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GIT Logs

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

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

Package: scRNAseq
Commit: f4f4a7f07b673cfa277303e798c29ed50ed417fa
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2024-02-26 08:51:02 -0800
Commit message:

 Purged all calls to the (now-deleted) cache moving code.
 
Package: gypsum
Commit: b3cdec5f1f11e664a05d9d38fc00135c72f863c7
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2024-02-26 08:30:30 -0800
Commit message:

 Removed unnecessary importFrom tags, bumped version and date.
 
Package: gypsum
Commit: 60af5a4b37f13c2aad21944ff9ab6720ffafa97d
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2024-02-26 08:24:21 -0800
Commit message:

 Cache publicS3Config response on disk to avoid hitting CF worker limits.

Otherwise this is requested once for every open R session, which could
easily blow past the 100000/month request limit that we're working with.
 
Package: sesame
Commit: 9b269f4b7284d577de1ad6a357d12a64d5bb551e
Author: Wanding Zhou <zhouwanding@gmail.com>
Date: 2024-02-26 11:26:18 -0500
Commit message:

 bump to 1.21.10
 
Package: saseR
Commit: e787c4cc8d450a5f3e146f9f2b3fd3aec2e2b277
Author: Alexandre Segers <alexandre.segers@ugent.be>
Date: 2024-02-26 17:14:48 +0100
Commit message:

 version update
 
Package: saseR
Commit: 5d83f225aa1d83ec9c459b3f292be6b5fcccefc1
Author: Alexandre Segers <alexandre.segers@ugent.be>
Date: 2024-02-26 17:03:41 +0100
Commit message:

 update vignette and beta phase arguments
 
Package: MGnifyR
Commit: 11bfc73d037641189a43aff18ab5d2a0d886eafb
Author: TuomasBorman <tvborm@utu.fi>
Date: 2024-02-26 16:20:21 +0200
Commit message:

 Fixed cache name
 
Package: MGnifyR
Commit: 8224063c4dc52c189cc5ea3494e9a2d577c2c8bc
Author: TuomasBorman <tvborm@utu.fi>
Date: 2024-02-26 13:42:31 +0200
Commit message:

 searchAnalysis: in addition of analysis ID, give also study/sample ID where that analysis belongs
 
Package: MGnifyR
Commit: be1f2306b8aa723632eea0215d4acb579ef9d1dd
Author: TuomasBorman <tvborm@utu.fi>
Date: 2024-02-26 13:22:55 +0200
Commit message:

 Minor fix to input check
 
Package: MGnifyR
Commit: 8145fca30bb1f3fd71d455f300f705c26e7e522f
Author: TuomasBorman <tvborm@utu.fi>
Date: 2024-02-26 10:30:13 +0200
Commit message:

 Minor typo fix
 
Package: MGnifyR
Commit: 983948e61f34a0030acf64815f1895a64d1d77ef
Author: TuomasBorman <tvborm@utu.fi>
Date: 2024-02-15 08:59:39 +0200
Commit message:

 Fix mgnify_client
 
Package: rawDiag
Commit: 398710486a4936f5b2f38130ba7a0b6128403aaf
Author: Christian Panse <cp@fgcz.ethz.ch>
Date: 2024-02-26 16:35:35 +0100
Commit message:

 feat: handle "Orbitrap Resolution:" in trailer

make it more robust for different Orbitrap devices
 
Package: rawDiag
Commit: 5a1fd4da781bbbbabeb44d4f61ea950464db0b9c
Author: Christian Panse <cp@fgcz.ethz.ch>
Date: 2024-02-26 16:34:43 +0100
Commit message:

 doc: replace EH4547(DIA) with EH3222(DDA)
 
Package: rawDiag
Commit: 5bf0b6c3e4ff4a985d8f288825f1712db5eb440d
Author: Christian Panse <cp@fgcz.ethz.ch>
Date: 2024-02-23 19:40:32 +0100
Commit message:

 doc: add generic visualization text
 
Package: rawDiag
Commit: d52a119c53778858b903edd70c124800b89cf5c1
Author: Christian Panse <cp@fgcz.ethz.ch>
Date: 2024-02-23 19:04:43 +0100
Commit message:

 doc: remove `paste` in `message()`
 
Package: rawDiag
Commit: 1176b738e55f98bb50b0349253c625b7494cd5c8
Author: Christian Panse <cp@fgcz.ethz.ch>
Date: 2024-02-23 19:00:09 +0100
Commit message:

 doc: remove commented code
 
Package: rawDiag
Commit: a721c63c7d26937f6f3c76c52b9eb7ba96b3216c
Author: Christian Panse <cp@fgcz.ethz.ch>
Date: 2024-02-23 18:58:03 +0100
Commit message:

 doc: remove echo = FALSE
 
Package: miRSM
Commit: d93b1a317627a2f5b65e55b5eb6ec7bd6f4c308d
Author: zhangjunpeng411 <zhangjunpeng_411@yahoo.com>
Date: 2024-02-26 22:18:31 +0800
Commit message:

 Merge branch 'devel' of github.com:zhangjunpeng411/miRSM into devel
 
Package: miRSM
Commit: a044d248a7d0c6e92a9337133271cc94e765ee6c
Author: Junpeng Zhang <zhangjunpeng411@gmail.com>
Date: 2024-02-06 14:17:20 +0800
Commit message:

 Update
 
Package: cola
Commit: 1456cfb5f913ce0e43845a1ffecae1f17251e660
Author: Zuguang Gu <jokergoo@gmail.com>
Date: 2024-02-26 14:40:57 +0100
Commit message:

 merge
 
Package: cola
Commit: 9c4a56b3b3e96f8cb5e449c154464a790f80c7d9
Author: Zuguang Gu <jokergoo@gmail.com>
Date: 2024-02-26 14:40:14 +0100
Commit message:

 solved conflicts between matrixStats and matrixGeneric
 
Package: cola
Commit: 8376b71ab216f69fd77b7af9f898048c5dfc6070
Author: Zuguang Gu <jokergoo@gmail.com>
Date: 2023-06-06 09:45:08 +0200
Commit message:

 update
 
Package: cola
Commit: c530e8fa9a751f688670a19bb5e8cf6b8800b69f
Author: Zuguang Gu <jokergoo@gmail.com>
Date: 2023-06-06 09:40:52 +0200
Commit message:

 update
 
Package: cola
Commit: 59134eda0c00f99cdf81c47e0391bd6a54ad3cc9
Author: Zuguang Gu <jokergoo@gmail.com>
Date: 2023-06-05 21:15:08 +0200
Commit message:

 update
 
Package: cola
Commit: a989217c9e393a7d715f02e801ca2372b3a5461b
Author: Zuguang Gu <jokergoo@gmail.com>
Date: 2023-06-05 20:18:10 +0200
Commit message:

 turn off parallel in collect_plots()
 
Package: cola
Commit: d50b6eb98c5812e0ce4f4c0b50b8f137ea6ce4dd
Author: Zuguang Gu <jokergoo@gmail.com>
Date: 2023-06-05 18:17:22 +0200
Commit message:

 explicitely reassign fun_name
 
Package: mobileRNA
Commit: ca36c4b4e439a77e5f3de8796d6a19835913efcd
Author: KJeynesCupper <kej031@student.bham.ac.uk>
Date: 2024-02-26 13:03:11 +0000
Commit message:

 Build-push
 
Package: mobileRNA
Commit: c51ddd3d5a3e3ec436cd29d1871c4c2593ee1b2c
Author: Katie Jeynes-Cupper <77631989+KJeynesCupper@users.noreply.github.com>
Date: 2024-02-26 12:52:58 +0000
Commit message:

 Update RNAsequences.R 
Package: sesame
Commit: 0ebf0ad0a8718149cc16177bacce4aba3c742c77
Author: Wanding Zhou <zhouwanding@gmail.com>
Date: 2024-02-26 07:37:49 -0500
Commit message:

 bump to 1.21.9
 
Package: sesame
Commit: 87c54e850de265380ec765aae750dd47e8171c4e
Author: Wanding Zhou <zhouwanding@gmail.com>
Date: 2024-02-26 07:37:27 -0500
Commit message:

 fix liftOver to use probe ID in address not in GRanges manifest
 
Package: mobileRNA
Commit: ecfb405846cca2fbdaa77ea35b3957dd534119b5
Author: KJeynesCupper <kej031@student.bham.ac.uk>
Date: 2024-02-26 12:30:55 +0000
Commit message:

 updated_v19
 
Package: mobileRNA
Commit: a16fee0d44b08afc96bdf67cbc3e5a8131d02aff
Author: Katie Jeynes-Cupper <77631989+KJeynesCupper@users.noreply.github.com>
Date: 2024-02-22 14:29:09 +0000
Commit message:

 Update plotSamplePCA.R 
Package: mobileRNA
Commit: 25f0eefc26a6aa976d06e1010d96cd105bb122d3
Author: Katie Jeynes-Cupper <77631989+KJeynesCupper@users.noreply.github.com>
Date: 2024-02-20 20:43:43 +0000
Commit message:

 Update RNAsummary.R 
Package: mobileRNA
Commit: 043d0b3fd688e5705f8c17894e69acdd4373c524
Author: Katie Jeynes-Cupper <77631989+KJeynesCupper@users.noreply.github.com>
Date: 2024-02-20 20:06:19 +0000
Commit message:

 Update RNAfeatures.R 
Package: mobileRNA
Commit: 60a04bef260ab5db3a15269c24ef853c39d839d4
Author: Katie Jeynes-Cupper <77631989+KJeynesCupper@users.noreply.github.com>
Date: 2024-02-20 16:29:12 +0000
Commit message:

 Update RNAfeatures.R 
Package: depmap
Commit: 3c5b0387c62bd3f19963858e7d21e47439262dd8
Author: Laurent Gatto <laurent.gatto@uclouvain.be>
Date: 2024-02-26 13:17:48 +0100
Commit message:

 remove old institution in 2nd vignette
 
Package: depmap
Commit: 40f081dddb2bfa8f7500307ab9c24f8ac0c41739
Author: Laurent Gatto <laurent.gatto@uclouvain.be>
Date: 2024-02-26 12:44:13 +0100
Commit message:

 no BiocCheck nor covr
 
Package: depmap
Commit: 124eba51b33c893b3f355b3333500699afea734c
Author: Laurent Gatto <laurent.gatto@uclouvain.be>
Date: 2024-02-26 12:24:40 +0100
Commit message:

 Merge branch 'master' of github.com:UCLouvain-CBIO/depmap
 
Package: depmap
Commit: c094d904dd45648e41ced9babf29ad91f5f42d8f
Author: Laurent Gatto <laurent.gatto@uclouvain.be>
Date: 2024-02-26 12:24:22 +0100
Commit message:

 udpate Rd
 
Package: depmap
Commit: 07d2395191cd358e655a8c79c6d0da321b053232
Author: Laurent Gatto <laurent.gatto@uclouvain.be>
Date: 2024-02-26 12:23:51 +0100
Commit message:

 fix man page
 
Package: depmap
Commit: 9fcacb488709c001841dc328bc13e6db4f512a5c
Author: Laurent Gatto <laurent.gatto@uclouvain.be>
Date: 2024-02-26 11:56:06 +0100
Commit message:

 suggest tidyverse
 
Package: depmap
Commit: 1237961d8e02b6bdd6aff738503d149b73f706d5
Author: Laurent Gatto <laurent.gatto@uclouvain.be>
Date: 2024-02-26 11:19:10 +0100
Commit message:

 suggest magick (needed to build vignette)
 
Package: depmap
Commit: 33efe59e997397df43da131a5d7ea55d3fee9c4a
Author: Laurent Gatto <laurent.gatto@uclouvain.be>
Date: 2024-02-26 11:08:16 +0100
Commit message:

 suggest dplyr
 
Package: depmap
Commit: 17985f82674aa448832e37c0f829337456c8c312
Author: Laurent Gatto <laurent.gatto@uclouvain.be>
Date: 2024-02-26 10:56:27 +0100
Commit message:

 add gha
 
Package: pgxRpi
Commit: ab4e77fa09753ea61502c342c277a890eb01c0eb
Author: hangjiaz <zhaohj314@gmail.com>
Date: 2024-02-26 13:06:32 +0100
Commit message:

 add dataset parameter; temporary fix of limit bug in covloader
 
Package: rols
Commit: 6f199151ff0e21793231129ee2f03ac5c95fbe76
Author: Laurent Gatto <laurent.gatto@uclouvain.be>
Date: 2024-02-26 12:28:02 +0100
Commit message:

 bump version
 
Package: rols
Commit: bec21e0a9dda5edf99282cbb1194412a19b92766
Author: Laurent Gatto <laurent.gatto@uclouvain.be>
Date: 2024-02-26 12:27:09 +0100
Commit message:

 add orcid
 
Package: rols
Commit: cd7a870730299d55710c4e93b3307e728b4738d5
Author: Laurent Gatto <laurent.gatto@uclouvain.be>
Date: 2024-02-16 16:58:07 +0100
Commit message:

 Fix different URI locations (see #42)
 
Package: rols
Commit: 1f85f319d8ebae6c7dcf539719150e5a4b2bf783
Author: lgatto <laurent.gatto@gmail.com>
Date: 2024-02-12 21:43:47 +0100
Commit message:

 bump and news
 
Package: rols
Commit: e8b300b2eb3f12b87192dbf22fc26960fd85c76f
Author: lgatto <laurent.gatto@gmail.com>
Date: 2024-02-12 21:42:40 +0100
Commit message:

 convert TRUE/FALSE to true/false
 
Package: sesameData
Commit: 32be2e019918d612d3a86952439cde9a340ff4b0
Author: Wanding Zhou <zhouwanding@gmail.com>
Date: 2024-02-26 06:43:19 -0500
Commit message:

 bump to 1.21.10, added silent option to platform check
 
Package: ginmappeR
Commit: 7beafa01665793690e744982d4af95eb894416ef
Author: Fernando Sola <fersolesp@alum.us.es>
Date: 2024-02-26 11:31:41 +0100
Commit message:

 Release 0.99.11
 
Package: muleaData
Commit: c8953364ef89d01d7b9755edc3ef663dda62579f
Author: barizona <barizona@barizona>
Date: 2024-02-26 11:12:51 +0100
Commit message:

 make BiocCheck::BiocCheck('new-package'=TRUE) run with OK-s
 
Package: muleaData
Commit: dd2200c528dccc8b8feb7ab1f0ab8b903546f3fd
Author: barizona <barizona@barizona>
Date: 2024-02-26 10:01:12 +0100
Commit message:

 .Rproj deleted
 
Package: autonomics
Commit: 43a1240f382a7ca4cd55002c23c6a09b4d66785e
Author: Aditya Bhagwat <aditya.bhagwat@uni-marburg.de>
Date: 2024-02-26 10:59:12 +0100
Commit message:

 unexport/undocument annotate_uniprot
 
Package: autonomics
Commit: 042fa33f8d646f46a704d41df325a84a49ffe7cc
Author: Aditya Bhagwat <aditya.bhagwat@uni-marburg.de>
Date: 2024-02-26 10:46:40 +0100
Commit message:

 Streamline msgs : tab -> spaces
 
Package: dorothea
Commit: aed86b06a488ec9a3fd8d3731065160dcf36ff15
Author: PauBadiaM <pau.badia@uni-heidelberg.de>
Date: 2024-02-26 10:44:45 +0100
Commit message:

 Bumped version
 
Package: dorothea
Commit: 29657a5b05ac15f6b83275be3ab84e025c0bc23a
Author: PauBadiaM <pau.badia@uni-heidelberg.de>
Date: 2024-02-26 10:41:31 +0100
Commit message:

 Adapted versioning
 
Package: dorothea
Commit: 1461fb75e23e110c2281860526d4333920925282
Author: PauBadiaM <pau.badia@uni-heidelberg.de>
Date: 2024-02-24 12:55:48 +0100
Commit message:

 Downgraded version
 
Package: dorothea
Commit: 2947186c45f9d62b9646b5844062924145d56250
Author: PauBadiaM <pau.badia@uni-heidelberg.de>
Date: 2024-02-24 12:54:07 +0100
Commit message:

 Bumper version
 
Package: dorothea
Commit: 96f8e1b81c163559447d6be2cdfaf1e7c763a475
Author: PauBadiaM <pau.badia@uni-heidelberg.de>
Date: 2024-02-24 11:40:01 +0100
Commit message:

 Deleted cahce github CI
 
Package: dorothea
Commit: 94dd50d55e8878042ab01d9da7d86854b4ec4570
Author: PauBadiaM <pau.badia@uni-heidelberg.de>
Date: 2024-02-22 11:16:44 +0100
Commit message:

 Modified CI
 
Package: dorothea
Commit: 0e0ecf38dd8be4435753ffb5dd588fc32c4022fe
Author: PauBadiaM <pau.badia@uni-heidelberg.de>
Date: 2024-02-22 11:10:42 +0100
Commit message:

 Changed github CI
 
Package: dorothea
Commit: 280e687e81861b249c50a0d92fbbf793d274a25e
Author: PauBadiaM <pau.badia@uni-heidelberg.de>
Date: 2024-02-22 11:03:36 +0100
Commit message:

 Updated git CI
 
Package: dorothea
Commit: 2a21d4df9ef14591745a8d9bbd126f56445a2cd5
Author: PauBadiaM <pau.badia@uni-heidelberg.de>
Date: 2024-02-22 10:30:24 +0100
Commit message:

 Bumped version
 
Package: dorothea
Commit: 580da5ddccf636b6ebd2966c0ff4072ef799aadc
Author: PauBadiaM <pau.badia@uni-heidelberg.de>
Date: 2024-02-22 10:29:58 +0100
Commit message:

 Fixed test for Seurat v5
 
Package: autonomics
Commit: 8b733481706fa83de6bfe8b00e4dd58d5e476453
Author: Aditya Bhagwat <aditya.bhagwat@uni-marburg.de>
Date: 2024-02-26 10:00:27 +0100
Commit message:

 read_maxquant_xxx : streamline msgs
 
Package: scRNAseq
Commit: c1b47503cd1ae19c2c7343abf20f49414ddc76d6
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2024-02-25 23:11:11 -0800
Commit message:

 Removed the old cache moving code and associated Suggests.

This is no longer necessary given that enough time has passed since the cache
relocation fiasco, I doubt anyone's still on the old cache locations.
 
Package: scRNAseq
Commit: ab8ba167142326487a0a2278e3ad1e3ccd43e446
Author: Aaron Lun <infinite.monkeys.with.keyboards@gmail.com>
Date: 2024-02-25 23:09:09 -0800
Commit message:

 Switch to gypsum backend for saving and loading datasets. (#42)

Similarly, we switch to the alabaster framework to store the data, rather than
RDS files. This should allow the files to be re-used in other languages.

Users can now grab SCEs directly from the gypsum backend with fetchDataset, and
they can perform listing and advanced searches directly on gypsum's SQLite
files. This lays the groundwork for removing dependencies on ExperimentHub.

All of the little per-dataset functions now call fetchDataset to retrieve
content, where it is back-compatible to do so. We plan to soft-deprecate all
per-dataset functions to simplify maintenance; users should just call
fetchDataset instead, and be responsible for any additional transformations.

We also provide functions for users to save and upload their own datasets.
This should simplify the process of making a contribution. 
Package: scRNAseq
Commit: 88575c83428da5199a03b5da316798777991e928
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2024-02-25 22:42:25 -0800
Commit message:

 Fixed the NEWS file.
 
Package: yamss
Commit: ea9e3bdecf833ea03c2439b45fb5fec4c76ce3ca
Author: lmyint <lmyint@macalester.edu>
Date: 2024-02-25 22:25:29 -0600
Commit message:

 Update examples causing C stack usage to be too close to the limit
 
Package: DelayedArray
Commit: 854795f8e8ff4c966df77c6a6ebf45877968f7c5
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2024-02-25 19:17:42 -0800
Commit message:

 another minor code reorg
 
Package: sesame
Commit: db554feed8521ce2dd9f2644757a5a14490a15fa
Author: Wanding Zhou <zhouwanding@gmail.com>
Date: 2024-02-25 20:51:32 -0500
Commit message:

 minor, message omitted
 
Package: sesame
Commit: 1e222ded6f8c9f6e6ee3cca6a6147ce7c6714d20
Author: Wanding Zhou <zhouwanding@gmail.com>
Date: 2024-02-25 20:51:20 -0500
Commit message:

 bump to 1.21.8, updated liftOver
 
Package: depmap
Commit: 3df31af82a70e8a937094d68a31a71f2074de613
Author: Laurent Gatto <laurent.gatto@uclouvain.be>
Date: 2024-02-26 01:34:36 +0100
Commit message:

 more vignette fixing and README update
 
Package: depmap
Commit: 2cd20d25dde650f6c01832723c9aaf0a5a03d754
Author: Laurent Gatto <laurent.gatto@uclouvain.be>
Date: 2024-02-26 01:29:31 +0100
Commit message:

 fix version
 
Package: depmap
Commit: 816235e6811547f2ea6c9ce6a24784cdd0064daa
Author: Laurent Gatto <laurent.gatto@uclouvain.be>
Date: 2024-02-26 01:27:06 +0100
Commit message:

 simplify and update vignettes
 
Package: alabaster.matrix
Commit: 6eb318ba1f44846d831060059138d4a100f046bc
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2024-02-25 10:49:53 -0800
Commit message:

 Improved robustness of coercion for WrapperArrays.

Wrapepd it in a try-catch, to fall back to DelayedArray coercion on failure.
 
Package: depmap
Commit: dd9c902aacc339f702df83704cec5f9316032ad4
Author: Laurent Gatto <laurent.gatto@uclouvain.be>
Date: 2024-02-25 21:06:25 +0100
Commit message:

 add new DepMapFiles
 
Package: DECIPHER
Commit: 41542b75d8f2475dcb7382b3f341be458a54b7c8
Author: Erik Wright <sixfoot10@Eriks-MacBook-Pro.local>
Date: 2024-02-25 07:36:27 -0500
Commit message:

 Changes to avoid build timeout among other things

 Committer: Erik Wright <eswright@pitt.edu>
 Changes to be committed:
	modified:   DESCRIPTION
	modified:   R/AlignSeqs.R
	modified:   R/Clusterize.R
	modified:   R/DetectRepeats.R
	modified:   R/FindNonCoding.R
	modified:   R/FindSynteny.R
	modified:   R/IdTaxa.R
	modified:   R/IndexSeqs.R
	modified:   R/LearnTaxa.R
	modified:   R/OrientNucleotides.R
	modified:   R/SearchIndex.R
	modified:   R/TreeLine.R
	modified:   man/MapCharacters.Rd
	modified:   man/OrientNucleotides.Rd
	modified:   src/DECIPHER.h
	modified:   src/DistanceMatrix.c
	modified:   src/EnumerateSequence.c
	modified:   src/Order.c
	modified:   src/PairwiseAlignment.c
	modified:   src/R_init_decipher.c
	modified:   src/Utils.c
	modified:   vignettes/SearchForResearch.Rnw
 
Package: ggtree
Commit: 38016ab1e3fde1ff88ec131e2e6e89aa4a234d9d
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2024-02-25 17:56:42 +0800
Commit message:

 compatible with ggplot2 3.5.0
 
Package: ggtree
Commit: 465e08d84c8350f044a30804c044c1a28b4e3086
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2024-02-13 01:24:28 +0800
Commit message:

 copy rect_to_poly, #601
 
Package: ggtree
Commit: ee1a177f0913ab5caa4876c7106c110824b7f836
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2024-02-13 01:09:00 +0800
Commit message:

 correct repo, #576
 
Package: ggtree
Commit: 33a07af48961d893c2a5dcbdc221881899d0456f
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2023-10-25 17:06:33 +0800
Commit message:

 update bioc version
 
Package: ggtree
Commit: 81f6b6ee7fa9affe0c189e16ceeefa635e66af96
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2023-10-25 17:06:22 +0800
Commit message:

 update bioc version
 
Package: gypsum
Commit: c28f9e24b3756e2b61a246a797eaff6ae5f1ad2a
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2024-02-25 00:09:38 -0800
Commit message:

 More careful normalization of paths before comparing them.

This is necessary to accurately convert symlinks into upload links, where the
prefix of the former's destination path is checked against the cache location.
 
Package: alabaster.matrix
Commit: 1b8b9d5f9ec66f91904c0aea6982a9a5b8af0526
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2024-02-24 23:44:30 -0800
Commit message:

 Store the absolute path in ReloadedArraySeed constructor.

This protects saveObject() calls from changes in the working directory, which
would break if a relative path was stored in the seed.
 
Package: gypsum
Commit: 72a27979bff5ec526e93a4bef67534ed5b549657
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2024-02-24 17:26:00 -0800
Commit message:

 Clarified prefix-based definition for relative paths in docs.
 
Package: gypsum
Commit: b7f4206782ba4f16bd391a4e29d778335dc83a83
Author: Aaron Lun <infinite.monkeys.with.keyboards@gmail.com>
Date: 2024-02-24 14:08:37 -0800
Commit message:

 Added text search on metadata based on tokens in the SQLite file. (#2)

This uses a dedicated 'gypsum.search.clause' class to allow users to assemble
complex queries with standard syntax. We also allow developers to just obtain
the WHERE filter directly if they want to assemble their own SQL queries. 
Package: ternarynet
Commit: ad33b2778b878b1d0c7bedbc86aea669001721ca
Author: mccallm <mccallm@gmail.com>
Date: 2024-02-24 09:23:37 -0500
Commit message:

 Change sprintf to snprintf in gn_Rwrap.c
 
Package: mzR
Commit: 5f500973666ee0cc719998ff7cc9322307e8ab94
Author: Laurent Gatto <laurent.gatto@uclouvain.be>
Date: 2024-02-24 15:18:16 +0100
Commit message:

 remove mentions of mzData
 
Package: mzR
Commit: a3ad6fac899922a0e97dd9a7050f0ed97d6f9317
Author: Steffen Neumann <sneumann@ipb-halle.de>
Date: 2023-11-07 15:08:36 +0100
Commit message:

 Bump github actions to BioC 3.19 devel
 
Package: mzR
Commit: a0d56e75c53ae0932c10a8d4bdfc3699466bd895
Author: Steffen Neumann <sneumann@ipb-halle.de>
Date: 2023-11-06 09:12:12 +0100
Commit message:

 Bump github actions to BioC 3.18 devel
 
Package: mzR
Commit: 5143a8f59a99db7c8c1f93af5f7d3cf5d5ea2552
Author: Steffen Neumann <sneumann@ipb-halle.de>
Date: 2023-11-03 08:34:10 +0100
Commit message:

 First attempt to fix compilation on centOS 7 / R-4.3.1 reported in #286
 
Package: DelayedArray
Commit: 3cace213e09594823178c4b52fedef8efd3e1cde
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2024-02-23 19:20:18 -0800
Commit message:

 minor code reorg
 
Package: pathlinkR
Commit: e9750954f9bd434cdd03714cff774d226ac7cfac
Author: Travis <travis.m.blimkie@gmail.com>
Date: 2024-02-23 10:42:52 -0800
Commit message:

 Merge pull request #12 from hancockinformatics/devel

Updated links in vignette to new github pages. 
Package: pathlinkR
Commit: 28ca4cbc291bfea749567eae08a4c60be70c482b
Author: Travis Blimkie <travis.m.blimkie@gmail.com>
Date: 2024-02-23 09:26:44 -0800
Commit message:

 Updated links in vignette to new github pages.
 
Package: DelayedArray
Commit: dbfb345b8605062c154c1dd7f48b41b6da3101dd
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2024-02-23 11:51:01 -0800
Commit message:

 small edit
 
Package: DelayedArray
Commit: 71d174954ec57d4b0173671e81b4408e86141fcf
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2024-02-23 11:46:11 -0800
Commit message:

 Rename supportedRealizationBackends -> registeredRealizationBackends
 
Package: timeOmics
Commit: de6b101f81c738d306c985b36e8201030339e988
Author: AntoineB <bodein.antoine@gmail.com>
Date: 2024-02-23 13:57:36 -0500
Commit message:

 version bump
 
Package: timeOmics
Commit: fd6ac08f7f2c4e907eda0ab78720838df64cfe75
Author: AntoineB <bodein.antoine@gmail.com>
Date: 2024-02-23 13:51:16 -0500
Commit message:

 version bump
 
Package: DeepTarget
Commit: 70ca8271de67041b1a4b7d1b46fcf833bdfe2171
Author: CBIIT-CGBB <yhu@mail.nih.gov>
Date: 2024-02-23 13:46:21 -0500
Commit message:

 adding doi
 
Package: DeepTarget
Commit: 9526332951ffd25bc8a3dae9a5baeb97c045396c
Author: CBIIT-CGBB <yhu@mail.nih.gov>
Date: 2024-02-23 13:45:13 -0500
Commit message:

 adding doi
 
Package: DelayedArray
Commit: 5c7c254bdc46566b36a38556aa66d3e69fa7d089
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2024-02-23 10:06:16 -0800
Commit message:

 Improvement to BLOCK_mult_Lgridi() and BLOCK_mult_Rgrid()

Internal functions BLOCK_mult_Lgrid() and BLOCK_mult_Rgrid() are the
workhorses behind matrix multiplication between a DelayedMatrix object
(or derivative) and a non-DelayedMatrix object.

This change implements the same improvement that was implemented in
BLOCK_rowsum() and BLOCK_colsum() at commit 1f6eeb4.

When 'BACKEND' is not NULL (e.g. is set to "HDF5Array" or "TENxMatrix"),
and 'BPPARAM' is NULL (i.e. grid strips are processed sequentially), then
most of the time we are now able to return a **pristine** DelayedMatrix
object instead of one made of a bunch of pristine DelayedMatrix objects
bound together (via rbind() or cbind()).
Situations where we cannot do it is when the internal walk on the input
matrix is incompatible with the chunking of the realization sink. This
happens for example with:

  m1 <- matrix(1:12, ncol=3)
  m2 <- matrix(101:115, nrow=3)
  BLOCK_mult_Lgrid(m1, m2, Lgrid=rowAutoGrid(m1, 2), BACKEND="TENxMatrix")

Here the returned object is a DelayedMatrix object obtained by rbind'ing
2 TENxMatrix objects together, instead of a single TENxMatrix object.
 
Package: gDNAx
Commit: afbc598dbb3f24fcacd867c092a7ae737479da64
Author: Robert Castelo <robert.castelo@upf.edu>
Date: 2024-02-23 18:59:48 +0100
Commit message:

 Several bugfixes on filtering BAM files, show method, etc.
 
Package: DeepTarget
Commit: cf89dcebf2ace3802185bb082925f3ac50736150
Author: CBIIT-CGBB <yhu@mail.nih.gov>
Date: 2024-02-23 12:57:11 -0500
Commit message:

 updating required functions for newly added function
 
Package: DeepTarget
Commit: 1ba3bd463414b2b9215550047098ad729f9987fc
Author: CBIIT-CGBB <yhu@mail.nih.gov>
Date: 2024-02-23 12:54:59 -0500
Commit message:

 adding Depmap2DeepTarget function for data retrieval and preparation as input for DeepTarget
 
Package: DeepTarget
Commit: 26dac9e99f416a2257fc82fbf10367fa0aaada1f
Author: CBIIT-CGBB <yhu@mail.nih.gov>
Date: 2024-02-23 12:54:09 -0500
Commit message:

 adding Depmap2DeepTarget function for data retrieval and preparation as input for DeepTarget
 
Package: DeepTarget
Commit: 6d1b274a70fd2b4fc587003e53c65bb393242964
Author: CBIIT-CGBB <yhu@mail.nih.gov>
Date: 2024-02-23 12:51:17 -0500
Commit message:

 updating version from 0.99.13 to 0.99.14: Adding function to retrieve data directly from Depmap and then do preprocessing when applicable
 
Package: TEKRABber
Commit: 34d358fb36761d0d61f525a060878d2719ab82b5
Author: ferygood <yaochung41@gmail.com>
Date: 2024-02-23 18:02:30 +0100
Commit message:

 update 1.7.2 to bioc devel
 
Package: TEKRABber
Commit: 95a17e4b9f1367490053f85b8282ff764e7e6db7
Author: ferygood <yaochung41@gmail.com>
Date: 2024-02-21 18:53:06 +0100
Commit message:

 fix typo in corrOrthologTE
 
Package: TEKRABber
Commit: 57485fa02bd55b5187eb6a22a74ada46c067b8fc
Author: ferygood <yaochung41@gmail.com>
Date: 2024-02-21 18:37:06 +0100
Commit message:

 modified the parallel computing
 
Package: TEKRABber
Commit: ff485bacde1af865806d357c91910cdbbe3782de
Author: ferygood <yaochung41@gmail.com>
Date: 2024-02-20 19:56:21 +0100
Commit message:

 try omp commit
 
Package: TEKRABber
Commit: 52de33ccd59010ec81e9454d1f83e19d47fc359a
Author: ferygood <yaochung41@gmail.com>
Date: 2024-02-20 10:00:11 +0100
Commit message:

 commit before using doParallel
 
Package: TEKRABber
Commit: 66021de498e6254836467a03155f9731983ba721
Author: ferygood <yaochung41@gmail.com>
Date: 2024-01-31 18:21:09 +0100
Commit message:

 write annotation for appTEKRABber function
 
Package: TEKRABber
Commit: 3c7b8ea7dce3804e6cde8464d9e831e4f00ced63
Author: ferygood <yaochung41@gmail.com>
Date: 2024-01-30 18:53:15 +0100
Commit message:

 change getRMSK to prepareRMSK
 
Package: TEKRABber
Commit: 6b9993cbb491d4dbdb4aef9a32869cee6d87458f
Author: ferygood <yaochung41@gmail.com>
Date: 2024-01-26 14:39:11 +0100
Commit message:

 create getRMSK function to get rmsk annotation from UCSC
 
Package: CytoMDS
Commit: 637e20e230ee0fc37812922f9235be2403c7c39c
Author: phauchamps <philippehauchamps@hotmail.com>
Date: 2024-02-23 16:57:27 +0100
Commit message:

 - updated copyight in all R source files
- re-factored package doc file
- bumped to version 0.99.11
 
Package: CytoPipelineGUI
Commit: 67109e2bf90de1c95a2e7907177e276d72f16f25
Author: phauchamps <philippehauchamps@hotmail.com>
Date: 2024-02-23 16:07:48 +0100
Commit message:

 - updated copyright in all R source files
- re-factored package documentation file
- bumped version to 1.1.3
 
Package: CytoPipeline
Commit: d83e80f18d3e6069b45e58d85d8666211c633054
Author: phauchamps <philippehauchamps@hotmail.com>
Date: 2024-02-23 16:00:18 +0100
Commit message:

 - updated unit tests to take into account new external package versions
- updated copyrights in all R files
- refactored package documentation file
 
Package: CytoPipeline
Commit: 97e31fc3ace53ad7399439adb7c9c04c44795e80
Author: phauchamps <philippehauchamps@hotmail.com>
Date: 2024-02-23 14:36:09 +0100
Commit message:

 - `execute()` now stores the nb of events retained at each pre-processing step,
to speed-up `collectNbOfRetainedEvents()`
- bumped version to 1.3.6
 
Package: gDRutils
Commit: c5d407926e602808dff7d4798f867c1c7a04e274
Author: j-smola <31825957+j-smola@users.noreply.github.com>
Date: 2024-02-23 15:35:03 +0100
Commit message:

 Merge pull request #107 from gdrplatform/GDR-2425_2

[GDR-2425] Update gDRdict and restore missing tooltips 
Package: gDRutils
Commit: e419c128e12a69ebd48122fa020fae61a99c2aef
Author: Janina Smola <janina.smola@contractors.roche.com>
Date: 2024-02-23 13:21:40 +0100
Commit message:

 Merge branch 'main' into GDR-2425_2
 
Package: gDRutils
Commit: 16c3f62b8b845347be452be467816ebb4c8337af
Author: Janina Smola <janina.smola@contractors.roche.com>
Date: 2024-02-23 13:04:40 +0100
Commit message:

 tests: restore tooltips in table
 
Package: gDRutils
Commit: 5f3300fc93421da4d2779f174511f57385527586
Author: Janina Smola <janina.smola@contractors.roche.com>
Date: 2024-02-23 13:04:23 +0100
Commit message:

 doc: restore tooltips in table
 
Package: gDRutils
Commit: 3cf5985bd0ff5debf98ec1ad8d0ed48e95be90c6
Author: Janina Smola <janina.smola@contractors.roche.com>
Date: 2024-02-23 13:03:57 +0100
Commit message:

 chore: restore tooltips in table
 
Package: gDRutils
Commit: 5e1fef3e38a7f91b8f36a5591eeb978f956dca4f
Author: Janina Smola <janina.smola@contractors.roche.com>
Date: 2024-02-23 13:02:55 +0100
Commit message:

 chore: update dependencies
 
Package: gDRutils
Commit: 4ae1a833a908c3d188ca17836a3a8211b28abad9
Author: Janina Smola <janina.smola@contractors.roche.com>
Date: 2024-02-22 20:43:00 +0100
Commit message:

 chore: restore tooltips in table
 
Package: TrajectoryGeometry
Commit: b73603124589d12beff71c8745ebebae738e24cb
Author: Michael Shapiro <michael.shapiro@crick.ac.uk>
Date: 2024-02-20 10:51:41 +0000
Commit message:

 Cleaned up vignette.
 
Package: CytoMDS
Commit: 33f7868a78384576d3e97ff3a7cfedd38fa91c9c
Author: phauchamps <philippehauchamps@hotmail.com>
Date: 2024-02-14 16:46:49 +0100
Commit message:

 - biplot now handles extVariables with missing values
- bumped to version 0.99.10
 
Package: CytoMDS
Commit: ed593a3f5b426b58225593dae29f6978a56ba644
Author: phauchamps <philippehauchamps@hotmail.com>
Date: 2024-02-09 12:23:02 +0100
Commit message:

 - in `ggplotSampleMDS()` : add label layer after `geom_point()` (no more before)
- bumped version to 0.99.9
 
Package: gDRtestData
Commit: 3df49e04b25c33177315e2d76d8abe25e5d22b57
Author: marcin-kam <marcin.kamianowski@gmail.com>
Date: 2024-02-23 13:13:59 +0100
Commit message:

 Merge pull request #63 from gdrplatform/GDR-2429

fix: standardize default branch 
Package: gDRtestData
Commit: 396826412a687b2f50638bae44297e59765a8152
Author: Marcin Kamianowski <marcin.kamianowski@contractors.roche.com>
Date: 2024-02-22 15:06:48 +0100
Commit message:

 fix: standardize default branch
 
Package: gDRtestData
Commit: 6f36d11c749fa60bac45cd8df24ee107bfe8121e
Author: Arek Gladki <41166437+gladkia@users.noreply.github.com>
Date: 2024-02-20 14:58:24 +0100
Commit message:

 Merge pull request #61 from gdrplatform/GDR-2371

Gdr 2371 
Package: gDRtestData
Commit: 00264a670bbf6758ee898648612c5a82aa90b9b5
Author: Arkadiusz Gladki <arkadiusz.gladki@contractors.roche.com>
Date: 2024-02-16 12:52:01 +0100
Commit message:

 build: trigger build
 
Package: gDRtestData
Commit: 26062e69034f74fa94437fba061487cf0cef46a1
Author: Arkadiusz Gladki <arkadiusz.gladki@contractors.roche.com>
Date: 2024-02-15 14:14:22 +0100
Commit message:

 chore: update DESCRIPTION
 
Package: gDRtestData
Commit: 29438960fa06164ac0cb8b218bb7152fb1b6aded
Author: Arkadiusz Gladki <arkadiusz.gladki@contractors.roche.com>
Date: 2024-02-15 09:42:58 +0100
Commit message:

 doc: update docs
 
Package: gDRtestData
Commit: 65a0a6944fe45b51f4d34e7913f14010768f5b54
Author: Arek Gladki <41166437+gladkia@users.noreply.github.com>
Date: 2024-02-15 09:40:29 +0100
Commit message:

 Update _pkgdown.yml

Co-authored-by: j-smola <31825957+j-smola@users.noreply.github.com> 
Package: gDRtestData
Commit: 89e801199d9cbeb248cf7e4bb3e8beeae5867006
Author: Arkadiusz Gladki <arkadiusz.gladki@contractors.roche.com>
Date: 2024-02-14 12:55:12 +0100
Commit message:

 build: clean-up/add info (GHA pkgdown.yaml)
 
Package: gDRtestData
Commit: 7a721a17732d91f3b8c5c475f03afa5c927932ca
Author: Arkadiusz Gladki <arkadiusz.gladki@contractors.roche.com>
Date: 2024-02-14 10:38:00 +0100
Commit message:

 build: add Dockerfile
 
Package: gDRtestData
Commit: 9c5d7cd2433524e734fbec2117a91afcd1ad0985
Author: Arkadiusz Gladki <arkadiusz.gladki@contractors.roche.com>
Date: 2024-02-14 10:31:14 +0100
Commit message:

 chore: bump v+c
 
Package: gDRtestData
Commit: 3c666df4fbc169691333803cb22c0b88bbd01826
Author: Arkadiusz Gladki <arkadiusz.gladki@contractors.roche.com>
Date: 2024-02-14 10:30:56 +0100
Commit message:

 build: add pkdown GHA pipeline
 
Package: gDRtestData
Commit: c26cc3cabfa4eb481fe262f58f667d0466266cfe
Author: Arkadiusz Gladki <arkadiusz.gladki@contractors.roche.com>
Date: 2024-02-14 10:30:37 +0100
Commit message:

 chore: update ignore rules
 
Package: gDRtestData
Commit: 9f762e9bbfd6d607219eaf40f37acbff6ef03070
Author: Bartek <32614650+bczech@users.noreply.github.com>
Date: 2024-02-08 11:07:45 +0100
Commit message:

 Merge pull request #56 from gdrplatform/GDR-2199

Gdr 2199 
Package: gDRtestData
Commit: 71d12eab392782cab0b562da3aa96d21b509d1a5
Author: czechb3 <bartosz.w.czech@gmail.com>
Date: 2024-02-08 10:27:57 +0100
Commit message:

 ci: trigger build
 
Package: gDRtestData
Commit: df7614ebbd6cceaf15bae30c0ee6609ecf038203
Author: czechb3 <bartosz.w.czech@gmail.com>
Date: 2024-02-07 20:35:13 +0100
Commit message:

 ci: trigger build
 
Package: gDRtestData
Commit: 2445ae1d395b757630fd38667d3ab8f37adda28a
Author: czechb3 <bartosz.w.czech@gmail.com>
Date: 2024-02-07 16:40:02 +0100
Commit message:

 ci: resolve conflict
 
Package: gDRtestData
Commit: 6ab1e74201490889fa0e19ded7758b03543b1cf1
Author: czechb3 <bartosz.w.czech@gmail.com>
Date: 2024-01-30 13:51:13 +0100
Commit message:

 chore: resolve conflict
 
Package: gDRtestData
Commit: 8bda4504d2c393375abf3a4e614ccdf9ab7b49e2
Author: czechb3 <bartosz.w.czech@gmail.com>
Date: 2024-01-22 10:39:26 +0100
Commit message:

 refactor: remove redundant script
 
Package: gDRtestData
Commit: f20c99c5306e4f81ba48e66138c9d72557a9fbaf
Author: czechb3 <bartosz.w.czech@gmail.com>
Date: 2024-01-19 11:50:17 +0100
Commit message:

 data: update datasets
 
Package: gDRtestData
Commit: 9011fae20579e304aa5e784f45d47978872bacfc
Author: czechb3 <bartosz.w.czech@gmail.com>
Date: 2024-01-12 16:03:33 +0100
Commit message:

 update: test data
 
Package: gDRtestData
Commit: 059255f99f089846f552541ca77cab0bbb0fbad5
Author: czechb3 <bartosz.w.czech@gmail.com>
Date: 2024-01-09 12:32:43 +0100
Commit message:

 chore: bump version and update NEWS.md
 
Package: gDRtestData
Commit: 9cb902d5021151e54f8a932fc3a03fd582c1de3d
Author: czechb3 <bartosz.w.czech@gmail.com>
Date: 2024-01-09 11:30:06 +0100
Commit message:

 data: update test data
 
Package: gDRcore
Commit: 6cd01ae9af7de147343679be11faaf6523bd7026
Author: gDR team <gdr-support-d@gene.com>
Date: 2024-02-23 12:12:11 +0000
Commit message:

 Merge branch 'main' into devel
 
Package: gDRcore
Commit: a126c226c45ee3ab9cc066e3d7f06295f992c125
Author: marcin-kam <marcin.kamianowski@gmail.com>
Date: 2024-02-23 13:11:56 +0100
Commit message:

 Merge pull request #139 from gdrplatform/GDR-2429

fix: standardize default branch 
Package: gDRcore
Commit: ed04b1a8492d1c9e7a6dc9e95255030837534335
Author: Marcin Kamianowski <marcin.kamianowski@contractors.roche.com>
Date: 2024-02-22 14:00:45 +0100
Commit message:

 fix: standardize default branch
 
Package: gDRutils
Commit: f56d8a1ad2213dd310a5080687a9111edbc0a2a6
Author: marcin-kam <marcin.kamianowski@gmail.com>
Date: 2024-02-23 13:09:04 +0100
Commit message:

 Merge pull request #106 from gdrplatform/GDR-2429

fix: standardize default branch 
Package: gDRutils
Commit: a04a0c22eef0009a4952e23a95d754d3ada74126
Author: Marcin Kamianowski <marcin.kamianowski@contractors.roche.com>
Date: 2024-02-22 15:08:16 +0100
Commit message:

 fix: standardize default branch
 
Package: gDRutils
Commit: 389d12eef3138600913bec77cb0672ad5a72fda9
Author: Arek Gladki <41166437+gladkia@users.noreply.github.com>
Date: 2024-02-14 13:41:11 +0100
Commit message:

 Merge pull request #104 from gdrplatform/GDR-2371

Gdr 2371 
Package: gDRutils
Commit: d97776e2ebeb837e37ca95a26e389d7b721efabb
Author: Arkadiusz Gladki <arkadiusz.gladki@contractors.roche.com>
Date: 2024-02-14 12:46:26 +0100
Commit message:

 build: clean-up/add info (GHA pkgdown.yaml)
 
Package: gDRutils
Commit: c42f8c457e23ceeb72ec4153e2f4d7870cfaad18
Author: Arkadiusz Gladki <arkadiusz.gladki@contractors.roche.com>
Date: 2024-02-14 07:11:36 +0100
Commit message:

 build: minor improvement
 
Package: gDRutils
Commit: 45a72be6e6a71692cb85c2bf9b5d02b4f9d93227
Author: Arkadiusz Gladki <arkadiusz.gladki@contractors.roche.com>
Date: 2024-02-14 07:10:15 +0100
Commit message:

 chore: bump v+c
 
Package: gDRutils
Commit: b18480fee9a3461d12c67978002fe0771a690c95
Author: Arkadiusz Gladki <arkadiusz.gladki@contractors.roche.com>
Date: 2024-02-13 17:58:42 +0100
Commit message:

 build: change base image
 
Package: gDRutils
Commit: d275d934cd47425d7821ab9addd4ab87b6f0dd58
Author: Arkadiusz Gladki <arkadiusz.gladki@contractors.roche.com>
Date: 2024-02-13 16:40:17 +0100
Commit message:

 build: trigger build
 
Package: gDRutils
Commit: 12f818d02e96d6c9a45c38e64d22c111022dc02c
Author: Arkadiusz Gladki <arkadiusz.gladki@contractors.roche.com>
Date: 2024-02-13 15:57:47 +0100
Commit message:

 build: trigger build
 
Package: gDRutils
Commit: 6d4b643670216fba417c4e4b0a78ebe778aaf1d0
Author: Arkadiusz Gladki <arkadiusz.gladki@contractors.roche.com>
Date: 2024-02-13 15:50:26 +0100
Commit message:

 build: trigger build
 
Package: gDRutils
Commit: 1bf195ba949787f864ff5da2c10cebdcd9cfe15d
Author: Arkadiusz Gladki <arkadiusz.gladki@contractors.roche.com>
Date: 2024-02-13 15:42:09 +0100
Commit message:

 build: trigger build
 
Package: gDRutils
Commit: d20e359c9b64bdcae2df21004f35db19a3ed237e
Author: Arkadiusz Gladki <arkadiusz.gladki@contractors.roche.com>
Date: 2024-02-13 15:39:07 +0100
Commit message:

 build: update yaml path in GA pipeline
 
Package: gDRutils
Commit: de5492c639d3b4c94a8db8322a36e44411d613dd
Author: Arkadiusz Gladki <arkadiusz.gladki@contractors.roche.com>
Date: 2024-02-13 15:36:25 +0100
Commit message:

 build: update GA pgkdown workflow
 
Package: gDRutils
Commit: f720fcd1df47d4a0e795db24521a400e5ba764cc
Author: Arkadiusz Gladki <arkadiusz.gladki@contractors.roche.com>
Date: 2024-02-13 13:40:50 +0100
Commit message:

 build: simplify/clean-up Dockerfile
 
Package: gDRutils
Commit: 09768d4f8474448dfedc08bbb4365737feae4f2b
Author: Arkadiusz Gladki <arkadiusz.gladki@contractors.roche.com>
Date: 2024-02-13 09:23:07 +0100
Commit message:

 build: trigger build
 
Package: gDRutils
Commit: 1a5491d8efecf1acc818f4cf2ae809518ac40aa9
Author: Arkadiusz Gladki <arkadiusz.gladki@contractors.roche.com>
Date: 2024-02-13 09:22:21 +0100
Commit message:

 build: trigger build
 
Package: gDRutils
Commit: 698f014b78654e27e97f83fbe1d8c4908d5dfd4e
Author: Arkadiusz Gladki <arkadiusz.gladki@contractors.roche.com>
Date: 2024-02-13 09:11:23 +0100
Commit message:

 build: trigger build
 
Package: gDRutils
Commit: 38bc84c2dc0517164c892e22b48a956ffc08158d
Author: Arkadiusz Gladki <arkadiusz.gladki@contractors.roche.com>
Date: 2024-02-13 08:31:40 +0100
Commit message:

 chore: trigger
 
Package: gDRutils
Commit: 6ea060b465361d4bcfabacd03e47e53f51e1937d
Author: Arkadiusz Gladki <arkadiusz.gladki@contractors.roche.com>
Date: 2024-02-13 08:25:56 +0100
Commit message:

 build: trigger build
 
Package: gDRutils
Commit: bc6dc5bd283c86f95b0bdeeeae9c701db284879f
Author: Arkadiusz Gladki <arkadiusz.gladki@contractors.roche.com>
Date: 2024-02-13 08:14:12 +0100
Commit message:

 chore: trigger
 
Package: gDRutils
Commit: 25f5a027bbdb244949d3aa35851071d862817fff
Author: Arkadiusz Gladki <arkadiusz.gladki@contractors.roche.com>
Date: 2024-02-13 08:07:46 +0100
Commit message:

 chore: trigger
 
Package: gDRutils
Commit: fcb76f291f3df82c7e529f98e3414dbbb183604f
Author: Arkadiusz Gladki <arkadiusz.gladki@contractors.roche.com>
Date: 2024-02-13 08:02:39 +0100
Commit message:

 build: trigger build
 
Package: gDRutils
Commit: 3ab8bdf79d66fd731cb3b150e2798bf4fdf6f45b
Author: Arkadiusz Gladki <arkadiusz.gladki@contractors.roche.com>
Date: 2024-02-13 07:49:22 +0100
Commit message:

 build: trigger
 
Package: gDRutils
Commit: f9771812e26bf3fdfbd1769bdfce6b943d658f34
Author: Arkadiusz Gladki <arkadiusz.gladki@contractors.roche.com>
Date: 2024-02-13 07:10:57 +0100
Commit message:

 build: trigger build
 
Package: gDRutils
Commit: 71b7e55fffbbd390f29030fe77324708055f538d
Author: Arkadiusz Gladki <arkadiusz.gladki@contractors.roche.com>
Date: 2024-02-12 23:05:51 +0100
Commit message:

 build: trigger build
 
Package: gDRutils
Commit: eba8ac36407e1b79e399760b75ad9b0449fb1744
Author: Arkadiusz Gladki <arkadiusz.gladki@contractors.roche.com>
Date: 2024-02-12 23:02:47 +0100
Commit message:

 build: trigger
 
Package: gDRutils
Commit: 3e035098aaf9d85b258a5b84bac71eae2b2274df
Author: Arkadiusz Gladki <arkadiusz.gladki@contractors.roche.com>
Date: 2024-02-12 22:58:49 +0100
Commit message:

 chore: trigger
 
Package: gDRutils
Commit: 2e957c88437bc31614eff0287e9f19642615ca91
Author: Arkadiusz Gladki <arkadiusz.gladki@contractors.roche.com>
Date: 2024-02-12 22:53:22 +0100
Commit message:

 chore: trigger
 
Package: gDRutils
Commit: 6b64d46d7c12eff261c2a1ecbddeb6bf169ed245
Author: Arkadiusz Gladki <arkadiusz.gladki@contractors.roche.com>
Date: 2024-02-12 22:35:04 +0100
Commit message:

 build: update pipeline
 
Package: gDRutils
Commit: 3a8f362b604bc7eff5c3b0ff60f0da1a14a93adf
Author: Arkadiusz Gladki <arkadiusz.gladki@contractors.roche.com>
Date: 2024-02-12 22:22:00 +0100
Commit message:

 chore: udpate dockerfile
 
Package: gDRutils
Commit: faa5866bd7d6a82e5d1e935a66e765c08190d97a
Author: Arkadiusz Gladki <arkadiusz.gladki@contractors.roche.com>
Date: 2024-02-12 22:11:42 +0100
Commit message:

 build: trigger build
 
Package: gDRutils
Commit: 26370921c2405cb787a373122d49f59f9373caca
Author: Arkadiusz Gladki <arkadiusz.gladki@contractors.roche.com>
Date: 2024-02-12 22:01:16 +0100
Commit message:

 build: trigger build
 
Package: gDRutils
Commit: 04c8de2c3ea7883760ea1438190146d9090e8b63
Author: Arkadiusz Gladki <arkadiusz.gladki@contractors.roche.com>
Date: 2024-02-12 17:36:37 +0100
Commit message:

 chore: trigger build
 
Package: gDRutils
Commit: b27732c348b6d3661ce0595865a3858d3098f1b3
Author: Arkadiusz Gladki <arkadiusz.gladki@contractors.roche.com>
Date: 2024-02-12 17:25:54 +0100
Commit message:

 build: update pipeline
 
Package: gDRutils
Commit: d10d259a48295124a2dbc9b61bbdabd720f372d7
Author: Arkadiusz Gladki <arkadiusz.gladki@contractors.roche.com>
Date: 2024-02-12 17:16:37 +0100
Commit message:

 build: update Dockerfile
 
Package: gDRutils
Commit: 8468232641ca29aae689fab4884be72dcd10ecfb
Author: Arkadiusz Gladki <arkadiusz.gladki@contractors.roche.com>
Date: 2024-02-12 17:12:02 +0100
Commit message:

 build: update Dockerfile
 
Package: gDRutils
Commit: 32f150348a2a6aa0d6138bc6dae3e4a5929fd71b
Author: Arkadiusz Gladki <arkadiusz.gladki@contractors.roche.com>
Date: 2024-02-12 17:01:37 +0100
Commit message:

 build: update Dockerfile
 
Package: gDRutils
Commit: acfa0a655b44c1d0cf432558b68a8755fbdaca2f
Author: Arkadiusz Gladki <arkadiusz.gladki@contractors.roche.com>
Date: 2024-02-12 16:55:24 +0100
Commit message:

 build: update Dockerfile
 
Package: gDRutils
Commit: 263e1d241b8fbf1937673749f219b17d34d14c67
Author: Arkadiusz Gladki <arkadiusz.gladki@contractors.roche.com>
Date: 2024-02-12 16:48:04 +0100
Commit message:

 build: update Dockerfile
 
Package: gDRutils
Commit: 88a767ff5d2c9966adb508b1a1a5c27252da2261
Author: Arkadiusz Gladki <arkadiusz.gladki@contractors.roche.com>
Date: 2024-02-12 16:28:18 +0100
Commit message:

 build: update Docker image in pipeline
 
Package: gDRutils
Commit: 0d5514abf9cf3c1bc84410ce455ddedf45ffd5f8
Author: Arkadiusz Gladki <arkadiusz.gladki@contractors.roche.com>
Date: 2024-02-12 16:26:26 +0100
Commit message:

 build: use BioC Docker image
 
Package: gDRutils
Commit: 9ab53be491c43c07b5945ccd2aaf2b5ec7041574
Author: Arkadiusz Gladki <arkadiusz.gladki@contractors.roche.com>
Date: 2024-02-12 12:53:35 +0100
Commit message:

 build: trigger build
 
Package: gDRutils
Commit: c04bf8e648fca5fbab810202b56706c73ebaa568
Author: Arkadiusz Gladki <arkadiusz.gladki@contractors.roche.com>
Date: 2024-02-12 12:40:34 +0100
Commit message:

 build: modify pkgdown pipeline
 
Package: gDRutils
Commit: 15035bde1e9962f612774808d6abb5f1b5962105
Author: Arkadiusz Gladki <arkadiusz.gladki@contractors.roche.com>
Date: 2024-02-12 12:21:52 +0100
Commit message:

 build: update Dockerfile setttings
 
Package: gDRutils
Commit: 7e1b4ac5c5d76100b17ad4df3eb25f168dc9e701
Author: Arkadiusz Gladki <arkadiusz.gladki@contractors.roche.com>
Date: 2024-02-12 11:53:37 +0100
Commit message:

 build: update pipeline
 
Package: gDRutils
Commit: b1eddd26094ecbc574fa638d3eef186da131e009
Author: Arkadiusz Gladki <arkadiusz.gladki@contractors.roche.com>
Date: 2024-02-12 11:49:07 +0100
Commit message:

 build: trigger build
 
Package: gDRutils
Commit: 45c5ba51481e6937a4fa9875ee90457900934090
Author: Arkadiusz Gladki <arkadiusz.gladki@contractors.roche.com>
Date: 2024-02-12 08:54:45 +0100
Commit message:

 build: fix Dockerfile
 
Package: gDRutils
Commit: cf7d15126ffc2f81d32342f1306901f72a7bd180
Author: Arkadiusz Gladki <arkadiusz.gladki@contractors.roche.com>
Date: 2024-02-12 08:50:34 +0100
Commit message:

 build: test build
 
Package: gDRutils
Commit: 05eba42596cb1feda188f4a03d459e17a7fcad05
Author: Arkadiusz Gladki <arkadiusz.gladki@contractors.roche.com>
Date: 2024-02-12 08:48:20 +0100
Commit message:

 build: test pkgdown.yaml CI
 
Package: gDRutils
Commit: 9544a13813683d9db1baacf9afa1326400374b1d
Author: Arkadiusz Gladki <arkadiusz.gladki@contractors.roche.com>
Date: 2024-02-12 07:58:38 +0100
Commit message:

 feat: add drat version of pkdgdown CI
 
Package: gDRutils
Commit: 32649cb59c94dc9cdba26e9cfc11873b312295fc
Author: Arkadiusz Gladki <arkadiusz.gladki@contractors.roche.com>
Date: 2024-02-12 07:57:44 +0100
Commit message:

 chore: update ignore rules
 
Package: gDRutils
Commit: c7b05b12d76f78ce513e2084ad3a33ab2f701ea1
Author: Bartek <32614650+bczech@users.noreply.github.com>
Date: 2024-02-08 11:08:03 +0100
Commit message:

 Merge pull request #102 from gdrplatform/GDR-2199

Gdr 2199 
Package: gDRutils
Commit: b19ad8a1780f80897474d9a0017030413a070767
Author: czechb3 <bartosz.w.czech@gmail.com>
Date: 2024-02-08 10:28:08 +0100
Commit message:

 ci: trigger build
 
Package: gDRutils
Commit: f37ab15145aa07b3dbb5738e88895c4999fb2876
Author: czechb3 <bartosz.w.czech@gmail.com>
Date: 2024-02-07 20:29:15 +0100
Commit message:

 ci: trigger build
 
Package: gDRutils
Commit: e426aecb495413d915b622bb00726da5261fdc62
Author: czechb3 <bartosz.w.czech@gmail.com>
Date: 2024-01-30 14:21:13 +0100
Commit message:

 refactor: remove margittr from dependencies
 
Package: gDRutils
Commit: fd31744f336deb906500307c2d435d4f3f3bc1ea
Author: czechb3 <bartosz.w.czech@gmail.com>
Date: 2024-01-30 14:03:21 +0100
Commit message:

 chore: resolve conflict
 
Package: gDRutils
Commit: af5038b7b2ab336f1436cd373ab1bde40a2a4812
Author: czechb3 <bartosz.w.czech@gmail.com>
Date: 2024-01-18 15:50:04 +0100
Commit message:

 refactor: update headers
 
Package: gDRutils
Commit: c7ab07bbcc534e63c2a42105503ad889acb2bd6d
Author: czechb3 <bartosz.w.czech@gmail.com>
Date: 2024-01-18 14:22:13 +0100
Commit message:

 refactor: update convert_mae_se_assay_to_dt function
 
Package: gDRutils
Commit: b3058ad24cef146b5afa6d3ef5882419532fa091
Author: czechb3 <bartosz.w.czech@gmail.com>
Date: 2024-01-18 13:28:36 +0100
Commit message:

 doc: update documentation
 
Package: gDRutils
Commit: 1aaea8dc746ae209e07f2ed02dd39b893889ab68
Author: czechb3 <bartosz.w.czech@gmail.com>
Date: 2024-01-18 11:50:31 +0100
Commit message:

 reoxygenate
 
Package: gDRutils
Commit: b087c8aa2e0104be7d58bd242b5e224ade368a3c
Author: czechb3 <bartosz.w.czech@gmail.com>
Date: 2024-01-17 14:32:27 +0100
Commit message:

 refactor: update unit tests
 
Package: gDRutils
Commit: 00bf666b6faafd4b5675aae353f97e265d66aafd
Author: czechb3 <bartosz.w.czech@gmail.com>
Date: 2024-01-17 14:32:16 +0100
Commit message:

 refactor: extend list of data columns
 
Package: gDRutils
Commit: 15655c2fe3f1542c7aa12fd46b00f084670f6743
Author: czechb3 <bartosz.w.czech@gmail.com>
Date: 2024-01-17 11:53:04 +0100
Commit message:

 restore: R/convert_mae_se_assay_to_dt.R
 
Package: gDRutils
Commit: fcf7bcda9344f1e4fc85374c7338e3472bf73f6d
Author: czechb3 <bartosz.w.czech@gmail.com>
Date: 2024-01-17 11:46:35 +0100
Commit message:

 refactor: appease lintr
 
Package: gDRutils
Commit: d4ced3ced359f12ecafd74cbcb93bc5619e07446
Author: czechb3 <bartosz.w.czech@gmail.com>
Date: 2024-01-16 16:18:08 +0100
Commit message:

 refactor: update headers list
 
Package: gDRutils
Commit: c88e132b428736242bef11b40fed0ebdb2d9ce30
Author: czechb3 <bartosz.w.czech@gmail.com>
Date: 2024-01-15 17:13:55 +0100
Commit message:

 refactor: update assay name
 
Package: gDRutils
Commit: cd9fe66054bdbc5c0b5ac7469e309fe1b375604e
Author: czechb3 <bartosz.w.czech@gmail.com>
Date: 2024-01-12 14:42:35 +0100
Commit message:

 feat: add function to convert field name into assay name
 
Package: gDRutils
Commit: 907a51e8c6b53e04015fbda1b87e2778f837de03
Author: czechb3 <bartosz.w.czech@gmail.com>
Date: 2024-01-11 16:22:31 +0100
Commit message:

 refactor: add functions for getting combo excess and scores field names
 
Package: gDRutils
Commit: 05cebe8acc8528711cffcee17a100b00a9724251
Author: czechb3 <bartosz.w.czech@gmail.com>
Date: 2024-01-11 10:26:42 +0100
Commit message:

 refactor: update combo table
 
Package: gDRutils
Commit: bbc3db222343d2e027eaf315c033e581d8825a95
Author: czechb3 <bartosz.w.czech@gmail.com>
Date: 2024-01-03 13:03:30 +0100
Commit message:

 refactor: fix typo
 
Package: gDRutils
Commit: 417838f4d9e0f57277478a72bd5151c90d61248f
Author: czechb3 <bartosz.w.czech@gmail.com>
Date: 2024-01-03 12:32:21 +0100
Commit message:

 chore: bump version and update NEWS.md
 
Package: gDRutils
Commit: 3e502387e8795303bc7b516ff6e79daef2244d6b
Author: czechb3 <bartosz.w.czech@gmail.com>
Date: 2024-01-03 12:31:59 +0100
Commit message:

 refactor: rename matrix into combination
 
Package: gDR
Commit: 7da40353a59b9203dc7bb8c64dae12ebbe77e312
Author: marcin-kam <marcin.kamianowski@gmail.com>
Date: 2024-02-23 13:06:25 +0100
Commit message:

 Merge pull request #48 from gdrplatform/GDR-2429

Gdr 2429 
Package: gDR
Commit: 12110eea2739f0730d0ffd76391c2bdefd37e4dc
Author: Marcin Kamianowski <marcin.kamianowski@contractors.roche.com>
Date: 2024-02-22 15:31:38 +0100
Commit message:

 fix: standardize default branch
 
Package: gDR
Commit: c8e11c52dd28039faa505e3ca83d697bead371a6
Author: Marcin Kamianowski <marcin.kamianowski@contractors.roche.com>
Date: 2024-02-22 15:30:09 +0100
Commit message:

 fix: standardize default branch
 
Package: gDRimport
Commit: 51bb99557d1354b291e13501f25bfec608de7947
Author: marcin-kam <marcin.kamianowski@gmail.com>
Date: 2024-02-23 12:53:52 +0100
Commit message:

 Merge pull request #78 from gdrplatform/GDR-2429

Gdr 2429 
Package: gDRimport
Commit: 109b4ff415cd70c047a96a7391e7e3691ceaf0ec
Author: Marcin Kamianowski <marcin.kamianowski@contractors.roche.com>
Date: 2024-02-22 15:29:34 +0100
Commit message:

 fix: standardize default branch
 
Package: gDRimport
Commit: bea53247a560c32482e6e5f8a625458e62ff27dc
Author: Marcin Kamianowski <marcin.kamianowski@contractors.roche.com>
Date: 2024-02-22 14:17:10 +0100
Commit message:

 fix: standardize default branch
 
Package: gDRstyle
Commit: 289971876f1fa89e5cc0971e92147130b7fdca90
Author: marcin-kam <marcin.kamianowski@gmail.com>
Date: 2024-02-23 12:52:59 +0100
Commit message:

 Merge pull request #74 from gdrplatform/GDR-2429

Gdr 2429 
Package: gDRstyle
Commit: 53d143fe7fe2945903e130d4ab9205878ed3b88a
Author: Marcin Kamianowski <marcin.kamianowski@contractors.roche.com>
Date: 2024-02-22 14:04:24 +0100
Commit message:

 fix: standardize default branch
 
Package: gDRstyle
Commit: 666b860a0cd8a9cfc73510324928db796f1b8bf8
Author: Marcin Kamianowski <marcin.kamianowski@contractors.roche.com>
Date: 2024-02-22 13:04:19 +0100
Commit message:

 fix: standardize default branch
 
Package: autonomics
Commit: f258eadbe8b166b1d8f8ec8bf59a97dd3fa8883d
Author: Aditya Bhagwat <aditya.bhagwat@uni-marburg.de>
Date: 2024-02-23 12:04:05 +0100
Commit message:

 Further streamlining of `annotate_maxquant`, `read_maxquant_proteingroups` and `read_maxquant_phosphosites`
 
Package: autonomics
Commit: 2748414fabd1481ee4706458ae13ec3679474c3c
Author: Aditya Bhagwat <aditya.bhagwat@uni-marburg.de>
Date: 2024-02-23 11:45:47 +0100
Commit message:

 annotate_maxquant : further streamlining
 
Package: autonomics
Commit: 6d70cfc91dcd4013a4faf97863c5f0e9fdb7efbd
Author: Aditya Bhagwat <aditya.bhagwat@uni-marburg.de>
Date: 2024-02-23 10:49:03 +0100
Commit message:

 (uniprot|maxquant|contaminant)dt -> (uniprot|maxquant|contaminant)hdrs
 
Package: autonomics
Commit: 58e6f834833650599359249914bafd248520cb20
Author: Aditya Bhagwat <aditya.bhagwat@uni-marburg.de>
Date: 2024-02-23 10:32:46 +0100
Commit message:

 annotate_maxquant : make msgs more intuitive
 
Package: UCell
Commit: 24fb4260e435608d231939c401fe7ab4bb89ee54
Author: Massimo Andreatta <massimo.andreatta@unil.ch>
Date: 2024-02-23 10:16:15 +0100
Commit message:

 Include SeuratObject in Suggests
 
Package: sketchR
Commit: 42162d80e81623fdf816638722ea1581828b2355
Author: Charlotte Soneson <charlottesoneson@gmail.com>
Date: 2024-02-23 08:49:08 +0100
Commit message:

 Merge pull request #13 from fmicompbio/review-additions

Review additions 
Package: sketchR
Commit: f273dbca044fb5eb288b175a7592287b229655fd
Author: Charlotte Soneson <charlottesoneson@gmail.com>
Date: 2024-02-23 07:33:34 +0100
Commit message:

 Update copyright holder
 
Package: sketchR
Commit: cb1d20a68ad7f5167ca1f745e96722b17da9b706
Author: Charlotte Soneson <charlottesoneson@gmail.com>
Date: 2024-02-23 06:41:15 +0100
Commit message:

 Update installation instructions
 
Package: sketchR
Commit: cf9daa1a1821127247885e0d396f53585e4f1c70
Author: Charlotte Soneson <charlottesoneson@gmail.com>
Date: 2024-02-22 21:53:43 +0100
Commit message:

 Expand vignette introduction
 
Package: sketchR
Commit: 5498bdaceafe78ce8420fa56b2f094890637d067
Author: Charlotte Soneson <charlottesoneson@gmail.com>
Date: 2024-02-22 20:35:28 +0100
Commit message:

 Add package man page
 
Package: sketchR
Commit: 926620b0097ec539a14b70edbe55f8286feedfe0
Author: Charlotte Soneson <charlottesoneson@gmail.com>
Date: 2024-02-22 20:31:05 +0100
Commit message:

 Bump version and update date
 
Package: sketchR
Commit: 8232d73b84401f3afe50c7eede4abd11f01c9a6b
Author: Charlotte Soneson <charlottesoneson@gmail.com>
Date: 2024-02-22 20:30:39 +0100
Commit message:

 Update year in license
 
Package: EpiMix
Commit: 8866c90dc93e8db563e6feea56e87d864705fdaf
Author: Eric Zheng <eric2021@crosswood.stanford.edu>
Date: 2024-02-22 21:30:14 -0800
Commit message:

 version bump in devel
 
Package: EpiMix
Commit: 5c53180b3e19602c68a016fbd76c8353d04b8c8e
Author: Eric Zheng <eric2021@crosswood.stanford.edu>
Date: 2024-02-22 21:29:08 -0800
Commit message:

 change description file
 
Package: ClassifyR
Commit: f69f5f32c46f4fc198b3e743514b45900643b1b2
Author: Dario Strbenac <dario@maths.usyd.edu.au>
Date: 2024-02-23 15:00:08 +1100
Commit message:

 crossValidate methods other than DataFrame also accept verbose from user. Fixes #101
 
Package: consensusSeekeR
Commit: d8c3500f59015ff53ae1b6f77483754a764c6817
Author: Astrid Deschenes <adeschen@hotmail.com>
Date: 2024-02-22 19:59:06 -0500
Commit message:

 Update package version to 1.31.2
 
Package: consensusSeekeR
Commit: a903441d124b09cff127a78301e99ed742cfc912
Author: Astrid Deschenes <adeschen@hotmail.com>
Date: 2024-02-22 19:48:07 -0500
Commit message:

 Update minimal R version required in DESCRIPTION file
 
Package: consensusSeekeR
Commit: 09e713ecf5c26acaaf963de786e22c4b67ec3c28
Author: Astrid Deschenes <adeschen@hotmail.com>
Date: 2024-02-22 19:22:34 -0500
Commit message:

 Update package version to 1.31.1
 
Package: consensusSeekeR
Commit: b3cb1ed4708db6abd95e4b63446beb9934727d50
Author: Astrid Deschenes <adeschen@hotmail.com>
Date: 2024-02-22 19:01:45 -0500
Commit message:

 Update assignation in function
 
Package: consensusSeekeR
Commit: a4016dec47193a942288c47da8b314f1f756546d
Author: Astrid Deschenes <adeschen@hotmail.com>
Date: 2024-02-22 18:09:32 -0500
Commit message:

 Merge remote-tracking branch 'upstream/master'
 
Package: consensusSeekeR
Commit: bbc13ef2b41bb19a51f9f265a87203815ce5842f
Author: Astrid Deschenes <adeschen@hotmail.com>
Date: 2024-02-22 18:08:36 -0500
Commit message:

 Adding encoding UTF-8 to man pages
 
Package: consensusSeekeR
Commit: da739338c9be4b0025db8897790acb373926efa0
Author: Astrid Deschenes <adeschen@hotmail.com>
Date: 2024-02-22 18:07:59 -0500
Commit message:

 Update comment in unit test
 
Package: consensusSeekeR
Commit: cc77eeb57ee42ce10951bd5625f5981a022a195a
Author: Astrid Deschenes <adeschen@hotmail.com>
Date: 2024-02-22 18:07:28 -0500
Commit message:

 Update abstract in vignette
 
Package: consensusSeekeR
Commit: 95e9297be36416b9af28569e37e78eb18eec0d56
Author: Astrid Deschenes <adeschen@hotmail.com>
Date: 2024-02-22 17:20:47 -0500
Commit message:

 Adding encoding UTF-8 to man pages
 
Package: consensusSeekeR
Commit: de513f85e48948c681237829ac900161c14f8460
Author: Astrid Deschenes <adeschen@hotmail.com>
Date: 2024-02-22 17:03:07 -0500
Commit message:

 Remove paste from condition signals
 
Package: consensusSeekeR
Commit: 9b1b670de64dcc2befdaa4dba9f3a685507d2924
Author: Astrid Deschenes <adeschen@hotmail.com>
Date: 2024-02-22 17:00:45 -0500
Commit message:

 Update description field in the DESCRIPTION file
 
Package: consensusSeekeR
Commit: 0f0aa4bc82d33eae8c155459bcb6d6e0acc96a0a
Author: Astrid Deschenes <adeschen@hotmail.com>
Date: 2024-02-22 16:57:53 -0500
Commit message:

 Update description field in the DESCRIPTION file
 
Package: consensusSeekeR
Commit: 11cbde09849c86c0e2b7fc95276cb7439604a4c2
Author: Astrid Deschenes <adeschen@hotmail.com>
Date: 2024-02-22 16:45:10 -0500
Commit message:

 Update codecov link in README
 
Package: consensusSeekeR
Commit: 9de424c5d9740c1805b9aa405ec0c8612dd99989
Author: Astrid Deschenes <adeschen@hotmail.com>
Date: 2024-02-22 16:26:39 -0500
Commit message:

 Update issue link in README
 
Package: consensusSeekeR
Commit: 03f8f3aec03925c23772d88cb6f5d9bdc9c3ee63
Author: Astrid Deschenes <adeschen@hotmail.com>
Date: 2024-02-22 16:21:24 -0500
Commit message:

 Update check-bioc action
 
Package: consensusSeekeR
Commit: c77435962e3e6961e7b4e0dd8daafab6dc91216f
Author: Astrid Deschenes <adeschen@hotmail.com>
Date: 2024-02-22 16:18:01 -0500
Commit message:

 Update check-bioc action
 
Package: consensusSeekeR
Commit: 81bc899f8daba6e4b76eb0c95ad880b95c1abadc
Author: Astrid Deschenes <adeschen@hotmail.com>
Date: 2024-02-22 16:13:08 -0500
Commit message:

 Add codecov upload task to check-bioc action
 
Package: consensusSeekeR
Commit: 428287423d14e9e563565ccb495969554834e3b3
Author: Astrid Deschenes <adeschen@hotmail.com>
Date: 2024-02-22 13:59:45 -0500
Commit message:

 Update README
 
Package: consensusSeekeR
Commit: 26061b5a7db9b2aaf5d118bc2a94000a27a8b46e
Author: Astrid Deschenes <adeschen@hotmail.com>
Date: 2024-02-21 23:07:56 -0500
Commit message:

 update actions/checkout to v4
 
Package: consensusSeekeR
Commit: 299d532d7479bf7aeed7b3fd7335120b0de71e35
Author: Astrid Deschenes <adeschen@hotmail.com>
Date: 2024-02-21 21:46:08 -0500
Commit message:

 Add license logo in README file
 
Package: consensusSeekeR
Commit: 4aaaab6b30861e88edb8abe3f09ea26304831e6c
Author: Astrid Deschenes <adeschen@hotmail.com>
Date: 2024-02-21 21:45:00 -0500
Commit message:

 Update README to point to new action workflow
 
Package: consensusSeekeR
Commit: 72742eff0f4a0e6be8d5d2478facaca97d674fdc
Author: Astrid Deschenes <adeschen@hotmail.com>
Date: 2024-02-21 21:35:20 -0500
Commit message:

 Removing Maintainer field from DESCRIPTION file
 
Package: consensusSeekeR
Commit: cfedde121bd8fa3b875b7e7d84d752c9f948c055
Author: Astrid Deschenes <adeschen@hotmail.com>
Date: 2024-02-21 21:12:09 -0500
Commit message:

 Adding github workflows
 
Package: consensusSeekeR
Commit: 3411b9c70cc61e2a0c171368cd90cd969efc7725
Author: Astrid Deschenes <adeschen@hotmail.com>
Date: 2024-02-21 21:08:16 -0500
Commit message:

 Update README file
 
Package: consensusSeekeR
Commit: 622a327783e17e3d9ccbb6fc68998bfcc5e844b0
Author: Astrid Deschenes <adeschen@hotmail.com>
Date: 2024-02-21 21:06:15 -0500
Commit message:

 Update code indentation
 
Package: gypsum
Commit: 22fbdd9224ae6e7e17b8680630ce3196b2e1231e
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2024-02-22 16:50:20 -0800
Commit message:

 Use write-and-rename to avoid caching incomplete downloads.

This is more common than one might think due to network interruptions.
If a partially downloaded file is cached, subsequent calls will think
that the whole file is already available and not restart the download.
 
Package: scde
Commit: f9e66508457f9548343b1b91cc22b05cbc06ff7c
Author: evanbiederstedt <evan.biederstedt@gmail.com>
Date: 2024-02-22 18:41:03 -0500
Commit message:

 fix Makevars files
 
Package: AUCell
Commit: 8dd84847c95be4a0249bc294f9cf51e79213876b
Author: Sara Aibar <sara.aibar@kuleuven.be>
Date: 2024-02-23 00:15:49 +0100
Commit message:

 Version
 
Package: mitch
Commit: f9c79729f4b543378f2a028c76a51b7e42404db3
Author: markziemann <markziemann@gmail.com>
Date: 2024-02-23 10:12:44 +1100
Commit message:

 vignette update
 
Package: AUCell
Commit: ce331cc3b429b7703a4691830dbfb5df5d8b8de5
Author: Sara Aibar <sara.aibar@kuleuven.beeval>
Date: 2024-02-23 00:00:43 +0100
Commit message:

 descr
 
Package: AUCell
Commit: 4d98b1211a63a700131ba803621b795e86c4e5a2
Author: Sara Aibar <20438544+s-aibar@users.noreply.github.com>
Date: 2024-02-22 23:50:16 +0100
Commit message:

 Version (devel) 
Package: AUCell
Commit: 0d9c4d9e763b9413cb359acf682479b039736f9e
Author: Gert Hulselmans <gert.hulselmans@kuleuven.be>
Date: 2024-02-16 17:03:57 +0100
Commit message:

 Remove "rbokeh" as it is removed from Bioconductor.

Remove "rbokeh" as it is removed from Bioconductor.
 
Package: CytoMethIC
Commit: da18c01efe164505eef59e1f1c05989f44e9fe2a
Author: Jacob Fanale <jakefanale@gmail.com>
Date: 2024-02-22 14:27:23 -0500
Commit message:

 minor, message omitted
 
Package: CytoMethIC
Commit: fdcda4e459a91713ae510dd0eccff8ba7748a4d5
Author: Jacob Fanale <jakefanale@gmail.com>
Date: 2024-02-22 14:00:03 -0500
Commit message:

 Bump version num
 
Package: CytoMethIC
Commit: 609d06d84943a1f75335430fc77b452877fab887
Author: Jacob Fanale <jakefanale@gmail.com>
Date: 2024-02-22 13:10:58 -0500
Commit message:

 Merge branch 'devel' of https://github.com/zhou-lab/CytoMethIC into devel
 
Package: CytoMethIC
Commit: 229770ce996c9a534904ce4760d6025e65377e9a
Author: Wanding Zhou <zhouwanding@gmail.com>
Date: 2024-02-22 12:00:15 -0500
Commit message:

 fix to check error
 
Package: alabaster.matrix
Commit: 62b3175a791b9fdf64f64a013ba05560ca53d13c
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2024-02-22 07:57:10 -0800
Commit message:

 Forgot to capitalize the name of the ReloadedArray saving option.
 
Package: TCGAutils
Commit: bba991f0334ddf8ac67355a0939114aa06616508
Author: LiNk-NY <marcel.ramos@roswellpark.org>
Date: 2024-02-22 15:56:16 +0000
Commit message:

 version bump 1.23.4
 
Package: TCGAutils
Commit: 62e78945385acb950973f22a762164e622e95819
Author: LiNk-NY <marcel.ramos@roswellpark.org>
Date: 2024-02-22 15:56:06 +0000
Commit message:

 more informative error, closes #34
 
Package: spoon
Commit: d96b8cdabdfd9eb5d2cfebff57e4772054412989
Author: Kinnary Shah <kinnaryshahh@gmail.com>
Date: 2024-02-22 10:20:59 -0500
Commit message:

 update version
 
Package: TrajectoryGeometry
Commit: 8354f60efa33bf76da8a161f2afd9df097464e89
Author: Michael Shapiro <michael.shapiro@crick.ac.uk>
Date: 2024-02-20 10:51:41 +0000
Commit message:

 Cleaned up vignette.
 
Package: CNVgears
Commit: 070e60b56e8c598689c5dbfb4c295c2afc9a6800
Author: lshep <lori.shepherd@roswellpark.org>
Date: 2024-02-22 08:16:26 -0500
Commit message:

 User requested deprecation
 
Package: iSEEindex
Commit: b14d858ca2597ae8deb7adea3a36cbfc59814b87
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2024-02-22 13:44:48 +0100
Commit message:

 Runr + more (#57)

* exposing the app title as parameter to be possibly chosen by the user upon launching iSEEindex()

* updting GHA workflow to run with Bioc 3.19 in devel

* version bump

---------

Co-authored-by: Kevin Rue-Albrecht <kevinrue67@gmail.com> 
Package: LACE
Commit: 93c58dc9eb9f2c49b71180ae8753460b20ff5e81
Author: DavideMaspero <d.maspero@campus.unimib.it>
Date: 2024-02-22 10:45:26 +0100
Commit message:

 Update DESCRIPTION
 
Package: MungeSumstats
Commit: f7bd3336deccdd623f396c9a083d9257624a42e5
Author: Al-Murphy <alanmurph94@hotmail.com>
Date: 2024-02-22 09:03:48 +0000
Commit message:

 longtests upstream
 
Package: alabaster.matrix
Commit: ba60c84b1ec86f4da2f72c4290b59fab7909050f
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2024-02-21 22:47:21 -0800
Commit message:

 Removed the output options when reading arrays/sparse matrices.

Callers can coerce it themselves, either manually or by setting an
altReadObject override - there's no need to do it in the default readers.

We also update the DelayedArray saveObject options to use the actual class
name for consistency with the new expectations in alabaster.base's docs.
 
Package: alabaster.se
Commit: 583dc959e618c74fd05e49a5e47baac7b8b11574
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2024-02-21 23:06:57 -0800
Commit message:

 Renamed SE saving options to align with alabaster.base's docs.
 
Package: alabaster.base
Commit: 7efe11931892c70dbf3ce17d6276f593e85f4aaa
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2024-02-21 22:27:05 -0800
Commit message:

 Clarified docs for save/readObject, especially for around '...'.

Options should now be prefixed by the case-sentivei class name (for saving) and
by the object type (for reading); this is what is used for dispatch and so is
guaranteed to be non-conflicting across methods.
 
Package: EasyCellType
Commit: e85e8187c540f66994b5ca12fe95f5d9eb95f1f5
Author: Li <RLi8@mdanderson.org>
Date: 2024-02-21 23:39:44 -0600
Commit message:

 add biocstyle to suggests
 
Package: alabaster.matrix
Commit: b627a2da377f6d32e4a1399da13bae8d30c5b3db
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2024-02-21 15:39:00 -0800
Commit message:

 Bumped version and date.
 
Package: alabaster.matrix
Commit: b9f154049b4fcac983785274b9b25e6f54ce4006
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2024-02-21 15:28:33 -0800
Commit message:

 Introduce a WrapperArray virtual class for coercion overrides.

This allows us to forward all the coercion methods to the seed without
having to implement this logic separately for the array/matrix classes
corresponding to the application-specific WrapperArraySeed subclass.
 
Package: alabaster.matrix
Commit: 9e1dbfd78e8fd548c996b818595e61c425fb4e3f
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2024-02-21 14:39:25 -0800
Commit message:

 Avoid type coercion if the types are already the same.

This avoids inefficiencies from another unnecessary delayed operation.
 
Package: projectR
Commit: fd96af342c3161a340f03958bbd38e9e2431bd9c
Author: dimalvovs <dlvovs1@jh.edu>
Date: 2024-02-21 15:43:00 -0500
Commit message:

 fix illegal bump
 
Package: projectR
Commit: b137e7c2ab40f21f159b4c1d264f6a3cad6f892b
Author: dimalvovs <dlvovs1@jh.edu>
Date: 2024-02-21 15:31:31 -0500
Commit message:

 make bump odd
 
Package: projectR
Commit: 39819a11004d4dbefc49268d40c169fcbf115901
Author: dimalvovs <dlvovs1@jh.edu>
Date: 2024-02-21 15:28:00 -0500
Commit message:

 bump version
 
Package: projectR
Commit: 83da394eec420e8388f1a970536deb2a3bd38ddd
Author: dimalvovs <dmitrijs.lvovs@gmail.com>
Date: 2024-02-21 15:08:03 -0500
Commit message:

 Merge pull request #38 from genesofeve/projectionDriveR

Projection drive r 
Package: projectR
Commit: 1d441270364c2adecf10ae3e055c0706cfb93abe
Author: rpalaganas <ryanpalaganas96@gmail.com>
Date: 2024-02-21 11:53:26 -0500
Commit message:

 Update projectR.Rmd
 
Package: projectR
Commit: 7f78f928dacc33cf73dc55ed8e47a8c7b035783f
Author: rpalaganas <ryanpalaganas96@gmail.com>
Date: 2024-02-21 10:40:33 -0500
Commit message:

 Update projectR.Rmd
 
Package: projectR
Commit: 713c55b49369c40c96bd934458841cf32b902539
Author: rpalaganas <ryanpalaganas96@gmail.com>
Date: 2024-02-21 09:46:43 -0500
Commit message:

 Update projectR.Rmd
 
Package: projectR
Commit: 9ac52250d0befb7456a7ce1eda56aa0958244617
Author: rpalaganas <ryanpalaganas96@gmail.com>
Date: 2024-02-21 09:44:17 -0500
Commit message:

 update vignette
 
Package: projectR
Commit: 5ed503425496ea858f3d461c716a63a875f7996f
Author: rpalaganas <ryanpalaganas96@gmail.com>
Date: 2024-02-21 09:15:19 -0500
Commit message:

 Update plotting.R

Removed unnecessary == FALSE/TRUE statements
 
Package: projectR
Commit: 8e731b223559e9cfaa857899417a5c272a4cf738
Author: rpalaganas <ryanpalaganas96@gmail.com>
Date: 2024-02-20 16:09:39 -0500
Commit message:

 Update projectR.html

Knit rmd using projectiondriver branch. Should be rerun after merge
 
Package: projectR
Commit: 55167e0c91efd9e4191e271d7e05e09a53ecd7ac
Author: rpalaganas <ryanpalaganas96@gmail.com>
Date: 2024-02-16 13:57:42 -0500
Commit message:

 Update plotting.R
 
Package: projectR
Commit: 2f96c605ccdd00aaf6c6b8f5db0566b6ece888c2
Author: rpalaganas <ryanpalaganas96@gmail.com>
Date: 2024-02-16 13:02:58 -0500
Commit message:

 Update examples

Added examples for PV mode projectionDrivers
Added fgsea examples for pdVolcano function
 
Package: projectR
Commit: bc1d94834f267f53182b01cb01d4e156b9c386ff
Author: rpalaganas <ryanpalaganas96@gmail.com>
Date: 2024-02-16 13:02:25 -0500
Commit message:

 Style updates

Incorporated some lintr suggestions
Added display options for volcano plots
 
Package: projectR
Commit: 08394c7d860df7a65ea1efed84d5eed9f43b8ab3
Author: rpalaganas <ryanpalaganas96@gmail.com>
Date: 2024-02-16 12:59:11 -0500
Commit message:

 Style updates

Incorporated some lintr suggestions
Resolved 'no visible binding for global variable'
Added automatic plotting
Condensed volcano plotting to one parametrized function
 
Package: projectR
Commit: b8009990ab257b03980b85a18992a6886337d105
Author: rpalaganas <ryanpalaganas96@gmail.com>
Date: 2024-02-16 12:56:42 -0500
Commit message:

 Style updates

updated roxygen2 documentation
 
Package: projectR
Commit: abe8c9d1785ffd5d784beaa467a5398a2254f79e
Author: rpalaganas <ryanpalaganas96@gmail.com>
Date: 2024-02-15 19:24:03 -0500
Commit message:

 Updated functions to reflect code review

Improved style consistency, incorporated lintr
Parameterized unweighted/weighted volcanos to one function
Updated vignette with more projectionDriveR examples
 
Package: projectR
Commit: 1b9d5573ee3b7ea6a9e07056be80042b391577fa
Author: dimalvovs <dlvovs1@jh.edu>
Date: 2024-01-19 16:49:12 -0500
Commit message:

 refactor to match new bioc
 
Package: projectR
Commit: 7f43d38f0301469aed88e4b5cb5fc1f7038e6446
Author: rpalaganas <ryanpalaganas96@gmail.com>
Date: 2024-01-17 15:35:05 -0500
Commit message:

 Update plotting.R

Removed plot print
 
Package: projectR
Commit: 3f37b5342cf17bdd41c4139e8490e918e9c45aa9
Author: rpalaganas <ryanpalaganas96@gmail.com>
Date: 2024-01-17 14:57:18 -0500
Commit message:

 update namespace
 
Package: projectR
Commit: 1188a94e0d05c74f2b88851fa32ef55462fe38b4
Author: rpalaganas <ryanpalaganas96@gmail.com>
Date: 2024-01-17 11:47:57 -0500
Commit message:

 Delete projectR.tex
 
Package: projectR
Commit: 6ea2ca7572d46e7642ea7aab125c9b4812ca4e15
Author: rpalaganas <ryanpalaganas96@gmail.com>
Date: 2024-01-17 11:46:08 -0500
Commit message:

 Build check

Removed cropping and magick from vignette
 
Package: projectR
Commit: 7af3d64fe3ae68738cc921ee57c1a7bc7f8f44f6
Author: rpalaganas <ryanpalaganas96@gmail.com>
Date: 2024-01-17 10:28:53 -0500
Commit message:

 Update projectR.Rmd
 
Package: projectR
Commit: ddf882610c72d43588dfcdc8be24ef7f44b86997
Author: rpalaganas <ryanpalaganas96@gmail.com>
Date: 2024-01-17 10:13:06 -0500
Commit message:

 removed dependencies ggpubr, magick
 
Package: projectR
Commit: 2c5f667cab6121be89fb8427ceaf1a8d645623ec
Author: rpalaganas <ryanpalaganas96@gmail.com>
Date: 2024-01-16 16:52:57 -0500
Commit message:

 vignette update
 
Package: projectR
Commit: 580877f3be8ad8d850e35ba2c5cf1f11c707e2cb
Author: rpalaganas <ryanpalaganas96@gmail.com>
Date: 2024-01-16 16:07:41 -0500
Commit message:

 Update DESCRIPTION
 
Package: projectR
Commit: 3634fa7e47cca1d6de0a39a31b025985a64c69e4
Author: rpalaganas <ryanpalaganas96@gmail.com>
Date: 2024-01-16 15:58:24 -0500
Commit message:

 Update namespace and description
 
Package: projectR
Commit: 0f44c1e4ba7f8b5e9d01f1fc3f3800261adc724a
Author: rpalaganas <ryanpalaganas96@gmail.com>
Date: 2024-01-16 15:35:21 -0500
Commit message:

 Updated man
 
Package: projectR
Commit: d2c36274b19464919a44ed9565d1443ecdb6f8bf
Author: rpalaganas <ryanpalaganas96@gmail.com>
Date: 2024-01-16 15:23:15 -0500
Commit message:

 update vignette

update projectR.html
 
Package: projectR
Commit: 6baf395c8fca8034ab40481c7e3577b3095540b5
Author: rpalaganas <ryanpalaganas96@gmail.com>
Date: 2024-01-16 15:04:15 -0500
Commit message:

 remove rmd

Removed rmd file to check if it is causing build errors
 
Package: projectR
Commit: 6c5bf026d26a7abc23fe6c131a3877459403009a
Author: rpalaganas <ryanpalaganas96@gmail.com>
Date: 2024-01-16 14:45:37 -0500
Commit message:

 Update projectR.Rmd

install specific branch
 
Package: projectR
Commit: 0777b3edd7f761deccafb2613505d48aea043db9
Author: rpalaganas <ryanpalaganas96@gmail.com>
Date: 2024-01-16 14:25:16 -0500
Commit message:

 Update plotting.R

include ggpubr import
 
Package: projectR
Commit: bf5ff9f1190829a36472024014e05c94f4152235
Author: rpalaganas <ryanpalaganas96@gmail.com>
Date: 2024-01-16 14:22:17 -0500
Commit message:

 Update projectR.Rmd

include magick package
 
Package: projectR
Commit: fcbab62dc8536d31615c75cb2274d1b2de3a96a2
Author: rpalaganas <ryanpalaganas96@gmail.com>
Date: 2024-01-16 13:47:42 -0500
Commit message:

 Updated vignette

Updated vignette to reflect updated projectionDriveR function
 
Package: projectR
Commit: 7aaf3ca50e91dafee1fbf8faa11cf9734a1d83f2
Author: rpalaganas <ryanpalaganas96@gmail.com>
Date: 2024-01-16 12:55:14 -0500
Commit message:

 Merge branch 'master' into projectionDriveR
 
Package: projectR
Commit: a38a12c15fd3edc16b97246245fc952baf422f6a
Author: rpalaganas <ryanpalaganas96@gmail.com>
Date: 2024-01-09 15:02:02 -0500
Commit message:

 Updated projectionDriveR function and added volcano plotting function

Updated projectionDriveR function with mode argument, user specifies generation of confidence intervals or pvalues

Updated plotting.R with volcano plotting function

Added tests for updated functions
 
Package: projectR
Commit: 5144edc982651425e7e319eb4550d30730760025
Author: rpalaganas <ryanpalaganas96@gmail.com>
Date: 2023-12-12 14:29:16 -0500
Commit message:

 Updated test_projectR.R and projectionDriveR functions

Added tests for projectionDriveR in test_projectR.R
Removed redundant confidence interval (CI) plotting function from projectionDriveRfun.R
Updated CI plotting function in plotting.R to include weighted vs unweighted CI plots
Removed redundant projectionDriveR function
 
Package: projectR
Commit: 7321f6af1fc27f03df7e67ea8d0180c5592600a6
Author: rpalaganas <ryanpalaganas96@gmail.com>
Date: 2023-12-12 13:48:53 -0500
Commit message:

 Merge branch 'master' into projectionDriveR
 
Package: projectR
Commit: ae55d44415e2aa618e8716e271bea0ae2056b347
Author: rpalaganas <105320146+rpalaganas@users.noreply.github.com>
Date: 2023-11-03 17:05:36 -0400
Commit message:

 moved projectionDriveRfun. location to the R subfolder 
Package: projectR
Commit: 824d3c69d43d7cd6a19947aecd394d60d243701f
Author: Ryan Palaganas <ryanpalaganas@Ryans-MacBook-Pro.local>
Date: 2023-11-03 16:59:13 -0400
Commit message:

 updated projectionDriveR function
 
Package: spoon
Commit: a4ae8270604c41fd1e7f2c0f00bd2b3ba3cd87f6
Author: Kinnary Shah <kinnaryshahh@gmail.com>
Date: 2024-02-21 14:55:13 -0500
Commit message:

 update version
 
Package: spoon
Commit: 5d43326dde90cd1882b3a79cad723a675139f949
Author: Kinnary Shah <kinnaryshahh@gmail.com>
Date: 2024-02-21 14:50:40 -0500
Commit message:

 update dependency
 
Package: gypsum
Commit: 7cc9f362a7b5d7cfea87e314a0478f14b7619a31
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2024-02-21 10:28:02 -0800
Commit message:

 Minor roxygenation, bumped version and date.
 
Package: gypsum
Commit: 990c8496c4ae8cb7eb5848d10e2cf7b75dbb323d
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2024-02-21 10:26:48 -0800
Commit message:

 Support link resolution in saveFile when precheck=TRUE.

It's too inconvenient for downstream users to handle it themselves,
given that they'd have to know about the ..links files.
 
Package: timeOmics
Commit: a5022a406bd9f73e37643b205629d99c1cd7168a
Author: AntoineB <bodein.antoine@gmail.com>
Date: 2024-02-21 13:30:17 -0500
Commit message:

 fix summary.getCluster examples
 
Package: CytoMethIC
Commit: 58e665ba6a17c652c6404b728bc234194c3fe2a9
Author: Jacob Fanale <jakefanale@gmail.com>
Date: 2024-02-21 13:13:25 -0500
Commit message:

 bump version number
 
Package: CytoMethIC
Commit: 3824eaf9c20815bf248af4396e7d6f48d9cce330
Author: Jacob Fanale <jakefanale@gmail.com>
Date: 2024-02-21 13:12:12 -0500
Commit message:

 Update Vignette
 
Package: CytoMethIC
Commit: 4496d8b207f25fe5a42275dd2d123d598a4c4706
Author: Wanding Zhou <zhouwanding@gmail.com>
Date: 2024-01-14 16:45:59 -0500
Commit message:

 minor, message omitted
 
Package: CytoMethIC
Commit: 0e80f375fdbf094a2bf566005b3576e83409c48b
Author: Wanding Zhou <zhouwanding@gmail.com>
Date: 2024-01-14 16:01:48 -0500
Commit message:

 minor, message omitted
 
Package: CytoMethIC
Commit: e07b5d2f2652d6388cf85d125ae581405df7046f
Author: Wanding Zhou <zhouwanding@gmail.com>
Date: 2024-01-14 15:54:09 -0500
Commit message:

 bump to 0.99.11
 
Package: CytoMethIC
Commit: 79cda4612951a51f4eb8b498b01534bb8f48ee31
Author: Wanding Zhou <zhouwanding@gmail.com>
Date: 2024-01-14 11:44:29 -0500
Commit message:

 added infer ethnicity
 
Package: MungeSumstats
Commit: a46a8fd2174d67640cd72dfec248e70e32569760
Author: Al-Murphy <alanmurph94@hotmail.com>
Date: 2024-02-21 17:59:56 +0000
Commit message:

 longtests upstream
 
Package: MungeSumstats
Commit: 83e5315f8caebfd2776913e4915d86f4d4b64595
Author: Al-Murphy <alanmurph94@hotmail.com>
Date: 2024-02-21 17:57:39 +0000
Commit message:

 longtests + bug fixes
 
Package: PharmacoGx
Commit: 650d0e533636b959e0c3dffa43d2b6d4f99b0cb8
Author: Jermiah <jermiahjoseph98@gmail.com>
Date: 2024-02-21 17:12:12 +0000
Commit message:

 Update cellline parameter in drugDoseResponseCurve function
 
Package: scRNAseqApp
Commit: a117853879bafbbd590c083e76c868d2673c1f2d
Author: JIANHONG OU <jianhong@users.noreply.github.com>
Date: 2024-02-21 10:55:42 -0500
Commit message:

 use withCallingHandlers to replace tryCatch.
 
Package: scRNAseqApp
Commit: 9896f4aa978b30e89a693c90ca171136cf0f3ad3
Author: JIANHONG OU <jianhong@users.noreply.github.com>
Date: 2024-02-21 10:47:26 -0500
Commit message:

 Add Wilcoxon test for violin plot
 
Package: UCell
Commit: 9169c3d190c7783cdcd873ef121717812302a46a
Author: Massimo Andreatta <massimo.andreatta@unil.ch>
Date: 2024-02-21 16:08:44 +0100
Commit message:

 Smaller test dataset; change default for chunk.size=100
 
Package: autonomics
Commit: de60ed5a1a5cfc4cea991ea7b879cd500a7066ae
Author: Aditya Bhagwat <aditya.bhagwat@uni-marburg.de>
Date: 2024-02-21 16:09:08 +0100
Commit message:

 Fix earlier commit
 
Package: autonomics
Commit: 3827f052a103570af521d806431f3d21829be897
Author: Aditya Bhagwat <aditya.bhagwat@uni-marburg.de>
Date: 2024-02-21 15:46:50 +0100
Commit message:

 Rewrite annotate_maxquant
 
Package: autonomics
Commit: fcb798ab6a9c9aae1376c7b694de23f986596496
Author: Aditya Bhagwat <aditya.bhagwat@uni-marburg.de>
Date: 2024-02-06 11:35:46 +0100
Commit message:

 3.2_read_proteingroups : `annotate_maxquantdt` unifies curate_annotate_(maxquant|fastafile) and fixes (mixed fwd rev proteingroups)
 
Package: MsQuality
Commit: 6078c89010e4707983bc7ba687360b7fb3c54c1c
Author: Thomas Naake <thomasnaake@googlemail.com>
Date: 2024-02-21 15:39:39 +0100
Commit message:

 version bump to 1.3.2 in devel
 
Package: MsQuality
Commit: edec868d352233e5fcb850ffa6180c155ec0d845
Author: Thomas Naake <thomasnaake@googlemail.com>
Date: 2024-02-21 15:38:41 +0100
Commit message:

 bug fix: MS:40000155 in specification file added, adjust tests
 
Package: MsQuality
Commit: 81d71566721f40e7c16ff46406369c65e657ffcf
Author: Thomas Naake <thomasnaake@googlemail.com>
Date: 2024-02-21 15:33:01 +0100
Commit message:

 Revert "bug fix: MS:40000155 in specification file added, adjust tests"

This reverts commit 85214ec06bbb539eb6288317a28d4fec3af2d38c.
 
Package: MsQuality
Commit: 85214ec06bbb539eb6288317a28d4fec3af2d38c
Author: Thomas Naake <thomasnaake@googlemail.com>
Date: 2024-02-21 15:30:46 +0100
Commit message:

 bug fix: MS:40000155 in specification file added, adjust tests
 
Package: tximeta
Commit: b73d868a07386ca6d2784032f17be4bff4160e2c
Author: Mike Love <mikelove@users.noreply.github.com>
Date: 2024-02-21 09:18:57 -0500
Commit message:

 changing docs to say digest
 
Package: CytoPipelineGUI
Commit: 88807746d51c2c8d79a649a04f3c289c751284b3
Author: phauchamps <philippehauchamps@hotmail.com>
Date: 2024-02-21 09:58:28 +0100
Commit message:

 - added CITATION file
- bumped version to 1.1.2
 
Package: CytoPipeline
Commit: 8a8681b488c9de7958bc74326480b91f5cfeb7dd
Author: phauchamps <philippehauchamps@hotmail.com>
Date: 2024-02-21 10:05:05 +0100
Commit message:

 removed 'é' from CITATION file
 
Package: CytoPipeline
Commit: 9a75cee2ad44fae31eee3ec2cad0c82e8de6427e
Author: phauchamps <philippehauchamps@hotmail.com>
Date: 2024-02-21 09:51:29 +0100
Commit message:

 - added CITATION file
- bumped version to 1.3.5
 
Package: QTLExperiment
Commit: d5649298696952b5f67d363586e435f5b1ae5bad
Author: dunstone-a <amelia.dunstone@gmail.com>
Date: 2024-02-21 18:50:35 +1100
Commit message:

 Update Roxygen to 7.2.3
 
Package: QTLExperiment
Commit: a490120b5784a5eee355a71fb452bfb634f2a825
Author: dunstone-a <amelia.dunstone@gmail.com>
Date: 2024-02-21 18:50:22 +1100
Commit message:

 Small changes and index fixes
 
Package: gypsum
Commit: 160a545dcf2144b5eeb73bacbf4f3538877b17e6
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2024-02-20 22:36:49 -0800
Commit message:

 Bumped version with another link in the description.
 
Package: gypsum
Commit: 568e5057aa98db1f5990cf7d9a45b25903ef05e7
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2024-02-20 22:33:40 -0800
Commit message:

 Updated the metadata fetchers to the new URL.

Also just include the file extension in the name for simplicity.
 
Package: gypsum
Commit: 160a545dcf2144b5eeb73bacbf4f3538877b17e6
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2024-02-20 22:36:49 -0800
Commit message:

 Bumped version with another link in the description.
 
Package: gypsum
Commit: 568e5057aa98db1f5990cf7d9a45b25903ef05e7
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2024-02-20 22:33:40 -0800
Commit message:

 Updated the metadata fetchers to the new URL.

Also just include the file extension in the name for simplicity.
 
Package: EasyCellType
Commit: d3c15ac57f42518f0609e1cf4d748942b67473d8
Author: Li <RLi8@mdanderson.org>
Date: 2024-02-20 23:57:55 -0600
Commit message:

 Added biocstyle
 
Package: GenomicPlot
Commit: 03356a8a4134429972376396276641df16da4915
Author: Shuye Pu <shuye2009@gmail.com>
Date: 2024-02-20 21:23:55 -0500
Commit message:

 update extdata
 
Package: GenomicPlot
Commit: 9aac8e770f6e9c782dfcb56d2292fad3e078c383
Author: Shuye Pu <shuye2009@gmail.com>
Date: 2024-02-20 19:45:33 -0500
Commit message:

 add functions set_seqinfo and custom_TxDb_from_GTF to enforce same seqlevels between input GRanges and txdb
 
Package: tidyomics
Commit: bf1f508e693839c464487af97c0a80a5200dc184
Author: william-hutchison <william.8191@fastmail.com>
Date: 2024-02-21 10:56:42 +1100
Commit message:

 Merge pull request #15 from tidyomics/improve-documentation

Improve documentation 
Package: tidyomics
Commit: fb82ab3413f6bfb38efe0f07868523c9a9d58c2a
Author: william-hutchison <william.8191@fastmail.com>
Date: 2024-02-21 10:54:23 +1100
Commit message:

 Version up 
Package: tidyomics
Commit: cbc07de281caa8af9fb6caf64c4b6d86a98873c1
Author: william-hutchison <william.8191@fastmail.com>
Date: 2024-02-21 10:54:06 +1100
Commit message:

 Fix typo 
Package: tidyomics
Commit: 737679ce1953b1b02989122d4ad901c99568aed6
Author: william-hutchison <william.8191@fastmail.com>
Date: 2024-02-21 10:53:31 +1100
Commit message:

 Version up 
Package: tidyomics
Commit: f11c98ac2352ba103d7ae0ab637a4e464816f308
Author: william-hutchison <william.8191@fastmail.com>
Date: 2024-02-21 10:53:19 +1100
Commit message:

 Remove BiocManager import 
Package: tidyomics
Commit: 57cdafdfadc98500a49084781c0abec60e37802e
Author: William Hutchison <william.8191@fastmail.com>
Date: 2024-02-20 16:29:21 +1100
Commit message:

 Version up
 
Package: tidyomics
Commit: a0214d1c34d81412cf3e5c2975fd5693f0afe94c
Author: William Hutchison <william.8191@fastmail.com>
Date: 2024-02-20 16:28:50 +1100
Commit message:

 Remove BiocManager import
 
Package: tidyomics
Commit: 1e11b6444fa9e3a0fcad205a291755053cf5679d
Author: William Hutchison <william.8191@fastmail.com>
Date: 2024-02-20 16:09:58 +1100
Commit message:

 Version up
 
Package: tidyomics
Commit: 9a3606fc850a674b763b27fbeebb21f7273d9c1e
Author: William Hutchison <william.8191@fastmail.com>
Date: 2024-02-20 16:08:53 +1100
Commit message:

 Update README and vignette
 
Package: tidyomics
Commit: bee20665bf1753141664c793c4dfe48cc35bced1
Author: William Hutchison <william.8191@fastmail.com>
Date: 2024-02-20 16:08:25 +1100
Commit message:

 Update function documentation
 
Package: tidyomics
Commit: b218995580a58628a071002bfc65562650c35b9b
Author: William Hutchison <william.8191@fastmail.com>
Date: 2024-02-20 14:52:59 +1100
Commit message:

 Add man page for package name
 
Package: pathlinkR
Commit: 5b52fd54851ef60b9654ed30b012c59f0e30a707
Author: Travis <travis.m.blimkie@gmail.com>
Date: 2024-02-20 10:12:06 -0800
Commit message:

 Merge pull request #11 from hancockinformatics/devel

Merg Devel 0.99.382 
Package: pathlinkR
Commit: 906e7466759a5fee6036256a01f9e68fd6d45109
Author: Travis Blimkie <travis.m.blimkie@gmail.com>
Date: 2024-02-16 14:22:12 -0800
Commit message:

 Edits to vignette to reduce build time a bit.
 
Package: pathlinkR
Commit: a4880c4f9ff11d4b00aefc14fb79d12ed85a221d
Author: Travis Blimkie <travis.m.blimkie@gmail.com>
Date: 2024-02-16 14:21:57 -0800
Commit message:

 Removed messages from ppiExtractSubnetwork and tweaked tests.
 
Package: pathlinkR
Commit: 98ca00b0072b6a870fe3dbd9078650980acef326
Author: Travis Blimkie <travis.m.blimkie@gmail.com>
Date: 2024-02-16 14:20:57 -0800
Commit message:

 Tweaked examples to reduce time.
 
Package: pathlinkR
Commit: 354c317510cd8db09d8a7ec67e3d6e86f3b0dcaf
Author: Travis Blimkie <travis.m.blimkie@gmail.com>
Date: 2024-02-16 13:55:38 -0800
Commit message:

 Updated or fixed tests where need to improve timings.
 
Package: pathlinkR
Commit: 64f2bc5e5ab9c7fef464ab1734efd3dca124e7d7
Author: Travis Blimkie <travis.m.blimkie@gmail.com>
Date: 2024-02-16 13:55:22 -0800
Commit message:

 Fixed igraph functions that had been deprecated.
 
Package: pathlinkR
Commit: b074b46d93b646a473e80beb975ec82a8485f908
Author: Travis Blimkie <travis.m.blimkie@gmail.com>
Date: 2024-02-16 13:17:16 -0800
Commit message:

 Removed Steiner method from network trimming since the package is no longer available at CRAN.
 
Package: pathlinkR
Commit: 36ddae2c02acbd690c275ef992290934ede54365
Author: Travis Blimkie <travis.m.blimkie@gmail.com>
Date: 2024-02-13 15:57:00 -0800
Commit message:

 Fixed some typos, trying to reduce check time.
 
Package: tidySpatialExperiment
Commit: 3395271d42d8ca105ee7d07985f82fed349b88c0
Author: william-hutchison <william.8191@fastmail.com>
Date: 2024-02-21 10:01:37 +1100
Commit message:

 Merge pull request #26 from william-hutchison/update-documentation

Update documentation 
Package: tidySpatialExperiment
Commit: 4b2e790bd06cb1bb8cf47fb3a6cd1a6814d846fd
Author: William Hutchison <william.8191@fastmail.com>
Date: 2024-02-21 09:42:22 +1100
Commit message:

 Version up
 
Package: tidySpatialExperiment
Commit: d154a349d25e9eff5e97ae40322e3cc637fa0c93
Author: William Hutchison <william.8191@fastmail.com>
Date: 2024-02-21 09:41:54 +1100
Commit message:

 Update NEWS
 
Package: tidySpatialExperiment
Commit: 1942e75096f32091067769063ccc569c84dae5de
Author: William Hutchison <william.8191@fastmail.com>
Date: 2024-02-21 09:40:35 +1100
Commit message:

 Add Bioconductor installation instructions
 
Package: bugsigdbr
Commit: ba3bc9c03ac81a9654952573e8c3546a2b11912c
Author: J Wokaty <jwokaty@users.noreply.github.com>
Date: 2024-02-20 17:02:07 -0500
Commit message:

 Bump version to 1.9.4
 
Package: bugsigdbr
Commit: a8821ec0ecf3c9a3d75dccd24dd3082c85ba4153
Author: J Wokaty <jwokaty@users.noreply.github.com>
Date: 2024-02-20 17:01:24 -0500
Commit message:

 Update man for importBugSigDB
 
Package: scRNAseqApp
Commit: 839bbd8054d95e214f1e35280532d51d334840b3
Author: JIANHONG OU <jianhong@users.noreply.github.com>
Date: 2024-02-20 16:53:59 -0500
Commit message:

 change dcast to dcast.data.table.
 
Package: scRNAseqApp
Commit: b3bf95cfc8b9928fe8b5c20be7db299a47038bb8
Author: JIANHONG OU <jianhong@users.noreply.github.com>
Date: 2024-02-20 16:51:00 -0500
Commit message:

 Add Chisq test for proportion
 
Package: bugsigdbr
Commit: 64c5a592824c4a4a38741964cae3ec3ba601e8fa
Author: J Wokaty <jwokaty@users.noreply.github.com>
Date: 2024-02-20 16:37:44 -0500
Commit message:

 Bump version to 1.9.3
 
Package: bugsigdbr
Commit: fa11ee829effaa506694df4d256ba413aefc46e5
Author: J Wokaty <jwokaty@users.noreply.github.com>
Date: 2024-02-20 16:27:04 -0500
Commit message:

 Add all Zenodo releases to documentation
 
Package: bugsigdbr
Commit: 944f6c81aee3e718f85e6c363a26d38058d1729a
Author: J Wokaty <jwokaty@users.noreply.github.com>
Date: 2024-02-07 09:57:17 -0500
Commit message:

 Update github action
 
Package: MouseAgingData
Commit: ccdac1cd6b0b5688640abefa8790c76460c98641
Author: tram-nguyen-n <tram_nguyen@hms.harvard.edu>
Date: 2024-02-20 20:46:33 +0000
Commit message:

 bumped version
 
Package: MouseAgingData
Commit: 21c57de5665f831c707a0011a3bbff6b34ef834f
Author: tram-nguyen-n <tram_nguyen@hms.harvard.edu>
Date: 2024-02-20 20:40:12 +0000
Commit message:

 typo
 
Package: MouseAgingData
Commit: 0d6a7de13864e720b40c604f5b1a8bc5cf728a92
Author: tram-nguyen-n <tram_nguyen@hms.harvard.edu>
Date: 2024-02-20 20:38:10 +0000
Commit message:

 fixed bug in authors
 
Package: MouseAgingData
Commit: 8bfc66ee49a830c93b33b0674594285f917f767b
Author: tram-nguyen-n <tram_nguyen@hms.harvard.edu>
Date: 2024-02-20 20:33:23 +0000
Commit message:

 added man back
 
Package: MouseAgingData
Commit: 96def8954e63eab0d0efa3587ece1cfc6be6548d
Author: tram-nguyen-n <tram_nguyen@hms.harvard.edu>
Date: 2024-02-20 20:32:23 +0000
Commit message:

 X to x
 
Package: MouseAgingData
Commit: c68791dc5e1634e16cb06c3cf24c2564c06b016c
Author: tram-nguyen-n <tram_nguyen@hms.harvard.edu>
Date: 2024-02-20 20:30:14 +0000
Commit message:

 deleted from github

Merge remote-tracking branch 'origin/devel' into devel

# Conflicts:
#	R/parabiosis10X.R
 
Package: MouseAgingData
Commit: c50b4be9a3a85055e97ab3b94ee9fa2fa64dcb3a
Author: tram-nguyen-n <tram_nguyen@hms.harvard.edu>
Date: 2024-02-20 20:28:58 +0000
Commit message:

 10X to 10x
 
Package: MouseAgingData
Commit: 24302003c611dba6493aea365787a9f6dd6ca006
Author: Tram Nguyen <150388074+tram-nguyen-n@users.noreply.github.com>
Date: 2024-02-20 15:25:56 -0500
Commit message:

 Delete R/parabiosis10X.R 
Package: MouseAgingData
Commit: aac23241afa14b51d52322dda972b36317da4d33
Author: tram-nguyen-n <tram_nguyen@hms.harvard.edu>
Date: 2024-02-20 20:25:29 +0000
Commit message:

 deleted parabiosis10X
 
Package: MouseAgingData
Commit: e7c04f920622137f8d654084ca4d8eedc526c558
Author: tram-nguyen-n <tram_nguyen@hms.harvard.edu>
Date: 2024-02-20 20:19:45 +0000
Commit message:

 match author to description
 
Package: MouseAgingData
Commit: f0197e5bb0dc457e3e6c26149e1f74497b0d9ff4
Author: tram-nguyen-n <tram_nguyen@hms.harvard.edu>
Date: 2024-02-20 20:17:03 +0000
Commit message:

 bumped version
 
Package: MouseAgingData
Commit: f7045848e15fed57663d628c16bf4ecf82e3006e
Author: tram-nguyen-n <tram_nguyen@hms.harvard.edu>
Date: 2024-02-20 20:16:45 +0000
Commit message:

 added collaborators
 
Package: BiocCheck
Commit: 122fb4dc171eb35e4ac61d0e4fc6083123e71a2c
Author: LiNk-NY <marcel.ramos@roswellpark.org>
Date: 2024-02-20 10:45:55 -0500
Commit message:

 version bump 1.39.26
 
Package: BiocCheck
Commit: 1418257ccd821bde27c243cf20edd53ca747260b
Author: LiNk-NY <marcel.ramos@roswellpark.org>
Date: 2024-02-20 10:45:52 -0500
Commit message:

 fix typo closes #210
 
Package: gDRimport
Commit: f400c97d44f7f4de80aace094ef2722c49ae1918
Author: Arek Gladki <41166437+gladkia@users.noreply.github.com>
Date: 2024-02-20 14:57:43 +0100
Commit message:

 Merge pull request #77 from gdrplatform/GDR-2371

Gdr 2371 
Package: gDRimport
Commit: 490eb563914c61023c902389f06f96a188d820f9
Author: Arkadiusz Gladki <arkadiusz.gladki@contractors.roche.com>
Date: 2024-02-19 10:30:57 +0100
Commit message:

 build: update notes
 
Package: gDRimport
Commit: 0c827cd52a1ca2fb40a8a404ea4f2de7b57b3186
Author: Arkadiusz Gladki <arkadiusz.gladki@contractors.roche.com>
Date: 2024-02-16 12:52:49 +0100
Commit message:

 build: trigger build
 
Package: gDRimport
Commit: 9bf176d5ab82e0625a0682dd7d1326ba2fa5c06c
Author: Arkadiusz Gladki <arkadiusz.gladki@contractors.roche.com>
Date: 2024-02-15 14:11:51 +0100
Commit message:

 chore: bump versions of dependencies
 
Package: gDRimport
Commit: 7802518b579950feb6f5a8063fb3e5a58ed9c1ee
Author: Arkadiusz Gladki <arkadiusz.gladki@contractors.roche.com>
Date: 2024-02-15 09:38:46 +0100
Commit message:

 doc: switch to Roxygen 7.3.0
 
Package: gDRimport
Commit: eec10eafbe19c3c4fafceb9bf0155a6ffde880df
Author: Arkadiusz Gladki <arkadiusz.gladki@contractors.roche.com>
Date: 2024-02-15 09:33:09 +0100
Commit message:

 build: update requirements for deps
 
Package: gDRimport
Commit: 7597cc459374d6e5a15a2d7c5b5a3184b7c1b098
Author: Arkadiusz Gladki <arkadiusz.gladki@contractors.roche.com>
Date: 2024-02-14 13:29:44 +0100
Commit message:

 doc: trim data in the vignette
 
Package: gDRimport
Commit: 3d2b6bc06fe1950d982caeb58d7e0f5d0bd8e173
Author: Arkadiusz Gladki <arkadiusz.gladki@contractors.roche.com>
Date: 2024-02-14 13:28:06 +0100
Commit message:

 build: fix  dependencies YAML
 
Package: gDRimport
Commit: b56920a8cd91cd2251b7e8579ed973d9c842baa7
Author: Arkadiusz Gladki <arkadiusz.gladki@contractors.roche.com>
Date: 2024-02-14 12:55:50 +0100
Commit message:

 build: clean-up/add info (GHA pkgdown.yaml)
 
Package: gDRimport
Commit: a5abfcc5ea23031616de8696607b481b455691d7
Author: Arkadiusz Gladki <arkadiusz.gladki@contractors.roche.com>
Date: 2024-02-14 10:55:17 +0100
Commit message:

 chore: bump v+c
 
Package: gDRimport
Commit: fa928d024c6bbed67bae870d484105a0191e5436
Author: Arkadiusz Gladki <arkadiusz.gladki@contractors.roche.com>
Date: 2024-02-14 10:55:03 +0100
Commit message:

 build: update Dockerfile
 
Package: gDRimport
Commit: 334cebaad3b65d055c9b4bcb219201871e75ee8c
Author: Arkadiusz Gladki <arkadiusz.gladki@contractors.roche.com>
Date: 2024-02-14 10:54:49 +0100
Commit message:

 build: add pkgdown GHA pipeline
 
Package: gDRimport
Commit: 6aca33ee443a4233f3239e1443d3d110ed41c17c
Author: Arkadiusz Gladki <arkadiusz.gladki@contractors.roche.com>
Date: 2024-02-14 10:54:28 +0100
Commit message:

 chore: update ignore rules
 
Package: gDR
Commit: 2204e9859fecea613e71c7009fdef9d76841ad0a
Author: Arek Gladki <41166437+gladkia@users.noreply.github.com>
Date: 2024-02-20 14:54:33 +0100
Commit message:

 Merge pull request #47 from gdrplatform/GDR-2371

Gdr 2371 
Package: gDR
Commit: 043df27f2c54ebe42c7b3074abe63e5671eec190
Author: Arkadiusz Gladki <arkadiusz.gladki@contractors.roche.com>
Date: 2024-02-16 12:54:10 +0100
Commit message:

 build: trigger build
 
Package: gDR
Commit: 76e35d0af8b25940d288ad90cd20acfcc6976c04
Author: Arkadiusz Gladki <arkadiusz.gladki@contractors.roche.com>
Date: 2024-02-15 14:18:56 +0100
Commit message:

 doc: update reqs
 
Package: gDR
Commit: 8bc34aa75ccd4adafe5bb881a0297e923bd526f5
Author: Arkadiusz Gladki <arkadiusz.gladki@contractors.roche.com>
Date: 2024-02-15 14:05:19 +0100
Commit message:

 doc: update README.md
 
Package: gDR
Commit: 53337d3faf4ca7847ca6088794d9c12500d04d1d
Author: Arkadiusz Gladki <arkadiusz.gladki@contractors.roche.com>
Date: 2024-02-15 13:48:20 +0100
Commit message:

 doc: update README
 
Package: gDR
Commit: bcb52f55984eab549263fe99b19ddfac82afe8dc
Author: Arkadiusz Gladki <arkadiusz.gladki@contractors.roche.com>
Date: 2024-02-15 13:41:58 +0100
Commit message:

 doc: add overview diagram
 
Package: gDR
Commit: 4ae37796e65e0f9b9d621636d9322b255c1110d8
Author: Arkadiusz Gladki <arkadiusz.gladki@contractors.roche.com>
Date: 2024-02-15 09:59:41 +0100
Commit message:

 doc: update docs
 
Package: gDR
Commit: 7d3f1550efb2ab4c9267f78b12c82bc7320e85d1
Author: Arek Gladki <41166437+gladkia@users.noreply.github.com>
Date: 2024-02-15 09:58:01 +0100
Commit message:

 Update _pkgdown.yml

Co-authored-by: j-smola <31825957+j-smola@users.noreply.github.com> 
Package: gDR
Commit: 5baacdf6c8b7f650041fe0b175e4803ccb6a3f9d
Author: Arkadiusz Gladki <arkadiusz.gladki@contractors.roche.com>
Date: 2024-02-14 15:11:23 +0100
Commit message:

 chore: update .Rbuildignore
 
Package: gDR
Commit: 646f6c299723445c37d6644a165aa7a980c68cc0
Author: Arkadiusz Gladki <arkadiusz.gladki@contractors.roche.com>
Date: 2024-02-14 14:32:04 +0100
Commit message:

 chore: bump v+c
 
Package: gDR
Commit: f949ea13fbccaa7cd023062a2dcc8cae43b8c7f3
Author: Arkadiusz Gladki <arkadiusz.gladki@contractors.roche.com>
Date: 2024-02-14 14:30:32 +0100
Commit message:

 build: update Docker build scenario
 
Package: gDR
Commit: 8c4a647963847d8db9acea2dba42432373f712f7
Author: Arkadiusz Gladki <arkadiusz.gladki@contractors.roche.com>
Date: 2024-02-14 14:30:12 +0100
Commit message:

 build: add GHA pipeline (pkgdown)
 
Package: gDR
Commit: 4023a98f6c71c92e790fa2ef6d01bd82232bc5af
Author: Arkadiusz Gladki <arkadiusz.gladki@contractors.roche.com>
Date: 2024-02-14 14:29:50 +0100
Commit message:

 chore: update ingore rules
 
Package: gDNAx
Commit: 137bca9c2c06eb3b047f8e66c87a468b6e335ef2
Author: Robert Castelo <robert.castelo@upf.edu>
Date: 2024-02-20 14:52:25 +0100
Commit message:

 Bumped version
 
Package: gDNAx
Commit: 81bc28a8fcbaea6296ee20076264853784e9aeb4
Author: Robert Castelo <robert.castelo@upf.edu>
Date: 2024-02-20 14:49:54 +0100
Commit message:

 Prompt an error when a 0-byte BAM file is passed as an argument
 
Package: decoupleR
Commit: 87fe87ef62a4a45402dd89a51d5959edd451bec0
Author: PauBadiaM <paubadiamompel@gmail.com>
Date: 2024-02-20 11:20:01 +0100
Commit message:

 CHanged github CI
 
Package: decoupleR
Commit: b7fc46f4a7a3e95465025cb6a41fece925d24141
Author: PauBadiaM <paubadiamompel@gmail.com>
Date: 2024-02-20 11:00:16 +0100
Commit message:

 Fixed progeny vignette bug
 
Package: decoupleR
Commit: 576cf86cc559ba76abf24a8b4cf57f35ce6f06a9
Author: PauBadiaM <paubadiamompel@gmail.com>
Date: 2024-01-16 16:51:21 +0100
Commit message:

 Updated docs
 
Package: CellBarcode
Commit: 5bccf2598ec7e59a76652b2a80f5ecfeee9336bf
Author: Wenjie Sun <wenjie1991@users.noreply.github.com>
Date: 2024-02-20 09:38:59 +0100
Commit message:

 [doc] Update documents
 
Package: CellBarcode
Commit: f34c0ec0662cf9e5421bce8e42bb4aa274be90fe
Author: Wenjie Sun <wenjie1991@users.noreply.github.com>
Date: 2024-02-20 09:36:44 +0100
Commit message:

 [doc] Update README file
 
Package: CellBarcode
Commit: 8cf0c4acf90f86897d889c261e1242f87876c996
Author: wenjie1991 <sunwjie@gmail.com>
Date: 2024-02-20 00:52:47 +0100
Commit message:

 [doc] add pkgdown link
 
Package: CellBarcode
Commit: d4d51f7c0e29c115b339ecc8433d54b98e72cce4
Author: wenjie1991 <sunwjie@gmail.com>
Date: 2024-02-20 00:45:24 +0100
Commit message:

 [misc] fix check doc error
 
Package: CellBarcode
Commit: fac88f34eda954890db608f9c1b08e7809858db2
Author: wenjie1991 <sunwjie@gmail.com>
Date: 2024-02-20 00:36:28 +0100
Commit message:

 [misc] Fix check error
 
Package: CellBarcode
Commit: 24504ea9a91db6a7800cafb5e35840f19969850b
Author: wenjie1991 <sunwjie@gmail.com>
Date: 2024-02-19 23:59:56 +0100
Commit message:

 [misc] fix check errors
 
Package: CellBarcode
Commit: 5188a1efc7ba00b78aa91b80dc706479c5ba8ff4
Author: wenjie1991 <sunwjie@gmail.com>
Date: 2024-02-19 23:44:39 +0100
Commit message:

 Merge branch 'devel' of github.com:wenjie1991/CellBarcode into devel
 
Package: CellBarcode
Commit: 99af8f4035298b39563aaee8711c066cc064a43a
Author: wenjie1991 <sunwjie@gmail.com>
Date: 2024-02-19 23:42:55 +0100
Commit message:

 [doc] update scSeq vignettes
 
Package: CellBarcode
Commit: 86fd4c2a22299b5a64ea79fd7604f9e16839310f
Author: wenjie1991 <sunwjie@gmail.com>
Date: 2024-02-19 23:31:42 +0100
Commit message:

 Add citation
 
Package: DegCre
Commit: 73e91599444a939c8044bcadc74489e446e3bfbb
Author: Brian Roberts <brianroberts1976@yahoo.com>
Date: 2024-02-19 17:23:27 -0600
Commit message:

 Fixed one more href
 
Package: DegCre
Commit: 6c1f17a6aa360cbd912369ceb05a17513e9851d4
Author: Brian Roberts <brianroberts1976@yahoo.com>
Date: 2024-02-19 17:04:30 -0600
Commit message:

 Fixed hrefs and R patch level in DESCRIPTION
 
Package: DegCre
Commit: 0fed590980d0029d59c5234b03f69f53bbbb3015
Author: Brian Roberts <brianroberts1976@yahoo.com>
Date: 2024-02-19 16:16:28 -0600
Commit message:

 Fixed runDegCre example
 
Package: DegCre
Commit: b89e13f52ba4572523e65bbd06a3f30373089255
Author: Brian Roberts <brianroberts1976@yahoo.com>
Date: 2024-02-19 15:47:18 -0600
Commit message:

 Changed test funs to subset GRs without which. Removed internal library(GenomicRanges) calls.
 
Package: ternarynet
Commit: e5c6079b1c4f84085acbcd71a73991167dc0c1d7
Author: mccallm <mccallm@gmail.com>
Date: 2024-02-19 15:32:42 -0500
Commit message:

 Version bump in DESCRIPTION
 
Package: gypsum
Commit: 323cdf5eb73e6250e465d8a37851eadc885a2031
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2024-02-19 10:46:23 -0800
Commit message:

 Elaborated on description for BiocCheck.
 
Package: gypsum
Commit: 240b531304d64594ab071b68f5c2c61a0295d5d4
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2024-02-15 08:32:53 -0800
Commit message:

 Updated the vignette with new calls, improved wording.
 
Package: gypsum
Commit: 7a69896e8a5f9d36fa26da2a948f7ad0e90f6fd3
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2024-02-14 17:21:12 -0800
Commit message:

 Added explicit tests for listFiles, remove* functions.
 
Package: gypsum
Commit: 323cdf5eb73e6250e465d8a37851eadc885a2031
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2024-02-19 10:46:23 -0800
Commit message:

 Elaborated on description for BiocCheck.
 
Package: DegCre
Commit: 14c1c9f1274e8326586f457ff25fa7e164d29605
Author: Brian Roberts <brianroberts1976@yahoo.com>
Date: 2024-02-19 11:37:33 -0600
Commit message:

 Fixed runnable examples to load GenomicRanges.
 
Package: POMA
Commit: dc99f5271408cab564939ab9d65dedb9b4ca22f8
Author: pcastellanoescuder <polcaes@gmail.com>
Date: 2024-02-19 09:04:44 -0600
Commit message:

 update R-CMD-Check workflow 5
 
Package: gDRcore
Commit: 3abbcdaedddd69c78111ac1dc096aafa094713a4
Author: Arkadiusz Gladki <arkadiusz.gladki@contractors.roche.com>
Date: 2024-02-19 15:23:32 +0100
Commit message:

 Merge branch 'master' into devel
 
Package: gDRcore
Commit: fdfb3fb198c2e64258fa755c8887a505d46399aa
Author: Bartek <32614650+bczech@users.noreply.github.com>
Date: 2024-02-16 08:09:14 +0100
Commit message:

 Merge pull request #137 from gdrplatform/GDR-2416

Gdr 2416 
Package: gDRcore
Commit: 2424dd40cbbe324947ce8ad8e868164b44bedfd1
Author: czechb3 <bartosz.w.czech@gmail.com>
Date: 2024-02-14 13:57:20 +0100
Commit message:

 ci: resolve conflict
 
Package: gDRcore
Commit: c8a362139c7b019598f7935cea65de3bd01a2b39
Author: Arek Gladki <41166437+gladkia@users.noreply.github.com>
Date: 2024-02-14 13:52:19 +0100
Commit message:

 Merge pull request #138 from gdrplatform/GDR-2371

Gdr 2371 
Package: gDRcore
Commit: 44c91a34f358e9c154809e82a6498e616ec4eb24
Author: czechb3 <bartosz.w.czech@gmail.com>
Date: 2024-02-14 12:58:19 +0100
Commit message:

 refactor: appease lintr
 
Package: gDRcore
Commit: 752fbe75d8451a4de22e565b86e2b918e8a9afba
Author: Arkadiusz Gladki <arkadiusz.gladki@contractors.roche.com>
Date: 2024-02-14 12:54:30 +0100
Commit message:

 build: clean-up/add info (GHA pkgdown.yaml)
 
Package: gDRcore
Commit: 4f6c5146105cce2ae1dedde1faab2ca55ce8798e
Author: czechb3 <bartosz.w.czech@gmail.com>
Date: 2024-02-14 12:30:55 +0100
Commit message:

 refactor: remove hardcoded vars
 
Package: gDRcore
Commit: 6678b23c43481b63448ec06939c1bc98fbc16b79
Author: czechb3 <bartosz.w.czech@gmail.com>
Date: 2024-02-14 12:29:35 +0100
Commit message:

 refactor: simplify logic and remove duplicates
 
Package: gDRcore
Commit: 24ea3a25902feed638f7db097e7651b0b608149b
Author: Arkadiusz Gladki <arkadiusz.gladki@contractors.roche.com>
Date: 2024-02-14 11:55:27 +0100
Commit message:

 chore: replace 'gdr_matches' with  'grr_matches'
 
Package: gDRcore
Commit: 2039b0e3f6e8b083a47416dbb65feed97c16eb02
Author: Arkadiusz Gladki <arkadiusz.gladki@contractors.roche.com>
Date: 2024-02-14 09:56:14 +0100
Commit message:

 chore: remove obsolete line
 
Package: gDRcore
Commit: 5cca27d4d568d242b38c3b1dcdcc26220b0a773c
Author: Arkadiusz Gladki <arkadiusz.gladki@contractors.roche.com>
Date: 2024-02-14 09:44:01 +0100
Commit message:

 chore: bump v+c
 
Package: gDRcore
Commit: 1eef167db384ef00576a320bce3557a461ec4ff3
Author: Arkadiusz Gladki <arkadiusz.gladki@contractors.roche.com>
Date: 2024-02-14 09:42:10 +0100
Commit message:

 build: add pkgdown GHA pipeline
 
Package: gDRcore
Commit: 7cb1046216e7be333a25de85be6dbe31ad38c840
Author: Arkadiusz Gladki <arkadiusz.gladki@contractors.roche.com>
Date: 2024-02-14 09:41:48 +0100
Commit message:

 doc: add pkgdown config
 
Package: gDRcore
Commit: d755c2cf64c0ae6cbff22e2b4e3ef3f9f1cfd45b
Author: Arkadiusz Gladki <arkadiusz.gladki@contractors.roche.com>
Date: 2024-02-14 09:41:26 +0100
Commit message:

 chore: add .Rbuildignore
 
Package: gDRcore
Commit: 7c0b91c7c2de3c46fd2689e9955f42a5f244a82e
Author: Arkadiusz Gladki <arkadiusz.gladki@contractors.roche.com>
Date: 2024-02-14 09:40:53 +0100
Commit message:

 chore: udpate .gitignore (pkgdown)
 
Package: gDRcore
Commit: fe95c69f71aace8531f93eba41b0421e7629a882
Author: Arkadiusz Gladki <arkadiusz.gladki@contractors.roche.com>
Date: 2024-02-14 09:37:31 +0100
Commit message:

 refactor: rename 'matches' to 'gdr_matches'

Details:
 - pkgdown can't hanlde exported function called 'matches'
 
Package: gDRcore
Commit: bce5acec25c41676f3954b514907673e517af2cc
Author: Arkadiusz Gladki <arkadiusz.gladki@contractors.roche.com>
Date: 2024-02-14 09:36:40 +0100
Commit message:

 chore: fix typo in vignette
 
Package: gDRcore
Commit: 631b8ddc62fd3e956a8f67ac95e63435c5e20b85
Author: Arkadiusz Gladki <arkadiusz.gladki@contractors.roche.com>
Date: 2024-02-14 09:36:06 +0100
Commit message:

 doc: remove obsolete importFrom record
 
Package: gDRcore
Commit: e1da5979f8f4642c13bb4f785082d9372e26a31a
Author: Arkadiusz Gladki <arkadiusz.gladki@contractors.roche.com>
Date: 2024-02-14 09:35:11 +0100
Commit message:

 build: update Dockerfile
 
Package: gDRcore
Commit: b0e9cda8a30f7f3e2c551dbc83adbaad031672e7
Author: czechb3 <bartosz.w.czech@gmail.com>
Date: 2024-02-13 14:21:41 +0100
Commit message:

 chore: bump version and update NEWS.md
 
Package: gDRcore
Commit: c16e5015046f25a55be3a2da978a05b0c260a21c
Author: czechb3 <bartosz.w.czech@gmail.com>
Date: 2024-02-13 14:20:41 +0100
Commit message:

 fix: bug with taking unique records from control samples
 
Package: gDRcore
Commit: f628c6fe13c70f890b6bbba92a5e548c4b9e5deb
Author: Bartek <32614650+bczech@users.noreply.github.com>
Date: 2024-02-12 16:42:20 +0100
Commit message:

 Merge pull request #136 from gdrplatform/GDR-2199_2

Fix tests for GRAN 
Package: gDRcore
Commit: 2f631acc2b70f75bf6646a314fcf9a323f7909db
Author: czechb3 <bartosz.w.czech@gmail.com>
Date: 2024-02-12 16:14:17 +0100
Commit message:

 ci: trigger build
 
Package: gDRcore
Commit: e8f2f79d4bda558b0f30e3124a3c0e8016523579
Author: czechb3 <bartosz.w.czech@gmail.com>
Date: 2024-02-12 14:26:07 +0100
Commit message:

 test: update unit tests
 
Package: gDRcore
Commit: c5e07ad1013767d8632f90138cdcae42b1b69bc3
Author: czechb3 <bartosz.w.czech@gmail.com>
Date: 2024-02-12 09:04:54 +0100
Commit message:

 chore: bump version and update NEWS.md