94636729b
Author: Giulia Pais <giuliapais1@gmail.com>
Date: 2022-11-30 17:11:17 +0100
Commit message:

 [FIX] Fixed code for tidyselect warnings, minor adjustments
 
Package: ISAnalytics
Commit: cc2874a7eb8cada5f3219c05a4c6fbfc2abf4c89
Author: Giulia Pais <giuliapais1@gmail.com>
Date: 2022-11-02 17:52:36 +0100
Commit message:

 [minor] Removed github actions from branch, fixed codecov file and README
 
Package: biodbLipidmaps
Commit: f3417835bc651afcad14ee7ea58e34b6decc639c
Author: Pierrick Roger <pk.roger@icloud.com>
Date: 2022-12-01 13:24:56 +0100
Commit message:

 Remove HTML from web service's reply. (#15)

 
Package: biodbLipidmaps
Commit: 1895f9a0a812bd1ce9ad5f1c4f5f5bf4213689ad
Author: Pierrick Roger <pk.roger@icloud.com>
Date: 2022-11-30 19:36:32 +0100
Commit message:

 Solve chk library deprecations. (#14)

 
Package: biodbLipidmaps
Commit: ca0b96e575dfa9a6de9748562a2414cc3f3795ae
Author: Pierrick Roger <pk.roger@icloud.com>
Date: 2022-11-24 23:20:16 +0100
Commit message:

 Merge branch 'remove_R_front'
 
Package: biodbLipidmaps
Commit: 9ad08731fb6ef63fa3119fe0d3f6e21897032168
Author: Pierrick Roger <pk.roger@icloud.com>
Date: 2022-11-24 22:51:11 +0100
Commit message:

 Remove R_front script.
 
Package: edgeR
Commit: 7dc6dd1fc01166e49e93ca64f8e37aab4a6e51ee
Author: Gordon Smyth <smyth@wehi.edu.au>
Date: 2022-12-01 22:10:20 +1100
Commit message:

 edgeR 3.41.2
- Update NAMESPACE for getNormLibSizes()
- Add getNormLibSizes() to calcNormFactors example.
 
Package: Rsubread
Commit: 743efc8da68ef2d4616b0e284c89fd7e7cdba02e
Author: Yang Liao <liao_y@svr2672.licr.unimelb.edu.au>
Date: 2022-12-01 19:42:54 +1100
Commit message:

 Fixex warning in cellCounts
 
Package: IntOMICS
Commit: a4b0fad3eb2ed5e4c9b71d51991fac2b11ced26b
Author: anna-pacinkova <ana.pacinkova@gmail.com>
Date: 2022-12-01 08:14:18 +0100
Commit message:

 BN_mod_res update
 
Package: IntOMICS
Commit: e089ba7f8b0ea43afc0bb382127c0c76983ec7c7
Author: anna-pacinkova <ana.pacinkova@gmail.com>
Date: 2022-11-27 19:26:55 +0100
Commit message:

 vignette error
 
Package: IntOMICS
Commit: ed2a8728205f0e02666697dc8984f7554af88237
Author: anna-pacinkova <ana.pacinkova@gmail.com>
Date: 2022-11-27 10:59:42 +0100
Commit message:

 omics_to_list add
 
Package: IntOMICS
Commit: f401fd1d4e5d8e027f6bb0c73ab8e667f43c7c4a
Author: anna-pacinkova <ana.pacinkova@gmail.com>
Date: 2022-11-26 20:20:53 +0100
Commit message:

 validity vignette man [ackage
 
Package: IntOMICS
Commit: 18b08b8fa887e5344f92d1500f9d9bb28d0e33db
Author: anna-pacinkova <ana.pacinkova@gmail.com>
Date: 2022-11-25 12:16:51 +0100
Commit message:

 edge_types simplified
 
Package: IntOMICS
Commit: cef900a95cab6bf072d90ea29a3004e0e39650d4
Author: anna-pacinkova <ana.pacinkova@gmail.com>
Date: 2022-11-25 09:37:58 +0100
Commit message:

 importFrom_internal_BiocStyle_dataLoad_pckgLinks
 
Package: IntOMICS
Commit: 9b1954859f926bb5806b273f840cb34b0fd93c1b
Author: anna-pacinkova <ana.pacinkova@gmail.com>
Date: 2022-11-21 22:31:18 +0100
Commit message:

 package:: removed
 
Package: IntOMICS
Commit: ae0bb14a9b41c4020244e301b398dfa28e075dc0
Author: anna-pacinkova <ana.pacinkova@gmail.com>
Date: 2022-11-21 22:05:15 +0100
Commit message:

 version update
 
Package: IntOMICS
Commit: c90e08b23bd189a0baa35adbea3106d9bb4323db
Author: anna-pacinkova <ana.pacinkova@gmail.com>
Date: 2022-11-21 22:00:07 +0100
Commit message:

 citation
 
Package: IntOMICS
Commit: dd30d8d8db33d0b581ddbdfb13b14af4cca7b743
Author: anna-pacinkova <ana.pacinkova@gmail.com>
Date: 2022-11-21 21:53:10 +0100
Commit message:

 DESCRIPTION updated
 
Package: IntOMICS
Commit: 17a9cdaad0c0c539fa52179e8459c4ff6e5eeebf
Author: anna-pacinkova <ana.pacinkova@gmail.com>
Date: 2022-11-21 21:40:16 +0100
Commit message:

 DESCRIPTION modified
 
Package: IntOMICS
Commit: a304be942b03ed222a5eac381e70c8067fddc418
Author: anna-pacinkova <ana.pacinkova@gmail.com>
Date: 2022-11-21 21:32:58 +0100
Commit message:

 MatchedAssayExperiment
 
Package: IntOMICS
Commit: 5fafe618808731002cab70f180b137471726cdeb
Author: anna-pacinkova <ana.pacinkova@gmail.com>
Date: 2022-11-20 23:34:46 +0100
Commit message:

 MatchedAssayExperiment hidden functions
 
Package: IntOMICS
Commit: af199913fa483849ec9160bfb96edcf78793fba3
Author: anna-pacinkova <ana.pacinkova@gmail.com>
Date: 2022-11-20 20:21:22 +0100
Commit message:

 readme added
 
Package: immunoClust
Commit: 4e6d709cc8a08242ec941152fe4d52b54404ebdb
Author: Till Sörensen <till-antoni.soerensen@charite.de>
Date: 2022-12-01 09:25:59 +0100
Commit message:

 problems with vignette build
 
Package: speckle
Commit: 58c04c6b39b26ca80c5baa325b69fd375b59bcee
Author: bphipson <12027703+bphipson@users.noreply.github.com>
Date: 2022-12-01 17:34:15 +1100
Commit message:

 try to fix edgeR error
 
Package: rfaRm
Commit: 83e2b1d1ca0677ef8eeec3be288c39b91d4c004d
Author: Lara Selles <lara.selles@oist.jp>
Date: 2022-12-01 15:26:30 +0900
Commit message:

 fix URL for clans
 
Package: speckle
Commit: 748128e8e501e0b29596657434798530d4a18366
Author: bphipson <12027703+bphipson@users.noreply.github.com>
Date: 2022-12-01 17:10:30 +1100
Commit message:

 bump version number
 
Package: speckle
Commit: b87a483d34e95c9b573d2c0e3553b02265bfe292
Author: bphipson <12027703+bphipson@users.noreply.github.com>
Date: 2022-12-01 17:07:55 +1100
Commit message:

 fix warning in bioconductor build (edgeR)
 
Package: spatialLIBD
Commit: 94388342546637dc6851f3f51dc3ac1d598038ab
Author: Leonardo Collado Torres <lcolladotor@gmail.com>
Date: 2022-11-30 23:36:50 -0500
Commit message:

 Fix some minor bugs while testing locally
 
Package: spatialLIBD
Commit: ce71aeeef148672ae347faa155d9030daaf4b017
Author: Leonardo Collado Torres <lcolladotor@gmail.com>
Date: 2022-11-30 22:49:47 -0500
Commit message:

 v1.11.2 -- tentative change
 
Package: spatialLIBD
Commit: 364ba0783b56314de93a5ada87b287e4ba6c6e59
Author: Leonardo Collado Torres <lcolladotor@gmail.com>
Date: 2022-11-30 22:48:17 -0500
Commit message:

 Try using fetch_data() for type = "spatialDLPFC_Visium"
 
Package: GenomeInfoDb
Commit: 06deb62aeff52a4f8042b379cfaf5861e4ab31fb
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2022-11-30 12:56:39 -0800
Commit message:

 Register some additional NCBI assemblies

- Assemblies bCatUst1.alt.v2 and bCatUst1.pri.v2 for Catharus ustulatus.
- Assemblies felCat9.1_X and F.catus_Fca126_mat1.0 for Felis catus.
 
Package: shinyMethyl
Commit: a315b087cc6b5c283fccec403deeaee808900742
Author: Jean-Philippe Fortin <fortin946@gmail.com>
Date: 2022-11-30 10:04:03 -0800
Commit message:

 Fixed testing
 
Package: BioPlex
Commit: 9b697729604320e89cfbadf5bbf569c51453eb15
Author: lgeistlinger <ludwig.geistlinger@gmail.com>
Date: 2022-11-30 12:07:35 -0500
Commit message:

 add pointers to data checks
 
Package: atena
Commit: 5700031248152d645c27684770de6a3dfbc402a0
Author: beacalvo <beacalvo96@gmail.com>
Date: 2022-11-30 17:13:59 +0100
Commit message:

 Fixed error in creating reassignment matrix in the atena method
 
Package: HiCDOC
Commit: 317e3015546d7457636ac5daf9d3a3ce9522876c
Author: Matthias Zytnicki <matthias.zytnicki@inra.fr>
Date: 2022-11-30 16:33:16 +0100
Commit message:

 Update news.
 
Package: HiCDOC
Commit: a2b05061c33909fb58d86dc1d65a40bdf1e3b31f
Author: Matthias Zytnicki <matthias.zytnicki@inra.fr>
Date: 2022-11-30 16:27:44 +0100
Commit message:

 Version bump.
 
Package: HiCDOC
Commit: bbbf8f3e7fdd1e7be2dd17fad8ae6372e6b1bc81
Author: Matthias Zytnicki <matthias.zytnicki@inra.fr>
Date: 2022-11-30 16:27:04 +0100
Commit message:

 Merge remote-tracking branch 'upstream/master'
 
Package: HiCDOC
Commit: 23d28c8c0c37c945179b4108b72915da9610acec
Author: Elise Maigné <elise.maigne@inrae.fr>
Date: 2022-11-30 16:14:40 +0100
Commit message:

 remove unused files
 
Package: HiCDOC
Commit: e099e7a744f9d7e37e47c87cd5fc3b66c7bdfe27
Author: Elise Maigné <elise.maigne@inrae.fr>
Date: 2022-11-30 16:12:20 +0100
Commit message:

 Merge pull request #5 from mzytnicki/selfInteractionRatio

Change the computation of selfInteraction (diagonal only) + review the distance normalisation 
Package: HiCDOC
Commit: 5349c3d06a3feb4a268830c6c3d5cd4a2bbc5f79
Author: Elise Maigné <elise.maigne@inrae.fr>
Date: 2022-11-30 16:12:07 +0100
Commit message:

 Merge branch 'master' into selfInteractionRatio 
Package: HiCDOC
Commit: 93e2faf7ed75c6f06d93dac401391387cb96c7a2
Author: Elise Maigné <elise.maigne@inrae.fr>
Date: 2022-11-30 15:47:23 +0100
Commit message:

 pass tests
 
Package: HiCDOC
Commit: 8e058dc948fbb287dba86ff973485721eee30415
Author: Elise Maigné <elise.maigne@inrae.fr>
Date: 2022-11-29 14:37:01 +0100
Commit message:

 change tests values
 
Package: HiCDOC
Commit: eacd1b613c5adf2e8420476f89b9adaada0352bb
Author: Elise Maigné <elise.maigne@inrae.fr>
Date: 2022-11-29 14:36:47 +0100
Commit message:

 recompile example data
 
Package: HiCDOC
Commit: e8117f2c584373cbd0ea5d2cff399dca50075102
Author: Elise Maigné <elise.maigne@inrae.fr>
Date: 2022-11-29 14:36:30 +0100
Commit message:

 handles error on tests (pb of data.table agregation format, needs to be all numeric)
 
Package: HiCDOC
Commit: ffe5633b1110a8fb435d4b86cf798040305d1107
Author: Elise Maigné <elise.maigne@inrae.fr>
Date: 2022-11-17 15:06:52 +0100
Commit message:

 add missing argument
 
Package: HiCDOC
Commit: 3e0463792aa6e56b5d314eddb02bc042ed41053d
Author: Elise Maigné <elise.maigne@inrae.fr>
Date: 2022-11-17 14:01:55 +0100
Commit message:

 correct roxygen
 
Package: HiCDOC
Commit: fd1e2a2d51fc5137d48f8dcf33d39674dac0e218
Author: Elise Maigné <elise.maigne@inrae.fr>
Date: 2022-11-17 14:01:15 +0100
Commit message:

 correct computation of selfInteractionRatios
 
Package: HiCDOC
Commit: 04e8f4732e5c615d472e99c6baaec85e4ee92ab4
Author: Elise Maigné <elise.maigne@inrae.fr>
Date: 2022-11-17 13:59:37 +0100
Commit message:

 add missing arguments in function
 
Package: HiCDOC
Commit: 0a91356479288db0594e7320f61c253e37ca5f7d
Author: Elise Maigné <elise.maigne@inrae.fr>
Date: 2022-11-16 16:38:36 +0100
Commit message:

 factorize the creation of the interactionSet in parsers, recreate the interacion on diagonal if there is only off diagonal interaction
 
Package: HiCDOC
Commit: b005fa2fe249beb808dbbadb2328378965f3da6e
Author: Elise Maigné <elise.maigne@inrae.fr>
Date: 2022-11-16 15:21:18 +0100
Commit message:

 keep zero lines
 
Package: HiCDOC
Commit: 4f28b855d2ecd63ff5cf3088b00a95498b885393
Author: Elise Maigné <elise.maigne@inrae.fr>
Date: 2022-10-26 16:57:59 +0200
Commit message:

 rechange compartments affectation, correct tests, recompile example data
 
Package: HiCDOC
Commit: fcb0eb0055ff9d2846facd21ad2e5baef57a1a1a
Author: Elise Maigné <elise.maigne@inrae.fr>
Date: 2022-10-26 16:03:22 +0200
Commit message:

 remove varif if NA values on the median (not allowed), already fixed before KR normalization.
 
Package: HiCDOC
Commit: 9b4514aa3513edcf039ae6edae3016be3098c436
Author: Elise Maigné <elise.maigne@inrae.fr>
Date: 2022-10-26 15:59:05 +0200
Commit message:

 allow results of only one condition
 
Package: HiCDOC
Commit: 60c470b7d3e14802d560263794abffdf6426d3b9
Author: Elise Maigné <elise.maigne@inrae.fr>
Date: 2022-10-24 19:23:09 +0200
Commit message:

 revert compartment assignement. Lower should be A. correct tests. rerun example data
 
Package: HiCDOC
Commit: 8e9caadd89fb25e28be95b6166d77329e246bd3e
Author: Elise Maigné <elise.maigne@inrae.fr>
Date: 2022-10-24 15:32:35 +0200
Commit message:

 change compartment assignment (higher = A). Recompile example data, change tests.
 
Package: HiCDOC
Commit: 0a48dd5b69e651be9c35ecf380c78ad19c232524
Author: Elise Maigné <elise.maigne@inrae.fr>
Date: 2022-10-24 10:48:53 +0200
Commit message:

 use median of others values if no value on diagonal
 
Package: HiCDOC
Commit: fd5e86b68423a6f9b5ca6f69d2881df821348dc0
Author: Elise Maigné <elise.maigne@inrae.fr>
Date: 2022-10-24 10:43:00 +0200
Commit message:

 correct tests according to changes on norm distance, ratios and new colors on plotInteractions
 
Package: HiCDOC
Commit: 17739faf8fab323fb30136d0a60235a66f1111ad
Author: Elise Maigné <elise.maigne@inrae.fr>
Date: 2022-10-24 10:31:54 +0200
Commit message:

 coorect test after add of +1 in positions
 
Package: HiCDOC
Commit: 240822b9a06bc1971d9bae03ddf831caef4d03a5
Author: Matthias Zytnicki <matthias.zytnicki@inra.fr>
Date: 2022-10-20 14:58:30 +0200
Commit message:

 Version bump.
 
Package: HiCDOC
Commit: 6433d11169cd65e2c1fc73860f77850de8cf0945
Author: Matthias Zytnicki <matthias.zytnicki@inra.fr>
Date: 2022-10-20 14:58:04 +0200
Commit message:

 Correct Windows bug.
 
Package: HiCDOC
Commit: 2ea0091475e2cd0861432bee02c774ab36ca66d2
Author: Elise Maigné <elise.maigne@inrae.fr>
Date: 2022-10-21 16:11:02 +0200
Commit message:

 allow a transformX parameter in plotDistanceEffect, 3 colours fo plotInteractions
 
Package: HiCDOC
Commit: c3081b35bd445075d0735a7a393b16079b22381b
Author: Elise Maigné <elise.maigne@inrae.fr>
Date: 2022-10-21 15:55:39 +0200
Commit message:

 removing the +1 in log(+1) in normdistance (after KR = no need). returning results in log to have a nice viz scale (around 0)
 
Package: HiCDOC
Commit: bbc571ecede79425de83dd9ab598238d6da484f6
Author: Elise Maigné <elise.maigne@inrae.fr>
Date: 2022-10-20 16:54:32 +0200
Commit message:

 normalization distance : put again results in original scale. Too hard to viz interactions and distance effect otherwise
 
Package: HiCDOC
Commit: 1a12582d13f8dc6dc6238f33a415b0666dbf65a6
Author: Elise Maigné <elise.maigne@inrae.fr>
Date: 2022-10-20 14:09:06 +0200
Commit message:

 reverse compartments attribution (same as before, to compare results)
 
Package: HiCDOC
Commit: bdfe7468e13e2a5e05f73f0a9dc4b4a245dac2a4
Author: Elise Maigné <elise.maigne@inrae.fr>
Date: 2022-10-20 13:29:45 +0200
Commit message:

 correct variance for variance by column (by replicate, condition)
 
Package: HiCDOC
Commit: 8dd96a16f3550858cb2419a6d1ce4eb97707ac0c
Author: Elise Maigné <elise.maigne@inrae.fr>
Date: 2022-10-20 12:57:26 +0200
Commit message:

 valids assays must have a non zero variance
 
Package: HiCDOC
Commit: 91486e54a1fb6b710b67f2118fcd03d038c52d93
Author: Elise Maigné <elise.maigne@inrae.fr>
Date: 2022-10-20 09:30:47 +0200
Commit message:

 rename compartment -> cluster when its cluster and not compartment
 
Package: HiCDOC
Commit: cc9cec3c0d7a8bb74e1c719638903ce353ed6436
Author: Elise Maigné <elise.maigne@inrae.fr>
Date: 2022-10-20 09:30:20 +0200
Commit message:

 correct in case of only 1 column matrix
 
Package: HiCDOC
Commit: f179d22e2ecbdb5662612982b5d260e5d7e23e85
Author: Elise Maigné <elise.maigne@inrae.fr>
Date: 2022-10-19 11:43:51 +0200
Commit message:

 log2 normalization for norm distance, keep in log2 after
 
Package: HiCDOC
Commit: 200eebe2cc6f228ad75a39a90810f535a546df61
Author: Elise Maigné <elise.maigne@inrae.fr>
Date: 2022-09-14 17:27:08 +0200
Commit message:

 take only diagonal to detectcompartments, change A to higher values
 
Package: HiCDOC
Commit: cae8f06ec4dc6a45b1dd58c43dd3cfb96d0cafe4
Author: Elise Maigné <elise.maigne@inrae.fr>
Date: 2022-09-14 17:26:29 +0200
Commit message:

 use log to normalize distance (loess done on log). Dividing by resulting value (equivalent to remove bias in log scale)
 
Package: HiContactsData
Commit: ddd1dc77fab00ddcbbf3dc4882361bc160127cd3
Author: js2264 <jacquesserizay@gmail.com>
Date: 2022-11-30 16:25:57 +0100
Commit message:

 bump to 1.1.6
 
Package: HiContactsData
Commit: aced6d43f486b939a33ba57d91c2ae4ad0cefdab
Author: js2264 <jacquesserizay@gmail.com>
Date: 2022-11-30 16:21:05 +0100
Commit message:

 add hicpro validPairs
 
Package: MungeSumstats
Commit: 7de01e900fafa8bb7ca5a349b9ac0557764ebe26
Author: Al-Murphy <alanmurph94@hotmail.com>
Date: 2022-11-30 15:16:55 +0000
Commit message:

 GHA update
 
Package: MungeSumstats
Commit: 57f4aa199b55fa95242aadbaa0cd9eaa988320ee
Author: Al-Murphy <alanmurph94@hotmail.com>
Date: 2022-11-30 15:09:43 +0000
Commit message:

 GHA update
 
Package: MungeSumstats
Commit: b210a7063ec3096fb025d5594de7400b70aeb9e7
Author: Al-Murphy <alanmurph94@hotmail.com>
Date: 2022-11-30 15:05:43 +0000
Commit message:

 GHA update
 
Package: MungeSumstats
Commit: 4ad1e0b876b97d3dd761f87e654229c47d275690
Author: Al-Murphy <alanmurph94@hotmail.com>
Date: 2022-11-30 15:02:09 +0000
Commit message:

 GHA update
 
Package: GRaNIE
Commit: d5f25893561555d2640f2642c5d8a7139e10f2f8
Author: Christian Arnold <christian.arnold@embl.de>
Date: 2022-11-30 13:26:52 +0100
Commit message:

 Changed link to TFBS files
 
Package: MsExperiment
Commit: 43f9c023af83094e5b7a731a6f31d9ba5f629946
Author: Johannes Rainer <5506112+jorainer@users.noreply.github.com>
Date: 2022-11-30 12:14:38 +0100
Commit message:

 Merge pull request #31 from rformassspectrometry/jomain

refactor: use grr::matches do match data to samples 
Package: MsExperiment
Commit: 3fcdbb92c9f96e7c368f65c110b042152aefaba1
Author: jorainer <johannes.rainer@gmail.com>
Date: 2022-11-30 09:35:15 +0100
Commit message:

 refactor: adapt to Sebastian's comments
 
Package: MsExperiment
Commit: 03248fa7f44e50e0267b8db38b2b135b7ec13b87
Author: Johannes Rainer <5506112+jorainer@users.noreply.github.com>
Date: 2022-11-30 07:56:02 +0100
Commit message:

 Update NEWS.md

Co-authored-by: Sebastian Gibb <mail@sebastiangibb.de> 
Package: MsExperiment
Commit: 4a496fe633ffc4574b5012e60e2a55149c58b57f
Author: jorainer <johannes.rainer@gmail.com>
Date: 2022-11-28 16:19:00 +0100
Commit message:

 refactor: use S4Vectors::findMatches instead of grr::matches
 
Package: MsExperiment
Commit: 99fe8a4e949a111f8bf05177cf517c69e5b4691a
Author: jorainer <johannes.rainer@gmail.com>
Date: 2022-11-15 14:59:21 +0100
Commit message:

 refactor: use grr::matches do match data to samples

- Use the `grr::matches` function instead of an `lapply` to find all matches
  between elements and samples in `linkSampleData`. This increases performance,
  especially for larger data sets.
 
Package: MsExperiment
Commit: 2118964fef7b4e2e226da9e27b68d8da8313457b
Author: jorainer <johannes.rainer@gmail.com>
Date: 2022-11-15 14:06:34 +0100
Commit message:

 ci: use R devel and BioC 3.17
 
Package: MsExperiment
Commit: af327547b42345e1ec137c4df550b2f812161eb2
Author: jorainer <johannes.rainer@gmail.com>
Date: 2022-11-15 14:03:46 +0100
Commit message:

 Merge branch 'master'
 
Package: MsExperiment
Commit: 4fd4c32b97aed2c3fd5012b1a2633bc1010baf10
Author: jorainer <johannes.rainer@gmail.com>
Date: 2022-10-17 17:25:18 +0200
Commit message:

 refactor: import spectra<- from ProtGenerics
 
Package: LEA
Commit: aa7e9a9fe19dfb9c25311c1d7b80aa504a86ac2a
Author: francois <francois@timc-bcm-66p.home>
Date: 2022-11-30 08:34:34 +0100
Commit message:

 fix dgetrf fast_inverse
 
Package: spaSim
Commit: 140e2baab378c46511aea09889bb104c1dc60942
Author: fuerzhou <“653540853@qq.com”>
Date: 2022-11-30 10:41:58 +1100
Commit message:

 Updated installation instructions.
 
Package: spaSim
Commit: f49dd0e2352d555daae9b6a8ed74c47496498222
Author: fuerzhou <“653540853@qq.com”>
Date: 2022-11-29 23:41:51 +1100
Commit message:

 Version bump in devel branch
 
Package: spaSim
Commit: e4f218220239bb23b0b359098ec130fcd792ee4a
Author: fuerzhou <“653540853@qq.com”>
Date: 2022-11-29 22:47:35 +1100
Commit message:

 Added RANN import
 
Package: spaSim
Commit: 382c64fc82cfed8d4aa0987d18a4e3c49f017dde
Author: fuerzhou <“653540853@qq.com”>
Date: 2022-11-29 22:31:44 +1100
Commit message:

 Added `jitter` parameter to `TIS()`.
 
Package: spaSim
Commit: 8f22f8840a74008a1e2ed5f5cc20be0f71fe9f72
Author: fuerzhou <“653540853@qq.com”>
Date: 2022-11-29 22:04:47 +1100
Commit message:

 Fixed "jitter" typo in documentation.
 
Package: spaSim
Commit: e6b6f1eaf800838cebe7b96c201c572c5155c23b
Author: fuerzhou <“653540853@qq.com”>
Date: 2022-11-29 22:04:21 +1100
Commit message:

 Fixed the incorrectly plotted image in README
 
Package: speckle
Commit: 65866a812ce2df505605aaebc7030bc00ed6c27f
Author: bphipson <12027703+bphipson@users.noreply.github.com>
Date: 2022-11-30 16:02:28 +1100
Commit message:

 Added changes to address issues for Bioconductor review
 
Package: speckle
Commit: 786bfe56d394c4e92f3a52d377f4cc0b69971fbc
Author: MelodyJIN-Y <Melody-Jin@outlook.com>
Date: 2022-11-14 11:40:36 +0800
Commit message:

 update unit test
 
Package: speckle
Commit: 1776c698e89284d90592d1d41e28509c297ad63d
Author: MelodyJIN-Y <Melody-Jin@outlook.com>
Date: 2022-11-14 11:28:40 +0800
Commit message:

 Update convertData.R 
Package: speckle
Commit: 456ed23d1edf4c695874fecabed4fd1f6d1e7de0
Author: MelodyJIN-Y <Melody-Jin@outlook.com>
Date: 2022-11-14 11:21:34 +0800
Commit message:

 change 1:3 construction to seq() 
Package: speckle
Commit: fb97ecd0d45247a9793e01ce0930e703f39d0d57
Author: MelodyJIN-Y <Melody-Jin@outlook.com>
Date: 2022-11-14 11:17:28 +0800
Commit message:

 Update propeller.anova.R 
Package: speckle
Commit: 25d62eeb7d9a56fcfa68e50bf651ce5a44700651
Author: MelodyJIN-Y <Melody-Jin@outlook.com>
Date: 2022-11-14 11:17:02 +0800
Commit message:

 Update propeller.ttest.R 
Package: speckle
Commit: de14b24fc5fd5afa09a0dc85d1141203c8b912a3
Author: MelodyJIN-Y <Melody-Jin@outlook.com>
Date: 2022-11-14 11:16:43 +0800
Commit message:

 Update normCounts.R 
Package: speckle
Commit: 8254e837ab44a528590a7c7e08296cb811346a59
Author: MelodyJIN-Y <Melody-Jin@outlook.com>
Date: 2022-11-14 11:16:30 +0800
Commit message:

 Update normCounts.R 
Package: speckle
Commit: 6ef3f96a908ff51ad443cf2f24cc9c34a0493fe3
Author: MelodyJIN-Y <Melody-Jin@outlook.com>
Date: 2022-11-14 11:15:45 +0800
Commit message:

 Update convertData.R 
Package: speckle
Commit: 35a6d33fcd8354e322dca1aa0612fc68f9462548
Author: MelodyJIN-Y <Melody-Jin@outlook.com>
Date: 2022-11-14 11:15:15 +0800
Commit message:

 Update speckle_example_data.R 
Package: speckle
Commit: b1352370aeed1b4641337c7e4424e6e73620909e
Author: MelodyJIN-Y <Melody-Jin@outlook.com>
Date: 2022-11-14 11:14:54 +0800
Commit message:

 Update propeller.anova.R 
Package: speckle
Commit: 3a5713bb93c14399336da68a3ca243b105d6e6f1
Author: MelodyJIN-Y <Melody-Jin@outlook.com>
Date: 2022-11-14 11:14:29 +0800
Commit message:

 Update propeller.ttest.R 
Package: speckle
Commit: 7ea6284d2f6c1957e61122fe00d669486bb23789
Author: MelodyJIN-Y <Melody-Jin@outlook.com>
Date: 2022-11-14 11:13:39 +0800
Commit message:

 Update propeller.anova.R 
Package: speckle
Commit: de89ebdee4024589bbd5af04cb4f151603ede9f8
Author: MelodyJIN-Y <Melody-Jin@outlook.com>
Date: 2022-11-14 11:13:17 +0800
Commit message:

 Update propeller.R 
Package: speckle
Commit: 89b8160fde0cfd4db1bbfa1dc94ed8b00855a7a1
Author: MelodyJIN-Y <Melody-Jin@outlook.com>
Date: 2022-11-14 11:11:59 +0800
Commit message:

 Update normCounts.R 
Package: speckle
Commit: 5eb18f6c2cc6a5216f86a9fbbf36c301068922b4
Author: MelodyJIN-Y <Melody-Jin@outlook.com>
Date: 2022-11-14 11:11:28 +0800
Commit message:

 Update ggplotColors.R 
Package: speckle
Commit: 1dfe2bdfd0c83a7f9687813918882810725aef5b
Author: MelodyJIN-Y <Melody-Jin@outlook.com>
Date: 2022-11-14 11:11:09 +0800
Commit message:

 Update getTransformedProps.R 
Package: speckle
Commit: 1a0c164ab8b23aafb692cc3dfe25cbeb27a53508
Author: MelodyJIN-Y <Melody-Jin@outlook.com>
Date: 2022-11-14 11:10:39 +0800
Commit message:

 Update estimateBetaParamsFromCounts.R 
Package: speckle
Commit: cacaddf66d27a42deaa15641e9458f4fa6b7854b
Author: MelodyJIN-Y <Melody-Jin@outlook.com>
Date: 2022-11-14 11:10:22 +0800
Commit message:

 Update estimateBetaParam.R 
Package: speckle
Commit: 383af35e2ee5b12c98ca97340a203b7f8a2ad257
Author: MelodyJIN-Y <Melody-Jin@outlook.com>
Date: 2022-11-14 11:10:01 +0800
Commit message:

 Update convertData.R 
Package: speckle
Commit: 1cdc07f4b594114134185e88c8cff3520eebbcd6
Author: MelodyJIN-Y <Melody-Jin@outlook.com>
Date: 2022-11-11 15:02:28 +0800
Commit message:

 include packages for unit test
 
Package: speckle
Commit: 3dc19d0a8086785acb35cceab84ecbbebf9607e2
Author: MelodyJIN-Y <Melody-Jin@outlook.com>
Date: 2022-11-11 15:01:44 +0800
Commit message:

 add unit tests
 
Package: speckle
Commit: f15ac11d95ad0bb721834a9616e0c69cc61ee221
Author: bphipson <12027703+bphipson@users.noreply.github.com>
Date: 2022-11-10 15:31:19 +1100
Commit message:

 Update DESCRIPTION

Add LazyData: TRUE 
Package: speckle
Commit: 1e3fa54dd5acc8a6a527e5ac8f6460bbe4bd65bc
Author: bphipson <12027703+bphipson@users.noreply.github.com>
Date: 2022-10-14 16:56:57 +1100
Commit message:

 Update README.md 
Package: speckle
Commit: 73afb9ff887a0e4364dae4160305c8507adffeb3
Author: bphipson <12027703+bphipson@users.noreply.github.com>
Date: 2022-10-14 16:54:41 +1100
Commit message:

 Update README.md 
Package: spatialLIBD
Commit: e16f4e0fa134e224cafd593853931149391e0a56
Author: Leonardo Collado Torres <lcolladotor@gmail.com>
Date: 2022-11-29 20:20:46 -0500
Commit message:

 v1.11.1 -- minor change in gene_set_enrichment() that provides more info
 
Package: spatialLIBD
Commit: cefc7db61a16e80b16c14f0df30b40701cfc788c
Author: Leonardo Collado Torres <lcolladotor@gmail.com>
Date: 2022-11-29 20:20:10 -0500
Commit message:

 Compute NumSig and SetSize like at https://github.com/LieberInstitute/HumanPilot/blob/master/Analysis/Layer_Guesses/check_clinical_gene_sets.R since it's useful info to have
 
Package: MAST
Commit: 339c6a71e727af549e8b802b4ea64e6259c592d5
Author: Andrew McDavid <andrew@ozette.com>
Date: 2022-11-29 16:59:28 -0800
Commit message:

 correct a few class == tests
 
Package: MAST
Commit: 16e90b42f071e0019d59db92ab58f41c5a9f7ab8
Author: Andrew McDavid <andrew@ozette.com>
Date: 2022-11-29 16:59:10 -0800
Commit message:

 Hack to resolve #175 and satijalab/seurat#6489
 
Package: openCyto
Commit: 3f60af92ad380aea9ff7cc0bf077c4f3a0321fc4
Author: mikejiang <mike@ozette.ai>
Date: 2022-11-29 16:33:29 -0800
Commit message:

 bump
 
Package: openCyto
Commit: a2949ed922e1e5529ac24f29b04af824b6eecaa6
Author: mikejiang <mike@ozette.ai>
Date: 2022-11-29 16:33:02 -0800
Commit message:

 dis able boost thread
 
Package: MAST
Commit: ac2f42e43c1067bccc06c3af93b9194ecab7cb9f
Author: Andrew McDavid <andrew@ozette.com>
Date: 2022-11-29 15:34:01 -0800
Commit message:

 Merge remote-tracking branch 'upstream/master'
 
Package: MAST
Commit: 8256845b3122274b691d7b3a410c1ad3ff9acf75
Author: Andrew McDavid <andrew@ozette.com>
Date: 2022-11-29 15:32:42 -0800
Commit message:

 attempt to fix stat_ell
 
Package: MAST
Commit: 60da6da0d76c6e8b2deaaaa4dec395fa2d45aac0
Author: Andrew McDavid <andrew.n.mcdavid@gmail.com>
Date: 2022-02-02 14:48:33 -0500
Commit message:

 Rerun pkgdown
 
Package: MAST
Commit: 6ff665c1f9638113461e7b1685c23dd45bd3ee9f
Author: Andrew McDavid <andrew.n.mcdavid@gmail.com>
Date: 2021-12-17 10:41:45 -0500
Commit message:

 Honeypot template
 
Package: MAST
Commit: 1f8d7c349fca820c5530aa7a18f9e47f0a620eb2
Author: Andrew McDavid <andrew.n.mcdavid@gmail.com>
Date: 2021-12-17 10:37:43 -0500
Commit message:

 Try adding an issue template to cut down on support questions to the issues
 
Package: MAST
Commit: 1daced13bd8b9f4332cdee905aee0ef4c8b26f40
Author: Andrew McDavid <andrew.n.mcdavid@gmail.com>
Date: 2021-12-17 10:36:32 -0500
Commit message:

 Didn't run document() to update melt_list_left example.
 
Package: MAST
Commit: 2b0cdf132a6a8162ac63cd4dd3cae2f21393057c
Author: Andrew McDavid <andrew.n.mcdavid@gmail.com>
Date: 2021-12-15 12:47:35 -0500
Commit message:

 Fixes #157

Also quell warnings about nobs.default
optimMsg was not being properly unlisted.
 
Package: MAST
Commit: 6f5d763983d8087447d9ab8f6d47745ec4fcf810
Author: Andrew McDavid <andrew.n.mcdavid@gmail.com>
Date: 2021-12-15 11:42:38 -0500
Commit message:

 Add `parallel` argument to `summary` and `lrTest`.
Fixes #169
 
Package: MAST
Commit: 97d14e9f9cb43d306109e8d7202b30314f04d018
Author: Nitesh Turaga <nitesh.turaga@gmail.com>
Date: 2021-10-26 16:30:38 +0000
Commit message:

 bump x.y.z version to odd y following creation of RELEASE_3_14 branch
 
Package: MAST
Commit: e7a03aaac4258830459424efd295faad35fc6e28
Author: Nitesh Turaga <nitesh.turaga@gmail.com>
Date: 2021-10-26 16:30:38 +0000
Commit message:

 bump x.y.z version to even y prior to creation of RELEASE_3_14 branch
 
Package: MAST
Commit: e3f45ab004e18a14f6400cc69388df04e5a482fe
Author: Nitesh Turaga <nitesh.turaga@gmail.com>
Date: 2021-05-19 16:23:40 +0000
Commit message:

 bump x.y.z version to odd y following creation of RELEASE_3_13 branch
 
Package: MAST
Commit: f9da1b9b0812a630f42440e7acd38996d5d745a6
Author: Nitesh Turaga <nitesh.turaga@gmail.com>
Date: 2021-05-19 16:23:40 +0000
Commit message:

 bump x.y.z version to even y prior to creation of RELEASE_3_13 branch
 
Package: MAST
Commit: f8fd6abb4746a5645f53627f224ab2bcb8bc900b
Author: Andrew McDavid <andrew.n.mcdavid@gmail.com>
Date: 2021-05-11 14:24:42 -0400
Commit message:

 Add a exprs_values slot to the ZlmFit class.

Needed to maintain state in lrTest and bootstrapping.
 
Package: MAST
Commit: 02c8b60c960531e6990ff32af8aa6435923ea278
Author: Andrew McDavid <andrew.n.mcdavid@gmail.com>
Date: 2021-05-10 13:26:44 -0400
Commit message:

 ebayes also needs to follow exprs_values
 
Package: MAST
Commit: ea948ebe13cb22a21ff0931d535276583becdb8f
Author: Andrew McDavid <andrew.n.mcdavid@gmail.com>
Date: 2021-05-07 08:56:10 -0400
Commit message:

 Add test RE: #158

unrelated: quell a couple warnings from lmer
 
Package: MAST
Commit: 9e88a7dd03918fa9820e8a8d080c85c6bfb83fae
Author: Andrew McDavid <andrew.n.mcdavid@gmail.com>
Date: 2021-05-07 08:55:26 -0400
Commit message:

 Fixes #158
 
Package: MAST
Commit: 48999d3b16f0c9655e6fe0179c0de387568ff5aa
Author: Andrew McDavid <andrew.n.mcdavid@gmail.com>
Date: 2021-02-16 15:37:36 -0500
Commit message:

 Fix link to MAST tag on support.bioconductor.org 
Package: MAST
Commit: 65e6bf9a30f2c7b87893769a50183b103bf15dfd
Author: Andrew McDavid <andrew.n.mcdavid@gmail.com>
Date: 2021-02-09 23:31:56 -0500
Commit message:

 Fix typo in vignette name. closes #150 
Package: HiContactsData
Commit: aebca197cb1aac51342e59c35ec5df3a59569d5f
Author: js2264 <jacquesserizay@gmail.com>
Date: 2022-11-30 00:08:14 +0100
Commit message:

 bump to 1.1.5
 
Package: HiContactsData
Commit: bff879f7cc9435ce5e6b7e813f6f7316112462fc
Author: js2264 <jacquesserizay@gmail.com>
Date: 2022-11-30 00:08:02 +0100
Commit message:

 add .hic and .hicpro files
 
Package: qvalue
Commit: f00c9060d92b1fe51471f329a5955e08a538379c
Author: Andrew Bass <andrewbass@Andrews-Mini.attlocal.net>
Date: 2022-11-29 16:44:31 -0500
Commit message:

 bump version number
 
Package: MungeSumstats
Commit: 42857d1781f6e849e45e566a6acc1ff3b135be8d
Author: Al-Murphy <alanmurph94@hotmail.com>
Date: 2022-11-29 20:52:53 +0000
Commit message:

 bug fix - chain file with offline run
 
Package: SFEData
Commit: 69bea0d473119a570cb37c376b05cb492b5579de
Author: Lambda Moses <dlu2@caltech.edu>
Date: 2022-11-29 12:26:49 -0800
Commit message:

 version bump before push
 
Package: SFEData
Commit: a03f41253150605fe35a058fe9bcf82665c43cc0
Author: Kayla Jackson <kaylajac@caltech.edu>
Date: 2022-11-28 16:29:02 -0800
Commit message:

 Add code for processing Lohoff, et al seqFISH data
 
Package: SFEData
Commit: 2fbfa94e2678d18c667c56e418e06a5a27154124
Author: Kayla Jackson <kaylajac@caltech.edu>
Date: 2022-11-28 15:30:28 -0800
Commit message:

 Change box file link for embryo 3
 
Package: SFEData
Commit: 69f223eb2d9fe40da4fa2d66b924506a2b0eeb13
Author: Kayla Jackson <kaylajac@caltech.edu>
Date: 2022-11-28 15:24:36 -0800
Commit message:

 Add mouse gastrulation seqFISH data
 
Package: SFEData
Commit: 2f3dce2c3e52c8a1c89909abf0aae5110fe0c253
Author: Kayla Jackson <kaylajac@caltech.edu>
Date: 2022-11-28 15:24:13 -0800
Commit message:

 Add mouse gastrulation seqFISH data
 
Package: SFEData
Commit: 37a3304625b55c94bb974ff83baa02808fd18ae3
Author: Kayla Jackson <kaylajac@caltech.edu>
Date: 2022-11-28 15:15:49 -0800
Commit message:

 Addition of seqFISH mouse gastrulation data
 
Package: SFEData
Commit: e0cc157f007528b4bf6773f4b07b793fb02db134
Author: Lambda Moses <dlu2@caltech.edu>
Date: 2022-11-03 10:31:04 -0700
Commit message:

 fixed Rd error
 
Package: GRaNIE
Commit: 8aa162c11e27508cc5fe5ad78ab2539fd3a75de1
Author: Christian Arnold <christian.arnold@embl.de>
Date: 2022-11-29 19:19:24 +0100
Commit message:

 README update
 
Package: GRaNIE
Commit: bd9b9e62596e740b5f1e01f6cf6461751c2a4abb
Author: Christian Arnold <christian.arnold@embl.de>
Date: 2022-11-29 19:01:52 +0100
Commit message:

 minor
 
Package: GRaNIE
Commit: 4656f59aaff1c2d069a5ea5ad78c96cbbf1fddbb
Author: Christian Arnold <christian.arnold@embl.de>
Date: 2022-11-29 18:53:49 +0100
Commit message:

 Documentation updates
 
Package: hpar
Commit: 26cc9533ec8ca1ca2a59ab1b105a77ee9f842ca9
Author: Laurent Gatto <laurent.gatto@uclouvain.be>
Date: 2022-11-29 15:52:04 +0100
Commit message:

 alias hpar
 
Package: hpar
Commit: 6c09034cb8fde6518ddaa3f9a5559f371eb7e171
Author: Laurent Gatto <laurent.gatto@uclouvain.be>
Date: 2022-11-29 15:49:27 +0100
Commit message:

 update hpar package man page
 
Package: hpar
Commit: b8559bf4181d782c62548eae5720b2f2a6d86ff3
Author: Laurent Gatto <laurent.gatto@uclouvain.be>
Date: 2022-11-22 17:12:59 +0100
Commit message:

 remove .rda from vignette and code/examples
 
Package: hpar
Commit: 7b7522e33d7b16a2410e9dac171883de25616dd2
Author: Laurent Gatto <laurent.gatto@uclouvain.be>
Date: 2022-11-22 16:59:39 +0100
Commit message:

 udpate metadata (remove .rda extension)
 
Package: hpar
Commit: dd4d6c3d1eedf9b936057dbce1ea7a0c0dcf1a5e
Author: Laurent Gatto <laurent.gatto@uclouvain.be>
Date: 2022-11-22 16:52:35 +0100
Commit message:

 add allHparData() to example
 
Package: hpar
Commit: 2d2d31a3af5a042245c18953c1ba03804bad46fd
Author: Laurent Gatto <laurent.gatto@uclouvain.be>
Date: 2022-11-22 16:42:39 +0100
Commit message:

 udpate code base to use EH
 
Package: hpar
Commit: 243ed50e342b27f318a66b3c032d9c02d0fb22b4
Author: Laurent Gatto <laurent.gatto@uclouvain.be>
Date: 2022-11-22 11:50:18 +0100
Commit message:

 fix sentence
 
Package: hpar
Commit: 33a2b7db83fdfff57e7770046ea4bc770a5eb07e
Author: Laurent Gatto <laurent.gatto@uclouvain.be>
Date: 2022-11-22 11:43:24 +0100
Commit message:

 use roxygen
 
Package: hpar
Commit: 5ffc1b54418c51fa0ff645f0456c2785148b6633
Author: Laurent Gatto <laurent.gatto@uclouvain.be>
Date: 2022-11-22 10:34:28 +0100
Commit message:

 update metadata.csv
 
Package: hpar
Commit: 0a94e5f23b62aff1cec9438f65fd4ad4932aec86
Author: Laurent Gatto <laurent.gatto@uclouvain.be>
Date: 2022-11-22 10:19:54 +0100
Commit message:

 update title names (omit extension)
 
Package: hpar
Commit: f54a653f5e503aadece1d1d8256870d5aea17e22
Author: Laurent Gatto <laurent.gatto@uclouvain.be>
Date: 2022-11-14 18:02:26 +0100
Commit message:

 fix: separate tags with colon instead of comma
 
Package: hpar
Commit: 528b39c68869d31d754086348d3f87d55df992fc
Author: Laurent Gatto <laurent.gatto@uclouvain.be>
Date: 2022-11-08 17:25:09 +0100
Commit message:

 feat: update package to use ExperimentHub
 
Package: hpar
Commit: 57e86b0e6d5bb2663f19c2fc84fec5576a54ccf9
Author: Laurent Gatto <laurent.gatto@uclouvain.be>
Date: 2022-11-08 14:17:17 +0100
Commit message:

 Merge branch 'devel'
 
Package: hpar
Commit: 538eb621cff671a98a3946888308ecb8fe654e70
Author: Laurent Gatto <laurent.gatto@uclouvain.be>
Date: 2022-11-08 14:16:58 +0100
Commit message:

 fix conflict
 
Package: hpar
Commit: ff5e3a35de6709211d172bd262697bb9010f19ec
Author: lgatto <laurent.gatto@gmail.com>
Date: 2022-10-31 22:21:18 +0100
Commit message:

 fix gha deploy 2
 
Package: hpar
Commit: 5db994099ba6936318563712300a2ddf0ae65f2b
Author: lgatto <laurent.gatto@gmail.com>
Date: 2022-10-31 22:03:33 +0100
Commit message:

 fix gha deploy
 
Package: hpar
Commit: 6ba932609b39cba313e9577c4f4b51c65cc08c26
Author: Laurent Gatto <laurent.gatto@uclouvain.be>
Date: 2022-10-31 18:18:49 +0100
Commit message:

 bump version
 
Package: hpar
Commit: f33800073442876d8bbb35df7e5e147a7846db22
Author: Laurent Gatto <laurent.gatto@uclouvain.be>
Date: 2022-10-31 18:17:43 +0100
Commit message:

 Merge branch 'ManonMartin-master'
 
Package: hpar
Commit: 489b1ad5d4fdd3206e2f955bf014f0014cecb78d
Author: Laurent Gatto <laurent.gatto@uclouvain.be>
Date: 2022-10-31 18:17:19 +0100
Commit message:

 fix errors
 
Package: hpar
Commit: 41877687a8f4043de616f3e4b279836afaaa8869
Author: Laurent Gatto <laurent.gatto@uclouvain.be>
Date: 2022-10-31 11:36:58 +0100
Commit message:

 fix: rename object in rnaGeneTissue21.0.rda
 
Package: hpar
Commit: 5a202c9c7f1ee708716391cfe50020e5d8642822
Author: Manon Martin <manmartin@mac-1T0-170.local>
Date: 2022-10-17 16:44:58 +0200
Commit message:

 updated to hpa 21.1
 
Package: hpar
Commit: b82d116986dca2194f6e8cfe609d10cca6a7d310
Author: Laurent Gatto <laurent.gatto@gmail.com>
Date: 2022-02-01 10:19:27 +0100
Commit message:

 Update check-bioc.yml 
Package: BiocFHIR
Commit: 10f9d06c5641a1d39e652944e8967c71bf78306c
Author: vjcitn <stvjc@channing.harvard.edu>
Date: 2022-11-29 09:48:55 -0500
Commit message:

 fix tests
 
Package: MsQuality
Commit: c1556102bdfa43701feb209d7ac7b1b1f6b95b7d
Author: tnaake <thomasnaake@gmx.de>
Date: 2022-11-29 14:42:47 +0100
Commit message:

 bump to 0.99.6
 
Package: MsQuality
Commit: 65e04a450321aea950db89a528e3a6e0a9a6d03f
Author: tnaake <thomasnaake@gmx.de>
Date: 2022-11-29 14:41:56 +0100
Commit message:

 Update check-bioc.yml
 
Package: MsQuality
Commit: 5eb9a07333dc27a14388efad22755db95f013a54
Author: tnaake <thomasnaake@gmx.de>
Date: 2022-11-29 13:32:34 +0100
Commit message:

 Update check-bioc.yml
 
Package: MsQuality
Commit: 61b60faacb74cfa64669e577de1b050947110047
Author: tnaake <thomasnaake@gmx.de>
Date: 2022-11-29 12:08:23 +0100
Commit message:

 Update check-bioc.yml
 
Package: MsQuality
Commit: 0552b84eedde4a4e790df8b224483374153475db
Author: tnaake <thomasnaake@gmx.de>
Date: 2022-11-29 10:22:10 +0100
Commit message:

 add partial_bundle in plotMetric
 
Package: MsQuality
Commit: 12f857b0ccbc07d426ac7b3ea36a41bb055242bb
Author: tnaake <thomasnaake@gmx.de>
Date: 2022-11-29 10:21:45 +0100
Commit message:

 create a script in inst/scripts/ for Lee2019-data
 
Package: MsQuality
Commit: c639a961d668a0993760be2ddc677d937587575a
Author: tnaake <thomasnaake@gmx.de>
Date: 2022-11-29 10:21:06 +0100
Commit message:

 use NEWS.md in markdown format
 
Package: MsQuality
Commit: b923959fcdf0a6baf2c39068b1c959fe1ceda868
Author: tnaake <thomasnaake@gmx.de>
Date: 2022-11-28 16:57:59 +0100
Commit message:

 add .github to .Rbuildignore
 
Package: MsQuality
Commit: e1f52ddc8a7e1305baf374a6fb0d060351921874
Author: tnaake <thomasnaake@gmx.de>
Date: 2022-11-23 12:59:42 +0100
Commit message:

 Update check-bioc.yml
 
Package: MsQuality
Commit: d47f08ac03b151df248b59f6f75b3307e5d40987
Author: tnaake <thomasnaake@gmx.de>
Date: 2022-11-23 12:48:51 +0100
Commit message:

 Update check-bioc.yml
 
Package: MsQuality
Commit: bc88593cc52f56b10026396fea6b810968464c4d
Author: tnaake <thomasnaake@gmx.de>
Date: 2022-11-23 12:46:44 +0100
Commit message:

 Update check-bioc.yml
 
Package: PhyloProfile
Commit: 48ea89e06cc6fd816d9145fd2178b04f79a3aca7
Author: trvinh <trvinh@gmail.com>
Date: 2022-11-29 14:42:25 +0100
Commit message:

 added interpro url; number of coorthologs and present taxa
 
Package: GRaNIE
Commit: 0ccc8610141fece1d3bd6279dbe01fad896fa301
Author: Christian Arnold <christian.arnold@embl.de>
Date: 2022-11-29 13:34:27 +0100
Commit message:

 Version bump devel
 
Package: GRaNIE
Commit: 83d6d42a3896910e35e617e4e853d95ca1fe759f
Author: Christian Arnold <christian.arnold@embl.de>
Date: 2022-11-29 13:33:46 +0100
Commit message:

 Bugfixes
 
Package: limma
Commit: 8b6c60082876e046640a04778e2a40e7e756eee3
Author: Gordon Smyth <smyth@wehi.edu.au>
Date: 2022-11-29 22:30:00 +1100
Commit message:

 29 Nov 2022: limma 3.55.1

- eBayes() now checks whether `fit` is a list object before
  undertaking other tests.

- Update limma-Tests.Rout.save for Bioc 3.16 annotation packages.
 
Package: hipathia
Commit: 95823e8f33525bff1db4eb63c2786327b65ccfc4
Author: Marta R. Hidalgo <marta.hidalgo@outlook.es>
Date: 2022-11-28 16:37:13 +0100
Commit message:

 fixing bugs for version 3.0 and bumping to version 2.99.0
 
Package: hipathia
Commit: e7c7b77d9d3e85764b6d7ece9ea432e5791efca1
Author: Marta R. Hidalgo <marta.hidalgo@outlook.es>
Date: 2022-11-22 14:40:06 +0100
Commit message:

 bumping version to 2.15.1
 
Package: hipathia
Commit: a3456c2a6a9e257572c3957f35748a08c35b9a7f
Author: Marta R. Hidalgo <marta.hidalgo@outlook.es>
Date: 2022-11-22 14:36:14 +0100
Commit message:

 Merge branch 'master' into devel
 
Package: hipathia
Commit: ba8f7c5154aa646ecc5fa7e3759170addd7cef26
Author: Marta R. Hidalgo <marta.hidalgo@outlook.es>
Date: 2022-11-22 14:28:58 +0100
Commit message:

 comentando el código nuevo
 
Package: hipathia
Commit: 1509b42131dcdd1e1d2390a7cb3acf19491fe9cb
Author: Marta R. Hidalgo <marta.hidalgo@outlook.es>
Date: 2022-11-04 13:12:21 +0100
Commit message:

 finishing new functions and fixing colors
 
Package: hipathia
Commit: 79d590932bae956b283515b2d91d77795f9f688f
Author: Marta R. Hidalgo <marta.hidalgo@outlook.es>
Date: 2022-11-03 11:11:39 +0100
Commit message:

 fixing correct Y coordinate in pathway layout in plotVG
 
Package: hipathia
Commit: 5b407ad1f51edc3011a3acbdfd2520d3eed9fc3e
Author: Marta R. Hidalgo <marta.hidalgo@outlook.es>
Date: 2022-11-03 11:09:54 +0100
Commit message:

 ultimando función visualización pathways, y añadiendo nueva de creación de reports (wrap)
 
Package: hipathia
Commit: c175f9f04374756c0cb8d48c44ba5afba85454ba
Author: Marta R. Hidalgo <marta.hidalgo@outlook.es>
Date: 2022-10-28 14:09:16 +0200
Commit message:

 updating devel.R
 
Package: hipathia
Commit: e37530270b6d982a584195052fd529a56e4774c3
Author: Marta R. Hidalgo <marta.hidalgo@outlook.es>
Date: 2022-10-26 17:02:12 +0200
Commit message:

 separating plotVG function into nodes, edges and plot
 
Package: hipathia
Commit: c3126a81f14907450229b79c270c42cfecb2a7d0
Author: Marta R. Hidalgo <marta.hidalgo@outlook.es>
Date: 2022-10-18 16:26:49 +0200
Commit message:

 fixing bugs, adding DAsummary pathways_summary functions
 
Package: hipathia
Commit: 55ac48e21d7a9c158eeae6223bc58686312dadbc
Author: Marta R. Hidalgo <marta.hidalgo@outlook.es>
Date: 2022-10-17 16:37:40 +0200
Commit message:

 changing hipathia structure to make uniprot and GO terms be computed inside main hipathia function and creating DApathways function, to compute all comparisons of all datasets in a single function (wrap to do_wilcoxon and do_limma)
 
Package: hipathia
Commit: da64a0fc9584a722fbe6f392588a726970ed482f
Author: Marta R. Hidalgo <marta.hidalgo@outlook.es>
Date: 2022-10-17 11:27:38 +0200
Commit message:

 adding devel.R file
 
Package: Rsubread
Commit: 6e5eafac965138e7efce7f12296780d160823a4e
Author: Yang Liao <liao_y@svr2672.licr.unimelb.edu.au>
Date: 2022-11-29 20:34:10 +1100
Commit message:

 fixed a bug of insufficient buffer
 
Package: immunoClust
Commit: 9c49a4e9036c8571a3530ad0ac66e92b942a89bc
Author: Till Sörensen <till-antoni.soerensen@charite.de>
Date: 2022-11-29 09:46:02 +0100
Commit message:

 meta.export
 
Package: immunoClust
Commit: ae98edfac8e65eff7d2e52a5c48d567cb61b920e
Author: Till Sörensen <till-antoni.soerensen@charite.de>
Date: 2022-11-29 09:45:14 +0100
Commit message:

 meta.export
 
Package: Rcwl
Commit: 72b36777871f639cea36580d498ce6b6795664e1
Author: Qian Liu <qliu7@buffalo.edu>
Date: 2022-11-28 22:57:52 -0500
Commit message:

 add add_meta() function
 
Package: Rsubread
Commit: 60aa1b1d3052fd861e880131b8bc3e5738928d18
Author: Yang Liao <liao_y@svr2672.licr.unimelb.edu.au>
Date: 2022-11-29 14:32:38 +1100
Commit message:

 Merge branch 'master' of git.bioconductor.org:packages/Rsubread
 
Package: Rsubread
Commit: 658156db3918573603a23ecc19780e1a32a91a1d
Author: Yang Liao <liao_y@svr2672.licr.unimelb.edu.au>
Date: 2022-11-29 14:31:52 +1100
Commit message:

 Use sparse martix for excluded cells.
 
Package: tomoseqr
Commit: 5eaee3607acff793005716f3547720f12b76502f
Author: shingenmochi <kinakomochi.work@gmail.com>
Date: 2022-11-29 11:53:30 +0900
Commit message:

 update NEWS
 
Package: tomoseqr
Commit: d93588af1f35e57dd5f0024c60146deb04af9ffc
Author: shingenmochi <kinakomochi.work@gmail.com>
Date: 2022-11-29 11:49:58 +0900
Commit message:

 bump version number
 
Package: tomoseqr
Commit: a4ab46730db1be0d0116a3bde8e82346b1400182
Author: shingenmochi <kinakomochi.work@gmail.com>
Date: 2022-11-29 11:42:07 +0900
Commit message:

 Merge branch 'update_Junker2014' into develop
 
Package: tomoseqr
Commit: 030bce9f55ef179b9f2244d92e01a1d41c01eb2d
Author: shingenmochi <kinakomochi.work@gmail.com>
Date: 2022-11-29 11:28:51 +0900
Commit message:

 update URL
 
Package: sesameData
Commit: c9051cfa7c6ddf20b04b877642905c9be17e3e37
Author: Wanding Zhou <zhouwanding@gmail.com>
Date: 2022-11-28 21:49:24 -0500
Commit message:

 bump to 1.17.3
 
Package: tomoseqr
Commit: bae988ed0172e5a98b16ec225ae45b1112a05d01
Author: shingenmochi <kinakomochi.work@gmail.com>
Date: 2022-11-29 11:35:45 +0900
Commit message:

 bump version number
 
Package: tomoseqr
Commit: cd07927aeae9707b6a7a4726acbf8c3ffd2cd1b0
Author: shingenmochi <kinakomochi.work@gmail.com>
Date: 2022-11-29 11:33:11 +0900
Commit message:

 Update RoxygenNote
 
Package: ensemblVEP
Commit: af762fac2254b11973335b479e3930446d257821
Author: vjcitn <stvjc@channing.harvard.edu>
Date: 2022-11-28 21:19:59 -0500
Commit message:

 passing check, using current 'vep' utility instead of a .pl program to use the API
the README mention of Windows may need attention
 
Package: sesame
Commit: bd470c0d5d8070d5a0c470ce2503121967f4b91a
Author: Wanding Zhou <zhouwanding@gmail.com>
Date: 2022-11-28 21:15:20 -0500
Commit message:

 1.17.2
 
Package: sesame
Commit: d3c4dc708b94aa41cf22384ee5fb44e1909461a9
Author: Wanding Zhou <zhouwanding@gmail.com>
Date: 2022-11-28 18:29:56 -0500
Commit message:

 bump to 1.17.1
 
Package: sesame
Commit: 486980210279af468fb5b0e7c3859752cfc1eb72
Author: Wanding Zhou <zhouwanding@gmail.com>
Date: 2022-11-10 21:30:05 -0500
Commit message:

 Merge remote-tracking branch 'upstream/master'
 
Package: sesame
Commit: 95dd0cf02a3daf0054b8aeb4106eb284f8833efb
Author: Wanding Zhou <zhouwanding@gmail.com>
Date: 2022-11-10 21:28:14 -0500
Commit message:

 update
 
Package: sesame
Commit: 9b4905d03e053a69a4e032361559e24eca9e739b
Author: Wanding Zhou <zhouwanding@gmail.com>
Date: 2022-10-19 09:27:17 -0400
Commit message:

 fix KYCG_loadDBs bug
 
Package: AnVILWorkflow
Commit: 1224e0c2e3d5ee170ce007dd37b3ea3b03c24329
Author: Sehyun Oh <sehyunoh@Sehyuns-MacBook-Air.local>
Date: 2022-11-28 16:26:41 -0500
Commit message:

 version bump
 
Package: AnVILWorkflow
Commit: 12e1cc453644d99b2a2082a7d33ed4d1adb950f3
Author: Sehyun Oh <sehyunoh@Sehyuns-MacBook-Air.local>
Date: 2022-11-28 16:26:31 -0500
Commit message:

 update vignette with the public workspace info
 
Package: AnVILWorkflow
Commit: a9d373961b88dc980a5ee17609f8a5f4a0f6d335
Author: Sehyun Oh <sehyunoh@Sehyuns-MacBook-Air.local>
Date: 2022-11-28 16:24:28 -0500
Commit message:

 update gh page title
 
Package: AnVILWorkflow
Commit: 875c94060483f6d06c675e669d9cbfeac7c8edbb
Author: Sehyun Oh <sehyunoh@Sehyuns-MacBook-Air.local>
Date: 2022-11-01 10:14:17 -0400
Commit message:

 updates to build site
 
Package: Rsubread
Commit: f99bcd0dee982b42329f2dc343c6f05546225cf0
Author: Yang Liao <yang.liao@onjcri.org.au>
Date: 2022-11-29 06:48:31 +1100
Commit message:

 Minor wording changes.
 
Package: nullranges
Commit: 087e653aed7b2645373e66b4282cc22c03bc0567
Author: mikelove <michaelisaiahlove@gmail.com>
Date: 2022-11-28 13:48:49 -0500
Commit message:

 typos in new text
 
Package: nullranges
Commit: f99357dc9003da3ff6a3605592a2e78f828d1891
Author: mikelove <michaelisaiahlove@gmail.com>
Date: 2022-11-28 08:51:36 -0500
Commit message:

 update overview vignette, bib
 
Package: excluderanges
Commit: f53e82dfbbc1e614fcb4bd23849493566e0165cb
Author: Mikhail Dozmorov <mikhail.dozmorov@gmail.com>
Date: 2022-11-28 07:01:27 -0500
Commit message:

 Logo version bump
 
Package: excluderanges
Commit: 988933cc647f0757ae2db4f1f5a134f50dcaf524
Author: Mikhail Dozmorov <mikhail.dozmorov@gmail.com>
Date: 2022-11-28 06:57:10 -0500
Commit message:

 Merge branch 'master' into RELEASE_3_16
 
Package: excluderanges
Commit: 29eccff290caeb279fccc5ecccd3bee6a97b0e45
Author: Mikhail Dozmorov <mikhail.dozmorov@gmail.com>
Date: 2022-11-21 07:44:51 -0500
Commit message:

 0.99.7
 

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