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

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Package: StatescopeR
Commit: 28adf6db482cb05760e01ec6fd02064ce8f3a090
Author: MSteketee <m.f.b.steketee@amsterdamumc.nl>
Date: 2025-07-28 19:02:21 +0200
Commit message:

 Added selected genes data for faster examples and tests. Harmonized all examples/tests/vignettes
Package: Rsamtools
Commit: e5e8fa08c8c8330fe7079f51d692e372a051ac81
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2025-07-28 09:29:06 -0700
Commit message:

 Rsamtools 2.25.2: Update serialized GAlignments instance
Package: scafari
Commit: 85df9877d2faf2be37eaba9278ccc333be3ae9a5
Author: swind <swind@uni-muenster.de>
Date: 2025-07-28 17:13:05 +0200
Commit message:

 formatting
Package: scafari
Commit: 4b11c696f44972f80459a26b0480b60c2db44441
Author: swind <swind@uni-muenster.de>
Date: 2025-07-28 17:12:53 +0200
Commit message:

 formatting
Package: scafari
Commit: 05a013d4f529065540ff165789629811dcf3988a
Author: swind <swind@uni-muenster.de>
Date: 2025-07-28 17:11:39 +0200
Commit message:

 add more metadata
Package: scafari
Commit: bade025053908e8c06cdee4824f634dd33772883
Author: swind <swind@uni-muenster.de>
Date: 2025-07-28 17:11:27 +0200
Commit message:

 add variables
Package: scafari
Commit: 444ac9fb4caa883f5b497d36d4f22db733100229
Author: swind <swind@uni-muenster.de>
Date: 2025-07-28 17:11:13 +0200
Commit message:

 formatting, adding leiden error handling
Package: scafari
Commit: 6fdc920a701e014815574dde2a69f658e8baa8aa
Author: swind <swind@uni-muenster.de>
Date: 2025-07-28 17:10:50 +0200
Commit message:

 formatting
Package: scafari
Commit: a603a012777f931c59c4d9fe8c7d1fdbf6ce87ef
Author: swind <swind@uni-muenster.de>
Date: 2025-07-28 17:10:25 +0200
Commit message:

 add missing metadata line
Package: scafari
Commit: 20d4e5067f5a76baf570d5df33e4510f28135eb2
Author: swind <swind@uni-muenster.de>
Date: 2025-07-28 17:07:24 +0200
Commit message:

 formatting
Package: scafari
Commit: f8673ab55330b8c7a4962a5f401ec7058dba870a
Author: swind <swind@uni-muenster.de>
Date: 2025-07-28 17:06:58 +0200
Commit message:

 update session info
Package: scafari
Commit: 611b2fdd28624a3f0d860b808b31250a697bdbf2
Author: swind <swind@uni-muenster.de>
Date: 2025-07-28 17:06:24 +0200
Commit message:

 raise version, add deps
Package: scafari
Commit: 38c3e39c56c9e2b555477ce95a95dc1bd27ad5dc
Author: Sophie Wind <sophie.wind@uni-muenster.de>
Date: 2025-07-28 10:29:29 +0200
Commit message:

 Merge branch 'rev_bi' into rev
Package: scafari
Commit: cd275fa1aecc86164011707f363a1d0ca219d31e
Author: Sophie Wind <sophie.wind@uni-muenster.de>
Date: 2025-07-18 10:57:26 +0200
Commit message:

 Merge branch 'merge-bc-bi' into rev
Package: scafari
Commit: a9cee3b0fd1e44e296009548a4e092a76eef3bf6
Author: sophiewind <sophie.wind@uni-muenster.de>
Date: 2025-06-10 06:41:32 +0000
Commit message:

 format docu
Package: scafari
Commit: bf2dfdbe13be0698af29e2be2025a302c6e15138
Author: sophiewind <sophie.wind@uni-muenster.de>
Date: 2025-06-10 06:41:16 +0000
Commit message:

 chnage max no of var
Package: scafari
Commit: ea67133d2fd25889ad118dcd085f6a6e9062f57e
Author: sophiewind <sophie.wind@uni-muenster.de>
Date: 2025-05-30 15:15:16 +0000
Commit message:

 change to ggbio
Package: scafari
Commit: 388cbeac416534fb621f0c2047d095bd0725ac55
Author: sophiewind <sophie.wind@uni-muenster.de>
Date: 2025-05-27 11:49:07 +0000
Commit message:

 add known canon in anno, change distplot to ggbio
Package: scafari
Commit: 1d6dfa49bcc661f5d12717ec34f7034713e6f4b6
Author: sophiewind <sophie.wind@uni-muenster.de>
Date: 2025-05-27 11:07:06 +0000
Commit message:

 change metadata
Package: scafari
Commit: b6900889c080594ede1c4637ec181e5eea70dc14
Author: sophiewind <sophie.wind@uni-muenster.de>
Date: 2025-05-27 09:16:43 +0000
Commit message:

 other metadata in demo
Package: scafari
Commit: 833ad806776fed4f38f1c9fe24ded93d67879975
Author: sophiewind <sophie.wind@uni-muenster.de>
Date: 2025-05-27 09:16:30 +0000
Commit message:

 deco changes
Package: scafari
Commit: a61f0d05b44220241f8625edcfe37c1af41d5095
Author: sophiewind <sophie.wind@uni-muenster.de>
Date: 2025-05-27 09:16:03 +0000
Commit message:

 ui changes
Package: scafari
Commit: b36da6d7279612fb7ff5155496bbf2758782dc99
Author: sophiewind <sophie.wind@uni-muenster.de>
Date: 2025-05-27 09:15:54 +0000
Commit message:

 change too meny cluster error conditions
Package: scafari
Commit: 03b35f7b7ebed2a2b6db29c4dc52a734b8985a17
Author: sophiewind <sophie.wind@uni-muenster.de>
Date: 2025-05-27 09:15:32 +0000
Commit message:

 ui changes
Package: scafari
Commit: 7ec5719fde0d4144ee3270356fb7188657c42cb9
Author: sophiewind <sophie.wind@uni-muenster.de>
Date: 2025-05-27 09:14:28 +0000
Commit message:

 add plotDensityEdge
Package: scafari
Commit: 1d4fa4049db41de94481ce9eb3d0c91c66089832
Author: swind <swind@uni-muenster.de>
Date: 2025-05-26 10:04:10 +0200
Commit message:

 add new seq plots
Package: scafari
Commit: 03b414153fd4258f45f8a7a3027bac957fe35b5c
Author: swind <swind@uni-muenster.de>
Date: 2025-05-26 10:03:53 +0200
Commit message:

 add new Seq plots
Package: scafari
Commit: 8bbba2818f9a7258a2cee64482d923683bf1b7cc
Author: sophiewind <sophie.wind@uni-muenster.de>
Date: 2025-05-20 06:43:14 +0000
Commit message:

 formatting
Package: scafari
Commit: a67e3633f3b1512a55045f3cd120c95188dca18c
Author: sophiewind <sophie.wind@uni-muenster.de>
Date: 2025-05-16 07:27:33 +0000
Commit message:

 correct var annot
Package: scafari
Commit: 84cb78b817bebed7189f4b719d4e83953cbb9237
Author: sophiewind <sophie.wind@uni-muenster.de>
Date: 2025-05-16 07:27:14 +0000
Commit message:

 adjust annotation in server, sanity check params, numeric inputs to sliders
Package: scafari
Commit: b9e7b0d3c5e8b86af0cfb87fb46ab6c8af2dc1d3
Author: sophiewind <sophie.wind@uni-muenster.de>
Date: 2025-05-15 14:33:23 +0000
Commit message:

 fix edgeplot
Package: scafari
Commit: 444334d4f45cfa315388ade231e89c36d1dcb768
Author: sophiewind <sophie.wind@uni-muenster.de>
Date: 2025-05-15 13:45:49 +0000
Commit message:

 add min.pts param
Package: scafari
Commit: 86a1e605c1fb8c8c0e3c3364138a2efa641e1119
Author: sophiewind <sophie.wind@uni-muenster.de>
Date: 2025-05-15 11:41:59 +0000
Commit message:

 show error, running leiden
Package: scafari
Commit: 1c1db3adc3cb0fc0d30ef1cd19cd138fe43802cd
Author: sophiewind <sophie.wind@uni-muenster.de>
Date: 2025-05-15 11:41:25 +0000
Commit message:

 show error, running leiden
Package: scafari
Commit: ca6c521db9726c5c4ce8b490834d95c562ba28c9
Author: sophiewind <sophie.wind@uni-muenster.de>
Date: 2025-05-15 09:29:23 +0000
Commit message:

 fix heatmap TODO ui error handling
Package: scafari
Commit: 1417a9a34c4f252f316c8fb3210acde7241d05f0
Author: sophiewind <sophie.wind@uni-muenster.de>
Date: 2025-05-15 09:19:19 +0000
Commit message:

 running version TODO heatmap
Package: scafari
Commit: 37eb3af6ad6a420f9257dd022a51dae487482ef3
Author: sophiewind <sophie.wind@uni-muenster.de>
Date: 2025-05-14 11:13:01 +0000
Commit message:

 running TODO no visible clusterPlot
Package: scafari
Commit: 714dd5c87a656d65a6ddf530d2c5b6da307f711d
Author: sophiewind <sophie.wind@uni-muenster.de>
Date: 2025-05-14 08:06:51 +0000
Commit message:

 working example with raising message but still some bugs
Package: scafari
Commit: 978c01442ccc82f352c72e78e97ad2a7cc4783e1
Author: sophiewind <sophie.wind@uni-muenster.de>
Date: 2025-05-13 15:00:27 +0000
Commit message:

 add clustering functions
Package: scafari
Commit: 846a02db45de93b2f9f9c5befd5170ad3c19a0a5
Author: sophiewind <sophie.wind@uni-muenster.de>
Date: 2025-05-13 15:00:08 +0000
Commit message:

 show different clustering methods in shiny
Package: scafari
Commit: 55874b6ba90c4ec068f13c9e3f00a0d22a937082
Author: sophiewind <sophie.wind@uni-muenster.de>
Date: 2025-05-13 14:14:53 +0000
Commit message:

 let explore var until cluster button is hit
Package: scafari
Commit: 862c52557afd9ec0289ff407a1b6a55cf0434dab
Author: sophiewind <sophie.wind@uni-muenster.de>
Date: 2025-05-13 13:37:39 +0000
Commit message:

 fix dbscan
Package: scafari
Commit: 9a505b65929401f26225df7fe50a472799d43954
Author: sophiewind <sophie.wind@uni-muenster.de>
Date: 2025-05-13 11:03:55 +0000
Commit message:

 fix leiden
Package: scafari
Commit: 5a93d56c5580611bcee34f36fcb82564e141ad3a
Author: sophiewind <sophie.wind@uni-muenster.de>
Date: 2025-05-13 08:51:19 +0000
Commit message:

 k means workin, leiden without hm working TOFO hm, TODO dbscan
Package: scafari
Commit: c0b59481a7e13f53b55fb478894a04700098433e
Author: sophiewind <sophie.wind@uni-muenster.de>
Date: 2025-05-13 08:05:03 +0000
Commit message:

 add clustering radio buttons
Package: scafari
Commit: ca28ae9371b6366822edbb2d2cf8bf31cdafe739
Author: sophiewind <sophie.wind@uni-muenster.de>
Date: 2025-05-12 15:19:35 +0000
Commit message:

 add leiden and dbscan option
Package: GenomicAlignments
Commit: 5227f2c66d3929d19cc508b41206bd68e1206cce
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2025-07-28 07:58:14 -0700
Commit message:

 GenomicAlignments 1.45.2: update updateObject() method for GAlignments objects
Package: DMRcate
Commit: b528894cfd4f9d64a54190aa4e0fcd5e7961649b
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2025-07-26 18:33:09 -0700
Commit message:

 DMRcate 3.5.1: Add Seqinfo to Imports

Also move GenomeInfoDb from Imports to Suggests.
Package: MSstatsConvert
Commit: 9d69415ac36a788b6e11db16f68bd8f46e20d363
Author: Mateusz Staniak <mtst@mstaniak.pl>
Date: 2025-07-28 14:38:51 +0200
Commit message:

 version bump
Package: MSstatsConvert
Commit: d3ceae992f06f41b967415e516184009d69a25da
Author: Mateusz Staniak <mtst@mstaniak.pl>
Date: 2025-07-28 14:38:01 +0200
Commit message:

 version bump
Package: MSstatsConvert
Commit: 8e38072ba52ac54793212f16a795f1e497f18c81
Author: tonywu1999 <wu.anthon@northeastern.edu>
Date: 2025-07-28 08:36:44 -0400
Commit message:

 feat(diann): Add support for DIANN 2.0 (#109)

* feat(diann): Add support for DIANN 2.0

* add unit tests - pending test files

* optimize code for large datasets

* use parquet file for input instead of CSV for examples

* update documentation for quantificationColumn

* edit docs for clean diann function

* refactor DIANN code to be more readable
Package: MSstatsConvert
Commit: ee9286cf3b61addfd9f64a5185a3e4d2c56bb56b
Author: tonywu1999 <wu.anthon@northeastern.edu>
Date: 2025-06-04 17:26:50 -0400
Commit message:

 feat(Metamorpheus): Remove decoys in converter for Metamorpheus; Add qvalue filtering when MBR is enabled (#108)
Package: MSstatsConvert
Commit: 6017c8bfcc1b322c8ab7cb44779c3afd2fae7b3d
Author: tonywu1999 <wu.anthon@northeastern.edu>
Date: 2025-05-14 11:43:45 -0400
Commit message:

 Add description in DIANN converter on DIANN 2.0 workaround (#107)
Package: looking4clusters
Commit: b34bbc58997291c377efb7408c4388dda89c2d43
Author: BioinfoUSAL <bioinfo@usal.es>
Date: 2025-07-28 13:51:20 +0200
Commit message:

 maintainer email changed
Package: gDRimport
Commit: 7ed1d40ca530b95bfd2d885621ca21a9a75aea9b
Author: Bartek <32614650+bczech@users.noreply.github.com>
Date: 2025-07-28 10:13:20 +0200
Commit message:

 Merge pull request #106 from gdrplatform/GDR-2986_2

Gdr 2986 2
Package: gDRimport
Commit: 0d2a893e3ac38a8ccf3ee1965357bc28d71c9307
Author: Bartek Czech <bartosz.w.czech@gmail.com>
Date: 2025-07-28 09:25:29 +0200
Commit message:

 ci: trigger build
Package: gDRimport
Commit: 6cecc705a1cc0adf09eecd7e878cdd55809403ae
Author: Bartek Czech <bartosz.w.czech@gmail.com>
Date: 2025-07-21 11:05:28 +0200
Commit message:

 ci: trigger build
Package: gDRimport
Commit: 54c7fb6a045158b30bb693888ffbc5955d9c9b64
Author: Bartek Czech <bartosz.w.czech@gmail.com>
Date: 2025-07-18 13:35:30 +0200
Commit message:

 refactor: update unit tests
Package: gDRimport
Commit: 845d508781f52ee9260312fe41727d525e15a79b
Author: Bartek Czech <bartosz.w.czech@gmail.com>
Date: 2025-07-17 17:04:52 +0200
Commit message:

 chore: bump version and update NEWS.md
Package: gDRimport
Commit: 29a315cf0a03a40c29eaa7993a8d0201a7ce5a29
Author: Bartek Czech <bartosz.w.czech@gmail.com>
Date: 2025-07-17 17:04:47 +0200
Commit message:

 refactor: code
Package: limma
Commit: 52065f89e221c0f77db46387613ad71171df1efe
Author: Gordon Smyth <smyth@wehi.edu.au>
Date: 2025-07-28 10:58:55 +1000
Commit message:

 limma 3.65.2

- New argument `span` for fitFDistUnequalDF1(), squeezeVar() and eBayes().

- Minor edits to poolVar() and update help page.

- Complete remaining dates for release versions in NEWS.Rd.
Package: Rsubread
Commit: 666b63dc50fa5d0e5cd4c9b7e805b6f6aa2f12f6
Author: Yang Liao (Monash University) <yliao@m3v107.massive.org.au>
Date: 2025-07-28 06:38:18 +1000
Commit message:

 Now the code is runnable on the large dataset.
Package: bettr
Commit: 0be6bfa63568a95e0551e8bda0f426c5d03a7af0
Author: Charlotte Soneson <charlottesoneson@gmail.com>
Date: 2025-07-27 20:50:02 +0200
Commit message:

 Expand vignette
Package: MetaScope
Commit: 9dcc93180e9437219ec8cf8073bf5d393102e65a
Author: Aubrey Odom <aodom@bu.edu>
Date: 2025-07-27 13:57:37 -0400
Commit message:

 Update Metablast to fix issue in R CMD CHECK
Package: MetaScope
Commit: c71a23b7ca823aeb701b19b51d02746fa3e7eb81
Author: Aubrey Odom <aodom@bu.edu>
Date: 2025-07-27 13:48:54 -0400
Commit message:

 Merge pull request #47 from seanlu96/master

fixed NA in fastas
Package: MetaScope
Commit: 8bb2ecbd6885c654429fb17d8de3080bf896b1fa
Author: Sean <89270441+seanlu96@users.noreply.github.com>
Date: 2025-07-26 12:33:35 -0400
Commit message:

 Merge branch 'devel' into master
Package: MetaScope
Commit: fa64687c8d6bc9db8043bde89156c29548045549
Author: Sean Lu <seanlu96@gmail.com>
Date: 2025-07-26 12:31:57 -0400
Commit message:

 fixed NA in fastas
Package: MetaScope
Commit: e6610476f5c546022bbaee9a821c9cb7acbd512d
Author: Aubrey Odom <aodom@bu.edu>
Date: 2025-07-25 12:27:21 -0400
Commit message:

 Update variable bindings
Package: MetaScope
Commit: f9163c23ae7e68b1de17138f87be10d79bd45474
Author: Aubrey Odom <aodom@bu.edu>
Date: 2025-07-25 12:18:47 -0400
Commit message:

 Merge pull request #46 from seanlu96/master

added compatibility with refseq 2020
Package: MetaScope
Commit: d1ed5fea4ad9f80446c6616fde317f108c61dd5a
Author: seanlu96 <89270441+seanlu96@users.noreply.github.com>
Date: 2025-07-25 12:06:49 -0400
Commit message:

 updated metablast for different databases
Package: MetaScope
Commit: 56d785fcdb5c35d3a0a6ba708cd932d898835e4e
Author: seanlu96 <89270441+seanlu96@users.noreply.github.com>
Date: 2025-07-25 11:25:33 -0400
Commit message:

 removed updated_fastas
Package: OSTA
Commit: c0fd1c1ff3c28776710e4acce95b9eceb166deb4
Author: Lukas Weber <lmweb012@gmail.com>
Date: 2025-07-27 13:30:39 -0400
Commit message:

 version
Package: OSTA
Commit: cd88d39e654309484fa0d487122571b0695e9c0a
Author: Lukas Weber <lmweb012@gmail.com>
Date: 2025-07-27 13:18:19 -0400
Commit message:

 fix possible formatting warning
Package: derfinderPlot
Commit: a397599e2c61a2009d033b70d1203347605fdbfe
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2025-07-26 18:31:38 -0700
Commit message:

 derfinderPlot 1.43.1: Add Seqinfo to Imports
Package: regionReport
Commit: 301f96deb84423d9efba1cb1648d1de6de3fee66
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2025-07-26 17:59:40 -0700
Commit message:

 small tweaks
Package: nullranges
Commit: 077bf27cf605282267500b4daee57c39f321ed81
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2025-07-26 17:45:40 -0700
Commit message:

 Add GenomeInfoDb to Suggests
Package: HicAggR
Commit: f3138ced74a0cbfc53eac9f73d4106f418140d51
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2025-07-26 17:33:32 -0700
Commit message:

 Add GenomeInfoDb to Suggests
Package: OSTA
Commit: 244dae4fd882cee33b454b78d0a59dac2efa61ae
Author: Lukas Weber <lmweb012@gmail.com>
Date: 2025-07-26 19:53:33 -0400
Commit message:

 version
Package: OSTA
Commit: dbca770ff4f1cd523615482aeca99558b6718809
Author: Lukas Weber <lmweb012@gmail.com>
Date: 2025-07-26 19:39:52 -0400
Commit message:

 remove commented sections
Package: OSTA
Commit: adb7bb2b44f618cd9a8a4f7c3582068d9aeba047
Author: Lukas Weber <lmweb012@gmail.com>
Date: 2025-07-26 19:35:22 -0400
Commit message:

 remove unnecessary output
Package: OSTA
Commit: 1bdb2dcd5e247dfb5b697bbb7b64748783384da8
Author: Lukas Weber <lmweb012@gmail.com>
Date: 2025-07-26 19:32:23 -0400
Commit message:

 fix duplicated label warning
Package: OSTA
Commit: 438500db73dbf35a230744960c6fd081c6e2b4b9
Author: Lukas Weber <lmweb012@gmail.com>
Date: 2025-07-26 19:30:55 -0400
Commit message:

 fix vignette stub warning
Package: OSTA
Commit: 23b82ef8eeb9fa8ae90cdbd9accf05866a288859
Author: Lukas Weber <lmweb012@gmail.com>
Date: 2025-07-26 19:24:56 -0400
Commit message:

 add EP, SR
Package: OSTA
Commit: ad15618688827a7d1bcc3d1e7214be4e83964da0
Author: Lukas Weber <lmweb012@gmail.com>
Date: 2025-07-26 19:20:32 -0400
Commit message:

 Merge branch 'sandbox-desc' into sandbox
Package: OSTA
Commit: 17aa0974a7ec0fa09118635210f2aa6ddbc8b36e
Author: Lukas Weber <lmweb012@gmail.com>
Date: 2025-07-26 16:59:16 -0400
Commit message:

 fix Intercept column name for spatialFDA::functionalGam() checks
Package: OSTA
Commit: a4fc2ae984ef332fe60924de54e4b5818f9c5271
Author: Lukas Weber <lmweb012@gmail.com>
Date: 2025-07-26 12:47:37 -0400
Commit message:

 skip parallelization due to segfault
Package: OSTA
Commit: 28c99492ead68cd27c7782f99b5abd3b8d75bca9
Author: Lukas Weber <lmweb012@gmail.com>
Date: 2025-07-25 14:39:28 -0400
Commit message:

 check build
Package: OSTA
Commit: fdbd0c8176cd222d32807b6fbf7cbf5031db3f27
Author: Lukas Weber <lmweb012@gmail.com>
Date: 2025-07-04 08:41:16 -0400
Commit message:

 install pkgs from source only in deps docker
Package: OSTA
Commit: 203b835fa5c7430d4cc1664fb8ee99e93e596e31
Author: Lukas Weber <lmweb012@gmail.com>
Date: 2025-07-04 08:19:13 -0400
Commit message:

 typo
Package: OSTA
Commit: 02907e920bd6b5d6fb990e4d6b1036caf2250332
Author: Lukas Weber <lmweb012@gmail.com>
Date: 2025-07-04 07:39:23 -0400
Commit message:

 trigger deps
Package: OSTA
Commit: 1cce66e01731f5672da756739a1298dc90da8e2e
Author: Lukas Weber <lmweb012@gmail.com>
Date: 2025-07-04 07:39:10 -0400
Commit message:

 install SPE and AUCell from source in both Docker files
Package: OSTA
Commit: 7d859d1297ec71ac28ad2f6b536386f258798e73
Author: Lukas Weber <lmweb012@gmail.com>
Date: 2025-07-04 06:40:27 -0400
Commit message:

 trigger deps sandbox-testing
Package: OSTA
Commit: a1f81aa3fc8b97c752ba71e0d678844df74a47c0
Author: HelenaLC <helena@crowell.eu>
Date: 2025-07-04 10:50:46 +0200
Commit message:

 up R dep, rmv Remotes:, add Mark
Package: netZooR
Commit: 2396daf13c923c7529fd86cb12c30ea7a22b26e1
Author: marouenbg <marouen.b.guebila@gmail.com>
Date: 2025-07-26 15:33:46 -0400
Commit message:

 update bioc
Package: OmicsMLRepoR
Commit: a3469d87af4166ea3a4295b0658aa81f0ec9c292
Author: Sehyun Oh <shbrief@gmail.com>
Date: 2025-07-26 14:09:08 -0400
Commit message:

 version bump
Package: OmicsMLRepoR
Commit: bf028a8c5cac3cfecba9cc53e5331f93302eaadd
Author: Sehyun Oh <shbrief@hotmail.com>
Date: 2025-07-26 13:52:38 -0400
Commit message:

 Merge pull request #50 from shbrief/feature_ontoSummarize

Feature onto summarize
Package: OmicsMLRepoR
Commit: fec4878db887b6f53ac2e1c84d5cec9ef4017e96
Author: Sehyun Oh <shbrief@hotmail.com>
Date: 2025-07-26 13:52:30 -0400
Commit message:

 Merge branch 'devel' into feature_ontoSummarize
Package: OmicsMLRepoR
Commit: 9f03f07211f7a9deb727ce6ca7574c0a731beb27
Author: Sehyun Oh <shbrief@gmail.com>
Date: 2025-07-26 13:48:31 -0400
Commit message:

 updated metadata
Package: OmicsMLRepoR
Commit: 199efbcec42e8512ef3b8d57d4a48d148eb40009
Author: Sehyun Oh <shbrief@gmail.com>
Date: 2025-07-26 13:45:20 -0400
Commit message:

 add cBioPortal data dictionary
Package: OmicsMLRepoR
Commit: 22bec061f05a59cdb67d0ccb6956d246c5012601
Author: Sehyun Oh <shbrief@gmail.com>
Date: 2025-07-26 13:41:57 -0400
Commit message:

 updated cMD data dictionary
Package: bettr
Commit: a595f9739d350ce5379755d40b2775f9658f2cdc
Author: Charlotte Soneson <charlottesoneson@gmail.com>
Date: 2025-07-26 18:18:15 +0200
Commit message:

 Bump version, update NEWS
Package: bettr
Commit: a1eab4017142c086587600223213e6e04307d193
Author: Charlotte Soneson <charlottesoneson@gmail.com>
Date: 2025-07-26 18:16:22 +0200
Commit message:

 Add possibility to specify the default weight
Package: bettr
Commit: 8b2bf09d568e3610f81c8f32b3935afc02ee67ac
Author: Charlotte Soneson <charlottesoneson@gmail.com>
Date: 2025-07-21 20:30:08 +0200
Commit message:

 Add contribution guidelines to README
Package: StatescopeR
Commit: 2402d30e125c75b17fef14cfbdffaabc25fa5760
Author: MSteketee <m.f.b.steketee@amsterdamumc.nl>
Date: 2025-07-26 14:11:24 +0200
Commit message:

 Version bump after nebbiolo2 storage issue
Package: RnBeads
Commit: 9c2201dd9c286464cb4ed87a82f561d8cf7f82ca
Author: Michael Scherer <michael.scherer@dkfz.de>
Date: 2025-07-26 14:25:01 +0200
Commit message:

 Merge branch 'devel' of git.bioconductor.org:packages/RnBeads into devel
Package: RnBeads
Commit: fdaa1038b7e79522fef6e2b19aa6bae83c3eda0d
Author: Scherer <m261r@b370-worker01.dkfz-heidelberg.de>
Date: 2025-07-26 12:18:30 +0200
Commit message:

 Fixed check WARNING
Package: RnBeads
Commit: 3c4a287af5eebc4fb4ca573f3ca83d1005768acd
Author: Scherer <m261r@b370-worker01.dkfz-heidelberg.de>
Date: 2025-07-26 11:45:23 +0200
Commit message:

 Smaller fixes, including documentation
Package: derfinder
Commit: 6a6364660083556e26d440d6305d1d58dc1d708a
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2025-07-25 15:41:35 -0700
Commit message:

 small tweak
Package: netZooR
Commit: 33ba46fd4ac926c88e5ab622f57c17e05da76636
Author: marouenbg <marouen.b.guebila@gmail.com>
Date: 2025-07-25 15:20:37 -0400
Commit message:

 bioc push
Package: netZooR
Commit: 5e459f85b4d2321bea8e2546669eb56678faf812
Author: Marouen <marouenbg@users.noreply.github.com>
Date: 2025-07-25 14:11:11 -0400
Commit message:

 Delete data/testDatasetMonster.RData
Package: netZooR
Commit: c212becebed0f8c76c1112ec669919344fc5e1c2
Author: Marouen <marouenbg@users.noreply.github.com>
Date: 2025-07-25 14:04:44 -0400
Commit message:

 Merge branch 'master' into devel
Package: netZooR
Commit: d4d5486fb0b0402e2517de69cd455516301150dc
Author: violafanfani <35488779+violafanfani@users.noreply.github.com>
Date: 2025-07-25 13:52:33 -0400
Commit message:

 Fix monster pvalues (#346)

* 1.6.2 (#339)

* Modified the LIONESS R code to disallow PANDA inference unless either a PPI or motif are provided

* add mode parameter to lioness (#336)

* update maintainer

* update maintainer

* update maintainer

* update maintainer (#337)

* update maintainer

* update maintainer

* Update ALPACA.R

* update sambar (#338)

---------

Co-authored-by: Tara Eicher <taraeicher@yahoo.com>

* Changing 'monsterCalculateTmPValues' to follow the same strategy as the plot. From '1' to '2', (rows and columns). Fixing Issue #335.

* Update main.yml

* Update main.yml

* Update main.yml

* Update README.md

* Update main.yml

* temporarily deactivating test

* checking that non-parametric works similar to zscore pvalue in monster

* fixing monster pvalue

* reconciling monster pvalues

* reconciling pvalues

* fixing testing and adding cases

* fixing testing

* adding test file

* adding test file

* moving data

* fixing test

* Delete data/monsterPvals.RData

* Update test-monster.R

---------

Co-authored-by: Marouen <marouenbg@users.noreply.github.com>
Co-authored-by: Tara Eicher <taraeicher@yahoo.com>
Co-authored-by: violafanfani <viol.fanfani@gmail.com>
Package: netZooR
Commit: 1f2f43bb658aaec4350f40bb5ae7686dd2353de5
Author: Marouen <marouenbg@users.noreply.github.com>
Date: 2025-07-24 19:39:08 -0400
Commit message:

 Devel (#352)

* update sambar

* update maintainer
Package: netZooR
Commit: bab46850e0aa306b520185554c1137d586d7e9fb
Author: Marouen <marouenbg@users.noreply.github.com>
Date: 2025-01-31 08:00:41 -0500
Commit message:

 1.6.2 (#339)

* Modified the LIONESS R code to disallow PANDA inference unless either a PPI or motif are provided

* add mode parameter to lioness (#336)

* update maintainer

* update maintainer

* update maintainer

* update maintainer (#337)

* update maintainer

* update maintainer

* Update ALPACA.R

* update sambar (#338)

---------

Co-authored-by: Tara Eicher <taraeicher@yahoo.com>
Package: musicatk
Commit: 5199a178c71705f74f756fc5147d94ca69eff7e2
Author: Josh Campbell <joshua-d-campbell@gmail.com>
Date: 2025-07-25 14:26:12 -0400
Commit message:

 merge bioc/devel
Package: musicatk
Commit: c8aa3ca53f5a8bd7425ac03bb004f8680374ff4d
Author: Joshua D. Campbell <joshua.d.campbell@gmail.com>
Date: 2025-07-24 16:15:22 -0400
Commit message:

 updated docs
Package: musicatk
Commit: d92d323362d17449b13b089e744f8364bd25d62d
Author: Josh Campbell <joshua-d-campbell@gmail.com>
Date: 2025-07-15 20:34:01 -0400
Commit message:

 version bump and news update
Package: musicatk
Commit: cb91127746abaf29106ba53080155dba12006f26
Author: Josh Campbell <joshua-d-campbell@gmail.com>
Date: 2025-07-15 20:29:04 -0400
Commit message:

 Merge remote-tracking branch 'campbio/devel' into devel
Package: musicatk
Commit: c7c2c9aa3e7cc7b468c27b752db8151fa67d41d6
Author: Joshua D. Campbell <joshua.d.campbell@gmail.com>
Date: 2025-07-15 20:27:56 -0400
Commit message:

 Merge pull request #87 from nqgurevich/refactor

Removal of conclust package
Package: musicatk
Commit: b2e2a29eb50349d2289e122eccdf15dffcb04edb
Author: Josh Campbell <joshua-d-campbell@gmail.com>
Date: 2025-07-15 20:26:45 -0400
Commit message:

 Merge branch 'RELEASE_3_21' into devel
Package: musicatk
Commit: fce19906e57abcbd47cd3b813b0ea7268dd4fb94
Author: Natasha Gurevich <ngurevich@dot1x-nat-10-222-36-127.bumc.bu.edu>
Date: 2025-07-15 14:04:29 -0400
Commit message:

 Adjustment for removal of conclust package from CRAN
Package: musicatk
Commit: e09d7a3ee24aa2b1600a2532f575c425a6e39966
Author: Natasha Gurevich <ngurevich@dot1x-nat-10-222-36-127.bumc.bu.edu>
Date: 2025-02-14 11:55:43 -0500
Commit message:

 Remove articles/articles in Shiny app help links
Package: musicatk
Commit: 0b2d43a681e3e711d6aab4462603586336afc4c6
Author: Natasha Gurevich <ngurevich@dot1x-nat-10-222-36-127.bumc.bu.edu>
Date: 2025-02-14 11:55:25 -0500
Commit message:

 Cosmetic changes to k value and plotting code
Package: musicatk
Commit: 85b25abcf97d5294721a5a79c8bce4028f7be99a
Author: nqgurevich <84352235+nqgurevich@users.noreply.github.com>
Date: 2025-01-24 16:09:54 -0500
Commit message:

 Merge pull request #86 from nqgurevich/refactor

Remove references to secondary articles folder
Package: musicatk
Commit: 349a865fed85dc31461c1f56a181a878c00cead4
Author: Natasha Gurevich <ngurevich@crc-dot1x-nat-10-239-201-206.bu.edu>
Date: 2025-01-21 16:19:14 -0500
Commit message:

 Heading fix for musicatk general vignette
Package: musicatk
Commit: 111c3e7b92ddbf5870d133051bc763763cdb0dde
Author: Natasha Gurevich <ngurevich@Natashas-MacBook-Pro.local>
Date: 2025-01-20 18:22:28 -0500
Commit message:

 Merge remote-tracking branch 'campbio/devel' into refactor
Package: musicatk
Commit: 8fe463ee0606f3caa5e95d9771d7a2b0049986bf
Author: Natasha Gurevich <ngurevich@Natashas-MacBook-Pro.local>
Date: 2025-01-20 18:22:08 -0500
Commit message:

 Redirect all articles to primary articles folder
Package: musicatk
Commit: a7f2c8ca5302e7ba18ebba1730249d2ab1755dea
Author: Joshua D. Campbell <joshua.d.campbell@gmail.com>
Date: 2025-01-17 14:13:03 -0500
Commit message:

 Merge pull request #84 from nqgurevich/refactor

Adjustment to point to primary articles folder
Package: musicatk
Commit: b628c5d1f1fe1ab29714de33b248b253faeb03aa
Author: Natasha Gurevich <ngurevich@dot1x-nat-10-222-36-127.bumc.bu.edu>
Date: 2025-01-17 11:55:28 -0500
Commit message:

 Adjustment to point to primary articles folder
Package: musicatk
Commit: 378c372b05b81041be710cc26a7e93dea05d768a
Author: Joshua D. Campbell <joshua.d.campbell@gmail.com>
Date: 2025-01-14 15:05:36 -0500
Commit message:

 Merge pull request #83 from nqgurevich/refactor

UI Tutorial
Package: musicatk
Commit: 90c24fd657379b208bc1b793e7c50b42546af883
Author: Natasha Gurevich <ngurevich@dot1x-nat-10-222-36-127.bumc.bu.edu>
Date: 2025-01-14 14:14:03 -0500
Commit message:

 create_result_model converted to add_result
Package: musicatk
Commit: 47d08bc1c898baca388f418f8269377349c81b99
Author: Natasha Gurevich <ngurevich@dot1x-nat-10-222-36-127.bumc.bu.edu>
Date: 2025-01-14 13:45:28 -0500
Commit message:

 Indel plotting bug fix
Package: musicatk
Commit: 4a61efe955a5cd4705f73cde913d3a3b3b40b3ae
Author: Natasha Gurevich <ngurevich@dot1x-nat-10-222-36-127.bumc.bu.edu>
Date: 2025-01-14 12:14:22 -0500
Commit message:

 index update

Merge remote-tracking branch 'campbio/devel' into refactor

# Conflicts:
#	inst/shiny/ui.R
Package: musicatk
Commit: f2b4989d6820f977666e9982c19a5892c45437e7
Author: Natasha Gurevich <ngurevich@dot1x-nat-10-222-36-127.bumc.bu.edu>
Date: 2025-01-14 12:09:32 -0500
Commit message:

 Delete duplicate files
Package: musicatk
Commit: 4a834580d2677498ce2225200cca12eae158cc40
Author: Natasha Gurevich <ngurevich@dot1x-nat-10-222-36-127.bumc.bu.edu>
Date: 2025-01-14 12:07:49 -0500
Commit message:

 UI tutorial updates - link to current website version
Package: musicatk
Commit: 173321bcafcc8851958c82a5d6b9475f83078066
Author: Natasha Gurevich <ngurevich@dot1x-nat-10-222-36-127.bumc.bu.edu>
Date: 2025-01-14 11:42:28 -0500
Commit message:

 UI tutorial updates
Package: musicatk
Commit: 7746e189eacb5683f4fde6ce29307ecdc00586e8
Author: Josh Campbell <joshua-d-campbell@gmail.com>
Date: 2024-12-23 08:21:10 -0500
Commit message:

 Updated help link to latest version in Shiny app
Package: musicatk
Commit: 3eeef7980518a313cb4f3bdbde73a535c7c079bd
Author: Joshua D. Campbell <joshua.d.campbell@gmail.com>
Date: 2024-12-21 15:47:44 -0500
Commit message:

 Merge pull request #82 from nqgurevich/refactor

Refactor - shiny/pkgdown
Package: musicatk
Commit: ea946cfc8f3843f9a03f2d68a9e1a99c1e3237f2
Author: Natasha Gurevich <ngurevich@Natashas-MacBook-Pro.local>
Date: 2024-12-20 11:15:20 -0500
Commit message:

 UI tutorial updates for refactor
Package: musicatk
Commit: 2d0804f675d39d96f85d347e8aa17beda2255963
Author: Natasha Gurevich <ngurevich@Natashas-MacBook-Pro.local>
Date: 2024-12-20 02:22:10 -0500
Commit message:

 Shiny updates for refactor
Package: musicatk
Commit: 8df0c3e6fe29e46fff91a8d621a26236d4742205
Author: Natasha Gurevich <ngurevich@dot1x-nat-10-222-36-127.bumc.bu.edu>
Date: 2024-12-17 11:53:58 -0500
Commit message:

 Musicatk package down site
Package: musicatk
Commit: c6ffbd5a1fd9c1df3471ce4734ca6cebd0c4a2e7
Author: Natasha Gurevich <ngurevich@Natashas-MacBook-Pro.local>
Date: 2024-12-16 16:01:13 -0500
Commit message:

 Remove GDC data
Package: musicatk
Commit: 528d09a7dcad350b9fc111f55afff5b102a751bc
Author: Natasha Gurevich <ngurevich@Natashas-MacBook-Pro.local>
Date: 2024-12-16 15:57:55 -0500
Commit message:

 Updates to packagedown site, news
Package: musicatk
Commit: e87155402b88fbf46728cfa1cd74a34ffc25e0b0
Author: nqgurevich <84352235+nqgurevich@users.noreply.github.com>
Date: 2024-12-02 19:45:51 -0500
Commit message:

 Update README.md

Updated CDM check badge and removed tutorial information
Package: musicatk
Commit: 8dce5557db05ecfd5cc2db28a15e2f92c72fad91
Author: Josh Campbell <joshua-d-campbell@gmail.com>
Date: 2024-11-26 13:47:00 -0500
Commit message:

 Decreased version number to match Bioc release
Package: escape
Commit: 59e0b129390607ea6824e8aaf8ad9277909ee3ba
Author: theHumanBorch <ncborch@gmail.com>
Date: 2025-07-25 12:48:23 -0500
Commit message:

 better alphanumeric sorting
Package: escape
Commit: d0adb16ae5bc1d69ea50e55712960d7578427860
Author: theHumanBorch <ncborch@gmail.com>
Date: 2025-07-23 14:19:12 -0500
Commit message:

 vizualization adjustments
Package: escape
Commit: 93b7862c08ba7ab945be7ecbe865cfd6a9ecc8fb
Author: theHumanBorch <ncborch@gmail.com>
Date: 2025-07-23 13:22:06 -0500
Commit message:

 Merge pull request #170 from BorchLab/ordering_correction

Adding sort to gseaEnrichment levels
Package: escape
Commit: 4e2ef664474151b1dfd3334a4f8a7249f0914258
Author: theHumanBorch <ncborch@gmail.com>
Date: 2025-07-23 13:10:29 -0500
Commit message:

 Adding sort to gseaEnrichment levels

#169 per issue
Package: escape
Commit: add68859c017ee0c9f06748a705ee03b8b16fd92
Author: theHumanBorch <ncborch@gmail.com>
Date: 2025-07-22 14:07:51 -0500
Commit message:

 Update test-coverage.yaml

converting to cobertura approach
Package: escape
Commit: 831395df70158c079f201847b70e055149c7e175
Author: theHumanBorch <ncborch@gmail.com>
Date: 2025-07-22 09:30:08 -0500
Commit message:

 Update test-coverage.yaml

Adding sending to codecov
Package: escape
Commit: 41cbe68852ff13f976bc7e727afeaa5dd13725ce
Author: theHumanBorch <ncborch@gmail.com>
Date: 2025-06-11 10:44:04 -0500
Commit message:

 Merge pull request #166 from toobiwankenobi/geyserSummary

fix color.by bug and introduce summarise.by feature for geyserEnrichment
Package: escape
Commit: 7b09b866225356eb6f3bab89e1745a9efa0dfc79
Author: toobiwankenobi <tobias.hoch@bluewin.ch>
Date: 2025-06-11 16:34:15 +0200
Commit message:

 fix checks to determine if color.by is a feature or metadata
Package: escape
Commit: b7ad30e4c2a8cd8ede63b46abfb34fd69c7f3492
Author: toobiwankenobi <tobias.hoch@bluewin.ch>
Date: 2025-06-11 15:44:00 +0200
Commit message:

 fix missing attribute error caused by gseaEnrichment and fix plotting of gseaEnrichment
Package: escape
Commit: 3b25b273955c318cf571b79495a009a83b32fe74
Author: toobiwankenobi <tobias.hoch@bluewin.ch>
Date: 2025-06-11 14:01:39 +0200
Commit message:

 version bump
Package: escape
Commit: 92a49df223efe6ea9b4c75d09d470c2e62f5c485
Author: toobiwankenobi <tobias.hoch@bluewin.ch>
Date: 2025-06-11 14:00:58 +0200
Commit message:

 enable dgCMatrix input. didnt work before.
Package: escape
Commit: d0211905d28d4768527be1b8da84a1078ec4c22b
Author: toobiwankenobi <tobias.hoch@bluewin.ch>
Date: 2025-06-11 09:31:56 +0200
Commit message:

 move summary function to utils since its now used across multiple functions
Package: escape
Commit: 256cb8839549d4098a18cd33eb7cc1e753344e7f
Author: toobiwankenobi <tobias.hoch@bluewin.ch>
Date: 2025-06-10 17:32:07 +0200
Commit message:

 enable color.by to use meta data that is different than other arguments such as group.by. Described in issue #163
Package: escape
Commit: 4f9de377bf1833607ed8458ffb24ef4439c8c69e
Author: toobiwankenobi <tobias.hoch@bluewin.ch>
Date: 2025-06-06 17:14:45 +0200
Commit message:

 fix formatting of param (was not correctly displayed before)
Package: escape
Commit: c10ffa36a34e6b5b0aacb6ffbbe9b201abfee36f
Author: toobiwankenobi <tobias.hoch@bluewin.ch>
Date: 2025-06-06 17:06:55 +0200
Commit message:

 roxygenise changes for geyserEnrichment
Package: escape
Commit: d809fc449843d4931049f5c4b2d2c3db2fa78955
Author: toobiwankenobi <tobias.hoch@bluewin.ch>
Date: 2025-06-06 17:06:02 +0200
Commit message:

 introduce summarise.by to collapse data (e.g. by patient ID) and enable color.by = NULL to remove coloring of data points.
Package: scRepertoire
Commit: 526c298e9adb71a6c613ab8e7e3f1e0a0d6f2085
Author: theHumanBorch <ncborch@gmail.com>
Date: 2025-07-25 12:33:26 -0500
Commit message:

 version
Package: scRepertoire
Commit: 29b33992fe7005d74e4964bb0ed257d0a264f418
Author: theHumanBorch <ncborch@gmail.com>
Date: 2025-07-25 11:00:59 -0500
Commit message:

 Merge pull request #520 from BorchLab/clonalSizeDistribution

clonalSizeDistribution optimization
Package: scRepertoire
Commit: 5674a0c0dc52b83414a579dc3d27dbd0ab194694
Author: theHumanBorch <ncborch@gmail.com>
Date: 2025-07-25 10:39:14 -0500
Commit message:

 Merge branch 'master' into clonalSizeDistribution
Package: scRepertoire
Commit: 6241952112638c7a6a18f1a4d0d0e3f5f7466902
Author: theHumanBorch <ncborch@gmail.com>
Date: 2025-07-25 10:37:43 -0500
Commit message:

 Update accompanying documentation

#507
Package: scRepertoire
Commit: 90c643b9aeba80b8cb7745e9dda07295e42798ad
Author: theHumanBorch <ncborch@gmail.com>
Date: 2025-07-25 10:37:31 -0500
Commit message:

 Update test-clonalSizeDistribution.R

#507 update unit testing - expand to the underlying distribution and distance functions
Package: scRepertoire
Commit: 8bb2307b315f67c1052506d4cc22269116fe0c46
Author: theHumanBorch <ncborch@gmail.com>
Date: 2025-07-25 10:37:06 -0500
Commit message:

 Update clonalSizeDistribution.R

#507 remove VGAM, truncdist, cubature dependencies and speed up function
Package: scRepertoire
Commit: 74fc82ab8d6811a6b2001d35dc8d01d30c72f16d
Author: theHumanBorch <ncborch@gmail.com>
Date: 2025-07-22 13:52:33 -0500
Commit message:

 Update test-coverage.yaml

Adding token
Package: scRepertoire
Commit: bac3dafb8f20fd03d977b69700853d578466a788
Author: theHumanBorch <ncborch@gmail.com>
Date: 2025-07-22 13:36:39 -0500
Commit message:

 Update test-coverage.yaml
Package: scRepertoire
Commit: bdf3dd033cdf41a6f9d73d50f37f63e371f6d14a
Author: theHumanBorch <ncborch@gmail.com>
Date: 2025-07-22 13:27:13 -0500
Commit message:

 Update test-coverage.yaml

testing cobertura usage
Package: scRepertoire
Commit: eac22931dbc18aa88952b33d3f8380660b266bfb
Author: theHumanBorch <ncborch@gmail.com>
Date: 2025-07-22 09:28:54 -0500
Commit message:

 Update test-coverage.yaml

Adding send to codecov
Package: scRepertoire
Commit: 27fcd1574036171a3b5fb9dc7ecfbacfb9fe7e7f
Author: theHumanBorch <ncborch@gmail.com>
Date: 2025-07-22 09:20:31 -0500
Commit message:

 Merge branch 'master' of https://github.com/BorchLab/scRepertoire
Package: scRepertoire
Commit: 652c3f97951ea2c441bfda3ab72dba06cde94f4e
Author: theHumanBorch <ncborch@gmail.com>
Date: 2025-07-22 09:20:23 -0500
Commit message:

 Update DESCRIPTION
Package: scRepertoire
Commit: f5f9eed823d64becd1ddfbb59c722943a2dd4138
Author: theHumanBorch <ncborch@gmail.com>
Date: 2025-07-22 09:10:40 -0500
Commit message:

 Merge pull request #519 from BorchLab/immunarch_fix

Immunarch fix
Package: scRepertoire
Commit: 5036a93705504c0918ac8b05f673e5c0223eae38
Author: theHumanBorch <ncborch@gmail.com>
Date: 2025-07-22 09:09:13 -0500
Commit message:

 updating vignette tidy
Package: scRepertoire
Commit: f03fb66a032f7a77fbb24d926e2b8b6f3576a0cf
Author: theHumanBorch <ncborch@gmail.com>
Date: 2025-07-22 08:30:41 -0500
Commit message:

 Update immunarch.Rmd

Expanding immunarch vignette and explaining the pairing
Package: scRepertoire
Commit: 0da212e32413beb8d2751525599ff612948ced96
Author: theHumanBorch <ncborch@gmail.com>
Date: 2025-07-21 15:31:04 -0500
Commit message:

 Merge pull request #517 from BorchLab/startracDiversity

Startrac diversity
Package: scRepertoire
Commit: 7e9fe48641852836bb6324c460f082c65601876d
Author: theHumanBorch <ncborch@gmail.com>
Date: 2025-07-21 15:09:03 -0500
Commit message:

 Plotting and check passes

#506
Package: scRepertoire
Commit: e8654f3ae52ed96ed24648edcdd3ca71add75200
Author: theHumanBorch <ncborch@gmail.com>
Date: 2025-07-21 08:59:54 -0500
Commit message:

 Pairwise and Index Plotting

#506 - Still need to work out plotting for pairwise comparisons
Package: scRepertoire
Commit: de665fe2c744c9aefbae46d693f6a1e2f626a731
Author: theHumanBorch <ncborch@gmail.com>
Date: 2025-07-21 07:23:27 -0500
Commit message:

 Merge pull request #516 from BorchLab/dandelionR

Update dandelionR.Rmd
Package: scRepertoire
Commit: 4df754223b9bef0bdae12da1507fd71e864b79d6
Author: theHumanBorch <ncborch@gmail.com>
Date: 2025-07-21 07:19:42 -0500
Commit message:

 Update dandelionR.Rmd

DandelionR vignette
Package: scRepertoire
Commit: e25c4a46d896e6907e2daa105600d1aa57a734cc
Author: theHumanBorch <ncborch@gmail.com>
Date: 2025-07-17 12:41:16 -0500
Commit message:

 Merge pull request #514 from BorchLab/additional_vignettes

Working on vignettes that are compatible with scRepertoire
Package: scRepertoire
Commit: 1d1525c0c3b8076aea7467d85555aede6bb2b0c6
Author: theHumanBorch <ncborch@gmail.com>
Date: 2025-07-17 12:40:35 -0500
Commit message:

 Working on vignettes that are compatible with scRepertoire
Package: scRepertoire
Commit: 6158594ef239f4f2717f7ce6b443bb03d02471d6
Author: theHumanBorch <ncborch@gmail.com>
Date: 2025-07-16 05:41:07 -0500
Commit message:

 Merge pull request #513 from Qile0317/citation-update

add CITATION.cff
Package: scRepertoire
Commit: 9b0707d3865194fe55bb5df6de5e7b8aae72d35f
Author: Qile0317 <qile0317@gmail.com>
Date: 2025-07-15 14:33:43 -0700
Commit message:

 add CITATION.cff
Package: scRepertoire
Commit: f2b14295c7d40838009bf027df68847e773df6ce
Author: theHumanBorch <ncborch@gmail.com>
Date: 2025-07-15 12:32:36 -0500
Commit message:

 Merge pull request #512 from BorchLab/positionalProperty_Refinement

Update positionalProperty.R
Package: scRepertoire
Commit: 1397f963a0212af114e16597df12e26918909878
Author: theHumanBorch <ncborch@gmail.com>
Date: 2025-07-15 09:39:41 -0500
Commit message:

 Update test-positionalProperty.R
Package: scRepertoire
Commit: 9b7a345c75d701b025d46694a179c953f85bf455
Author: theHumanBorch <ncborch@gmail.com>
Date: 2025-07-15 08:59:04 -0500
Commit message:

 update positionalProperty Unittests
Package: scRepertoire
Commit: 92ddf9be0ab1799877bf614fadb8c7e2786be0b9
Author: theHumanBorch <ncborch@gmail.com>
Date: 2025-07-15 08:28:16 -0500
Commit message:

 Update positionalProperty.R

Update CI interval 0 for residues with 2 or < observations
Plot and Legend Formatting
Package: scRepertoire
Commit: d137a0c13dea69f8a1756ef91b651e31f4bef185
Author: theHumanBorch <ncborch@gmail.com>
Date: 2025-07-15 07:48:37 -0500
Commit message:

 Documentation Cleaning
Package: scRepertoire
Commit: 023e2f3619f4682ebbfee0d20e8a4c8e49015afc
Author: theHumanBorch <ncborch@gmail.com>
Date: 2025-07-14 11:59:46 -0500
Commit message:

 Merge pull request #511 from BorchLab/documentation_update

Documentation update
Package: scRepertoire
Commit: 59337e0fc647252ddb124fde92d3075a9d862139
Author: theHumanBorch <ncborch@gmail.com>
Date: 2025-07-14 10:54:55 -0500
Commit message:

 Update vignette documentation
Package: scRepertoire
Commit: aa5bd2afc3d42adf957a549afca12e5c8e481d80
Author: theHumanBorch <ncborch@gmail.com>
Date: 2025-07-13 15:23:32 -0500
Commit message:

 Universalizing function documentation
Package: scRepertoire
Commit: 3f06939aac448d1c460e98db969c097351b6180d
Author: theHumanBorch <ncborch@gmail.com>
Date: 2025-07-12 07:00:05 -0500
Commit message:

 minimizing global variables
Package: scRepertoire
Commit: 2fa1ba9d222105a7f28d6c3eb647eb646145786e
Author: theHumanBorch <ncborch@gmail.com>
Date: 2025-07-12 05:41:13 -0500
Commit message:

 Merge branch 'master' of https://github.com/BorchLab/scRepertoire
Package: scRepertoire
Commit: 493cd3f681a9ac4a3d61e5657ae75f9c40564e8b
Author: theHumanBorch <ncborch@gmail.com>
Date: 2025-07-12 05:41:11 -0500
Commit message:

 updating site links
Package: scRepertoire
Commit: 9e8a404abaaeeef626328c2e4329fe550c94588f
Author: theHumanBorch <ncborch@gmail.com>
Date: 2025-07-12 05:37:05 -0500
Commit message:

 Merge pull request #510 from BorchLab/theme

Add themeRepertoire
Package: scRepertoire
Commit: b7864dbaa27c3d63c3f9d480c0ed23c217f2ee73
Author: theHumanBorch <ncborch@gmail.com>
Date: 2025-07-12 05:36:25 -0500
Commit message:

 Update NEWS.md
Package: scRepertoire
Commit: 3a3367801357287576ebf861e67b5d6e5a652894
Author: theHumanBorch <ncborch@gmail.com>
Date: 2025-07-12 05:35:16 -0500
Commit message:

 Add themeRepertoire
Package: scRepertoire
Commit: a6b52dd57702a8752575587b8d86809628d86033
Author: theHumanBorch <ncborch@gmail.com>
Date: 2025-07-11 19:03:34 -0500
Commit message:

 Merge pull request #508 from BorchLab/dev

v2.4.99999
Package: scRepertoire
Commit: aec63a9248d6633bfd02bf382c87f42d80c4b1ff
Author: theHumanBorch <ncborch@gmail.com>
Date: 2025-07-11 15:08:41 -0500
Commit message:

 Update test-positionalProperty.R
Package: scRepertoire
Commit: 567ef1f248519a3b1961177e640dfabc78d6c68b
Author: theHumanBorch <ncborch@gmail.com>
Date: 2025-07-11 12:04:14 -0500
Commit message:

 Add peptides as suggest
Package: scRepertoire
Commit: bbdaeccfbb0e36b47b78572f566a2dc0adbfac2a
Author: theHumanBorch <ncborch@gmail.com>
Date: 2025-07-11 10:59:40 -0500
Commit message:

 vignette-based cleaning
Package: scRepertoire
Commit: 28d66aa108738fb156838d67c5f2a959d6855567
Author: theHumanBorch <ncborch@gmail.com>
Date: 2025-07-11 10:08:09 -0500
Commit message:

 Merge branch 'master' into dev
Package: scRepertoire
Commit: ef2c289fb0c025ad2e8a6c36f7258e5e0f3c9656
Author: theHumanBorch <ncborch@gmail.com>
Date: 2025-07-11 09:59:04 -0500
Commit message:

 R CMD Final Checks
Package: scRepertoire
Commit: 7adf63b4667dbe41171cde5810f263ae4cb9b761
Author: theHumanBorch <ncborch@gmail.com>
Date: 2025-07-11 09:40:06 -0500
Commit message:

 Update clonalDiversity.R

fixing issue with orderingFunction() call parameters
Package: scRepertoire
Commit: 9aed5ea18eaf7ef6ed6d2b0ba7fdacfcd14ec4ef
Author: theHumanBorch <ncborch@gmail.com>
Date: 2025-07-11 09:14:23 -0500
Commit message:

 Fixed issue with spliting strings in loadContigs for TRUST4
Package: scRepertoire
Commit: eaf3d73dc4dc8695d6ea8454e8da97c0d321aaa7
Author: theHumanBorch <ncborch@gmail.com>
Date: 2025-07-11 08:41:39 -0500
Commit message:

 Update percentGeneUsage.R

adding group.by if NULL to multiple chains
Package: scRepertoire
Commit: 5505c38d02a4fb6a9392f3392e9399f5c980d1fb
Author: theHumanBorch <ncborch@gmail.com>
Date: 2025-07-11 08:41:19 -0500
Commit message:

 remove assert_that()
Package: scRepertoire
Commit: 878f587c383e679140192d0ec2907d2bba63f61f
Author: theHumanBorch <ncborch@gmail.com>
Date: 2025-07-11 08:41:05 -0500
Commit message:

 Spelling and common devtools::check() issues
Package: scRepertoire
Commit: 014bef9b344196d82f277afd755367c74222996c
Author: theHumanBorch <ncborch@gmail.com>
Date: 2025-07-11 07:52:39 -0500
Commit message:

 Adding examples to percentGeneUsage documentation
Package: scRepertoire
Commit: b9971a353e120718e49ecccdc70d9667eea557cb
Author: theHumanBorch <ncborch@gmail.com>
Date: 2025-07-11 07:45:30 -0500
Commit message:

 Getting group.by to work correctly for percentGeneUsage and aliases
Package: scRepertoire
Commit: 0d73f03b92502e40e67a26d7db292955a077369c
Author: theHumanBorch <ncborch@gmail.com>
Date: 2025-07-11 07:21:24 -0500
Commit message:

 updating vignettes for percentGeneUsage()
Package: scRepertoire
Commit: 53f8527c182ee6455a116ac51bc6442b786a700f
Author: theHumanBorch <ncborch@gmail.com>
Date: 2025-07-10 16:12:34 -0500
Commit message:

 percentGeneUsage draft
Package: scRepertoire
Commit: e473c99b000137b32beaba2b70a6498f72041078
Author: theHumanBorch <ncborch@gmail.com>
Date: 2025-07-06 15:15:37 -0500
Commit message:

 remove last reshape2 melt calls
Package: scRepertoire
Commit: 29bfc8fea01c77ee41380b19288b8c0066189eff
Author: theHumanBorch <ncborch@gmail.com>
Date: 2025-07-06 15:01:36 -0500
Commit message:

 documentation edit
Package: scRepertoire
Commit: da993ce892d5a42c2be91f7a13fb715f8781b8b4
Author: theHumanBorch <ncborch@gmail.com>
Date: 2025-07-06 15:01:24 -0500
Commit message:

 clonalCluster vignette edits
Package: scRepertoire
Commit: 7353f236bcd2b3b5227209cd69a5d23ead38aaef
Author: theHumanBorch <ncborch@gmail.com>
Date: 2025-07-06 15:01:08 -0500
Commit message:

 Update startracDiversity.R

remove false plyr call
Package: scRepertoire
Commit: 8fee7f79ee0950ce0c1ca70b02bd2bcd977cd70b
Author: theHumanBorch <ncborch@gmail.com>
Date: 2025-07-06 15:00:44 -0500
Commit message:

 Update scRepertoire-package.R

removing autoload importfrom
Package: scRepertoire
Commit: fda63eb3f0c68d603365cb158eb185702c62d4fb
Author: theHumanBorch <ncborch@gmail.com>
Date: 2025-07-06 15:00:28 -0500
Commit message:

 Update clonalCluster.R

Add ggrouping vertices variable
remove samples
compoenents specifically call weak
pseudocount for matching sequences
Package: scRepertoire
Commit: f8557caae6d580f4c7a52babe8409f06844a772a
Author: theHumanBorch <ncborch@gmail.com>
Date: 2025-07-06 14:59:45 -0500
Commit message:

 Update combineContigs.R

combineBCR default is now use V and J gene segments
Package: scRepertoire
Commit: 28e73130184505b22553193bf683463e2b23ffdd
Author: theHumanBorch <ncborch@gmail.com>
Date: 2025-07-06 14:59:10 -0500
Commit message:

 Update percentGenes.R

removing stringr import
Package: scRepertoire
Commit: 9e242340f0162f7964aef04b5f8565d196730249
Author: theHumanBorch <ncborch@gmail.com>
Date: 2025-07-06 14:59:03 -0500
Commit message:

 Update percentVJ.R

removing stringr import
Package: scRepertoire
Commit: 05affbecb79b88e63209923354a382658f357cbe
Author: theHumanBorch <ncborch@gmail.com>
Date: 2025-07-06 14:58:55 -0500
Commit message:

 Update vizGenes.R

removing stringr import
Package: scRepertoire
Commit: 6d2997691b0f95200e63ebc6d9c62e79dec2c156
Author: theHumanBorch <ncborch@gmail.com>
Date: 2025-07-06 07:27:16 -0500
Commit message:

 Update Combining_Contigs.Rmd
Package: scRepertoire
Commit: 0aa6b857212193ab14c44066156bb8810eb647fc
Author: theHumanBorch <ncborch@gmail.com>
Date: 2025-07-06 07:27:11 -0500
Commit message:

 vignette working

Adding peptides and refactor vignette
Package: scRepertoire
Commit: 419c824d379325ff7fad56731a03fa9fcdaec470
Author: theHumanBorch <ncborch@gmail.com>
Date: 2025-07-06 07:26:41 -0500
Commit message:

 update clonalHomeostasis melting
Package: scRepertoire
Commit: c3ee89183be795a4e20adfc74ea4601c14c663b8
Author: theHumanBorch <ncborch@gmail.com>
Date: 2025-07-06 07:26:17 -0500
Commit message:

 removing old rcpp exports
Package: scRepertoire
Commit: 7a7e67cdf48fa3930eb7f8f20491b6b1fba30984
Author: theHumanBorch <ncborch@gmail.com>
Date: 2025-07-06 06:50:54 -0500
Commit message:

 Update DESCRIPTION

remove plyr import in description
Package: scRepertoire
Commit: ed3318cee3f09b2fe517c26d821d8489fd5f8d4b
Author: theHumanBorch <ncborch@gmail.com>
Date: 2025-07-05 14:33:36 -0500
Commit message:

 Update test-getCirclize.R

formatting
Package: scRepertoire
Commit: 60d8f09a1886bc64310f1241345adc867ca839d8
Author: theHumanBorch <ncborch@gmail.com>
Date: 2025-07-05 14:33:29 -0500
Commit message:

 Update test-vizGenes.R

blanked for now
Package: scRepertoire
Commit: f85bcecb6a0892cd1ce74ea9d1a698e6ff6c15cf
Author: theHumanBorch <ncborch@gmail.com>
Date: 2025-07-05 14:33:22 -0500
Commit message:

 Update test-quietVDJgenes.R

No longer storing data
Package: scRepertoire
Commit: ca12baacc4d7ed6ce8fcd8ce7a35012e64c24045
Author: theHumanBorch <ncborch@gmail.com>
Date: 2025-07-05 14:33:08 -0500
Commit message:

 remove all snapshots
Package: scRepertoire
Commit: 31b9e2f9c052255dd7b0fce2632272d40bf454d5
Author: theHumanBorch <ncborch@gmail.com>
Date: 2025-07-05 14:32:56 -0500
Commit message:

 Update utils.R

groupList now ensures df is a list
Package: scRepertoire
Commit: 40b6f9159458f52a8060d075ad19adfbbb40f78f
Author: theHumanBorch <ncborch@gmail.com>
Date: 2025-07-05 14:32:38 -0500
Commit message:

 Update positionalProperty.R

import .padded.strings and define amino.acids
Package: scRepertoire
Commit: 9a4f66ea44fe62a490f249f492756b98dafee6ac
Author: theHumanBorch <ncborch@gmail.com>
Date: 2025-07-05 14:32:18 -0500
Commit message:

 Update getCircilize.R

use sort to get the columns orders
Package: scRepertoire
Commit: 00ba28959d7bfb740a89485e2a1b58eeaefb0d95
Author: theHumanBorch <ncborch@gmail.com>
Date: 2025-07-05 14:04:19 -0500
Commit message:

 Update test-percentVJ.R

temp not having VJ unit tests while that is refactored
Package: scRepertoire
Commit: 9f81f44c8e1aeedc94f007c77b76f4c99ba83016
Author: theHumanBorch <ncborch@gmail.com>
Date: 2025-07-05 14:03:58 -0500
Commit message:

 remove getData() calls
Package: scRepertoire
Commit: 7282a67df219447486e1b08c22e41ebd7a39777c
Author: theHumanBorch <ncborch@gmail.com>
Date: 2025-07-05 14:03:32 -0500
Commit message:

 Update test-loadContigs.R

removing awkward data load calls
Package: scRepertoire
Commit: 2865cf8afb8355a3f218f341a4eb1bb729463d48
Author: theHumanBorch <ncborch@gmail.com>
Date: 2025-07-05 14:03:17 -0500
Commit message:

 Update test-combineExpression.R

dumb unit tests calls the wrong function
Package: scRepertoire
Commit: 04eb8667667f8678110360199436edbe5782c129
Author: theHumanBorch <ncborch@gmail.com>
Date: 2025-07-05 14:02:59 -0500
Commit message:

 remove assertthat calls
Package: scRepertoire
Commit: 625b47a29a41144d33312379a148feda677a81cb
Author: theHumanBorch <ncborch@gmail.com>
Date: 2025-07-05 14:02:44 -0500
Commit message:

 add processStrings
Package: scRepertoire
Commit: c99143323c1a255eb50d13887447acb069f08e54
Author: theHumanBorch <ncborch@gmail.com>
Date: 2025-07-05 13:44:14 -0500
Commit message:

 Update test-combineContigs.R

combineBCR no longer requires sample
Package: scRepertoire
Commit: fae8f21c16eb7bf1c20573a974b4944f5dd24554
Author: theHumanBorch <ncborch@gmail.com>
Date: 2025-07-05 13:44:02 -0500
Commit message:

 Update test-combineExpression.R

remove group by testing added to the Seurat object - that does not make sense
Package: scRepertoire
Commit: 7be64c5f4f05e6c3aeb45b58bb410ba966ea5a03
Author: theHumanBorch <ncborch@gmail.com>
Date: 2025-07-05 13:43:36 -0500
Commit message:

 Update test-clonalScatter.R

removed group.by testing
Package: scRepertoire
Commit: 578f9000196022bfb3f3ef414623635b6cb63368
Author: theHumanBorch <ncborch@gmail.com>
Date: 2025-07-05 13:43:20 -0500
Commit message:

 Update test-clonalOverlap.R

clonal overlap testing no longer matches string for expect_error
Package: scRepertoire
Commit: 521d3eba66d13c069906dc8646219137aa356fac
Author: theHumanBorch <ncborch@gmail.com>
Date: 2025-07-05 13:43:00 -0500
Commit message:

 Update clonalNetwork.R

Ensure correct camelCase for internal functions
Package: scRepertoire
Commit: 614ace456fbd6dc5ebb7af28af40ea40d7c80dc9
Author: theHumanBorch <ncborch@gmail.com>
Date: 2025-07-05 13:42:44 -0500
Commit message:

 Update test-clonalNetwork.R

Update clonal network exportClones test
Package: scRepertoire
Commit: c425e742b8a824d3234576644513d45717124eec
Author: theHumanBorch <ncborch@gmail.com>
Date: 2025-07-05 13:42:30 -0500
Commit message:

 Update test-clonalCompare.R

move to grepl instead of stringr in the unit tests
Package: scRepertoire
Commit: 8281b717ac1093c96a9189e8964415cc3e2953ab
Author: theHumanBorch <ncborch@gmail.com>
Date: 2025-07-05 13:42:05 -0500
Commit message:

 Update combineContigs.R

Make sure passing the right object into clonalCluster
Package: scRepertoire
Commit: ab71d12847679b7200f4dbe2b54103fac3545ed5
Author: theHumanBorch <ncborch@gmail.com>
Date: 2025-07-05 13:41:46 -0500
Commit message:

 import igraph for cluster unit tests
Package: scRepertoire
Commit: a42cb9487d44c076f9b0ef68891aaf626fad156e
Author: theHumanBorch <ncborch@gmail.com>
Date: 2025-07-05 13:11:27 -0500
Commit message:

 Update clonalNetwork.R

Updating new internal function camelCase reference
Package: scRepertoire
Commit: 23a118a6391695bfe94e5fe366bf8d71339d8d23
Author: theHumanBorch <ncborch@gmail.com>
Date: 2025-07-05 13:11:11 -0500
Commit message:

 combineExpression low memory overhead

re-implementing Qiles addition
Package: scRepertoire
Commit: b2df3d5d888c58f1848905d07f1dcf056e5f63f1
Author: theHumanBorch <ncborch@gmail.com>
Date: 2025-07-05 13:10:38 -0500
Commit message:

 Update clonalBias.R

Update camelCase for internal function
Package: scRepertoire
Commit: 1dd0deb0ec12884068f92a09ca1d5339ecc9ea3b
Author: theHumanBorch <ncborch@gmail.com>
Date: 2025-07-05 13:10:20 -0500
Commit message:

 getting clonalCluster igraph imports right
Package: scRepertoire
Commit: b36381ce598e6c1ff6da914983c5c4ec372cc5f9
Author: theHumanBorch <ncborch@gmail.com>
Date: 2025-07-03 12:37:10 -0500
Commit message:

 updating function documentation
Package: scRepertoire
Commit: a7f9fa5d3f5ac9bc4ee984380d82d7f966d2e847
Author: theHumanBorch <ncborch@gmail.com>
Date: 2025-07-03 12:17:08 -0500
Commit message:

 Working through unit testing
Package: scRepertoire
Commit: 75f90e96fb52f93b1dffb2b8a3a8c1e426362de4
Author: theHumanBorch <ncborch@gmail.com>
Date: 2025-07-02 09:19:08 -0500
Commit message:

 Update clonalCluster.R

1) passed labeling and filtering directly to buildNetwork in immApex
2) Add chain information for vertex if exportGraph = TRUE
Package: scRepertoire
Commit: 692521964d81c43fc8ea698f1035c1d433d66035
Author: theHumanBorch <ncborch@gmail.com>
Date: 2025-07-01 11:46:38 -0500
Commit message:

 updating combineBCR() for more adaptable calling

#424 updated to allow for selective V/J filtering, use of normalzied to raw edit distances, single or multichains. Feeds into new clonalClusters()
Package: scRepertoire
Commit: f9ac613c678bddbc5e428b60bf5e4284fc8a5940
Author: theHumanBorch <ncborch@gmail.com>
Date: 2025-07-01 08:43:46 -0500
Commit message:

 Expanded clonalCluster

#480 #495 now has v/j filtering optionality, returns adjacency matrix, graph or clusters
Package: scRepertoire
Commit: 11bd55703aac51bed22a6bce3357f17b46f0557e
Author: theHumanBorch <ncborch@gmail.com>
Date: 2025-06-30 15:41:33 -0500
Commit message:

 Update clonalCluster.R

Working on 2 chains for clonalCluster
Package: scRepertoire
Commit: 921ffd5745de10b9aead0f8c11b14524b5abd39e
Author: theHumanBorch <ncborch@gmail.com>
Date: 2025-06-30 12:47:32 -0500
Commit message:

 removing stringr and reshape-based dependencies
Package: scRepertoire
Commit: f61fc31aec731f238a1ecd749dc1a3d23664e1c0
Author: theHumanBorch <ncborch@gmail.com>
Date: 2025-06-30 11:56:43 -0500
Commit message:

 update citation information
Package: scRepertoire
Commit: c2da4030c608f112685944dd8de0e7683a0382ee
Author: theHumanBorch <ncborch@gmail.com>
Date: 2025-06-27 09:55:53 -0500
Commit message:

 proper grouping for clonalDiversity

#504 allow for both x.axis and group.by
Package: scRepertoire
Commit: 60b81e9a2b978c6d45e6eee4fec07dbaf8c579aa
Author: theHumanBorch <ncborch@gmail.com>
Date: 2025-06-26 15:23:32 -0500
Commit message:

 removing assertthat from package
Package: scRepertoire
Commit: d12126899a66e16ee2940f6ad5776af766cd90a6
Author: theHumanBorch <ncborch@gmail.com>
Date: 2025-06-26 15:18:03 -0500
Commit message:

 removing stringdist from import
Package: scRepertoire
Commit: 49b504ed0ca2004ee974828839c0e80721d9b510
Author: theHumanBorch <ncborch@gmail.com>
Date: 2025-06-26 10:24:19 -0500
Commit message:

 update loadContigs unit tests
Package: scRepertoire
Commit: 04f205e7fdf288068ff3b47cf2e4cd808c7d77c3
Author: theHumanBorch <ncborch@gmail.com>
Date: 2025-06-26 10:15:24 -0500
Commit message:

 Removing testdata
Package: scRepertoire
Commit: 8502a7842ecc0153822504974e9cc8b6360887fc
Author: theHumanBorch <ncborch@gmail.com>
Date: 2025-06-26 10:14:32 -0500
Commit message:

 remove seurat_commands.R

I don't think these were used?
Package: scRepertoire
Commit: e829cc7f5543c3b9b5f8c312dd0cdfe0cf3b2e1a
Author: theHumanBorch <ncborch@gmail.com>
Date: 2025-06-26 10:13:42 -0500
Commit message:

 updating unit tests - remove vdiffR
Package: scRepertoire
Commit: 53fede607d8c6bc81b4863d9eeb40c5e212a66d2
Author: theHumanBorch <ncborch@gmail.com>
Date: 2025-06-26 09:22:26 -0500
Commit message:

 removing mini_contig_list
Package: scRepertoire
Commit: a05a51771d1ca28512cf1e1ecff23f200721be04
Author: theHumanBorch <ncborch@gmail.com>
Date: 2025-06-26 08:11:46 -0500
Commit message:

 clonalScatter fix for combineTCR/BCR grouping
Package: scRepertoire
Commit: 3addbdf9ac429e82790c573b5ff8482960fb8e15
Author: theHumanBorch <ncborch@gmail.com>
Date: 2025-06-26 07:33:44 -0500
Commit message:

 clonalHomeostasis proper axis labeling
Package: scRepertoire
Commit: 32dc5207022facd52dcbd27a369b5054572bfed2
Author: theHumanBorch <ncborch@gmail.com>
Date: 2025-06-26 07:23:41 -0500
Commit message:

 Update clonalCompare and unit tests

Fix issue with nrow() = 0 leading not leading to error message
Package: scRepertoire
Commit: d789f170d67d9f32fca834a816433d1664312fe9
Author: theHumanBorch <ncborch@gmail.com>
Date: 2025-06-25 15:48:07 -0500
Commit message:

 Updating the utils formatting, removing dependencies
Package: scRepertoire
Commit: 296737d0df354490c940bfabe159069befc57b9e
Author: theHumanBorch <ncborch@gmail.com>
Date: 2025-06-23 10:54:40 -0500
Commit message:

 update vignettes for positionalProperty
Package: scRepertoire
Commit: 77d6f761812274658470bafcea39b6dae3ee4db4
Author: theHumanBorch <ncborch@gmail.com>
Date: 2025-06-23 10:18:48 -0500
Commit message:

 Merge branch 'dev' of https://github.com/BorchLab/scRepertoire into dev
Package: scRepertoire
Commit: 74c032f37739f5668f4d319c7be89f3c0e0aa8ce
Author: theHumanBorch <ncborch@gmail.com>
Date: 2025-06-23 10:18:47 -0500
Commit message:

 update positionalProperty
Package: scRepertoire
Commit: d86cc67495273e2d068d78a61717d33af6783ef1
Author: theHumanBorch <ncborch@gmail.com>
Date: 2025-06-19 06:57:27 -0500
Commit message:

 rm export clones unit test data
Package: scRepertoire
Commit: 3a6501eb35ea23385ec92afddff67a36e959e728
Author: theHumanBorch <ncborch@gmail.com>
Date: 2025-06-18 08:09:20 -0500
Commit message:

 remove percent gene testthat
Package: scRepertoire
Commit: b30fe929d6edc1d346e3ba7026a70a04766e3b40
Author: theHumanBorch <ncborch@gmail.com>
Date: 2025-06-18 08:07:51 -0500
Commit message:

 updating percentGenes
Package: scRepertoire
Commit: eca12ce65899129eee6917d3805bbe97ffd7d93b
Author: theHumanBorch <ncborch@gmail.com>
Date: 2025-06-17 07:56:12 -0500
Commit message:

 update percentKmer
Package: scRepertoire
Commit: 03ae5f9e85840feba3bd883be6764712214d945e
Author: theHumanBorch <ncborch@gmail.com>
Date: 2025-06-16 10:44:44 -0500
Commit message:

 updating vignettes and documentation
Package: scRepertoire
Commit: 3d5a2f472d154b918dcd6719bdbae9e7874d7669
Author: theHumanBorch <ncborch@gmail.com>
Date: 2025-06-16 10:44:16 -0500
Commit message:

 polish export clones
Package: scRepertoire
Commit: f6fd43977e0fdd53eadce2c903cf77285affe477
Author: theHumanBorch <ncborch@gmail.com>
Date: 2025-06-16 10:43:58 -0500
Commit message:

 updating clonalDiversity
Package: scRepertoire
Commit: 4a8d0ce36dc2b2fe78a6ec1175ede96aa7be9eb0
Author: theHumanBorch <ncborch@gmail.com>
Date: 2025-06-15 15:00:51 -0500
Commit message:

 Add support for immunarch in exportClones
Package: scRepertoire
Commit: 4c5d6a3db773093adffc696af6ac615a405e1b8e
Author: theHumanBorch <ncborch@gmail.com>
Date: 2025-06-15 14:57:37 -0500
Commit message:

 adding immunarch vignette
Package: scRepertoire
Commit: 4380ad8373e9fea4279154e89a06c8ac0cbd8e9b
Author: theHumanBorch <ncborch@gmail.com>
Date: 2025-06-13 10:44:56 -0500
Commit message:

 update documentation
Package: scRepertoire
Commit: 9fc98cfd950872f183050f31cbe015814c1bf060
Author: theHumanBorch <ncborch@gmail.com>
Date: 2025-06-13 10:44:46 -0500
Commit message:

 reafctored positionalEntropy

Goal is base R + immApex usage
Package: scRepertoire
Commit: 6b443c55a55de889f8cc89494ba0bd09e7c9ec95
Author: theHumanBorch <ncborch@gmail.com>
Date: 2025-06-13 10:44:15 -0500
Commit message:

 refactor percentAA

Goal is base R + immApex usage
Package: scRepertoire
Commit: a5f9a24528af8b5ad25d3c876053f9c91caeb884
Author: theHumanBorch <ncborch@gmail.com>
Date: 2025-06-13 08:35:36 -0500
Commit message:

 Update tcrpheno.Rmd

working now
Package: scRepertoire
Commit: d55bd9c01cab15f37fa3281ba426819f749f8e41
Author: theHumanBorch <ncborch@gmail.com>
Date: 2025-06-13 08:35:25 -0500
Commit message:

 Update exportClones.R

refining tcrpheno export
Package: scRepertoire
Commit: 30f4c56a24ea0811eea3d4ef4da3c468ab0c4cf9
Author: theHumanBorch <ncborch@gmail.com>
Date: 2025-06-12 08:57:40 -0500
Commit message:

 Update annotateInvariant.R

get data frames and not 1 column
Package: scRepertoire
Commit: d444c27677b34fc207e75375e7b04b467b1d7453
Author: theHumanBorch <ncborch@gmail.com>
Date: 2025-06-12 08:56:57 -0500
Commit message:

 Cleaning other articles
Package: scRepertoire
Commit: ced9d302450e595d8f7e61fbfad2ec858fdaf255
Author: theHumanBorch <ncborch@gmail.com>
Date: 2025-06-12 08:56:37 -0500
Commit message:

 Add support for TCRpheno
Package: scRepertoire
Commit: 334b18505d511323cdc09e450c30a027fe288a30
Author: theHumanBorch <ncborch@gmail.com>
Date: 2025-06-11 14:56:21 -0500
Commit message:

 Adding dandelionR vignette to site

@zktuong - Adapting the old scRep vignette to use on the site. Let me know if you have any suggestions
Package: scRepertoire
Commit: 645f3cc0899610902226d4f98d87fc12850583ac
Author: theHumanBorch <ncborch@gmail.com>
Date: 2025-06-11 10:17:24 -0500
Commit message:

 Update immApex.Rmd
Package: scRepertoire
Commit: 77ed927cb3b62a5622d5222b5b004664640dedfe
Author: theHumanBorch <ncborch@gmail.com>
Date: 2025-05-28 09:41:47 -0500
Commit message:

 Merge pull request #502 from mihem/fix_annotateInvariant

Fix annotate invariant
Package: scRepertoire
Commit: 536b081f34cbc535b4415ca50d335de575c2a25f
Author: theHumanBorch <ncborch@gmail.com>
Date: 2025-05-28 09:39:19 -0500
Commit message:

 Update unit tests and author list
Package: scRepertoire
Commit: 2566f512ba35f60e49e6ced4c4f4818d13018adb
Author: theHumanBorch <ncborch@gmail.com>
Date: 2025-05-28 05:29:09 -0500
Commit message:

 Merge pull request #498 from zjsyj/quickfix-clonalQuant

quick fix clonalQuant, respect order.by parameter
Package: scRepertoire
Commit: 3e0ac6466cdc9c470635fa50ddd593e4881ef506
Author: theHumanBorch <ncborch@gmail.com>
Date: 2025-05-28 05:28:55 -0500
Commit message:

 Merge pull request #500 from mihem/add_alpha_size_vis

Add alpha size vis
Package: scRepertoire
Commit: d6506eb8a25f6c0e9d4db6fb1e0a1daa24743f1a
Author: mischko <mhem@mailbox.org>
Date: 2025-05-28 10:38:52 +0200
Commit message:

 Revert "change scores"

This reverts commit ac4511566b5e6e9340c1c32ea7cce39d44d6386a.
Package: scRepertoire
Commit: c9775401bfd308acf37cff537a1b956a50a16f91
Author: mischko <mhem@mailbox.org>
Date: 2025-05-28 10:38:01 +0200
Commit message:

 Revert "updated docs"

This reverts commit 978723026f5ab3490a13eb5ef8a4e28bf4382414.
Package: scRepertoire
Commit: 978723026f5ab3490a13eb5ef8a4e28bf4382414
Author: mischko <mhem@mailbox.org>
Date: 2025-05-28 00:37:18 +0200
Commit message:

 updated docs
Package: scRepertoire
Commit: ac4511566b5e6e9340c1c32ea7cce39d44d6386a
Author: mischko <mhem@mailbox.org>
Date: 2025-05-28 00:20:31 +0200
Commit message:

 change scores

remove TRA.length and score each criterion
Package: scRepertoire
Commit: 2602848f498db63d90bddcfb621f2da51fc6743a
Author: mischko <mhem@mailbox.org>
Date: 2025-05-27 23:36:09 +0200
Commit message:

 fix bug
Package: scRepertoire
Commit: b40576bc69254fc841c8245e4a157fe4b33bc750
Author: mischko <mhem@mailbox.org>
Date: 2025-05-27 23:32:06 +0200
Commit message:

 replace %in% with grepl
Package: scRepertoire
Commit: 9705933b3582688ac24d07f96161114f7495d169
Author: theHumanBorch <ncborch@gmail.com>
Date: 2025-05-27 07:26:33 -0500
Commit message:

 Clarify installation on pkgdown site

#496 Clarify installation on pkgdown site
Package: scRepertoire
Commit: 22f96d12a26d846be3a1a2e0f7d9033627a972ba
Author: mischko <mhem@mailbox.org>
Date: 2025-05-26 17:22:20 +0200
Commit message:

 update docs for clonalOverlay
Package: scRepertoire
Commit: 087fa3dd2d0baa260f8f386d26184c9b49e8a95e
Author: mischko <mhem@mailbox.org>
Date: 2025-05-26 17:10:37 +0200
Commit message:

 add pt.size and pt.alpha in clonalOverlay
Package: scRepertoire
Commit: eb0c0d1bf3a75179013a4ec076a0b685b8b0ee49
Author: theHumanBorch <ncborch@gmail.com>
Date: 2025-05-22 10:42:14 -0500
Commit message:

 adding table for diversity metrics
Package: scRepertoire
Commit: e8a6d80078fc9aa2013a32d15b7faabdd97130d2
Author: theHumanBorch <ncborch@gmail.com>
Date: 2025-05-22 09:41:07 -0500
Commit message:

 Merge branch 'dev' of https://github.com/BorchLab/scRepertoire into dev
Package: scRepertoire
Commit: 1323d85ea216612877b39689727190eeb2119640
Author: theHumanBorch <ncborch@gmail.com>
Date: 2025-05-22 09:41:06 -0500
Commit message:

 update loadcontigs
Package: scRepertoire
Commit: 6813c952da1f3bdd28745841f13feb1f3e67d36d
Author: theHumanBorch <ncborch@gmail.com>
Date: 2025-05-20 17:09:07 -0500
Commit message:

 Update Running_Escape.Rmd
Package: scRepertoire
Commit: 397ab30c88cf24b3e499e501baa3302e91d72e64
Author: jiasheng <astrognss@gmail.com>
Date: 2025-05-16 20:41:09 -0400
Commit message:

 quick fix clonalQuant, respect order.by parameter
Package: scRepertoire
Commit: abe7e160e5f2b9248c58bd442066b40ed5ccc00a
Author: theHumanBorch <ncborch@gmail.com>
Date: 2025-03-29 09:49:05 -0500
Commit message:

 Adding details to function
Package: scRepertoire
Commit: 6cf3eb47cb3db1309a3f653c622c1009c8ff2cd6
Author: theHumanBorch <ncborch@gmail.com>
Date: 2025-03-28 05:12:26 -0500
Commit message:

 update load contigs auto detect
Package: scRepertoire
Commit: 97ac123daf3b467bae8987d2d88c3f67348cc3b7
Author: theHumanBorch <ncborch@gmail.com>
Date: 2025-03-21 07:28:19 -0500
Commit message:

 update loadContigs() function
Package: scRepertoire
Commit: 78d05708039e34c656442d1893b65194f95b0e53
Author: theHumanBorch <ncborch@gmail.com>
Date: 2025-03-21 07:03:19 -0500
Commit message:

 Merge pull request #486 from BorchLab/master

rebasing dev branch
Package: MSstatsBioNet
Commit: 0fde597a351f7ce0f420d5365a04c247da1237de
Author: tonywu1999 <wu.anthon@northeastern.edu>
Date: 2025-07-25 12:20:32 -0400
Commit message:

 remove collapsing by interaction type (#51)
Package: rrvgo
Commit: a24df68fd9b929113c63762d3b23029a755bedbd
Author: ssayols <ssayols@almirall.com>
Date: 2025-07-25 17:29:23 +0200
Commit message:

 add pkgdown documentation
Package: rrvgo
Commit: 6d8ebc0b312aef1b9b0a22090ec38a0b0f67977f
Author: ssayols <ssayols@almirall.com>
Date: 2025-07-25 17:22:27 +0200
Commit message:

 fix typo in manpage
Package: StatescopeR
Commit: ba9f29dc135780b66d7922edbc0d4b88943b4cc8
Author: MSteketee <m.f.b.steketee@amsterdamumc.nl>
Date: 2025-07-25 17:18:09 +0200
Commit message:

 Created intermediate Statescope objects for use in examples
Package: rrvgo
Commit: 0241fcfad590173fa1d6c94698683ae67d7ab282
Author: ssayols <ssayols@almirall.com>
Date: 2025-07-25 17:00:55 +0200
Commit message:

 Add new parameter to keep in the output of calculateSimMatrix() terms without IC
Package: MSstatsBioNet
Commit: d465bd0c62b2e99083776558fd9982a89de688c6
Author: tonywu1999 <wu.anthon@northeastern.edu>
Date: 2025-07-25 10:29:04 -0400
Commit message:

 adjust error handling for zero edges and handling of issue column (#50)
Package: spatialFDA
Commit: 5e8d7cecf649661ee8407cec960ca67d427dff26
Author: mjemons <martin.emons@gmail.com>
Date: 2025-07-25 15:18:13 +0200
Commit message:

 changed default fGAM to gaussian with log link
Package: rrvgo
Commit: 74efd4e986fe881c92c7b59993eeb488323e081e
Author: ssayols <ssayols@almirall.com>
Date: 2025-07-25 16:02:26 +0200
Commit message:

 version bump
Package: rrvgo
Commit: a2bc04744f83374504d33fe5d753db5d8a358af2
Author: ssayols <ssayols@almirall.com>
Date: 2025-07-25 16:01:16 +0200
Commit message:

 Fixed warning calling `calculateSimMatrix()` with default value for the `semdata` parameter
Package: iSEEfier
Commit: 26d9e8da20a450a6a248e741da3565744967f495
Author: Najla Abassi <abassi.nejla96@gmail.com>
Date: 2025-07-25 15:21:57 +0200
Commit message:

 Updating iSEEfier version-Merge remote-tracking branch 'upstream/devel' into devel
Package: iSEEfier
Commit: dd9d77f6cddbade447d863e59d45be18086777d6
Author: Najla Abassi <abassi.nejla96@gmail.com>
Date: 2025-07-23 12:21:49 +0200
Commit message:

 adjusting logo position
Package: iSEEfier
Commit: fed96358fb7c89ad99f4425da336783b5e4c7006
Author: Najla Abassi <112277365+NajlaAbassi@users.noreply.github.com>
Date: 2025-07-23 12:06:37 +0200
Commit message:

 Merge pull request #11 from NajlaAbassi/iSEEfier_update

adding iSEEfier logo
Package: iSEEfier
Commit: 84df40d8187cfb34f6f0539567d15b7180e8d2a7
Author: Najla Abassi <abassi.nejla96@gmail.com>
Date: 2025-07-23 12:04:25 +0200
Commit message:

 adding iSEEfier logo
Package: iSEEfier
Commit: f099184073bd7f8a971dff4a84adea328456817b
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2025-03-07 14:49:45 +0100
Commit message:

 updating GHA to a more recent cache version
Package: iSEEfier
Commit: 95ff690c0e01fca33c12bf1287683687f83d49f1
Author: Najla Abassi <abassi.nejla96@gmail.com>
Date: 2025-02-08 22:33:08 +0100
Commit message:

 updating vignette
Package: LOBSTAHS
Commit: 020f76bde33b8b9bcf6175890c7cb89c9f7d9ff3
Author: Henry Holm <32178231+hholm@users.noreply.github.com>
Date: 2025-07-25 08:40:43 -0400
Commit message:

 Pushing version number 1.35.0 --> 1.35.1
Package: StatescopeR
Commit: 6add0ce158adc8b135a7c42747ce9daa7d05bd15
Author: MSteketee <m.f.b.steketee@amsterdamumc.nl>
Date: 2025-07-25 14:39:18 +0200
Commit message:

 Decreased number of genes for vignette/examples to speed up building and checking
Package: AnnotationHub
Commit: 11758ef932695f2b2294f0a81376b64ef7065f87
Author: lshep <lori.shepherd@roswellpark.org>
Date: 2025-07-25 08:12:30 -0400
Commit message:

 Merge pull request #63 from Bioconductor/selectSome

use BiocBaseUtils::selectSome
Package: AnnotationHub
Commit: f3bfe3e99b22f3eb9caf3a428f5022e039580e5d
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-07-17 15:28:50 -0400
Commit message:

 use BiocBaseUtils::selectSome
Package: SmartPhos
Commit: b8ecd16efd5a69e9cfbb95ec6ac13f7ed59cbc13
Author: shubh2565 <catchshubham2565@gmail.com>
Date: 2025-07-25 12:36:25 +0200
Commit message:

 modify news file
Package: SmartPhos
Commit: 2ef1721f5ca6b9226c1874b55cb8c33935da1212
Author: shubh2565 <catchshubham2565@gmail.com>
Date: 2025-07-25 11:46:56 +0200
Commit message:

 add NEWS file
Package: DESeq2
Commit: 6a2a0ee60fa29c9152b997b6cbb3f3aeb0f32e7b
Author: mikelove <michaelisaiahlove@gmail.com>
Date: 2025-07-25 11:28:48 +0200
Commit message:

 glmGamPoi and parallel error instead of warning, fixes #116
Package: StatescopeR
Commit: 9abc0828cbe46dbe9461d6b34a9686c0112c2894
Author: MSteketee <m.f.b.steketee@amsterdamumc.nl>
Date: 2025-07-25 10:57:37 +0200
Commit message:

 Merge branch 'devel' of git.bioconductor.org:packages/StatescopeR into devel
Package: StatescopeR
Commit: 2b3889bfa4a22847e90d91fb569b4ee471cffc40
Author: MSteketee <m.f.b.steketee@amsterdamumc.nl>
Date: 2025-07-25 10:51:11 +0200
Commit message:

 Added option to choose n_hvg_genes for quicker examples/vignette
Package: StatescopeR
Commit: 7fd62f29c74e95e5e55bd1ceffaccc71d9df5c23
Author: MSteketee <m.f.b.steketee@amsterdamumc.nl>
Date: 2025-07-25 10:51:11 +0200
Commit message:

 Added option to choose n_hvg_genes for quicker examples/vignette
Package: alabaster.base
Commit: d259a755a6fe0879205d5efce3d3ce75b93039ee
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2025-07-25 01:32:40 -0700
Commit message:

 Silence unnecessary warnings when hard linking fails.
Package: alabaster.base
Commit: 006d1c0af31c2decdbbfa51829e736001628f1f9
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2025-07-25 01:15:41 -0700
Commit message:

 Avoid considering '.' as absolute during path decomposition.

Also added some more tests to check for proper path absolution.
Package: scafari
Commit: 3f535854861491466cc0676e4d44a48415ce200e
Author: swind <swind@uni-muenster.de>
Date: 2025-07-25 09:14:12 +0200
Commit message:

 add globals
Package: scafari
Commit: 015e5c81f7d313338535d003237a430746c9f1a7
Author: swind <swind@uni-muenster.de>
Date: 2025-07-25 09:13:40 +0200
Commit message:

 raise version
Package: scafari
Commit: 5dfe2bfa3b9430210f1cea9df224de14fea55c30
Author: swind <swind@uni-muenster.de>
Date: 2025-07-25 09:12:30 +0200
Commit message:

 add global variables
Package: scafari
Commit: 3f8b37232d5cded9864e1e470e1d361f49d2512e
Author: swind <swind@uni-muenster.de>
Date: 2025-07-25 08:54:08 +0200
Commit message:

 update news
Package: scafari
Commit: 64c94f953b0e9e2d780a26dfe46cc0e8172a3549
Author: swind <swind@uni-muenster.de>
Date: 2025-07-25 08:53:16 +0200
Commit message:

 raise version
Package: scafari
Commit: 7564997e5c440ba5d7062b2e8cc0a87578879d8f
Author: swind <swind@uni-muenster.de>
Date: 2025-07-25 08:52:03 +0200
Commit message:

 set doctype to package
Package: scafari
Commit: 63cef78b269e91d6adf6cecf31f357e03a768cd0
Author: swind <swind@uni-muenster.de>
Date: 2025-07-24 18:13:52 +0200
Commit message:

 raise version, rm double mentioning
Package: scafari
Commit: 751af424f0f47906a3c4a10bb0463a81a506dcfb
Author: swind <swind@uni-muenster.de>
Date: 2025-07-24 18:13:13 +0200
Commit message:

 rm space
Package: scafari
Commit: 02c81fd9bd12353503894625706736a380b62274
Author: swind <swind@uni-muenster.de>
Date: 2025-07-24 18:12:24 +0200
Commit message:

 rm uneccesary line
Package: scafari
Commit: 6ba91b467f96872e0dff3755182389f46f125c63
Author: swind <swind@uni-muenster.de>
Date: 2025-07-24 18:12:00 +0200
Commit message:

 adjust tests to checksce fct
Package: scafari
Commit: 7d30e9bb0fe0ba8efcda374255fd9b768a972c89
Author: swind <swind@uni-muenster.de>
Date: 2025-07-24 18:11:37 +0200
Commit message:

 add checksce fct
Package: scafari
Commit: f2dd4fd63fdd286df599bb97ba9d927c9eb7a186
Author: swind <swind@uni-muenster.de>
Date: 2025-07-24 18:11:22 +0200
Commit message:

 make it shorter
Package: scafari
Commit: 02b5743edac8f496405d9bd89e7db9c805aa1da8
Author: swind <swind@uni-muenster.de>
Date: 2025-07-24 18:09:59 +0200
Commit message:

 reformatting
Package: scafari
Commit: 14825959f4895fad28356b828ade446fef657cf7
Author: swind <swind@uni-muenster.de>
Date: 2025-07-24 18:09:44 +0200
Commit message:

 rm double mentioning
Package: scafari
Commit: 18876b69ca3a35d6985e29a77150ff960ddf6aaa
Author: swind <swind@uni-muenster.de>
Date: 2025-07-24 14:37:43 +0200
Commit message:

 add scafari help
Package: scafari
Commit: eef75d1bc4feacfeadcab1f8dd9a98833939961d
Author: swind <swind@uni-muenster.de>
Date: 2025-07-24 14:11:33 +0200
Commit message:

 add missing fcts
Package: scafari
Commit: 438b07e8fb694f48f4f807a9949325367161161c
Author: swind <swind@uni-muenster.de>
Date: 2025-07-24 14:11:08 +0200
Commit message:

 delete license -> look package docu
Package: scafari
Commit: 9b20a0a11b972a33da254863eb84ad82c4385e03
Author: swind <swind@uni-muenster.de>
Date: 2025-07-24 14:10:45 +0200
Commit message:

 delete old package docu
Package: scafari
Commit: 15aaa498d9a4845b3eeda27060da1dd9c08fb257
Author: swind <swind@uni-muenster.de>
Date: 2025-07-24 14:10:21 +0200
Commit message:

 add package docu
Package: scafari
Commit: 15d1dfa7cc2ffcebda5f17b43999ee97a67ae77b
Author: swind <swind@uni-muenster.de>
Date: 2025-07-24 12:42:54 +0200
Commit message:

 add chunk labels
Package: scafari
Commit: 690c0b1d02169637a63d2c6593f603d649a7f0dd
Author: swind <swind@uni-muenster.de>
Date: 2025-07-24 10:47:19 +0200
Commit message:

 fix typo
Package: MSstatsBioNet
Commit: 4fdc7172371a977b56ed9b67bf2770f53973aac9
Author: Tony Wu <wu.anthon@northeastern.edu>
Date: 2025-07-24 22:03:26 -0400
Commit message:

 modify logfc_cutoff validation to enable logfc cutoff of 0
Package: MetaScope
Commit: b07091086ec53f30d4338c76a1ce1dd57b38fc02
Author: Aubrey Odom <aodom@bu.edu>
Date: 2025-07-24 20:19:43 -0400
Commit message:

 Update sparse matrix max-finding in metascope_id to be more efficient
Package: MetaScope
Commit: 83984bec7ebf7de08912cd7d17b0312a42f18b7e
Author: Aubrey Odom <aodom@bu.edu>
Date: 2025-07-24 12:51:01 -0400
Commit message:

 Updated metascope id exported value
Package: netZooR
Commit: b225a26899c27755c03e4df98aaeca4a4c730b6c
Author: marouenbg <marouen.b.guebila@gmail.com>
Date: 2025-07-24 19:50:02 -0400
Commit message:

 update maintainer
Package: netZooR
Commit: 9edac655c1e47ab20ed89b04d043721b7b06247b
Author: marouenbg <marouen.b.guebila@gmail.com>
Date: 2025-07-24 19:47:19 -0400
Commit message:

 update maintainer
Package: netZooR
Commit: 9e120982e31c266712912bf069f11ffd961565cc
Author: marouenbg <marouen.b.guebila@gmail.com>
Date: 2025-07-24 19:42:07 -0400
Commit message:

 update maintainer
Package: netZooR
Commit: d5a943076e3645a8b4334062f718cdcd354a1034
Author: marouenbg <marouen.b.guebila@gmail.com>
Date: 2025-07-24 19:37:24 -0400
Commit message:

 update maintainer
Package: netZooR
Commit: 2578ee39f41c66e2ccddfe67578f9814c8ca4e2a
Author: marouenbg <marouen.b.guebila@gmail.com>
Date: 2025-07-24 19:34:41 -0400
Commit message:

 Merge remote-tracking branch 'upstream/devel' into devel
Package: netZooR
Commit: 11ca8be24c1fa5188329992c796a8ef1583828fc
Author: Marouen <marouenbg@users.noreply.github.com>
Date: 2025-06-09 22:20:23 -0400
Commit message:

 Otter patch 2 (#347)

* update sambar

* update OTTER

* Update main.yml

* Update main.yml
Package: netZooR
Commit: 41e5256c0d55139a795b95290630813ddb88bb54
Author: marouenbg <marouen.b.guebila@gmail.com>
Date: 2025-06-09 16:16:32 -0400
Commit message:

 Merge remote-tracking branch 'upstream/devel' into devel
Package: netZooR
Commit: 9335a7bc74a458d942e31cac58767707c6fa442f
Author: Tara Eicher <taraeicher@yahoo.com>
Date: 2025-02-11 10:39:22 -0500
Commit message:

 Converted factor to character in network for plotting (#340)
Package: netZooR
Commit: 3508799b4babc25b035642932e04cc806889bc60
Author: marouenbg <marouen.b.guebila@gmail.com>
Date: 2024-12-31 10:42:03 -0500
Commit message:

 update sambar
Package: srnadiff
Commit: b23c87f601e36853b1441201994f3b0d795baebf
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2025-07-24 16:40:35 -0700
Commit message:

 srnadiff 1.29.1: Replace GenomeInfoDb with Seqinfo
Package: soGGi
Commit: 827dbf0c7f6957c4da0574b537ff1edc3dc68ae1
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2025-07-24 16:39:30 -0700
Commit message:

 soGGi 1.41.1: Replace GenomeInfoDb with Seqinfo
Package: scanMiR
Commit: e8349657724c291c3e4ebcf0adab9062c3aaca27
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2025-07-24 16:38:07 -0700
Commit message:

 scanMiR 1.15.1: Replace GenomeInfoDb with Seqinfo
Package: rnaEditr
Commit: 50b92cd54f611a3d56decf7dc9f6741737a2be5d
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2025-07-24 16:37:08 -0700
Commit message:

 rnaEditr 1.19.1: Replace GenomeInfoDb with Seqinfo
Package: rigvf
Commit: 865002e39b4b50b97818cd8b8cf50ff5eb6cd9f4
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2025-07-24 16:34:46 -0700
Commit message:

 rigvf 1.1.3: Replace GenomeInfoDb with Seqinfo
Package: rCGH
Commit: e2612d3e15963edeb89a87c2b16beadf15a18536
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2025-07-24 16:33:28 -0700
Commit message:

 rCGH 1.39.1: Replace GenomeInfoDb with Seqinfo
Package: r3Cseq
Commit: 87fafb1ae9ad359ea44ea1371deb21c97b6202bc
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2025-07-24 16:32:26 -0700
Commit message:

 r3Cseq 1.55.1: Replace GenomeInfoDb with Seqinfo
Package: podkat
Commit: 27b54a9e65111f9e3feb06de274635e3e508fd92
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2025-07-24 16:31:29 -0700
Commit message:

 podkat 1.41.1: Replace GenomeInfoDb with Seqinfo
Package: periodicDNA
Commit: 61bc1bbd15928c1532ce15435bf0f5f10a9f3f79
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2025-07-24 16:30:32 -0700
Commit message:

 periodicDNA 1.19.1: Replace GenomeInfoDb with Seqinfo
Package: msgbsR
Commit: d37534a289e2241f275c603d69a349f8bd9cc11b
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2025-07-24 16:29:09 -0700
Commit message:

 msgbsR 1.33.1: Replace GenomeInfoDb with Seqinfo
Package: mosaics
Commit: eb4f56d30dbe18b360560cd8ac1ed36219c5bd73
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2025-07-24 16:28:20 -0700
Commit message:

 mosaics 2.47.1: Replace GenomeInfoDb with Seqinfo
Package: MetabolomicsPipeline
Commit: 402b6cc54ed44c4951231e36c9a26a49fb739188
Author: joelparkeruofa <joelparker@arizona.edu>
Date: 2025-07-24 16:27:46 -0700
Commit message:

 removing files which are not needed
Package: MetabolomicsPipeline
Commit: 2d2465e5ef31296d8f973c46ccee537a94432b3d
Author: joelparkeruofa <joelparker@arizona.edu>
Date: 2025-07-24 16:25:49 -0700
Commit message:

 adding subWithinSuperpathResults
Package: MetabolomicsPipeline
Commit: 69bc491a02f3144c3180a5aa8bb1cdf640bead1d
Author: joelparkeruofa <joelparker@arizona.edu>
Date: 2025-07-24 16:25:04 -0700
Commit message:

 updating naming covention of subWithinSuperpathResults
Package: MetabolomicsPipeline
Commit: f1090769281958daab399c937076e9cfc633b1dd
Author: joelparkeruofa <joelparker@arizona.edu>
Date: 2025-07-24 16:23:46 -0700
Commit message:

 adding subWithinSuperResults
Package: MetabolomicsPipeline
Commit: 72be79a7d95f5de383d4cbce461c66faa6b2da4e
Author: joelparkeruofa <joelparker@arizona.edu>
Date: 2025-07-24 16:22:39 -0700
Commit message:

 updating the options for pvalue adjustments
Package: methylSig
Commit: 908b58913742fda78d970336f30d13f46c1432fd
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2025-07-24 16:27:01 -0700
Commit message:

 methylSig 1.21.1: Replace GenomeInfoDb with Seqinfo
Package: groHMM
Commit: 29bb2bc9a42779cf5282bb99d2f84780a9660ffa
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2025-07-24 16:25:12 -0700
Commit message:

 groHMM 1.43.1: Replace GenomeInfoDb with Seqinfo
Package: genomation
Commit: 9230c4440b91917fc1cb1a5bcdb232a71212cffb
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2025-07-24 16:24:03 -0700
Commit message:

 genomation 1.41.1: Replace GenomeInfoDb with Seqinfo
Package: geneAttribution
Commit: b3fd8272c9ceebce0f0064fedb8ce3b1bd8c641e
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2025-07-24 16:23:18 -0700
Commit message:

 geneAttribution 1.35.1: Replace GenomeInfoDb with Seqinfo
Package: gcapc
Commit: 6895d0f47abce7fff5630546767ba543dd1ee91b
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2025-07-24 16:21:43 -0700
Commit message:

 gcapc 1.33.1: Replace GenomeInfoDb with Seqinfo
Package: epivizrStandalone
Commit: bdfb19d037b3b1b9ae01e785e8ca92c32e13c8e1
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2025-07-24 16:20:41 -0700
Commit message:

 epivizrStandalone 1.37.1: Replace GenomeInfoDb with Seqinfo
Package: demuxSNP
Commit: f1693e202b5b3501a164f46759ebbf0f6a01e2c2
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2025-07-24 16:19:11 -0700
Commit message:

 demuxSNP 1.7.1: Replace GenomeInfoDb with Seqinfo
Package: conumee
Commit: a54093b70c0f97c1f764276c649c845239dd624c
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2025-07-24 16:14:19 -0700
Commit message:

 conumee 1.43.1: Replace GenomeInfoDb with Seqinfo
Package: consensusSeekeR
Commit: 56b21cfc95651679d4dd6cb7563d63d581ba0a06
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2025-07-24 16:13:25 -0700
Commit message:

 consensusSeekeR 1.37.1: Replace GenomeInfoDb with Seqinfo
Package: SplicingGraphs
Commit: c0064771d03a2e3ffd882f6bcd7106712c902117
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2025-07-24 16:12:12 -0700
Commit message:

 SplicingGraphs 1.49.1: Replace GenomeInfoDb with Seqinfo
Package: SparseSignatures
Commit: 4b9c2c5b394c20a1d1ced40bcb6e7072a49077d6
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2025-07-24 16:10:53 -0700
Commit message:

 SparseSignatures 2.19.1: Replace GenomeInfoDb with Seqinfo
Package: ShortRead
Commit: d2f69b822facfab578029f21838a34488f52ac2e
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2025-07-24 16:09:36 -0700
Commit message:

 ShortRead 1.67.1: Replace GenomeInfoDb with Seqinfo
Package: SPLINTER
Commit: 32067e4d1015cb4fb09f956a9d279043d84fb8b5
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2025-07-24 16:08:16 -0700
Commit message:

 SPLINTER 1.35.1: Replace GenomeInfoDb with Seqinfo
Package: Repitools
Commit: 7fae43e7e67aff0a0c125f116e9e70dbd173b831
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2025-07-24 16:06:50 -0700
Commit message:

 Repitools 1.55.1: Replace GenomeInfoDb with Seqinfo
Package: RTCGAToolbox
Commit: 979497cc2a3357d4386ba2ac229e85c438eafa82
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2025-07-24 16:05:50 -0700
Commit message:

 RTCGAToolbox 2.39.1: Replace GenomeInfoDb with Seqinfo
Package: RESOLVE
Commit: 1c7856908ab6b2d9e1c37e8bcb279912c505da4e
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2025-07-24 16:04:31 -0700
Commit message:

 RESOLVE 1.11.1: Replace GenomeInfoDb with Seqinfo
Package: OMICsPCA
Commit: a1ad83ba9040638133005beae2869015132ea8f1
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2025-07-24 16:03:31 -0700
Commit message:

 OMICsPCA 1.27.1: Replace GenomeInfoDb with Seqinfo
Package: MinimumDistance
Commit: 1585ce6fb4f44d74a32687f75f110ed45b916296
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2025-07-24 16:02:19 -0700
Commit message:

 MinimumDistance 1.53.1: Replace GenomeInfoDb with Seqinfo
Package: HTSeqGenie
Commit: 87943f46ed29301c9926c79640467cdf29a080fd
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2025-07-24 15:59:43 -0700
Commit message:

 HTSeqGenie 4.39.1: Replace GenomeInfoDb with Seqinfo
Package: GenomicInteractionNodes
Commit: be6bbd0f6cfe56cb8191679986db1f09f82d0d16
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2025-07-24 15:58:06 -0700
Commit message:

 GenomicInteractionNodes 1.13.1: Replace GenomeInfoDb with Seqinfo
Package: geomeTriD
Commit: 832ae3ff6e51e26de038f1bc308509eab7894cfa
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2025-07-22 22:45:10 -0700
Commit message:

 geomeTriD 1.3.16: Import Seqinfo instead of GenomeInfoDb
Package: dmGsea
Commit: 64b0934d5538acb2fec4bbb18a86b965e2830181
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2025-07-24 15:42:59 -0700
Commit message:

 dmGsea 0.99.9: Replace GenomeInfoDb with Seqinfo

NOTE TO THE MAINTAINER OF THE dmGsea PACKAGE: Your package doesn't
make any use of GenomeInfoDb so please do NOT import it.
Package: EpiMix
Commit: f378cd31c0b57a71365edcfea9d0e65131335ea2
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2025-07-24 15:29:54 -0700
Commit message:

 EpiMix 1.11.1: Replace GenomeInfoDb with Seqinfo
Package: CSAR
Commit: 6b5b524249f8a3adb40d80ce8f47bc3f31504502
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2025-07-24 15:27:20 -0700
Commit message:

 CSAR 1.61.1: Replace GenomeInfoDb with Seqinfo
Package: CINdex
Commit: c04e6515556bbdcffe4adb92465c876112b5b227
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2025-07-24 15:24:54 -0700
Commit message:

 CINdex 1.37.2: Replace GenomeInfoDb with Seqinfo
Package: BiSeq
Commit: 3b6b7d234a76b7b72a45847a69c78a0fed07f2b9
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2025-07-24 15:21:35 -0700
Commit message:

 BiSeq 1.49.1: Replace GenomeInfoDb with Seqinfo
Package: BasicSTARRseq
Commit: 5dfb043264cc45df0ef47e06aca0a906ad0c23a1
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2025-07-24 15:19:23 -0700
Commit message:

 BasicSTARRseq 1.37.1: Replace GenomeInfoDb with Seqinfo
Package: MSstatsBioNet
Commit: f49147002087ce7df24e958195e4647346feb627
Author: tonywu1999 <wu.anthon@northeastern.edu>
Date: 2025-07-24 18:14:05 -0400
Commit message:

 add logfc filter and filter exempt proteins filter (#49)
Package: microbiome
Commit: 7c4e0e863627816ed6c30523969c7826f2357166
Author: antagomir <leo.lahti@iki.fi>
Date: 2025-07-25 00:36:09 +0300
Commit message:

 test fix
Package: Rsubread
Commit: a466eadceed34d9c25f84bb2463561179ed6299a
Author: Yang Liao (Monash University) <yliao@m3v107.massive.org.au>
Date: 2025-07-25 06:59:47 +1000
Commit message:

 Added exon counting.
Package: SmartPhos
Commit: cbf70bd374cd4536972d04fbb6e886558d1fcb39
Author: shubh2565 <catchshubham2565@gmail.com>
Date: 2025-07-24 19:09:24 +0200
Commit message:

 minor bug fix
Package: miaDash
Commit: bc94910c6a91d4581ae0921359679db09fe63983
Author: Giulio Benedetti <giuliobene2000@gmail.com>
Date: 2025-07-24 17:52:37 +0300
Commit message:

 Merge pull request #24 from microbiome/qc_tab

Introduce tab for Quality Control
Package: miaDash
Commit: 99c10a264bd4ab5fbec090b71fbf6bb14ba87649
Author: Giulio Benedetti <giuliobene2000@gmail.com>
Date: 2025-07-24 17:42:17 +0300
Commit message:

 Introduce tab for Quality Control
Package: SmartPhos
Commit: d3188b41cd013dd6658bcd07849122b75fc684b4
Author: shubh2565 <catchshubham2565@gmail.com>
Date: 2025-07-24 18:32:28 +0200
Commit message:

 bug fix in enrichDifferential function
Package: SanityR
Commit: 30898e58c276c2433b20dfb55b4a2d8539ea8575
Author: Teo Sakel <teo@intelligentbiodata.com>
Date: 2025-07-24 17:57:50 +0200
Commit message:

 Bump pre-release version
Package: SanityR
Commit: 5dd084b86ec044821302ea7916c208727cfa598c
Author: teo <TeoSakel@users.noreply.github.com>
Date: 2025-07-24 17:50:58 +0200
Commit message:

 Improve test coverage (#5)

* Expand test coverage

* Minor fixes and tests to handle edge cases.

---------

Co-authored-by: Teo Sakel <teo@intelligentbiodata.com>
Package: SanityR
Commit: fa795ef7f6b840b990361166ff13062797053e68
Author: Teo Sakel <teo@intelligentbiodata.com>
Date: 2025-07-24 15:15:04 +0200
Commit message:

 Minor fix in test setup.

Ignore warnings about high entropy normalization.
Package: SanityR
Commit: 2e6f1d91448ad83eb5ed39e9f728a833e8d9511e
Author: Teo Sakel <teo@intelligentbiodata.com>
Date: 2025-07-24 15:14:11 +0200
Commit message:

 Changing coding style to address BiocCheck NOTES
Package: SanityR
Commit: 899d94cdb47e1713b6ab67a721ecca6091d01969
Author: Teo Sakel <teo@intelligentbiodata.com>
Date: 2025-07-22 13:36:52 +0200
Commit message:

 Fix typos
Package: Banksy
Commit: 098ad3f371861c10c337c7e409b79bfa7327dfe0
Author: jleechung <joseph.lee@u.nus.edu>
Date: 2025-07-24 16:48:52 +0100
Commit message:

 Support sparse matrices for PCA
Package: Banksy
Commit: 82253bc9f56083a4d1e6812a680f9b9cc56adc3e
Author: jleechung <joseph.lee@u.nus.edu>
Date: 2025-07-24 16:48:22 +0100
Commit message:

 igraph as.undirected deprecated
Package: biodbUniprot
Commit: 54ad981df5fc02e6329a6d80f780bfec4eb85faa
Author: lshep <lori.shepherd@roswellpark.org>
Date: 2025-07-24 10:48:06 -0400
Commit message:

 Deprecated
 - unresponsive
Package: biodbNcbi
Commit: ad86d6af2f1cbcb1d6b1b61018d56d03d164c232
Author: lshep <lori.shepherd@roswellpark.org>
Date: 2025-07-24 10:47:22 -0400
Commit message:

 Deprecate
 - unresponsive
Package: biodbNci
Commit: 658b5cb47c28d1dfc84f6603f495af6f1a07dd73
Author: lshep <lori.shepherd@roswellpark.org>
Date: 2025-07-24 10:46:27 -0400
Commit message:

 Deprecate

- unresponsive
Package: biodbHmdb
Commit: fa89c02cb07043a14d6c2011fb2afe049829f5c6
Author: lshep <lori.shepherd@roswellpark.org>
Date: 2025-07-24 10:45:35 -0400
Commit message:

 Deprecate
- unresponsive
Package: SARC
Commit: 111563487b652d21cfc35d94a57eb4a8a6b29e86
Author: lshep <lori.shepherd@roswellpark.org>
Date: 2025-07-24 10:08:10 -0400
Commit message:

 Deprecated

- unresponsive
Package: LinTInd
Commit: c409c9c694cf2760dfc4c7cf4578a02e1abb0e8d
Author: lshep <lori.shepherd@roswellpark.org>
Date: 2025-07-24 10:04:02 -0400
Commit message:

 Deprecated
 - unresponsive
Package: DominoEffect
Commit: 8af1ec45113a6bd4be44ead114490dee1c8f6668
Author: lshep <lori.shepherd@roswellpark.org>
Date: 2025-07-24 09:59:07 -0400
Commit message:

 Deprecated

- unresponsive
Package: CINdex
Commit: 0d2652f4711077c4d79fae091fcbe4eda395db0e
Author: lshep <lori.shepherd@roswellpark.org>
Date: 2025-07-24 09:52:05 -0400
Commit message:

 Deprecated

 - unresponsive
Package: txcutr
Commit: 1920197c9c7cf40843938320cad87041a1cf669a
Author: lshep <lori.shepherd@roswellpark.org>
Date: 2025-07-24 09:47:58 -0400
Commit message:

 Deprecated

 - unresponsive
Package: traviz
Commit: 3aa81b6aa97274b26a9638a2881c8aa577c0e32d
Author: lshep <lori.shepherd@roswellpark.org>
Date: 2025-07-24 09:45:40 -0400
Commit message:

 Deprecated
 - unresponsive
Package: rGADEM
Commit: c61c6c194f6ad2e99878de785286ac2a80dbc331
Author: lshep <lori.shepherd@roswellpark.org>
Date: 2025-07-24 09:18:37 -0400
Commit message:

 Deprecate

 - unresponsive
Package: SmartPhos
Commit: b0fed2cde0521407ea9441f5a98a06869681aab1
Author: shubh2565 <catchshubham2565@gmail.com>
Date: 2025-07-24 15:14:58 +0200
Commit message:

 update vignette
Package: oppti
Commit: ee33a14a2183587555c8d99ea18ca6e6534c534e
Author: lshep <lori.shepherd@roswellpark.org>
Date: 2025-07-24 09:13:45 -0400
Commit message:

 Deprecated

 - unresponsive
Package: hypeR
Commit: 6dfa3844c960535553f5181cca94db28921b303b
Author: lshep <lori.shepherd@roswellpark.org>
Date: 2025-07-24 09:07:27 -0400
Commit message:

 deprecated

- unresponsive
Package: gpuMagic
Commit: 7dae4045d98074971d86e81356aab0f8332f3338
Author: lshep <lori.shepherd@roswellpark.org>
Date: 2025-07-24 09:05:11 -0400
Commit message:

 Deprecate

 - user requested
Package: cisPath
Commit: fc02cd0072324e723252b06c18df98bf6b2e131f
Author: lshep <lori.shepherd@roswellpark.org>
Date: 2025-07-24 09:01:31 -0400
Commit message:

 Deprecated

- unresponsive
Package: ccmap
Commit: b597bdfa3a7d2a765895ec5619edf7902cc48f2c
Author: lshep <lori.shepherd@roswellpark.org>
Date: 2025-07-24 08:58:40 -0400
Commit message:

 Deprecate

- unresponsive

 - dependency crossmeta deprecated in 3.21
Package: TransView
Commit: b52656635ce077666c2188b8d5d6fc5959ddd3dd
Author: lshep <lori.shepherd@roswellpark.org>
Date: 2025-07-24 08:36:41 -0400
Commit message:

 Deprecated

 - unresponsive
Package: TitanCNA
Commit: eed2321f669bed90ebc750c8f1baefb6de4ab07b
Author: lshep <lori.shepherd@roswellpark.org>
Date: 2025-07-24 08:31:07 -0400
Commit message:

 Deprecated

- unresponsive
Package: CellScore
Commit: ec8b9680f85aa66087a8b7ec7709ee028f552039
Author: lshep <lori.shepherd@roswellpark.org>
Date: 2025-07-24 08:10:50 -0400
Commit message:

 Deprecated

 - unresponsive
Package: miaDash
Commit: f2d53d61bbd0b6d9f584b2d49182964eb8a43673
Author: Giulio Benedetti <giuliobene2000@gmail.com>
Date: 2025-07-24 13:51:29 +0300
Commit message:

 Merge pull request #23 from microbiome/dbb

Improve and extend importers
Package: miaDash
Commit: 60c3926a2b642f070562ae7ccba864a307b2a240
Author: Giulio Benedetti <giuliobene2000@gmail.com>
Date: 2025-07-24 13:36:16 +0300
Commit message:

 Improve and extend importers
Package: DspikeIn
Commit: 552052b0768ff6d5716713fce3180186b1d028b6
Author: mghotbi <mitra.ghotbi@gmail.com>
Date: 2025-07-24 10:41:05 +0200
Commit message:

 Fix CITATION encoding: declare UTF-8 and ensure ASCII-only content
Package: DspikeIn
Commit: faa914aba68be7f7847a4d902e94b5d556109248
Author: mghotbi <mitra.ghotbi@gmail.com>
Date: 2025-07-24 10:38:00 +0200
Commit message:

 Fix CITATION encoding: declare UTF-8 and ensure ASCII-only content
Package: DspikeIn
Commit: 8b36644fca2f0e2898a6d1135a806594e7300133
Author: mghotbi <mitra.ghotbi@gmail.com>
Date: 2025-07-24 09:25:26 +0200
Commit message:

 Bump to 0.99.16 to trigger Bioconductor build
Package: DspikeIn
Commit: 1f743b65a923dc9bf974caaca32631589d0bacdf
Author: mghotbi <mitra.ghotbi@gmail.com>
Date: 2025-07-24 09:14:19 +0200
Commit message:

 Version 0.99.15: Add CITATION, set LazyData to false, ready for Bioconductor
Package: TEQC
Commit: e5bd9e12928ea75397b56aa4bdffe4611329febb
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2025-07-23 16:34:41 -0700
Commit message:

 TEQC 4.31.1: Add S4Vectors, Seqinfo, and GenomicRanges to Imports

NOTE TO THE MAINTAINER: This package still has important issues that
need your attention:
- it still misses many imports;
- it still references RangedData objects which have been removed from
  Bioconductor 5 years ago.
See output of 'R CMD check' for the details.
Package: icetea
Commit: 94f284e3a41d1b6d1ec60bb0af400dc5808ae73b
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2025-07-23 16:14:12 -0700
Commit message:

 icetea 1.27.1: Add GenomeInfoDb to Suggests
Package: methrix
Commit: dab0a7ce95feb97223a97d04e769f83a25ebcdcd
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2025-07-23 16:08:50 -0700
Commit message:

 methrix 1.23.1: Use GenomeInfoDb::standardChromosomes() instead of standardChromosomes()
Package: trackViewer
Commit: 08abfdd42e40422d68fb91b6f1ce36e036217543
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2025-07-23 15:41:03 -0700
Commit message:

 trackViewer 1.45.2: Add Seqinfo to Imports
Package: iModMixData
Commit: bf1c88bdaa9b42086d299e2caeb4370238c0c160
Author: IsisNarvaez <isis.narvaez@upr.edu>
Date: 2025-07-23 17:32:08 -0400
Commit message:

 Remove iModMixData.Rproj from Git tracking
Package: transmogR
Commit: 8bf2d9891231bde1780fcdfa855f6056945b51d7
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2025-07-23 15:26:36 -0700
Commit message:

 transmogR 1.5.1: Import Seqinfo instead of GenomeInfoDb
Package: sitadela
Commit: adb286ba87bb95172353ada8450e8acbdea8eea9
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2025-07-23 15:20:06 -0700
Commit message:

 sitadela 1.17.1: Add Seqinfo to Imports

Also move GenomeInfoDb from Imports to Suggests.
Package: DspikeIn
Commit: 88b0f85359a20547619a8b2d69b2d24ea26da23f
Author: mghotbi <mitra.ghotbi@gmail.com>
Date: 2025-07-24 00:15:08 +0200
Commit message:

 Prepare version 0.99.15 for Bioconductor: fix LazyData, citation, vignette cleanup
Package: tadar
Commit: 94180a41c5651bc3fa8ce634293c6cd3a7abaa5e
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2025-07-23 15:12:37 -0700
Commit message:

 tadar 1.7.1: Import Seqinfo instead of GenomeInfoDb
Package: tRNAscanImport
Commit: a80cbf349a4095ba1684f49cd291720c49e7556c
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2025-07-23 15:09:32 -0700
Commit message:

 tRNAscanImport 1.29.1: Import Seqinfo instead of GenomeInfoDb
Package: strandCheckR
Commit: 5fec2b207c919ff88cb534cdefee0f091090f89d
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2025-07-23 15:07:14 -0700
Commit message:

 strandCheckR 1.27.1: Import Seqinfo instead of GenomeInfoDb
Package: spatzie
Commit: 319405d6f91b3cb1860ca60fe70e7f8eb7553904
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2025-07-23 15:03:34 -0700
Commit message:

 spatzie 1.15.1: Import Seqinfo instead of GenomeInfoDb
Package: sevenC
Commit: fe55d8917864fb8fa51b02b7afca4e3e254c7ce2
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2025-07-23 14:52:54 -0700
Commit message:

 sevenC 1.29.1: Import Seqinfo instead of GenomeInfoDb
Package: seqsetvis
Commit: c75429da225c9cce1afa1eda071e34da8febf443
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2025-07-23 14:50:06 -0700
Commit message:

 seqsetvis 1.29.1: Add Seqinfo to Imports

Also move GenomeInfoDb from Imports to Suggests.
Package: seqArchRplus
Commit: c98e60e38824cad1ee733eec7e10c061dfdea7f3
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2025-07-23 14:35:45 -0700
Commit message:

 seqArchRplus 1.9.1: Import Seqinfo instead of GenomeInfoDb
Package: segmentSeq
Commit: 86958e37c603aea186dd3f8ff180440d00b81b98
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2025-07-23 14:33:37 -0700
Commit message:

 segmentSeq 2.43.1: Import Seqinfo instead of GenomeInfoDb
Package: iModMixData
Commit: 82a7266f5983a19aa529c4afa16e1080aadfff48
Author: IsisNarvaez <isis.narvaez@upr.edu>
Date: 2025-07-23 10:57:58 -0400
Commit message:

 Add funding information, all checks, and bump version to 0.99.1
Package: ribosomeProfilingQC
Commit: 155968b589e349157acaac7a02cf5e118556a194
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2025-07-23 13:29:57 -0700
Commit message:

 ribosomeProfilingQC 1.21.2: Add Seqinfo to Imports
Package: riboSeqR
Commit: fa520188cb16533b01a54e1a807da70e71f70454
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2025-07-23 13:25:21 -0700
Commit message:

 riboSeqR 1.43.1: Add Seqinfo to Imports
Package: rfPred
Commit: 330c58d2245f3897b599c250ee469c2d98b292cf
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2025-07-23 13:22:54 -0700
Commit message:

 rfPred 1.47.1: Add Seqinfo to Imports
Package: recoup
Commit: 8a07c44b67466c220d141f336b74a6c2be8db423
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2025-07-23 13:19:41 -0700
Commit message:

 recoup 1.37.1: Add Seqinfo to Imports

Move GenomeInfoDb from Imports to Suggests.
Package: regionReport
Commit: f91143b2187585a112b42af57c24f003ab7f3404
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2025-07-23 13:04:15 -0700
Commit message:

 regionReport 1.43.1: Add Seqinfo to Imports
Package: raer
Commit: cabc5a19b83695cbd47a1ac21d76701c4deb85d4
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2025-07-23 12:52:44 -0700
Commit message:

 raer 1.7.2: Add Seqinfo to Imports
Package: GloScope
Commit: a36bf0219931f8c9f54725fd286a1f5d8a01d70d
Author: William Torous <38775272+wtorousa@users.noreply.github.com>
Date: 2025-07-23 12:08:21 -0700
Commit message:

 Fix merge conflict devel origin and upstream
Package: GloScope
Commit: 8f8ebe2613d94b8f03a10145fbe813b79be13a62
Author: William Torous <38775272+wtorousa@users.noreply.github.com>
Date: 2025-07-23 10:57:44 -0700
Commit message:

 Tested update of default number of GMM components
Package: GloScope
Commit: abab60da7056a573a1f33f2d40b5907cc41b8b16
Author: William Torous <38775272+wtorousa@users.noreply.github.com>
Date: 2025-07-23 09:48:43 -0700
Commit message:

 Sync GitHub with BioC release 3.21
Package: GloScope
Commit: a661703cd4627f327e973b0519a0f28b2a1af99d
Author: William Torous <38775272+wtorousa@users.noreply.github.com>
Date: 2024-08-02 16:47:51 -0700
Commit message:

 Remove renamed file
Package: GloScope
Commit: a029e5052811ce4617315a719e8956a6300f02fd
Author: William Torous <38775272+wtorousa@users.noreply.github.com>
Date: 2024-08-02 16:44:44 -0700
Commit message:

 Merge branch 'RELEASE_3_19' into main
Package: GloScope
Commit: 5adbc88093f8a9ffc9c2cc0fffa46819970577d2
Author: William Torous <38775272+wtorousa@users.noreply.github.com>
Date: 2024-08-02 16:34:32 -0700
Commit message:

 Version bump in release branch
Package: GloScope
Commit: c7968747f1c4f1cedf73aa1265b2a926c885611b
Author: William Torous <38775272+wtorousa@users.noreply.github.com>
Date: 2024-08-02 12:16:07 -0700
Commit message:

 bug fix: the  fn. was not properly exported
Package: GloScope
Commit: bf950903e9ac7049c3a9c408b6e8b412478664ae
Author: William Torous <38775272+wtorousa@users.noreply.github.com>
Date: 2024-06-04 09:57:28 -0400
Commit message:

 Update documentation
Package: GloScope
Commit: da355e49ab601a65443d98151d244049a731a9ce
Author: William Torous <wgwtorous@gmail.com>
Date: 2024-05-26 20:25:21 -0700
Commit message:

 Fix typo in vignette
Package: Pedixplorer
Commit: 2a9e17654cb39721042d8fd1cb3515bb21e8468f
Author: Louis Le Nézet <58640615+LouisLeNezet@users.noreply.github.com>
Date: 2025-07-23 20:59:33 +0200
Commit message:

 Fix bug alone individual in Pedigree (#33)

* Fix reading with inconsistent number of row

* Fix align_parents unchecked shiny

* Fix besthint

* Update test

* Add label_dist and label_cex

* Fix lint

* Update changelog

* Bump version

* Update max individual to plot on shiny

* Update news

* Fix parameter

* Fix test

* Remove readr usage

* Update pkgdown version

* Fix print cat usage

* Fix rd value

* Fix cat usage

* Fix error paste0 usage

* Fix value in rescale

* Fix line length

* Fix lines length

* Remove old author description

* Fix vignette

---------

Co-authored-by: Louis Le Nezet <louislenezet@gamil.com>
Package: Pedixplorer
Commit: 92517ee57b01797a7176cc210d12105a508f6138
Author: Louis Le Nézet <58640615+LouisLeNezet@users.noreply.github.com>
Date: 2025-07-15 16:46:47 +0200
Commit message:

 Improve logo (#32)

* Update logo

* Update test

* Update logo

* Update logo

---------

Co-authored-by: Louis Le Nezet <louislenezet@gamil.com>
Package: Pedixplorer
Commit: a0c210226749371de5fab5e368b50359a98a43b9
Author: Louis Le Nézet <58640615+LouisLeNezet@users.noreply.github.com>
Date: 2025-07-04 19:13:00 +0200
Commit message:

 Fix data.table import (#31)
Package: RTNsurvival
Commit: 824130f401765b0d321f3c822e1c8bc880eb97b8
Author: Mauro Castro <mauro.a.castro@gmail.com>
Date: 2025-07-23 15:55:28 -0300
Commit message:

 regular maintenance
Package: qsea
Commit: 7800f6780d7d0496c41fd1dd1c9d76336fabe477
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2025-07-23 11:53:03 -0700
Commit message:

 qsea 1.35.1: Import Seqinfo instead of GenomeInfoDb
Package: profileplyr
Commit: adab25ce348035d44ef18b7c760721a7ae37ee83
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2025-07-23 11:50:47 -0700
Commit message:

 profileplyr 1.25.1: Add Seqinfo to Imports

Also move GenomeInfoDb from Imports to Suggests.