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

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Package: iModMixData
Commit: 7623b9a35bcc5ba53667afa9d13fd2d5c850b776
Author: Isis Narvaez-Bandera <isis.narvaez@upr.edu>
Date: 2025-08-28 13:29:27 -0400
Commit message:

 biocViews: ExperimentData, ExpressionData, MassSpectrometryData, ExperimentHub
Package: biomaRt
Commit: 7b4e1102fd100e2c5da681276f89750b4028db74
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-08-28 19:08:06 +0200
Commit message:

 Remove dependencies superseded by new functions in tools (#140)
Package: biomaRt
Commit: 17bff63203ee6efd7e50e886679ef96ef695e37e
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-08-28 11:54:00 +0200
Commit message:

 Add revdep/ to .Rbuildignore
Package: biomaRt
Commit: 3e4945f36e8189c65a8f20d38af8bfb9777f9339
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-08-28 11:53:27 +0200
Commit message:

 Add revdep working folders in gitignore
Package: Pirat
Commit: 61999326e7a0673fc477d18c4fe238fa16930123
Author: Lucas Etourneau <lucas.etourneau@berkeley.edu>
Date: 2025-08-28 10:02:55 -0700
Commit message:

 Add channels
Package: punKEGGer
Commit: d46c8479cb0106588d8ed2fff721b29814276ea1
Author: gdj <gdeanda@inmegen.edu.mx>
Date: 2025-08-28 11:01:52 -0600
Commit message:

 Fix DESCRIPTION DCF (no leading ')', clean Authors@R) - v0.99.6
Package: Pirat
Commit: 2bed5c798e1e08732f26c6bbbd519e04c66061b5
Author: Lucas Etourneau <lucas.etourneau@berkeley.edu>
Date: 2025-08-28 09:52:09 -0700
Commit message:

 Change channel & package
Package: spatialFDA
Commit: 60ac7c86e8b499acc970fa62cc76f7a516018431
Author: mjemons <martin.emons@gmail.com>
Date: 2025-08-28 17:09:09 +0200
Commit message:

 major change in min threshold to calculate curves on - set to >1 point - print Rsq.adjust
Package: punKEGGer
Commit: 23de149f42d2b706328b8d7337ada7a314b1418c
Author: gdj <gdeanda@inmegen.edu.mx>
Date: 2025-08-28 10:31:16 -0600
Commit message:

 Version bump to 0.99.6 (force SPB rebuild)
Package: GSEABase
Commit: f9e1f78d51fcdf8b87daf79e65492aeef07fd4ca
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-08-28 11:42:23 -0400
Commit message:

 version bump 1.71.1
Package: GSEABase
Commit: 451a4471f883490ca935e2a8198f9f4d92ec8fcd
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-08-28 11:43:47 -0400
Commit message:

 add ignore files
Package: GSEABase
Commit: 60aaab4d5fe13311348354db0cd92c59257399c4
Author: Copilot <198982749+Copilot@users.noreply.github.com>
Date: 2025-08-28 11:37:03 -0400
Commit message:

 Add support for MSigDB mouse collection categories in BroadCollection (#12)

* Add support for MSigDB mouse collection categories

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Package: GSEABase
Commit: 8843b908da13c9b6eb6c59334e6de1a0c50d9159
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-08-27 11:07:39 -0400
Commit message:

 add copilot instructions
Package: BiocFileCache
Commit: 1fc61764ec373e29bb6436fe47551c8a0b0dd974
Author: lshep <lori.shepherd@roswellpark.org>
Date: 2025-08-28 11:38:51 -0400
Commit message:

 Merge pull request #68 from Bioconductor/trycatch_download

use tryCatch for bfcdownload when resource is unreliable
Package: BiocFileCache
Commit: d4b686589269ca2e02e84db532ed5b137b8d4311
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-08-27 12:46:25 -0400
Commit message:

 use tryCatch for bfcdownload when resource is unreliable
Package: mzR
Commit: 7a0319adc132af38fdcdc22e57d1e521dfa67abe
Author: Steffen Neumann <sneumann@ipb-halle.de>
Date: 2025-08-28 15:26:28 +0200
Commit message:

 Bump version
Package: mzR
Commit: f04857874fa81bccdbc9edd8171709e889ec1b19
Author: Adriano Rutz <adriano.rutz@hotmail.com>
Date: 2025-08-15 16:46:30 +0200
Commit message:

 ignore more NaNs
Package: mzR
Commit: bcb82e383a618a7bc3d66a20ecbdc32ade625b18
Author: Adriano Rutz <adriano.rutz@hotmail.com>
Date: 2025-08-15 08:44:08 +0200
Commit message:

 ignore more NaNs
Package: mzR
Commit: b97523ca6318bbe5bbd983a25283fd89030ff560
Author: Adriano Rutz <adriano.rutz@hotmail.com>
Date: 2025-08-14 17:11:32 +0200
Commit message:

 ignore nan energies
Package: mzR
Commit: c24f9afdef20987cba491e0cc8eee8a4bb5c8332
Author: Adriano Rutz <adriano.rutz@hotmail.com>
Date: 2025-08-14 12:58:41 +0200
Commit message:

 add `electronBeamEnergy`
Package: mzR
Commit: 27c8edb42604522358b18573bda0c10ac88f78f9
Author: Adriano Rutz <adriano.rutz@hotmail.com>
Date: 2025-08-14 07:51:51 +0200
Commit message:

 ran `updateCvParams.sh`
Package: mzR
Commit: 0e6f9e9d42c1112e2a6a78e1216d7c3d473d7f71
Author: Steffen Neumann <sneumann@ipb-halle.de>
Date: 2025-08-12 22:37:39 +0200
Commit message:

 Merge pull request #309 from sneumann/sneumann-patch-5

Bump BioC Versions in github action
Fixes GH actions failure on Linux
Package: mzR
Commit: a9041f108127ccb2ed0908299bc8cc23883c7ec5
Author: Steffen Neumann <sneumann@ipb-halle.de>
Date: 2025-08-12 22:04:15 +0200
Commit message:

 Bump BioC Versions in github action
Package: tximportData
Commit: 04d30a42107dcd5e68444e1143520f84764376f2
Author: Mike Love <mikelove@users.noreply.github.com>
Date: 2025-08-28 08:12:34 -0400
Commit message:

 update number of novel in oarfish
Package: msa
Commit: 72ebbc23c46e5938093565e72fa39662c1970041
Author: Ulrich Bodenhofer <ulrichbodenhofer@TAMMISAARI.local>
Date: 2025-08-28 13:38:53 +0200
Commit message:

 fixed compilations problems for arm64; version number bumped to 1.41.1
Package: Rarr
Commit: 3fb74aaeeffb45be70f601e7daab3ed108d02722
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-08-28 11:44:55 +0200
Commit message:

 Fix rchk PROTECT issues (#40)
Package: Rarr
Commit: d944a2efd2c735577773db11563e89b79990a790
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-08-28 11:42:34 +0200
Commit message:

 Add note in README about lack of v3 support (#41)
Package: Rarr
Commit: 219dcad29b3aca5d662d44c629832c1fed8705ec
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-08-28 09:18:17 +0200
Commit message:

 Use readBin() on a connection (#36)
Package: Rarr
Commit: ed3c844ce39ebb96f47760d55bd1884ad05be323
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-08-28 08:17:51 +0200
Commit message:

 Set up r-hub to test on more uncommon platforms (#38)
Package: peakCombiner
Commit: 1a8c64bb8a6a8272ca38ff97c7a9482a6ea452af
Author: Muckenhuber, Markus <markus.muckenhuber@novartis.com>
Date: 2025-08-27 11:02:04 -0400
Commit message:

 Updated version to 0.99.60 for second round of review
Package: peakCombiner
Commit: fe6b778c8c37463534129d85a846c5ab95bc7d8e
Author: Muckenhuber, Markus <markus.muckenhuber@novartis.com>
Date: 2025-08-25 05:52:31 -0400
Commit message:

 Add Vignette as HTML and update gitignore
Package: peakCombiner
Commit: 96040a6c0897bd83219766339eb83446a59702d9
Author: Muckenhuber, Markus <markus.muckenhuber@novartis.com>
Date: 2025-08-22 09:07:02 -0400
Commit message:

 Updated test with new parameter removeFlankOverlap
Package: peakCombiner
Commit: e95697f44e02959e6b5938defdfc6ca4bdb6c4d1
Author: Muckenhuber, Markus <markus.muckenhuber@novartis.com>
Date: 2025-08-22 09:06:49 -0400
Commit message:

 Updated man with new parameter removeFlankOverlap
Package: peakCombiner
Commit: 559eeb41b81fe8aaef04e178c8601b679498c215
Author: Muckenhuber, Markus <markus.muckenhuber@novartis.com>
Date: 2025-08-22 09:06:21 -0400
Commit message:

 Added new parameter removeFlankOverlaps
Package: peakCombiner
Commit: 02a9a43cca9e4dcab87ad81a4592bebbf22a4c50
Author: Muckenhuber, Markus <markus.muckenhuber@novartis.com>
Date: 2025-08-22 09:05:54 -0400
Commit message:

 Added hex sticker to ignore
Package: peakCombiner
Commit: 7f58cd410c36bd50004d5e5ac95496798992f4b5
Author: Muckenhuber, Markus <markus.muckenhuber@novartis.com>
Date: 2025-08-22 09:04:50 -0400
Commit message:

 New version
Package: peakCombiner
Commit: 7644c840b70c18d07af07aac61dd79167a1e8f0d
Author: Muckenhuber, Markus <markus.muckenhuber@novartis.com>
Date: 2025-08-18 09:08:09 -0400
Commit message:

 Readd GenomeInfoDb
Package: peakCombiner
Commit: 9ce6b61cff8a0dfcdfe83ac324d561b4c6181142
Author: Muckenhuber, Markus <markus.muckenhuber@novartis.com>
Date: 2025-08-18 08:55:43 -0400
Commit message:

 Correct typo in parameter startsAreBased
Package: peakCombiner
Commit: 17ff90e30d6961594c4c410d46d2e3a6e0615fcb
Author: Muckenhuber, Markus <markus.muckenhuber@novartis.com>
Date: 2025-08-14 05:07:41 -0400
Commit message:

 For now added
Package: peakCombiner
Commit: ee62ba828b188dfe03ba466f6780654effe38207
Author: Muckenhuber, Markus <markus.muckenhuber@novartis.com>
Date: 2025-08-14 04:27:23 -0400
Commit message:

 For now add gitproject
Package: peakCombiner
Commit: 68dffe7a375bc7d4e8ff1d5bdbfcecc9442b174b
Author: Muckenhuber, Markus <markus.muckenhuber@novartis.com>
Date: 2025-08-14 04:24:11 -0400
Commit message:

 Replace GenomeInfoDB with Seqinfo (in devel now will be released with new BC version)
Package: peakCombiner
Commit: 3bd71a54fea850275a6602a3a15c930b86b576a9
Author: Muckenhuber, Markus <markus.muckenhuber@novartis.com>
Date: 2025-08-14 04:23:36 -0400
Commit message:

 For the moment remove one test as it seems the new seqinfo package is failing
Package: peakCombiner
Commit: 90ba8e1ad65af4e367eee274395bf028c8e61861
Author: Muckenhuber, Markus <markus.muckenhuber@novartis.com>
Date: 2025-08-14 04:23:09 -0400
Commit message:

 Update man with new package
Package: peakCombiner
Commit: 34e53e9a49f64315f970729542c66fc8ec51fed0
Author: Muckenhuber, Markus <markus.muckenhuber@novartis.com>
Date: 2025-08-14 04:22:54 -0400
Commit message:

 Replaced seqinfos with new package Seqinfo
Package: peakCombiner
Commit: e4b9198a73c4e14bffbf5092ce7f28938846bc6d
Author: Markus Muckenhuber <141941160+MarkusMuck@users.noreply.github.com>
Date: 2025-08-13 14:46:27 +0200
Commit message:

 Delete peakCombiner-git.Rproj
Package: peakCombiner
Commit: e8852ada59436e61eda000a26a9a45a427e0779f
Author: Muckenhuber, Markus <markus.muckenhuber@novartis.com>
Date: 2025-08-13 08:09:54 -0400
Commit message:

 Corrected expected values in tests
Package: peakCombiner
Commit: 708cb72992a7bea4676a33bf16987e9e7346a019
Author: Muckenhuber, Markus <markus.muckenhuber@novartis.com>
Date: 2025-08-13 08:09:38 -0400
Commit message:

 Removed wrong line from man
Package: peakCombiner
Commit: d7f199160e716741a88b53418381a72cad7dca75
Author: Muckenhuber, Markus <markus.muckenhuber@novartis.com>
Date: 2025-08-13 08:09:25 -0400
Commit message:

 Readded name column
Package: peakCombiner
Commit: d03b4cdbce292f0b189424ed14226c2bc941950f
Author: Muckenhuber, Markus <markus.muckenhuber@novartis.com>
Date: 2025-08-13 08:09:09 -0400
Commit message:

 Removed commend which created error in Check
Package: peakCombiner
Commit: 963cfa45f34b391e3c7b88aada8c52593d5ccf04
Author: Muckenhuber, Markus <markus.muckenhuber@novartis.com>
Date: 2025-08-13 05:24:10 -0400
Commit message:

 Include setting 0-based option if needed
Package: peakCombiner
Commit: e8167d700b6def6b24a9843f000a4388445012dd
Author: Muckenhuber, Markus <markus.muckenhuber@novartis.com>
Date: 2025-08-13 05:23:45 -0400
Commit message:

 Update tests to new functions and syndata
Package: peakCombiner
Commit: 88d1039f8ed3aef0f2065860bcdc2633e87aa365
Author: Muckenhuber, Markus <markus.muckenhuber@novartis.com>
Date: 2025-08-13 05:23:27 -0400
Commit message:

 Update syn data
Package: peakCombiner
Commit: c09ad565258cf5de3c7f689720157ab1b0efb42c
Author: Muckenhuber, Markus <markus.muckenhuber@novartis.com>
Date: 2025-08-13 05:23:10 -0400
Commit message:

 Move hidding error messages to front of function and to reset default at the end
Package: peakCombiner
Commit: 0e1bc6f34961c430e82c17da6d39b81f1e8cef55
Author: Muckenhuber, Markus <markus.muckenhuber@novartis.com>
Date: 2025-08-13 05:22:44 -0400
Commit message:

 Set default to showMessages True
Package: peakCombiner
Commit: 17e0d24cae1fd4140e2f6a0763df11543b128936
Author: Muckenhuber, Markus <markus.muckenhuber@novartis.com>
Date: 2025-08-13 05:22:27 -0400
Commit message:

 Changed used dats
Package: peakCombiner
Commit: d644e001cff8221eaeb69dff7d4fe5d1b3d50ca2
Author: Muckenhuber, Markus <markus.muckenhuber@novartis.com>
Date: 2025-08-13 05:22:16 -0400
Commit message:

 Removed reset of error messages
Package: peakCombiner
Commit: 9c0f165204858e6dd37ec2efe5a90879d75af612
Author: Muckenhuber, Markus <markus.muckenhuber@novartis.com>
Date: 2025-08-12 10:22:44 -0400
Commit message:

 Added usage of blacklist to vignette
Package: peakCombiner
Commit: 7483bbf0cbe40c1bc8798825e4994591f126c522
Author: Muckenhuber, Markus <markus.muckenhuber@novartis.com>
Date: 2025-08-12 10:22:18 -0400
Commit message:

 Downloaded blacklist added to gitignore
Package: peakCombiner
Commit: 00d7a75c83e8dc82132129492952049abeaa7f37
Author: Muckenhuber, Markus <markus.muckenhuber@novartis.com>
Date: 2025-08-12 10:21:26 -0400
Commit message:

 Added new ShowMessages parameter
Package: peakCombiner
Commit: 64c042f3e43bacfc69582b55a7f9c882d7dc7db5
Author: Muckenhuber, Markus <markus.muckenhuber@novartis.com>
Date: 2025-08-12 10:21:08 -0400
Commit message:

 Changed order to silence messages and removed resets to default by error. And added the showMessages option to the check
Package: peakCombiner
Commit: 3fe1b3d7066ba8782ddc4d8d65067e5d1836c20d
Author: Muckenhuber, Markus <markus.muckenhuber@novartis.com>
Date: 2025-08-12 10:20:52 -0400
Commit message:

 Changed order to silence messages and removed resets to default by error. And added the showMessages option to the check. Added showMessagesto helper function
Package: peakCombiner
Commit: 8ee66a1c10c651b35a6d33944ebe54704191a1ef
Author: Muckenhuber, Markus <markus.muckenhuber@novartis.com>
Date: 2025-08-12 10:20:22 -0400
Commit message:

 Changed order to silence messages and removed resets to default by error. And added the showMessages option to the check
Package: peakCombiner
Commit: 9adac3f48d13ed04687c5952dd4ed7ebe121e4d5
Author: Muckenhuber, Markus <markus.muckenhuber@novartis.com>
Date: 2025-08-12 10:20:09 -0400
Commit message:

 Changed order to silence messages and removed resets to default by error. And added the showMessages option to the check
Package: peakCombiner
Commit: f24ac292c13ed946d60f41cd164de1e989d5ae6b
Author: Muckenhuber, Markus <markus.muckenhuber@novartis.com>
Date: 2025-08-12 10:19:44 -0400
Commit message:

 Added silence messages and removed resets to default by error
Package: peakCombiner
Commit: ed7308ff4adce67a64c1f695beaeb8ece26b07e3
Author: Muckenhuber, Markus <markus.muckenhuber@novartis.com>
Date: 2025-08-12 10:19:26 -0400
Commit message:

 Changed order to silence messages and removed resets to default by error
Package: peakCombiner
Commit: e12b1765c19e2058d915a8900e6d9060d796c290
Author: Muckenhuber, Markus <markus.muckenhuber@novartis.com>
Date: 2025-08-12 09:34:25 -0400
Commit message:

 Changed some parameters to camelCase.
Update information how to use blacklists and where to get them
Package: peakCombiner
Commit: 21c5ba2d65bc1a51edceb1da8756827e4f3479a6
Author: Muckenhuber, Markus <markus.muckenhuber@novartis.com>
Date: 2025-08-12 09:33:42 -0400
Commit message:

 Mayor updates on test to fit new parameter and function names. Check for new parameter and updated expected results for tests
Package: peakCombiner
Commit: edd22c7575d29ee9fd95027d72b73c36d566cb42
Author: Muckenhuber, Markus <markus.muckenhuber@novartis.com>
Date: 2025-08-12 09:33:04 -0400
Commit message:

 Updated tests to allow checking for correctly provided genome
Package: peakCombiner
Commit: b774b33b630e02f8914eb2f5e3a57d7ec8771841
Author: Muckenhuber, Markus <markus.muckenhuber@novartis.com>
Date: 2025-08-12 09:32:32 -0400
Commit message:

 Updated man
Package: peakCombiner
Commit: f14a3a65efc3d38da6fe8d2056aa2736cf1a3fda
Author: Muckenhuber, Markus <markus.muckenhuber@novartis.com>
Date: 2025-08-12 09:32:05 -0400
Commit message:

 New manual for re-named functions and parameters to follow camelCase
Package: peakCombiner
Commit: 82dcf65cb579d30655caa7611ee7bf04b69aeebf
Author: Muckenhuber, Markus <markus.muckenhuber@novartis.com>
Date: 2025-08-12 09:31:29 -0400
Commit message:

 Update how trimming is handeled and how genome infos are maintained
Package: peakCombiner
Commit: c221a86f0a27e501fda3ad9b3eecefc400075ee0
Author: Muckenhuber, Markus <markus.muckenhuber@novartis.com>
Date: 2025-08-12 09:30:49 -0400
Commit message:

 Update the way syn data is made to follow bed tools standards
Package: peakCombiner
Commit: b966293b5c4213a61e98428897f3fa7ef8e3f3b2
Author: Muckenhuber, Markus <markus.muckenhuber@novartis.com>
Date: 2025-08-12 09:30:20 -0400
Commit message:

 Update syn data to follow BED tool standards
Package: peakCombiner
Commit: 9701e143a0787b9cf38153f0869cc957c8a285db
Author: Muckenhuber, Markus <markus.muckenhuber@novartis.com>
Date: 2025-08-12 09:29:57 -0400
Commit message:

 Add new options to provide Genome information which is also maintained. Add the option to inform if input is 1 or 0-based. Outpu is now always 1-based
Package: peakCombiner
Commit: c6c39ad76067c33a8be005cb4bedc6774da7a8c0
Author: Muckenhuber, Markus <markus.muckenhuber@novartis.com>
Date: 2025-08-12 09:28:28 -0400
Commit message:

 Update usage of Blacklist doc and code. Also extract seqinfo from GRanges input and add it to output
Package: peakCombiner
Commit: 336ea86206cb8879c091b9024b1c6b0f00a6df9b
Author: Muckenhuber, Markus <markus.muckenhuber@novartis.com>
Date: 2025-08-12 09:27:46 -0400
Commit message:

 Extract SeqInfo from GRanges input and add it to outpu
Package: peakCombiner
Commit: 8028ff99915d77396653525840fad5f9e093e732
Author: Muckenhuber, Markus <markus.muckenhuber@novartis.com>
Date: 2025-08-12 09:27:07 -0400
Commit message:

 Update input test files to 0-based to follow BED tool standards
Package: peakCombiner
Commit: db511643de58669204b07942b143181801c3eae2
Author: Muckenhuber, Markus <markus.muckenhuber@novartis.com>
Date: 2025-08-12 09:26:34 -0400
Commit message:

 Rename function and options to camleCase
Package: peakCombiner
Commit: 745d7f4da30f22325a2554c76e56961976dd88e4
Author: Muckenhuber, Markus <markus.muckenhuber@novartis.com>
Date: 2025-08-12 09:26:04 -0400
Commit message:

 Implement solution to have all in 1-based and a way to extract genome info from input
Package: peakCombiner
Commit: 2fe0f2d031786de7109b11c15ce2a4fbd2d93df7
Author: Muckenhuber, Markus <markus.muckenhuber@novartis.com>
Date: 2025-08-12 09:24:56 -0400
Commit message:

 Added Annotation Hub to package list
Package: peakCombiner
Commit: 99865415fc85cd1605fbceb33c55d43089040514
Author: Muckenhuber, Markus <markus.muckenhuber@novartis.com>
Date: 2025-08-05 10:48:54 -0400
Commit message:

 Update parameter names to camaleCase from snake_case
Package: peakCombiner
Commit: 37a66a61b0d87daaf33cae8167d85f9100559da2
Author: Muckenhuber, Markus <markus.muckenhuber@novartis.com>
Date: 2025-08-05 10:05:07 -0400
Commit message:

 Change back the test push
Package: peakCombiner
Commit: 17daaf0dda01f10e9a69da63541582516fb0a536
Author: Muckenhuber, Markus <markus.muckenhuber@novartis.com>
Date: 2025-08-05 08:10:35 -0400
Commit message:

 Test pushing US
Package: peakCombiner
Commit: ea91f07f7e6c0283811032b48f2db6a8092256f8
Author: Markus Muckenhuber <141941160+MarkusMuck@users.noreply.github.com>
Date: 2025-08-04 15:09:19 +0200
Commit message:

 Update centerExpandRegions.R

Adjusted man
Package: peakCombiner
Commit: 3d9bc06c17fe5bbfefe4ef599eb4b2f5222a8d8f
Author: Markus Muckenhuber <141941160+MarkusMuck@users.noreply.github.com>
Date: 2025-08-04 14:50:19 +0200
Commit message:

 Update peakCombiner.Rmd

Not execute install.package
Package: peakCombiner
Commit: 1481dc1fe5d1f373320ec56501c6d994eb66a8ba
Author: Markus Muckenhuber <141941160+MarkusMuck@users.noreply.github.com>
Date: 2025-08-04 14:43:53 +0200
Commit message:

 Update peakCombiner.Rmd

Update how to install and load PeakCombiner
Package: peakCombiner
Commit: 48254b3ad303ed2d8eeb7003124616de307f5833
Author: Markus Muckenhuber <141941160+MarkusMuck@users.noreply.github.com>
Date: 2025-08-04 14:40:12 +0200
Commit message:

 Update peakCombiner.Rmd
Package: peakCombiner
Commit: b4afbb7a5eca6063822a773d6ba447615d97acb5
Author: Markus Muckenhuber <141941160+MarkusMuck@users.noreply.github.com>
Date: 2025-08-04 14:35:16 +0200
Commit message:

 Update peakCombiner.Rmd

Removed one opts_chunl$set
Package: peakCombiner
Commit: 9f1a0b17ed994ebd6eea10178302a9c90eece1db
Author: Markus Muckenhuber <141941160+MarkusMuck@users.noreply.github.com>
Date: 2025-08-04 14:27:36 +0200
Commit message:

 Update peakCombiner.Rmd

Correct error in calling makeGRangesFromDataFrame
Package: peakCombiner
Commit: a13d8de38522345d3a1bf26c51c9093a11b5203a
Author: Markus Muckenhuber <141941160+MarkusMuck@users.noreply.github.com>
Date: 2025-08-04 14:22:48 +0200
Commit message:

 Update peakCombiner.Rmd
Package: peakCombiner
Commit: 6af872a29b2437252674bf59266324d0a58a78b4
Author: Markus Muckenhuber <muckema1@vv7q2gf9jc.eu.novartis.net>
Date: 2025-07-31 16:13:27 +0200
Commit message:

 Triggering GitHub Action
Package: peakCombiner
Commit: ca9634f3f734c4efe9ddfcfcd9dde89db0c31ac2
Author: Muckenhuber, Markus <markus.muckenhuber@novartis.com>
Date: 2025-07-30 15:52:03 +0200
Commit message:

 Updated the vignette to align with changed parameters and functionalities of the package
Package: peakCombiner
Commit: d7a54eb2ffe29349a8624d08f8d077d11d35dde7
Author: Muckenhuber, Markus <markus.muckenhuber@novartis.com>
Date: 2025-07-29 16:20:33 +0200
Commit message:

 Added BiocManager to suggestions
Package: peakCombiner
Commit: ae5f58684e86050684068067a8bd07e9b6a78bc1
Author: Muckenhuber, Markus <markus.muckenhuber@novartis.com>
Date: 2025-07-29 16:17:50 +0200
Commit message:

 Update the way the package is loaded and how some data sets are loaded
Package: peakCombiner
Commit: 10357883110098736589064174cd8171635baf47
Author: Muckenhuber, Markus <markus.muckenhuber@novartis.com>
Date: 2025-07-29 16:17:31 +0200
Commit message:

 Updated the test results
Package: peakCombiner
Commit: 0d4d92708a4188d1bef81416b45ed0434eb01446
Author: Muckenhuber, Markus <markus.muckenhuber@novartis.com>
Date: 2025-07-29 16:16:57 +0200
Commit message:

 Correct some errors in the description of required imputs
Package: peakCombiner
Commit: a6dc40a2b54a2a4c1a3f5cc77d832d8aa57846a0
Author: Muckenhuber, Markus <markus.muckenhuber@novartis.com>
Date: 2025-07-29 16:16:31 +0200
Commit message:

 Change the default parameter for trim_start
Package: peakCombiner
Commit: 72b06438b63aabc609f082e65e3c086406aa67fe
Author: Muckenhuber, Markus <markus.muckenhuber@novartis.com>
Date: 2025-07-29 15:40:52 +0200
Commit message:

 Correct some mistakes in the test of vignette
Package: peakCombiner
Commit: 5eb33f102cb041d54da8f13c4f9443487d0d31f4
Author: Muckenhuber, Markus <markus.muckenhuber@novartis.com>
Date: 2025-07-29 15:40:22 +0200
Commit message:

 Add test to see non-unique entries in sample_sheet
Package: peakCombiner
Commit: 666b42cbac5e2985a429f7542ac742970692602c
Author: Muckenhuber, Markus <markus.muckenhuber@novartis.com>
Date: 2025-07-29 15:35:14 +0200
Commit message:

 Added an check if values in "score_columns" are unique
Package: peakCombiner
Commit: 4886f03d5ffe6f228e5e0f2c9dfc7d840af54f3d
Author: Muckenhuber, Markus <markus.muckenhuber@novartis.com>
Date: 2025-07-29 15:34:25 +0200
Commit message:

 Errors in documentation about col names for sample sheet, which should be "file_path" not "path_peaks"
Package: peakCombiner
Commit: 26f8b04d047bbd58787c77100f1f3f426fb3bd23
Author: Muckenhuber, Markus <markus.muckenhuber@novartis.com>
Date: 2025-07-29 15:33:30 +0200
Commit message:

 Changed the default for trim_start to be true
Package: peakCombiner
Commit: b0be3e5465b3c99a7f649f0835242660f3be214a
Author: Muckenhuber, Markus <markus.muckenhuber@novartis.com>
Date: 2025-07-25 11:47:04 +0200
Commit message:

 Adjusted vignette with new options in functions
Package: peakCombiner
Commit: 574263441a98678a34e5f0909ddf9ea187596efb
Author: Muckenhuber, Markus <markus.muckenhuber@novartis.com>
Date: 2025-07-25 11:46:45 +0200
Commit message:

 Adjusted test for new options and test them
Package: peakCombiner
Commit: 46b9b898ca3bc334f73cc3d98d88ead897a04a94
Author: Muckenhuber, Markus <markus.muckenhuber@novartis.com>
Date: 2025-07-25 11:46:26 +0200
Commit message:

 Adjusted man with new options and their explanations
Package: peakCombiner
Commit: d1e609863631f4b413b059b247dd8e87e7ae032e
Author: Muckenhuber, Markus <markus.muckenhuber@novartis.com>
Date: 2025-07-25 11:46:07 +0200
Commit message:

 Added the GenomicRanges way to test if expanded regions are beyong chrom boarders. Then trim them
Package: peakCombiner
Commit: a1a49d7b02e6df2bae210cd05792512acb3cfd1b
Author: Muckenhuber, Markus <markus.muckenhuber@novartis.com>
Date: 2025-07-25 11:45:01 +0200
Commit message:

 Added GenomeInfoDB package for genome reference
Package: peakCombiner
Commit: 772e7666274f3967e23c661d50cc7f3c11676fc8
Author: Muckenhuber, Markus <markus.muckenhuber@novartis.com>
Date: 2025-07-23 16:44:30 +0200
Commit message:

 Rename main functions to camelCase
Package: peakCombiner
Commit: 2f9197d9fb29a543c7b2d839789b3bfeca266b18
Author: Muckenhuber, Markus <markus.muckenhuber@novartis.com>
Date: 2025-07-23 16:44:04 +0200
Commit message:

 Rename main functions to camelCase
Package: peakCombiner
Commit: 94704c7dd3710ea2fe17c036b5e58aefdb64e692
Author: Muckenhuber, Markus <markus.muckenhuber@novartis.com>
Date: 2025-07-23 15:33:21 +0200
Commit message:

 Improved code to solve error in test
Package: peakCombiner
Commit: 26521be3165e3fed06a57e17849b86c24c87b9ce
Author: Muckenhuber, Markus <markus.muckenhuber@novartis.com>
Date: 2025-07-23 15:32:58 +0200
Commit message:

 Fix error in transforming GenomicRanges to tibble
Package: peakCombiner
Commit: e6172f325d68b7667b141a7ae86cbe20c4b57698
Author: Muckenhuber, Markus <markus.muckenhuber@novartis.com>
Date: 2025-07-22 17:43:28 +0200
Commit message:

 Allow Granges Object as input
Package: peakCombiner
Commit: 6231fcb5fe7d13575a86c13ef71ef00dfb3f3025
Author: Muckenhuber, Markus <markus.muckenhuber@novartis.com>
Date: 2025-07-22 17:17:58 +0200
Commit message:

 Added the output_format to all function
Package: peakCombiner
Commit: af080a67d672bc0459f010f35501be20993a90f0
Author: Muckenhuber, Markus <markus.muckenhuber@novartis.com>
Date: 2025-07-22 16:58:34 +0200
Commit message:

 Missed one function to add the output_data
Package: peakCombiner
Commit: aba6e8154260884a6537c77d9e7225ccc4514927
Author: Muckenhuber, Markus <markus.muckenhuber@novartis.com>
Date: 2025-07-22 16:55:37 +0200
Commit message:

 Error in file name after adding the output_structur option
Package: peakCombiner
Commit: d1ab2e0879ef4640f4c2d890475dc1077ff04676
Author: Muckenhuber, Markus <markus.muckenhuber@novartis.com>
Date: 2025-07-22 16:53:38 +0200
Commit message:

 Add the output_format as option to the code
Package: peakCombiner
Commit: 20d1320b1514279332b11ad73167645cccbdd9d7
Author: Muckenhuber, Markus <markus.muckenhuber@novartis.com>
Date: 2025-07-22 16:53:22 +0200
Commit message:

 Add the output_format option to all required functions
Package: peakCombiner
Commit: 617c1969bf234b6dc6bf9e00c21bfee6b423e5a9
Author: Muckenhuber, Markus <markus.muckenhuber@novartis.com>
Date: 2025-07-22 16:53:03 +0200
Commit message:

 Add the output_format as option and the required code to check input and output
Package: peakCombiner
Commit: 955602417587aef9f8a92eb3bac0b6d410c16157
Author: Muckenhuber, Markus <markus.muckenhuber@novartis.com>
Date: 2025-07-22 16:52:56 +0200
Commit message:

 Add the output_format as option and the required code to check input and output
Package: peakCombiner
Commit: f98eb45ece96c9b69db4e9ef86ff7200af1ebf1b
Author: Muckenhuber, Markus <markus.muckenhuber@novartis.com>
Date: 2025-07-22 16:52:51 +0200
Commit message:

 Add the output_format as option and the required code to check input and output
Package: peakCombiner
Commit: dea24fe2c82f3487cd27922ef1d5ae677028bcc1
Author: Muckenhuber, Markus <markus.muckenhuber@novartis.com>
Date: 2025-07-22 16:52:41 +0200
Commit message:

 Add the output_format as option and the required code to check input and output
Package: peakCombiner
Commit: a0c23cf768e363ca645efea9edf112939bf0d2f6
Author: Muckenhuber, Markus <markus.muckenhuber@novartis.com>
Date: 2025-07-22 15:13:29 +0200
Commit message:

 Added to change the strand when transforming into a tibble
Package: peakCombiner
Commit: 113f394ea375330c7dddb4d0a27614429449928b
Author: Muckenhuber, Markus <markus.muckenhuber@novartis.com>
Date: 2025-07-22 15:12:58 +0200
Commit message:

 Added the new option to define output file format
Package: peakCombiner
Commit: 2a363c38ac7105d56442652104004bf2cc1f2938
Author: Muckenhuber, Markus <markus.muckenhuber@novartis.com>
Date: 2025-07-22 15:12:34 +0200
Commit message:

 Adjusted manual how midpoint is now calculated
Package: peakCombiner
Commit: 18b75a8793b897ffbc87048c5c05995e8b55101d
Author: Muckenhuber, Markus <markus.muckenhuber@novartis.com>
Date: 2025-07-22 15:12:15 +0200
Commit message:

 Remove the blacklisted files from ENCODE
Package: peakCombiner
Commit: 23b570e10a3df4d904099c9f65d9ef3294228ec3
Author: Muckenhuber, Markus <markus.muckenhuber@novartis.com>
Date: 2025-07-22 15:11:30 +0200
Commit message:

 Format adjusted
Package: peakCombiner
Commit: f5bbba553a61859699e1db3fa81331fb4e22664b
Author: Muckenhuber, Markus <markus.muckenhuber@novartis.com>
Date: 2025-07-22 15:11:15 +0200
Commit message:

 Removed Encode black list reference
Package: peakCombiner
Commit: c2b290892ffea9da85e5621eb9df7c0bc219afb0
Author: Muckenhuber, Markus <markus.muckenhuber@novartis.com>
Date: 2025-07-22 15:10:47 +0200
Commit message:

 Added option to define output format in prepare intput
Package: peakCombiner
Commit: 8ab7561b8aa75404797fcffc5e7409169014562f
Author: Muckenhuber, Markus <markus.muckenhuber@novartis.com>
Date: 2025-07-21 18:02:30 +0200
Commit message:

 Fixed an error witthin the if else
Package: peakCombiner
Commit: d9e4c654e22bbb9fba009d405f08819ceceeaf65
Author: Muckenhuber, Markus <markus.muckenhuber@novartis.com>
Date: 2025-07-21 18:02:08 +0200
Commit message:

 Removed blacklist files
Package: peakCombiner
Commit: b750086cd2883ca95b5c232ed72db0ada198c471
Author: Muckenhuber, Markus <markus.muckenhuber@novartis.com>
Date: 2025-07-21 17:37:55 +0200
Commit message:

 Fix test filtering after updating blacklist
Package: peakCombiner
Commit: 1a1c64cda7f0ae9385e681fb2bce7ca14d61d333
Author: Muckenhuber, Markus <markus.muckenhuber@novartis.com>
Date: 2025-07-21 17:37:38 +0200
Commit message:

 Delete package provided blacklists
Package: peakCombiner
Commit: 4721255f0836eac6aa965d4d8feeed53d63da762
Author: Muckenhuber, Markus <markus.muckenhuber@novartis.com>
Date: 2025-07-21 17:37:23 +0200
Commit message:

 Removed encode blacklists for file
Package: peakCombiner
Commit: 9e62bc2c59875e8274e3667c02b2cdbaf8c4a2e0
Author: Muckenhuber, Markus <markus.muckenhuber@novartis.com>
Date: 2025-07-21 17:37:01 +0200
Commit message:

 Update text how midpoint is calculated
Package: peakCombiner
Commit: 2be3958154f6a7b62a7ccfd31a18b49b1a8f5662
Author: Muckenhuber, Markus <markus.muckenhuber@novartis.com>
Date: 2025-07-21 17:36:41 +0200
Commit message:

 Add Rporj to ignor
Package: peakCombiner
Commit: 8a1069e30626c79b11c8007efbd4e373b1ddffe1
Author: Muckenhuber, Markus <markus.muckenhuber@novartis.com>
Date: 2025-07-21 16:10:36 +0200
Commit message:

 Remove value "hg38" from tests
Package: peakCombiner
Commit: f98b89f8aaa7874c99e2197e5985285f9ee8ad0f
Author: Muckenhuber, Markus <markus.muckenhuber@novartis.com>
Date: 2025-07-21 16:08:34 +0200
Commit message:

 Remove hg38 from test for blacklist
Package: peakCombiner
Commit: 2db7fd9a32ccae62eefa154d76588e97423d1eb7
Author: Muckenhuber, Markus <markus.muckenhuber@novartis.com>
Date: 2025-07-21 16:07:29 +0200
Commit message:

 Added package to make Genomic Ranges object
Package: peakCombiner
Commit: d7e694a223ecff6bcdadc12bec71d23d9b644a97
Author: Muckenhuber, Markus <markus.muckenhuber@novartis.com>
Date: 2025-07-21 16:05:46 +0200
Commit message:

 Use resite instead of calculation of midpoint
Package: peakCombiner
Commit: 089996907c8a7f0073a6828d2ba5833f441a3d57
Author: Muckenhuber, Markus <markus.muckenhuber@novartis.com>
Date: 2025-07-21 14:45:34 +0200
Commit message:

 Add excluderanges to vignette
Package: peakCombiner
Commit: f5fc440a92c233457e5269eb1776f9f8d0479867
Author: Muckenhuber, Markus <markus.muckenhuber@novartis.com>
Date: 2025-07-21 14:43:01 +0200
Commit message:

 Update the test to run with the new script by not providing the encode blacklists
Package: peakCombiner
Commit: 0c807ba1e61faadbf210f375f0f219d7984bc20e
Author: Muckenhuber, Markus <markus.muckenhuber@novartis.com>
Date: 2025-07-21 14:42:36 +0200
Commit message:

 Changed the refernces to the encode blacklists
Package: peakCombiner
Commit: f8ad296b329bfcf153ad8c0963aeb5c804296ef6
Author: Muckenhuber, Markus <markus.muckenhuber@novartis.com>
Date: 2025-07-21 14:36:35 +0200
Commit message:

 Remove pre-loading of HG38 and mm10 from ENCODE
Package: peakCombiner
Commit: dea402d99705a661958ea8fecd4e99f2f1814ba5
Author: Muckenhuber, Markus <markus.muckenhuber@novartis.com>
Date: 2025-07-21 11:54:05 +0200
Commit message:

 Added a new RProject
Package: Spectra
Commit: 0afa29917e224747e8c4e20af4e056e3d2ed5ce6
Author: Johannes Rainer <5506112+jorainer@users.noreply.github.com>
Date: 2025-08-28 10:10:43 +0200
Commit message:

 Merge pull request #364 from rformassspectrometry/jomain

Add longForm methods
Package: Spectra
Commit: f3ca46552859df814cbe5f2f9e300617ec3b2cd9
Author: Johannes Rainer <johannes.rainer@gmail.com>
Date: 2025-08-28 10:10:09 +0200
Commit message:

 address Phili's comments
Package: Spectra
Commit: fbfdc6a8a117905d297b9e3a2fccd4583a2267c8
Author: Johannes Rainer <johannes.rainer@gmail.com>
Date: 2025-08-27 14:36:14 +0200
Commit message:

 feat: add longForm,Spectra (issue 360)
Package: Spectra
Commit: 82bf71ec9555e39bc9de1f691251b4fe497c31de
Author: Johannes Rainer <johannes.rainer@gmail.com>
Date: 2025-08-27 13:55:34 +0200
Commit message:

 feat: add longForm,MsBackend method (issue #360)
Package: Ularcirc
Commit: 8cd13d1d073af53fdb3ff935e5c68e5c8a46d11a
Author: David Humphreys <dth569@gadi-login-07.gadi.nci.org.au>
Date: 2025-08-28 14:33:28 +1000
Commit message:

 Remove mirBase.db dependency
Package: SeqArray
Commit: 6e66555b817378a5b3e964a3843fceaeda12c2f7
Author: Xiuwen Zheng <zhengxwen@gmail.com>
Date: 2025-08-27 23:30:36 -0500
Commit message:

 version bump
Package: punKEGGer
Commit: 8967c7a9aac52fbb8fece4eb2200ff21d9057729
Author: gdj <gdeanda@inmegen.edu.mx>
Date: 2025-08-27 18:05:09 -0600
Commit message:

 Bump version to 0.99.5
Package: basilisk
Commit: 9942970f6957217a867f7fee0c60188781f38fcb
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2025-08-27 14:46:34 -0700
Commit message:

 Remove references to Conda in the README.
Package: basilisk.utils
Commit: 112f90d25fd6b41041ef2f310869d411e616c515
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2025-08-27 14:50:54 -0700
Commit message:

 Updated README for the new purpose of this package, added badges.
Package: BiocPkgTools
Commit: 68dd50d5b75f07a3fe99f29eddbdb0b71d0491a8
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-08-27 16:14:54 -0400
Commit message:

 version bump 1.27.12
Package: BiocPkgTools
Commit: 3eedadca944f28dff16810b7dab4489d8cce8054
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-08-27 15:47:15 -0400
Commit message:

 use \code{} for type specs in docs
Package: BiocPkgTools
Commit: 910b4a9f314b1b5d745d1e5770bb90a0e1f1af2e
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-08-27 15:40:26 -0400
Commit message:

 minor remove spaces
Package: BiocPkgTools
Commit: c302ed2902d8de90a49cc686d903f75f849fcfb0
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-08-27 15:40:18 -0400
Commit message:

 use markdown for roxygen2 cross-refs
Package: BiocPkgTools
Commit: d4e93c293f096a2581947e1d1d91a9a20f3ca01c
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-08-27 15:36:04 -0400
Commit message:

 use markdown in roxygen2 blocks
Package: BiocPkgTools
Commit: f71a2ca3d14886e3853ab9fbb58401465b0570ee
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-08-27 14:52:29 -0400
Commit message:

 version bump 1.27.11
Package: BiocPkgTools
Commit: dadaeab2ec4d56fe48499bd74d9b94d33220d1d7
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-08-27 14:52:20 -0400
Commit message:

 update arg in examples
Package: BiocPkgTools
Commit: ae1b13b4f986a8a2a76f9bc3ae3190c4afcfd662
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-08-27 14:51:14 -0400
Commit message:

 exclude soon to be deprecated rorcid package
Package: DropletUtils
Commit: d85890b5222828f6fbb288cf372a1dd613d0ddee
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2025-08-27 10:53:10 -0700
Commit message:

 Bugfix for two-pass Matrix Market parsing.
Package: plyxp
Commit: d9d960c6eac7e0c4eab89aff588a0aa05fee9a23
Author: jtlandis <jtlandis314@gmail.com>
Date: 2025-08-27 13:38:05 -0400
Commit message:

 some unneeded code
Package: plyxp
Commit: 1f73ff763b1a8b81e0caed7726aed3fb0b33603f
Author: jtlandis <jtlandis314@gmail.com>
Date: 2025-08-26 22:57:38 -0400
Commit message:

 had a typo in argument
Package: plyxp
Commit: 7cd34d6bd9461acf38f5e5bac50fc9a15f11f091
Author: jtlandis <jtlandis314@gmail.com>
Date: 2025-08-26 22:52:26 -0400
Commit message:

 Update PlySummarizedExperiment-methods.Rd
Package: plyxp
Commit: 9bd2849eb66eeb4904d90615409942f5bc3ee93e
Author: jtlandis <jtlandis314@gmail.com>
Date: 2025-08-26 22:52:03 -0400
Commit message:

 fixing errors
Package: plyxp
Commit: cf95700faba397ebaf94b52969c08f3e969a39f9
Author: jtlandis <jtlandis314@gmail.com>
Date: 2025-08-26 17:42:50 -0400
Commit message:

 writing docs
Package: plyxp
Commit: e124fdf1e0f533663a66ef41d1c1d36863d665dc
Author: jtlandis <jtlandis314@gmail.com>
Date: 2025-08-26 17:42:05 -0400
Commit message:

 accidently removed this method...
Package: plyxp
Commit: be1ce2e78e281dbdd1d6dfd88ab493c8b19e4451
Author: jtlandis <jtlandis314@gmail.com>
Date: 2025-08-26 17:39:48 -0400
Commit message:

 adding docs
Package: plyxp
Commit: 28389c984a2db21d6e1a527ec28dcd128d4ca042
Author: jtlandis <jtlandis314@gmail.com>
Date: 2025-08-26 17:39:41 -0400
Commit message:

 trying to align with dplyr in that results are now grouped if object is
grouped
Package: plyxp
Commit: 077b95944db211e708d5544c0787b89f8119c5c0
Author: jtlandis <jtlandis314@gmail.com>
Date: 2025-08-26 17:38:51 -0400
Commit message:

 refactor manager to use an apply function. exposing a "get_chop()"
function for plyxp_mask
Package: plyxp
Commit: ad5a332f4fb5eeb7cdad7ffc0722f27d0946985e
Author: jtlandis <jtlandis314@gmail.com>
Date: 2025-08-26 15:10:12 -0400
Commit message:

 making an assignment function
Package: plyxp
Commit: d689cb77f4c15fd7c73aa7da93e9e7e81becff2f
Author: jtlandis <jtlandis314@gmail.com>
Date: 2025-08-26 15:08:46 -0400
Commit message:

 formatting
Package: plyxp
Commit: c5945ab69afe70aaf5a0a2015b9a9276422a81ab
Author: jtlandis <jtlandis314@gmail.com>
Date: 2025-08-26 15:07:42 -0400
Commit message:

 Update test_dplyr_group_by.R
Package: plyxp
Commit: f6d7698453d9c7cc59415b489cbabc851031a9c4
Author: jtlandis <jtlandis314@gmail.com>
Date: 2025-08-26 15:07:03 -0400
Commit message:

 Add result method to plyxp_mask and plyxp_manager classes. Using the
`result` method to pull ony specific values from mask within slice
method
Package: plyxp
Commit: c4b7a6feee6c3f9197cd2709088a796fdbb7f7c1
Author: jtlandis <jtlandis314@gmail.com>
Date: 2025-08-26 15:05:00 -0400
Commit message:

 Update connect_masks.R
Package: plyxp
Commit: 2104086fb5877f74256d2d5c32faf6e50fa2e01d
Author: jtlandis <jtlandis314@gmail.com>
Date: 2025-08-26 14:22:10 -0400
Commit message:

 deleting browser()
Package: plyxp
Commit: 0b917ae36ac4e47e910659e929f22812b1df3454
Author: jtlandis <jtlandis314@gmail.com>
Date: 2025-08-26 10:04:08 -0400
Commit message:

 Update NEWS
Package: plyxp
Commit: fed69e4854356f73d891b980d9ca650e1d3a1a6a
Author: jtlandis <jtlandis314@gmail.com>
Date: 2025-08-25 15:01:19 -0400
Commit message:

 Condensing down logic revolving around slicing the summarized Experiment
with `[`. Now `plyxp_slice_se()` will handle this case appropriately for
these opperations (even with groups)
Package: plyxp
Commit: 1ff3813772f8e41108c211c6ecd84f999c172af5
Author: jtlandis <jtlandis314@gmail.com>
Date: 2025-08-25 14:21:22 -0400
Commit message:

 Implement missing methods for PlySummarizedExperiment objects
Package: punKEGGer
Commit: 2d8e292a78946ddc4538448ac0282db6476d5ca0
Author: gdj <gdeanda@inmegen.edu.mx>
Date: 2025-08-27 10:47:39 -0600
Commit message:

 Bump version to 0.99.4
Package: punKEGGer
Commit: 2d01158b36aee17ae9d4712b973ad84f0aaf93f6
Author: gdj <gdeanda@inmegen.edu.mx>
Date: 2025-08-27 10:47:39 -0600
Commit message:

 Stop tracking IDE files
Package: punKEGGer
Commit: 3419ff5ac5f15a1573b1cf1908a8c41325fb6da7
Author: gdj <gdeanda@inmegen.edu.mx>
Date: 2025-08-27 10:13:10 -0600
Commit message:

 Add KEGG biocView, URL/BugReports, ORCID; bump to 0.99.3
Package: punKEGGer
Commit: e0259e6ceba256d5d10838976552ff31b54f501d
Author: gdj <gdeanda@inmegen.edu.mx>
Date: 2025-08-27 10:12:51 -0600
Commit message:

 Add KEGG biocView, URL/BugReports, ORCID; bump to 0.99.1
Package: punKEGGer
Commit: 0f6fad7fe3c02b36b6821163e6824644585b9f6e
Author: gdj <gdeanda@inmegen.edu.mx>
Date: 2025-08-27 10:12:14 -0600
Commit message:

 Add KEGG biocView, URL/BugReports, ORCID; bump to 0.99.1
Package: punKEGGer
Commit: 560d85e19af96d0706c145f5df2e2683ec6b25ca
Author: gdj <gdeanda@inmegen.edu.mx>
Date: 2025-08-27 10:10:58 -0600
Commit message:

 Add provenance script for extdata (KEGG + BioMart sources)
Package: punKEGGer
Commit: 5330bfac0adbe36d85a99fd9f736db2829dac7e4
Author: gdj <gdeanda@inmegen.edu.mx>
Date: 2025-08-27 10:05:18 -0600
Commit message:

 Fix LICENSE DCF stub for MIT license
Package: punKEGGer
Commit: caeab784ba194fc0f93757af2312e5a63dfa25be
Author: gdj <gdeanda@inmegen.edu.mx>
Date: 2025-08-27 10:04:43 -0600
Commit message:

 Stop tracking RStudio project files; keep locally via .gitignore
Package: immunotation
Commit: 8fdfeecc0dbc44e6af97414b648b0d2d397d63eb
Author: Katharina Imkeller <ag.imkeller@gmail.com>
Date: 2025-08-27 16:09:25 +0200
Commit message:

 fix decoding check
Package: immunotation
Commit: 21116bd1d5eb33748222fdf20adae6a193a5ef65
Author: Katharina Imkeller <ag.imkeller@gmail.com>
Date: 2025-08-25 13:22:18 +0200
Commit message:

 version correct 2
Package: immunotation
Commit: 0663fe32118ad981f15d0dfeae891f1947fc7777
Author: Katharina Imkeller <ag.imkeller@gmail.com>
Date: 2025-08-25 13:21:47 +0200
Commit message:

 version correct
Package: immunotation
Commit: 72931ca1c664a1e8a9c8405deef73a26366bb1bf
Author: Katharina Imkeller <ag.imkeller@gmail.com>
Date: 2025-08-25 13:14:57 +0200
Commit message:

 version 1.17.2
Package: biomaRt
Commit: f11e024327aab53d10e7e9c0b76d716c948f5fc0
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-08-27 15:49:48 +0200
Commit message:

 Recognize ENSEMBL_MART_ENSEMBL as ensembl in martCheck() (#131)
Package: Pigengene
Commit: 126d6fd9eaaa2d0e12eb4a1cc0ae40eab975bc22
Author: Habil Zare <zare@uthscsa.edu>
Date: 2025-08-27 08:50:33 -0500
Commit message:

 Move
Package: biomaRt
Commit: e93e00b00509e3b92e2d1628d6112c93acba6057
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-08-26 16:32:58 +0200
Commit message:

 Convert roxygen documentation to markdown syntax (#135)
Package: Rarr
Commit: c4c61c4de85ee1aa57b9c12723084c44761b3206
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-08-27 13:22:52 +0200
Commit message:

 Remove unused stringr dependency (#34)
Package: Rarr
Commit: 63932ea88fffed39a168b13b082c1acef796fa59
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-08-27 13:21:35 +0200
Commit message:

 Support "other" numeric datatype
Package: Rarr
Commit: 1c36508071fd7354efeff26eba62db969e8be0e0
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-08-27 13:16:12 +0200
Commit message:

 Use pretty = 4 rather than pretty = TRUE

Default is 2 spaces.
4 spaces is consistent with python and previous versions of this package.
Package: Rarr
Commit: 6dc676877f9b193c965853ce20058f4545c9385b
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-08-26 17:23:27 +0200
Commit message:

 Use curl directly rather than httr (#31)
Package: Rarr
Commit: 5acac5541bf110927bdfa8674992dd08053f3e9b
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-08-26 16:25:17 +0200
Commit message:

 Document lintr changes in NEWS
Package: Rarr
Commit: fc4bdeea9ea844adc547d3eccd5cc8e6d6437c8b
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-08-26 14:43:03 +0200
Commit message:

 Import selectively from jsonlite namespace
Package: Rarr
Commit: d48b0a2efb98baa42f99fa502618a04390d86934
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-08-26 12:53:19 +0200
Commit message:

 Use write_json() directly and rm .format_json()
Package: Rarr
Commit: ab23ae5d775cfac24a70b4802bb8970cf9ed9388
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-08-26 13:41:52 +0200
Commit message:

 Add lintr config file and GitHub Action
Package: Rarr
Commit: 0d8529421209a1114866caff2991c1fc644b2b58
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-08-26 13:39:43 +0200
Commit message:

 Reduce nesting
Package: Rarr
Commit: 5c75d4088c61ade1961836ce147c1bdb6fec7171
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-08-26 13:39:26 +0200
Commit message:

 Add nolint comments for false positives
Package: Rarr
Commit: 46a63b80c0e237e8b799197ec392b07cc5a4899b
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-08-26 14:03:52 +0200
Commit message:

 Use stop() early in the function
Package: Rarr
Commit: d165fd50bbf26b55462b26885814c476cd2b9a98
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-08-26 14:15:12 +0200
Commit message:

 Use paste() where appropriate
Package: Rarr
Commit: b753a4fc025db460a2d561a471b91dafb517fe08
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-08-26 13:26:44 +0200
Commit message:

 Remove commented code
Package: Rarr
Commit: fa25b0ba221ac298d0a8267cb5775f515e1b0805
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-08-26 13:10:16 +0200
Commit message:

 Fix whitespace in Rmd documents
Package: Rarr
Commit: 603f507b275447582dd02aaf4e37eb27a6bc88dd
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-08-26 12:43:13 +0200
Commit message:

 Avoid exists() approach
Package: Rarr
Commit: 51a6ed40b14af0fab0c1c5a08549db8f3df62c43
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-08-26 12:42:48 +0200
Commit message:

 Set on.exit() next to connection opening step
Package: Rarr
Commit: f5494c5fe4a5fbc60990daf891398d6ba340b732
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-08-26 11:44:13 +0200
Commit message:

 Simplify raw vector initialization
Package: Rarr
Commit: 9738a20ae5d0ae82cde4de14a8492a5256975378
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-08-26 11:43:58 +0200
Commit message:

 Fix typo
Package: Rarr
Commit: 4ff3273e5ce9166482b58ac1408e267023ac7093
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-08-25 10:13:58 +0200
Commit message:

 Use %||% where appropriate
Package: Rarr
Commit: 00d5a210190d17f1820d17e20f4d9daee264f12c
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-08-23 20:40:17 +0200
Commit message:

 Simplify zarray creation
Package: Rarr
Commit: 586ee23833ad988d3d15bb408cf6ce2bec53c473
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-08-23 20:26:10 +0200
Commit message:

 Get boolean directly without ifelse()
Package: Rarr
Commit: b4f9b537c98e2ac6dd555ccf9c16f27472cc04a4
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-08-23 20:25:53 +0200
Commit message:

 Use fixed = TRUE in regexes where relevant
Package: Rarr
Commit: d34cbd6d63a3b1a6b15d10f2d498b80f931a01a0
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-08-18 10:47:06 +0200
Commit message:

 Remove unnecessary c()
Package: Rarr
Commit: 61d5a1697a27ce204ae3bdf78b1d2f54fd583e35
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-08-18 10:46:54 +0200
Commit message:

 Use lengths()
Package: Rarr
Commit: 28cf5969e411debd8248417852b907901430763c
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-08-15 15:32:56 +0200
Commit message:

 Remove unused variable
Package: Rarr
Commit: 0b1c9debdbcff9cea352191858074521fa37b83e
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-07-25 19:08:55 +0200
Commit message:

 Fix variable initialization

rep() doesn't have an n= argument and this call currently always returns FALSE (length 1)
Package: Rarr
Commit: c834110002eb354e278f67cda17c66adbb3c4b7d
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-07-18 19:40:12 +0200
Commit message:

 Use double logical operators in if
Package: Rarr
Commit: a307ad9151f62e6635d1802360311375df78e249
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-08-26 14:32:03 +0200
Commit message:

 Convert to upper or lower only once
Package: Rarr
Commit: f439833f58dad0b4647adcf20c50981099bebb83
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-08-26 12:43:59 +0200
Commit message:

 Set R CMD check to a stricter setting and fix NOTEs and WARNINGs (#27)
Package: Rarr
Commit: 1118f8cb1bfbafb2323591e7010fb818be838719
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-08-26 10:58:30 +0200
Commit message:

 Consolidate NEWS under a single version header (#29)
Package: Rarr
Commit: c4766950ecda0a526ebed6fb5a3df0a7cce4a841
Author: Artür Manukyan <artur-man@hotmail.com>
Date: 2025-08-25 17:11:10 +0200
Commit message:

 add support for reading, writing and updating attributes (#19)

Co-authored-by: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Package: Rarr
Commit: 78c8cc05201aea2be05eee861d0b5bc21c112220
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-08-25 11:41:14 +0200
Commit message:

 Add air commit to git-blame-ignore-revs

To keep git blame simple and clean
Package: Rarr
Commit: 18cdd7b4142a9485127b71c384aac69556025a47
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-08-22 16:50:15 +0200
Commit message:

 Set up and run air (#26)
Package: Rarr
Commit: 47d52da77ac581d3357b8faac852cb3949f10905
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-08-22 14:47:36 +0200
Commit message:

 Expand .normalize_zarr_path() tests and fix edge cases (#25)
Package: smoppix
Commit: adeab581d5f43b6a30dc6444b293a30e38265e79
Author: stijn <stijn.hawinkel@psb.ugent.be>
Date: 2025-08-27 11:16:45 +0200
Commit message:

 export loadbalancebplapply in news and description
Package: smoppix
Commit: 3a54c8dfef75423f400219e5c7aab9dabacc1279
Author: stijn <stijn.hawinkel@psb.ugent.be>
Date: 2025-08-27 11:15:27 +0200
Commit message:

 export loadBalanceBplapply for use in other packages
Package: gDRimport
Commit: 9a5a6dda54f7d8182dfb27a275b5f30b4791c91a
Author: Bartek <32614650+bczech@users.noreply.github.com>
Date: 2025-08-27 11:07:35 +0200
Commit message:

 Merge pull request #107 from gdrplatform/GDR-771

Gdr 771
Package: gDRimport
Commit: 8564d3fd7a02b3eb9dfc09239f9ab94565f09e44
Author: Bartek Czech <bartosz.w.czech@gmail.com>
Date: 2025-08-27 10:06:56 +0200
Commit message:

 ci: trigger build
Package: gDRimport
Commit: dd64ed881ea0abeb66c09f876747ec529d4803cd
Author: Bartek Czech <bartosz.w.czech@gmail.com>
Date: 2025-08-26 16:08:51 +0200
Commit message:

 ci: trigger build
Package: gDRimport
Commit: a6d8b2a3d9348536cbb4e7ce0f682fa556673a5c
Author: Bartek Czech <bartosz.w.czech@gmail.com>
Date: 2025-08-26 16:08:21 +0200
Commit message:

 ci: trigger build
Package: gDRimport
Commit: ff1e1bb2e04c511b7233e62137e4aad0b6d46a4f
Author: Bartek <32614650+bczech@users.noreply.github.com>
Date: 2025-08-21 09:24:22 +0200
Commit message:

 refactor: Update load_files.R
Package: gDRimport
Commit: c02dd6c5af03d935485a1e31c62d7e6aabbd261c
Author: Bartek Czech <bartosz.w.czech@gmail.com>
Date: 2025-08-12 08:20:32 +0200
Commit message:

 chore: bump version and update NEWS.md
Package: gDRimport
Commit: 860d1a541b89190651d711c0ba45980d48d44bbd
Author: Bartek Czech <bartosz.w.czech@gmail.com>
Date: 2025-08-12 08:20:28 +0200
Commit message:

 fix: usage of ifelse
Package: gDRutils
Commit: 7911c112086d0b92c1267261153b0fefcc567dfa
Author: Bartek <32614650+bczech@users.noreply.github.com>
Date: 2025-08-27 11:07:29 +0200
Commit message:

 Merge pull request #172 from gdrplatform/GDR-771

Gdr 771
Package: gDRutils
Commit: 35b969c8bf5d2176709b8ecfc57d040ed293792b
Author: Bartek Czech <bartosz.w.czech@gmail.com>
Date: 2025-08-27 10:09:00 +0200
Commit message:

 ci: trigger build
Package: gDRutils
Commit: 90cdac64a238fba9c74725909b399bd8e84eeb72
Author: Bartek Czech <bartosz.w.czech@gmail.com>
Date: 2025-08-26 16:09:20 +0200
Commit message:

 ci: trigger build
Package: gDRutils
Commit: f7bf7c70df30c567ca26407703504888bccc49ad
Author: Bartek <32614650+bczech@users.noreply.github.com>
Date: 2025-08-21 09:18:50 +0200
Commit message:

 refactor: Update fit_curves.R
Package: gDRutils
Commit: 3d36b43c1ffb2948f6fc8666d22876a063d14af4
Author: Bartek Czech <bartosz.w.czech@gmail.com>
Date: 2025-08-12 07:46:11 +0200
Commit message:

 chore: bump version and update NEWS.md
Package: gDRutils
Commit: 071e05fab457b4451881a3cf4f1dec67bc93c98a
Author: Bartek Czech <bartosz.w.czech@gmail.com>
Date: 2025-08-12 07:45:35 +0200
Commit message:

 refactor: fix usage of ifelse
Package: scGraphVerse
Commit: 0b6084409f0a7ea950bbe0fe257fcf60c340bd44
Author: francescoc <francesco.cecerengs@gmail.com>
Date: 2025-08-27 10:22:13 +0200
Commit message:

 fix count_matrices to 2
Package: scGraphVerse
Commit: 4539d637b39c545634ca787a59f1a988905d6f8e
Author: francescoc <francesco.cecerengs@gmail.com>
Date: 2025-08-27 09:49:08 +0200
Commit message:

 fix WARN time
Package: SeqArray
Commit: 4cc25c2cf8ac710174c922c0acf099b86d2beb6f
Author: Xiuwen Zheng <zhengxwen@gmail.com>
Date: 2025-08-26 23:27:11 -0500
Commit message:

 improved workload balancing
Package: EnrichmentBrowser
Commit: 2ce1126725e4d694e2e377aebd84e628cdd4b5d4
Author: lgeistlinger <ludwig.geistlinger@gmail.com>
Date: 2025-08-26 22:46:53 -0400
Commit message:

 getGenesets: fix msigdb mouse collections
Package: EnrichmentBrowser
Commit: 700e85006f7dee6b98bd0ff5dbefd5d1208e1d7e
Author: lgeistlinger <ludwig.geistlinger@gmail.com>
Date: 2025-08-26 22:34:56 -0400
Commit message:

 getGenesets: fix msigdb mouse collections
Package: EnrichmentBrowser
Commit: aa9388bbf540528de1b928479e737c8893f10ef4
Author: lgeistlinger <ludwig.geistlinger@gmail.com>
Date: 2025-08-18 16:30:24 -0400
Commit message:

 pull upstream changes
Package: EnrichmentBrowser
Commit: bec2c849fcd40bfc542ba82238af1a6cbb706a58
Author: lgeistlinger <ludwig.geistlinger@gmail.com>
Date: 2025-07-10 11:15:01 -0400
Commit message:

 Bump version and update date
Package: EnrichmentBrowser
Commit: d081f32513ec5f63689999edf2f83484060f2960
Author: lgeistlinger <ludwig.geistlinger@gmail.com>
Date: 2025-07-10 10:49:24 -0400
Commit message:

 Bump version and update date
Package: scRNAseqApp
Commit: 0b21d81422b0b64c2d31d27d9fc6452cb226dd99
Author: Jianhong Ou <jianhong.ou@gmail.com>
Date: 2025-08-26 20:59:40 -0400
Commit message:

 add support for dark mode.
Package: scGraphVerse
Commit: ff7668fcede03a98655b7e04a87c7ad69e4a9c59
Author: francescoc <francesco.cecerengs@gmail.com>
Date: 2025-08-27 00:47:59 +0200
Commit message:

 fix compare_consensus example
Package: scGraphVerse
Commit: 10e47e984922fb2365a4fdef66d533ac4c466dd6
Author: francescoc <francesco.cecerengs@gmail.com>
Date: 2025-08-27 00:07:30 +0200
Commit message:

 fix time WARN
Package: cellmig
Commit: c94f7bcfcbcdda6cc50bf07714b78444b72eaae1
Author: snaketron <simo.kitanovski@uni-due.de>
Date: 2025-08-26 23:38:24 +0200
Commit message:

 more tests, dev-cov >80%
Package: scGraphVerse
Commit: db29f1e9d52a0769561bc76ffcd765b41e88aefc
Author: francescoc <francesco.cecerengs@gmail.com>
Date: 2025-08-26 23:36:09 +0200
Commit message:

 fix selgene example
Package: SETA
Commit: aab1357007bec58b198f2127dcaa719f7f24b903
Author: kylekimler <kylejkimler@gmail.com>
Date: 2025-08-26 14:02:58 -0400
Commit message:

 version bump and remote setup
Package: SETA
Commit: 98606b59a3149c4c3f54a8b5dc2d207b30c81746
Author: kylekimler <kylejkimler@gmail.com>
Date: 2025-08-22 17:56:22 -0400
Commit message:

 special char cleanup
Package: SETA
Commit: df14ec4069feb9cba43ab685d2760a54a8a5e71f
Author: kylekimler <kylejkimler@gmail.com>
Date: 2025-08-22 17:48:29 -0400
Commit message:

 ubuntu latex ERROR updates and other notes from bioconductor
Package: scRNAseqApp
Commit: 7e14a8f87825cc387581ec3da2bdccb59cf0efaa
Author: Jianhong Ou <jianhong.ou@gmail.com>
Date: 2025-08-26 10:55:22 -0400
Commit message:

 update search table when updateGeneExprPlot.
Package: scRNAseqApp
Commit: db52296c907ed758fa76f7f9ef802c91dbfcff65
Author: Jianhong Ou <jianhong.ou@gmail.com>
Date: 2025-08-26 09:53:26 -0400
Commit message:

 remove duplicated removeModal()
Package: scRNAseqApp
Commit: bed2dd71b121b39af6bbd5d447020c5538190046
Author: Jianhong Ou <jianhong.ou@gmail.com>
Date: 2025-08-26 09:42:32 -0400
Commit message:

 Add support for config.dcf file
Package: gDRcore
Commit: 440ba6de8647b91b268f061cb20e8de0d2a8c7cb
Author: Bartek <32614650+bczech@users.noreply.github.com>
Date: 2025-08-26 16:47:20 +0200
Commit message:

 Merge pull request #182 from gdrplatform/GDR-771

Gdr 771
Package: gDRcore
Commit: 7c301bdef1f640b41ee2d64fd864505f0652785f
Author: Bartek Czech <bartosz.w.czech@gmail.com>
Date: 2025-08-26 16:09:04 +0200
Commit message:

 ci: trigger build
Package: gDRcore
Commit: 39b49720229d4465e7c883adfede59d8cb85a3ff
Author: Bartek <32614650+bczech@users.noreply.github.com>
Date: 2025-08-21 09:34:52 +0200
Commit message:

 refactor: Update normalize_SE.R
Package: gDRcore
Commit: 13aca1e789dfa1826e03fa0330d77b9745b4b075
Author: Bartek <32614650+bczech@users.noreply.github.com>
Date: 2025-08-21 09:32:42 +0200
Commit message:

 refactor: Update fit_SE.combinations.R
Package: gDRcore
Commit: 19fdb4619b0980c5c04f9ec2469805d560798837
Author: Bartek Czech <bartosz.w.czech@gmail.com>
Date: 2025-08-12 08:00:18 +0200
Commit message:

 chore: bump version and update NEWS.md
Package: gDRcore
Commit: abf92d4c798ee73277b3ec4796fb631a8b5efa36
Author: Bartek Czech <bartosz.w.czech@gmail.com>
Date: 2025-08-12 07:59:37 +0200
Commit message:

 fix: usage of ifelse
Package: MSstatsShiny
Commit: fdef91afbfac6637ca78197bb37ea898b502a0fa
Author: tonywu1999 <anthonywu92@gmail.com>
Date: 2025-08-26 10:28:04 -0400
Commit message:

 Bump version from 1.11.3 to 1.11.4
Package: MSstatsShiny
Commit: 882ff3fdf10e1fed6e4ee562f28791d61eaf8566
Author: tonywu1999 <anthonywu92@gmail.com>
Date: 2025-08-26 10:27:06 -0400
Commit message:

 fix(download-button): Add error handling for download button (#112)
Package: MSstatsShiny
Commit: a3205e305e0f7a1769cf64590895532d49d6fa8b
Author: tonywu1999 <anthonywu92@gmail.com>
Date: 2025-08-26 10:10:58 -0400
Commit message:

 feat(network-interpretation): Add button to download network analysis code (#111)
Package: damidBind
Commit: 15fe5a105d38572382d284cc71c3102050b3eb48
Author: Owen Marshall <owen.marshall@utas.edu.au>
Date: 2025-08-26 11:58:23 +0000
Commit message:

 Added data provenance markdown detailing generation pipeline for files in inst/extdata
Package: spatialFDA
Commit: fc15443378ea7c2ca7e42b1b0b0cd320b8fc544a
Author: mjemons <martin.emons@gmail.com>
Date: 2025-08-26 13:30:06 +0200
Commit message:

 new weighting, bubble plot
Package: MSnbase
Commit: ec1e05c5e1b87d323bc4bbd70f0538ad4ab93952
Author: Laurent Gatto <lgatto@protonmail.ch>
Date: 2025-08-26 13:16:43 +0200
Commit message:

 fix PSMatch dependency version
Package: Pedixplorer
Commit: 34518cb7f59a244a3b0e1cc892e5db5b80cbde03
Author: Louis Le Nézet <58640615+LouisLeNezet@users.noreply.github.com>
Date: 2025-08-26 12:40:01 +0200
Commit message:

 Add Ggplot legend (#36)

* Simplify message kindepth error

* Try fix legend ggplot

* Fix ggplot legend

* Update documentation and tests

* Update test plot legend

* Update version and News

* Add missing new line

* Fix vignettte

* Fix vignette

---------

Co-authored-by: Louis Le Nezet <louislenezet@gamil.com>
Package: Pedixplorer
Commit: b21a6dcbf80300575c308982e82bde0dcc516067
Author: Louis Le Nézet <58640615+LouisLeNezet@users.noreply.github.com>
Date: 2025-07-24 10:19:43 +0200
Commit message:

 Update to Bioconductor (#35)

Co-authored-by: Louis Le Nezet <louislenezet@gamil.com>
Package: SpectriPy
Commit: e09cc13033857fb2ace2350af0fbdd05fed06e1a
Author: Johannes Rainer <5506112+jorainer@users.noreply.github.com>
Date: 2025-08-26 07:56:00 +0200
Commit message:

 Merge pull request #82 from rformassspectrometry/py_require

Use reticulate's py_require() to manage the Python installation and environment
Package: SpectriPy
Commit: 8a8c9b23b5f063b822906e3f84b3e0c86b306035
Author: jorainer <johannes.rainer@gmail.com>
Date: 2025-08-26 07:36:10 +0200
Commit message:

 Address Marilyn's comments
Package: SpectriPy
Commit: 6096093611c0397f25e6a8b8ad8c25a4a5aa512c
Author: jorainer <johannes.rainer@gmail.com>
Date: 2025-08-25 15:17:48 +0200
Commit message:

 Remove links to BioC release
Package: SpectriPy
Commit: 93b4fe60a5f4325882a99ed2a999291601a5547e
Author: jorainer <johannes.rainer@gmail.com>
Date: 2025-08-22 08:49:13 +0200
Commit message:

 Merge remote-tracking branch 'origin/main' into py_require
Package: SpectriPy
Commit: 81004544045e3e6c7084cec0f157ca6257e4a4d5
Author: jorainer <johannes.rainer@gmail.com>
Date: 2025-08-22 08:02:09 +0200
Commit message:

 docs: complete installation and troubleshooting
Package: SpectriPy
Commit: eb653805d13ebf7fff625f12d1d607cab9007193
Author: jorainer <johannes.rainer@gmail.com>
Date: 2025-08-22 07:19:12 +0200
Commit message:

 docs: add/expand installation instructions
Package: SpectriPy
Commit: 47f3f38c8f864e154d0b5c0995962d0fdfb09e2e
Author: jorainer <johannes.rainer@gmail.com>
Date: 2025-08-21 07:38:53 +0200
Commit message:

 tests: add unit tests for package loading
Package: SpectriPy
Commit: d435ffc7e94b4af7c547f1b59b9aff6137a58942
Author: Johannes Rainer <5506112+jorainer@users.noreply.github.com>
Date: 2025-07-09 10:21:26 +0200
Commit message:

 Merge pull request #80 from rformassspectrometry/jomain

Add support for `setBackend`
Package: SpectriPy
Commit: d442b7865002c8ac19d17dfc2dd23219a3f42e9b
Author: jorainer <johannes.rainer@gmail.com>
Date: 2025-06-18 16:42:47 +0200
Commit message:

 feat: add support for parameter data to backendInitialize

- Add support for parameter `data` to `backendInitialize,MsBackendPy`: enables
  changing the backend of a `Spectra` object with `setBackend()` to a
  `MsBackendPy`.
Package: SpectriPy
Commit: 572b41dfee75e84583e15a6729d79d598da0ac3d
Author: jorainer <johannes.rainer@gmail.com>
Date: 2025-06-18 06:25:48 +0200
Commit message:

 Merge branch 'main' into jomain
Package: SpectriPy
Commit: d3cb4b398b58b4e7beb2fb4ce9715e87b76eb842
Author: jorainer <johannes.rainer@gmail.com>
Date: 2025-05-22 07:40:42 +0200
Commit message:

 tests: refactor zzz.R and add unit tests
Package: SpectriPy
Commit: b6d0297448f9426fe73d43793f92812a01286e11
Author: jorainer <johannes.rainer@gmail.com>
Date: 2025-05-21 16:23:49 +0200
Commit message:

 Merge branch 'bioc_submission' into jomain
Package: SpectriPy
Commit: 41f965baf58542faf92dcb2ab3f377ea88fccb51
Author: jorainer <johannes.rainer@gmail.com>
Date: 2025-05-21 08:19:11 +0200
Commit message:

 refactor: package loading
Package: SpectriPy
Commit: 7d6456d18887ce1c1dfc2e12fb48f1bd330c877a
Author: jorainer <johannes.rainer@gmail.com>
Date: 2025-05-20 08:19:25 +0200
Commit message:

 tests: add more unit tests
Package: SpectriPy
Commit: ac0d0b0c521c590aff452a17ce16d6e8d6aa883e
Author: jorainer <johannes.rainer@gmail.com>
Date: 2025-05-05 07:38:34 +0200
Commit message:

 tests: add unit tests for zzz.R
Package: SpectriPy
Commit: 3e8d07bc88fd9d524f9580ad31228f5b6cad75a4
Author: jorainer <johannes.rainer@gmail.com>
Date: 2025-05-05 06:44:01 +0200
Commit message:

 Merge branch 'main' into jomain
Package: SpectriPy
Commit: 22d5f81a89f976179a051896ed3b19b7028b38f9
Author: jorainer <johannes.rainer@gmail.com>
Date: 2025-04-22 07:50:04 +0200
Commit message:

 feat: add support for data parameter in backendInitialize()
Package: SpectriPy
Commit: cee534239964a6d2ac60a988d59e64f5c2f8f667
Author: jorainer <johannes.rainer@gmail.com>
Date: 2025-04-18 08:47:36 +0200
Commit message:

 feat: backendInitialize to support data parameter
Package: scGraphVerse
Commit: 1ccc84fc18640ed6f19bfe0b088d2f1aa3f98f09
Author: francescoc <francesco.cecerengs@gmail.com>
Date: 2025-08-26 09:44:23 +0200
Commit message:

 fix example union
Package: vsclust
Commit: b9dd6eb2947a402c52015c44251a19b370f6537f
Author: veitveit <veits@bmb.sdu.dk>
Date: 2025-08-09 09:34:06 +0200
Commit message:

 fixed order of returned table for extenal apps
Package: vsclust
Commit: 28b6145ac739ed057d80018802f12b516ff430fc
Author: veitveit <veits@bmb.sdu.dk>
Date: 2025-07-07 10:20:40 +0200
Commit message:

 Merge branch 'master' of github.com:computproteomics/vsclust
Package: vsclust
Commit: 7433cddd520b6dfc972d6d39628a04196d0f2a9b
Author: Veit Schwämmle <veitveit@gmail.com>
Date: 2025-03-11 11:10:57 +0100
Commit message:

 Update README.md
Package: openCyto
Commit: 8bdcadeeec798931f539809c59070f9863fefb7b
Author: Mike Jiang <mike@ozette.com>
Date: 2025-08-25 17:02:07 -0700
Commit message:

 bump
Package: openCyto
Commit: e8b2a1744420f52e8237e2c8f0ce03629aec9094
Author: Mike Jiang <mike@ozette.com>
Date: 2025-08-25 17:01:38 -0700
Commit message:

 Merge remote-tracking branch 'conductor/devel' into devel
Package: openCyto
Commit: a2d54be05b72c3490bc919aeddfdb6e852ab8a73
Author: Mike Jiang <mike@ozette.com>
Date: 2025-08-25 16:56:35 -0700
Commit message:

 remove unused offensive include that breaks mac build #272
Package: scGraphVerse
Commit: 68410d331aeaaa16e8a82fb66ea56169c351168c
Author: francescoc <francesco.cecerengs@gmail.com>
Date: 2025-08-26 01:34:25 +0200
Commit message:

 fix toy examples
Package: scGraphVerse
Commit: 05286fd0519b84c28e93324ebea469f28b559534
Author: francescoc <francesco.cecerengs@gmail.com>
Date: 2025-08-26 01:01:12 +0200
Commit message:

 fix toy data£
Package: scGraphVerse
Commit: 09b1e94a50685ba3bee7abe10dcd427de3231c6c
Author: francescoc <francesco.cecerengs@gmail.com>
Date: 2025-08-26 00:11:44 +0200
Commit message:

 fix init_py and WARN time
Package: scGraphVerse
Commit: 4997a1dbc95fd549c742e4cc02399c8a225db75a
Author: francescoc <francesco.cecerengs@gmail.com>
Date: 2025-08-25 23:34:08 +0200
Commit message:

 fix WARN time and ERROR init_py
Package: MungeSumstats
Commit: 3b59105b8849be2aa76ff9408701f70602f5ed07
Author: Al-Murphy <alanmurph94@hotmail.com>
Date: 2025-08-25 17:10:21 -0400
Commit message:

 Remove unnecessary internet connection test
Package: scGraphVerse
Commit: 2ba423a8e5187dd58e5f3366578c703635a87388
Author: francescoc <francesco.cecerengs@gmail.com>
Date: 2025-08-25 22:14:08 +0200
Commit message:

 fix dependencies Build
Package: scGraphVerse
Commit: a615a73a9ea47f9de6fa2cd2f4b4759d3cd6947d
Author: francescoc <francesco.cecerengs@gmail.com>
Date: 2025-08-25 21:32:51 +0200
Commit message:

 fix systemInfo ERROR
Package: scGraphVerse
Commit: 58bd62b57ef6dd314cd46a19d99ca49761272634
Author: francescoc <francesco.cecerengs@gmail.com>
Date: 2025-08-25 20:54:40 +0200
Commit message:

 fix version
Package: scGraphVerse
Commit: 514dde0a035f03d8a51a0ae66826cb812af1c0d8
Author: francescoc <francesco.cecerengs@gmail.com>
Date: 2025-08-25 20:54:17 +0200
Commit message:

 fix connections left open
Package: scGraphVerse
Commit: 423b795b9da1142adcbb4afca78c08e36163dd9d
Author: francescoc <francesco.cecerengs@gmail.com>
Date: 2025-08-25 19:55:34 +0200
Commit message:

 fix Bump version
Package: scGraphVerse
Commit: bdfa7eb0b2620ffb98ded65a533b25dafd90e27f
Author: francescoc <francesco.cecerengs@gmail.com>
Date: 2025-08-25 19:55:05 +0200
Commit message:

 fix ERROR GenomeInfoDb and NOTES
Package: scGraphVerse
Commit: 85bcfbee12ee9f9dd241ab81c5832761167d2ad9
Author: francescoc <francesco.cecerengs@gmail.com>
Date: 2025-08-25 18:52:22 +0200
Commit message:

 bump package version
Package: GEOquery
Commit: deb63a18e0e6e8ab424dc7af922443ce7ca353fc
Author: Sean Davis <seandavi@gmail.com>
Date: 2025-08-25 12:30:39 -0400
Commit message:

 quarto vignette
Package: GEOquery
Commit: abf99f6e73642d0cd8b1f65d642d7070411ba871
Author: Sean Davis <seandavi@gmail.com>
Date: 2025-08-25 12:28:03 -0400
Commit message:

 vignette builder now quarto
Package: scRNAseqApp
Commit: c360b019aa48d66131ccd93a4f1232a4fbf901af
Author: Jianhong Ou <jianhong.ou@gmail.com>
Date: 2025-08-25 11:14:46 -0400
Commit message:

 update css.
Package: biomaRt
Commit: 398d17b5da91ad82ba98260126adcd34452d2fa0
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-08-25 16:15:13 +0200
Commit message:

 Document support on R 4.1.0
Package: DeeDeeExperiment
Commit: 101435d700f4de7814c743eb2bf6aaa2416138d8
Author: Najla Abassi <112277365+NajlaAbassi@users.noreply.github.com>
Date: 2025-08-25 15:05:50 +0200
Commit message:

 Merge pull request #9 from imbeimainz/bioc_review

Bioc review
Package: DeeDeeExperiment
Commit: 8eb9e2bd680e8ad75dd3927d4763901068de7c26
Author: Najla Abassi <abassi.nejla96@gmail.com>
Date: 2025-08-25 15:04:02 +0200
Commit message:

 version bump 0.99.5
Package: DeeDeeExperiment
Commit: 4e7b5268aa76390bcfb014cdc9ec4d0fee519daa
Author: Najla Abassi <abassi.nejla96@gmail.com>
Date: 2025-08-25 15:03:46 +0200
Commit message:

 remove redundant class definition
Package: BiocFileCache
Commit: f5c504ad42978a4f0eaccfc3ed24ee66ab4167df
Author: lshep <lori.shepherd@roswellpark.org>
Date: 2025-08-25 08:42:10 -0400
Commit message:

 version bump for test update
Package: BiocFileCache
Commit: eb912664194e6267f7095c942c9b4c24d84a15bd
Author: lshep <lori.shepherd@roswellpark.org>
Date: 2025-08-25 08:41:23 -0400
Commit message:

 Merge pull request #67 from Bioconductor/sqlite_file_update

update sqlite test file location
Package: BiocFileCache
Commit: 762d9ddd28c57f38bc28d30411210396f2afb06f
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-08-22 15:28:49 -0400
Commit message:

 update sqlite test file location
Package: biomaRt
Commit: b80f2ea761e47e2b4ead42be3a0ae4db2c281ad8
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-08-25 11:36:17 +0200
Commit message:

 Add NEWS about R CMD check NOTE and WARNINGs
Package: biomaRt
Commit: 722340125aeea898890ef8198cc673c36c046b35
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-08-25 10:39:48 +0200
Commit message:

 Use r-lib version of check action

To be able to set custom level of alert in R CMD check
Package: biomaRt
Commit: 005440e8254378ccde552d87da78d2edede0b2bd
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-08-25 11:31:28 +0200
Commit message:

 Use aliases approach for biomaRt-deprecated

To avoid having a usage section that causes warnings about undocumented arguments
Package: biomaRt
Commit: 92a21a603dd67f89809f20adbab89e3814bb9e23
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-08-25 10:49:48 +0200
Commit message:

 Document object parameter
Package: biomaRt
Commit: 4108a84221c48c9b79d7ebb0eec1f72efc5a237a
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-08-25 10:47:16 +0200
Commit message:

 Use rdname rather than alias
Package: XAItest
Commit: 1f7a5f7a475a497b12b07008dbdad4101386cb71
Author: gui <ghislain.fievet@gmail.com>
Date: 2025-08-25 14:18:00 +0200
Commit message:

 fix genScenario
Package: immunotation
Commit: f3d1e519b9f032095703480125a8a0f60715ff21
Author: Katharina Imkeller <ag.imkeller@gmail.com>
Date: 2025-08-25 13:14:57 +0200
Commit message:

 version 1.17.2
Package: immunotation
Commit: 39e414d76b7bdf932ef5dc99a5d77927e7f65013
Author: Katharina Imkeller <ag.imkeller@gmail.com>
Date: 2025-08-25 13:08:03 +0200
Commit message:

 fixed URL update from AFND
Package: cellmig
Commit: 22c37baef31ae8aff88aa1d035b9fa4f2015d7ec
Author: snaketron <simo.kitanovski@uni-due.de>
Date: 2025-08-25 12:30:59 +0200
Commit message:

 bump, fix DESCRIPTION, add news
Package: TFEA.ChIP
Commit: 249fa53ecfb2d54d7c3fa0a9e87287ecbbce27f1
Author: yosra <yosraberrouayel@gmail.com>
Date: 2025-08-25 11:23:25 +0200
Commit message:

 modif gitignore
Package: FLAMES
Commit: 1f17e9d7f01e7ee1029f3e82e608a26b86e6ab6f
Author: Changqing Wang <wang.ch@wehi.edu.au>
Date: 2025-08-25 16:02:57 +1000
Commit message:

 chore: set no model-coverage default for oarfish
Package: FLAMES
Commit: 01d612d4c0ff83bc472d204837befed2cc268126
Author: Changqing Wang <wang.ch@wehi.edu.au>
Date: 2025-08-25 12:00:38 +1000
Commit message:

 feat: add additional_arguments for BLAZE
Package: iModMixData
Commit: 0854a28a4bf4935d4d9e736938e96323603e21dc
Author: Isis Narvaez-Bandera <isis.narvaez@upr.edu>
Date: 2025-08-24 22:27:03 -0400
Commit message:

 Citation with doi
Package: iModMixData
Commit: b113e2ef008e4fd401d1eccccff662ec75e4375b
Author: Isis Narvaez-Bandera <isis.narvaez@upr.edu>
Date: 2025-08-24 22:01:21 -0400
Commit message:

 Version: 0.99.4
Package: iModMixData
Commit: b1aae30105dfcf4c0304cb454daee5c90b66b81e
Author: Isis Narvaez-Bandera <isis.narvaez@upr.edu>
Date: 2025-08-24 21:57:19 -0400
Commit message:

 BioCheck 0 ERRORS | ⚠ 0 WARNINGS | ℹ 2 NOTES
Package: FLAMES
Commit: 9b07c70510c359fb4cc3a370460f1e9b665170f1
Author: Changqing Wang <wang.ch@wehi.edu.au>
Date: 2025-08-22 12:35:45 +1000
Commit message:

 feat: add additional_arguments for oarfish
Package: FLAMES
Commit: 3f809af0e09e739e96e98455e4d44e4de8f19b10
Author: Changqing Wang <wang.ch@wehi.edu.au>
Date: 2025-08-22 11:22:09 +1000
Commit message:

 feat: add plot_durations
Package: iModMixData
Commit: 2cab5515e2257132a4171d9827c7b7d2964fa68e
Author: Isis Narvaez-Bandera <isis.narvaez@upr.edu>
Date: 2025-08-24 17:26:10 -0400
Commit message:

 Update version
Package: iModMixData
Commit: f9c771bb07f891ea4fb48e5f74c974d8eb86168c
Author: Isis Narvaez-Bandera <isis.narvaez@upr.edu>
Date: 2025-08-24 17:24:11 -0400
Commit message:

 Bioconductor suggestions
Package: XAItest
Commit: 88b736dd4b78721a138a49d201654bdf237ea933
Author: gui <ghislain.fievet@gmail.com>
Date: 2025-08-24 15:23:24 +0200
Commit message:

 add scenario generation and addSimThresh fct
Package: scRNAseqApp
Commit: 6e74ad937968aed1dad9cbfc234fc24e39086b99
Author: Jianhong Ou <jianhong.ou@gmail.com>
Date: 2025-08-23 20:08:51 -0400
Commit message:

 Add close and delete button for issues.
Package: SuperCellCyto
Commit: f631cc60bdd46bcacc67ce01c5b9cee7f5b3f42b
Author: Givanna Putri <ghar1821@users.noreply.github.com>
Date: 2025-08-23 18:48:26 +1000
Commit message:

 Merge pull request #3 from phipsonlab/fix-bioc-error

Fix bioc error
Package: SuperCellCyto
Commit: b9c2ef3f81c5cfb42b424718b24611838de6db15
Author: Givanna Putri <givanna.h@gmail.com>
Date: 2025-08-23 12:01:54 +1000
Commit message:

 bump version
Package: SuperCellCyto
Commit: 73fa665f032d7461347e8cb76b8280c8efc07510
Author: Givanna Putri <givanna.h@gmail.com>
Date: 2025-08-23 11:58:52 +1000
Commit message:

 move data to inst and add chunk labels
Package: SuperCellCyto
Commit: 982db8f4c1bf1495deddc41475e89fd8c6c88a9b
Author: Givanna Putri <givanna.h@gmail.com>
Date: 2025-08-23 10:05:11 +1000
Commit message:

 changed paste to sprintf
Package: RbowtieCuda
Commit: 0fa036d62633ce263832151aa2e17ef79af7cba8
Author: FranckRICHARD01 <franckrichard033@gmail.com>
Date: 2025-08-23 11:50:58 +0200
Commit message:

 version 1.1.8
Package: scGraphVerse
Commit: 46dde01bec3f1240e69f7e08cb4a33d640ea1b0a
Author: francescoc <francesco.cecerengs@gmail.com>
Date: 2025-08-23 10:49:22 +0200
Commit message:

 add authors
Package: scGraphVerse
Commit: 104d10fba3bd6135f1ca416d4b39354f1fbfa555
Author: francescoc <francesco.cecerengs@gmail.com>
Date: 2025-08-23 09:51:18 +0200
Commit message:

 fix vignettes
Package: scRNAseqApp
Commit: d89c979ac4a9f23e1066d8659d9e4a36b259fc3d
Author: Jianhong Ou <jianhong.ou@gmail.com>
Date: 2025-08-22 19:51:36 -0400
Commit message:

 Update css for issues
Package: scRNAseqApp
Commit: 2f1a4c3a20661ffd7e8badbedc97a1d52760217c
Author: Jianhong Ou <jianhong.ou@gmail.com>
Date: 2025-08-22 13:15:26 -0400
Commit message:

 add css for issues.
Package: TBSignatureProfiler
Commit: 6f942dcfff3a694adf7ca971f388255058426f83
Author: Kiloni Quiles <kiloni@Kilonis-MacBook-Pro.local>
Date: 2025-08-22 10:52:09 -0400
Commit message:

 Updating package maintainer details
Package: TBSignatureProfiler
Commit: 6eeb75e2aa05def2554b1efa1d8c2724df4ea44c
Author: Aubrey Odom <aodom@bu.edu>
Date: 2025-07-18 16:58:17 -0400
Commit message:

 Fix column arg
Package: biomaRt
Commit: c18befa8257b4c3bd206e98f8267a5bb02720335
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-08-18 17:16:39 +0200
Commit message:

 Document internal change to roxygen
Package: biomaRt
Commit: 67c4aa1a43edac10aeb313f874bc1e1bda4fc2ee
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-08-22 14:46:54 +0200
Commit message:

 Use \pkg{} rather than \sQuote{}
Package: biomaRt
Commit: 0923b9f7e82a210c940ef87a4534c5c5ad7d8559
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-08-22 14:45:56 +0200
Commit message:

 Use rdname instead of alias

To ensure both usages are reflected in the generated Rd documentation
Package: biomaRt
Commit: f468de6553645b27396b414062fe6d3d05ae582e
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-08-18 17:01:15 +0200
Commit message:

 Run devtools::document()
Package: biomaRt
Commit: 50a99bb24558292f047ae16d83aac8e9f08edf6f
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-08-18 17:01:03 +0200
Commit message:

 Render NAMESPACE via roxygen2
Package: biomaRt
Commit: b62514ebc2bfef3af93d32f581bb80f67eae9f64
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-08-18 17:00:45 +0200
Commit message:

 Add pkg-level doc to Collate
Package: biomaRt
Commit: 0e1f602455f5f11ce64692c8c4adf215a7b2bf31
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-08-18 16:38:21 +0200
Commit message:

 Add missing import tags
Package: biomaRt
Commit: 59ca2695871d24f81ab3655894793249c05ab283
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-08-18 16:38:07 +0200
Commit message:

 Add missing export tags
Package: biomaRt
Commit: a0320b5869fe097510aeeea6281d601e00cf1482
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-08-18 16:24:50 +0200
Commit message:

 Import generics
Package: biomaRt
Commit: 0482cf7c9152b6f85421af940f492489d2b6e64a
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-08-18 16:24:43 +0200
Commit message:

 Render pkg-level documentation
Package: biomaRt
Commit: ef20a58f907e55589f374b4b7d81203ac57690ab
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-08-18 16:14:03 +0200
Commit message:

 Imports methods globally
Package: biomaRt
Commit: cb3778c61636d3c6af6fcee7417eb146c2d12cab
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-08-18 15:01:23 +0200
Commit message:

 Move select-methods doc source to methods-Mart
Package: biomaRt
Commit: 417a8867cfa569c9a392bf2f575c8d2689bf0005
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-08-18 14:55:45 +0200
Commit message:

 Document Mart-class in methods-Mart
Package: biomaRt
Commit: d1bc09d0ce52fc600b6b579e0a9eb43332899470
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-08-18 14:53:24 +0200
Commit message:

 Ensure internal functions don't get Rd
Package: biomaRt
Commit: 7b25f94b2adfe88fa9bf2704a9a3a6f23e4f9238
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-08-18 14:46:30 +0200
Commit message:

 Fix biomartCache manually
Package: biomaRt
Commit: 3dd4b6da014876923387cdbebae37833cae69324
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-08-18 14:44:29 +0200
Commit message:

 Fix biomaRt-deprecated manually
Package: biomaRt
Commit: e9f527464373593233c3a622b75c8f1d02c890f2
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-08-18 14:04:29 +0200
Commit message:

 Re-render man/ pages with roxygen
Package: biomaRt
Commit: fcd98a64d644666516022bf5ef70b90825daa0ff
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-08-18 14:42:00 +0200
Commit message:

 Remove extra whitespace
Package: biomaRt
Commit: 35c0acd88746e4c91037536fe2b55472941c81a4
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-08-18 11:14:21 +0200
Commit message:

 Run Rd2roxygen()
Package: scDblFinder
Commit: 4088b789d305eb2fd43b6f64e6d4b573834a95ea
Author: plger <pl.germain@gmail.com>
Date: 2025-08-11 13:14:13 +0200
Commit message:

 fix #134
Package: DEP
Commit: 96d07f14cca02b5942bea9b411980db504cee3da
Author: lshep <lori.shepherd@roswellpark.org>
Date: 2025-08-22 08:28:23 -0400
Commit message:

 Deprecate

 - maintainer indicated no longer can maintain
Package: TFEA.ChIP
Commit: bf9f162f915f54e6c14a0987700e9c1d643f688f
Author: yosra <yosraberrouayel@gmail.com>
Date: 2025-08-22 14:13:04 +0200
Commit message:

 corrected errors
Package: cellmig
Commit: 5e40821f4e3b102a590d3de767dd753836c56b22
Author: snaketron <simo.kitanovski@uni-due.de>
Date: 2025-08-22 12:57:51 +0200
Commit message:

 shorter functions
Package: markeR
Commit: 1e9d3839e566a7f521053ece8ef9ec7102cc3eac
Author: Rita Silva <ritamtbsilva@gmail.com>
Date: 2025-08-21 16:57:21 +0100
Commit message:

 Update markeR.Rmd
Package: markeR
Commit: 0fff716a9103c9f84a4d166f49cbde1d3ed8dd2c
Author: Rita Silva <ritamtbsilva@gmail.com>
Date: 2025-08-21 16:55:01 +0100
Commit message:

 update vignette to be more useful
Package: markeR
Commit: c9d8c158e3b1f26afb2924c3602157f4f5eb12ec
Author: Rita Silva <55759937+ritamtbsilva@users.noreply.github.com>
Date: 2025-08-21 12:27:40 +0100
Commit message:

 Update pkgdown.yaml
Package: markeR
Commit: dae89f9fd6c048b62c9b269577b1992312595ae8
Author: Rita Silva <ritamtbsilva@gmail.com>
Date: 2025-08-21 12:25:40 +0100
Commit message:

 Update NEWS.md
Package: markeR
Commit: e1ca040a17138ce9eae1a5b6cbba4d1d65870587
Author: Rita Silva <55759937+ritamtbsilva@users.noreply.github.com>
Date: 2025-08-21 12:14:04 +0100
Commit message:

 Merge pull request #73 from DiseaseTranscriptomicsLab/default

update main from default
Package: markeR
Commit: c80697289828e6bea68f03f4e34476a7b114ee95
Author: Rita Silva <55759937+ritamtbsilva@users.noreply.github.com>
Date: 2025-08-21 12:12:57 +0100
Commit message:

 Merge pull request #72 from DiseaseTranscriptomicsLab/main

remove optional in parenthesis
Package: markeR
Commit: 01a64e883622219201ad341c2eab998be3c3df13
Author: Rita Silva <ritamtbsilva@gmail.com>
Date: 2025-08-21 12:12:18 +0100
Commit message:

 remove optional in parenthesis
Package: markeR
Commit: 3af81143122842db2356a7b58d6fd5eefa3315e2
Author: Rita Silva <ritamtbsilva@gmail.com>
Date: 2025-08-21 12:11:17 +0100
Commit message:

 Merge branch 'default' of https://github.com/DiseaseTranscriptomicsLab/markeR into default
Package: markeR
Commit: 70bf477d6b005d76c796218ae9bcf7ca676e6a69
Author: Rita Silva <ritamtbsilva@gmail.com>
Date: 2025-08-21 12:10:49 +0100
Commit message:

 Update .gitignore
Package: markeR
Commit: 0cbccb2452569174203849918c50bc0b900f4d0d
Author: Rita Silva <55759937+ritamtbsilva@users.noreply.github.com>
Date: 2025-08-21 12:09:19 +0100
Commit message:

 Merge pull request #71 from DiseaseTranscriptomicsLab/main

Merge pull request #70 from DiseaseTranscriptomicsLab/default
Package: markeR
Commit: 246d8a15872a983f162d8abfe3d26b099598c9d2
Author: Rita Silva <55759937+ritamtbsilva@users.noreply.github.com>
Date: 2025-08-21 12:08:45 +0100
Commit message:

 Merge pull request #70 from DiseaseTranscriptomicsLab/default

update main
Package: markeR
Commit: 5be84f17dc7cd618b433a5c3d35133432072735a
Author: Rita Silva <55759937+ritamtbsilva@users.noreply.github.com>
Date: 2025-08-21 12:07:53 +0100
Commit message:

 Merge pull request #69 from DiseaseTranscriptomicsLab/main

Bioconductor reviews
Package: markeR
Commit: 262cb986a28dca12deac886354009e509081082f
Author: Rita Silva <ritamtbsilva@gmail.com>
Date: 2025-08-21 11:52:13 +0100
Commit message:

 removing optional (again)
Package: markeR
Commit: 79670ecd5d3d772773b8c927b1751b9ae018a444
Author: Rita Silva <ritamtbsilva@gmail.com>
Date: 2025-08-21 10:47:58 +0100
Commit message:

 Merge branch 'main' of https://github.com/DiseaseTranscriptomicsLab/markeR
Package: markeR
Commit: 92cf89f14acc1c08a23e736316916a54dd2c2af7
Author: Rita Silva <ritamtbsilva@gmail.com>
Date: 2025-08-21 10:47:49 +0100
Commit message:

 update main vignette to remove optional tags for individual gene and comparison with gene sets
Package: markeR
Commit: b6a7260a3c42b19698ae78d1ca09983e5f143285
Author: Rita Silva <55759937+ritamtbsilva@users.noreply.github.com>
Date: 2025-08-21 10:40:54 +0100
Commit message:

 Update R-CMD-check.yaml
Package: markeR
Commit: 5b20e2e200fe60ca61fcaaf83e23f3d1eca38be7
Author: Rita Silva <ritamtbsilva@gmail.com>
Date: 2025-08-21 10:33:50 +0100
Commit message:

 remove rminversion workflow from github

As the required version is 4.5.0, it just enough to run R CMD
Package: markeR
Commit: e9ca0b5607d2e00094f76588067a6e10aeab6d26
Author: Rita Silva <ritamtbsilva@gmail.com>
Date: 2025-08-21 10:24:31 +0100
Commit message:

 fix broken link workflow image
Package: markeR
Commit: 40c86ca5cbbeb6627b0ff574617a7c9314659c12
Author: Rita Silva <ritamtbsilva@gmail.com>
Date: 2025-08-21 10:21:39 +0100
Commit message:

 update workflow image in main
Package: markeR
Commit: d794294cec8818a27f99acb286befb32793e06d4
Author: Rita Silva <ritamtbsilva@gmail.com>
Date: 2025-08-20 17:33:15 +0100
Commit message:

 Merge branch 'main' of https://github.com/DiseaseTranscriptomicsLab/markeR
Package: markeR
Commit: 42cf9b2720cf5c99735eee60d71780b99f2ad37f
Author: Rita Silva <ritamtbsilva@gmail.com>
Date: 2025-08-20 17:33:06 +0100
Commit message:

 fix bug calculateDE preventing pkgdown from compiling article
Package: markeR
Commit: 08bbb73943b045445819e18717508c5aa5816bd7
Author: Rita Silva <55759937+ritamtbsilva@users.noreply.github.com>
Date: 2025-08-20 17:25:40 +0100
Commit message:

 Update bioc-check.yml
Package: markeR
Commit: 59bf7127e2aa600f81d4c362698d6b970ac51f33
Author: Rita Silva <55759937+ritamtbsilva@users.noreply.github.com>
Date: 2025-08-20 17:25:18 +0100
Commit message:

 Update bioc-check.yml
Package: markeR
Commit: 692f8dd88fb670ade90e47da5e2120feeefc1b2a
Author: Rita Silva <ritamtbsilva@gmail.com>
Date: 2025-08-20 17:22:48 +0100
Commit message:

 remove unecessary badges from readme, for bioconductor submission
Package: markeR
Commit: 8f8190d80ce6cf7a5d2f3f4234d70a029815902d
Author: Rita Silva <ritamtbsilva@gmail.com>
Date: 2025-08-20 17:19:57 +0100
Commit message:

 remove unecessary commented code
Package: markeR
Commit: 795790d8743e0550dd6b36b02ec73cd94029f3a7
Author: Rita Silva <ritamtbsilva@gmail.com>
Date: 2025-08-20 17:11:19 +0100
Commit message:

 fix BiocCheck notes
Package: markeR
Commit: 83ffd91d410d9092ca0f7619e9f6e39fc5d22724
Author: Rita Silva <ritamtbsilva@gmail.com>
Date: 2025-08-19 17:01:53 +0100
Commit message:

 fix R CMD check notes
Package: markeR
Commit: eafdda0aacbf79dcd5e2dfb2fa362ce7fa91c76e
Author: Rita Silva <ritamtbsilva@gmail.com>
Date: 2025-08-19 12:48:11 +0100
Commit message:

 add runnable example VariableAssociation
Package: markeR
Commit: 829ba0b34a224641d07c02c4d3ddb2f802854a0b
Author: Rita Silva <ritamtbsilva@gmail.com>
Date: 2025-08-19 12:22:16 +0100
Commit message:

 fix NAMESPACE and DESCRIPTION's imports
Package: markeR
Commit: 86fe730d55565d5b4bddaf601874fc4d242e6627
Author: Rita Silva <ritamtbsilva@gmail.com>
Date: 2025-08-19 11:43:44 +0100
Commit message:

 Update required R version to > 4.4.0
Package: markeR
Commit: 880f08be6eaa7a981608baccfaa4a4afca8ada81
Author: Rita Silva <ritamtbsilva@gmail.com>
Date: 2025-08-19 11:43:18 +0100
Commit message:

 update date and author vignettes
Package: markeR
Commit: 441a665f7ee001f31791349342d8f8d92803f1cc
Author: Rita Silva <ritamtbsilva@gmail.com>
Date: 2025-08-19 10:44:07 +0100
Commit message:

 update links introduction vignette
Package: markeR
Commit: 8f2f5da549c992991ccb14e496b29e5480e7ceea
Author: Rita Silva <ritamtbsilva@gmail.com>
Date: 2025-08-18 20:13:33 +0100
Commit message:

 Update .gitignore
Package: markeR
Commit: 237ae5c633b29ea80356448fe1755dda30ed7c9d
Author: Rita Silva <ritamtbsilva@gmail.com>
Date: 2025-08-18 20:01:18 +0100
Commit message:

 update readme
Package: markeR
Commit: 7f24fd3e92da186d26e442e502d87596e4414618
Author: Rita Silva <ritamtbsilva@gmail.com>
Date: 2025-08-18 19:43:59 +0100
Commit message:

 convert vignettes to article and add general vignette
Package: markeR
Commit: 92e2058384f9fe9709040b30c4505848835ee288
Author: Rita Silva <55759937+ritamtbsilva@users.noreply.github.com>
Date: 2025-08-18 13:03:42 +0100
Commit message:

 Merge pull request #68 from DiseaseTranscriptomicsLab/default

update branches to run checks
Package: markeR
Commit: 65857894354e4ea31e15e40bf456c68b2380141e
Author: Rita Silva <ritamtbsilva@gmail.com>
Date: 2025-08-18 13:02:53 +0100
Commit message:

 update branches to run checks
Package: markeR
Commit: 4c1f543ad0361282a2386f898e1b44ffb22bebc4
Author: Rita Silva <ritamtbsilva@gmail.com>
Date: 2025-08-18 13:01:54 +0100
Commit message:

 Update .gitignore
Package: markeR
Commit: 8ddcb77b402cc14f71efeb510c577748fa2d991a
Author: Rita Silva <55759937+ritamtbsilva@users.noreply.github.com>
Date: 2025-08-18 13:01:05 +0100
Commit message:

 Merge pull request #67 from DiseaseTranscriptomicsLab/default

Update pkgdown.yaml
Package: markeR
Commit: e6e44c1a246dae757181d5e9f11cde435a1d507d
Author: Rita Silva <55759937+ritamtbsilva@users.noreply.github.com>
Date: 2025-08-18 13:00:15 +0100
Commit message:

 Update pkgdown.yaml
Package: markeR
Commit: 4cab87e9792d8580fb108e1ff667607608a199c9
Author: Rita Silva <ritamtbsilva@gmail.com>
Date: 2025-08-14 17:12:11 +0100
Commit message:

 Revert "Delete"

This reverts commit 7acf2175651e6c2ecf11d5057c44f765709f53e1.
Package: markeR
Commit: 7acf2175651e6c2ecf11d5057c44f765709f53e1
Author: Rita Silva <ritamtbsilva@gmail.com>
Date: 2025-08-14 17:08:16 +0100
Commit message:

 Delete
Package: markeR
Commit: 971889f08905a54751ebd65fa040c50c87cfad92
Author: Rita Silva <55759937+ritamtbsilva@users.noreply.github.com>
Date: 2025-08-14 17:01:45 +0100
Commit message:

 Update bioc-check.yml
Package: markeR
Commit: 9c038a01476bdad619e648f45036422d0456fde2
Author: Rita Silva <55759937+ritamtbsilva@users.noreply.github.com>
Date: 2025-08-14 17:01:28 +0100
Commit message:

 Update Rminversion.yaml
Package: markeR
Commit: 5f32fa8ed9004a0c8d0f16f2d387ee63086c345b
Author: Rita Silva <55759937+ritamtbsilva@users.noreply.github.com>
Date: 2025-08-14 17:01:03 +0100
Commit message:

 Update R-CMD-check.yaml
Package: markeR
Commit: 2724c16a6aa0dd7d922ddd39538bd55669692544
Author: Rita Silva <55759937+ritamtbsilva@users.noreply.github.com>
Date: 2025-08-14 17:00:21 +0100
Commit message:

 Update pkgdown.yaml
Package: markeR
Commit: c904d64ef5511512c6eee0f2505fef339db6b2af
Author: Rita Silva <ritamtbsilva@gmail.com>
Date: 2025-08-14 16:48:14 +0100
Commit message:

 adapt readme to include visualisation plots for enrichment in benchmarking mode
Package: markeR
Commit: c833748c97b6ce437d56598e0bde824b47d13ece
Author: Rita Silva <ritamtbsilva@gmail.com>
Date: 2025-08-12 18:08:49 +0100
Commit message:

 Delete LICENSE
Package: markeR
Commit: 5635b1aeadf506dd2d690b6d20e339597cd2a4d2
Author: Rita Silva <ritamtbsilva@gmail.com>
Date: 2025-08-12 18:02:57 +0100
Commit message:

 add info on paper scripts to readme file
Package: markeR
Commit: 079c73bc9152bb86d7b887c0a01bac8339aa7ecc
Author: Rita Silva <ritamtbsilva@gmail.com>
Date: 2025-08-12 17:14:45 +0100
Commit message:

 Remove paper figures and preprocessing scripts

Deleted all figures, RMarkdown files, and preprocessing scripts from the inst/Paper directory. Updated .gitignore to exclude the entire inst/Paper directory instead of just its data subfolder.
Package: markeR
Commit: 4e8c2452c50c6007c76751732bda754e71490057
Author: Rita Silva <ritamtbsilva@gmail.com>
Date: 2025-07-23 17:39:34 +0100
Commit message:

 temporarily remove faulty badges
Package: spatialFDA
Commit: de7274c2c36d40be96d6efd31d7ad525b4da1cac
Author: mjemons <martin.emons@gmail.com>
Date: 2025-08-22 10:58:09 +0200
Commit message:

 adjusted p-values and coefficient subsetting
Package: gDRstyle
Commit: a0a5e6fa4175a9de8719241da4362871695746d3
Author: Bartek <32614650+bczech@users.noreply.github.com>
Date: 2025-08-22 10:50:20 +0200
Commit message:

 Merge pull request #93 from gdrplatform/GDR-771

Gdr 771
Package: gDRstyle
Commit: ae1265635d5af2a4cd5d1b62f6be98e243913037
Author: Bartek <32614650+bczech@users.noreply.github.com>
Date: 2025-08-21 09:26:07 +0200
Commit message:

 refactor: Update build_tools.R
Package: gDRstyle
Commit: 8f56731b3439b163b6c0f74a68bb4fa24ca988fa
Author: Bartek Czech <bartosz.w.czech@gmail.com>
Date: 2025-08-12 08:04:47 +0200
Commit message:

 chore: bump version and update NEWS.md
Package: gDRstyle
Commit: 98445f97136aa4c0e48484d3c402d2e17e506f57
Author: Bartek Czech <bartosz.w.czech@gmail.com>
Date: 2025-08-12 08:04:42 +0200
Commit message:

 fix: usage of ifelse
Package: Spectra
Commit: 0473acc069a6b6b23494529f6429a60ba98b4406
Author: Johannes Rainer <johannes.rainer@gmail.com>
Date: 2025-08-22 10:19:45 +0200
Commit message:

 readme: add link to preprint
Package: Spectra
Commit: 6b1674f8fc197ad638116694781f0cc81440e493
Author: Johannes Rainer <5506112+jorainer@users.noreply.github.com>
Date: 2025-08-22 10:12:29 +0200
Commit message:

 Merge pull request #363 from rformassspectrometry/jomain

docs: fix documentation and unit tests
Package: Spectra
Commit: cea90aeeb228dac2948a39811abbd3f4451e369d
Author: Johannes Rainer <johannes.rainer@gmail.com>
Date: 2025-08-22 10:01:18 +0200
Commit message:

 docs: add link from filterPrecursorScan to fragmentGroupIndex
Package: Spectra
Commit: 90cbd8404fd2d8b0e92b7ccabd10cc822f2a3006
Author: Johannes Rainer <johannes.rainer@gmail.com>
Date: 2025-08-22 08:46:38 +0200
Commit message:

 docs: fix documentation and unit tests
Package: Spectra
Commit: 0117bc7de3dbe693aaf34655f00d5f40b4844a31
Author: Johannes Rainer <5506112+jorainer@users.noreply.github.com>
Date: 2025-08-22 07:37:19 +0200
Commit message:

 Merge pull request #359 from Ahlammentag/main

Add precursorPurity function
Package: Spectra
Commit: a86ba343994c4de502e86cd6b2ffc88987051b01
Author: Johannes Rainer <5506112+jorainer@users.noreply.github.com>
Date: 2025-08-22 07:36:11 +0200
Commit message:

 Merge pull request #362 from rformassspectrometry/phili

addition of `groupMsFragments` to get an index of which MSn goes with which MS1
Package: Spectra
Commit: ccd8061e20e1bec5aa830d238aeaeda4b109a5d2
Author: Philippine Louail <127301965+philouail@users.noreply.github.com>
Date: 2025-08-21 23:18:48 +0200
Commit message:

 Update check-bioc.yml
Package: Spectra
Commit: 1ca072f627361f1597b04d74670abfa0f9b1f1dc
Author: Philippine Louail <127301965+philouail@users.noreply.github.com>
Date: 2025-08-21 23:16:26 +0200
Commit message:

 Update test_Spectra-functions.R
Package: Spectra
Commit: a0138f6e86fa3ff92132413fcc6247fefd992a9c
Author: Philippine Louail <127301965+philouail@users.noreply.github.com>
Date: 2025-08-21 23:13:38 +0200
Commit message:

 Update test_Spectra-functions.R
Package: Spectra
Commit: a206e681a91594a3228e801a7c034fe64f54febe
Author: Philippine Louail <127301965+philouail@users.noreply.github.com>
Date: 2025-08-21 23:04:44 +0200
Commit message:

 fix based on jo comments
Package: Spectra
Commit: 4556cacc7d39ef3c0d39085f81b2b3b79c3dc4da
Author: Philippine Louail <127301965+philouail@users.noreply.github.com>
Date: 2025-07-28 16:41:49 +0200
Commit message:

 fix output cbind2
Package: Spectra
Commit: 21bdefb5f97a3eedbfaccdabaa8a75c67105e3a4
Author: Philippine Louail <127301965+philouail@users.noreply.github.com>
Date: 2025-07-22 16:11:56 +0200
Commit message:

 fix test object
Package: Spectra
Commit: 35111f014dc21bdb9434420750e8c9b238f9ecc5
Author: Philippine Louail <127301965+philouail@users.noreply.github.com>
Date: 2025-07-22 15:57:05 +0200
Commit message:

 Update test_Spectra-functions.R
Package: Spectra
Commit: c04043d257cab107a86dfd0cba6a67c5744e73f5
Author: Philippine Louail <127301965+philouail@users.noreply.github.com>
Date: 2025-07-22 15:44:18 +0200
Commit message:

 fix fct name
Package: Spectra
Commit: 6c761cc686af631a3b6452732777b6761180a7d1
Author: Philippine Louail <127301965+philouail@users.noreply.github.com>
Date: 2025-07-22 15:32:56 +0200
Commit message:

 bump versioon
Package: Spectra
Commit: 54bd49283ed3f62574eaf9c79eeda137a7ceacf9
Author: Philippine Louail <127301965+philouail@users.noreply.github.com>
Date: 2025-07-22 15:14:55 +0200
Commit message:

 Update Spectra-functions.R
Package: Spectra
Commit: 7835ebf6e98be0ea4e53285ab471a388ed517c09
Author: Philippine Louail <127301965+philouail@users.noreply.github.com>
Date: 2025-07-21 15:18:50 +0200
Commit message:

 additon of groupMsFragments
Package: Spectra
Commit: 325a29b635ce779c9689ca8c5e51ab36a0a321a3
Author: Ahlam Mentag <ahlammentag63@gmail.com>
Date: 2025-07-02 13:52:50 +0200
Commit message:

 fix exports
Package: Spectra
Commit: 2a118bb093699eaedd178ebfaf4fab5d8ecbf146
Author: Ahlam Mentag <ahlammentag63@gmail.com>
Date: 2025-07-02 13:22:49 +0200
Commit message:

 Add precursorPurity function
Package: cellmig
Commit: 25d32b7610c134e60241662197f141945fbea0da
Author: snaketron <simo.kitanovski@uni-due.de>
Date: 2025-08-22 09:49:03 +0200
Commit message:

 bump
Package: cellmig
Commit: 43bdd5406f7480d6f88dfcff49bf9cec28be02dd
Author: snaketron <simo.kitanovski@uni-due.de>
Date: 2025-08-22 09:48:53 +0200
Commit message:

 Bugfix
Package: cellmig
Commit: 775d9395f64f5cfc9656dee51db5b96e350c4c17
Author: snaketron <simo.kitanovski@uni-due.de>
Date: 2025-08-22 09:43:45 +0200
Commit message:

 explain how mini was generated
Package: cellmig
Commit: 105cd3901ea49fd5d0622d49efa3d2b3a595ba4f
Author: snaketron <simo.kitanovski@uni-due.de>
Date: 2025-08-22 09:43:36 +0200
Commit message:

 bump and shorter description
Package: cellmig
Commit: ccd0ba07a383543610c705c30c8da292e869f0d9
Author: snaketron <simo.kitanovski@uni-due.de>
Date: 2025-08-22 09:17:06 +0200
Commit message:

 bump
Package: cellmig
Commit: 3617f0b9bc0df5db6991a1c732f0fba261b061fd
Author: snaketron <simo.kitanovski@uni-due.de>
Date: 2025-08-22 09:12:16 +0200
Commit message:

 commit d_mini version, should speed things up
Package: cellmig
Commit: e90ad5e0909d1cb8629cbb20bd476699b78d17e9
Author: snaketron <simo.kitanovski@uni-due.de>
Date: 2025-08-22 09:00:21 +0200
Commit message:

 even more comp. time red. + bump
Package: jazzPanda
Commit: 63b2d7f5d64fa299d826b45e55ed1f3e8540afcc
Author: Melody <Melody-Jin@outlook.com>
Date: 2025-08-22 16:27:01 +1000
Commit message:

 Fix test names; resolve conflict when porting changes to devel
Package: biocmake
Commit: 02027f30f3ace195edbf5a8b6e5823dd048a6384
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2025-08-21 20:42:11 -0700
Commit message:

 Propagate compiler flags for release builds, use release builds on Windows.

We set the build type on Windows because we assume we're building with mingw.
No need to consider multi-config generators because R doesn't use them anyway.

We propagate the compiler flags into the CMAKE_C(XX)_FLAGS_RELEASE variable
to avoid clobbering R's flags with Cmake's defaults for the Release build.
Package: Rigraphlib
Commit: 18619b99fdbbc59a4664ebbfacd7137e7cefa186
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2025-08-21 21:01:15 -0700
Commit message:

 No need for Windows-specific --config as Rtools just uses Makefiles anyway.
Package: igblastr
Commit: 63cf93f0512c65918d4bef5ccd73c436cc15192a
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2025-08-21 16:52:17 -0700
Commit message:

 igblastr 0.99.13

Add _IMGT.rat.IGH.202508 to list of built-in C-region dbs.
Package: leapR
Commit: 43a9f5bede650f53e99ffd3b5ae99233e01c4762
Author: Sara JC Gosline <sara.gosline@pnnl.gov>
Date: 2025-08-21 16:20:01 -0700
Commit message:

 Merge branch 'master' into devel
Package: leapR
Commit: 7724c3f3784cc2e539a9ca50ae0fce1a1c923286
Author: Sara JC Gosline <sara.gosline@pnnl.gov>
Date: 2025-08-04 10:46:31 -0700
Commit message:

 Merge pull request #53 from pnnl/bioc-data

updated version
Package: leapR
Commit: d077aa539d1bdbbb63fe549eaa5f8b50cc132b73
Author: Sara JC Gosline <sara.gosline@pnnl.gov>
Date: 2025-08-04 10:39:52 -0700
Commit message:

 updated version
Package: leapR
Commit: 85ede1a105cb8a50d934283bf08a38ac68c711a7
Author: Sara JC Gosline <sara.gosline@pnnl.gov>
Date: 2025-08-04 10:39:09 -0700
Commit message:

 Merge remote-tracking branch 'origin/master' into bioc-data
Package: leapR
Commit: 0dc562cec5eb873466b67e2b813939610fb0f937
Author: Sara JC Gosline <sara.gosline@pnnl.gov>
Date: 2025-08-04 10:38:54 -0700
Commit message:

 Merge pull request #52 from pnnl/bioc-data

Bioc package uptdates
Package: leapR
Commit: 8bc1ff74408cb2ff6a8dcb7c3d65121066242b7a
Author: Sara JC Gosline <sara.gosline@pnnl.gov>
Date: 2025-08-04 10:32:11 -0700
Commit message:

 Merge remote-tracking branch 'upstream/devel' into bioc-data
Package: leapR
Commit: 8216b9755bbb6d79f7649dda459553a815ab350a
Author: Sara JC Gosline <sara.gosline@pnnl.gov>
Date: 2025-08-04 10:14:59 -0700
Commit message:

 removed r history
Package: leapR
Commit: 00b8a237cd3ae1c2087719796d6cb18f2c8d1118
Author: Sara JC Gosline <sara.gosline@pnnl.gov>
Date: 2025-08-04 10:14:38 -0700
Commit message:

 added readme for extdata and removed extra files
Package: scRNAseqApp
Commit: ce73629bbaaf2cffc7bc8717a63e5327233fc6e5
Author: Jianhong Ou <jianhong.ou@gmail.com>
Date: 2025-08-21 16:34:32 -0400
Commit message:

 add a comment previewer.
Package: iscream
Commit: 8a4373d5b22d3733f076ab75f20ec5c86885fe7e
Author: James Eapen <james.eapen@vai.org>
Date: 2025-08-21 16:23:05 -0400
Commit message:

 chore(DESCRIPTION): bump version after watching tag on support site
Package: iscream
Commit: 9ac5cb4d67d14171981181cab2eba444a9f7462b
Author: James Eapen <james.eapen@vai.org>
Date: 2025-08-21 16:10:32 -0400
Commit message:

 chore(DESCRIPTION): bump version after updating support site email
Package: iscream
Commit: aeab47a59f2ce38cfe846f944ff1023dd6ec57f0
Author: James Eapen <james.eapen@vai.org>
Date: 2025-08-20 14:31:07 -0400
Commit message:

 chore(DESCRIPTION): add tabix in SystemRequirements
Package: MetaScope
Commit: 1f63097232a02dc81834a817706e220f4829488e
Author: seanlu96 <89270441+seanlu96@users.noreply.github.com>
Date: 2025-08-21 15:15:35 -0400
Commit message:

 fixed man 16S refseq
Package: MetaScope
Commit: ebfd543059a7079ba34231fa318011b0f48d5b24
Author: seanlu96 <89270441+seanlu96@users.noreply.github.com>
Date: 2025-08-21 15:14:31 -0400
Commit message:

 updated 16S refseq

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

# Conflicts:
#	man/download_refseq_16S.Rd
Package: MetaScope
Commit: 228b5725534c411c9505a1a3a1f39b18f4deb761
Author: seanlu96 <89270441+seanlu96@users.noreply.github.com>
Date: 2025-08-21 14:46:36 -0400
Commit message:

 updated documentation download_refseq_16S
Package: MetaScope
Commit: cfcde867872df61f1e458082f242d2d5bb9c201d
Author: seanlu96 <89270441+seanlu96@users.noreply.github.com>
Date: 2025-08-21 14:46:36 -0400
Commit message:

 updated documentation download_refseq_16S
Package: MetaScope
Commit: c5546bae9bdacc7f1bcaca124f8b1c11c7bfd8de
Author: seanlu96 <89270441+seanlu96@users.noreply.github.com>
Date: 2025-08-21 09:45:04 -0400
Commit message:

 update Version and Authors
Package: MetaScope
Commit: db372d7c036e643bdbb28306ac0861be76af91d0
Author: Sean <89270441+seanlu96@users.noreply.github.com>
Date: 2025-08-20 13:52:39 -0400
Commit message:

 Merge pull request #48 from seanlu96/master

added download function for 16S refseq
Package: MetaScope
Commit: ff934f09d7bde30988c03d51d87f2c1e4fab56a8
Author: Sean Lu <seanlu96@gmail.com>
Date: 2025-08-20 13:51:53 -0400
Commit message:

 added download function for 16S refseq
Package: cellmig
Commit: df857e221eec1c178e573e1674f0258830b181a4
Author: snaketron <simo.kitanovski@uni-due.de>
Date: 2025-08-21 19:35:09 +0200
Commit message:

 bump
Package: cellmig
Commit: de6e669e6270743d2cde2df912d74bc8191c48ea
Author: snaketron <simo.kitanovski@uni-due.de>
Date: 2025-08-21 19:34:33 +0200
Commit message:

 make things faster
Package: Rarr
Commit: 8863d77cc352ece3b97bf53e312f120bb597ea8c
Author: Artür Manukyan <artur-man@hotmail.com>
Date: 2025-08-21 18:59:27 +0200
Commit message:

 fixing chunkdim vs dim (#17)

Fix #16
Package: Rarr
Commit: 7df11225ad67a549d303adbf58fa40fe258e645e
Author: Artür Manukyan <artur-man@hotmail.com>
Date: 2025-08-21 14:37:00 +0200
Commit message:

 Add nchar as argument to writeZarrArray() (#15)
Package: Rarr
Commit: f4626f14bf98320c0a76c0ef2706bdc7bf95a88e
Author: Sharla Gelfand <sharla.gelfand@gmail.com>
Date: 2025-06-19 12:08:34 -0400
Commit message:

 Take port into account, allow colons in bucket names when parsing urls (#21)
Package: Rarr
Commit: 09b0889c6022263095d48d131579f658595f420d
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-06-04 16:55:51 +0000
Commit message:

 Fix minor typos (#23)
Package: MSstatsBioNet
Commit: f41191a3b69bc0073d88d3fc108ed50deb8049b5
Author: tonywu1999 <wu.anthon@northeastern.edu>
Date: 2025-08-21 12:39:13 -0400
Commit message:

 tests(visualizeNetworksWithHTML): Add unit tests for generateCytoscapeConfig (#55)
Package: scRNAseqApp
Commit: d86c796cd40d04c95e326a5e4974443a509944d7
Author: Jianhong Ou <jianhong.ou@gmail.com>
Date: 2025-08-21 11:22:37 -0400
Commit message:

 Add markdown support for issues.
Package: netZooR
Commit: 09bc7a3fb123a557b48cf7ad2029e7d6b6cd34c1
Author: Tara Eicher <taraeicher@yahoo.com>
Date: 2025-08-21 10:46:13 -0400
Commit message:

 Added fix for cmdstanr bug
Package: netZooR
Commit: 8139e474ec10f12184656d292833b9117a6c772b
Author: Tara Eicher <taraeicher@yahoo.com>
Date: 2025-08-19 14:32:57 -0400
Commit message:

 Added cmdstanr with Additional_repositories specification
Package: jazzPanda
Commit: bc88713a9f5284485fd00cacb64aa31dee3e1263
Author: Melody <Melody-Jin@outlook.com>
Date: 2025-08-22 00:12:53 +1000
Commit message:

 Port fix from release 1.0.2 to devel 1.1.1
Package: cellmig
Commit: 3ba65b91ca767a2a9919228cf5f5bdce2a2ad78d
Author: snaketron <simo.kitanovski@uni-due.de>
Date: 2025-08-21 16:16:35 +0200
Commit message:

 shorter runtime to avoid timeout
Package: cellmig
Commit: 780820867f5b55abd017e65f67a27d6e66426181
Author: snaketron <simo.kitanovski@uni-due.de>
Date: 2025-08-21 15:57:01 +0200
Commit message:

 bump version
Package: cellmig
Commit: d1d1e11f27a340b632ca66c9d14d5ab00fb17dcf
Author: snaketron <simo.kitanovski@uni-due.de>
Date: 2025-08-21 15:56:46 +0200
Commit message:

 remove .Rproj
Package: goatea
Commit: 886d2f3435cf8945838d72f74bc07eb6b9144b1d
Author: Maurits Unkel <mauritsunkel@gmail.com>
Date: 2025-08-21 14:09:40 +0200
Commit message:

 Updated README with installation steps and vignette with table of content
Package: goatea
Commit: 5463995e3d742a1fe6915b02f4b072496deeb0ae
Author: Maurits Unkel <mauritsunkel@gmail.com>
Date: 2025-08-21 14:06:54 +0200
Commit message:

 Updated exported functions runnable examples to work with inst/data/