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GIT Logs

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

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Package: GSVA
Commit: 87df5a545fe901d62f42511062e09e3330277efb
Author: Robert Castelo <robert.castelo@upf.edu>
Date: 2026-04-07 21:04:08 +0200
Commit message:

 Some C code cleanup
Package: GSVA
Commit: 08fac60387b9448fc2c0ac214eef91fe8039e541
Author: Robert Castelo <robert.castelo@upf.edu>
Date: 2026-04-07 20:39:37 +0200
Commit message:

 Code cleanup and added unit tests for parameter objects and gene sets
Package: AnVILVRS
Commit: 70f940eb2c9e343b22b9dc1f48c82f9b394b0a0f
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2026-04-07 14:15:33 -0400
Commit message:

 version bump 0.99.19
Package: AnVILVRS
Commit: 3c37c4f105c37f22b1b5bb1fe7549a5d6df6ce1e
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2026-04-07 14:15:28 -0400
Commit message:

 prompt user before cloning
Package: AnVILVRS
Commit: 89b60efae40a2ee556df3c5b146a82b94f716af1
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2026-04-07 14:03:51 -0400
Commit message:

 version bump 0.99.18
Package: AnVILVRS
Commit: 61d65a323d072ea86bcb6226064c2a7b7d856483
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2026-04-07 14:03:46 -0400
Commit message:

 add package doc with roxygen2
Package: AnVILVRS
Commit: f9d3d949072d52fe36d4d22e541394e31d8ebe3e
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2026-04-07 13:54:20 -0400
Commit message:

 version bump 0.99.17
Package: AnVILVRS
Commit: 3ab0d7b38e6041cdc0611332b2d6cc3037c13b36
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2026-04-07 13:54:05 -0400
Commit message:

 include sessionInfo output in README.md
Package: AnVILVRS
Commit: 54e4b54b7f88c60ef547de51d9b8f618a3fecf7f
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2026-04-07 13:50:51 -0400
Commit message:

 run get_caf example in README.md
Package: AnVILVRS
Commit: a1025afdacd2bf5b1e19e70403ca71c23d075548
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2026-04-07 13:46:54 -0400
Commit message:

 update prose in README.md
Package: AnVILVRS
Commit: 4f105f0e7bb066576e760927135ae2363b2442a0
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2026-04-07 13:46:14 -0400
Commit message:

 update outputs in README.md
Package: AnVILVRS
Commit: bc4be0548bb4f2e84be40099a76dd5c86ac3f83a
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2026-04-07 13:42:49 -0400
Commit message:

 update get_caf chunk in vignette
Package: AnVILVRS
Commit: 270c9c9d90fa563bb0c4042e6000ec724fa2b56a
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2026-04-07 13:17:01 -0400
Commit message:

 remove auto install from vignette
Package: ClustIRR
Commit: 1a6eca634f8a42f8115a5d7bcce614429dc383a2
Author: sktron <simo.kitanovski@uni-due.de>
Date: 2026-04-07 19:29:06 +0200
Commit message:

 tests fixed, minor bugfix in selecting NAs
Package: ClustIRR
Commit: c0617c95db698a044175009bfc7ce36b3d9557d4
Author: sktron <simo.kitanovski@uni-due.de>
Date: 2026-04-07 18:50:36 +0200
Commit message:

 bugfix nweight no longer input
Package: ClustIRR
Commit: 68a5c02622bbb2e3dacce196a50e0ed5926208f4
Author: sktron <simo.kitanovski@uni-due.de>
Date: 2026-04-07 18:49:37 +0200
Commit message:

 transit blaster -> rBLAST, warning fixes, man fixes, dependencies
Package: RcwlPipelines
Commit: a60693c035308b9fe4ab479fdf379812a9f74a90
Author: qhu <qiang.hu@roswellpark.org>
Date: 2026-04-07 13:07:53 -0400
Commit message:

 add UnsupportedPlatforms
Package: Rcwl
Commit: 260b79e7a1682aad7ab220ed2dbe1f0e38afdaf8
Author: hubentu <qiang.hu@roswellpark.org>
Date: 2026-04-07 13:04:26 -0400
Commit message:

 fix step bugs
Package: AnVILVRS
Commit: 321d3768267e31132a4813f2f0061aec24092707
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2026-04-07 12:02:01 -0400
Commit message:

 version bump 0.99.16
Package: AnVILVRS
Commit: e6e99db0af8d1bf312e641bf21d6b1b946e78515
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2026-04-07 12:01:45 -0400
Commit message:

 bug fix get_pop_descriptor saves to cache location

- force arg added
Package: ENmix
Commit: dbede0f64bfdfdcdb2dd9eddcf41e65f4137df2f
Author: xuz1 <xuz@niehs.nih.gov>
Date: 2026-04-07 11:23:46 -0400
Commit message:

 bugfix

Signed-off-by: xuz1 <xuz@niehs.nih.gov>
Package: MSstatsLiP
Commit: 7131096b77e912de6264cb823fc57b7973da6b9e
Author: tonywu1999 <anthonywu92@gmail.com>
Date: 2026-04-07 11:01:10 -0400
Commit message:

 refactor(groupComparisonLiP): Use ptm_label_type and protein_label_type for groupComparisonPTM dependency (#47)
Package: TraianProt
Commit: b8befbe745bf56127ecb236db3f06dc2ca759d45
Author: Samuel <sdelacam@ucm.es>
Date: 2026-04-07 16:22:21 +0200
Commit message:

 Fix example scope in impute_KNN_data and update version
Package: TraianProt
Commit: 580b5a83e299c8b15e914bdf7d475469f7263d22
Author: Samuel <sdelacam@ucm.es>
Date: 2026-04-07 16:21:01 +0200
Commit message:

 Fix example scope in impute_KNN_data and update version
Package: TraianProt
Commit: e7a75eb5ac869ecd9a7f34f4d53888a69e56717f
Author: Samuel <sdelacam@ucm.es>
Date: 2026-04-07 16:07:00 +0200
Commit message:

 Update version to 0.99.11 to trigger build
Package: TraianProt
Commit: 53613db5db3c34916a9c0d2f3cfbd30a16816a49
Author: Samuel <sdelacam@ucm.es>
Date: 2026-04-07 15:42:44 +0200
Commit message:

 Ready for Bioconductor submission: all checks passed
Package: Chromatograms
Commit: e121edc922b8394f6ca0365d12dc1f049e69360d
Author: Philippine Louail <philippine.louail@outlook.com>
Date: 2026-04-03 08:59:49 +0200
Commit message:

 Merge pull request #52 from rformassspectrometry/phili

Improve efficiency by pre-filtering Spectra object before summarizing it
Package: Chromatograms
Commit: 21a18fe9baa5caa1e0bfbeb07cc3cf22c450b84d
Author: Philippine Louail <127301965+philouail@users.noreply.github.com>
Date: 2026-04-02 17:08:50 +0200
Commit message:

 Improve efficiency
Package: Chromatograms
Commit: 9d4ac58fa44d091da2656b504fef491aebf3b647
Author: Philippine Louail <philippine.louail@outlook.com>
Date: 2026-04-02 13:04:41 +0200
Commit message:

 Merge pull request #51 from rformassspectrometry/phili

Adding compareChromatograms() method
Package: Chromatograms
Commit: c440e49f5aee03234df704b62b3542998fda0601
Author: Philippine Louail <127301965+philouail@users.noreply.github.com>
Date: 2026-04-02 12:51:48 +0200
Commit message:

 fix label param in test
Package: Chromatograms
Commit: 15b665862ac74dbd0ec2367dcb614e65ec9c4a4a
Author: Philippine Louail <127301965+philouail@users.noreply.github.com>
Date: 2026-04-02 12:32:49 +0200
Commit message:

 Update using-a-chromatograms-object.Rmd
Package: Chromatograms
Commit: 01f50c61d81430dca0c1f481256b16c3b11b9b87
Author: Philippine Louail <127301965+philouail@users.noreply.github.com>
Date: 2026-04-02 12:26:23 +0200
Commit message:

 fix documentation
Package: Chromatograms
Commit: 6dfe240f9565e81df49e51c2216132000443601b
Author: Philippine Louail <127301965+philouail@users.noreply.github.com>
Date: 2026-04-02 12:13:54 +0200
Commit message:

 fix matchRtime()
Package: Chromatograms
Commit: 935cef59868bea43fbe87f39c584d603353f8ce8
Author: Philippine Louail <127301965+philouail@users.noreply.github.com>
Date: 2026-04-02 08:50:12 +0200
Commit message:

 simplify helper code
Package: Chromatograms
Commit: 63e810ba773d9d013cbae716aca302d67f55e5bd
Author: Philippine Louail <127301965+philouail@users.noreply.github.com>
Date: 2026-03-31 13:19:20 +0200
Commit message:

 fix jo's comments
Package: Chromatograms
Commit: dfe08b11b3628440a6d48305c12474a353399c38
Author: Philippine Louail <127301965+philouail@users.noreply.github.com>
Date: 2026-03-30 15:24:07 +0200
Commit message:

 fix issue in self comparing
Package: Chromatograms
Commit: dd5c8410c47ff782124f338740fa0f8b8435b771
Author: Philippine Louail <127301965+philouail@users.noreply.github.com>
Date: 2026-03-30 13:23:21 +0200
Commit message:

 Update helpers.R
Package: Chromatograms
Commit: 07f9c702b0b3375876274fd8ef7e531d4da8c1ec
Author: Philippine Louail <127301965+philouail@users.noreply.github.com>
Date: 2026-03-27 15:23:40 +0100
Commit message:

 fix return
Package: Chromatograms
Commit: 600dbc157a442bab7ccc88e069cc662a0be1c948
Author: Philippine Louail <127301965+philouail@users.noreply.github.com>
Date: 2026-03-27 14:37:40 +0100
Commit message:

 update to compareChromatograms()
Package: Chromatograms
Commit: c85d32f949c342638b26400455a1fa0d24aa9d6a
Author: Philippine Louail <127301965+philouail@users.noreply.github.com>
Date: 2026-03-27 11:03:05 +0100
Commit message:

 Adding correlate method
Package: sosta
Commit: 196c8276a2bbb8890224479a2eec0560800ca2e0
Author: sgunz <samuel.gunz@uzh.ch>
Date: 2026-03-26 14:20:20 +0100
Commit message:

 version bum 1.3.4
Package: sosta
Commit: d4629cde6c2066edff9a292175e016e827e482b4
Author: sgunz <samuel.gunz@uzh.ch>
Date: 2026-03-26 14:12:55 +0100
Commit message:

 remove failing GHA bioc-checks
Package: snifter
Commit: e08497783c83d3f151146e3d4ef00fd12ffdb46d
Author: Alan O'Callaghan <alan.ocallaghan@outlook.com>
Date: 2026-04-07 13:50:54 +0100
Commit message:

 Merge branch 'devel' of git.bioconductor.org:packages/snifter into devel
Package: snifter
Commit: 287c9da9b924b48182e8c3e2b2d32b8b58bb6218
Author: Alan O'Callaghan <alan.ocallaghan@outlook.com>
Date: 2026-04-07 13:49:54 +0100
Commit message:

 Remove BBSoptions
Package: densvis
Commit: c13c29a7ef8685e35be89ddc4a041c002c928a5f
Author: Alan O'Callaghan <alan.ocallaghan@outlook.com>
Date: 2026-04-07 13:50:23 +0100
Commit message:

 Remove BBSoptions
Package: scrapper
Commit: d63efcd75d2c2bb9159b0ad90add2d06844197fc
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2026-04-07 22:11:35 +1000
Commit message:

 Allow scoreMarkers to only return the indices of the top markers.

This avoids having to call the DFrame constructor for a bit of efficiency if
the user doesn't care about the effect sizes. If we do need a DFrame, we create
it directly in Rcpp to avoid calling the S4Vectors::DFrame constructor.
Package: gutenTAG
Commit: b74827a52f23ca63a13cd3d0dbe9f7f8a267c20b
Author: John Abbey <john@dqbm-nbm-joab.local>
Date: 2026-04-07 13:51:16 +0200
Commit message:

 update README
Package: gutenTAG
Commit: 68951426602b9c4632959cf30b6cd34100adccb2
Author: John Abbey <john@dqbm-nbm-joab.local>
Date: 2026-04-07 13:50:49 +0200
Commit message:

 update readme
Package: gutenTAG
Commit: 7df65d9313ef497eaa82ccc8d3f3d641ae09ea2b
Author: John Abbey <john@dqbm-nbm-joab.local>
Date: 2026-04-07 13:35:47 +0200
Commit message:

 add reticulate to suggests
Package: Rarr
Commit: 6f05b272b274dece617fd0e548ebe684c2d7af99
Author: Hugo Gruson <git@hugogruson.fr>
Date: 2026-04-07 13:10:36 +0200
Commit message:

 Remove ZarrArray for Suggests for now
Package: Rarr
Commit: 370c58250743fbb5ca35f5fb01f28a72b0247486
Author: Hugo Gruson <git@hugogruson.fr>
Date: 2026-04-07 13:04:54 +0200
Commit message:

 Bump version
Package: Rarr
Commit: 78bd4965924ca8c26ef8261fbd817400acd1d804
Author: Hugo Gruson <git@hugogruson.fr>
Date: 2026-04-07 13:04:38 +0200
Commit message:

 Remove unnecessary R headers from snappy copy
Package: Rarr
Commit: 40a3bd14709762c6904b57c86749d7a3fa16cd7c
Author: Hugo Gruson <git@hugogruson.fr>
Date: 2026-04-07 13:00:15 +0200
Commit message:

 Use lifecycle pkg for ZarrArray deprecation
Package: gutenTAG
Commit: 6c6bcf97927d2353c5db325c470fc20b336387cb
Author: John Abbey <john@dqbm-nbm-joab.local>
Date: 2026-04-07 13:00:56 +0200
Commit message:

 anndata to suggests
Package: scTypeEval
Commit: 5efb5bf6abb4e432e813fbdc3a9b27e8b9f0f725
Author: JGarnica22 <j.garnica22@gmail.com>
Date: 2026-04-07 11:44:28 +0200
Commit message:

 bump: R 4.6.0
Package: scTypeEval
Commit: 354fa0d809d491310eec99f39a0a30e3f14ce4d6
Author: JGarnica22 <j.garnica22@gmail.com>
Date: 2026-04-07 11:29:35 +0200
Commit message:

 update version 0.99.30
Package: scTypeEval
Commit: 6f9fd07918c515305fdbdc0a4d000330c9a7a97f
Author: JGarnica22 <j.garnica22@gmail.com>
Date: 2026-04-07 11:23:00 +0200
Commit message:

 bump higher version
Package: scTypeEval
Commit: f7714a79bc47d19efd95bdd19fc0d84849d6dd8e
Author: JGarnica22 <j.garnica22@gmail.com>
Date: 2026-04-07 11:13:12 +0200
Commit message:

 fix: avoid 1:
Package: scTypeEval
Commit: 712a66632c307ebc02e7108c050aaacdf8a7e5aa
Author: JGarnica22 <j.garnica22@gmail.com>
Date: 2026-04-02 16:14:09 +0200
Commit message:

 add: higher version
Package: scTypeEval
Commit: 38d8439d6912e3ab5f85da283a7d9137bfe4c4a1
Author: JGarnica22 <j.garnica22@gmail.com>
Date: 2026-04-02 15:46:12 +0200
Commit message:

 fix: revision of roxygen documentation
Package: scTypeEval
Commit: 89cded2edb8d3b1fa056bc70d1ea600c1add8bc5
Author: JGarnica22 <j.garnica22@gmail.com>
Date: 2026-04-02 13:55:35 +0200
Commit message:

 fix: defulat dissimilarity method to Pseudobulk:Euclidean
Package: scTypeEval
Commit: ff4728977b362433713c825028472fa2703df839
Author: JGarnica22 <j.garnica22@gmail.com>
Date: 2026-04-02 13:39:20 +0200
Commit message:

 fix: default black_list as NULL
Package: scTypeEval
Commit: 411de8f5714ad466d55c564c3a8ba19b3005a363
Author: JGarnica22 <j.garnica22@gmail.com>
Date: 2026-04-02 13:38:35 +0200
Commit message:

 fix: default black_list as NULL
Package: scTypeEval
Commit: bc2dc43ff46066a515710432656ab223b0d0214d
Author: JGarnica22 <j.garnica22@gmail.com>
Date: 2026-04-02 13:18:48 +0200
Commit message:

 rm: get_optimal_clustering function
Package: scTypeEval
Commit: bf23be9c79c0b36c1a50007f6b0d352adce345c4
Author: JGarnica22 <j.garnica22@gmail.com>
Date: 2026-04-02 12:53:08 +0200
Commit message:

 add: loading of black_list
Package: scTypeEval
Commit: 51c8e76d167419d6e3ed301afd6463d39dea35b2
Author: JGarnica22 <j.garnica22@gmail.com>
Date: 2026-04-02 12:28:27 +0200
Commit message:

 rm: global metrics of clustering agreement depending on aricode, NMI and ARI
Package: scTypeEval
Commit: 4643d9c4d043705646487afb502a27dbc4ce0cd3
Author: JGarnica22 <j.garnica22@gmail.com>
Date: 2026-04-02 12:24:10 +0200
Commit message:

 fix: remove `eval=FALSE`, warnings, and not used arguments
Package: scTypeEval
Commit: f9b0a9cfdbbe91ee3c0bf59a555a63bffd64e20b
Author: JGarnica22 <j.garnica22@gmail.com>
Date: 2026-04-02 09:23:35 +0200
Commit message:

 fix: void 1:...; use seq_len() or seq_along() and avoid sapply(); use
vapply().
Package: scTypeEval
Commit: 95db7c30b81343fc46d2b3784ad91ef5c96412da
Author: JGarnica22 <j.garnica22@gmail.com>
Date: 2026-04-01 18:39:37 +0200
Commit message:

 fix: change all functions and variables to snake_case
Package: scTypeEval
Commit: 2c2c2e42d7235b154349da63e654167978e3e99d
Author: JGarnica22 <j.garnica22@gmail.com>
Date: 2026-02-27 17:24:56 +0100
Commit message:

 fix: lines length
Package: scTypeEval
Commit: 3fb9ea987c6e24df53a4f72350a6df897f247efa
Author: JGarnica22 <j.garnica22@gmail.com>
Date: 2026-02-27 17:19:53 +0100
Commit message:

 fix: typo
Package: scTypeEval
Commit: fd9ca5041cdd52689ee2d6609ffaf21983403ab2
Author: JGarnica22 <j.garnica22@gmail.com>
Date: 2026-02-27 17:14:13 +0100
Commit message:

 fix text
Package: scTypeEval
Commit: ffdc448fafa170e77aed9245781e613d88327450
Author: JGarnica22 <j.garnica22@gmail.com>
Date: 2026-02-27 17:01:20 +0100
Commit message:

 add benchmark results
Package: scTypeEval
Commit: a73905ec69cce6d809705b75d636df9816befae2
Author: JGarnica22 <j.garnica22@gmail.com>
Date: 2026-02-27 16:30:47 +0100
Commit message:

 add: benchmarking fig
Package: PSMatch
Commit: 91fe6d80e22bc9ca2c73301b7fd5db496af771e1
Author: Laurent Gatto <lgatto@protonmail.ch>
Date: 2026-04-07 12:35:23 +0200
Commit message:

 Merge branch 'main' into devel
Package: PSMatch
Commit: 792268de906bebbc1b0cfb907ac446fea8765c68
Author: Laurent Gatto <lgatto@protonmail.ch>
Date: 2026-04-07 12:35:10 +0200
Commit message:

 bump version
Package: PSMatch
Commit: 4e784ddd28d4516f3630b1c47a16c7ca97cee4c9
Author: Laurent Gatto <lgatto@protonmail.ch>
Date: 2026-04-07 12:32:48 +0200
Commit message:

 Merge branch 'main' into devel
Package: PSMatch
Commit: dc3d6e34910d660b780de06c4ea3600f5dafb116
Author: Laurent Gatto <lgatto@protonmail.ch>
Date: 2026-04-07 12:32:27 +0200
Commit message:

 depend on PTMods 0.99.4
Package: PSMatch
Commit: 3bf94113445befce9abb85c303e1a167f2ee7886
Author: Laurent Gatto <lgatto@protonmail.ch>
Date: 2026-04-07 12:29:28 +0200
Commit message:

 Merge branch 'main' into devel
Package: PSMatch
Commit: 77592b31f01edef6dbdbdc79c84b6348b2044e05
Author: Laurent Gatto <lgatto@protonmail.ch>
Date: 2026-04-07 12:28:24 +0200
Commit message:

 fix indentation
Package: PSMatch
Commit: 7fe4e6ed6fb5172cdf89137bf4bd043d66e8766a
Author: Laurent Gatto <laurent.gatto@uclouvain.be>
Date: 2026-04-07 12:24:29 +0200
Commit message:

 Merge pull request #43 from guideflandre/main

docs: added clarifications on the use of addCarbamidomethyl = TRUE  default
Package: PSMatch
Commit: 31bef1a11b2cbc472bd5c3992c1629956a914582
Author: Guillaume Deflandre <guill.deflandre@gmail.com>
Date: 2026-04-07 12:22:48 +0200
Commit message:

 docs: completed vignette with PTMods references
Package: PSMatch
Commit: 5f59ee490fbe27fd9c6314412a91515f0a2bc80b
Author: Guillaume Deflandre <guill.deflandre@gmail.com>
Date: 2026-04-07 11:42:48 +0200
Commit message:

 docs: wrong formulation in documentation
Package: PSMatch
Commit: 13d84b829d6b75eff05b7cebaaa37aae5d19374c
Author: Guillaume Deflandre <guill.deflandre@gmail.com>
Date: 2026-04-07 11:39:51 +0200
Commit message:

 Docs: add addCarbamidomethyl as a parameter in plotSpectraPTM
Package: PSMatch
Commit: b5afd7c23024b9e974a6bc88d77b475f5ac515bc
Author: Guillaume Deflandre <guill.deflandre@gmail.com>
Date: 2026-04-06 22:55:17 +0200
Commit message:

 build: bump the cache version to .4
Package: PSMatch
Commit: 1927ffff6257d9925ea11206639609eb51aa3542
Author: Guillaume Deflandre <guill.deflandre@gmail.com>
Date: 2026-04-06 22:25:16 +0200
Commit message:

 docs: added clarifications on the use of addCarbamidomethyl = TRUE by default
Package: biomaRt
Commit: d8106a4fc751ec239858328b80e458be8f0f0a04
Author: Hugo Gruson <git@hugogruson.fr>
Date: 2026-04-07 12:21:05 +0200
Commit message:

 Fix pkgdown index
Package: biomaRt
Commit: 98b8fb404da8d5cdf79d2e2fdf7dbeb1a0b67f52
Author: Hugo Gruson <git@hugogruson.fr>
Date: 2026-04-07 12:12:24 +0200
Commit message:

 Bump version
Package: biomaRt
Commit: 484b4c33c6971ffe52b7705ad1251fb9a9d4e45f
Author: Hugo Gruson <git@hugogruson.fr>
Date: 2026-04-07 12:12:06 +0200
Commit message:

 Mention SSL setting change in NEWS
Package: biomaRt
Commit: 51d9f9531f14b0d2807c76eeec648be48f6c94d8
Author: Hugo Gruson <git@hugogruson.fr>
Date: 2026-04-07 12:09:50 +0200
Commit message:

 Reimport req_user_agent()
Package: biomaRt
Commit: 41d8b5831106809d5bef1281ae2da349016f697c
Author: Hugo Gruson <git@hugogruson.fr>
Date: 2026-04-07 12:09:36 +0200
Commit message:

 Remove forced SSL settings
Package: biomaRt
Commit: 4ff37395e0fe9635a923b490a3c14e5da3cc81a9
Author: Hugo Gruson <git@hugogruson.fr>
Date: 2026-04-07 12:08:41 +0200
Commit message:

 Move non biomart utilities to dedicated pkgdown section
Package: kissDE
Commit: 5088686fd0d7f492f825fb1d608299c8cfc0f479
Author: Aurélie Siberchicot <aurelie.siberchicot@univ-lyon1.fr>
Date: 2026-04-07 11:12:46 +0200
Commit message:

 Update the R-CMD-check workflow
Package: gutenTAG
Commit: e518bcf39c32f39c38a9144878cc85574668a969
Author: John Abbey <john@dqbm-nbm-joab.local>
Date: 2026-04-07 10:58:45 +0200
Commit message:

 change license
Package: gutenTAG
Commit: 953d314a280944c82ad9c4e40f6955fae6ceae71
Author: John Abbey <john@dqbm-nbm-joab.local>
Date: 2026-04-07 10:44:06 +0200
Commit message:

 fix warning in test-asAnnData
Package: arrayQualityMetrics
Commit: 3acb7cb4fb20f6c9c194c8643c45438d38c4d2ba
Author: Hugo Gruson <git@hugogruson.fr>
Date: 2026-04-07 10:24:08 +0200
Commit message:

 Bump version
Package: arrayQualityMetrics
Commit: 7bffb37fff7c3aef4dee639d87437d2405948712
Author: Hugo Gruson <git@hugogruson.fr>
Date: 2026-04-07 10:23:50 +0200
Commit message:

 Use jsonlite instead of custom code

jsonlite is already an indirect dependency
Package: TraianProt
Commit: 7bfb290443e801eadd7978716712d7ef4afe5391
Author: Samuel <sdelacam@ucm.es>
Date: 2026-04-07 10:34:26 +0200
Commit message:

 Eliminado library(rsconnect) del codigo fuente y actualizacion de version
Package: TraianProt
Commit: 027b92bacef6b351cf3c179cb1203c9cc95887a4
Author: Samuel <sdelacam@ucm.es>
Date: 2026-04-07 10:18:52 +0200
Commit message:

 Sincronizando historial con Bioconductor y actualizando archivos
Package: betterChromVAR
Commit: 4c97fb42b17b03efce945c5b71196dea54ca4e45
Author: plger <pl.germain@gmail.com>
Date: 2026-04-07 09:12:02 +0200
Commit message:

 version bump to trigger new build...
Package: wavFeatExt
Commit: d4abe01d2ab7a2883f4a7aa87ce2383e51c5c126
Author: Maharani Ahsani Ummi <maharaniahsani@itb.ac.id>
Date: 2026-04-07 12:43:01 +0700
Commit message:

 Address reviewer comments: documentation, vignette, naming, examples
Package: HDF5Array
Commit: b7bc1f300e2383768723a36b2a52d107e1db7399
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2026-04-06 22:37:18 -0700
Commit message:

 HDF5Array 1.39.1: Internal util compute_max_string_size() is now in h5mread
Package: VISTA
Commit: e0b8a1a4367f0ff1b6f57797e292cd95b333d69e
Author: Chirag Parsania <chirag.parsania@gmail.com>
Date: 2026-04-07 15:35:33 +1000
Commit message:

 Increment version number to 0.99.5
Package: VISTA
Commit: cbf5c9294df624657990c79241d1f366f1cd175e
Author: Chirag Parsania <chirag.parsania@gmail.com>
Date: 2026-04-07 15:17:17 +1000
Commit message:

 Refactor package state handling and clean reviewer-facing package metadata

- remove <<- usage from exporting, reporting, and visualization helpers
- keep explicit local state for manifests, report assets, enrichment outputs, and plot messages
- restore selective SummarizedExperiment replacement imports for rowData<- and colData<-
- clean DESCRIPTION metadata and dependency duplication
- tighten namespace imports and address BiocCheck style issues for vapply and seq_len/seq_along
- simplify pkgdown articles by dropping the redundant reference guide entry
Package: h5mread
Commit: 288d616620851a16391f17b20172c6f69caf0bc8
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2026-04-06 22:16:56 -0700
Commit message:

 h5mread 1.3.3: Small twaek to h5writeDimnames()

Avoid annoying warning when using h5writeDimnames() to write the dimnames
of a dataset with at least one dimension > 1e6.
Package: wavFeatExt
Commit: b86764ac0fdefa331e31de5249f3b640bbb1459a
Author: Maharani Ahsani Ummi <maharaniahsani@itb.ac.id>
Date: 2026-04-07 12:06:12 +0700
Commit message:

 Address reviewer comments: documentation, vignette, naming, examples
Package: wavFeatExt
Commit: 40f82124629880595bee1b9907efbb8287caf232
Author: Maharani Ahsani Ummi <maharaniahsani@itb.ac.id>
Date: 2026-04-07 12:02:01 +0700
Commit message:

 Address reviewer comments: documentation, vignette, naming, examples
Package: scran
Commit: 83da94719ea3d0d91ec272374a87812507943cc1
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2026-04-07 13:56:41 +1000
Commit message:

 Throttle down to 2 cores to avoid CHECK errors.
Package: scran
Commit: 7c3e04c4922c7a12b1739ed87360c32e291f6896
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2026-04-07 12:30:38 +1000
Commit message:

 Strip down vignette to remove mentions of deprecated functionality.
Package: scran
Commit: 9a31089ab3cebc27ca0ed4fbb5089213a2a667f4
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2026-04-07 11:27:01 +1000
Commit message:

 Bypass some warnings now that we've deprecated everything.
Package: scran
Commit: b7de0f5303fd0433db3eb3ade67e719dedc52dcd
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2026-04-07 02:47:47 +1000
Commit message:

 Deprecate a lot of old functions.

Some of them have improved versions in scrapper, and others just aren't used.
Package: wavFeatExt
Commit: 5ce814c104d2c0218cb12cb3f64bc61c57a1705c
Author: Maharani Ahsani Ummi <maharaniahsani@itb.ac.id>
Date: 2026-04-07 10:49:52 +0700
Commit message:

 Address reviewer comments: documentation, vignette, naming, examples
Package: SpiecEasi
Commit: 54bbc2cb31be11faade0a3a39b26613f95837566
Author: Zachary Kurtz <zdkurtz@gmail.com>
Date: 2026-04-06 23:47:19 -0400
Commit message:

 Bump version: 1.99.4 → 1.99.5
Package: SpiecEasi
Commit: 423c866335a393c48a36a17a1e257870150a4b61
Author: Zachary Kurtz <zdkurtz@gmail.com>
Date: 2026-04-06 23:47:12 -0400
Commit message:

 fix versioning
Package: SpiecEasi
Commit: 7c713bf44bbb4d660ad0d004295c411d42d4a4ca
Author: Zachary Kurtz <zdkurtz@gmail.com>
Date: 2026-04-06 23:29:27 -0400
Commit message:

 resolve estFun before passing to pulsar
Package: limpa
Commit: dc9427f92cb57ecb2b1d67432d013b77440e2bb5
Author: Gordon Smyth <smyth@wehi.edu.au>
Date: 2026-04-07 13:44:14 +1000
Commit message:

 limpa 1.3.11
- dpc() now calls either dpcON() or dpcCN() depending on `model` argument.
- Original dpc() renamed to dpcLegacy().
- New arguments for EListFromLongFormatFile(), readDIANN() and readSpectronaut().
- readSpectronaut() now reads run information columns.
Package: CSOA
Commit: af52b3992c2823f6dc4377d20d605431cdf1daa1
Author: andrei-stoica26 <andreistoica@foxmail.com>
Date: 2026-04-07 10:26:53 +0800
Commit message:

 Bumped version number
Package: CSOA
Commit: 83e866e8549991d5be57561cf6d28b870f3594e6
Author: andrei-stoica26 <andreistoica@foxmail.com>
Date: 2026-04-07 10:26:09 +0800
Commit message:

 Removed bayesbio dependency
Package: scuttle
Commit: 68f3482d6461e4315a9b5f7eb4b653a7475be782
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2026-04-06 21:46:10 +1000
Commit message:

 Just use scran_aggregate for the across-cells aggregation for now.

This ensures that the fast path (i.e., no medians) works for all matrices, not
just dgCMatrices. This is not written with a particularly great deal of love
but whatever, we'll be throwing it out in the next release cycle anyway.
Package: scuttle
Commit: 7d809619f5a19ae31bb3521abfa82f747a7cd157
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2026-04-06 21:23:05 +1000
Commit message:

 Cleaned out vignettes to reflect the historical nature of this package.
Package: scuttle
Commit: 8f25a577b499a7b9615fe533953c1d2b9b72f622
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2026-04-06 16:00:40 +1000
Commit message:

 Slap deprecation warnings on every function with a scrapper equivalent.
Package: metagenomeSeq
Commit: 201033db18b652b0992de3a0a420f93fba3c1965
Author: Joseph Paulson <josephpaulson@gmail.com>
Date: 2026-04-06 09:44:01 -0700
Commit message:

 remove interactiveDisplay
Package: AnVILVRS
Commit: 510033d0bd78cb9fc1d198cadce495ccc7244a3b
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2026-04-06 17:12:45 -0400
Commit message:

 .Rbuildignore cache folders
Package: AnVILVRS
Commit: ee4bc1edfc8677c325ba9afaff8416b64181ef9f
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2026-04-06 17:06:45 -0400
Commit message:

 version bump 0.99.15
Package: AnVILVRS
Commit: 1161edefa1b6e44240977fa52b82c2cc519a53da
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2026-04-06 17:06:39 -0400
Commit message:

 doc options(AnVILVRS.toolkit_path = ...)
Package: AnVILVRS
Commit: aed32396d5becec7713565ff8c05cf181b94f6e3
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2026-04-06 16:04:12 -0400
Commit message:

 update get_caf example
Package: AnVILVRS
Commit: 147156e65dc4010bb277cd5b07fbec68707cd679
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2026-04-06 16:04:00 -0400
Commit message:

 update toolkit_dir default

- use setup_vrs_toolkit as default
Package: AnVILVRS
Commit: 2f9aaa6cf59566ff2f187b7aa6d2ac5e25318cc1
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2026-04-06 15:59:36 -0400
Commit message:

 add build_vrs_index and setup_vrs_toolkit helpers
Package: AnVILVRS
Commit: 27ea0a7a305d8ae15aa85085e9f8eb5fb0efc3e3
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2026-04-06 15:57:41 -0400
Commit message:

 fix vrs-anvil-toolkit name in message
Package: AnVILVRS
Commit: 8a1b5ce241c0b0f45f6902d6d8354aefad55dd4d
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2026-04-06 15:41:08 -0400
Commit message:

 unexport local calls
Package: PTMods
Commit: 9484aa383cf19b9f5f02deea559ff077808c8aa4
Author: Guillaume Deflandre <guill.deflandre@gmail.com>
Date: 2026-04-06 23:00:21 +0200
Commit message:

 Build: bump version to 0.99.4
Package: PTMods
Commit: d48b99b3aae691f39350cb247bb66612295d7b52
Author: Guillaume Deflandre <37773040+guideflandre@users.noreply.github.com>
Date: 2026-03-31 11:40:05 +0200
Commit message:

 Merge pull request #23 from rformassspectrometry/convertAnnotation

Feat: keep NAs in input vector for addModfications
Package: PTMods
Commit: cceca430bdf096423ee4afb1a22bbba528a70e68
Author: GuillaumeDeflandre <potamoidef@gmail.com>
Date: 2026-03-31 11:36:16 +0200
Commit message:

 Feat: keep NAs in input vector for addModfications
Package: PTMods
Commit: 9f0404a7073d2ff2af80c08f70175d0ecf7d8974
Author: Guillaume Deflandre <37773040+guideflandre@users.noreply.github.com>
Date: 2026-03-25 15:00:55 +0100
Commit message:

 Merge pull request #22 from rformassspectrometry/addModifications

Add getModificationsCounts and throw error when multiple modifications in add modfications
Package: PTMods
Commit: 5f12de34992a96618118b2f7211e33e67d41a253
Author: GuillaumeDeflandre <potamoidef@gmail.com>
Date: 2026-03-25 14:25:38 +0100
Commit message:

 docs: keep version to 0.99.3 for now
Package: PTMods
Commit: 0ee6126f09afb010266ad35d2fe23983eb0ce501
Author: GuillaumeDeflandre <potamoidef@gmail.com>
Date: 2026-03-25 14:25:15 +0100
Commit message:

 feat: add getModificationsCounts and throw error when multiple modifications on amino acid

getModificationsCounts gives a named numerical vector with all
modifications and their counts in given sequences.

addFixed and VariableModifications used to take the first instance of
given modifications on the same amino acid. Because this is not
supported, it is preferred to throw an error.
Package: phylobar
Commit: 8e88a06024412581bd33b8a881bd8fbec638fbc9
Author: Kris Sankaran <sankaran.kris@gmail.com>
Date: 2026-04-06 15:45:39 -0500
Commit message:

 bump version
Package: phylobar
Commit: 5621f0a8ca725b679c0bfa7d9fd4c9b824dae605
Author: Kris Sankaran <sankaran.kris@gmail.com>
Date: 2026-04-06 15:39:56 -0500
Commit message:

 ensure 'wb' mode for windows systems
Package: RFGeneRank
Commit: 7bc34fcb3553297afd20d2c57203e85da6aa3f37
Author: Abdulaziz Albeshri <a.z.a1410@hotmail.com>
Date: 2026-04-06 23:26:11 +0300
Commit message:

 Updated R dependency to R (>= 4.6)
Package: DropletUtils
Commit: 0ffac763314fa0e226cf83b063168216aa798f77
Author: Jonathan Griffiths <7976085+jonathangriffiths@users.noreply.github.com>
Date: 2026-04-06 20:33:16 +0100
Commit message:

 test with Csparsematrix for scuttle change
Package: betterChromVAR
Commit: 0b3f9b71c847b52468a00d11c1bd7828f60debcf
Author: plger <pl.germain@gmail.com>
Date: 2026-04-06 20:46:37 +0200
Commit message:

 version bump
Package: betterChromVAR
Commit: 45b50fb93ca75932afa5fe228eb13a222bc2e1f5
Author: plger <pl.germain@gmail.com>
Date: 2026-04-06 20:46:20 +0200
Commit message:

 fixed imports
Package: betterChromVAR
Commit: bca597284ca8382b5fb361adb9c8929a798d4e2d
Author: plger <pl.germain@gmail.com>
Date: 2026-04-06 18:57:07 +0200
Commit message:

 added doc for the methods
Package: betterChromVAR
Commit: d247e671fcb07a741edd3f65bd9357d2cdd83038
Author: plger <pl.germain@gmail.com>
Date: 2026-04-06 18:36:37 +0200
Commit message:

 major refactoring of the interface, breaking main function in steps
Package: betterChromVAR
Commit: 318504af471edc0f398dd602c15155c601aec8ad
Author: plger <pl.germain@gmail.com>
Date: 2026-04-01 22:27:05 +0200
Commit message:

 added sampleBackgroundPeaks
Package: betterChromVAR
Commit: b57b66d557866da70da812f4ef3e471337e356c8
Author: plger <pl.germain@gmail.com>
Date: 2026-03-31 13:16:30 +0200
Commit message:

 updated doc
Package: betterChromVAR
Commit: fe84dd9db4ea36f3056a0e14088d912da0323712
Author: plger <pl.germain@gmail.com>
Date: 2026-03-31 13:16:08 +0200
Commit message:

 updated doc
Package: betterChromVAR
Commit: 25ebfd8a7cceecacd3e8654c0101799a04150a94
Author: plger <pl.germain@gmail.com>
Date: 2026-03-31 13:11:24 +0200
Commit message:

 catch flbias
Package: scp
Commit: 41ea7687e627693efea31e3d6e79a8fd28e9d811
Author: Laurent Gatto <lgatto@protonmail.ch>
Date: 2026-04-06 19:53:16 +0200
Commit message:

 bump version
Package: scp
Commit: b6288777e883ce4e945c76b980099d000e9397bb
Author: Laurent Gatto <lgatto@protonmail.ch>
Date: 2026-04-06 19:51:56 +0200
Commit message:

 Merge branch 'devel'
Package: scp
Commit: 08b965223a81e7c57b7b439cc15478669b18515c
Author: Christophe Vanderaa <43441105+cvanderaa@users.noreply.github.com>
Date: 2026-02-09 14:42:48 +0100
Commit message:

 Changed my email
Package: trio
Commit: c6f8de730e5e6f436b80584f298aa6076a6b9c60
Author: holgerschw <holgerschw@users.noreply.github.com>
Date: 2026-04-06 19:42:38 +0200
Commit message:

 Removed dependency from haplo.stats and corrected some flaws.
Package: RFGeneRank
Commit: f85576b0a04a3eb2056943c1dddd1cd2f3fea17b
Author: Abdulaziz Albeshri <a.z.a1410@hotmail.com>
Date: 2026-04-06 20:42:57 +0300
Commit message:

 Replace class() with inherits() in sign_importance; bump version to 0.99.3
Package: QFeatures
Commit: 23506f8e7ee7f8481e2db17f2ea9dbf822082481
Author: Laurent Gatto <lgatto@protonmail.ch>
Date: 2026-04-06 17:49:11 +0200
Commit message:

 bump version, update news
Package: QFeatures
Commit: 390dd5efad5dfd8ea713a0a7d3b4fd0f8f44f671
Author: Laurent Gatto <laurent.gatto@uclouvain.be>
Date: 2026-04-06 17:46:13 +0200
Commit message:

 Merge pull request #255 from leopoldguyot/readqfeatures_verbose

aggregate redundant messages in aggregateFeatures + aggregateFeatures/readQFeatures progress bar
Package: QFeatures
Commit: b813c131968825c5218edfde6278283b73fe2537
Author: Léopold Guyot <leopold.guyot13@gmail.com>
Date: 2026-03-26 11:20:13 +0100
Commit message:

 Merge branch 'rformassspectrometry:master' into readqfeatures_verbose
Package: QFeatures
Commit: db9a8107a696d7098d832b1f9e140499ec3ae027
Author: leopoldguyot <leopold.guyot13@gmail.com>
Date: 2026-01-20 11:47:06 +0100
Commit message:

 fix set name printing for message aggregation
Package: QFeatures
Commit: 72645bc772cfb2112792b0ca3088b3ceb53a9e1c
Author: leopoldguyot <leopold.guyot13@gmail.com>
Date: 2026-01-20 11:28:06 +0100
Commit message:

 add verbose argument to .splitSE
Package: QFeatures
Commit: 77cdbf20c3c81d1f25f1b175e6a22c67f1870067
Author: leopoldguyot <leopold.guyot13@gmail.com>
Date: 2026-01-20 10:58:03 +0100
Commit message:

 aggregate messages in readQFeatues and add progress bar to aggregateFeatures and readQFeatures
Package: scater
Commit: f23aaa1bf12b28f0f8d653d5d71eb3d3e6538bad
Author: Alan O'Callaghan <alan.ocallaghan@outlook.com>
Date: 2026-04-06 16:59:47 +0100
Commit message:

 Merge branch 'devel' of git.bioconductor.org:packages/scater into devel
Package: scater
Commit: c7f852599739aefd879849bfc9048b0d94cd578a
Author: Aaron Lun <infinite.monkeys.with.keyboards@gmail.com>
Date: 2026-04-07 01:57:36 +1000
Commit message:

 Implement replacement for the now-deprecated summarizeAssayByGroup. (#225)

* Implement replacement for the now-deprecated summarizeAssayByGroup.
Package: HuBMAPR
Commit: d489fca9b6f810ab8a7eda609bae1add4bb76bb5
Author: christinehou11 <chou11@jh.edu>
Date: 2026-04-06 10:25:26 -0500
Commit message:

 bump upg

:wq
:wQ
Package: HuBMAPR
Commit: d912ca5e0eb975801a700a12bad5b2451946399f
Author: christinehou11 <chou11@jh.edu>
Date: 2026-04-06 10:05:45 -0500
Commit message:

 bug fix
Package: immGLIPH
Commit: 31b663f805fc1bc3788a398a6c5c77b1702facdc
Author: theHumanBorch <ncborch@gmail.com>
Date: 2026-03-23 12:36:48 -0500
Commit message:

 Merge pull request #6 from BorchLab/roxygen

blank in data Rd
Package: immGLIPH
Commit: 5abfe5ea202269f6247c0bf41e21cbe303660ad4
Author: theHumanBorch <ncborch@gmail.com>
Date: 2026-03-23 12:35:30 -0500
Commit message:

 blank in data Rd
Package: PlinkMatrix
Commit: 6ad2847ef6da0d97a569e1f2244b1ba7de16a331
Author: vjcitn <stvjc@channing.harvard.edu>
Date: 2026-04-06 06:18:33 -0400
Commit message:

 fix vignette
Package: PlinkMatrix
Commit: 9af70616fa233abe64a057a8e4860743f4760fd5
Author: vjcitn <stvjc@channing.harvard.edu>
Date: 2026-04-06 06:13:33 -0400
Commit message:

 remove redundancies
Package: PlinkMatrix
Commit: 398d6acabefdde0e369ef5ccaec41326b722390f
Author: vjcitn <stvjc@channing.harvard.edu>
Date: 2026-04-06 06:11:52 -0400
Commit message:

 first NEWS file
Package: PlinkMatrix
Commit: 158b25da766ead4443bf0d98003fe75f6a034129
Author: vjcitn <stvjc@channing.harvard.edu>
Date: 2026-04-06 06:09:51 -0400
Commit message:

 change package doc
Package: PlinkMatrix
Commit: 8d611384b18d0dc4209ae6a32993a59104fbff9e
Author: vjcitn <stvjc@channing.harvard.edu>
Date: 2026-04-06 05:54:07 -0400
Commit message:

 add installation text in two places
Package: PlinkMatrix
Commit: ff03fafdaaa2a41952648f56f1803e000296a003
Author: vjcitn <stvjc@channing.harvard.edu>
Date: 2026-04-06 05:51:34 -0400
Commit message:

 fix shorttitle
Package: PlinkMatrix
Commit: fced5312ae57f29625786a438c25a19c4d76568d
Author: vjcitn <stvjc@channing.harvard.edu>
Date: 2026-04-06 05:48:42 -0400
Commit message:

 fix PlinkArray reference in README.md
Package: augere.solo
Commit: 49db6e7139874c5d7640ac655e4dfc41d319f883
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2026-04-06 18:54:15 +1000
Commit message:

 Bumped version to trigger a SPB rebuild.
Package: SeqArray
Commit: 03061a1ba0d3ed59db8e02cf83bae3959f8f1c76
Author: Xiuwen Zheng <zhengxwen@gmail.com>
Date: 2026-04-05 19:54:36 -0500
Commit message:

 fix C warnings
Package: APAlyzer
Commit: c080147770542c8a82ccccecb7e1401c1284dd6e
Author: RJWANGbioinfo <rjwang.bioinfo@gmail.com>
Date: 2026-04-05 14:15:31 -0700
Commit message:

 Update README badges to hardcoded version numbers
Package: APAlyzer
Commit: 5c716a6cf891847d169a893e1131ecc4c633d20c
Author: RJWANGbioinfo <rjwang.bioinfo@gmail.com>
Date: 2026-04-05 14:09:24 -0700
Commit message:

 Update README badges to use dynamic Bioconductor shields
Package: APAlyzer
Commit: e0fc7273ce539e863ab28cd4c1ab0379af33296f
Author: RJWANGbioinfo <rjwang.bioinfo@gmail.com>
Date: 2026-04-05 14:09:12 -0700
Commit message:

 Merge upstream/devel; reactivate package and fix BioC 3.22/3.23 compatibility

- Remove deprecation (zzz.R, PackageStatus: Deprecated)
- Bump version to 1.25.2
- Fix ggplot2 4.0+ S7 compatibility in tests
- Replace library(HybridMTest) with requireNamespace(); move to Suggests
- Migrate makeTxDbFromGRanges from GenomicFeatures to txdbmaker
- Add txdbmaker, rlang, S4Vectors to Imports
- Fix undefined globals and deprecated ggplot2 args
- Add .Rbuildignore; update License field
Package: APAlyzer
Commit: 2dfc96e180d2ea9912c7e0bd83d6cec3372421c1
Author: RJWANGbioinfo <rjwang.bioinfo@gmail.com>
Date: 2026-04-05 13:49:08 -0700
Commit message:

 Fix compatibility with R-devel and Bioconductor 3.22/3.23

- Fix test failure: ggplot2 4.0+ S7 objects return typeof "object" not "list"
- Replace deprecated element_line(size=) with element_line(linewidth=)
- Replace library(HybridMTest) with requireNamespace(); move to Suggests
- Migrate makeTxDbFromGRanges import from GenomicFeatures to txdbmaker
- Add txdbmaker, rlang, S4Vectors to Imports
- Fix undefined globals (Print, queryHits, download.file, aes vars)
- Add .Rbuildignore; update License field in DESCRIPTION
- Bump version to 1.9.5
Package: APAlyzer
Commit: ea1e797b990e90c87f5a3d0e36785817a7010029
Author: Ruijia Wang <51307984+RJWANGbioinfo@users.noreply.github.com>
Date: 2024-12-02 12:14:16 -0500
Commit message:

 Update README.md

added email of Bin
Package: APAlyzer
Commit: eb200b8d039b11f964703fa9b4e75c655e0b69da
Author: Ruijia Wang <51307984+RJWANGbioinfo@users.noreply.github.com>
Date: 2022-07-04 15:55:40 -0400
Commit message:

 Update README.md
Package: GenomicRanges
Commit: 1f405cacb7f243be9ddc2887afc29b62fe51fe42
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2026-04-05 12:50:30 -0700
Commit message:

 GenomicRanges 1.63.2

o Use TxDb.Athaliana.BioMart.plantsmart51 instead of
  TxDb.Athaliana.BioMart.plantsmart22 in vignette.

o Remove C code.

o Small tweak to restrict() method for GenomicRanges object.
Package: GenomicFeatures
Commit: a1a980ec8037f78c3cb28a3fa861d4d636cdf37b
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2026-04-05 12:55:16 -0700
Commit message:

 GenomicFeatures 1.63.2: Move C code from GenomicRanges

The C code supporting transcriptLocs2refLocs() and transcriptWidths()
used to be in GenomicRanges and is now in GenomicFeatures.
Package: GSVA
Commit: 78670ba965c7b2d274727e46672af5f9c0145e0f
Author: Robert Castelo <robert.castelo@upf.edu>
Date: 2026-04-05 21:42:48 +0200
Commit message:

 Added support for ssGSEA to work with large datasets stored using a DelayedArray backend, such as HDF5. Several other fixes in the code and documentation. Added unit tests for HDF5 backend and parallelization
Package: LimROTS
Commit: 90ca4a0bee54b1c47bb679abeb516a676367f012
Author: Ali Youssef <aliali.mostafa99@gmail.com>
Date: 2026-04-05 22:30:09 +0300
Commit message:

 Bump the version
Package: LimROTS
Commit: 5d0d2a9a01084901d9e810cc0067a70fdd2ac97b
Author: Ali Youssef <aliali.mostafa99@gmail.com>
Date: 2026-04-05 22:09:40 +0300
Commit message:

 fix for BiocCheck
Package: LimROTS
Commit: 34ebff704c5ce4b3b6693c780deae17a7653cbc5
Author: Ali Youssef <aliali.mostafa99@gmail.com>
Date: 2026-04-05 21:54:28 +0300
Commit message:

 add survival vignettes
Package: LimROTS
Commit: ed6febd786695cc24111a4f8570e84d5d0422627
Author: Ali Youssef <aliali.mostafa99@gmail.com>
Date: 2026-04-05 21:09:24 +0300
Commit message:

 LimROTS_survival vignettes
Package: LimROTS
Commit: 540d9d774087ef85db73f89608a8ecddc1706f4e
Author: Ali Youssef <aliali.mostafa99@gmail.com>
Date: 2026-04-05 20:42:03 +0300
Commit message:

 add assay.type to LimROTS_survival
Package: LimROTS
Commit: 52230c8b4405839b1773dadff505919f30f2028d
Author: Ali Youssef <aliali.mostafa99@gmail.com>
Date: 2026-04-05 20:28:08 +0300
Commit message:

 Updating vignettes LimROTS
Package: LimROTS
Commit: eb305532330523c78f4876296c3e113320236377
Author: Ali Youssef <aliali.mostafa99@gmail.com>
Date: 2026-04-05 19:55:56 +0300
Commit message:

 unit tests for LimROTS and survival
Package: LimROTS
Commit: 2f280fd3a306315952a8e2da2aa456db85ea8fa5
Author: Ali Youssef <aliali.mostafa99@gmail.com>
Date: 2026-04-05 19:14:48 +0300
Commit message:

 group.name to group
Package: LimROTS
Commit: 92365085a5db43505323818354c401dfe0af92fe
Author: Ali Youssef <aliali.mostafa99@gmail.com>
Date: 2026-04-05 19:10:01 +0300
Commit message:

 data.exp to x
Package: LimROTS
Commit: 56151852e3094a6c6819febfd888f4c68288df53
Author: Ali Youssef <aliali.mostafa99@gmail.com>
Date: 2026-04-05 19:02:39 +0300
Commit message:

 fix Description
Package: LimROTS
Commit: cfb3432c6132673c29cde5f862c81d4b64a5e235
Author: Ali Youssef <aliali.mostafa99@gmail.com>
Date: 2026-04-05 18:46:10 +0300
Commit message:

 remove log2 FC keep only corrected one
Package: LimROTS
Commit: e64f86b7f453f7e030520025a4dbf171af82293f
Author: Ali Youssef <aliali.mostafa99@gmail.com>
Date: 2026-04-05 18:27:14 +0300
Commit message:

 Fix Description Link to Doi
Package: MsDataHub
Commit: 0075d6186311527dbc71dd54ca178d4e813af8c8
Author: Laurent Gatto <lgatto@protonmail.ch>
Date: 2026-04-05 20:26:04 +0200
Commit message:

 Merge branch 'guideflandre-main'
Package: MsDataHub
Commit: 93e36183f45945667e7c4dcfb0ab706d0a19fef5
Author: Laurent Gatto <lgatto@protonmail.ch>
Date: 2026-04-05 20:24:53 +0200
Commit message:

 fix news
Package: MsDataHub
Commit: c4624d5a4d3caafa195da04834e326a440023496
Author: GuillaumeDeflandre <potamoidef@gmail.com>
Date: 2026-04-05 17:56:51 +0200
Commit message:

 Docs: bump version and add NEWS entry
Package: MsDataHub
Commit: ded38e21fafdb136163e23a4f6ac123bc1c11d18
Author: GuillaumeDeflandre <potamoidef@gmail.com>
Date: 2026-04-02 10:24:29 +0200
Commit message:

 docs: correcting the filepath to MASSIVE data
Package: MsDataHub
Commit: 1d696d21fd059571d2b5764cda899be146931ef4
Author: GuillaumeDeflandre <potamoidef@gmail.com>
Date: 2026-04-02 09:51:17 +0200
Commit message:

 docs: wrong documentation corrected
Package: MsDataHub
Commit: b09d2eef2db99d478ee76d3124c0684ee3e148c8
Author: GuillaumeDeflandre <potamoidef@gmail.com>
Date: 2026-04-01 17:08:50 +0200
Commit message:

 docs: add missing zenodo link
Package: MsDataHub
Commit: c53d00720a34ae659e6b2e2448e2588ec6582776
Author: GuillaumeDeflandre <potamoidef@gmail.com>
Date: 2026-04-01 17:01:51 +0200
Commit message:

 Feat: add Boekweg datasets
Package: MsDataHub
Commit: 4e24c72bce79f4753860ab2146a4b94a3a3111a6
Author: Laurent Gatto <lgatto@protonmail.ch>
Date: 2026-03-20 18:58:19 +0100
Commit message:

 fix alias
Package: MsDataHub
Commit: dd997e68f8fd7fb693b8f11bcd278a36c77d598c
Author: Laurent Gatto <laurent.gatto@uclouvain.be>
Date: 2026-03-20 18:59:49 +0100
Commit message:

 Merge pull request #15 from rformassspectrometry/tmtms3

Tmtms3
Package: MsDataHub
Commit: 7ffe701f965478e9e748a057389628d060e65620
Author: Laurent Gatto <lgatto@protonmail.ch>
Date: 2026-03-20 18:59:02 +0100
Commit message:

 merge
Package: MsDataHub
Commit: 05eb480cf25025900c5deaf83baa1828a4726f46
Author: Laurent Gatto <laurent.gatto@uclouvain.be>
Date: 2026-03-20 18:06:25 +0100
Commit message:

 Merge branch 'main' into tmtms3
Package: MsDataHub
Commit: 12e4d7ade4f3307ef67cad9deeaa2ac4017e2ce3
Author: Laurent Gatto <lgatto@protonmail.ch>
Date: 2026-03-20 18:03:33 +0100
Commit message:

 add ms3 to vignette
Package: MsDataHub
Commit: e79530257f4ee2eb89769e32b2868f52c25842b1
Author: Laurent Gatto <lgatto@protonmail.ch>
Date: 2026-03-20 18:04:43 +0100
Commit message:

 merge
Package: MsDataHub
Commit: 8ad97a4365e87135e9c82e44afc95fccb041975a
Author: Laurent Gatto <lgatto@protonmail.ch>
Date: 2026-03-20 17:53:16 +0100
Commit message:

 add man
Package: MsDataHub
Commit: 5375a1950286761affcd490a0910681cb05b8b41
Author: Laurent Gatto <lgatto@protonmail.ch>
Date: 2026-03-20 12:31:10 +0100
Commit message:

 add tmtms3 data
Package: R453Plus1Toolbox
Commit: 8022a29a2b49103e5495c3ec65930faa8ec5578f
Author: huklein <hansulrich.klein@gmail.com>
Date: 2026-04-05 11:55:23 -0400
Commit message:

 Refactor biomaRt usage in plotVariants and disable calls during vignette build
Package: tximeta
Commit: 681d166eeaa8bf8a3cd72d9c9eab3e32c5c23aa7
Author: Mike Love <mikelove@users.noreply.github.com>
Date: 2026-04-04 17:48:32 -0400
Commit message:

 working on #97
Package: mzID
Commit: 6be48831b83c0ed0a8b7e569e707800ad2627593
Author: Laurent Gatto <lgatto@protonmail.ch>
Date: 2026-04-05 13:42:19 +0200
Commit message:

 fix partial argument match of 'along' to 'along.with
Package: MouseFM
Commit: 6cd9eac8556253c343bddf66ea1ca0536b02f0ac
Author: Matthias Munz <matthias.munz@gmx.de>
Date: 2026-03-22 17:16:45 +0100
Commit message:

 version bump in devel
Package: MouseFM
Commit: 3b24e5e5454240fa82a9654b9680f68bec4255ef
Author: Matthias Munz <matthias.munz@gmx.de>
Date: 2026-03-22 17:16:37 +0100
Commit message:

 bug fix: avoid online example checks and improve biomaRt errors
Package: postNet
Commit: 8a267437a287f177ccf49be0295a5e0553b27f35
Author: Krzysztof Szkop <krzysztof.szkop@gmail.com>
Date: 2026-04-05 10:21:42 +0100
Commit message:

 KS
Package: fRagmentomics
Commit: 70ba26a27aa599005d09e79f4ef3ab593a4779e3
Author: Killian Maudet <maudet.killian.loq@gmail.com>
Date: 2026-03-31 14:07:34 +0200
Commit message:

 Prepare Bioconductor devel release 0.99.12
Package: PSMatch
Commit: 52447ce5ef7f11787c9ad8dfc6213f64c4cd45b6
Author: Laurent Gatto <lgatto@protonmail.ch>
Date: 2026-04-05 08:12:08 +0200
Commit message:

 Merge branch 'main' into devel
Package: PSMatch
Commit: 70ac012fa12dde15665b9d65e6667dddf6c5a0ae
Author: Laurent Gatto <laurent.gatto@uclouvain.be>
Date: 2026-04-05 08:11:04 +0200
Commit message:

 Merge pull request #42 from rformassspectrometry/guideflandre-PTModsDependency

Guideflandre pt mods dependency
Package: PSMatch
Commit: 5e8f96921d6f0bd15740d3be21400d6ebb61cdc2
Author: Laurent Gatto <laurent.gatto@uclouvain.be>
Date: 2026-04-05 08:10:22 +0200
Commit message:

 Merge pull request #41 from guideflandre/PTModsDependency

Add PTMods dependencies
Package: PSMatch
Commit: bea0b45aa7a3e5a0e0cf9adb6411bc8c18d61b8a
Author: Laurent Gatto <lgatto@protonmail.ch>
Date: 2026-04-05 07:32:08 +0200
Commit message:

 bump cache version
Package: PSMatch
Commit: 271ac7ed9413ad5cea32ff89da6cd3e704b85814
Author: GuillaumeDeflandre <potamoidef@gmail.com>
Date: 2026-04-05 00:05:58 +0200
Commit message:

 Build: bump cache version
Package: PSMatch
Commit: 9b1dee7bc7e77c62c8f6b013477ca66159a94d8c
Author: GuillaumeDeflandre <potamoidef@gmail.com>
Date: 2026-04-04 23:28:01 +0200
Commit message:

 Docs: missing PTMods import
Package: PSMatch
Commit: f33ff8a027876f3986c3f58c987f612b6f7aa51d
Author: GuillaumeDeflandre <potamoidef@gmail.com>
Date: 2026-04-04 14:35:01 +0200
Commit message:

 docs: revert to 1.15.2
Package: PSMatch
Commit: 3ed2243dfe2ea5abf32f56327e1f0f4460b00b98
Author: GuillaumeDeflandre <potamoidef@gmail.com>
Date: 2026-04-04 14:13:45 +0200
Commit message:

 docs: bump version and adjust NEWS
Package: PSMatch
Commit: e9a5721de6bbf47e4e9fb880b9cb4df3dcd9a39f
Author: Guillaume Deflandre <guill.deflandre@gmail.com>
Date: 2026-04-04 00:28:01 +0200
Commit message:

 docs: trigger git build again
Package: PSMatch
Commit: d58f71ade57d50262ccca63f5bccc01b9c814b80
Author: Guillaume Deflandre <37773040+guideflandre@users.noreply.github.com>
Date: 2026-04-03 23:35:50 +0200
Commit message:

 Merge branch 'main' into PTModsDependency
Package: PSMatch
Commit: b0629b39b50ce7011fccb576c406311484fce0e0
Author: Guillaume Deflandre <guill.deflandre@gmail.com>
Date: 2026-04-03 23:26:46 +0200
Commit message:

 build: trigger github activity
Package: PSMatch
Commit: aec2248c26092b498c13df093ce4310e6e8d11c9
Author: GuillaumeDeflandre <potamoidef@gmail.com>
Date: 2026-04-03 10:46:35 +0200
Commit message:

 Docs: improve example in plotSpectraPTM
Package: PSMatch
Commit: 86aa77493362c92b04a10c26e23e83db161c9dc7
Author: GuillaumeDeflandre <potamoidef@gmail.com>
Date: 2026-04-03 10:40:40 +0200
Commit message:

 Docs: include PTMods dependency in vignettes
Package: PSMatch
Commit: f3841a4e13619492afcf08795df6568d546fe4f9
Author: GuillaumeDeflandre <potamoidef@gmail.com>
Date: 2026-04-02 22:39:46 +0200
Commit message:

 Docs: doesn't support data(Boekweg) yet
Package: PSMatch
Commit: 3b5a1ab9f90ce4c4596a18783ba5d3e86421f658
Author: GuillaumeDeflandre <potamoidef@gmail.com>
Date: 2026-04-02 22:35:34 +0200
Commit message:

 Docs: completed the vignette
Package: PSMatch
Commit: da03d98f13e68a2fd8e9d59e883d2b40c1474865
Author: GuillaumeDeflandre <potamoidef@gmail.com>
Date: 2026-04-02 22:25:14 +0200
Commit message:

 tests: add correct tests for plots
Package: PSMatch
Commit: eb25d34fff8bb6a8e19b6656de54cb3ca6ea09f7
Author: GuillaumeDeflandre <potamoidef@gmail.com>
Date: 2026-04-02 22:22:14 +0200
Commit message:

 Feat: match closest fragment instead of common in label fragments to avoid longer object warning
Package: PSMatch
Commit: 148e595348185fbb13edcd91741e5b7d5ac4fc95
Author: GuillaumeDeflandre <potamoidef@gmail.com>
Date: 2026-04-02 22:19:09 +0200
Commit message:

 Feat: add parameters in plotSpectraPTM to include variableMods and fixedMods
Package: PSMatch
Commit: 467291bed41c93c276129befe449f8b36b0b075d
Author: GuillaumeDeflandre <potamoidef@gmail.com>
Date: 2026-03-25 17:07:03 +0100
Commit message:

 tests: corrected the failing tests
Package: PSMatch
Commit: bd2b3dcd01d2d86db899c465d5a3cf500039b8fd
Author: GuillaumeDeflandre <potamoidef@gmail.com>
Date: 2026-03-25 16:23:43 +0100
Commit message:

 build: correct dependency structure
Package: PSMatch
Commit: 45c239b7cc3de2595de08be345c88165250d744b
Author: GuillaumeDeflandre <potamoidef@gmail.com>
Date: 2026-03-25 16:05:18 +0100
Commit message:

 Build: add PTMods dependency in .github workflow
Package: PSMatch
Commit: 095c7cc3f3511b455acbdc153e41b40a99525f11
Author: GuillaumeDeflandre <potamoidef@gmail.com>
Date: 2026-03-25 15:16:52 +0100
Commit message:

 Merge branch 'PTModsDependency' of github.com:guideflandre/PSMatch into PTModsDependency
Package: PSMatch
Commit: 8190d26a416d8dca87a8340a293d0d6e429b9da9
Author: GuillaumeDeflandre <potamoidef@gmail.com>
Date: 2026-03-25 15:16:48 +0100
Commit message:

 tests: improve tests from calculateFragments
Package: PSMatch
Commit: cd1a1d3a9c997ca9b7d0994de8e7038fd994b087
Author: GuillaumeDeflandre <potamoidef@gmail.com>
Date: 2026-03-25 14:50:43 +0100
Commit message:

 tests: remove the tests that have migrated to PTMods
Package: PSMatch
Commit: 7fb41ad6d9529659b46b156e1eb6e457c89be891
Author: Guillaume Deflandre <37773040+guideflandre@users.noreply.github.com>
Date: 2026-03-25 14:41:01 +0100
Commit message:

 Merge branch 'rformassspectrometry:main' into PTModsDependency
Package: PSMatch
Commit: b34360ce9752483012bb71e6cd578f0d25f69c27
Author: GuillaumeDeflandre <potamoidef@gmail.com>
Date: 2026-03-25 13:57:05 +0100
Commit message:

 feat: add addCarbamidomethyl
Package: PSMatch
Commit: e87b90819e68ecad7d695226dff9721e79bef08a
Author: GuillaumeDeflandre <potamoidef@gmail.com>
Date: 2026-03-24 14:48:40 +0100
Commit message:

 docs: correct NEWS
Package: PSMatch
Commit: 6c04a241945b3144fb8dea1c5ef5617158a4820f
Author: GuillaumeDeflandre <potamoidef@gmail.com>
Date: 2026-03-24 14:42:09 +0100
Commit message:

 docs: added contribution guidelines and CoC
Package: PSMatch
Commit: 46554b638b6c6c36435f193a5c7416bb841ace56
Author: GuillaumeDeflandre <potamoidef@gmail.com>
Date: 2026-03-24 13:27:31 +0100
Commit message:

 style: plotSpectraPTM includes new PTMods dependencies and bold peptide
Package: PSMatch
Commit: 4993b14d25a317b762f80c4622d208c72999cac8
Author: GuillaumeDeflandre <potamoidef@gmail.com>
Date: 2026-03-16 14:01:23 +0100
Commit message:

 build: added PTMods dependency
Package: PSMatch
Commit: 5d26e09ebfe6d0f6ee0cdff4836daf2ac9dba81d
Author: GuillaumeDeflandre <potamoidef@gmail.com>
Date: 2026-02-19 12:12:03 +0100
Commit message:

 Docs: modified example of error thrown when both positional and variable mods are present
Package: PSMatch
Commit: 49207ba2b4dd68cff288ad47fdf25116a66d5501
Author: GuillaumeDeflandre <potamoidef@gmail.com>
Date: 2026-02-19 11:16:53 +0100
Commit message:

 test: Fixed errors in tests for .parseModifiedSequence
Package: PSMatch
Commit: 01250f1fe5e25bf4e30a2b67beacd1712ad97202
Author: GuillaumeDeflandre <potamoidef@gmail.com>
Date: 2026-02-19 10:51:48 +0100
Commit message:

 Doc: removed late NEWS addition
Package: PSMatch
Commit: 391e62471648a75fcd6b20e8a543fcc26bff3deb
Author: GuillaumeDeflandre <potamoidef@gmail.com>
Date: 2026-02-19 10:48:44 +0100
Commit message:

 Doc: add NEWS info
Package: PSMatch
Commit: 4a6e56577ff2a5f049bc63094a2864e206d2f7d8
Author: GuillaumeDeflandre <potamoidef@gmail.com>
Date: 2026-02-12 15:52:26 +0100
Commit message:

 style: remove unnecessary comments
Package: PSMatch
Commit: 747896cf16e4e598a219d887c7bd20e1b8ed769e
Author: Guillaume Deflandre <37773040+guideflandre@users.noreply.github.com>
Date: 2026-01-02 15:34:22 +0100
Commit message:

 Merge branch 'main' into calculateFragments
Package: PSMatch
Commit: b2c85b673d4773228cc8ab922660bc513c4f410c
Author: GuillaumeDeflandre <potamoidef@gmail.com>
Date: 2026-01-02 15:09:25 +0100
Commit message:

 Optimise parseModifiedSequence based on PR remarks
Package: PSMatch
Commit: efc36fff6114ac78ed86c4adc8cbb3c8d77210f5
Author: Guillaume Deflandre <37773040+guideflandre@users.noreply.github.com>
Date: 2026-01-02 12:05:43 +0100
Commit message:

 Update R/fragments-calculate.R

Co-authored-by: Sebastian Gibb <mail@sebastiangibb.de>
Package: PSMatch
Commit: 889882e6a33f3ca8da75371d850aeadc6f6653c9
Author: Guillaume Deflandre <37773040+guideflandre@users.noreply.github.com>
Date: 2026-01-02 12:05:28 +0100
Commit message:

 Update R/fragments-calculate.R

Co-authored-by: Sebastian Gibb <mail@sebastiangibb.de>
Package: PSMatch
Commit: 3a54c4dc1e604f7f32e8ffbfd0cfa4d55c424a47
Author: GuillaumeDeflandre <potamoidef@gmail.com>
Date: 2026-01-02 12:02:04 +0100
Commit message:

 add missing documentation
Package: PSMatch
Commit: 7d301af0003517d39b02c88a0ac60bcebd03f7e7
Author: GuillaumeDeflandre <potamoidef@gmail.com>
Date: 2025-12-18 16:51:51 +0100
Commit message:

 add NEWS info
Package: PSMatch
Commit: 25bd52a9f45cb50517a8aed8d8c8d892ad442279
Author: GuillaumeDeflandre <potamoidef@gmail.com>
Date: 2025-12-18 12:22:04 +0100
Commit message:

 Correct documentation
Package: PSMatch
Commit: 74d1e1e06921178bd9be21f8eb8bbe98e17c113e
Author: GuillaumeDeflandre <potamoidef@gmail.com>
Date: 2025-12-18 12:02:07 +0100
Commit message:

 update selenocysteine and pyrrolysine masses
Package: PSMatch
Commit: dc86d8c63b6574cf16ca1232d8ce20a89bdaf4c3
Author: GuillaumeDeflandre <potamoidef@gmail.com>
Date: 2025-12-18 11:41:31 +0100
Commit message:

 Test lazygit commit
Package: PSMatch
Commit: f8e524e6cd626a1dc7739197b3495aaf0661c1b8
Author: GuillaumeDeflandre <potamoidef@gmail.com>
Date: 2025-12-17 15:17:02 +0100
Commit message:

 remove old test commit
Package: PSMatch
Commit: 2cc24f56dfbf2f2d673ea0b46b71eed610c1da53
Author: GuillaumeDeflandre <potamoidef@gmail.com>
Date: 2025-12-17 15:16:10 +0100
Commit message:

 test commit
Package: PSMatch
Commit: 2d5510a62d9955dafb839c1dffbe9635b4f03b9a
Author: GuillaumeDeflandre <potamoidef@gmail.com>
Date: 2025-12-17 14:57:56 +0100
Commit message:

 add unimod import dependency
Package: PSMatch
Commit: ddc2a8c6469911479fb39f70417ba1d46fe3d65d
Author: Guitou1 <potamoidef@gmail.com>
Date: 2025-12-16 17:14:08 +0100
Commit message:

 Keep fixed modifications and preview for annotation parser
Package: PSMatch
Commit: 9a3dd15b2c43222b0c10305e85b601826014ea94
Author: Guitou1 <potamoidef@gmail.com>
Date: 2025-12-16 11:37:14 +0100
Commit message:

 Merge branch 'calculateFragments' of https://github.com/guideflandre/PSMatch into calculateFragments
Package: PSMatch
Commit: ff3c5869a639e1776f7eaf228514f855c1fb6887
Author: Guitou1 <potamoidef@gmail.com>
Date: 2025-12-16 11:35:16 +0100
Commit message:

 Merge branch 'calculateFragments' of https://github.com/guideflandre/PSMatch into calculateFragments
Package: PSMatch
Commit: 323bf27187ac67932e6ea3971f18c526b1b1af04
Author: Guitou1 <potamoidef@gmail.com>
Date: 2025-12-16 11:35:16 +0100
Commit message:

 Merge branch 'calculateFragments' of https://github.com/guideflandre/PSMatch into calculateFragments
Package: PSMatch
Commit: 24086abe35c5589e1d7294d8779f814a80cf813b
Author: Guitou1 <potamoidef@gmail.com>
Date: 2025-12-16 11:33:31 +0100
Commit message:

 correct documentation error
Package: PSMatch
Commit: 8a770892220553e7fc57e9692ccb7be8524bbd21
Author: Guillaume Deflandre <37773040+guideflandre@users.noreply.github.com>
Date: 2025-10-16 11:56:12 +0200
Commit message:

 Merge branch 'rformassspectrometry:main' into calculateFragments
Package: PSMatch
Commit: 56d6f4b7174bbabe8695fea9545a2c9570961427
Author: Guitou1 <potamoidef@gmail.com>
Date: 2025-07-24 14:46:09 +0200
Commit message:

 Add positional modifications
Package: postNet
Commit: a2c1a13d8e1c5f9b05b7f8cd37e789f2e8916889
Author: Krzysztof Szkop <krzysztof.szkop@gmail.com>
Date: 2026-04-05 02:12:06 +0100
Commit message:

 KS
Package: postNet
Commit: 5684fbba1af84cfcd2149900dcabf9883c3fa800
Author: Krzysztof Szkop <krzysztof.szkop@gmail.com>
Date: 2026-04-04 23:34:40 +0100
Commit message:

 KS
Package: postNet
Commit: 65898918828d475d6b569e622dd4c24011066486
Author: Krzysztof Szkop <krzysztof.szkop@gmail.com>
Date: 2026-04-04 23:03:23 +0100
Commit message:

 KS
Package: postNet
Commit: 53c2beea5620bde001160380832a179e9a6c26a5
Author: Krzysztof Szkop <krzysztof.szkop@gmail.com>
Date: 2026-04-04 22:51:00 +0100
Commit message:

 KS
Package: postNet
Commit: 69e4b465fbfe5d4c5bdca81bad44b67628d782bb
Author: Krzysztof Szkop <krzysztof.szkop@gmail.com>
Date: 2026-04-04 22:50:00 +0100
Commit message:

 KS
Package: CyTOFpower
Commit: f06ceb3266caeb82a9d4abcaea61e39022ac0be8
Author: Andreas Gschwind <andreas.gschwind@stanford.edu>
Date: 2026-04-04 14:36:23 -0700
Commit message:

 bump version
Package: CyTOFpower
Commit: 6fe8e1cb92f10ad674a544b3551989933e2f60b0
Author: Andreas Gschwind <andreas.gschwind@stanford.edu>
Date: 2026-04-04 14:33:29 -0700
Commit message:

 remove the expected warning string, throwing error on windows
Package: postNet
Commit: 37cfeb75a7455bd21734e2ed566daf3968556b3f
Author: Krzysztof Szkop <krzysztof.szkop@gmail.com>
Date: 2026-04-04 22:23:19 +0100
Commit message:

 KS
Package: postNet
Commit: dc216bf4cfc14b693c1d9893f6d832e5cf56a21f
Author: Krzysztof Szkop <krzysztof.szkop@gmail.com>
Date: 2026-04-04 21:51:55 +0100
Commit message:

 KS
Package: S4Vectors
Commit: 8dd94e8c9d743ed88fb2db4d37eb5837aaa82677
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2026-04-04 13:28:26 -0700
Commit message:

 version bump (0.49.1)
Package: S4Vectors
Commit: f7a31cf7c7c1de9203636ef311279abaf69fcde2
Author: Pieter Lenaerts <plenae@disroot.org>
Date: 2026-04-04 22:26:32 +0200
Commit message:

 Allow tolerance in tests to accomodate the riscv64 architecture (#133)
Package: postNet
Commit: 5cecbafba1ab9a8cf8db53007b7ee89d281b7572
Author: Krzysztof Szkop <krzysztof.szkop@gmail.com>
Date: 2026-04-04 21:14:51 +0100
Commit message:

 KS
Package: postNet
Commit: 28ca0022fd1d21e082ce5ed8478e7b3ac5a4c7ec
Author: Krzysztof Szkop <krzysztof.szkop@gmail.com>
Date: 2026-04-04 21:13:32 +0100
Commit message:

 KS
Package: postNet
Commit: 182827a08eda20e0bfddbe4fe393b7d04ae2964b
Author: Krzysztof Szkop <krzysztof.szkop@gmail.com>
Date: 2026-04-04 20:44:45 +0100
Commit message:

 KS
Package: postNet
Commit: bfe6083cc30ece6d8d59d781c5fd36b27ec94449
Author: Krzysztof Szkop <krzysztof.szkop@gmail.com>
Date: 2026-04-04 20:32:59 +0100
Commit message:

 KS
Package: postNet
Commit: 8be209d07343974869c731ea65565de1bcf75271
Author: Krzysztof Szkop <krzysztof.szkop@gmail.com>
Date: 2026-04-04 20:29:48 +0100
Commit message:

 KS
Package: CBN2Path
Commit: 1cee7fec0bc4e0d3ba2dc447954b3d72d8f0ced1
Author: William Choi-Kim <will.choi.kim@gmail.com>
Date: 2026-04-04 14:19:17 -0500
Commit message:

 remove BBSoptions
Package: CBN2Path
Commit: 0889da37b5ce42e3f367ae157786d49c78ae9bca
Author: William Choi-Kim <will.choi.kim@gmail.com>
Date: 2026-04-04 14:16:50 -0500
Commit message:

 bump v
Package: CBN2Path
Commit: fcd1bcd937bd2f8780925d508792f6b4ba2ac844
Author: William Choi-Kim <will.choi.kim@gmail.com>
Date: 2026-04-04 14:16:22 -0500
Commit message:

 update DESCRIPTION for new Bioc release
Package: SpatialArtifacts
Commit: 9d54adcfb1269bc5b7516203a97d5cd7a9ed7a9f
Author: Jiali He <jialihe@umich.edu>
Date: 2026-04-04 12:36:02 -0400
Commit message:

 Bump version to 0.99.8
Package: SpatialArtifacts
Commit: ccea6e99bf09271d1c601d2c2fc02678eb4a0052
Author: Jiali He <jialihe@umich.edu>
Date: 2026-04-04 12:33:04 -0400
Commit message:

 Final cleanup: removed Date field
Package: universalmotif
Commit: b7d9f6dab249f2ca972fb55cad70ff1ac763b30e
Author: bjmt <benjmtremblay@gmail.com>
Date: 2026-04-04 10:25:27 +0100
Commit message:

 test create_sequences fix (#32)
Package: CGRphylo2
Commit: c3425c9337166c4f574a33aa1e6ae8cb42b42ee8
Author: Amarinder Thind <thind.amarinder@gmail.com>
Date: 2026-04-04 19:40:36 +1100
Commit message:

 Fix BiocCheck issues: runnable examples, Biostrings integration, remove global env assign
Package: scuttle
Commit: fe00d56ce2c252e56c2ca10087af443394c7284c
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2026-04-04 18:47:19 +1100
Commit message:

 Switch back to blockApply for parallelized fitLinearModel.

LAPACK is not reliably thread-safe so it's too risky to call.
Package: CGRphylo2
Commit: 640f5d3589a13f4a9f77f7fbdfd25cfa73278523
Author: Amarinder Thind <thind.amarinder@gmail.com>
Date: 2026-03-27 11:52:19 +1100
Commit message:

 Remove .Rproj from tracking; add to .gitignore
Package: TileDBArray
Commit: a6a1f3f0644b3ce047d90b9c183afc6461e5e417
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2026-04-04 16:05:04 +1100
Commit message:

 Workaround to enable writing of high-dimensional dense arrays.

Seems to be an issue with the underlying tiledb package, but whatever.
Package: ZarrArray
Commit: 7f4701ef9692b0c8c39941758458b653d79dd9b5
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2026-04-03 16:58:16 -0700
Commit message:

 ZarrArray 0.99.3: Drop underscore prefix from class names

S4 classes ZarrArraySeed, ZarrArray, ZarrMatrix, and ZarrRealizationSink
were originally defined in the Rarr package but were recently removed
from it, as planned. So, moving forward with the transition plan, we can
now drop the temporary underscore prefix from the corresponding classes
defined in the ZarrArray package, that is, from _ZarrArraySeed,
_ZarrArray, _ZarrMatrix, and _ZarrRealizationSink. Note that this prefix
was only a temporary hack to avoid class name conflicts.
Package: PSMatch
Commit: 4164a3dbaae8430aacbb35b7dc587efe90705df6
Author: Laurent Gatto <lgatto@protonmail.ch>
Date: 2026-04-03 23:24:27 +0200
Commit message:

 Merge branch 'main' into devel
Package: PSMatch
Commit: 804e7cbc1ca03850c70cb0f01a699c7f4029bcf4
Author: Laurent Gatto <lgatto@protonmail.ch>
Date: 2026-04-03 23:23:11 +0200
Commit message:

 install magick in workflow
Package: PSMatch
Commit: a9e84c43d7e5912b432b3a7dabac52119980bf08
Author: Laurent Gatto <lgatto@protonmail.ch>
Date: 2026-04-03 23:21:14 +0200
Commit message:

 use MsDataHub
Package: PSMatch
Commit: 8ebe013bf1226ea20808cc60e8ceb98241ce7778
Author: Laurent Gatto <laurent.gatto@uclouvain.be>
Date: 2026-03-16 22:10:28 +0100
Commit message:

 Merge pull request #39 from guideflandre/citation

docs: changed to correct citation link
Package: PSMatch
Commit: 7df8abca3216126dda16f212bb388c2bbe224dd0
Author: GuillaumeDeflandre <potamoidef@gmail.com>
Date: 2026-03-16 14:06:21 +0100
Commit message:

 docs: changed to correct citation link
Package: AnVILAz
Commit: 07f81c6c63f48c4c79b59011940ae8713332b975
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2026-04-03 15:54:36 -0400
Commit message:

 version bump 1.5.1
Package: AnVILAz
Commit: 097ff5ced228311d4a10b9e0cef94609a3273ba5
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2026-04-03 15:49:58 -0400
Commit message:

 sanitize args when error reporting in .az_do
Package: AnVILAz
Commit: 8c0bade7e4466bf6aa47ae1f36b39a67cb44b4a4
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2026-04-03 15:41:00 -0400
Commit message:

 update RoxygenNote
Package: drugfindR
Commit: 6d429bfd676a8caf88fd08671faf31c193c8bdcf
Author: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com>
Date: 2026-03-27 04:53:37 +0000
Commit message:

 chore(deps): pin dependencies (#189)

Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com>
Package: drugfindR
Commit: 95ad740a48c36c015af40a55b0cca6880d6c60fa
Author: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com>
Date: 2026-02-27 06:01:56 +0000
Commit message:

 chore(deps): update actions/upload-artifact action to v7 (#188)

Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com>
Package: drugfindR
Commit: a06ad511838113e379c89d435fc6494878f1e1c6
Author: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com>
Date: 2026-02-19 06:05:05 +0000
Commit message:

 chore(deps): update pre-commit hook compilerla/conventional-pre-commit to v4.4.0 (#187)

Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com>
Package: scRepertoire
Commit: a7f3953f2c38b7bb3482750501955461e65ff6be
Author: theHumanBorch <ncborch@gmail.com>
Date: 2026-04-03 13:45:48 -0500
Commit message:

 Update combineBCR.Rd
Package: immApex
Commit: bd6eb8d9c99c5040bf62208b4905c6179701e468
Author: theHumanBorch <ncborch@gmail.com>
Date: 2026-04-03 13:30:26 -0500
Commit message:

 fix inferCDR
Package: scRepertoire
Commit: 4d84200eaebf2163e399165ea884268e7af824d7
Author: theHumanBorch <ncborch@gmail.com>
Date: 2026-04-03 13:10:39 -0500
Commit message:

 v2.7.3
Package: tLOH
Commit: 3d7cdb965669de648fed9a4cb3361b10edda0804
Author: lshep <lori.shepherd@roswellpark.org>
Date: 2026-04-03 14:01:45 -0400
Commit message:

 Deprecated
unresponsive
Package: supersigs
Commit: 880dd6428973eee63c6e19a22293f44a006a9b41
Author: lshep <lori.shepherd@roswellpark.org>
Date: 2026-04-03 14:00:33 -0400
Commit message:

 Deprecated
unresponsive
Package: netprioR
Commit: 673e21f6c54d62e8338eea4d0205ab948f15e208
Author: lshep <lori.shepherd@roswellpark.org>
Date: 2026-04-03 13:59:25 -0400
Commit message:

 Deprecated
unresponsive
Package: geneXtendeR
Commit: 122ed6a6426bc5e88ce5d9c3c6394c12a3f67e41
Author: lshep <lori.shepherd@roswellpark.org>
Date: 2026-04-03 13:58:15 -0400
Commit message:

 Deprecated
 unresponsive
Package: biobroom
Commit: 9636fba7b8e7dd977f9433fcd160b1d64769f916
Author: lshep <lori.shepherd@roswellpark.org>
Date: 2026-04-03 13:56:48 -0400
Commit message:

 Deprecated
unresponsive
Package: RTCGA
Commit: cf38102146137117aa4227c2bf1bfd4f832dc657
Author: lshep <lori.shepherd@roswellpark.org>
Date: 2026-04-03 13:54:05 -0400
Commit message:

 Deprecated
unresponsive
Package: MethReg
Commit: ad56b40ea1a86f65558c6af55d0af012cca457c2
Author: lshep <lori.shepherd@roswellpark.org>
Date: 2026-04-03 13:52:35 -0400
Commit message:

 Deprecated
 unresponsive
Package: MSPrep
Commit: 5555cbbacb3d6dc726e00e49b8ce6c875c3ed169
Author: lshep <lori.shepherd@roswellpark.org>
Date: 2026-04-03 13:51:13 -0400
Commit message:

 Deprecated
unresponsive
Package: GNET2
Commit: 67528ee2dcf659d03bf2de62ba87d2bdb2ea7d8f
Author: lshep <lori.shepherd@roswellpark.org>
Date: 2026-04-03 13:49:47 -0400
Commit message:

 Deprecate
unresponsive
Package: scRepertoire
Commit: f93abd9c29c16cd67d1dda1c323ed8c77d3430e1
Author: theHumanBorch <ncborch@gmail.com>
Date: 2026-04-03 12:04:32 -0500
Commit message:

 Merge pull request #573 from BorchLab/bioc-3.24-release

Bioc 3.24 release
Package: scRepertoire
Commit: 9e66595bee8d3780a8f3788dadaa6d71b0dd8ecf
Author: theHumanBorch <ncborch@gmail.com>
Date: 2026-04-03 12:04:15 -0500
Commit message:

 Merge branch 'devel' into bioc-3.24-release
Package: scRepertoire
Commit: 471e720e72484e3eeda2b39d70a56227ea37a8b7
Author: theHumanBorch <ncborch@gmail.com>
Date: 2026-04-03 12:00:47 -0500
Commit message:

 Update pkgdown.yml

wesbite update
Package: scRepertoire
Commit: d88302914da1458be09091595e1700ab6566caee
Author: theHumanBorch <ncborch@gmail.com>
Date: 2026-04-03 10:51:36 -0500
Commit message:

 Update immcantation.Rmd

adding tryCatch() arround findThreshold()
Package: scRepertoire
Commit: a8902d9edee3220f3e81adec6018fc7dab6502b2
Author: theHumanBorch <ncborch@gmail.com>
Date: 2026-04-03 10:36:25 -0500
Commit message:

 update site
Package: scRepertoire
Commit: e250811c811ec7fe65a7246a54f908a9685bd1db
Author: theHumanBorch <ncborch@gmail.com>
Date: 2026-04-03 10:36:10 -0500
Commit message:

 Update _pkgdown.yml
Package: scRepertoire
Commit: 5e71c9c36b8d74878f8340f8afbfebca76cc0130
Author: theHumanBorch <ncborch@gmail.com>
Date: 2026-04-03 10:35:57 -0500
Commit message:

 syncing index and README
Package: scRepertoire
Commit: 588f7dfd1407f97bbe263fcb279f0c8678d22ea9
Author: theHumanBorch <ncborch@gmail.com>
Date: 2026-04-03 10:35:42 -0500
Commit message:

 add cross-linking
Package: scRepertoire
Commit: f0f8a276ced7dfbc32fad299d585abdc07c7a149
Author: theHumanBorch <ncborch@gmail.com>
Date: 2026-04-03 10:34:16 -0500
Commit message:

 Create immReferent.Rmd
Package: scRepertoire
Commit: d28ed3de3b6305cff8a4bec89d13ef734e35087e
Author: theHumanBorch <ncborch@gmail.com>
Date: 2026-04-03 08:49:19 -0500
Commit message:

 Create release.yaml
Package: scRepertoire
Commit: 24b6c4cdea6ea8e407684e1fb3b06d81fcc8b628
Author: theHumanBorch <ncborch@gmail.com>
Date: 2026-04-03 08:47:09 -0500
Commit message:

 switch to devel default
Package: scRepertoire
Commit: 842f09475e8fa33b58a81803ece8ab2f8b4bb219
Author: theHumanBorch <ncborch@gmail.com>
Date: 2026-04-03 08:38:39 -0500
Commit message:

 defaults on combineBCR

Per issue #570
Package: scRepertoire
Commit: f35e70486216579a32838c5da96c5201a77b1748
Author: theHumanBorch <ncborch@gmail.com>
Date: 2026-04-03 08:35:17 -0500
Commit message:

 versioning
Package: scRepertoire
Commit: f7eb2615fa7cf0a68d3a28a44354f1219b3ae5d5
Author: theHumanBorch <ncborch@gmail.com>
Date: 2026-04-03 08:29:42 -0500
Commit message:

 Update combineExpression.R
Package: scRepertoire
Commit: c848c26ae3fc95105d0e374fd6d6094255ebe364
Author: theHumanBorch <ncborch@gmail.com>
Date: 2026-04-03 08:07:25 -0500
Commit message:

 Merge pull request #572 from BorchLab/bc-dev-branch

Bc dev branch
Package: scRepertoire
Commit: 23e3cdf16676cd9ba67abe7b074e7b54e8e33c2d
Author: theHumanBorch <ncborch@gmail.com>
Date: 2026-04-03 08:04:11 -0500
Commit message:

 Merge pull request #571 from BorchLab/expanding-site

Updating pkgdown website
Package: scRepertoire
Commit: a4458eacbfb8955c3be4dfa046b8d424a1d7f4d3
Author: theHumanBorch <ncborch@gmail.com>
Date: 2026-04-03 08:03:11 -0500
Commit message:

 Update immLynx.Rmd
Package: scRepertoire
Commit: 17815f39ee72196100ce6ac1a4ccacf8e136fa73
Author: theHumanBorch <ncborch@gmail.com>
Date: 2026-03-09 10:34:08 -0500
Commit message:

 reorganizing the site
Package: scRepertoire
Commit: e6ae7fa6d7f8d2c53c046714faa5c1a5126a68ce
Author: theHumanBorch <ncborch@gmail.com>
Date: 2026-02-28 06:01:06 -0600
Commit message:

 updating the immGLIPH vignette
Package: scRepertoire
Commit: 4eb7964890066e7d6cd414dfff382f85bf7efd71
Author: theHumanBorch <ncborch@gmail.com>
Date: 2026-02-19 07:25:59 -0600
Commit message:

 adding immLynx and immGLIPH
Package: scRepertoire
Commit: 07269791364b5a687df064628b59d89a5ec6ed83
Author: theHumanBorch <ncborch@gmail.com>
Date: 2026-01-27 13:40:21 -0600
Commit message:

 add clonalBin function
Package: scRepertoire
Commit: 9ea24925042d2ba58a5cdadd85890722cbd37e3b
Author: theHumanBorch <ncborch@gmail.com>
Date: 2026-01-27 08:15:33 -0600
Commit message:

 Update test-utils.R
Package: scRepertoire
Commit: ab1b4e1ddef8679011c69f359b387f66425a5a04
Author: theHumanBorch <ncborch@gmail.com>
Date: 2026-01-27 08:05:31 -0600
Commit message:

 refining unit tests
Package: scRepertoire
Commit: 78f545208991c10220ebf4d7d9df45d7f566bbb4
Author: theHumanBorch <ncborch@gmail.com>
Date: 2026-01-27 07:07:00 -0600
Commit message:

 update documentation
Package: scRepertoire
Commit: d443ef6974439ec2caf1213d4f13302d1c718fe2
Author: theHumanBorch <ncborch@gmail.com>
Date: 2026-01-27 07:06:49 -0600
Commit message:

 #536 Expanding alluvial funcitonality
Package: scRepertoire
Commit: 6faa47e58ae19533576f80c8305e831f63f9b367
Author: theHumanBorch <ncborch@gmail.com>
Date: 2026-01-27 07:05:37 -0600
Commit message:

 fix undefined variables
Package: scRepertoire
Commit: c33c42fd6e84d904bbbcaadda3a04e097a351ea1
Author: theHumanBorch <ncborch@gmail.com>
Date: 2026-01-27 07:05:13 -0600
Commit message:

 update getCirclize

More ooptions and add vizCirclise
Package: scRepertoire
Commit: 2792b32a96c40a35330b44710c85763c6edba374
Author: theHumanBorch <ncborch@gmail.com>
Date: 2026-01-27 06:59:43 -0600
Commit message:

 updating unit tests for new dot.notataion
Package: scRepertoire
Commit: 325a2d4646eafbb37b9a668babf5ce168d9e9cbb
Author: theHumanBorch <ncborch@gmail.com>
Date: 2026-01-27 06:58:47 -0600
Commit message:

 adding articles to rbuildignore
Package: scRepertoire
Commit: 297062936e3e3d807af946abae008c555fa0119b
Author: theHumanBorch <ncborch@gmail.com>
Date: 2026-01-26 08:39:01 -0600
Commit message:

 converting to dot.notation

universal argument annotation from camelCase to dot.notation
Package: scRepertoire
Commit: b013e59cb686ce308cee7bf013ad5856d44ab606
Author: theHumanBorch <ncborch@gmail.com>
Date: 2026-01-08 12:27:11 -0600
Commit message:

 Update index.md

update data link in pkgdwn site
Package: scRepertoire
Commit: 6d6d906d6eafd2f501639c41d8eee73a645b12b2
Author: theHumanBorch <ncborch@gmail.com>
Date: 2026-01-08 10:33:26 -0600
Commit message:

 Update README.md
Package: ENmix
Commit: 66fd07ad6be87816be3af69bff09c2afb7a84e89
Author: xuz1 <xuz@niehs.nih.gov>
Date: 2026-04-03 12:58:09 -0400
Commit message:

 bugfix

Signed-off-by: xuz1 <xuz@niehs.nih.gov>
Package: SpatialArtifacts
Commit: 044fbe1fa405105cc096a73a0b074cc5bcbeb506
Author: Jiali He <jialihe@umich.edu>
Date: 2026-04-03 12:11:34 -0400
Commit message:

 Add unit tests, fix license, add NEWS.md, update installation instructions, bump version to 0.99.6
Package: immLynx
Commit: 90a3c1cb18639bd2a1373c80b8efebde523fac6b
Author: theHumanBorch <ncborch@gmail.com>
Date: 2026-03-23 17:37:12 -0500
Commit message:

 Merge pull request #15 from BorchLab/timeout-testthat

Timeout testthat
Package: immLynx
Commit: 8841c2d20731bc5305dbb98562bf381a00840aa3
Author: theHumanBorch <ncborch@gmail.com>
Date: 2026-03-23 17:33:42 -0500
Commit message:

 Update documentation
Package: immLynx
Commit: 1b837d616e208caf63cf8139c9668be52910fe4f
Author: theHumanBorch <ncborch@gmail.com>
Date: 2026-03-23 17:33:30 -0500
Commit message:

 Removed the umbrella roxygen block
Package: immLynx
Commit: 4fadff980720b8875316839b345c1dbaec8d2e5c
Author: theHumanBorch <ncborch@gmail.com>
Date: 2026-03-23 17:32:52 -0500
Commit message:

 Skipping unit tests on bioc
Package: hpAnnot
Commit: c6a0578576b71fef80560020eb258726e6e169f2
Author: lshep <lori.shepherd@roswellpark.org>
Date: 2026-04-03 11:49:07 -0400
Commit message:

 Deprecated
Package: immReferent
Commit: ec10da35cf0c7751649c58730b3676b0173bd550
Author: theHumanBorch <ncborch@gmail.com>
Date: 2026-04-03 10:29:39 -0500
Commit message:

 fixing export names
Package: immReferent
Commit: 95f50956c1a34f9324cd92bf91132cbe0a4c3916
Author: theHumanBorch <ncborch@gmail.com>
Date: 2026-04-03 10:38:15 -0500
Commit message:

 moving towards devel default
Package: immReferent
Commit: 15223c348df16bb35d774acc661437894f2cfb37
Author: theHumanBorch <ncborch@gmail.com>
Date: 2026-01-04 15:03:57 -0600
Commit message:

 Update README.md
Package: immReferent
Commit: 23e23faed3415ac2d76c4fc4e0af7f0d174b5858
Author: theHumanBorch <ncborch@gmail.com>
Date: 2026-04-03 10:43:18 -0500
Commit message:

 version bumping
Package: toppgene
Commit: 3e5f69e773c74d56b6c8f380790c80e638e40913
Author: Pariksheet Nanda <pan79@pitt.edu>
Date: 2026-04-03 11:37:32 -0400
Commit message:

 REL: Forgot to increment version in the DESCRIPTION
Package: knowYourCG
Commit: 7c12644a0ddac930ec41602b2ba1555e907ebc21
Author: Wanding Zhou <zhouwanding@gmail.com>
Date: 2026-04-03 10:42:21 -0400
Commit message:

 minor, message omitted
Package: knowYourCG
Commit: e731436277960caec4803db798300c2558416c22
Author: Wanding Zhou <zhouwanding@gmail.com>
Date: 2026-04-03 07:46:49 -0400
Commit message:

 attempting to fix build on windows
Package: Ibex
Commit: 38bb71dc9ed0a983b1d6d4118e31d46e2d8653e3
Author: theHumanBorch <ncborch@gmail.com>
Date: 2026-04-03 09:16:27 -0500
Commit message:

 syncing with Bioconductor
Package: Ibex
Commit: 001c5c2bd18f9c277e698b2c4e415e4578390117
Author: theHumanBorch <ncborch@gmail.com>
Date: 2026-04-03 08:52:53 -0500
Commit message:

 Update README.md
Package: Ibex
Commit: 8a4114ec1a7e7353631f86fb6f674e79956ff84c
Author: theHumanBorch <ncborch@gmail.com>
Date: 2026-04-03 09:46:55 -0500
Commit message:

 Delete settings.local.json
Package: Ibex
Commit: 8efc54a168f7980efd41f1f6fa0430722b49d0d2
Author: theHumanBorch <ncborch@gmail.com>
Date: 2026-04-03 09:42:12 -0500
Commit message:

 Merge origin/devel into devel: resolve conflicts for CI, NEWS.md, DESCRIPTION, README

- CI workflows: keep devel-only branch targets
- DESCRIPTION: version 1.1.1, keep contributor additions (Qile Yang, lifecycle, RoxygenNote 7.3.3)
- NEWS: delete plain-text NEWS, keep NEWS.md with improved formatting from both sides
- README: combine Bioconductor badges with improved heading hierarchy
Package: Ibex
Commit: a5f6f5c3dad52ae2692eb0390474cce000b263e2
Author: theHumanBorch <ncborch@gmail.com>
Date: 2025-12-10 08:07:04 -0600
Commit message:

 Merge pull request #27 from Qile0317/vec-input

Allow `Ibex_matrix()` to take in AA character vectors
Package: Ibex
Commit: 02fff1f7c87cfc08a9e134f13142e57e72f3ba06
Author: Qile0317 <qile0317@gmail.com>
Date: 2025-12-09 01:53:30 -0800
Commit message:

 increment dev version
Package: Ibex
Commit: 19eb6674e7199600c62b11ef3e31e983052d62b4
Author: Qile0317 <qile0317@gmail.com>
Date: 2025-12-09 01:52:14 -0800
Commit message:

 make ibex matrix accept vectors
Package: Ibex
Commit: fdea76e95a9c0580036a943ffe7dd84101be9710
Author: Qile0317 <qile0317@gmail.com>
Date: 2025-12-09 01:34:22 -0800
Commit message:

 sync news
Package: Ibex
Commit: f6664efcc194b12ae423de88c20c9874fda8c939
Author: Qile0317 <qile0317@gmail.com>
Date: 2025-12-09 01:32:45 -0800
Commit message:

 fix verbosity
Package: Ibex
Commit: 4305271037250d8e02aa1166b29dc59da0b4d962
Author: theHumanBorch <ncborch@gmail.com>
Date: 2025-11-04 11:12:12 -0600
Commit message:

 Merge pull request #26 from Qile0317/reimpl

Reimplement some overwritten changes from #20
Package: Ibex
Commit: 270807625bdaf8f7431a8d8d8665649b84467994
Author: Qile0317 <qile0317@gmail.com>
Date: 2025-11-02 20:12:39 -0800
Commit message:

 minor NEWS formatting
Package: Ibex
Commit: da9907830e462e4eee4d161765d082b12e81d5c5
Author: Qile0317 <qile0317@gmail.com>
Date: 2025-11-02 12:58:15 -0800
Commit message:

 make actions work on devel
Package: Ibex
Commit: e97f2a6a56b6230f90c07203b91ddde1c14f0122
Author: Qile0317 <qile0317@gmail.com>
Date: 2025-11-02 12:54:43 -0800
Commit message:

 improve testing and update wordlist
Package: Ibex
Commit: 51c636994fb6bbc082bdbe55eedd215bf8f106f5
Author: Qile0317 <qile0317@gmail.com>
Date: 2025-11-02 12:47:07 -0800
Commit message:

 format readme
Package: Ibex
Commit: fadeab49c63d5f15e1eefd444c3e907b3693c317
Author: Qile0317 <qile0317@gmail.com>
Date: 2025-11-02 12:44:57 -0800
Commit message:

 add configure files for basilisk
Package: Ibex
Commit: 04ca1768c2194fd6951b9ff6cea36c20c9dc5bb8
Author: Qile0317 <qile0317@gmail.com>
Date: 2025-11-02 12:33:49 -0800
Commit message:

 markdownlint
Package: Ibex
Commit: c7248c89dca0cf8d29952a422525b037c2a991d8
Author: Qile0317 <qile0317@gmail.com>
Date: 2025-11-02 12:28:56 -0800
Commit message:

 docker
Package: Ibex
Commit: 5e5b10c9e3ed909a0108fcc70dc62f61dc5ef153
Author: Qile0317 <qile0317@gmail.com>
Date: 2025-11-02 12:26:18 -0800
Commit message:

 add bbsoptions
Package: Ibex
Commit: a407b1bf593fdf93ab993e866aa8bd4bcd22033b
Author: Qile0317 <qile0317@gmail.com>
Date: 2025-11-02 12:25:08 -0800
Commit message:

 Increment version number to 1.0.0.9000
Package: Ibex
Commit: 93c492bdd42630e819efc7d3ea18bdb003fc761c
Author: Qile0317 <qile0317@gmail.com>
Date: 2025-11-02 12:24:12 -0800
Commit message:

 update NEWS formatting
Package: Ibex
Commit: f238de551abcd24a27dde360a157a93a05aeb122
Author: Qile0317 <qile0317@gmail.com>
Date: 2025-11-02 12:16:36 -0800
Commit message:

 remove rlang import
Package: Ibex
Commit: 51b951dc37a916f148d086f434d09ac6a9f92712
Author: Qile0317 <qile0317@gmail.com>
Date: 2025-11-02 00:13:18 -0700
Commit message:

 Merge branch 'main' of https://github.com/BorchLab/Ibex
Package: Ibex
Commit: b78e1bb077daaca43e1077da790029f5741a7b2a
Author: Qile0317 <qile0317@gmail.com>
Date: 2025-10-02 00:06:29 -0700
Commit message:

 Merge branch 'main' of https://github.com/BorchLab/Ibex
Package: Ibex
Commit: 37a6631f69cb2e6272d34bb5515e0efe080ad533
Author: Qile0317 <qile0317@gmail.com>
Date: 2025-09-27 01:01:19 -0700
Commit message:

 Merge branch 'main' of https://github.com/BorchLab/Ibex
Package: Ibex
Commit: 29759544bfb553cb863beabac6bd693e98027733
Author: Qile0317 <qile0317@gmail.com>
Date: 2025-08-17 12:33:36 -0700
Commit message:

 Merge branch 'main' of https://github.com/BorchLab/Ibex
Package: Ibex
Commit: c54e85197d1cac63cd431780b8ff1407200accc8
Author: Qile0317 <qile0317@gmail.com>
Date: 2025-07-31 16:36:43 -0700
Commit message:

 minor adjust to gitignore and man
Package: Ibex
Commit: 77aafeb10b56eb9a37e557fa05b5855f90538ce8
Author: Qile0317 <qile0317@gmail.com>
Date: 2025-07-31 21:18:35 +0000
Commit message:

 add .vscode to gitignore
Package: Ibex
Commit: 772809f2c56c84ed530f1a1f2618ae7980231d64
Author: theHumanBorch <ncborch@gmail.com>
Date: 2026-04-03 09:29:36 -0500
Commit message:

 Merge main into devel, resolve DESCRIPTION version to 1.1.1
Package: escape
Commit: 38f2be35c1bfa7b7d8db8c1fec4f1bd174a045ce
Author: theHumanBorch <ncborch@gmail.com>
Date: 2026-04-03 08:56:37 -0500
Commit message:

 Merge branch 'devel' of git.bioconductor.org:packages/escape into devel
Package: escape
Commit: 60cef1e51c1a00b4e9ccfaa6fd98e8efe94267e9
Author: theHumanBorch <ncborch@gmail.com>
Date: 2026-04-03 08:21:42 -0500
Commit message:

 updating CI
Package: escape
Commit: 2f40e0cf0628b755f4b3ea89a8bd0da767304219
Author: theHumanBorch <ncborch@gmail.com>
Date: 2026-04-03 08:16:14 -0500
Commit message:

 assay handling

#140

Working on checking assay and object versions
Package: escape
Commit: 004bda5fb79af2bdc496590cf92c3805eac9f8b4
Author: theHumanBorch <ncborch@gmail.com>
Date: 2026-04-03 08:19:49 -0500
Commit message:

 Update README.md
Package: escape
Commit: 127c119199d8edf1e90cf9909dc665129eb79511
Author: theHumanBorch <ncborch@gmail.com>
Date: 2026-04-03 08:21:42 -0500
Commit message:

 updating CI
Package: escape
Commit: eccbd0cc6259f45f3a4e9cd6845b3f673888dcc5
Author: theHumanBorch <ncborch@gmail.com>
Date: 2026-04-03 08:16:55 -0500
Commit message:

 Update README.md
Package: escape
Commit: 72ed1c12ae63b3cab947e607f7694b3be9a68593
Author: theHumanBorch <ncborch@gmail.com>
Date: 2026-04-03 08:16:14 -0500
Commit message:

 assay handling

#140

Working on checking assay and object versions
Package: immApex
Commit: ac82a8c1ebaf3fbc2fec4640b500d86a1cf5c992
Author: theHumanBorch <ncborch@gmail.com>
Date: 2026-04-03 07:35:52 -0500
Commit message:

 correcting version
Package: immApex
Commit: 60999dfc53d26abfcf1dcd5a9e4e5e51afd3e55e
Author: theHumanBorch <ncborch@gmail.com>
Date: 2026-04-03 07:34:51 -0500
Commit message:

 update readme
Package: immApex
Commit: c52586205746cd43b74a6892e035777ae16f8d60
Author: theHumanBorch <ncborch@gmail.com>
Date: 2026-04-03 07:15:35 -0500
Commit message:

 Switch CI to devel/RELEASE branches and add automated releases

Update workflow triggers from main/master to devel/RELEASE_3_* to align
with Bioconductor's branch model. Add release.yaml workflow that
automatically creates GitHub Releases from NEWS.md when version tags are
pushed or RELEASE branches are created.

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
Package: immApex
Commit: ed6ed30b5285a48964549a91c94abab5c4040817
Author: theHumanBorch <ncborch@gmail.com>
Date: 2026-02-06 09:03:47 -0600
Commit message:

 Merge pull request #20 from BorchLab/immreferent-use

Immreferent use
Package: immApex
Commit: d3d4a0be3795e178fd97189726e6c340b56b4a12
Author: theHumanBorch <ncborch@gmail.com>
Date: 2026-02-06 09:03:30 -0600
Commit message:

 Merge branch 'devel' into immreferent-use
Package: immApex
Commit: f504aced79225621b39850a744f86d87afee90c9
Author: theHumanBorch <ncborch@gmail.com>
Date: 2026-02-06 09:01:22 -0600
Commit message:

 Merge branch 'main' into immreferent-use
Package: immApex
Commit: 75d8ee90b6e14347204a5ef2da7d752a61996522
Author: theHumanBorch <ncborch@gmail.com>
Date: 2026-02-06 08:57:41 -0600
Commit message:

 using immReferent

moving away from pulling directly from IMGT due to instability
Package: immApex
Commit: 25421e667014003bf5921f2324194fde7bd450ab
Author: theHumanBorch <ncborch@gmail.com>
Date: 2026-02-06 07:59:48 -0600
Commit message:

 Merge pull request #18 from Qile0317/qile

Add informative error for missing Peptides Package + minor changes
Package: immApex
Commit: 173c98ef5ba2b5f2364fb714856594528a7ecefd
Author: theHumanBorch <ncborch@gmail.com>
Date: 2026-02-06 07:59:17 -0600
Commit message:

 hash is needed for getIMGT
Package: immApex
Commit: 2576a5fa8da4b203b90ab52910137b56462c36dd
Author: Qile0317 <qile0317@gmail.com>
Date: 2026-02-04 16:55:59 -0800
Commit message:

 update wordlist
Package: immApex
Commit: 749ec6c07b695a76e5972a4ec1abc5a19b54c4f1
Author: Qile0317 <qile0317@gmail.com>
Date: 2026-02-04 16:55:08 -0800
Commit message:

 run devtools::document()
Package: immApex
Commit: 41cea9abb97e5bc4a6cfbe6090e0b90437083fb7
Author: Qile0317 <qile0317@gmail.com>
Date: 2026-02-04 16:53:54 -0800
Commit message:

 revert test buildnetwork
Package: immApex
Commit: 46bc858142cf4938b169c416ea18d43058359b0a
Author: Qile0317 <qile0317@gmail.com>
Date: 2026-02-04 16:52:53 -0800
Commit message:

 revert fastEdges change
Package: immApex
Commit: 4660d60b80eaa0dde9fbe27fb097b03c3069dbae
Author: Qile0317 <qile0317@gmail.com>
Date: 2026-02-04 16:51:35 -0800
Commit message:

 revert buildNetwork change
Package: immApex
Commit: e8fba4a8d9f6c82a23c455034f2bf0297e77f9eb
Author: Qile <43093685+Qile0317@users.noreply.github.com>
Date: 2026-02-04 16:47:25 -0800
Commit message:

 Merge branch 'devel' into qile
Package: immApex
Commit: b3df8d1246d6bf92eb5a953d5dc87ce2a6b44eb4
Author: Qile0317 <qile0317@gmail.com>
Date: 2026-02-04 16:35:33 -0800
Commit message:

 remove hash from deps
Package: immApex
Commit: daedf51874c28914299266367276b04553c793c5
Author: Qile0317 <qile0317@gmail.com>
Date: 2026-02-04 16:31:18 -0800
Commit message:

 increment dev version and add to news
Package: immApex
Commit: d4230547d643b47dd0166bffa7eee08e463a7056
Author: Qile0317 <qile0317@gmail.com>
Date: 2026-02-04 16:29:41 -0800
Commit message:

 improve error message for immApex properties
Package: immApex
Commit: 14614749baf8396dc31fd9325bcd484b58c621ad
Author: theHumanBorch <ncborch@gmail.com>
Date: 2025-12-22 10:27:09 -0600
Commit message:

 fix aggregate networks
Package: postNet
Commit: 938070478c8c72fe12f484d3162581af7fec6d45
Author: Krzysztof Szkop <krzysztof.szkop@gmail.com>
Date: 2026-04-03 11:58:01 +0100
Commit message:

 KS
Package: RankMap
Commit: 5a0da7323759bd83fe032fa3c6577a9cb2e6bd90
Author: jinming-cheng <jinming.cheng2018@gmail.com>
Date: 2026-04-03 16:22:45 +0800
Commit message:

 Update R version
Package: RankMap
Commit: 7e5547301daf2342e2296e345df795dd7191bdb8
Author: jinming-cheng <jinming.cheng2018@gmail.com>
Date: 2026-04-03 12:41:25 +0800
Commit message:

 Edits to address comments from Bioconductor reviewer
Package: Spectra
Commit: 9b287fb000de4ec6c119a9474e753db9425b1480
Author: Johannes Rainer <5506112+jorainer@users.noreply.github.com>
Date: 2026-04-03 09:17:39 +0200
Commit message:

 Merge pull request #383 from rformassspectrometry/jomain

feat: add shiftPeaks function
Package: Spectra
Commit: d09be806c09d68c1954a49bb2d060e2f4fdd52cc
Author: Johannes Rainer <johannes.rainer@gmail.com>
Date: 2026-04-03 08:32:53 +0200
Commit message:

 refactor: use two different functions for shiftPeaks()
Package: Spectra
Commit: bfd9d84d78544b2ff4d26eec71a67563b8fb9b48
Author: Johannes Rainer <johannes.rainer@gmail.com>
Date: 2026-04-02 12:51:00 +0200
Commit message:

 refactor: add parameter onlyCore to dropNaSpectraVariables()

- Add parameter `onlyCore = FALSE` to `dropNaSpectraVariables()`.
Package: Spectra
Commit: 96ee974a8b1c0942e74332ffe5515f94e5bfbd6b
Author: Johannes Rainer <johannes.rainer@gmail.com>
Date: 2026-04-02 10:18:15 +0200
Commit message:

 feat: add shiftPeaks function

- Add function `shiftPeaks()` that allows to shift mass peaks in m/z dimension
  by an offset, which can be a single number or value(s) from a spectra variable.
Package: ZarrArray
Commit: 41a978d1d311cf6ca3108de959230c87be03daa2
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2026-04-02 23:19:02 -0700
Commit message:

 ZarrArray 0.99.2: Add 'zarr_version' argument to writeZarrArray()

Default value for 'zarr_version' is 3.
Package: SeqArray
Commit: 5b30be469c04ca2de2f67d9a7c624e0877225afb
Author: Xiuwen Zheng <zhengxwen@gmail.com>
Date: 2026-04-03 01:11:30 -0500
Commit message:

 fix seqAsVCF()
Package: CyTOFpower
Commit: 6551d87b6a96b8c42c57c9fe7919623c3b2725ba
Author: Andreas Gschwind <andreas.gschwind@stanford.edu>
Date: 2026-04-02 21:11:47 -0700
Commit message:

 version bump
Package: CyTOFpower
Commit: acf8f9f055930597a89444101492d79188e6129a
Author: Andreas Gschwind <andreas.gschwind@stanford.edu>
Date: 2026-04-02 21:07:48 -0700
Commit message:

 remove .data$
Package: CyTOFpower
Commit: 624a2a7a518ad9676735ef02cdf29530e2d3c1ca
Author: Andreas Gschwind <andreas.gschwind@stanford.edu>
Date: 2026-04-02 21:07:06 -0700
Commit message:

 reframe instead of summarize
Package: CyTOFpower
Commit: 51a4342536730a9a20b93852adfe721374b0b799
Author: Andreas Gschwind <andreas.gschwind@stanford.edu>
Date: 2026-04-02 21:06:42 -0700
Commit message:

 remove .data$
Package: CyTOFpower
Commit: 66ff598b260dcefbec29f5beec215e45661d3d7c
Author: Andreas Gschwind <andreas.gschwind@stanford.edu>
Date: 2026-04-02 21:05:27 -0700
Commit message:

 global variables because tidyverse complains about .data$
Package: CyTOFpower
Commit: 1c1da014f3d4bb90c48e585ffdbc6b5f089d32cb
Author: Andreas Gschwind <andreas.gschwind@stanford.edu>
Date: 2026-04-02 21:04:23 -0700
Commit message:

 initial release message added
Package: DeMixT
Commit: d5587c37bc8d039f0b6aea552182781977e3e025
Author: wwylab <wwang7@mdanderson.org>
Date: 2026-04-02 15:28:19 -0500
Commit message:

 Add bounds check before calloc to fix -Walloc-size-larger-than warning
Package: Rarr
Commit: 0f461abd3327e55364b56376cc277a8555ffe4d6
Author: Hugo Gruson <git@hugogruson.fr>
Date: 2026-04-02 22:25:38 +0200
Commit message:

 Fix iterator type
Package: biomaRt
Commit: caf88d1bcec5cd112fe8bdaaaca3eae1f6fa1bff
Author: Hugo Gruson <git@hugogruson.fr>
Date: 2026-04-02 21:50:16 +0200
Commit message:

 Remove loadNamespace() call
Package: RESOLVE
Commit: 4d61d9e6985007a9c5cff12d572f28a24541f39b
Author: Luca De Sano <luca.desano@gmail.com>
Date: 2026-04-02 18:37:34 +0200
Commit message:

 update to 1.13.1
Package: OncoScore
Commit: bcc86a07252c4195fcbc5ee1a6b4f41897ef133f
Author: Luca De Sano <luca.desano@gmail.com>
Date: 2026-04-02 18:02:49 +0200
Commit message:

 update to 1.39.1
Package: SparseSignatures
Commit: cc8943cfa6da63bf1a98a3b973e8dd0e413139d5
Author: Luca De Sano <luca.desano@gmail.com>
Date: 2026-04-02 17:52:16 +0200
Commit message:

 update to 2.21.1
Package: SpatialArtifacts
Commit: daa534134e6c776eed5e322f37457cdbdd028d3a
Author: Jiali He <jialihe@umich.edu>
Date: 2026-04-02 11:49:08 -0400
Commit message:

 Final fix for spe_vignette.Rd value section and bump to 0.99.5
Package: DMRsegaldata
Commit: 3907489a041f584e10ee8c30effb3d93c83800dc
Author: vaslem <vaslemonidis@hotmail.com>
Date: 2026-04-02 17:46:59 +0200
Commit message:

 Remove autogenerated comment from NAMESPACE file
Package: DMRsegaldata
Commit: ff9d84210ba86d98a3646b0b2ef1cea88e5611f6
Author: vaslem <vaslemonidis@hotmail.com>
Date: 2026-04-02 17:45:38 +0200
Commit message:

 Bump package version to 0.99.7 in DESCRIPTION
Package: crisprScore
Commit: cbd6f9f60dc7fb50d14b90485b9561d582caf21e
Author: Jean-Philippe Fortin <fortin946@gmail.com>
Date: 2026-04-02 11:45:33 -0400
Commit message:

 Modified bbsoptions
Package: DMRsegaldata
Commit: d7f23a7c0d2d02f6c29af4133857c8d55c1b326a
Author: vaslem <vaslemonidis@hotmail.com>
Date: 2026-04-02 17:45:12 +0200
Commit message:

 Add import statement for ExperimentHub in NAMESPACE
Package: crisprBwa
Commit: 97195ce55b1915b9a6423cda8fdedce6554fc8b2
Author: Jean-Philippe Fortin <fortin946@gmail.com>
Date: 2026-04-02 11:42:49 -0400
Commit message:

 Removed bboptions
Package: Rbwa
Commit: 5cbabaa6d8593f15fc1bdec47bf8e87d01f80b6a
Author: Jean-Philippe Fortin <fortin946@gmail.com>
Date: 2026-04-02 11:41:26 -0400
Commit message:

 Removed bbsoptions
Package: Rbwa
Commit: c3c527aa284bccda4b53fdc456547f1eaa00e445
Author: Jean-Philippe Fortin <fortin946@gmail.com>
Date: 2026-04-02 11:41:14 -0400
Commit message:

 removed bbsoptions
Package: SpatialArtifacts
Commit: f7af0a045913441e717f7e7997065dddb0aced4d
Author: Jiali He <jialihe@umich.edu>
Date: 2026-04-02 11:34:19 -0400
Commit message:

 Fix spe_vignette @return warning and version bump to 0.99.4
Package: Rbwa
Commit: 8ee27d4143bd4eaecf18831a4eda27c38d46b058
Author: Jean-Philippe Fortin <fortin946@gmail.com>
Date: 2026-04-02 11:37:18 -0400
Commit message:

 Added confi to description
Package: SpatialArtifacts
Commit: a0b7f1aae9f7688c3f0d397646db0f662bb137bf
Author: Jiali He <jialihe@umich.edu>
Date: 2026-04-02 11:16:44 -0400
Commit message:

 Bump version to 0.99.3
Package: jvecfor
Commit: 375f4ff5f611fb95f28b14e187f296c7d4ce7a68
Author: Anestis Gkanogiannis <ganoyan@gmail.com>
Date: 2026-04-02 16:54:29 +0200
Commit message:

 Bump version to 0.99.7
Package: jvecfor
Commit: 66f41311eba4849e0d12cbaf94c6bb62aae74b3b
Author: Anestis Gkanogiannis <ganoyan@gmail.com>
Date: 2026-04-02 16:41:39 +0200
Commit message:

 Remove git LFS
Package: biocViews
Commit: 241cd863d066d78bb87f54e8c7535ba89a8ae0f3
Author: A Wokaty <awokaty@users.noreply.github.com>
Date: 2026-04-02 10:32:40 -0400
Commit message:

 1.79.5
Package: biocViews
Commit: a8e0f51ee8c8c3427a9eb23bedc38dfab4b688a8
Author: A Wokaty <awokaty@users.noreply.github.com>
Date: 2026-04-02 10:31:14 -0400
Commit message:

 Revert "Add Config/Bioconductor/UnsupportedPlatforms"

This reverts commit 8f9b228833a6154cb0287334173e9b755fca59ca.
Package: SpectriPy
Commit: 4f7beb5699abc211b67ebef2b02d59fb7a19c161
Author: Johannes Rainer <5506112+jorainer@users.noreply.github.com>
Date: 2026-04-02 15:08:14 +0200
Commit message:

 Merge pull request #88 from rformassspectrometry/jomain

feat: add a setBackend method specifically for MsBackendPy
Package: SpectriPy
Commit: a81c664774877c91d49078b4b7e3cdcaf7ad56f4
Author: jorainer <johannes.rainer@gmail.com>
Date: 2026-04-02 14:09:00 +0200
Commit message:

 feat: add a setBackend method specifically for MsBackendPy

- `setBackend()` for `MsBackendPy` allows to apply the processing queue before
  transferring the data (parameter `applyProcessing = TRUE`).
Package: LimROTS
Commit: 3a965b506600154b29bf5033e77574e4080699f4
Author: Ali Youssef <aliali.mostafa99@gmail.com>
Date: 2026-04-02 15:24:17 +0300
Commit message:

 fix docs
Package: LimROTS
Commit: 70f8589c3753fba5b09f13030bd0713ad604f4a9
Author: Ali Youssef <aliali.mostafa99@gmail.com>
Date: 2026-04-02 15:13:37 +0300
Commit message:

 Bump the version
Package: LimROTS
Commit: aaa61597469df2d4e00e7f495296249b80d99e89
Author: Ali Youssef <aliali.mostafa99@gmail.com>
Date: 2026-04-02 15:12:27 +0300
Commit message:

 adding correlation_block to all functions
Package: LimROTS
Commit: dcfc4dec413e1a1bd6c9bdcddbf76825d527e4d6
Author: Ali Youssef <aliali.mostafa99@gmail.com>
Date: 2026-04-02 13:52:22 +0300
Commit message:

 adding bootstrapSamples_limRots_block
Package: LimROTS
Commit: bfb2b9f2f2bf1faf4aaf164a4a2fb21a934a08d8
Author: Ali Youssef <aliali.mostafa99@gmail.com>
Date: 2026-04-02 13:30:23 +0300
Commit message:

 update Description
Package: LimROTS
Commit: 1cd4af1be0a721584406292c05110cd202b2bef6
Author: Ali Youssef <aliali.mostafa99@gmail.com>
Date: 2026-04-02 13:28:55 +0300
Commit message:

 update ReadME
Package: plyranges
Commit: c2ff9bc597c85867c08a9fee502402c08431f1d8
Author: Mike Love <mikelove@users.noreply.github.com>
Date: 2026-04-02 07:34:18 -0400
Commit message:

 news update for 1.32
Package: CellMentor
Commit: 7660309498904e3743529843f8e68ea5c9d36853
Author: Petrenko Kate <petrenko.kate@icloud.com>
Date: 2026-04-02 14:33:07 +0300
Commit message:

 Move scRNAseq from Imports to Suggests to fix install error

scRNAseq is only used in convenience dataset-loading functions,
not core algorithm. Using requireNamespace() checks instead of
hard dependency. Bumps version to 0.99.3.
Package: CellMentor
Commit: 42e1d04eb76c516d8090622f372eb4ae4c026349
Author: Petrenko Kate <petrenko.kate@icloud.com>
Date: 2025-12-10 19:09:05 +0200
Commit message:

 CHANGES FOR BIOCONDUCTOR REVIEW
Package: CellMentor
Commit: 894827683a0e2795b420afdbc71a7564699eed6a
Author: Petrenko Kate <petrenko.kate@icloud.com>
Date: 2025-12-10 19:02:01 +0200
Commit message:

 CHANGES FOR BIOCONDUCTOR REVIEW
Package: postNet
Commit: 559929367c1dcbc6c540e21b114c7a27d8251ed9
Author: Krzysztof Szkop <krzysztof.szkop@gmail.com>
Date: 2026-04-02 12:07:01 +0100
Commit message:

 KS
Package: TVTB
Commit: 5534769ea55919ba1ef761924bc411ce6fbd940c
Author: Kevin Rue-Albrecht <kevinrue67@gmail.com>
Date: 2026-04-02 11:28:08 +0100
Commit message:

 add unsupported platform entry to description file (#19)

* add unsupported platform entry to description file

* update bioc version in github action

---------

Co-authored-by: Kevin Rue <kevinrue@users.noreply.github.com>
Package: postNet
Commit: 03b2a0e750525f8e083887e9469e8fe76da6f8fc
Author: Krzysztof Szkop <krzysztof.szkop@gmail.com>
Date: 2026-04-02 11:03:59 +0100
Commit message:

 KS
Package: postNet
Commit: 38899b66ddb3bfa0e42f8a4604563cbdde738800
Author: Krzysztof Szkop <krzysztof.szkop@gmail.com>
Date: 2026-04-02 10:50:28 +0100
Commit message:

 KS
Package: sketchR
Commit: 3e1f1af6dabbf862d3a8a9c99c2ba9223f752fb5
Author: Charlotte Soneson <charlottesoneson@gmail.com>
Date: 2026-04-02 10:37:47 +0200
Commit message:

 Remove .BBSoptions (UnsupportedPlatforms: win32)
Package: sketchR
Commit: c04fe6bb8aeb5d5c1ce16aae3b67cbf3761825aa
Author: Charlotte Soneson <charlottesoneson@gmail.com>
Date: 2025-10-29 20:19:37 +0100
Commit message:

 Merge remote-tracking branch 'upstream/devel' into devel
Package: sketchR
Commit: d23d807b1e75bb35a0627a2c061092bc82cc4df0
Author: Charlotte Soneson <charlottesoneson@gmail.com>
Date: 2025-10-02 19:34:45 +0200
Commit message:

 Replace macos-13 GHA runner (will be retired in Dec 2025)
Package: wavFeatExt
Commit: 9dfd6097fb436a80d11f2c73559251c1b103480e
Author: Maharani Ahsani Ummi <maharaniahsani@itb.ac.id>
Date: 2026-04-02 15:15:41 +0700
Commit message:

 Address reviewer comments: documentation, vignette, naming, examples
Package: wavFeatExt
Commit: e04309f5f5f0931892b5f7e1e4b909fab4eedc1c
Author: Maharani Ahsani Ummi <maharaniahsani@itb.ac.id>
Date: 2026-04-02 15:10:17 +0700
Commit message:

 Address reviewer comments: documentation, vignette, naming, examples
Package: Macarron
Commit: 729ef2cc5dfcebee29c48697893b6e63e16cd57c
Author: sagun <sagun_90@hotmail.com>
Date: 2026-04-02 02:38:34 -0400
Commit message:

 decorateID fix v1.15.1
Package: dnaEPICO
Commit: 5ae2a2a84a99d8d2f8b17aaa8306513bc2939e8a
Author: Paul Ruiz <ruizpint@qut.edu.au>
Date: 2026-04-02 14:07:56 +1000
Commit message:

 Bioconductor pack::fun and dnaEPICO.Rmd 0.99.10
Package: dnaEPICO
Commit: 1c2fea3d9f2e539a222087d3db069f96ea1d6575
Author: Paul Ruiz <ruizpint@qut.edu.au>
Date: 2026-04-02 13:47:32 +1000
Commit message:

 Bioconductor pack::fun and dnaEPICO.Rmd 0.99.10
Package: dnaEPICO
Commit: 798c4fd6475616255348c461904584c61aa8b0ba
Author: Paul Ruiz <ruizpint@qut.edu.au>
Date: 2026-04-02 13:23:05 +1000
Commit message:

 Bioconductor pack::fun and dnaEPICO.Rmd 0.99.10
Package: Rsubread
Commit: d66685a96d2e0035933bc45cdcc230697614bd45
Author: Yang Liao (Monash University) <yliao@m3-login2.massive.org.au>
Date: 2026-04-02 14:44:15 +1100
Commit message:

 added switch of soft-clipping in cellCounts
Package: MicrobiotaProcess
Commit: 916270ccf65f2d86c0df632a2556d1dae04f5bfe
Author: xiangpin <xshuangbin@163.com>
Date: 2026-04-02 11:31:10 +0800
Commit message:

 update news and bump version
Package: MicrobiotaProcess
Commit: d1582c6eab8712dddc56ed73732f97a5fee0a57e
Author: xiangpin <xshuangbin@163.com>
Date: 2026-04-02 11:29:40 +0800
Commit message:

 fix the issue due to new biomformat
Package: MicrobiotaProcess
Commit: 6c0f73b80999893a66efdb5ad00f810c6ab1b6e1
Author: xiangpin <xshuangbin@163.com>
Date: 2025-11-03 14:39:05 +0800
Commit message:

 update news
Package: octad
Commit: 0c1ec0772a0160952b6bcc7db70837d7b99a6d59
Author: Lionir <eygen.chekalin@gmail.com>
Date: 2026-04-01 20:29:35 -0700
Commit message:

 dplyr fix
Package: octad
Commit: 4b9dc79215a6463eb89424028c8531546ff199de
Author: Lionir <eygen.chekalin@gmail.com>
Date: 2026-04-01 20:29:06 -0700
Commit message:

 dplyr fix
Package: cfTools
Commit: 76650a4e5f35a261d610b906c886d58e0dd2d322
Author: RoseHuRan <huran@ucla.edu>
Date: 2026-04-01 22:49:06 -0400
Commit message:

 exclude a platform
Package: octad
Commit: 084a64ceeabe47b08610fc9b28015a74f4795ec9
Author: Lionir <eygen.chekalin@gmail.com>
Date: 2026-04-01 20:03:45 -0700
Commit message:

 bug fix
Package: SpatialArtifacts
Commit: 0e08eb288a1540e3fe653aa290e27743c66fc0bb
Author: Jiali He <jialihe@umich.edu>
Date: 2026-04-01 22:55:11 -0400
Commit message:

 Final cleanup
Package: proDA
Commit: abe7b978ba0b9b835e07037ad40eb00fa182d63b
Author: const-ae <artjom31415@googlemail.com>
Date: 2026-04-01 21:33:47 +0100
Commit message:

 Bump version
Package: proDA
Commit: 87aceb137d520352aa1180713d3ca8f9b53a6f3c
Author: const-ae <artjom31415@googlemail.com>
Date: 2026-04-01 21:33:31 +0100
Commit message:

 Remove DEP dependency
Package: netboost
Commit: 4e016d867f2f0c7dc120720ecf8dad69683f05b5
Author: PascalSchlosser <pascal.schlosser@uniklinik-freiburg.de>
Date: 2026-04-01 22:17:06 +0200
Commit message:

 Replace .BBSoptions with Config/Bioconductor/UnsupportedPlatforms in DESCRIPTION

Bioconductor is transitioning to R Universe which does not support
.BBSoptions. Move the Windows unsupported platform declaration to
DESCRIPTION and remove the now-redundant Windows check in install.libs.R.
Package: koinar
Commit: e21971e53ab7ae90c340a4404863a0d6e8dea0de
Author: Ludwig Lautenbacher <llautenbacher@monterosatx.com>
Date: 2026-04-01 21:01:36 +0200
Commit message:

 Bump version
Package: koinar
Commit: b5c3eb1cf39afd3461b03d05a7b6249e6422aa9d
Author: Ludwig Lautenbacher <llautenbacher@monterosatx.com>
Date: 2026-04-01 20:56:27 +0200
Commit message:

 Add mzR as suggested dependency
Package: koinar
Commit: a99ed734400269b48664a697f5a8d6bbbbb014bb
Author: Ludwig Lautenbacher <llautenbacher@monterosatx.com>
Date: 2026-04-01 20:49:04 +0200
Commit message:

 Add default Rproj file.
Package: MetaGxOvarian
Commit: f7961b3fcce3a0c3c7160b435395036dd5bcc164
Author: Michael Tran <mtran256@uwo.ca>
Date: 2026-04-01 12:02:53 -0400
Commit message:

 fix: use rmarkdown vignette engine
Package: StatescopeR
Commit: 4a30922a63e1c260d42e7b0705ab4feca5179edf
Author: MSteketee <m.f.b.steketee@amsterdamumc.nl>
Date: 2026-04-01 17:34:05 +0200
Commit message:

 Limited number of basilisk environment, now using statescope-autogenes
Package: enrichplot
Commit: f344fd649f4d3d8f35fa234662e1761db758925a
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2026-04-01 23:05:04 +0800
Commit message:

 bump version