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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: FLAMES
Commit: 53d0c2f729bd430eb791b04b883a3f509dc94615
Author: Changqing Wang <wang.ch@wehi.edu.au>
Date: 2025-04-14 00:33:16 +1000
Commit message:

 odd y version number
Package: FLAMES
Commit: ac1dafb51dc744f964618996b40448a0567c70b8
Author: youyupei <youyupei@gmail.com>
Date: 2025-04-10 17:44:29 +1000
Commit message:

 Bump version to 2.2.0 and update quantify_gene function to 1. fix one bug in UMI deduplication. 2. improved mem usage.
Package: FLAMES
Commit: bf4c4857601c880ffc00db741ffb4b062fbf35fe
Author: youyupei <youyupei@gmail.com>
Date: 2025-04-10 11:31:13 +1000
Commit message:

 Bug Fix UMI collapsing
Package: motifTestR
Commit: d2aa59ca37be7cb55b69d153ae81caeb0bd77129
Author: Stevie Ped <stephen.pederson.au@gmail.com>
Date: 2025-04-13 15:06:42 +0930
Commit message:

 Bugfix in prior counts for poisson enrichment testing
Package: MultiModalGraphics
Commit: 9b5a11ebf7953b827ed43347d8d393c5a5fbb948
Author: Malick Fall <malick.fall@gmail.com>
Date: 2025-04-12 21:02:40 -0400
Commit message:

 dataset source documentation
Package: TrIdent
Commit: bdec1afcbf13eb1a54da5a20c4aaa6dfea46accd
Author: jlmaier <jlmaier@ncsu.edu>
Date: 2025-04-11 23:27:02 -0400
Commit message:

 Update version
Package: TrIdent
Commit: e565b271da13babe4ee14c8de3284ee80d39be6c
Author: jlmaier <jlmaier@ncsu.edu>
Date: 2025-04-11 23:21:38 -0400
Commit message:

 temporarily disable unit tests
Package: RAIDS
Commit: f9c7db5deb437e8f6ac3ed2a21543b0e19b984af
Author: belleau <belleau@belleauMBP.home>
Date: 2025-04-11 17:14:42 -0400
Commit message:

 Update to version 1.5.1
Package: atena
Commit: 97fbc1394b3e2b558a764efc2a0bfc384e9e8faa
Author: Robert Castelo <robert.castelo@upf.edu>
Date: 2025-04-11 23:19:37 +0200
Commit message:

 Use match.fun() in annotaTEs() to avoid triggering a cryptic error when parsefun is a character string
Package: GSVA
Commit: 9406633021a400295dcd5fa39a9344cfce10f77c
Author: Robert Castelo <robert.castelo@upf.edu>
Date: 2025-04-11 23:07:19 +0200
Commit message:

 Be less conservative in checking for zero bandwidth
Package: RAIDS
Commit: adf231fd868e273d23058cf47cd74bdbdf1a09d5
Author: belleau <belleau@belleauMBP.home>
Date: 2025-04-11 16:58:39 -0400
Commit message:

 Merge remote-tracking branch 'upstream/devel'
Package: RAIDS
Commit: 1f226157fe17bf49a87a67e3a2b63eaa37af6606
Author: belleau <belleau@belleauMBP.home>
Date: 2025-04-11 16:50:41 -0400
Commit message:

 Merge branch 'main' of https://github.com/KrasnitzLab/RAIDS
Package: RAIDS
Commit: 7391a7edbb8b251511896564d1800be8bee67856
Author: Astrid Deschênes <adeschen@users.noreply.github.com>
Date: 2025-04-11 16:24:37 -0400
Commit message:

 Merge pull request #580 from belleau/main

Add function generateProfileGDS
Package: RAIDS
Commit: f91aa8028ee5359cd2cba9ea6cc32dbb2ec9d49c
Author: belleau <belleau@belleauMBP.home>
Date: 2025-04-11 16:07:54 -0400
Commit message:

 Merge branch 'main' of https://github.com/belleau/RAIDS
Package: RAIDS
Commit: dd2ee0427ca637aeee707bd4088734850affabf1
Author: belleau <belleau@belleauMBP.home>
Date: 2025-04-11 16:07:00 -0400
Commit message:

 Add function generateProfileGDS
Package: RAIDS
Commit: fb60b8f57f233fc99563c167b4e563b85b83d0ef
Author: Astrid Deschênes <adeschen@users.noreply.github.com>
Date: 2025-04-11 15:49:26 -0400
Commit message:

 Merge pull request #579 from adeschen/main

Add unit test for processPileupChrBin() function
Package: RAIDS
Commit: b698dd361773594fcf6c8568e5e16f4696d05536
Author: adeschen <adeschen@hotmail.com>
Date: 2025-04-11 14:26:43 -0400
Commit message:

 Merge branch 'main' of https://github.com/adeschen/RAIDS
Package: RAIDS
Commit: 26c72ca4b9d25f96a75bb2449780b96c5dd91137
Author: adeschen <adeschen@hotmail.com>
Date: 2025-04-11 14:26:34 -0400
Commit message:

 Add unit test for processPileupChrBin() function
Package: RAIDS
Commit: e2ac16f6f596204abb919b2924c174780f0ef2d8
Author: Astrid Deschênes <adeschen@users.noreply.github.com>
Date: 2025-04-11 13:49:22 -0400
Commit message:

 Merge pull request #5 from KrasnitzLab/main

Merge with Krasnitz RAIDS
Package: RAIDS
Commit: 64aa87a3c346989735c63f355d47696cb2221aa4
Author: Astrid Deschênes <adeschen@users.noreply.github.com>
Date: 2025-04-11 13:48:03 -0400
Commit message:

 Merge pull request #578 from adeschen/main

Update doc and format processPileupChrBin() function
Package: RAIDS
Commit: 5b04cad74d6be32cc1f03090c9b919febc88d0d0
Author: krasnitz <krasnitz@cshl.edu>
Date: 2025-04-11 13:33:30 -0400
Commit message:

 Update RAIDS.Rmd
Package: RAIDS
Commit: 8cc8b65e271b6c5b2c75972632ee0294be84d0bb
Author: adeschen <adeschen@hotmail.com>
Date: 2025-04-11 13:28:56 -0400
Commit message:

 Update doc and format processPileupChrBin() function
Package: RAIDS
Commit: 5b03a90153710904548659625dcbe50964f90f16
Author: Astrid Deschênes <adeschen@users.noreply.github.com>
Date: 2025-04-11 12:58:31 -0400
Commit message:

 Merge pull request #577 from belleau/main

Add function readSNVBAM
Package: RAIDS
Commit: 4e774b05ec2833ca207f1ccca5fd54560e8a5885
Author: belleau <belleau@belleauMBP.home>
Date: 2025-04-11 12:43:27 -0400
Commit message:

 Merge branch 'main' of https://github.com/belleau/RAIDS
Package: RAIDS
Commit: 30c59978b6f99621c8d62c1c1e9cf75d5f07fed9
Author: belleau <belleau@belleauMBP.home>
Date: 2025-04-11 12:43:17 -0400
Commit message:

 Add function readSNVBAM
Package: RAIDS
Commit: 70620b9289bee56c7c2b46c5712f2c43e147f19a
Author: Astrid Deschênes <adeschen@users.noreply.github.com>
Date: 2025-04-11 12:29:01 -0400
Commit message:

 Merge pull request #576 from adeschen/main

Adding tests for extractNucleotide() function
Package: RAIDS
Commit: bf8e02bc406b4a205e4a204f08288bbce41b1140
Author: adeschen <adeschen@hotmail.com>
Date: 2025-04-10 15:31:38 -0400
Commit message:

 Adding tests for extractNucleotide() function
Package: RAIDS
Commit: ec7902a6bd5bf28df5e2e0571a5e9160acc187ee
Author: Astrid Deschênes <adeschen@users.noreply.github.com>
Date: 2025-04-10 15:08:39 -0400
Commit message:

 Merge pull request #575 from adeschen/main

Update doc for extractNucleotid() function
Package: RAIDS
Commit: 34eb2fef5b4304211fc8f11459ae8bab2bcaa7b8
Author: adeschen <adeschen@hotmail.com>
Date: 2025-04-10 14:37:57 -0400
Commit message:

 Correct extractNucleotide() function
Package: RAIDS
Commit: b2d024a4d70a65b803334e9d345b5dfb2425fd32
Author: adeschen <adeschen@hotmail.com>
Date: 2025-04-10 14:03:40 -0400
Commit message:

 Update doc for extractNucleotid() function
Package: RAIDS
Commit: 204f21ecc554196eb59b4b8d5f752a487d4e7e4d
Author: Astrid Deschênes <adeschen@users.noreply.github.com>
Date: 2025-04-10 13:35:46 -0400
Commit message:

 Merge pull request #4 from KrasnitzLab/main

Merge with Krasnitz
Package: RAIDS
Commit: 5145ad988fea01b46e943f360cf54c199f36038a
Author: Astrid Deschênes <adeschen@users.noreply.github.com>
Date: 2025-04-10 12:24:32 -0400
Commit message:

 Merge pull request #574 from belleau/main

Add functions for BAM file
Package: RAIDS
Commit: a5a1bf8b5b11eea0a5681dde46e69862a82d55c0
Author: Astrid Deschênes <adeschen@users.noreply.github.com>
Date: 2025-04-10 12:11:58 -0400
Commit message:

 Merge pull request #573 from adeschen/main

Update README
Package: RAIDS
Commit: 5da36d09e06d6f89d2005603c89c3c4b1b5b718b
Author: adeschen <adeschen@hotmail.com>
Date: 2025-04-10 11:55:35 -0400
Commit message:

 Merge branch 'main' of https://github.com/adeschen/RAIDS
Package: RAIDS
Commit: f2ae83d27f45034a51e776c6b880fad7a8f2d0aa
Author: adeschen <adeschen@hotmail.com>
Date: 2025-04-10 11:53:26 -0400
Commit message:

 Update README
Package: RAIDS
Commit: c47f0e4d5aa429683b2dd94230600b39b69bc91f
Author: belleau <belleau@belleauMBP.home>
Date: 2025-04-10 09:01:34 -0400
Commit message:

 Merge branch 'main' of https://github.com/belleau/RAIDS
Package: RAIDS
Commit: 33e0327dcbdc8e9bde0cc21836089d7b49f4939d
Author: belleau <belleau@belleauMBP.home>
Date: 2025-04-10 08:59:31 -0400
Commit message:

 Add function extractNucleotide and processPileupChrBin
Package: RAIDS
Commit: ba92d064725684cf10593fe2a111f5332e553c59
Author: Astrid Deschênes <adeschen@users.noreply.github.com>
Date: 2025-04-09 21:09:40 -0400
Commit message:

 Merge pull request #572 from adeschen/main

Update check-bioc
Package: RAIDS
Commit: d7bdaeabd77e1695778d6631c49a9aa69e542095
Author: adeschen <adeschen@hotmail.com>
Date: 2025-04-09 20:40:52 -0400
Commit message:

 Update check-bioc
Package: RAIDS
Commit: cf9bc69d547c12a4c1b7b0c56e023a65f5996c57
Author: Astrid Deschênes <adeschen@users.noreply.github.com>
Date: 2025-04-09 19:58:20 -0400
Commit message:

 Merge pull request #571 from adeschen/main

Update vignette title
Package: RAIDS
Commit: 00c1ba27155372d144b3c0f3dfd0f37e4e55ffdf
Author: adeschen <adeschen@hotmail.com>
Date: 2025-04-09 19:33:41 -0400
Commit message:

 Update vignette title
Package: RAIDS
Commit: ce9c260e1d8ca05f8af926cb0b9b4659a46426c3
Author: Astrid Deschênes <adeschen@users.noreply.github.com>
Date: 2025-04-09 19:27:06 -0400
Commit message:

 Merge pull request #570 from adeschen/main

Update title in DESCRIPTION file
Package: RAIDS
Commit: 7ba504a57ada88e8951faae34f10a88530ee61ca
Author: adeschen <adeschen@hotmail.com>
Date: 2025-04-09 18:13:44 -0400
Commit message:

 Update title in DESCRIPTION file
Package: GSVA
Commit: bda0b775f551912a45a658279eb13473f54d2b61
Author: Robert Castelo <robert.castelo@upf.edu>
Date: 2025-04-11 22:26:39 +0200
Commit message:

 Added missing dependency to suggests
Package: gINTomics
Commit: 1e2d8095e60c04b2621cf29a80830916f940cd4b
Author: angeve96 <angeve89@gmail.com>
Date: 2025-04-11 20:50:44 +0200
Commit message:

 version bump
Package: gINTomics
Commit: 45c99b40dd81b578bf7735471d2e9317a5e8c4ed
Author: angeve96 <angeve89@gmail.com>
Date: 2025-04-11 20:47:34 +0200
Commit message:

 diff class
Package: gINTomics
Commit: a086eb99b0a46d565568b50786cb78a2eca7d3a2
Author: angeve96 <angeve89@gmail.com>
Date: 2025-04-04 19:09:41 +0200
Commit message:

 genomic diff
Package: gINTomics
Commit: 668af9352c14fe5dddddbeb82307a1a13f30ad85
Author: angeve96 <angeve89@gmail.com>
Date: 2025-03-05 11:52:54 +0100
Commit message:

 adding Class attr
Package: gINTomics
Commit: c42256631d365689126b47d7a49e8a80981330be
Author: angeve96 <angeve89@gmail.com>
Date: 2025-02-26 17:24:18 +0100
Commit message:

 update gene download
Package: gINTomics
Commit: c3929d8977c0e2e938a80a12a658042a453a348d
Author: angeve96 <angeve89@gmail.com>
Date: 2025-02-26 17:23:35 +0100
Commit message:

 new class mode
Package: xCell2
Commit: 9affd038a15f972b6817eb7b71afaa4b385c9ad1
Author: AlmogAngel <almogangel@gmail.com>
Date: 2025-04-11 21:01:47 +0300
Commit message:

 Fix sparse matrix binding in ScToPseudoBulk

Convert underrepresented cell type matrices (dgCMatrix) to dense data frames using as.data.frame(as.matrix(tmp))
to prevent errors during dplyr::bind_cols.
Package: xCell2
Commit: 8cbb2590a1f467dffddf31e81438e8fa6729591c
Author: AlmogAngel <almogangel@gmail.com>
Date: 2025-04-11 20:56:34 +0300
Commit message:

 Fix sparse matrix binding in ScToPseudoBulk

Convert underrepresented cell type matrices (dgCMatrix) to dense data frames using as.data.frame(as.matrix(tmp))
to prevent errors during dplyr::bind_cols.
Package: GSVA
Commit: 7f625fe91a6a54dffeddab63b3c1b4f965dc5da2
Author: Robert Castelo <robert.castelo@upf.edu>
Date: 2025-04-11 19:55:43 +0200
Commit message:

 Merge pull request #242 from rcastelo/115-update-gsva-vignette

Updated vignette
Package: GSVA
Commit: c75f0e090648c2cc24792fe72a855b6f3734f6f3
Author: Robert Castelo <robert.castelo@upf.edu>
Date: 2025-04-11 19:54:29 +0200
Commit message:

 Updated vignette
Package: gDRstyle
Commit: 1a46c4cecd4441bddabab897409f1e0f5a9d6cf1
Author: darsoo <daro.scig@gmail.com>
Date: 2025-04-11 19:55:30 +0200
Commit message:

 Merge pull request #87 from gdrplatform/GDR-2951_1

Gdr 2951 1
Package: gDRstyle
Commit: f271adcd5d5a90c9787447b4222471332fac8674
Author: darsoo <daro.scig@gmail.com>
Date: 2025-04-11 16:40:06 +0200
Commit message:

 Update NEWS.md
Package: gDRstyle
Commit: 69cfbe7d9d543bee1a66138cc1b370f5dcca150c
Author: darsoo <daro.scig@gmail.com>
Date: 2025-04-11 16:38:57 +0200
Commit message:

 Update DESCRIPTION
Package: gDRstyle
Commit: 485255c1a95437d1dd5f6d439dc24e25d1d41946
Author: darsoo <daro.scig@gmail.com>
Date: 2025-04-11 16:38:09 +0200
Commit message:

 Update linters_config.R
Package: Motif2Site
Commit: eecc9cb72290a5fafeba254d411870b569690fa5
Author: peymanzarrineh <peyman.zarrineh@manchester.ac.uk>
Date: 2025-04-11 15:31:34 +0100
Commit message:

 Fixing the Bioconductor stated bug
Package: SynExtend
Commit: 7884b6a52e4de5373f2e7b9476cbf2863d5cd284
Author: npcooley <npcooley@gmail.com>
Date: 2025-04-11 12:14:01 -0400
Commit message:

 missing FDR assignment
Package: CytoMDS
Commit: 8c0dfe600e2032705c387aa684bd126b912f821f
Author: phauchamps <philippehauchamps@hotmail.com>
Date: 2025-04-11 16:53:57 +0200
Commit message:

 GHA: migrated to actions/cache@v4 from v2
Package: CytoMDS
Commit: 528641746fd2c22c3e20a22785c7c1937dd95eb5
Author: phauchamps <philippehauchamps@hotmail.com>
Date: 2025-04-11 16:37:37 +0200
Commit message:

 - changed package citation (and in README.md) to peer reviewed journal article
- bumped to version 1.3.7
Package: CytoMDS
Commit: d942e53dc53454797ed07e4103b76bfb938937a3
Author: phauchamps <philippehauchamps@hotmail.com>
Date: 2025-02-25 15:41:39 +0100
Commit message:

 - `ggplotMarginalDensities()`: corrected a bug when channels were specified as
marker names
- made the corresponding doc more clear
Package: signifinder
Commit: 72b3918e4db764123f0d1410a086d16b4b8b0e54
Author: Stefania Pirrotta <s.pirrotta.sp@gmail.com>
Date: 2025-04-11 17:01:39 +0200
Commit message:

 update description
Package: MLP
Commit: 33458e57a8e1fa3ba1aa41f6163479fa89c26aa6
Author: Laure Cougnaud <laure.cougnaud@openanalytics.eu>
Date: 2025-04-11 15:19:40 +0200
Commit message:

 doc: remove description-like items in itemize (R-devel 11/10/2023)
Package: MLP
Commit: 55f2390a35da8eab0ca9b808cd9f037c2b406a6b
Author: Laure Cougnaud <laure.cougnaud@openanalytics.eu>
Date: 2025-04-11 15:10:32 +0200
Commit message:

 addGeneSetDescription: fix issue KEGG
Package: sosta
Commit: c0b4d4154447d766e6740708c3cdc825866c144e
Author: sgunz <samuel.gunz@uzh.ch>
Date: 2025-04-11 15:46:19 +0200
Commit message:

 update news and vignettes
Package: rcellminer
Commit: 913b4a361510fd454cd201aed2395d5e77f731ce
Author: Fathi Elloumi <fathi.elloumi@nih.gov>
Date: 2025-04-11 09:34:06 -0400
Commit message:

 Added number of samples in the 2D plot
Package: rcellminerData
Commit: 7eabea8b5f53f1dd71396ba9775d9170a2359e21
Author: Fathi Elloumi <fathi.elloumi@nih.gov>
Date: 2025-04-11 09:30:20 -0400
Commit message:

 Uploaded NCI60 drug data v2_14
Package: SynExtend
Commit: f55c32a3244e0aa3e8d7e41239c9e2f006d6f8d7
Author: npcooley <npcooley@gmail.com>
Date: 2025-04-11 08:18:42 -0400
Commit message:

 man pages and stuff
Package: SynExtend
Commit: 3772bfdbc2b39ca598c65b24aad9a3c7cd62c81e
Author: Nicholas Cooley <39340402+npcooley@users.noreply.github.com>
Date: 2025-04-11 07:51:54 -0400
Commit message:

 Merge pull request #76 from ahl27/master

fix issue
Package: SynExtend
Commit: 0738efffb0d91f2713004c2d75f2af450ff84d92
Author: ahl27 <ahl27@pitt.edu>
Date: 2025-04-11 07:38:21 -0400
Commit message:

 fix to tests
Package: SynExtend
Commit: 75f27e668f68f9bc70517e90fc7fb66fcfe2777b
Author: ahl27 <ahl27@pitt.edu>
Date: 2025-04-11 07:35:38 -0400
Commit message:

 minor fixes to testing
Package: SynExtend
Commit: b1d22102d6345f58b37f1326df11806468994cc0
Author: ahl27 <ahl27@pitt.edu>
Date: 2025-04-11 07:26:37 -0400
Commit message:

 fix issue
Package: SynExtend
Commit: c9587c3086fe54d36a7060ecf64e20e8a8517174
Author: npcooley <npcooley@gmail.com>
Date: 2025-04-11 01:16:24 -0400
Commit message:

 more man page additions
Package: SynExtend
Commit: 0eec29a932d56fa08b72946150a8e9d1d87beb9f
Author: npcooley <npcooley@gmail.com>
Date: 2025-04-11 00:54:43 -0400
Commit message:

 bug and man fixes
Package: SynExtend
Commit: 96cabcc64af8d3068776317724d2687476a39dbe
Author: Nicholas Cooley <39340402+npcooley@users.noreply.github.com>
Date: 2025-04-10 23:59:10 -0400
Commit message:

 Merge pull request #75 from ahl27/master

fix: Critical fix to `ExoLabel`
Package: SynExtend
Commit: 360800fde2ddb592e071cf006d87ec059773314c
Author: npcooley <npcooley@gmail.com>
Date: 2025-04-10 23:58:35 -0400
Commit message:

 yolo
Package: SynExtend
Commit: 2f19bc401c906c6f1fbf8d691ca3545f0083dc44
Author: ahl27 <ahl27@pitt.edu>
Date: 2025-04-10 15:56:13 -0400
Commit message:

 disables consensus clustering in code
Package: SynExtend
Commit: 879add7976bb33557e27694bad8e7e4501e21091
Author: ahl27 <ahl27@pitt.edu>
Date: 2025-04-10 15:55:50 -0400
Commit message:

 disables consensus clustering in man page
Package: SynExtend
Commit: 86fe32e8d2b0d6dbbfc4bc3f4ed4990a5e8bedf2
Author: ahl27 <ahl27@pitt.edu>
Date: 2025-04-10 15:53:04 -0400
Commit message:

 disables consensus clustering
Package: SynExtend
Commit: 78d22e18d7a829c37e68f829c1aeb9c2321d1ccb
Author: ahl27 <ahl27@pitt.edu>
Date: 2025-04-10 15:48:43 -0400
Commit message:

 fixes issue with output not matching number of vertices
Package: SynExtend
Commit: 023a4f8fb466c3f42cd49c6b2ccf4e0d73d7cc53
Author: ahl27 <ahl27@pitt.edu>
Date: 2025-04-10 15:44:39 -0400
Commit message:

 fixes issue with reporting of file sizes during merge sort
Package: SynExtend
Commit: c53022c48601e7f1078678dcc09ba80f625c511d
Author: ahl27 <ahl27@pitt.edu>
Date: 2025-04-10 15:31:30 -0400
Commit message:

 slight improvement to output
Package: SynExtend
Commit: 880033ca72feef1dcf3b78a6f5b932215c4e2866
Author: ahl27 <ahl27@pitt.edu>
Date: 2025-04-10 15:24:21 -0400
Commit message:

 fix bioccheck warning
Package: SynExtend
Commit: d7b78de55d2af2a173c95363f6c14e4a2232b598
Author: ahl27 <ahl27@pitt.edu>
Date: 2025-04-10 15:21:12 -0400
Commit message:

 update namespace
Package: SynExtend
Commit: 3efefb0ce4b822f2f174f76279bfe2b2480fbf55
Author: ahl27 <ahl27@pitt.edu>
Date: 2025-04-10 15:13:51 -0400
Commit message:

 adds test to check compression accuracy
Package: SynExtend
Commit: a18d79dbb48924bd4c6495ff00946c3b84ac6e02
Author: ahl27 <ahl27@pitt.edu>
Date: 2025-04-10 12:20:25 -0400
Commit message:

 fixes issue where disjoint sets could differ in tests due to numerical inaccuracy
Package: SynExtend
Commit: 11b92b963da3802675e664cb11f8b9e432bc5c7a
Author: ahl27 <ahl27@pitt.edu>
Date: 2025-04-10 12:10:19 -0400
Commit message:

 adds testing file
Package: SynExtend
Commit: 22d48bbfb8d40fab10789a048f624334e721e349
Author: ahl27 <ahl27@pitt.edu>
Date: 2025-04-10 11:52:21 -0400
Commit message:

 adds unit testing and debugging for consistent checking in the future
Package: SynExtend
Commit: 3c7a15309f1e21005af4ab8abf45a2c7c5f5d58c
Author: ahl27 <ahl27@pitt.edu>
Date: 2025-04-09 21:09:34 -0400
Commit message:

 much faster edge comparison function, makes reading in nodes a lot faster
Package: SynExtend
Commit: 532ca5ac200bf1c31c229ab58321c4943b5519cc
Author: ahl27 <ahl27@pitt.edu>
Date: 2025-04-09 20:52:36 -0400
Commit message:

 small updates to printing
Package: SynExtend
Commit: 99422e2c245b4ae0e8bef5ef1083a7ddb1c52e28
Author: ahl27 <ahl27@pitt.edu>
Date: 2025-04-09 20:47:18 -0400
Commit message:

 why did i forget a debug statement in code
Package: SynExtend
Commit: eda19f9fb6bd706d406cd9b0b08dea41a7f56efb
Author: ahl27 <ahl27@pitt.edu>
Date: 2025-04-09 20:46:20 -0400
Commit message:

 fixes another stupid bug
Package: SynExtend
Commit: c657d4219dc8fd22e1cbec23ed6fdc1aa4ad689c
Author: ahl27 <ahl27@pitt.edu>
Date: 2025-04-09 13:42:56 -0400
Commit message:

 moves report on iteration autofill inside clustering
Package: SynExtend
Commit: ad297c957bd7651aeab9fac1238fc1c19f1e7b73
Author: ahl27 <ahl27@pitt.edu>
Date: 2025-04-09 13:39:32 -0400
Commit message:

 fix issue with easter egg
Package: SynExtend
Commit: 709dee87ac5b1bcb2e9a568fe491497a7d6d67c2
Author: ahl27 <ahl27@pitt.edu>
Date: 2025-04-08 16:31:54 -0400
Commit message:

 updates man page, exposes dist_scaling parameter, code cleanup
Package: SynExtend
Commit: 21e825cccb677f4d7563860becc72391ae3852d4
Author: ahl27 <ahl27@pitt.edu>
Date: 2025-04-08 15:24:03 -0400
Commit message:

 improves precision of weight compression
Package: SynExtend
Commit: aeb350030b0fd44ee3fce0a0fe643f75b14db35d
Author: ahl27 <ahl27@pitt.edu>
Date: 2025-04-08 13:26:54 -0400
Commit message:

 Fixes a ton of bugs: merge sort on multiple files fixed, better weight compression, better output formatting, fewer incorrect comments in code
Package: SynExtend
Commit: fa22493dfd8692893e0945356c8a5851f7492f27
Author: ahl27 <ahl27@pitt.edu>
Date: 2025-04-07 19:22:08 -0400
Commit message:

 last commit before changing algorithm a lot
Package: Ibex
Commit: ff9e8e11d9e7792f4898bb090e8052644ffd9c27
Author: theHumanBorch <ncborch@gmail.com>
Date: 2025-04-11 07:08:57 -0500
Commit message:

 version 0.99.10
Package: gDRimport
Commit: 93d52fbc77bb14fa1fbdf43cf7a8d376a05d654a
Author: darsoo <daro.scig@gmail.com>
Date: 2025-04-11 11:49:25 +0200
Commit message:

 Merge pull request #102 from gdrplatform/GDR-2951

Gdr 2951
Package: gDRimport
Commit: 738d0771d30bd2a4e2251c32f707814598a667d5
Author: Dariusz Scigocki <daro.scig@gmail.com>
Date: 2025-04-10 17:12:51 +0000
Commit message:

 bump version
Package: gDRimport
Commit: 77eb04d974cea11f43cbf86c78cd1c9161066b8b
Author: Dariusz Scigocki <daro.scig@gmail.com>
Date: 2025-04-10 17:12:00 +0000
Commit message:

 replaced with_mock with with_mocked_bindings
Package: gDRstyle
Commit: 64a295fa7a088d53b03b2e8fcd708713a5ad9ed4
Author: darsoo <daro.scig@gmail.com>
Date: 2025-04-11 11:00:37 +0200
Commit message:

 Merge pull request #86 from gdrplatform/GDR-2951

Gdr 2951
Package: gDRstyle
Commit: 5d7d379fadbf8cc29a97ff413ebc6ba93a429e6d
Author: Dariusz Scigocki <daro.scig@gmail.com>
Date: 2025-04-10 17:18:18 +0000
Commit message:

 CI
Package: gDRstyle
Commit: ef08d02a371fc68f3c44f7e3fbe771fef84730b2
Author: Dariusz Scigocki <daro.scig@gmail.com>
Date: 2025-04-10 11:59:06 +0200
Commit message:

 added comment
Package: gDRstyle
Commit: 29bbc89c6fdd16555911e3b547e6ef86c47c1692
Author: Dariusz Scigocki <daro.scig@gmail.com>
Date: 2025-04-09 13:12:41 +0200
Commit message:

 updated lintr config
Package: gDRstyle
Commit: efcb3c314f5c256872c754f5f346eb6054950738
Author: Dariusz Scigocki <daro.scig@gmail.com>
Date: 2025-04-09 12:06:19 +0200
Commit message:

 removed suppressWarnings
Package: gDRstyle
Commit: 3f9541f29f6ced9bab2094315811c995b7adeca4
Author: Dariusz Scigocki <daro.scig@gmail.com>
Date: 2025-04-09 11:24:26 +0200
Commit message:

 added support for non-defaults options in linters_config
Package: gDRstyle
Commit: 06ed4364136dfc80c0eb422cacc8e3a81cb33219
Author: darsoo <daro.scig@gmail.com>
Date: 2025-04-09 10:07:49 +0200
Commit message:

 Update linters_config.R
Package: gDRstyle
Commit: a6283c2379bc805f4e0264fa01912529012c02fc
Author: Dariusz Scigocki <daro.scig@gmail.com>
Date: 2025-04-09 09:24:11 +0200
Commit message:

 removed checking rplatform deps
Package: gDRstyle
Commit: cae5f9548cc1d5593efb5473eedc7c1b738126ee
Author: Dariusz Scigocki <daro.scig@gmail.com>
Date: 2025-04-08 23:21:04 +0200
Commit message:

 bump version
Package: gDRstyle
Commit: 211fa8e404b3dca8aefb35b31188451e217475d5
Author: Dariusz Scigocki <daro.scig@gmail.com>
Date: 2025-04-08 23:19:39 +0200
Commit message:

 updated lintr config
Package: miaTime
Commit: ecf0d50809d76e7cef447ec3902e22ce4df2cbc7
Author: TuomasBorman <tvborm@utu.fi>
Date: 2025-04-11 09:18:08 +0300
Commit message:

 Sync with bioc
Package: miaTime
Commit: 33dbe05497555007a068a6be63eee5a7d3d4b65d
Author: Muluh <127390183+Daenarys8@users.noreply.github.com>
Date: 2025-04-11 07:13:51 +0100
Commit message:

 remove citation as no doi yet (#109)

Signed-off-by: Daena Rys <rysdaena8@gmail.com>
Package: miaTime
Commit: f071a98e0ba2ae4cbc9aefbeaed8a817dc121e92
Author: Daena Rys <rysdaena8@gmail.com>
Date: 2025-04-11 08:51:18 +0300
Commit message:

 remove citation as no doi yet

Signed-off-by: Daena Rys <rysdaena8@gmail.com>
Package: miaTime
Commit: 3df4ba1287495c72e75c60c29d57492fe264fb72
Author: Daena Rys <rysdaena8@gmail.com>
Date: 2025-04-11 08:48:22 +0300
Commit message:

 Merge branch 'devel' into tests
Package: miaTime
Commit: cd9a5df222d4eb844c02840bb1af722fe219a324
Author: Daena Rys <rysdaena8@gmail.com>
Date: 2025-04-06 08:57:11 +0300
Commit message:

 Fix latex xter error

Signed-off-by: Daena Rys <rysdaena8@gmail.com>
Package: PSMatch
Commit: d00b69ae13dcee4d3760d24dd8b61ccef65e4a97
Author: Laurent Gatto <laurent.gatto@uclouvain.be>
Date: 2025-04-11 07:54:26 +0200
Commit message:

 Merge pull request #23 from guideflandre/PSMatch-PTM

plotSpectraPTM correct annotations
Package: PSMatch
Commit: 74f84d8aaa9bc46d71da1f5e5847ac5495e428dd
Author: Guitou1 <potamoidef@gmail.com>
Date: 2025-04-10 18:05:25 +0200
Commit message:

 missing import
Package: PSMatch
Commit: c101a40176b060b6bb4d30bd505548eeb14eb08f
Author: Guitou1 <potamoidef@gmail.com>
Date: 2025-04-10 17:31:48 +0200
Commit message:

 comment out bugging test
Package: PSMatch
Commit: 6e218556a4e0d0fbc4df2f79cbadf19cf9241282
Author: Guitou1 <potamoidef@gmail.com>
Date: 2025-04-10 17:23:49 +0200
Commit message:

 depend on vdiffr
Package: PSMatch
Commit: 8cd19695156882e451e5e7455161c6023ddb3f84
Author: Guitou1 <potamoidef@gmail.com>
Date: 2025-04-10 15:18:17 +0200
Commit message:

 More space for plots
Package: PSMatch
Commit: b01e6550417298d6ec1ee3b3b7f539139a3d0094
Author: Guitou1 <potamoidef@gmail.com>
Date: 2025-04-10 15:10:57 +0200
Commit message:

 complete review comment on documentation
Package: PSMatch
Commit: eacd8e55c7eb060a8ef6873496dbf058eb3f2a00
Author: Guitou1 <potamoidef@gmail.com>
Date: 2025-04-10 15:05:51 +0200
Commit message:

 Correct documentation on main
Package: PSMatch
Commit: c332111cff76a462e57bf487fb8b5b0e28bb6a3c
Author: Guillaume <guillaume@def-pc.home>
Date: 2025-04-10 14:05:16 +0200
Commit message:

 change annotation function name
Package: PSMatch
Commit: ffb6229470920935c056071a62139129ebaaf9a6
Author: Guillaume <guillaume@def-pc.home>
Date: 2025-04-10 12:52:57 +0200
Commit message:

 correct test files
Package: PSMatch
Commit: 51f02a5755eb598e6fd6b54a3d4f652047d990df
Author: Guillaume <guillaume@def-pc.home>
Date: 2025-04-10 12:48:33 +0200
Commit message:

 see previous commit
Package: PSMatch
Commit: 9ab019acb3c3da5edaf5040187218b2bd1fd0cf8
Author: Guillaume <guillaume@def-pc.home>
Date: 2025-04-10 12:48:15 +0200
Commit message:

 Correct annotations
Package: PSMatch
Commit: 8537b254e7efcd4bd27da6c26a84a83db66d3863
Author: Laurent Gatto <laurent.gatto@uclouvain.be>
Date: 2025-04-10 07:13:48 +0200
Commit message:

 fix man pages
Package: PSMatch
Commit: e3245fa892a9bb64006b2831af3b6e70cb0a7edc
Author: Laurent Gatto <laurent.gatto@uclouvain.be>
Date: 2025-04-10 06:52:56 +0200
Commit message:

 Merge branch 'guideflandre-PSMatch-PTM'
Package: PSMatch
Commit: f86008717d6e31b70b394a57c05d9e6cf82fea11
Author: Laurent Gatto <laurent.gatto@uclouvain.be>
Date: 2025-04-10 06:52:29 +0200
Commit message:

 fix errors
Package: PSMatch
Commit: ceb5db59aea14af6f0fd7173f24fff73adf177b3
Author: Guillaume <guillaume@def-pc.home>
Date: 2025-04-10 00:57:16 +0200
Commit message:

 Updates based on reviews
Package: PSMatch
Commit: 552d0cf7daee43b18843d9efc97170a306cb2659
Author: Guillaume <guillaume@def-pc.home>
Date: 2025-04-09 23:39:15 +0200
Commit message:

 see previous commit
Package: PSMatch
Commit: f1e095da0ac2f7f55b674d1dce696338d3545306
Author: Guillaume <guillaume@def-pc.home>
Date: 2025-04-09 23:29:31 +0200
Commit message:

 Merge branch 'PSMatch-PTM' of https://github.com/guideflandre/PSMatch into PSMatch-PTM
Package: PSMatch
Commit: 78e07224b5fd6961a5162fcf75d336e4fa5b0cf2
Author: Guillaume <guillaume@def-pc.home>
Date: 2025-04-09 23:27:28 +0200
Commit message:

 Update based on reviews
Package: PSMatch
Commit: 0973364793478db66e9d58cdb0cc6d9a3c7ec13a
Author: Guillaume Deflandre <37773040+guideflandre@users.noreply.github.com>
Date: 2025-04-09 23:26:33 +0200
Commit message:

 Update R/plotSpectra-PTM.R

Co-authored-by: Sebastian Gibb <mail@sebastiangibb.de>
Package: PSMatch
Commit: 54f78bf44823f3bd7b1268cdc99557bc6c4f0850
Author: Guillaume Deflandre <37773040+guideflandre@users.noreply.github.com>
Date: 2025-04-09 23:19:51 +0200
Commit message:

 Update R/fragments-label.R

Co-authored-by: Sebastian Gibb <mail@sebastiangibb.de>
Package: PSMatch
Commit: 8c1a4452c18810db3623e4db489d373ea02d75d1
Author: Guillaume <guillaume@def-pc.home>
Date: 2025-04-09 20:41:04 +0200
Commit message:

 Spectra to imports, R to dependencies
Package: PSMatch
Commit: 760723b3f1e1866e6a322a55b4dbedfbb264c6b6
Author: Guillaume <guillaume@def-pc.home>
Date: 2025-04-09 20:27:08 +0200
Commit message:

 rmarkdown syntax
Package: PSMatch
Commit: 5c614adefc4beaddc36425a6683b2b0618fd0d64
Author: Guillaume <guillaume@def-pc.home>
Date: 2025-04-09 17:25:16 +0200
Commit message:

 see previous commit
Package: PSMatch
Commit: d4a858d110514568ca669c8bde4474d64b92b09c
Author: Guillaume <guillaume@def-pc.home>
Date: 2025-04-09 17:17:10 +0200
Commit message:

 Keep deltaMz as TRUE or FALSE. Add deltaMzData instead
Package: PSMatch
Commit: 747d404bd0c6bb6b1c1adc37275aa9ef1d0bae21
Author: Guillaume <guillaume@def-pc.home>
Date: 2025-04-09 16:52:44 +0200
Commit message:

 correctly place snapshots from test file
Package: PSMatch
Commit: 6606c6116d8f0ed40f9b240929c16e6a62a88ab7
Author: Guillaume <guillaume@def-pc.home>
Date: 2025-04-09 16:42:05 +0200
Commit message:

 Update plotSpectraPTM documentation based on review
Package: PSMatch
Commit: b6f546d3e354bf337bc5f1f04c3cadf440df5467
Author: Guillaume <guillaume@def-pc.home>
Date: 2025-04-09 15:55:04 +0200
Commit message:

 Change plotSpectraPTM based on reviews
Package: PSMatch
Commit: 8686b488eaa0521e36ad7952c66a601f5ac6d022
Author: Guitou1 <potamoidef@gmail.com>
Date: 2025-04-09 10:17:47 +0200
Commit message:

 specify what in deprecated addFragments
Package: PSMatch
Commit: e647aeed65bb8c972e27634f4d94d6895e506e1c
Author: Guitou1 <potamoidef@gmail.com>
Date: 2025-04-09 09:43:41 +0200
Commit message:

 Updates based on review (correct labelFragments )
Package: PSMatch
Commit: f522589ca2779ae57a9f3c3e10488a2b93add4b1
Author: Guitou1 <potamoidef@gmail.com>
Date: 2025-04-08 22:28:52 +0200
Commit message:

 Additional unit test to labelFragments
Package: PSMatch
Commit: 6ce6f9c73df2daa015b67bd07bf317316710c446
Author: Guitou1 <potamoidef@gmail.com>
Date: 2025-04-08 22:26:48 +0200
Commit message:

 Add mz to labelFragments, plotSpectraPTM and new unit tests
Package: PSMatch
Commit: 650375d57fb584995a9c68f65afe1c8f32e18898
Author: Guillaume Deflandre <37773040+guideflandre@users.noreply.github.com>
Date: 2025-04-08 22:01:17 +0200
Commit message:

 Merge branch 'rformassspectrometry:main' into PSMatch-PTM
Package: PSMatch
Commit: d29a4777890f116505645d09605dc65dd4a4b84e
Author: Laurent Gatto <laurent.gatto@uclouvain.be>
Date: 2025-04-08 12:12:32 +0200
Commit message:

 install latest spectra
Package: PSMatch
Commit: bac7632c38ca57590da5239565d9f0ca7ebf37af
Author: Laurent Gatto <laurent.gatto@uclouvain.be>
Date: 2025-04-08 12:08:16 +0200
Commit message:

 bump devel version
Package: PSMatch
Commit: c0f3eabb1c341501b2e39a28c923441c48f0633c
Author: Guitou1 <potamoidef@gmail.com>
Date: 2025-01-27 10:09:21 +0100
Commit message:

 add plotSpectra-PTM
Package: MSnbase
Commit: 852fcdef60377da4ef67df4d2a28dfb510697eca
Author: Laurent Gatto <laurent.gatto@gmail.com>
Date: 2025-04-11 07:28:53 +0200
Commit message:

 Merge pull request #609 from lgatto/methods-fragments

chore: remove R/methods-fragments.R (moved to PSMatch)
Package: MSnbase
Commit: 8d7781fdca203d9c47eaa843fa2521b8f5ebbea9
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2025-04-10 23:23:07 +0200
Commit message:

 chore: remove R/methods-fragments.R (moved to PSMatch)
Package: MSnbase
Commit: bee84832e8d54277a56c13f11aeb3f5a3f7f7891
Author: Laurent Gatto <laurent.gatto@gmail.com>
Date: 2025-03-17 11:32:08 +0100
Commit message:

 Update check-bioc.yml
Package: MSnbase
Commit: d2f33c5a0bd36a4ac16ea8e03a683a0f0032f281
Author: Laurent Gatto <laurent.gatto@gmail.com>
Date: 2025-03-17 11:30:11 +0100
Commit message:

 Update check-bioc.yml
Package: systemPipeShiny
Commit: 78fbb7db68f97c67b14801c8a8a9ab9d562aca72
Author: lz100 <35240440+lz100@users.noreply.github.com>
Date: 2025-04-10 22:01:12 -0700
Commit message:

 Merge pull request #107 from lz100/devel

prepare for 1.18 bug fix and changes
Package: systemPipeShiny
Commit: d3e29aa84752d64e314e8c43a50f59bacb44921a
Author: Le Zhang <35240440+lz100@users.noreply.github.com>
Date: 2025-04-10 22:00:24 -0700
Commit message:

 chore: update NEWS.md for systemPipeShiny 1.18.0 release; add major and minor changes, and bug fixes
Package: systemPipeShiny
Commit: e6be4bec18973133b90c22e6fb341442bb8c7e0a
Author: Le Zhang <35240440+lz100@users.noreply.github.com>
Date: 2025-04-10 21:54:45 -0700
Commit message:

 chore: update Roxygen version and clean up documentation for various functions
Package: systemPipeShiny
Commit: 1f21850cad71cc003694f836422976aa014a599a
Author: Le Zhang <35240440+lz100@users.noreply.github.com>
Date: 2025-04-10 21:50:21 -0700
Commit message:

 feat: add new workflow options for Single Cell RNAseq, BLAST, and Cheminformatics; update compatibility information
Package: systemPipeShiny
Commit: 1a5b6d60d888c1769f11afbce9d7407392561ed8
Author: Le Zhang <35240440+lz100@users.noreply.github.com>
Date: 2025-04-10 21:19:49 -0700
Commit message:

 fix: correct container function name in vs_esqUI to match esquisse package
Package: systemPipeShiny
Commit: 6512369da537a8fa929583d016d44991e3f50877
Author: Le Zhang <35240440+lz100@users.noreply.github.com>
Date: 2025-04-10 21:11:47 -0700
Commit message:

 fix: remove hover effect and transition from header logo in welcome page
Package: systemPipeShiny
Commit: 103b523c1cef63e903aca033e43d369cf7b918fd
Author: Le Zhang <35240440+lz100@users.noreply.github.com>
Date: 2025-04-10 20:53:19 -0700
Commit message:

 fix: wf page buttons not working due to shiny update , switch method to init input and update css
Package: systemPipeShiny
Commit: db03356037b60be629978d43610a9df9c401b360
Author: Le Zhang <35240440+lz100@users.noreply.github.com>
Date: 2025-04-10 20:04:52 -0700
Commit message:

 fix: update return statement in checkModulePkgs_internal to use glue for missing package installation instructions
Package: systemPipeShiny
Commit: 83abcb7840a36ea286f07cb4e1540901683ea6a6
Author: Le Zhang <35240440+lz100@users.noreply.github.com>
Date: 2025-04-10 20:04:41 -0700
Commit message:

 feat: bump version to 1.17.1 and update package dependencies;
Package: cfTools
Commit: cbbfd667e42b4c5f351b401d98173a9f41a779ab
Author: RoseHuRan <huran@ucla.edu>
Date: 2025-04-10 22:55:12 -0400
Commit message:

 update NEWS
Package: ADAMgui
Commit: 99a5a06a2a6fabb4c263635c0daad880cf1498e4
Author: jrybarczyk <jose.luiz@unesp.br>
Date: 2025-04-10 23:25:33 -0300
Commit message:

 update vignette
Package: topdownr
Commit: 7b8a713a22dd207595079a1e83354daf19a429e2
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2025-04-10 23:11:18 +0200
Commit message:

 fix: adapt to new argument name
Package: topdownr
Commit: 7cc10c8d3b112bba59a0d69b31fd128ff54d6040
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2025-04-10 22:27:16 +0200
Commit message:

 docs: add newlines
Package: topdownr
Commit: 226ada55bd9fe7e655d01adf192ab7928d159b98
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2025-04-10 22:23:28 +0200
Commit message:

 ci: update bioc-check gha workflow
Package: topdownr
Commit: dabb6227f5ebd3d21fa045591efafdc305764048
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2025-04-10 22:09:05 +0200
Commit message:

 refactor: adapt to changed return value of PSMatch::calculateFragments introduced in rformassspectrometry/PSMatch#19
Package: topdownr
Commit: f66e1eccce20291e478a83f445241f691f971a0c
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2025-04-10 21:54:48 +0200
Commit message:

 docs: fix typo
Package: topdownr
Commit: 98a76c35a39dd146d4957f220c35a5ba9dea6b8f
Author: Sebastian Gibb <mail@sebastiangibb.de>
Date: 2025-04-10 21:53:43 +0200
Commit message:

 refactor: use complete argument names to avoid partial matching warning
Package: mspms
Commit: 186ccbbc083f90015780705ea53cf755246f8a6f
Author: Charlie Bayne <baynec2@gmail.com>
Date: 2025-04-07 20:43:24 -0700
Commit message:

 Added support for limma based statistics.
Package: mspms
Commit: 4a2ab326e1279b5539f0fbe0455df524a285210f
Author: Charlie Bayne <baynec2@gmail.com>
Date: 2025-01-28 01:07:35 -0500
Commit message:

 added limma based statistics
Package: mspms
Commit: 826a77f090a197971841b1caccab89b09bbed725
Author: Charlie Bayne <baynec2@gmail.com>
Date: 2025-01-28 01:07:17 -0500
Commit message:

 Added limma based statistics.
Package: mspms
Commit: f89f846a9164a84cf42eb4693e552eb33b3be574
Author: Charlie Bayne <baynec2@gmail.com>
Date: 2025-01-17 16:21:42 -0800
Commit message:

 fixed p.adj.signif bug
Package: mspms
Commit: a11a254823cd4662639cc4b0777a492e8ad27be8
Author: Charlie Bayne <baynec2@gmail.com>
Date: 2025-01-17 16:21:11 -0800
Commit message:

 fixed "p.adj.signif" bug
Package: geomeTriD
Commit: 8dc8e7fcdd446417f60ca9305146f521499d6bb4
Author: Jianhong Ou <jou@JNXKY095H1.local>
Date: 2025-04-10 15:37:32 -0400
Commit message:

 add createTADGeometries function.
Package: BreastSubtypeR
Commit: d8c15cf50a2d76bde32e77191edb6a1c8b68d950
Author: yqkiuo <44391853+yqkiuo@users.noreply.github.com>
Date: 2025-04-10 20:51:23 +0200
Commit message:

 Fix vignette build error by adding BiocStyle to Suggests
Package: gDNAx
Commit: 5dbeed5ef12e6fb5553a49fe05977dc4a2665c12
Author: Robert Castelo <robert.castelo@upf.edu>
Date: 2025-04-10 20:13:52 +0200
Commit message:

 Bump version to see if the Windows build works again
Package: MetaboDynamics
Commit: 5a4b2e2e578d233171b008e1a4420cf6fe476a16
Author: ada697e <katja.danielzik@uni-due.de>
Date: 2025-04-10 19:57:39 +0200
Commit message:

 take get_ORA_annotations out
Package: Ibex
Commit: a28b36486f61aee69c5ed74e1a56886d770b3246
Author: theHumanBorch <ncborch@gmail.com>
Date: 2025-04-10 12:30:15 -0500
Commit message:

 update data documentation
Package: Ibex
Commit: 5c4cf1ba01f869ce5d87569c3f7a41e7255c3cfc
Author: theHumanBorch <ncborch@gmail.com>
Date: 2025-04-09 11:33:25 -0500
Commit message:

 Update Ibex.matrix.R

remove ifelse
Package: splatter
Commit: c455be9cdeae79d74b469a4ccd76d17d74074108
Author: Luke Zappia <lazappi@users.noreply.github.com>
Date: 2025-04-10 19:10:52 +0200
Commit message:

 Update NEWS for release
Package: splatter
Commit: ed5a25aca0668f69f67f396d93243e5a028c50d8
Author: Luke Zappia <lazappi@users.noreply.github.com>
Date: 2025-02-25 07:24:32 +0100
Commit message:

 Merge pull request #180 from Oshlack/dependabot/github_actions/JamesIves/github-pages-deploy-action-4.7.3
Package: splatter
Commit: 7c20220c7e5b05e4448ace61a08c5fb7a4094c38
Author: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Date: 2025-02-24 16:32:24 +0000
Commit message:

 Bump JamesIves/github-pages-deploy-action from 4.7.2 to 4.7.3

Bumps [JamesIves/github-pages-deploy-action](https://github.com/jamesives/github-pages-deploy-action) from 4.7.2 to 4.7.3.
- [Release notes](https://github.com/jamesives/github-pages-deploy-action/releases)
- [Commits](https://github.com/jamesives/github-pages-deploy-action/compare/v4.7.2...v4.7.3)

---
updated-dependencies:
- dependency-name: JamesIves/github-pages-deploy-action
  dependency-type: direct:production
  update-type: version-update:semver-patch
...

Signed-off-by: dependabot[bot] <support@github.com>
Package: splatter
Commit: 33ff7952e306d6b62964fda70117da2c6dc04361
Author: Luke Zappia <lazappi@users.noreply.github.com>
Date: 2024-12-10 07:25:29 +0100
Commit message:

 Merge pull request #179 from Oshlack/dependabot/github_actions/JamesIves/github-pages-deploy-action-4.7.2

Bump JamesIves/github-pages-deploy-action from 4.6.9 to 4.7.2
Package: splatter
Commit: 7f7ca71d8ccaef42b482fe8a81ad4678a667b834
Author: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Date: 2024-12-09 16:16:02 +0000
Commit message:

 Bump JamesIves/github-pages-deploy-action from 4.6.9 to 4.7.2

Bumps [JamesIves/github-pages-deploy-action](https://github.com/jamesives/github-pages-deploy-action) from 4.6.9 to 4.7.2.
- [Release notes](https://github.com/jamesives/github-pages-deploy-action/releases)
- [Commits](https://github.com/jamesives/github-pages-deploy-action/compare/v4.6.9...v4.7.2)

---
updated-dependencies:
- dependency-name: JamesIves/github-pages-deploy-action
  dependency-type: direct:production
  update-type: version-update:semver-minor
...

Signed-off-by: dependabot[bot] <support@github.com>
Package: zellkonverter
Commit: 7493c5c6b1ee9a3a5245a56a6327da1df8604416
Author: Luke Zappia <lazappi@users.noreply.github.com>
Date: 2025-04-10 19:02:54 +0200
Commit message:

 Prepare NEWS for release
Package: zellkonverter
Commit: cc72eceba8cf5b6b1ebb6e64ffe086c194e09c1f
Author: Luke Zappia <lazappi@users.noreply.github.com>
Date: 2025-04-10 19:02:33 +0200
Commit message:

 Bump devel version
Package: zellkonverter
Commit: a6c053daec65385c6c2f911fd5992e7dc728f76b
Author: Luke Zappia <lazappi@users.noreply.github.com>
Date: 2025-04-10 19:01:41 +0200
Commit message:

 Modify SCE2AnnData() to return dgRMatix assays
Package: zellkonverter
Commit: 27390e94d9a63f058f491edb0896c9bb17058e9f
Author: Luke Zappia <lazappi@users.noreply.github.com>
Date: 2025-04-10 17:24:51 +0200
Commit message:

 Add tests for anndata v0.10.9
Package: pRoloc
Commit: 6f7c028a9197cd94bede619322bb17c0f54e89e9
Author: Lisa Breckels <lms79@cam.ac.uk>
Date: 2025-04-10 17:43:45 +0100
Commit message:

 remove long title from mcmc_plot_probs
Package: Coralysis
Commit: 97623d9cc8141bf2bc39dac8f92ec82e2b869289
Author: antonioggsousa <antonioggsousa@gmail.com>
Date: 2025-04-10 19:09:55 +0300
Commit message:

 Fixing function examples
Package: Coralysis
Commit: e3b0c0fc4ba40cb77378bd961522993c8f087ee5
Author: antonioggsousa <antonioggsousa@gmail.com>
Date: 2025-04-10 18:11:33 +0300
Commit message:

 Adding testthat
Package: Coralysis
Commit: 8161fc6b4676d44063f9b72d12df9d776108cd38
Author: antonioggsousa <antonioggsousa@gmail.com>
Date: 2025-04-10 18:11:01 +0300
Commit message:

 Re-running vignettes for v.0.99.4
Package: Coralysis
Commit: 77f5ab9d87e0eb84aa6677895b60be41d3c3ef19
Author: antonioggsousa <antonioggsousa@gmail.com>
Date: 2025-04-10 18:10:25 +0300
Commit message:

 Version 0.99.4
Package: Coralysis
Commit: 7d9d99cbc07bc50105efedd964945d1126acf0d3
Author: antonioggsousa <antonioggsousa@gmail.com>
Date: 2025-04-10 18:09:50 +0300
Commit message:

 Fine-tune functions to address Bioconductor requirements
Package: Coralysis
Commit: c023e26d68a825f20e38e4e4d1bf9d6ccc53f54e
Author: antonioggsousa <antonioggsousa@gmail.com>
Date: 2025-04-03 13:14:25 +0300
Commit message:

 Changing vignettes format to meet BioStyle required by Bioconductor
Package: Moonlight2R
Commit: f025fe83b8b155cfdb4df0a4c710d179ec9103c2
Author: Matteo Tiberti <matteo.tiberti@gmail.com>
Date: 2025-04-10 17:08:05 +0200
Commit message:

 changed default argument of `stabClassMAVISp` in TFinfluence docs (#137)

* changed default in TFinfluence docs

* updated man file using roxygen

* version bump
Package: orthos
Commit: ba13760507095b57fb23ee4aaed5c3d023506a2f
Author: Panagiotis Papasaikas <panp80@gmail.com>
Date: 2025-04-10 16:13:34 +0200
Commit message:

 Merge pull request #15 from fmicompbio/update-envs-202504

Update envs
Package: orthos
Commit: a8498e5cff4016f6e89dc82c732bdcfdaf7754c3
Author: Charlotte Soneson <charlottesoneson@gmail.com>
Date: 2025-04-10 11:58:09 +0200
Commit message:

 Use linewidth instead of size for geom_violin
Package: orthos
Commit: 241beaa807e49da7af59bef6171bf6a2e68ff433
Author: Charlotte Soneson <charlottesoneson@gmail.com>
Date: 2025-04-10 11:43:50 +0200
Commit message:

 Bump version
Package: orthos
Commit: 18cf4c8eeeb53d99452ed4f0952929292d0a871a
Author: Charlotte Soneson <charlottesoneson@gmail.com>
Date: 2025-04-10 10:39:49 +0200
Commit message:

 Adjust package versions
Package: orthos
Commit: 454784f0192420eb7e158c9da1e4715b87496d19
Author: Charlotte Soneson <charlottesoneson@gmail.com>
Date: 2025-04-10 09:25:59 +0200
Commit message:

 Add Intel mac runner
Package: orthos
Commit: 8e6d391fa2c192308e1bd13ff6d979d2bd65ff1c
Author: Charlotte Soneson <charlottesoneson@gmail.com>
Date: 2025-04-10 09:25:03 +0200
Commit message:

 Update environments
Package: miaTime
Commit: 063b7d76affccb8098aea94356525955cf204f7a
Author: Muluh <127390183+Daenarys8@users.noreply.github.com>
Date: 2025-04-06 09:47:10 +0100
Commit message:

 Fix latex xter error (#108)

Signed-off-by: Daena Rys <rysdaena8@gmail.com>
Package: BiocBookDemo
Commit: 99acc283c42c3686da425b824da7060ed41160eb
Author: js2264 <jacquesserizay@gmail.com>
Date: 2025-04-10 13:40:07 +0200
Commit message:

 bump to 1.5.1
Package: BiocBookDemo
Commit: 046901676d275025dc2c53da2b1c9db0ec613e4a
Author: js2264 <jacquesserizay@gmail.com>
Date: 2025-04-10 13:33:45 +0200
Commit message:

 fix: deactivate pdf rendering for now
Package: BiocBookDemo
Commit: 42e84cd89e920dabfba02576fa4e6e1bad29e7b9
Author: js2264 <jacquesserizay@gmail.com>
Date: 2025-04-10 13:09:14 +0200
Commit message:

 fix: add title to stub
Package: BiocBookDemo
Commit: 97e648ce27876fff91670ee11037e4f3a7429ce2
Author: js2264 <jacquesserizay@gmail.com>
Date: 2025-04-10 13:02:03 +0200
Commit message:

 fix: move yml config keys around
Package: BiocBookDemo
Commit: d19309e78887f29e2b6f6deae728da31cc6d6cc7
Author: js2264 <jacquesserizay@gmail.com>
Date: 2025-04-10 13:01:47 +0200
Commit message:

 ci: update actions
Package: ExpressionAtlas
Commit: 421bf7024a2d7756b3b03854da376d1c8826969d
Author: Pedro Madrigal <pmadrigal@ebi.ac.uk>
Date: 2025-04-10 11:44:35 +0100
Commit message:

 add date
Package: ExpressionAtlas
Commit: 57cc9dafc0f0f80fa6e5722f4ea73b7ad6d36d5e
Author: Pedro Madrigal <pmadrigal@ebi.ac.uk>
Date: 2025-04-10 11:42:28 +0100
Commit message:

 Merge branch 'master-rel-3-20' of https://github.com/ebi-gene-expression-group/bioconductor-ExpressionAtlas into master-rel-3-20

# Conflicts:
#	DESCRIPTION
Package: ExpressionAtlas
Commit: 838632ddb1212ee2c11420b7f6b92ff2ce51a65a
Author: Pedro Madrigal <pmadrigal@ebi.ac.uk>
Date: 2025-04-10 11:16:00 +0100
Commit message:

 1.99.6
Package: RFLOMICS
Commit: cdd4f7d9d7417927a0d5279758f78c76dac502e8
Author: HULOT Audrey <audrey.hulot@inrae.fr>
Date: 2025-04-10 11:56:39 +0200
Commit message:

 bump version
Package: RFLOMICS
Commit: cadc3807238a8855056354d35756b1c27a18c07e
Author: HULOT Audrey <audrey.hulot@inrae.fr>
Date: 2025-04-10 11:44:52 +0200
Commit message:

 add condition to skip test.
Package: MSstats
Commit: bb51b2064056de99ca12e384cc3e44b41f27e191
Author: Mateusz Staniak <mtst@mstaniak.pl>
Date: 2025-04-10 10:17:42 +0200
Commit message:

 version bump
Package: MSstats
Commit: a6f295844d877670b95d82280b96f3c108eb5108
Author: tonywu1999 <wu.anthon@northeastern.edu>
Date: 2025-04-07 13:49:51 -0400
Commit message:

 docs(groupComparison): Provide documentation on edge cases in ComparisonResult table (#159)

* docs(groupComparison): Provide documentation on edge cases in ComparisonResult table

* bug(linear-summary): Fix bug regarding bitwise operator
Package: MSstats
Commit: a1ae61d18d45f85add8547e6a12c3b189e805ad8
Author: tonywu1999 <wu.anthon@northeastern.edu>
Date: 2025-04-07 10:02:05 -0400
Commit message:

 chore(MSstatsSummarize): Deprecate MSstatsSummarize function (#158)
Package: MSstats
Commit: ef67267d353f2eca2425a0909ce4e374a0835e06
Author: tonywu1999 <wu.anthon@northeastern.edu>
Date: 2025-03-12 17:32:27 -0400
Commit message:

 docs(vignette): Add information on how to adjust for covariates (#157)
Package: MSstatsConvert
Commit: 3c1d0085fceaf874a77c23792ac19ca64cb1c95c
Author: Mateusz Staniak <mtst@mstaniak.pl>
Date: 2025-04-10 10:07:40 +0200
Commit message:

 version bump
Package: MSstatsConvert
Commit: 62fbca28104b3ba7c14280b1fd07fd9a1eb3abed
Author: tonywu1999 <wu.anthon@northeastern.edu>
Date: 2025-04-07 10:00:55 -0400
Commit message:

 fix(pd-converter): Remove QuanInfo column after cleaning up PD data (#106)

* fix(pd-converter): Remove QuanInfo column after cleaning up PD data
Package: MSstatsConvert
Commit: 02e15072d1ed4e934616e51d2c5865915570eed2
Author: tonywu1999 <wu.anthon@northeastern.edu>
Date: 2025-03-20 19:30:07 -0400
Commit message:

 add initial validation function for spectronaut columns (#105)
Package: MSstatsConvert
Commit: 1730441913a4e14a19304b9803264303b266bcdd
Author: tonywu1999 <wu.anthon@northeastern.edu>
Date: 2025-01-17 18:07:58 -0500
Commit message:

 docs(DIANN): Update documentation on DIANN converter q-value filters (#104)
Package: MSstatsConvert
Commit: 01c991bcdf183b084d73ddac7e419aeabc6bb208
Author: tonywu1999 <wu.anthon@northeastern.edu>
Date: 2025-01-16 17:57:41 -0500
Commit message:

 docs(MSstatsBalancedDesign): Updated description of fill_incomplete parameter (#103)

* docs(MSstatsBalancedDesign): Updated description of fill_incomplete parameter

* remove man file for .validatePDTMTInputColumns
Package: BioNAR
Commit: 5e880595906fbcf14fd3a7313317e22270324861
Author: Anatoly Sorokin <lptolik@gmail.com>
Date: 2025-04-10 16:11:17 +0900
Commit message:

 Fix News before release
Package: BioNAR
Commit: 0f485cc1ee888ad0496a8838ecf5b6a2076a9da0
Author: Anatoly Sorokin <lptolik@gmail.com>
Date: 2025-03-27 11:25:44 +0900
Commit message:

 minor corrections in documentation
Package: TENET
Commit: 04162f44d755530b6db6fdb0bfc311605d49eae0
Author: Ethan Nelson-Moore <nelsonmo@usc.edu>
Date: 2025-04-09 22:02:20 -0700
Commit message:

 v0.99.8: Regenerate documentation (missed in previous release)
Package: ClassifyR
Commit: 95a55cc9759a50df21f5c0de5ceea5d8af4b7afd
Author: Dario Strbenac <dario@maths.usyd.edu.au>
Date: 2025-04-10 13:20:12 +1000
Commit message:

 lineColours check works if it is a vector longer than one.
Package: limpa
Commit: 61ca22da8b4a4cc73c1d4a6fd787846efd04ad45
Author: Gordon Smyth <smyth@wehi.edu.au>
Date: 2025-04-10 13:00:14 +1000
Commit message:

 limpa 0.99.13
- Simply NEWS.Rd ready for Bioc 3.21 release.
Package: limpa
Commit: 89bbcdc7b1d5df421988a75a68dbac3f3b557044
Author: Gordon Smyth <smyth@wehi.edu.au>
Date: 2025-04-10 10:51:10 +1000
Commit message:

 Bump dates
Package: limpa
Commit: d9022ff1f7f89fe80e5c934fd5e9443310e2af48
Author: Gordon Smyth <smyth@wehi.edu.au>
Date: 2025-04-10 10:46:47 +1000
Commit message:

 limpa 0.99.12
- dpcQuant() and peptides2Proteins() now return essentially equal values if there are
multiple entirely imputed values for the same protein.
- Update readSpectronaut() to allow more flexibility regarding which columns are read.
- Bug fix to voomaLmFitWithImputation() for proteins
that are almost entirely imputed and have no remaining
degrees of freedom for estimating the residual variance.
Previously the degrees of freedom were not always being recognized as zero
because of floating point errors.
- New calculation of lost degrees of freedom in voomaLmFitWithImputation().
The new method always returns integer residual degrees of freedom and no longer assumes that entirely imputed values are all equal for the same gene.
- Remove reference to DIA in vignette, because limpa works for both DIA and DDA.
Package: sparrow
Commit: 1f03bea5db6dbb160067c8262cee934258b54fd4
Author: Steve Lianoglou <slianoglou@gmail.com>
Date: 2025-04-09 15:57:45 -0700
Commit message:

 trying to squach WARNINGS about some documentation defficiencies
Package: dada2
Commit: d50ef09fbafd99c41090ede4ac91b76ebf120716
Author: Ben Callahan <bcallah@ncsu.edu>
Date: 2025-04-09 14:41:53 -0400
Commit message:

 Fix error introduced in previous commit

Note to self, don't check in even seemingly trivial changes without running a package check!
Package: ProteinGymR
Commit: 8809c8adb63424558b70f9dce2b65a2d662882c0
Author: Tram Nguyen <tram_nguyen@hms.harvard.edu>
Date: 2025-04-09 14:24:23 -0400
Commit message:

 Merge pull request #39 from ccb-hms/update_heatmap

Update functions
Package: ProteinGymR
Commit: 5d4fbc641d3b4fd0ef894baf86309b06b1355d36
Author: tram-nguyen-n <tram_nguyen@hms.harvard.edu>
Date: 2025-04-09 18:22:24 +0000
Commit message:

 add correlation to visualization vignette
Package: ProteinGymR
Commit: c26285ac4d07a9e005dccfc76385104c2c184ce4
Author: tram-nguyen-n <tram_nguyen@hms.harvard.edu>
Date: 2025-04-09 16:25:40 +0000
Commit message:

 updated NAMESPACE related to marginals
Package: ProteinGymR
Commit: 3aba259e036869f3da81f9fd05e46f29cfd9f77b
Author: tram-nguyen-n <tram_nguyen@hms.harvard.edu>
Date: 2025-04-09 16:24:54 +0000
Commit message:

 added corr plot to visualization vignette
Package: ProteinGymR
Commit: 40a2f3d2ab16d580bbe5decb387f986fd3c895d3
Author: tram-nguyen-n <tram_nguyen@hms.harvard.edu>
Date: 2025-04-09 16:24:33 +0000
Commit message:

 update 79 models for available_models()
Package: ProteinGymR
Commit: 11f227f984c0345af0429b2372deb6b20fe0fa78
Author: tram-nguyen-n <tram_nguyen@hms.harvard.edu>
Date: 2025-04-09 16:24:11 +0000
Commit message:

 marginals for corr plot
Package: ProteinGymR
Commit: 14a0ebbf5c83dcfe3091ce2cea299cd5e4d15744
Author: tram-nguyen-n <tram_nguyen@hms.harvard.edu>
Date: 2025-04-08 20:40:34 +0000
Commit message:

 update metadata for all new v1.2 datasets
Package: ProteinGymR
Commit: 7be4dbd0023f3dc39e846c155672780fe828e01e
Author: tram-nguyen-n <tram_nguyen@hms.harvard.edu>
Date: 2025-04-08 20:39:53 +0000
Commit message:

 make 79 supervised model RDS data
Package: ProteinGymR
Commit: a86f959dc2d495023dd7747ec7212dcf26ffcf43
Author: tram-nguyen-n <tram_nguyen@hms.harvard.edu>
Date: 2025-04-08 20:39:06 +0000
Commit message:

 update zero show raw scores and 5 summary metrics benchmarks for v1.2 (79 models)
Package: ProteinGymR
Commit: 2e1c83620a5e89f275fb3407480912b53269c394
Author: tram-nguyen-n <tram_nguyen@hms.harvard.edu>
Date: 2025-04-08 20:14:40 +0000
Commit message:

 add v1.2 zero shot scores
Package: ProteinGymR
Commit: 34eda019a1a085e075c546e63c958ae2656688c0
Author: tram-nguyen-n <tram_nguyen@hms.harvard.edu>
Date: 2025-03-26 18:28:58 +0000
Commit message:

 metadata for all pdb files individually
Package: ProteinGymR
Commit: b06031a45293339a6024a1f464089c54a6ddb45b
Author: Tram Nguyen <tram_nguyen@hms.harvard.edu>
Date: 2025-03-25 17:22:40 -0400
Commit message:

 Merge pull request #38 from ccb-hms/devel

Merge pull request #37 from ccb-hms/update_heatmap
Package: ProteinGymR
Commit: bc546756421e7fca74c6ca4617eb192eef516caa
Author: tram-nguyen-n <tram_nguyen@hms.harvard.edu>
Date: 2025-03-25 21:20:54 +0000
Commit message:

 add marginals to correlation plot
Package: ProteinGymR
Commit: 0b573f9ba5c02b7e5722bf6d1b090f5c23a92365
Author: Tram Nguyen <tram_nguyen@hms.harvard.edu>
Date: 2025-03-21 14:06:54 -0400
Commit message:

 Merge pull request #37 from ccb-hms/update_heatmap

Update heatmap and vignettes
Package: ProteinGymR
Commit: 54a3d01b9b35d8dc79f539e6fb740ff1ad5ae5f8
Author: Tram Nguyen <tram_nguyen@hms.harvard.edu>
Date: 2025-03-21 14:03:38 -0400
Commit message:

 Merge pull request #36 from ccb-hms/devel

Merge pull request #33 from ccb-hms/update_heatmap
Package: ProteinGymR
Commit: beb786e8b34677ad22529767bec474b2303b0c49
Author: tram-nguyen-n <tram_nguyen@hms.harvard.edu>
Date: 2025-03-21 18:01:47 +0000
Commit message:

 edits to vignette
- separate Import from Visualization
- new vignette visualizing heatmap + 3d structure
Package: ProteinGymR
Commit: 9824aa9ecf0228fe663ac1e113aaf853dd384533
Author: tram-nguyen-n <tram_nguyen@hms.harvard.edu>
Date: 2025-03-21 18:00:56 +0000
Commit message:

 if `model_data` missing, load default.
Package: ProteinGymR
Commit: b74d64578173e7e834257e640f75710441d196e6
Author: tram-nguyen-n <tram_nguyen@hms.harvard.edu>
Date: 2025-03-21 18:00:08 +0000
Commit message:

 if `dms_data` missing, load default
Package: ProteinGymR
Commit: d32102509cf8e10007b0a9b97f9c032497103164
Author: tram-nguyen-n <tram_nguyen@hms.harvard.edu>
Date: 2025-03-14 00:54:04 +0000
Commit message:

 added additional models to `available_models()`
Package: ProteinGymR
Commit: 8ebb3f93283e5e99ac21a15d29a0eb2df520037c
Author: Tram Nguyen <tram_nguyen@hms.harvard.edu>
Date: 2025-03-13 20:05:02 -0400
Commit message:

 Merge pull request #33 from ccb-hms/update_heatmap

merge `update_heatmap` branch to `devel`
Package: ProteinGymR
Commit: fabaacbc0a3ae91975aac80b99813071911e986a
Author: tram-nguyen-n <tram_nguyen@hms.harvard.edu>
Date: 2025-03-14 00:03:51 +0000
Commit message:

 added back blue in heatmap
Package: ProteinGymR
Commit: 9d9861461adbeaaa1fad0745a72852ffc9442498
Author: tram-nguyen-n <tram_nguyen@hms.harvard.edu>
Date: 2025-03-13 23:59:42 +0000
Commit message:

 - added function for model heatmap `plot_zeroshot_heatmap()`

- script for downloading and making zero shot score Rdata list
Package: ProteinGymR
Commit: e0832c5d99dfce6c4d3cdc8e3a515d988456e906
Author: tram-nguyen-n <tram_nguyen@hms.harvard.edu>
Date: 2025-03-13 20:42:33 +0000
Commit message:

 add `@Returns` description for `plot_dms_heatmap()`
Package: ProteinGymR
Commit: 649dbc09b1a4ff5fcd44a0902113f3abe5053c7c
Author: tram-nguyen-n <tram_nguyen@hms.harvard.edu>
Date: 2025-03-13 19:24:02 +0000
Commit message:

 removed `pdb_structure` export
Package: GSVA
Commit: f58cefe792fcfc28eff7b5c6c1ee998685f67da7
Author: Robert Castelo <robert.castelo@upf.edu>
Date: 2025-04-09 19:12:31 +0200
Commit message:

 Avoid bandwith values close to zero in kernel ECDF calculations
Package: ExpressionAtlas
Commit: cb8f254ac795ce1d4d089aacff9001b62253749a
Author: Pedro Madrigal <pmadrigal@ebi.ac.uk>
Date: 2025-04-09 16:26:52 +0100
Commit message:

 roll back
Package: ExpressionAtlas
Commit: feeebb7efd1ab759437d1afd768db15adc5bd459
Author: Pedro Madrigal <pmadrigal@ebi.ac.uk>
Date: 2025-04-09 16:22:53 +0100
Commit message:

 Solve the Error -  Illegal version bump from 1.99.4 to 1.35.1
Package: ExpressionAtlas
Commit: 5ebf3839509ebc7d770db7f883fa22a89ecd0666
Author: Pedro Madrigal <pmadrigal@ebi.ac.uk>
Date: 2025-04-09 16:14:26 +0100
Commit message:

 roll back
Package: mitology
Commit: 39f1b2b538cd462788545788d178829d83b33052
Author: Stefania Pirrotta <s.pirrotta.sp@gmail.com>
Date: 2025-04-09 17:04:20 +0200
Commit message:

 adjust R version in description file
Package: BSgenomeForge
Commit: a05fb73a8ad32555cbaa6de2846e962364f60ec7
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2025-04-09 07:40:54 -0700
Commit message:

 add a few missing Rd \link{} targets package anchors
Package: orthos
Commit: b22595c71983b4ba9f5ab1950525af6606220aaa
Author: Charlotte Soneson <charlottesoneson@gmail.com>
Date: 2025-04-09 12:49:23 +0200
Commit message:

 Merge pull request #14 from fmicompbio/reticulate-1.42

Reticulate 1.42
Package: orthos
Commit: f6ecc7e3dc2a0fe18977e88716b0edef09329b69
Author: Charlotte Soneson <charlottesoneson@gmail.com>
Date: 2025-04-09 09:13:37 +0200
Commit message:

 Avoid warnings about non-existing variable
Package: orthos
Commit: 7dc623cfcbe87da535c16f04200339a658e55d28
Author: Charlotte Soneson <charlottesoneson@gmail.com>
Date: 2025-04-09 08:47:09 +0200
Commit message:

 Set RETICULATE_ENABLE_PYTHON_FINALIZER to "yes"
Package: GSVA
Commit: 5cf33306fb66b0ed4889f3dd874cb2236738aa95
Author: Robert Castelo <robert.castelo@upf.edu>
Date: 2025-04-09 12:14:58 +0200
Commit message:

 Bump version
Package: GSVA
Commit: 7dc9e40069d36a7cfa647f1071892fcd6a4502dc
Author: Axel Klenk <72612834+axelklenk@users.noreply.github.com>
Date: 2025-04-08 20:42:31 +0200
Commit message:

 Merge pull request #241 from rcastelo/240-examplereadgmt-exceeds-run-time-limit-of-5-seconds

use a smaller GMT file in the example for readGMT() and suppress pack…
Package: GSVA
Commit: 0494acf82df83899ccc1eb8af089053612f46d10
Author: Axel Klenk <axel.klenk@gmail.com>
Date: 2025-04-08 20:36:20 +0200
Commit message:

 use a smaller GMT file in the example for readGMT() and suppress package startup messages in all examples
Package: limma
Commit: 1d3c7bbdd1c13b4adfe06b12209b280df65d3d11
Author: Gordon Smyth <smyth@wehi.edu.au>
Date: 2025-04-09 20:07:59 +1000
Commit message:

 limma 3.63.13

- plotSA() no longer plots genes with df.residual=0 and no longer
  gives a warning when such genes are present.
Package: crupR
Commit: 2e245f89513abf2614760e661d40f66f99586fb5
Author: akbariomgba <persiaakom@hotmail.com>
Date: 2025-04-09 11:33:43 +0200
Commit message:

 Removed the package file (hopefully)
Package: PhyloProfile
Commit: 250856b2fd165b6092f53b154c893873c8672c47
Author: AnnamTran <trvinh@gmail.com>
Date: 2025-04-09 10:27:17 +0200
Commit message:

 fixed high rank filter
Package: GBScleanR
Commit: 670b62269b7cc17b4392f051a328791a3985f20c
Author: tomoyukif <f.tomoyuki@okayama-u.ac.jp>
Date: 2025-04-09 16:38:13 +0900
Commit message:

 Update manuals
Package: msa
Commit: c653d2dee94244e7ecb9571f65d6eb57cc7c7749
Author: UBod <ulrich@bodenhofer.com>
Date: 2025-04-09 09:29:55 +0200
Commit message:

 fix to avoid crash in ClustalOmega code; version number bumped to 1.39.5
Package: msa
Commit: cf5e66463a879d7d5a9ac7896dd51db8a6494b02
Author: UBod <ulrich@bodenhofer.com>
Date: 2025-04-09 09:10:19 +0200
Commit message:

 Merge pull request #36 from rualmey/devel

fix segfault when doing profile alignment
Package: msa
Commit: 1d388d7e15c87a5d374415b820035dec007c824d
Author: Ruben Almey <94168719+rualmey@users.noreply.github.com>
Date: 2025-04-08 14:05:11 +0000
Commit message:

 fix segfault when doing profile alignment
Package: extraChIPs
Commit: 2657841b2a2e836676e58b981b7320ab60361fb2
Author: Stevie Ped <stephen.pederson.au@gmail.com>
Date: 2025-04-08 23:48:12 +0930
Commit message:

 Added fill to plotPCA
Package: gemma.R
Commit: 4b07e3f5c619ddd3ff842727244386c399f6fed8
Author: OganM <ogan.mancarcii@gmail.com>
Date: 2025-04-08 16:35:46 -0700
Commit message:

 specification dump
Package: gemma.R
Commit: 235ecd377542cb44fa1f55eff12a9ec336bdf913
Author: OganM <ogan.mancarcii@gmail.com>
Date: 2025-04-08 16:35:19 -0700
Commit message:

 update news
Package: gemma.R
Commit: 87f68176a9be3e15f2d7a7a7bf83f26c7cc6e4ae
Author: OganM <ogan.mancarcii@gmail.com>
Date: 2025-04-03 16:22:34 -0700
Commit message:

 fix get_dataset_design example
Package: gemma.R
Commit: 8e282a3bd47564b227ffc0b82e8b31f6e19ff39b
Author: OganM <ogan.mancarcii@gmail.com>
Date: 2025-04-03 16:01:51 -0700
Commit message:

 version bump
Package: gemma.R
Commit: 0e7d3eba0f410da0ca5e3f119362e2c4a4cd0eca
Author: OganM <ogan.mancarcii@gmail.com>
Date: 2025-04-03 16:01:23 -0700
Commit message:

 documentation
Package: gemma.R
Commit: 666a25c2a2853600bb2af48d5cceecb9bcc0cde5
Author: OganM <ogan.mancarcii@gmail.com>
Date: 2025-04-03 14:44:40 -0700
Commit message:

 move subset functions to internal for now
Package: gemma.R
Commit: 659a9e39e23e9790cf143fd2fa17f62a56e3a965
Author: OganM <ogan.mancarcii@gmail.com>
Date: 2025-04-03 13:27:56 -0700
Commit message:

 subset documentation
Package: gemma.R
Commit: 8f82ae41e47826cfaaa353ab3c8aea9a05dda63b
Author: OganM <ogan.mancarcii@gmail.com>
Date: 2025-04-02 21:15:27 -0700
Commit message:

 subset functions required to process samples
Package: gemma.R
Commit: 33e0c274ea2f61a0d20b2e3c448946d83160f38f
Author: OganM <ogan.mancarcii@gmail.com>
Date: 2025-04-01 18:57:46 -0700
Commit message:

 typo
Package: gemma.R
Commit: f5ae9e0fd6cfeac1be9b89366b5d6434e83777d9
Author: OganM <ogan.mancarcii@gmail.com>
Date: 2025-04-01 18:57:20 -0700
Commit message:

 reorder out of place endpoints
Package: gemma.R
Commit: f88e5d94c78568d86ff322aecba4d6c29bfabee7
Author: OganM <ogan.mancarcii@gmail.com>
Date: 2025-04-01 18:34:42 -0700
Commit message:

 deprecate get_child_terms
Package: gemma.R
Commit: 4a0ac139f979bb18c1108421cf4e16c8634832a7
Author: OganM <ogan.mancarcii@gmail.com>
Date: 2025-04-01 18:34:27 -0700
Commit message:

 make get_dataset_design internal. not removed for possible debugging utility
Package: gemma.R
Commit: f894e721c70c28a6c1b24da87c5a7f03d3756241
Author: OganM <ogan.mancarcii@gmail.com>
Date: 2025-04-01 15:35:41 -0700
Commit message:

 test fix
Package: gemma.R
Commit: 6286f47040acaab719df7133c6cacf3c376268a7
Author: OganM <ogan.mancarcii@gmail.com>
Date: 2025-03-31 20:31:29 -0700
Commit message:

 documentation fix
Package: gemma.R
Commit: e626e7ff03e4e27b541287250efa628197582ccf
Author: OganM <ogan.mancarcii@gmail.com>
Date: 2025-03-31 20:21:12 -0700
Commit message:

 documentation
Package: gemma.R
Commit: b0e971034793ce2804388e86c8d0ef767d5871b2
Author: OganM <ogan.mancarcii@gmail.com>
Date: 2025-03-31 20:20:51 -0700
Commit message:

 get_annotation_children and get_annotation_parents
Package: gemma.R
Commit: f05312ee250963d6f3ac2a602fdc1b44efea3a96
Author: OganM <ogan.mancarcii@gmail.com>
Date: 2025-03-31 20:01:48 -0700
Commit message:

 registry re-run
Package: gemma.R
Commit: 69f6d72f668fb11b2111dff38a3176be47acf9df
Author: OganM <ogan.mancarcii@gmail.com>
Date: 2025-03-31 19:50:21 -0700
Commit message:

 gemma.R vignette fix
Package: gemma.R
Commit: 77a33770d98f60cf0ce5a81db3fb1a21972960f1
Author: OganM <ogan.mancarcii@gmail.com>
Date: 2025-03-31 19:09:17 -0700
Commit message:

 allow accessing out of data component
Package: gemma.R
Commit: 0bfaed1753c09578bf545344ca76ff392ef3ac21
Author: OganM <ogan.mancarcii@gmail.com>
Date: 2025-03-31 18:44:26 -0700
Commit message:

 allow title overrides in registry
Package: gemma.R
Commit: 80a10411891a1d3fdc2a6238086a27cd1e1a5c57
Author: OganM <ogan.mancarcii@gmail.com>
Date: 2025-03-31 17:35:20 -0700
Commit message:

 add annotation keyword
Package: gemma.R
Commit: 414d82f7b243c10904be81017b7fa5386f153a95
Author: ogan Mancarci <ogan.mancarci@gmail.com>
Date: 2024-12-11 13:47:11 -0800
Commit message:

 error message extraction fix for json output
Package: gemma.R
Commit: ef00dac95c09181eab04f8a33b2149192c8d79ae
Author: ogan Mancarci <ogan.mancarci@gmail.com>
Date: 2024-12-11 13:29:40 -0800
Commit message:

 get_dataset_expression_levels_for_genes resolves gene symbols correctly if all datasets is of the same taxon
Package: gemma.R
Commit: 63c6e845221edd3cef1172f9718f4323ab0512e3
Author: ogan Mancarci <ogan.mancarci@gmail.com>
Date: 2024-12-11 10:19:44 -0800
Commit message:

 convenience function to merge get_gene_differential_expression_values and the taxon specified version
Package: gemma.R
Commit: c08c8d0c7761a99d005bdcbba51646cef2bd0a23
Author: ogan Mancarci <ogan.mancarci@gmail.com>
Date: 2024-12-08 13:15:51 -0800
Commit message:

 pass HTTP error messages to users
Package: gemma.R
Commit: cf9e402ddd945e539ad62f5a534b1474b0db5244
Author: ogan Mancarci <ogan.mancarci@gmail.com>
Date: 2024-12-03 05:45:07 -0800
Commit message:

 Merge branch 'devel' of github.com:PavlidisLab/gemma.R into devel
Package: gemma.R
Commit: e82c5e0903f82520a168fbd34a568d9a1a9d3081
Author: Paul Pavlidis <paul@msl.ubc.ca>
Date: 2024-11-27 15:44:44 -0800
Commit message:

 Merge branch 'devel' of https://github.com/PavlidisLab/gemma.R into devel
Package: gemma.R
Commit: 9e2b638722aaa939d1b85b6dc98ac5053b2a7860
Author: ogan Mancarci <ogan.mancarci@gmail.com>
Date: 2024-11-26 12:33:49 -0800
Commit message:

 import kableExtra instead of suggest
Package: gemma.R
Commit: 28087686b84a64df74995ca469cd0ba992ed2fdb
Author: OganM <ogan.mancarci@gmail.com>
Date: 2024-10-22 14:02:55 -0700
Commit message:

 test for get_dataset_object consolidation tests
Package: imageTCGA
Commit: abf6c6c99abc8fc66d7208ab32364e4178ae20f3
Author: billila <ilaria.billato@studenti.unipd.it>
Date: 2025-04-09 01:04:14 +0200
Commit message:

 bump version
Package: imageTCGA
Commit: 410e037c784e3e822589a81c53214c525e115d2f
Author: billila <ilaria.billato@studenti.unipd.it>
Date: 2025-04-09 00:41:37 +0200
Commit message:

 add package in suggests
Package: imageTCGA
Commit: d607a18ee80aa420d8f0282d19128e4db004105a
Author: billila <ilaria.billato@studenti.unipd.it>
Date: 2025-04-09 00:38:37 +0200
Commit message:

 fix typo
Package: BloodCancerMultiOmics2017
Commit: 371b69d9fdf91b27833663129fd2a2113bba66f8
Author: MalgorzataOles <dr.malgorzata.oles@gmail.com>
Date: 2025-04-09 00:39:56 +0200
Commit message:

 Excluding IHW pckg from being loaded
Package: imageTCGA
Commit: db5da9194aea6536971a200480715bbbb5767b4f
Author: billila <ilaria.billato@studenti.unipd.it>
Date: 2025-04-08 21:46:16 +0200
Commit message:

 update README.md
Package: PhyloProfile
Commit: 79a5fc475b24a6976fea58cbfd197b2a9bc9572a
Author: AnnamTran <trvinh@gmail.com>
Date: 2025-04-08 22:07:22 +0200
Commit message:

 replace placeholder for orthoDB ver
Package: PhyloProfile
Commit: 9d3e36edf21b9c214db53384596ecf086b8e077f
Author: AnnamTran <trvinh@gmail.com>
Date: 2025-04-08 21:49:25 +0200
Commit message:

 scale var1/var2 to 0-1
Package: RbowtieCuda
Commit: b5a0f006f52c1b16171d2c93e636f039733e8108
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2025-04-08 11:55:05 -0700
Commit message:

 small tweak to .BBSoptions
Package: RbowtieCuda
Commit: b6c6cb2efb4207080b849c945dae3ae14eb8f288
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2025-04-08 11:07:56 -0700
Commit message:

 add .BBSoptions file
Package: Ibex
Commit: 61be251f8870a24f13fe9bb1473ddf10cfbafcae
Author: theHumanBorch <ncborch@gmail.com>
Date: 2025-04-08 12:44:24 -0500
Commit message:

 v0.99.9
Package: Ibex
Commit: 2ae029d5d73b63e5d894a99233349e833f484d9b
Author: theHumanBorch <ncborch@gmail.com>
Date: 2025-04-08 11:38:54 -0500
Commit message:

 Adding conditional for examples
Package: AnnotationDbi
Commit: c7bc88802af14c08eba01bca64b448d58a3c1683
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2025-04-08 10:39:15 -0700
Commit message:

 AnnotationDbi 1.69.1

- Fix unit tests
- Fix some minor formatting issues in man pages
Package: immApex
Commit: 5a14e60155c251d7935f7e1a26ebdd244445f90d
Author: theHumanBorch <ncborch@gmail.com>
Date: 2025-04-08 12:39:27 -0500
Commit message:

 Merge branch 'main' into devel

Updated single IMGT test pull for new nomenclature
Package: immApex
Commit: 0649a32dcce723c5ad8dd2c190e758ae8e0ef0e7
Author: theHumanBorch <ncborch@gmail.com>
Date: 2025-04-08 12:04:32 -0500
Commit message:

 update IMGT testthat data
Package: PhyloProfile
Commit: 44824bb9e44c58be54fba45c024e1ae20944575c
Author: AnnamTran <trvinh@gmail.com>
Date: 2025-04-08 19:20:26 +0200
Commit message:

 fixed orthoDB URL for seed IDs
Package: zellkonverter
Commit: e0950036cddc006f9fc84b5d4909a17a26e16265
Author: Luke Zappia <lazappi@users.noreply.github.com>
Date: 2025-04-08 18:21:34 +0200
Commit message:

 Bump dev version
Package: zellkonverter
Commit: fb329700e39d4be720619e2c6bdcb5b31482394e
Author: Luke Zappia <lazappi@users.noreply.github.com>
Date: 2025-04-08 18:20:25 +0200
Commit message:

 Style code
Package: zellkonverter
Commit: 9472bbb35096fcdb4df2c43c457a50a921e82d8d
Author: Luke Zappia <lazappi@users.noreply.github.com>
Date: 2025-04-08 18:06:33 +0200
Commit message:

 Add an environment for anndata v0.11.4
Package: zellkonverter
Commit: 870cc47ba5637e0d7ca6bb1ab9396294a281d023
Author: Luke Zappia <lazappi@users.noreply.github.com>
Date: 2025-04-08 17:11:51 +0200
Commit message:

 Disable anndata v0.7.6 tests on aarch64 Linux
Package: CexoR
Commit: 88a4e05d62d59e917bde3831217127c00434d8c0
Author: Pedro Madrigal <8195212+pmb59@users.noreply.github.com>
Date: 2025-04-07 17:48:43 +0100
Commit message:

 Update DESCRIPTION
Package: fCCAC
Commit: 16a208b873a5d0a088192b5bd536ea07b4bd711d
Author: Pedro Madrigal <pmadrigal@ebi.ac.uk>
Date: 2025-04-07 18:12:41 +0100
Commit message:

 Merge remote-tracking branch 'upstream/devel'
Package: fCCAC
Commit: f0a88b926590c0674bf067536e1692e35e387ed9
Author: Pedro Madrigal <8195212+pmb59@users.noreply.github.com>
Date: 2025-04-07 17:47:43 +0100
Commit message:

 Update DESCRIPTION
Package: GSVA
Commit: 4ae0f3780b3281fcf2d0c4235962a496e2eb9d42
Author: Robert Castelo <robert.castelo@upf.edu>
Date: 2025-04-08 17:57:12 +0200
Commit message:

 Bump version
Package: GSVA
Commit: 22c0328b8112c44aa0b55be2f71eb6f7d7dd5711
Author: Axel Klenk <72612834+axelklenk@users.noreply.github.com>
Date: 2025-04-08 15:30:03 +0200
Commit message:

 Merge pull request #239 from rcastelo/235-r-cmd-check-notes-caused-by-documentation

fix NOTE about 'non-topic package-anchored links'
Package: GSVA
Commit: ccef93a0174ae694eced8aa3773be9d6a3a7a01d
Author: Axel Klenk <axel.klenk@gmail.com>
Date: 2025-04-08 15:20:24 +0200
Commit message:

 fix NOTE about 'non-topic package-anchored links'
Package: ExpressionAtlas
Commit: 74f3a2a5d267f6933de102bf7262811451863ff4
Author: Pedro Madrigal <pmadrigal@ebi.ac.uk>
Date: 2025-04-08 16:51:39 +0100
Commit message:

 ensure version bump propagates to the repository visible to BiocManager::install()
Package: ExpressionAtlas
Commit: 69e9684656eadef58dd536e1428cdeb1aa2a7037
Author: Pedro Madrigal <pmadrigal@ebi.ac.uk>
Date: 2025-04-08 15:03:51 +0100
Commit message:

 change colour scale in two umap plots; bump version
Package: OmnipathR
Commit: 7e5f894b628444f6206e4fb7781c48bc8f53bad0
Author: deeenes <turei.denes@gmail.com>
Date: 2025-04-08 17:45:46 +0200
Commit message:

 Version bump: 3.15.14 → 3.15.99
Package: OmnipathR
Commit: ebb67afeaa63e6785512063145058489927b2912
Author: deeenes <turei.denes@gmail.com>
Date: 2025-04-08 17:43:16 +0200
Commit message:

 added news for upcoming release `4.0.0` (BioC 3.21)
Package: crupR
Commit: 545c02ab354f63d16645667a7d792de95aed88c2
Author: akbariomgba <persiaakom@hotmail.com>
Date: 2025-04-08 16:40:21 +0200
Commit message:

 Added the three final notes
Package: signifinder
Commit: 3abd8999bfa6c3e23c306613acab709a40876e3b
Author: Stefania Pirrotta <s.pirrotta.sp@gmail.com>
Date: 2025-04-08 16:20:54 +0200
Commit message:

 increase version number
Package: signifinder
Commit: 6ebc1165c8b45a6f3bf61f5d507c6431d908e572
Author: Stefania Pirrotta <s.pirrotta.sp@gmail.com>
Date: 2025-04-08 13:04:23 +0200
Commit message:

 adjust citation and description
Package: signifinder
Commit: f987e4c7ce0b5d86d79b36e785b1edbd81a06dcc
Author: Stefania Pirrotta <s.pirrotta.sp@gmail.com>
Date: 2025-04-08 13:04:06 +0200
Commit message:

 Adjust functions and tests
Package: ChemmineR
Commit: e65d9a61551a2fcd0a377bd7e497f264ad4c9a00
Author: khoran <khoran@cs.ucr.edu>
Date: 2025-04-03 08:11:41 -0700
Commit message:

 fixed bug with sdfid<- not working
Package: ChemmineR
Commit: 368bbd3bbc81a6fc86a7cadfcd2d5e72e09ba84a
Author: khoran <khoran@cs.ucr.edu>
Date: 2025-04-03 07:45:09 -0700
Commit message:

 fix bug with MASS value in V3000 formated SDFs
Package: imageTCGA
Commit: 9033338d02c1b794655f273363441ed6db269729
Author: billila <ilaria.billato@studenti.unipd.it>
Date: 2025-04-08 16:14:35 +0200
Commit message:

 update README.md
Package: imageTCGA
Commit: ec24557013277aae0a0380e485e6d92ea449f9ff
Author: billila <ilaria.billato@studenti.unipd.it>
Date: 2025-04-08 16:10:39 +0200
Commit message:

 bump version
Package: imageTCGA
Commit: b8b4cc036be3e3af8ac4370a96865f90c94d2b03
Author: billila <ilaria.billato@studenti.unipd.it>
Date: 2025-04-08 16:09:35 +0200
Commit message:

 update README and vignette
Package: imageTCGA
Commit: 510e4689dd3c6a808965807486f8fc5bde87c161
Author: billila <ilaria.billato@studenti.unipd.it>
Date: 2025-04-08 16:05:12 +0200
Commit message:

 remove R dep
Package: imageTCGA
Commit: 6257660f298ea7c41f3ebf0f16501cbd81f5ae65
Author: billila <ilaria.billato@studenti.unipd.it>
Date: 2025-04-08 15:37:16 +0200
Commit message:

 add app.R
Package: imageTCGA
Commit: 3e111e39e3a5c3b81888c9da2b569ae923c62571
Author: Ilaria Billato <78036851+billila@users.noreply.github.com>
Date: 2025-04-08 15:30:05 +0200
Commit message:

 Merge pull request #1 from PeteHaitch/devel

Corrections to package installation instructions
Package: imageTCGA
Commit: ff58b150126fb1f1a4aec7aea711eab9e7da185a
Author: Peter Hickey <peter.hickey@gmail.com>
Date: 2025-04-08 08:39:55 +1000
Commit message:

 Corrections to package installation instructions
Package: TargetSearch
Commit: be1ba75303de6d347e3011d1f011efe99f38cacc
Author: Alvaro Cuadros-Inostroza <acuadros+github@gmail.com>
Date: 2025-04-08 15:49:18 +0200
Commit message:

 Version 2.9.2
Package: TargetSearch
Commit: c10a520a3657c9c7698f4e5e26b65131b5287256
Author: Alvaro Cuadros-Inostroza <acuadros+github@gmail.com>
Date: 2025-04-08 15:48:17 +0200
Commit message:

 Update NEWS
Package: TargetSearch
Commit: 7e3d9cc84d6c07fefde36e3da420c38a0403c6a7
Author: Alvaro Cuadros-Inostroza <acuadros+github@gmail.com>
Date: 2024-12-20 16:12:21 +0100
Commit message:

 Feature: new method `libUID`

Implements method libUID to get/set the library's unique identifiers.
Also add tests and improve documentation on the the `tsLib` methods
man page.
Package: TargetSearch
Commit: c170e380b72f65d769f12c853a8e3978070ff0fa
Author: Alvaro Cuadros-Inostroza <acuadros+github@gmail.com>
Date: 2024-12-20 10:41:58 +0100
Commit message:

 docs: add note on deprecated `libId` method
Package: TargetSearch
Commit: ff2888b11663f67c187b6cbc66e32e9528cc7262
Author: Alvaro Cuadros-Inostroza <acuadros+github@gmail.com>
Date: 2024-12-19 12:11:35 +0100
Commit message:

 refactor: internal function .setLibrary and .set_uid

Split the logic that remove artifacs from the `libData` slot into a
separated function.

Create a new internal function `.set_uid` which takes cares of setting
or getting the unique identifiers for each library element.

Add a test that checks an expected warning, and also check that the
library object is created cleanly.
Package: KEGGREST
Commit: 5c3511f243f55a1bf4c5ba7b4763452565d7d1c4
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-04-02 18:39:32 -0400
Commit message:

 version bump 1.47.1
Package: KEGGREST
Commit: b9132b53ecc8ba501e5976994fa7429568cd171c
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-04-02 18:37:36 -0400
Commit message:

 handle cases where lastField is NA
Package: lpsymphony
Commit: 83374749a76fa18c414b260c90d91c3fd370afa6
Author: Mike Smith <grimbough@gmail.com>
Date: 2025-04-08 14:01:29 +0200
Commit message:

 Update linux runner
Package: lpsymphony
Commit: 7eeddc1e0f89a58e5836554f1fd01d95f082f523
Author: Mike Smith <grimbough@gmail.com>
Date: 2025-04-08 14:01:07 +0200
Commit message:

 Update gitignore
Package: lpsymphony
Commit: 9a34703a32633e24ae10e8d4d9ad9930ae3618da
Author: Mike Smith <grimbough@gmail.com>
Date: 2025-04-08 13:58:32 +0200
Commit message:

 Version bump
Package: lpsymphony
Commit: 669fc5fc930b619c37464bd9a66c011ed2f7bee5
Author: Mike Smith <grimbough@gmail.com>
Date: 2025-04-08 13:58:25 +0200
Commit message:

 Update to configure script to cope with -std=gnu2x being added to the default CC command
Package: ClustIRR
Commit: 5fca0b685de7341e475f9f7b908e8ca9a3c83c5e
Author: snaketron <simo.kitanovski@proton.me>
Date: 2025-04-08 13:45:47 +0200
Commit message:

 bugfix
Package: ADaCGH2
Commit: 0b6372e563914bb0acf2e0afb11671226a952a0f
Author: Ramon @ Triturus
Date: 2025-04-08 13:17:16 +0200
Commit message:

 2.47.2: updated NEWS for BioC 3.21
</div>
Package: PSMatch
Commit: 327301ac7ccfe3611af17b43318b173b7b92490c
Author: Laurent Gatto <laurent.gatto@uclouvain.be>
Date: 2025-04-08 12:06:28 +0200
Commit message:

 suggest spectra 1.17.10
Package: PSMatch
Commit: 9d216a8bc3ff78fd007f5d047cafc632a1fe58ef
Author: Laurent Gatto <laurent.gatto@uclouvain.be>
Date: 2025-04-08 12:03:19 +0200
Commit message:

 Merge pull request #20 from guideflandre/main

Fix error when calling multiple Spectra objects in addFragments
Package: PSMatch
Commit: 407b2c10b1ac61d3d63a6394133a6ce40e43f6f9
Author: Laurent Gatto <laurent.gatto@uclouvain.be>
Date: 2025-04-08 10:34:31 +0200
Commit message:

 check R 4.5 and on workflow dispatch
Package: PSMatch
Commit: a3ec24449358ea115ac69eaf39430bb8e6be052f
Author: Laurent Gatto <laurent.gatto@uclouvain.be>
Date: 2025-04-08 10:31:26 +0200
Commit message:

 bump version, update cache
Package: PSMatch
Commit: 3aaa30fc29f1ad1cd55a8588053df6a271871527
Author: Guitou1 <potamoidef@gmail.com>
Date: 2025-03-06 14:08:11 +0100
Commit message:

 update documentation
Package: PSMatch
Commit: 33a149e1958eec695ededb814a9480ed21df98c3
Author: Guitou1 <potamoidef@gmail.com>
Date: 2025-02-28 15:14:14 +0100
Commit message:

 Merge branch 'main' of https://github.com/guideflandre/PSMatch
Package: PSMatch
Commit: e668386e812b7b446f37c1e967a0165194b56f20
Author: Guitou1 <potamoidef@gmail.com>
Date: 2025-02-28 11:46:22 +0100
Commit message:

 Call labelFragments when addFragments is called
Package: PSMatch
Commit: 80178e254e1478df69dabb10b268c8e00bf965a8
Author: Guitou1 <potamoidef@gmail.com>
Date: 2025-02-28 11:46:22 +0100
Commit message:

 Call labelFragments when addFragments is called
Package: PSMatch
Commit: fd4d3842deb4c479c66c84011b55591832bb977a
Author: Guitou1 <potamoidef@gmail.com>
Date: 2025-02-28 11:24:41 +0100
Commit message:

 Update addFragments
Package: PSMatch
Commit: 54f2d5c1aadb6731270c0b8826dd4944d7238c24
Author: Guillaume Deflandre <37773040+guideflandre@users.noreply.github.com>
Date: 2025-02-28 11:22:37 +0100
Commit message:

 Merge branch 'main' into main
Package: PSMatch
Commit: d8d8239023c9ac6f2e9ebf969b725fb3b859716f
Author: Guitou1 <potamoidef@gmail.com>
Date: 2025-02-28 11:18:48 +0100
Commit message:

 Decprecate addFragments correctly
Package: PSMatch
Commit: 21c2f30e2c02a38d247a9295a1c94fb06cfa706e
Author: Guitou1 <potamoidef@gmail.com>
Date: 2025-02-28 10:59:28 +0100
Commit message:

 fix indent
Package: PSMatch
Commit: 924cb46fa6dc9ed84df2d71c90e9ac84f3567552
Author: Guitou1 <potamoidef@gmail.com>
Date: 2025-02-28 10:44:20 +0100
Commit message:

 Resolved merge conflict in 
 </pre>
    </div>
  
    

      Package: PSMatch

      Commit: 10071d1d756a19de4fb8ac5e4c67dd982587b251

      Author:  Guitou1 <potamoidef@gmail.com> 

      Date: 2025-02-28 10:33:47 +0100

      Commit message:


	  
		
 Update documentations
 

    

  
    

      Package: PSMatch

      Commit: 302ab525c0e0eca580b71f3edebf59ae67136716

      Author:  Guitou1 <potamoidef@gmail.com> 

      Date: 2025-02-28 10:33:47 +0100

      Commit message:


	  
		
 Update documentations
 

    

  
    

      Package: PSMatch

      Commit: aedbcbd7c7f7b8f9a54ee132ce1f93d4ee3c1884

      Author:  Guitou1 <potamoidef@gmail.com> 

      Date: 2025-02-20 16:33:59 +0100

      Commit message:


	  
		
 Change addFragments name and update NEWS
 

    

  
    

      Package: PSMatch

      Commit: a7367d03149daf199075752c92af06addfc77271

      Author:  Guitou1 <potamoidef@gmail.com> 

      Date: 2025-02-03 15:07:05 +0100

      Commit message:


	  
		
 Replace addFragments documentation with labelFragments
 

    

  
    

      Package: PSMatch

      Commit: f97c14bb977c1aa5b729b2738a7c83013ad0b6b1

      Author:  Guitou1 <potamoidef@gmail.com> 

      Date: 2025-02-03 14:35:33 +0100

      Commit message:


	  
		
 remove old addFragments test and R
 

    

  
    

      Package: PSMatch

      Commit: fb4403d2702592295efd43d5ccd79a862f2116bd

      Author:  Guitou1 <potamoidef@gmail.com> 

      Date: 2025-02-03 14:34:20 +0100

      Commit message:


	  
		
 deprecate addLabels
 

    

  
    

      Package: PSMatch

      Commit: 7b1d929ed7356ec71f67ff9d2bac7b6b6019d8dc

      Author:  Guitou1 <potamoidef@gmail.com> 

      Date: 2025-02-03 14:03:19 +0100

      Commit message:


	  
		
 Add attribute
 

    

  
    

      Package: PSMatch

      Commit: 70edf96137f72436347455b4f3005ecc46765307

      Author:  Guitou1 <potamoidef@gmail.com> 

      Date: 2025-01-31 15:56:06 +0100

      Commit message:


	  
		
 Update based on PR review
 

    

  
    

      Package: PSMatch

      Commit: df39f37f668c2327d23412199a5d9d515fd49012

      Author:  Guitou1 <potamoidef@gmail.com> 

      Date: 2025-01-31 15:42:15 +0100

      Commit message:


	  
		
 Remove unnecessary test
 

    

  
    

      Package: PSMatch

      Commit: 898d8f5c801299e9b5e171bbd3374b7a52734e97

      Author:  Guitou1 <potamoidef@gmail.com> 

      Date: 2025-01-31 15:41:53 +0100

      Commit message:


	  
		
 Update documentation
 

    

  
    

      Package: PSMatch

      Commit: 8a6284901812075dce3611c6d1db57ad0ab9997e

      Author:  Guillaume Deflandre <37773040+guideflandre@users.noreply.github.com> 

      Date: 2025-01-31 15:32:26 +0100

      Commit message:


	  
		
 Update test_addFragments.R 

    

  
    

      Package: PSMatch

      Commit: b2b12d95b94a2bb9eb6ed9630c205762388e58ab

      Author:  Guillaume Deflandre <37773040+guideflandre@users.noreply.github.com> 

      Date: 2025-01-31 15:15:26 +0100

      Commit message:


	  
		
 Update R/fragments-add.R

Co-authored-by: Sebastian Gibb <mail@sebastiangibb.de> 

    

  
    

      Package: PSMatch

      Commit: 868918de3f4a66de6088f4ebe282f4a0699cfde9

      Author:  Guitou1 <potamoidef@gmail.com> 

      Date: 2025-01-27 10:01:30 +0100

      Commit message:


	  
		
 remove plotting function for PR
 

    

  
    

      Package: PSMatch

      Commit: b07d1a49b1d30e036ff18a599380d271cc36c442

      Author:  Guitou1 <potamoidef@gmail.com> 

      Date: 2025-01-24 16:15:33 +0100

      Commit message:


	  
		
 add PlotSpectraPTM
 

    

  
    

      Package: PSMatch

      Commit: 7c3c3682551d759a693fb8462bd60eae0a2fa222

      Author:  Guitou1 <potamoidef@gmail.com> 

      Date: 2025-01-24 15:51:51 +0100

      Commit message:


	  
		
 Remove attribute in addFragments
 

    

  
    

      Package: PSMatch

      Commit: 264390c84ff8fefede069a61a2b88cc64a83f7d9

      Author:  Guitou1 <potamoidef@gmail.com> 

      Date: 2025-01-23 11:04:03 +0100

      Commit message:


	  
		
 Update tests addFragments
 

    

  
    

      Package: PSMatch

      Commit: a3c3adae40af6ae1c6a1a6b3f8550b798c81b2cb

      Author:  Guitou1 <potamoidef@gmail.com> 

      Date: 2025-01-22 17:15:00 +0100

      Commit message:


	  
		
 addFragments correcion
 

    

  
    

      Package: PSMatch

      Commit: f0b1f2a84badd18f9135f3c65d60b1baff0d8421

      Author:  Guitou1 <potamoidef@gmail.com> 

      Date: 2025-01-22 17:09:44 +0100

      Commit message:


	  
		
 Update documentation
 

    

  
    

      Package: PSMatch

      Commit: 8203f6dfb0933226900082792ca5075445ad3643

      Author:  Guitou1 <potamoidef@gmail.com> 

      Date: 2025-01-22 16:46:33 +0100

      Commit message:


	  
		
 Remove check for variable modifications as they are now included in Spectra
 

    

  
    

      Package: PSMatch

      Commit: 775859caec1fc5c308ed40154aa061aa189ba848

      Author:  Guitou1 <potamoidef@gmail.com> 

      Date: 2025-01-22 15:53:58 +0100

      Commit message:


	  
		
 Update addFragments to generate a list
 

    

  
    

      Package: PSMatch

      Commit: 11834aa92533f7c2de1d1f38f669fa591394145f

      Author:  Guitou1 <potamoidef@gmail.com> 

      Date: 2025-01-22 15:41:40 +0100

      Commit message:


	  
		
 Merge branch 'main' of https://github.com/guideflandre/PSMatch
 

    

  
    

      Package: PSMatch

      Commit: 56aec17557320009a229e37a854b05b81dc95f82

      Author:  Guitou1 <potamoidef@gmail.com> 

      Date: 2025-01-21 21:57:06 +0100

      Commit message:


	  
		
 Update comments in addFragments
 

    

  
    

      Package: PSMatch

      Commit: 5f4615292ecd2def441903ad4a7bd9ba840e8e0d

      Author:  Guitou1 <potamoidef@gmail.com> 

      Date: 2025-01-21 14:18:02 +0100

      Commit message:


	  
		
 Updated failed unit test
 

    

  
    

      Package: PSMatch

      Commit: 4f5795aaab653147b85274334645d831c4a9bb81

      Author:  Guitou1 <potamoidef@gmail.com> 

      Date: 2025-01-21 12:56:23 +0100

      Commit message:


	  
		
 Remove redundancies and update calculateFragments based on PR
 

    

  
    

      Package: PSMatch

      Commit: 7107718cb747761c1383abeae266ce1cdaf2e894

      Author:  Guitou1 <potamoidef@gmail.com> 

      Date: 2025-01-21 00:29:25 +0100

      Commit message:


	  
		
 Merge calculateFragments and calculateFragments2 into one true calculateFragments
 

    

  
    

      Package: PSMatch

      Commit: 3d6bc0c4c9accc9e1f8100e351d62fcea3c5f95f

      Author:  Guitou1 <potamoidef@gmail.com> 

      Date: 2025-01-20 23:39:13 +0100

      Commit message:


	  
		
 update documentaton

Merge branch 'main' of https://github.com/guideflandre/PSMatch

# Conflicts:
#	R/fragments-calculate2.R
 

    

  
    

      Package: PSMatch

      Commit: bdd7cd8669c921d0c86d69aae2f1fdd6ca326595

      Author:  Guitou1 <potamoidef@gmail.com> 

      Date: 2025-01-20 19:40:41 +0100

      Commit message:


	  
		
 update documentation
 

    

  
    

      Package: PSMatch

      Commit: 2526ccd07dc345f002fd3af82743ffc47279abb2

      Author:  Guitou1 <potamoidef@gmail.com> 

      Date: 2025-01-20 18:37:24 +0100

      Commit message:


	  
		
 Update documentation
 

    

  
    

      Package: PSMatch

      Commit: f4a5d0ff6cdf939227b1e7e8ae3e619efc1188af

      Author:  Guitou1 <potamoidef@gmail.com> 

      Date: 2025-01-20 13:51:21 +0100

      Commit message:


	  
		
 Remove redundancy in strplit(sequence)
 

    

  
    

      Package: PSMatch

      Commit: 0525f860346484c26af6f69c9dd6be9b5b7c4681

      Author:  Guitou1 <potamoidef@gmail.com> 

      Date: 2025-01-17 16:22:04 +0100

      Commit message:


	  
		
 Add warning for modifications parameter
 

    

  
    

      Package: PSMatch

      Commit: a39cbeee777a85496ab9c15036709ba4774e0012

      Author:  Guillaume Deflandre <37773040+guideflandre@users.noreply.github.com> 

      Date: 2025-01-10 11:10:38 +0100

      Commit message:


	  
		
 Update fragments-calculate2.R

Change modified peptide layout into AGC[57.02]AK instead of AG[C]AK to specify the modified mass 

    

  
    

      Package: PSMatch

      Commit: 5c0344e6bb98b944775a9a9edd8e6fdfc25b6110

      Author:  Guitou1 <potamoidef@gmail.com> 

      Date: 2025-01-07 14:45:41 +0100

      Commit message:


	  
		
 update variable_modifications default to empty numeric
 

    

  
    

      Package: PSMatch

      Commit: 9d5b9ff19c2ed19415b8b971c0d66e1be684a9ff

      Author:  Guitou1 <potamoidef@gmail.com> 

      Date: 2025-01-07 11:17:11 +0100

      Commit message:


	  
		
 update: testthat .cumsumFragmentMasses
 

    

  
    

      Package: PSMatch

      Commit: f5b8b06b6fe99587f7683fe557690e0390026a0c

      Author:  Guitou1 <potamoidef@gmail.com> 

      Date: 2025-01-07 10:54:04 +0100

      Commit message:


	  
		
 update .cumsumFragmentMasses
 

    

  
    

      Package: PSMatch

      Commit: 6d2591592f51eaf86d7296d754a852d5694fbee2

      Author:  Guitou1 <potamoidef@gmail.com> 

      Date: 2025-01-07 09:48:40 +0100

      Commit message:


	  
		
 git ignore Rproj file
 

    

  
    

      Package: PSMatch

      Commit: 7c8afd63e952624b5dcd2802195d33afb1c413b4

      Author:  Guillaume Deflandre <37773040+guideflandre@users.noreply.github.com> 

      Date: 2025-01-06 16:17:17 +0100

      Commit message:


	  
		
 Update DESCRIPTION 

    

  
    

      Package: PSMatch

      Commit: 5c4ce492b2d63e028c14d86dfce09dbeaea049a3

      Author:  Guillaume Deflandre <37773040+guideflandre@users.noreply.github.com> 

      Date: 2025-01-06 16:03:52 +0100

      Commit message:


	  
		
 Update fragments-calculate2.R

Corrected .cumsumFragmentMasses 

    

  
    

      Package: PSMatch

      Commit: ebb867314cc0d7f5abf24aedf7923e9c23603ee8

      Author:  Guillaume Deflandre <37773040+guideflandre@users.noreply.github.com> 

      Date: 2025-01-02 10:45:12 +0100

      Commit message:


	  
		
 Update fragments-calculate2.R 

    

  
    

      Package: PSMatch

      Commit: 046cca0eaf0b29187bf8b6dde51295bb3e891560

      Author:  Guillaume Deflandre <37773040+guideflandre@users.noreply.github.com> 

      Date: 2025-01-02 10:40:51 +0100

      Commit message:


	  
		
 Update R/fragments-calculate2.R

Co-authored-by: Sebastian Gibb <mail@sebastiangibb.de> 

    

  
    

      Package: PSMatch

      Commit: befd86a5338c721a68d3f6eb626d039e4c92d1a1

      Author:  Guillaume Deflandre <37773040+guideflandre@users.noreply.github.com> 

      Date: 2024-12-24 16:11:41 +0100

      Commit message:


	  
		
 Update test_fragments2.R

Updates according to reviewed PR 

    

  
    

      Package: PSMatch

      Commit: 9d1ea080e2ee1742f37da2e49495b103cc543b93

      Author:  Guillaume Deflandre <37773040+guideflandre@users.noreply.github.com> 

      Date: 2024-12-24 15:55:44 +0100

      Commit message:


	  
		
 Update fragments-calculate2.R

Updates based on reviewed PR 

    

  
    

      Package: PSMatch

      Commit: 7c8f6c9a628ff0db03726d736ea3478e6c5d081c

      Author:  Guillaume Deflandre <37773040+guideflandre@users.noreply.github.com> 

      Date: 2024-12-24 15:48:39 +0100

      Commit message:


	  
		
 Update DESCRIPTION 

    

  
    

      Package: PSMatch

      Commit: dfeaa2ed32e1460548438bb040851d46a29761e5

      Author:  Guillaume Deflandre <37773040+guideflandre@users.noreply.github.com> 

      Date: 2024-12-24 15:42:17 +0100

      Commit message:


	  
		
 Update NEWS.md 

    

  
    

      Package: PSMatch

      Commit: ea262a07c92ca5a840cc08c9795ca1dd251d72a6

      Author:  Guillaume Deflandre <37773040+guideflandre@users.noreply.github.com> 

      Date: 2024-12-24 15:40:03 +0100

      Commit message:


	  
		
 Delete PSMatch.Rproj 

    

  
    

      Package: PSMatch

      Commit: f3b7ba7060b4d21afe20a64bd67854cea4d50444

      Author:  Guitou1 <potamoidef@gmail.com> 

      Date: 2024-12-20 10:40:56 +0100

      Commit message:


	  
		
 Update documentation
 

    

  
    

      Package: PSMatch

      Commit: b75af03d68c8be0449bcb883de3c7b432a070506

      Author:  Guitou1 <potamoidef@gmail.com> 

      Date: 2024-12-19 17:21:57 +0100

      Commit message:


	  
		
 Update documentation
 

    

  
    

      Package: PSMatch

      Commit: d505a3d26a39d1d0394f44168656d8be9640f1f4

      Author:  Guillaume Deflandre <37773040+guideflandre@users.noreply.github.com> 

      Date: 2024-12-19 16:52:35 +0100

      Commit message:


	  
		
 Update fragments-calculate2.R 

    

  
    

      Package: PSMatch

      Commit: d1951bb83af6a1b21032d24e41111e6fa0e7d116

      Author:  Guillaume Deflandre <37773040+guideflandre@users.noreply.github.com> 

      Date: 2024-12-19 16:48:42 +0100

      Commit message:


	  
		
 Update fragments-calculate2.R 

    

  
    

      Package: PSMatch

      Commit: ab015512ec923dfe2488b51678880bded2c8684b

      Author:  Guillaume Deflandre <37773040+guideflandre@users.noreply.github.com> 

      Date: 2024-12-19 16:46:03 +0100

      Commit message:


	  
		
 Update fragments-calculate2.R 

    

  
    

      Package: PSMatch

      Commit: 32dd91b87c16862e45262c63b6ec4862a088e244

      Author:  Guillaume Deflandre <37773040+guideflandre@users.noreply.github.com> 

      Date: 2024-12-19 16:34:28 +0100

      Commit message:


	  
		
 Create test_fragments2.R

feat: tests for calculateFragments2 

    

  
    

      Package: PSMatch

      Commit: 11d943c2f5b471b41ab751b1261c0d7b3b5dcb34

      Author:  Guillaume Deflandre <37773040+guideflandre@users.noreply.github.com> 

      Date: 2024-12-19 16:33:04 +0100

      Commit message:


	  
		
 Create fragments-calculate2.R

feat: calculateFragments2 
Provides modifications to the generated theoretical fragments 

    

  
    

      Package: ResidualMatrix

      Commit: 45c38ea5a69f448177832252c2ec8c4e3ddb36f1

      Author:  LTLA <infinite.monkeys.with.keyboards@gmail.com> 

      Date: 2025-04-08 02:06:20 -0700

      Commit message:


	  
		
 Support DelayedMatrix seeds in extract_array().

This just involves working around the lack of a isometric binary subtraction
between a DelayedArray and a non-DelayedArray.
 

    

  
    

      Package: PSMatch

      Commit: 5dc7a07f8baac027aea7a073813078076f167a46

      Author:  Laurent Gatto <laurent.gatto@uclouvain.be> 

      Date: 2025-02-01 16:23:48 +0100

      Commit message:


	  
		
 fix indent
 

    

  
    

      Package: PSMatch

      Commit: e64e13b1c0eca2120e594e64408c660ea4afcbe8

      Author:  Sebastian Gibb <mail@sebastiangibb.de> 

      Date: 2025-01-22 10:38:04 +0100

      Commit message:


	  
		
 chore: bump version
 

    

  
    

      Package: PSMatch

      Commit: 6799e09779481f84420f597444696d7c450666f6

      Author:  Sebastian Gibb <mail@sebastiangibb.de> 

      Date: 2025-01-22 10:37:48 +0100

      Commit message:


	  
		
 docs: add PR urls to NEWS.md
 

    

  
    

      Package: PSMatch

      Commit: 84df4258a23a737553fb78157af3a65ad7c5e116

      Author:  Guillaume Deflandre <37773040+guideflandre@users.noreply.github.com> 

      Date: 2025-01-22 10:34:54 +0100

      Commit message:


	  
		
 refactor: merge calculateFragments and calculateFragments2 (#19)

* Create fragments-calculate2.R

feat: calculateFragments2 
Provides modifications to the generated theoretical fragments

* Create test_fragments2.R

feat: tests for calculateFragments2

* Update fragments-calculate2.R

* Update fragments-calculate2.R

* Update fragments-calculate2.R

* Update documentation

* Update documentation

* Delete PSMatch.Rproj

* Update NEWS.md

* Update DESCRIPTION

* Update fragments-calculate2.R

Updates based on reviewed PR

* Update test_fragments2.R

Updates according to reviewed PR

* Update R/fragments-calculate2.R

Co-authored-by: Sebastian Gibb <mail@sebastiangibb.de>

* Update fragments-calculate2.R

* Update fragments-calculate2.R

Corrected .cumsumFragmentMasses

* Update DESCRIPTION

* git ignore Rproj file

* update .cumsumFragmentMasses

* update: testthat .cumsumFragmentMasses

* update variable_modifications default to empty numeric

* Update fragments-calculate2.R

Change modified peptide layout into AGC[57.02]AK instead of AG[C]AK to specify the modified mass

* Add warning for modifications parameter

* Remove redundancy in strplit(sequence)

* Update documentation

* update documentation

* Merge calculateFragments and calculateFragments2 into one true calculateFragments

* Remove redundancies and update calculateFragments based on PR

* Updated failed unit test

* Update comments in addFragments

---------

Co-authored-by: Sebastian Gibb <mail@sebastiangibb.de> 

    

  
    

      Package: PSMatch

      Commit: b0421575011f5140cba43f5f5a4ef0d02a1ee5bd

      Author:  Sebastian Gibb <mail@sebastiangibb.de> 

      Date: 2025-01-20 22:36:30 +0100

      Commit message:


	  
		
 fix: import combn from utils
 

    

  
    

      Package: PSMatch

      Commit: a046b32ce46f233502c4118d6b1750ca2ece72d5

      Author:  Guillaume Deflandre <37773040+guideflandre@users.noreply.github.com> 

      Date: 2025-01-20 22:32:13 +0100

      Commit message:


	  
		
 feat: add calculateFragments2 supporting fixed and variable modifications (closes #16)

* Create fragments-calculate2.R

feat: calculateFragments2 
Provides modifications to the generated theoretical fragments

* Create test_fragments2.R

feat: tests for calculateFragments2

* Update fragments-calculate2.R

* Update fragments-calculate2.R

* Update fragments-calculate2.R

* Update documentation

* Update documentation

* Delete PSMatch.Rproj

* Update NEWS.md

* Update DESCRIPTION

* Update fragments-calculate2.R

Updates based on reviewed PR

* Update test_fragments2.R

Updates according to reviewed PR

* Update R/fragments-calculate2.R

Co-authored-by: Sebastian Gibb <mail@sebastiangibb.de>

* Update fragments-calculate2.R

* Update fragments-calculate2.R

Corrected .cumsumFragmentMasses

* Update DESCRIPTION

* git ignore Rproj file

* update .cumsumFragmentMasses

* update: testthat .cumsumFragmentMasses

* update variable_modifications default to empty numeric

* Update fragments-calculate2.R

Change modified peptide layout into AGC[57.02]AK instead of AG[C]AK to specify the modified mass

* Add warning for modifications parameter

* Remove redundancy in strplit(sequence)

* Update documentation

* update documentation

---------

Co-authored-by: Sebastian Gibb <mail@sebastiangibb.de> 

    

  
    

      Package: PSMatch

      Commit: 2920d3412ccc986c6798ccc2e00ac52b429cdf99

      Author:  Laurent Gatto <laurent.gatto@uclouvain.be> 

      Date: 2024-12-12 15:57:50 +0100

      Commit message:


	  
		
 use bioc devel
 

    

  
    

      Package: PSMatch

      Commit: f07b40b39991aa3e1b5aabb15a43c9eebc27d2a3

      Author:  Laurent Gatto <laurent.gatto@uclouvain.be> 

      Date: 2024-12-12 14:46:42 +0100

      Commit message:


	  
		
 new devel version
 

    

  
    

      Package: SeqArray

      Commit: 44473f683500ac62c7786fb2b7fbb4e41e2fe8f5

      Author:  Xiuwen Zheng <zhengxwen@gmail.com> 

      Date: 2025-04-08 02:45:05 -0500

      Commit message:


	  
		
 update
 

    

  
    

      Package: dada2

      Commit: 12a00d4791b299290f1fec33b9b80e3415ddbc2f

      Author:  Ben Callahan <bcallah@ncsu.edu> 

      Date: 2025-04-08 01:22:28 -0400

      Commit message:


	  
		
 Bump
 

    

  
    

      Package: dada2

      Commit: 84dede81babb50cc9e19e797f72a4c0c35a1b981

      Author:  Ben Callahan <bcallah@ncsu.edu> 

      Date: 2025-04-08 01:21:13 -0400

      Commit message:


	  
		
 Update errorModels.R

Remove default values for binnedQ - require the user to pass the binned quality scores to binnedQualErrfun
 

    

  
    

      Package: spacexr

      Commit: 3664366e0d35bd00ffba3172319f1a86066b3430

      Author:  ggrajeda <gabriel.grajeda@gmail.com> 

      Date: 2025-04-07 22:32:40 -0400

      Commit message:


	  
		
 Fix call to getCounts

Now passing in the name of the experiment object when creating a SpatialRNA object.
 

    

  
    

      Package: spacexr

      Commit: 9755f5bf9a4512cfa135b087e3513510c6a5682f

      Author:  ggrajeda <gabriel.grajeda@gmail.com> 

      Date: 2025-04-02 15:51:16 -0400

      Commit message:


	  
		
 Add citation information to README
 

    

  
    

      Package: mixOmics

      Commit: 79bc89bb324b3e8049a87bdc0114cfa6a314c018

      Author:  Kim-Anh Lê Cao <mixomicsdeveloper@gmail.com> 

      Date: 2025-04-08 11:35:25 +1000

      Commit message:


	  
		
 Merge remote-tracking branch 'bioc/devel' into HEAD
 

    

  
    

      Package: mixOmics

      Commit: 1f4a4139ed8392ba29a30ec46172abd94a83647c

      Author:  Eva Hamrud <50098063+evaham1@users.noreply.github.com> 

      Date: 2025-04-08 11:32:25 +1000

      Commit message:


	  
		
 version 6.31.5
 

    

  
    

      Package: mixOmics

      Commit: ed3c8d2f0aad98440d26afe1f2995e651e270036

      Author:  Eva Hamrud <50098063+evaham1@users.noreply.github.com> 

      Date: 2025-04-08 11:30:18 +1000

      Commit message:


	  
		
 Merge pull request #362 from mixOmicsTeam/345-ggplot-plotloadings

345 ggplot plotloadings 

    

  
    

      Package: mixOmics

      Commit: c2efdf04a8308cdf93d658b54c401d59b26b28d3

      Author:  Eva Hamrud <50098063+evaham1@users.noreply.github.com> 

      Date: 2025-04-08 10:45:47 +1000

      Commit message:


	  
		
 comment out tests which give margin errors
 

    

  
    

      Package: mixOmics

      Commit: 55c26c0c93b8839f3d9a0122369e4f20d912f776

      Author:  Eva Hamrud <50098063+evaham1@users.noreply.github.com> 

      Date: 2025-04-08 10:04:26 +1000

      Commit message:


	  
		
 skip making these plot tests when on cran
 

    

  
    

      Package: mixOmics

      Commit: 183f99e7cc14cb24e58e564d3cc175661551b060

      Author:  Eva Hamrud <50098063+evaham1@users.noreply.github.com> 

      Date: 2025-04-08 09:35:45 +1000

      Commit message:


	  
		
 use par to adjust plot margins
 

    

  
    

      Package: mixOmics

      Commit: 5e78a97ed98437b4366e89e607a2504da5fcdaab

      Author:  Eva Hamrud <50098063+evaham1@users.noreply.github.com> 

      Date: 2025-04-08 09:03:45 +1000

      Commit message:


	  
		
 increase png size for plotting
 

    

  
    

      Package: mixOmics

      Commit: 77afae7732c108ebfe5a43a751b3fe8df695b134

      Author:  Eva Hamrud <50098063+evaham1@users.noreply.github.com> 

      Date: 2025-04-07 17:10:49 +1000

      Commit message:


	  
		
 update failed unit tests due to plotting margins - added png and dev.off lines
 

    

  
    

      Package: mixOmics

      Commit: 483bcd33639e4fb06e2191a591d9be2c6879dc3b

      Author:  Eva Hamrud <50098063+evaham1@users.noreply.github.com> 

      Date: 2025-04-07 16:40:59 +1000

      Commit message:


	  
		
 updated plotLoadings examples
 

    

  
    

      Package: mixOmics

      Commit: d9b5b69a362a4d3e6c48304a014923b0c7b4fa1a

      Author:  Eva Hamrud <50098063+evaham1@users.noreply.github.com> 

      Date: 2025-04-07 16:33:43 +1000

      Commit message:


	  
		
 example file too long
 

    

  
    

      Package: mixOmics

      Commit: 010174971eaff0c0b160cb7929cd70d7e4d8393c

      Author:  Eva Hamrud <50098063+evaham1@users.noreply.github.com> 

      Date: 2025-04-07 16:11:47 +1000

      Commit message:


	  
		
 update docs
 

    

  
    

      Package: mixOmics

      Commit: 5272e4b274f39a04df5b84f30c29022dd5cdb36f

      Author:  Eva Hamrud <50098063+evaham1@users.noreply.github.com> 

      Date: 2025-04-07 15:57:39 +1000

      Commit message:


	  
		
 full unit test passes
 

    

  
    

      Package: mixOmics

      Commit: 4d83b2ca5d23fe3be623dbfb6f3f029ff04c0cd5

      Author:  Eva Hamrud <50098063+evaham1@users.noreply.github.com> 

      Date: 2025-04-07 15:38:59 +1000

      Commit message:


	  
		
 plotLoadings.mint.plsda passess unit tests
 

    

  
    

      Package: mixOmics

      Commit: f7c9b8a7d877af71d310ced4be23969027b4931e

      Author:  Eva Hamrud <50098063+evaham1@users.noreply.github.com> 

      Date: 2025-04-07 15:33:58 +1000

      Commit message:


	  
		
 update file
 

    

  
    

      Package: mixOmics

      Commit: 3778cd3c6105aa74f2e75c21631d4980c021f1ad

      Author:  Eva Hamrud <50098063+evaham1@users.noreply.github.com> 

      Date: 2025-04-07 15:33:21 +1000

      Commit message:


	  
		
 fixed plotLoadings.mint.plsda
 

    

  
    

      Package: mixOmics

      Commit: 8b5cc0c835aa71d739539597011f21dd185f4ea8

      Author:  Eva Hamrud <50098063+evaham1@users.noreply.github.com> 

      Date: 2025-04-07 15:26:07 +1000

      Commit message:


	  
		
 works on ggplot and graphics
 

    

  
    

      Package: mixOmics

      Commit: 31603ba2733735d8833ef4ef3bbe0fa8f2922e31

      Author:  Eva Hamrud <50098063+evaham1@users.noreply.github.com> 

      Date: 2025-04-07 14:16:40 +1000

      Commit message:


	  
		
 last fixes
 

    

  
    

      Package: mixOmics

      Commit: c5791396b0a5e418a2b81f05cc9c4711f41b1edd

      Author:  Eva Hamrud <50098063+evaham1@users.noreply.github.com> 

      Date: 2025-04-07 14:16:17 +1000

      Commit message:


	  
		
 plotLoadings.mint.plsda works for graphics on global study
 

    

  
    

      Package: mixOmics

      Commit: 18ff5fd1f94f402736982018bc5cad1002547dd8

      Author:  Eva Hamrud <50098063+evaham1@users.noreply.github.com> 

      Date: 2025-04-07 13:40:08 +1000

      Commit message:


	  
		
 plotLoadings.mint.pls passes unit tests
 

    

  
    

      Package: mixOmics

      Commit: 48a8a6645b1861ad49f3277ea941a82e27ef816c

      Author:  Eva Hamrud <50098063+evaham1@users.noreply.github.com> 

      Date: 2025-04-07 13:39:58 +1000

      Commit message:


	  
		
 ggplot2 functionality for plotLoadings.mint.pls
 

    

  
    

      Package: mixOmics

      Commit: 42e98b15c13ba5d80f6f9effa5cde0a51ea7997e

      Author:  Eva Hamrud <50098063+evaham1@users.noreply.github.com> 

      Date: 2025-04-07 13:31:49 +1000

      Commit message:


	  
		
 plotLoadings.mint.pls passes for all graphics tests
 

    

  
    

      Package: mixOmics

      Commit: 93c6cbbb1a3d099189901441d23f13620551b1f3

      Author:  Eva Hamrud <50098063+evaham1@users.noreply.github.com> 

      Date: 2025-04-07 12:09:57 +1000

      Commit message:


	  
		
 fixed grid layout issue for all.partial plots
 

    

  
    

      Package: mixOmics

      Commit: ca08db33a9fa1026917f3bf6bf11fc78b4544fb3

      Author:  Eva Hamrud <50098063+evaham1@users.noreply.github.com> 

      Date: 2025-04-07 12:04:35 +1000

      Commit message:


	  
		
 fixed functionality to specify block when choosing all.partial or specific study
 

    

  
    

      Package: mixOmics

      Commit: 344be1576b1d2886d3d9e1f70a5928e2599c8065

      Author:  Eva Hamrud <50098063+evaham1@users.noreply.github.com> 

      Date: 2025-04-07 11:51:58 +1000

      Commit message:


	  
		
 clean up generic plotLoadings file
 

    

  
    

      Package: mixOmics

      Commit: cb7639cda3e132b6c3c6d1112d843a54d9200722

      Author:  Eva Hamrud <50098063+evaham1@users.noreply.github.com> 

      Date: 2025-04-04 13:14:04 +1100

      Commit message:


	  
		
 removed depcreated arg from plotLoadings.mint.pls
 

    

  
    

      Package: mixOmics

      Commit: e5b76e57538559e7f3808f99b14c6eb7a8d6a86e

      Author:  Eva Hamrud <50098063+evaham1@users.noreply.github.com> 

      Date: 2025-04-04 13:07:28 +1100

      Commit message:


	  
		
 plotLoadings.plsda checked
 

    

  
    

      Package: mixOmics

      Commit: 5c0f9df1e844a051ec989c293e392683d129f91e

      Author:  Eva Hamrud <50098063+evaham1@users.noreply.github.com> 

      Date: 2025-04-04 13:02:43 +1100

      Commit message:


	  
		
 checked plotLoadings.pls
 

    

  
    

      Package: mixOmics

      Commit: e8de9ed7475a067a41bf28b1cc9b2432f47feff1

      Author:  Eva Hamrud <50098063+evaham1@users.noreply.github.com> 

      Date: 2025-04-04 12:57:17 +1100

      Commit message:


	  
		
 updated plotLoadings.pca to remove deprecated args
 

    

  
    

      Package: mixOmics

      Commit: 34fbff0c7bfcc5eba785d0c5fb3cf4b656b0bcbd

      Author:  Eva Hamrud <50098063+evaham1@users.noreply.github.com> 

      Date: 2025-04-04 12:51:26 +1100

      Commit message:


	  
		
 reorg plotLoadings functions into separate scripts
 

    

  
    

      Package: mixOmics

      Commit: f8fd1d95d09a5c0f729c64271c12639c9f069e6d

      Author:  Eva Hamrud <50098063+evaham1@users.noreply.github.com> 

      Date: 2025-04-03 17:25:32 +1100

      Commit message:


	  
		
 make tests silent
 

    

  
    

      Package: mixOmics

      Commit: 684ad731c55705c7ea712c9e36009c30c5cccb69

      Author:  Eva Hamrud <50098063+evaham1@users.noreply.github.com> 

      Date: 2025-04-03 17:22:09 +1100

      Commit message:


	  
		
 added mint.plsda unit tests
 

    

  
    

      Package: mixOmics

      Commit: c0f20e06f400101bc0ed7b756a594eef11cf9a3e

      Author:  Eva Hamrud <50098063+evaham1@users.noreply.github.com> 

      Date: 2025-04-03 17:15:17 +1100

      Commit message:


	  
		
 fix ggplot layouts
 

    

  
    

      Package: mixOmics

      Commit: b1deae34e32aeb210d79ac562f8760ecbd2e0b50

      Author:  Eva Hamrud <50098063+evaham1@users.noreply.github.com> 

      Date: 2025-04-03 17:12:24 +1100

      Commit message:


	  
		
 fix col and border issues
 

    

  
    

      Package: mixOmics

      Commit: 57ed92a3008067dd55b2f6371f4e96e47a14939f

      Author:  Eva Hamrud <50098063+evaham1@users.noreply.github.com> 

      Date: 2025-04-03 17:04:56 +1100

      Commit message:


	  
		
 add black border if boxes are white
 

    

  
    

      Package: mixOmics

      Commit: 6bcb5a92d8189a3e9dfa46f70a6a7b035929fe1d

      Author:  Eva Hamrud <50098063+evaham1@users.noreply.github.com> 

      Date: 2025-04-03 16:43:56 +1100

      Commit message:


	  
		
 plot across studies global, all.partial and each study individually
 

    

  
    

      Package: mixOmics

      Commit: ba447783111a02a848aac96fc027704edf0d61c5

      Author:  Eva Hamrud <50098063+evaham1@users.noreply.github.com> 

      Date: 2025-04-03 16:36:10 +1100

      Commit message:


	  
		
 checks for multiblock objects or args in plotLoadings.mint.plsda
 

    

  
    

      Package: mixOmics

      Commit: 4c46338daa7681ab7586b6504c6becffb618623d

      Author:  Eva Hamrud <50098063+evaham1@users.noreply.github.com> 

      Date: 2025-04-03 16:32:39 +1100

      Commit message:


	  
		
 fixed border issues
 

    

  
    

      Package: mixOmics

      Commit: 9d6732c98e125e2da8921041f9d21f7237f13fd6

      Author:  Eva Hamrud <50098063+evaham1@users.noreply.github.com> 

      Date: 2025-04-03 16:25:50 +1100

      Commit message:


	  
		
 fix border arg passing issue
 

    

  
    

      Package: mixOmics

      Commit: 86344f40f25ff4671757888a0e2d7186d1446761

      Author:  Eva Hamrud <50098063+evaham1@users.noreply.github.com> 

      Date: 2025-04-03 16:21:38 +1100

      Commit message:


	  
		
 add extra aesth args to plotLoadings.mint.plsda
 

    

  
    

      Package: mixOmics

      Commit: 4f2ae1fed4fe3ddd62253095d4f58c82949040b3

      Author:  Eva Hamrud <50098063+evaham1@users.noreply.github.com> 

      Date: 2025-04-03 15:28:12 +1100

      Commit message:


	  
		
 before changes
 

    

  
    

      Package: mixOmics

      Commit: 57bdbf9d009ce5239171fb4868bbe4186d49e710

      Author:  Eva Hamrud <50098063+evaham1@users.noreply.github.com> 

      Date: 2025-04-03 15:25:22 +1100

      Commit message:


	  
		
 reorder and add args
 

    

  
    

      Package: mixOmics

      Commit: 5ef648defb037eb9d8f144cdfc6d17b8c3ca4502

      Author:  Eva Hamrud <50098063+evaham1@users.noreply.github.com> 

      Date: 2025-04-03 15:13:07 +1100

      Commit message:


	  
		
 add unit tests for plotLoadings.mint.pls
 

    

  
    

      Package: mixOmics

      Commit: 9ecf6b30c45475d7279e01ace38826537ab03982

      Author:  Eva Hamrud <50098063+evaham1@users.noreply.github.com> 

      Date: 2025-04-03 15:01:55 +1100

      Commit message:


	  
		
 add ggplot2 functionality
 

    

  
    

      Package: mixOmics

      Commit: af7bc355d974657884786a56d4a8a869b0ab1958

      Author:  Eva Hamrud <50098063+evaham1@users.noreply.github.com> 

      Date: 2025-04-03 14:47:49 +1100

      Commit message:


	  
		
 update plotLoadings.mixo.pls to allow for ggplot2
 

    

  
    

      Package: mixOmics

      Commit: e38c3eeaa75c4e0f2b49d6fb38dd7c64026b30e0

      Author:  Eva Hamrud <50098063+evaham1@users.noreply.github.com> 

      Date: 2025-04-03 13:57:33 +1100

      Commit message:


	  
		
 edit plotLoadings.mint.pls
 

    

  
    

      Package: mixOmics

      Commit: e68ca7e159493ef513686fcd203842b081508e91

      Author:  Eva Hamrud <50098063+evaham1@users.noreply.github.com> 

      Date: 2025-04-03 11:34:57 +1100

      Commit message:


	  
		
 updated plotLoadings.mint.pls for better functionality and to control block plotted
 

    

  
    

      Package: mixOmics

      Commit: 9ffea24d75efef28d05e0ef6dfe26d44b2d907b8

      Author:  Eva Hamrud <50098063+evaham1@users.noreply.github.com> 

      Date: 2025-04-03 10:37:08 +1100

      Commit message:


	  
		
 unit testing for plotLoadings on diablo obj
 

    

  
    

      Package: mixOmics

      Commit: a1a8fbe86d4f71c9d231fc4111eb0fd8f5ac75f3

      Author:  Eva Hamrud <50098063+evaham1@users.noreply.github.com> 

      Date: 2025-04-02 16:51:26 +1100

      Commit message:


	  
		
 edited plotLoadings.plsda and added unit tests
 

    

  
    

      Package: mixOmics

      Commit: 81e5a639d2b19e89064bc9cad99bc704cca6c4b2

      Author:  Eva Hamrud <50098063+evaham1@users.noreply.github.com> 

      Date: 2025-04-02 16:15:26 +1100

      Commit message:


	  
		
 allow ggplot2 functionality in plotLoadings.plsda
 

    

  
    

      Package: mixOmics

      Commit: f59eaf3a5b4180fbdad53e89d28256fef98727d5

      Author:  Eva Hamrud <50098063+evaham1@users.noreply.github.com> 

      Date: 2025-04-02 15:55:18 +1100

      Commit message:


	  
		
 add aes functionality and remove 'plot' arg from plotLoadings.mixo_plsda
 

    

  
    

      Package: mixOmics

      Commit: 6aee38eec25ea6b200db8fecd054cc317742ddcb

      Author:  Eva Hamrud <50098063+evaham1@users.noreply.github.com> 

      Date: 2025-04-02 15:21:47 +1100

      Commit message:


	  
		
 added tests for plotLoadings.pls
 

    

  
    

      Package: mixOmics

      Commit: 8230d1e81a962eb6f4579f3cb74b192f5e161d7c

      Author:  Eva Hamrud <50098063+evaham1@users.noreply.github.com> 

      Date: 2025-04-02 15:09:58 +1100

      Commit message:


	  
		
 update plotLoadings.pls
 

    

  
    

      Package: mixOmics

      Commit: 5f959119c66e094e467f3fa3f6071edcdb489897

      Author:  Eva Hamrud <50098063+evaham1@users.noreply.github.com> 

      Date: 2025-04-01 14:34:38 +1100

      Commit message:


	  
		
 update plotLoadings.pca docs
 

    

  
    

      Package: mixOmics

      Commit: 63b86fb22de9ad734e1a7997774784da8dd8b068

      Author:  Eva Hamrud <50098063+evaham1@users.noreply.github.com> 

      Date: 2025-04-01 14:32:52 +1100

      Commit message:


	  
		
 add unit tests including vdiffr tests for plotLoadings.pca
 

    

  
    

      Package: mixOmics

      Commit: c0691afd72067311c1cf9859b6286361585ea237

      Author:  Eva Hamrud <50098063+evaham1@users.noreply.github.com> 

      Date: 2025-04-01 14:32:32 +1100

      Commit message:


	  
		
 updated plotLoadings.pca to allow for ggplot2 plotting and extra customisability
 

    

  
    

      Package: scHiCcompare

      Commit: 245661374d427598a410ddaf76c8b7b8db6a2904

      Author:  hamy12398 <hamy.12398@gmail.com> 

      Date: 2025-04-07 19:54:36 -0400

      Commit message:


	  
		
 Merge remote-tracking branch 'origin/devel'
 

    

  
    

      Package: scHiCcompare

      Commit: 84674d1c9a324ee27d49877425043385172923fa

      Author:  hamy12398 <93464589+hamy12398@users.noreply.github.com> 

      Date: 2025-04-07 19:53:26 -0400

      Commit message:


	  
		
 Merge pull request #32 from dozmorovlab/main

Merge pull request #31 from dozmorovlab/devel 

    

  
    

      Package: scHiCcompare

      Commit: a1e15ea8f2f9069354c1d0badc082566a1c79ef6

      Author:  hamy12398 <hamy.12398@gmail.com> 

      Date: 2025-04-07 19:52:40 -0400

      Commit message:


	  
		
 merge changes
 

    

  
  


</div>

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