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GIT Logs

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

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

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

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

 Replace .BBSoptions with Config/Bioconductor/UnsupportedPlatforms in DESCRIPTION

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

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

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

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

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

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

 bump version
Package: enrichplot
Commit: 968daa2c599ec6e9b064e350bbb6a31cf1e437a9
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2026-04-01 23:04:50 +0800
Commit message:

 support stat parameter, #343
Package: enrichplot
Commit: a79704947a7f8533394eef0735f64d2bfc45e094
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2026-03-26 11:00:39 +0800
Commit message:

 manhattanplot
Package: enrichplot
Commit: 7461c01e1b95a21bd228362fa396d02e433785b5
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2026-03-02 14:16:11 +0800
Commit message:

 update docs
Package: enrichplot
Commit: b9006f8b557b747869432be2e36963775dab9c16
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2026-03-02 12:04:24 +0800
Commit message:

 format
Package: enrichplot
Commit: 69ebe466530a27fb89f4831aec8db5bc65106607
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2026-03-02 12:01:19 +0800
Commit message:

 bug fixed
Package: enrichplot
Commit: ce10a97230aba512b033d3e44f65c9717e0e8273
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2026-02-26 10:56:36 +0800
Commit message:

 bug fixed in dotplot
Package: BulkSignalR
Commit: 85593551d91063a6ff81fdde87e1ab1b2ace24e9
Author: jcolinge <65902924+jcolinge@users.noreply.github.com>
Date: 2026-04-01 16:35:44 +0200
Commit message:

 corrected typo
Package: BulkSignalR
Commit: 7d5dcb5e295d8020c2d46673cbe1bfb3c0dd6bc6
Author: jcolinge <65902924+jcolinge@users.noreply.github.com>
Date: 2026-03-30 14:45:54 +0200
Commit message:

 update README and DESCRIPTION
Package: iModMix
Commit: d5546042e77fa6820d19d621a192b32c4a154fc5
Author: IsisNarvaez <isis.narvaez@upr.edu>
Date: 2026-04-01 10:28:31 -0400
Commit message:

 "left" out
Package: philr
Commit: c10d8f47146b5b431cdf1ae7ea8223c32c965714
Author: Justin Silverman <jsilve24@gmail.com>
Date: 2026-04-01 09:27:12 -0400
Commit message:

 change: updating news
Package: philr
Commit: 38d8fac247a1c4cb1e8e62be465615b210e0d62f
Author: Justin Silverman <jsilve24@gmail.com>
Date: 2026-04-01 09:22:24 -0400
Commit message:

 fix: updating .Rbuildignore
Package: philr
Commit: 1ec4eec9022d39d35e15ed11dd842d00c537f9d3
Author: Justin Silverman <jsilve24@gmail.com>
Date: 2026-04-01 09:18:30 -0400
Commit message:

 feat: adding CLAUDE.md
Package: philr
Commit: bc6129f93ce37186035c521cf3f3566f08acda2d
Author: Justin Silverman <jsilve24@gmail.com>
Date: 2026-04-01 09:17:19 -0400
Commit message:

 fix: updating documentation, making counts rather than relabund clear
Package: philr
Commit: bf7ce8cf07c18e2110f34cadf12d236954e222fa
Author: Justin Silverman <jsilve24@gmail.com>
Date: 2026-04-01 09:17:01 -0400
Commit message:

 feat: adding .Rbuildignore
Package: philr
Commit: bc0061b1b6347da528c37726ec6796ed59920787
Author: Justin Silverman <jsilve24@gmail.com>
Date: 2026-04-01 08:58:07 -0400
Commit message:

 Merge remote-tracking branch 'Bioconductor/devel'
Package: philr
Commit: 71d3c3398302d49321799e7d7a6fdaedd9051e25
Author: Justin Silverman <jsilve24@gmail.com>
Date: 2024-10-15 11:50:59 -0400
Commit message:

 change: updating news files
Package: plyranges
Commit: c2f2b4177b047d678e34f4f5cc8724ee8fb0ef91
Author: Mike Love <mikelove@users.noreply.github.com>
Date: 2026-03-31 17:12:45 -0400
Commit message:

 fixing pipe
Package: plyranges
Commit: e5ce86cd3b2a72dcfdfb0c685cf15261554d8bf2
Author: Mike Love <mikelove@users.noreply.github.com>
Date: 2026-03-31 17:12:30 -0400
Commit message:

 fixing docs probs
Package: plyranges
Commit: e5d83ec20b6dd78483fe0b6c58caa82495c1d619
Author: Mike Love <mikelove@users.noreply.github.com>
Date: 2026-03-31 10:56:03 -0400
Commit message:

 try fix test_slice
Package: plyranges
Commit: e7c4591daf5e1a9565466b1ac5c7733a636a093c
Author: Michael Love <mikelove@users.noreply.github.com>
Date: 2026-03-31 09:55:39 -0400
Commit message:

 Merge pull request #124 from tidyomics/new-slices

New slices
Package: plyranges
Commit: 4ea5b1c185230838df9a1f6c97fb4f0969d8b58b
Author: Mike Love <mikelove@users.noreply.github.com>
Date: 2026-03-24 14:24:57 -0400
Commit message:

 more work on new slice functions, testing
Package: plyranges
Commit: 41eb383b7643b5b03f1956f57c56119d645b3b9d
Author: Mike Love <mikelove@users.noreply.github.com>
Date: 2026-03-18 09:30:01 -0400
Commit message:

 to test: new slice functionality code
Package: GSVA
Commit: 6c3dd1bdbe80526a9457c33919fe7b8d9f13a254
Author: Robert Castelo <robert.castelo@upf.edu>
Date: 2026-04-01 14:05:51 +0200
Commit message:

 Further code cleaning
Package: clusterProfiler
Commit: 34939c3fadd8e29a763c474b0e1b847a4d2866be
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2026-04-01 19:13:36 +0800
Commit message:

 bump version
Package: clusterProfiler
Commit: 6089ea5da3dd9205d0dc38d16f120713d002d19d
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2026-04-01 12:12:13 +0800
Commit message:

 Merge branch 'devel' of github.com:YuLab-SMU/clusterProfiler into devel
Package: clusterProfiler
Commit: d1607ab675bac1643cadc862ab9304bf1df3acf6
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2026-04-01 12:11:10 +0800
Commit message:

 Merge pull request #812 from xiayh17/master

Refactor LLM interpretation with aisdk and update documentation
Package: clusterProfiler
Commit: 061f3d9d12e47b7bb0b6893f5466be0ed76c93fa
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2026-04-01 12:10:50 +0800
Commit message:

 bug fixed
Package: clusterProfiler
Commit: b621681081832c201d72a36a1d29e6578590247d
Author: Young Sherlock <xiayh17@gmail.com>
Date: 2026-04-01 00:18:03 +0800
Commit message:

 feat: use aisdk default model for interpret helpers
Package: clusterProfiler
Commit: 524ac04f6c3a537bcaa4bff8af082c882a1c44da
Author: Young Sherlock <xiayh17@gmail.com>
Date: 2026-03-31 23:14:32 +0800
Commit message:

 Merge branch 'devel' into master
Package: clusterProfiler
Commit: 47160ec2947333951d5e7391a143e87cbe060c2f
Author: Young Sherlock <xiayh17@gmail.com>
Date: 2026-03-01 02:51:17 +0800
Commit message:

 fix: address R CMD check warnings and notes (undocumented args, missing imports)
Package: clusterProfiler
Commit: 641a889290e19a88d27c253b12a7e173457de68d
Author: Young Sherlock <xiayh17@gmail.com>
Date: 2026-03-01 02:32:50 +0800
Commit message:

 feat: Replace fanyi with aisdk for LLM-based interpretation
Package: clusterProfiler
Commit: 056609c77754500a7a61c0618d4a62dc3db93e70
Author: Young Sherlock <xiayh17@gmail.com>
Date: 2026-03-01 02:28:10 +0800
Commit message:

 refactor: migrate to aisdk structured output and update documentation
Package: clusterProfiler
Commit: a52882ff38a4399fc775e8f91a6da4fbaec41827
Author: Young Sherlock <xiayh17@gmail.com>
Date: 2026-03-01 02:23:46 +0800
Commit message:

 refactor: clean up and simplify print.interpretation method
Package: clusterProfiler
Commit: 818182e59ac34ea2a680c82fe675c1aa1c81b1ec
Author: Young Sherlock <xiayh17@gmail.com>
Date: 2026-03-01 01:21:12 +0800
Commit message:

 docs: update documentation for interpret functions
Package: clusterProfiler
Commit: ce59da68a826e0fb74c37edf2175a2589734f351
Author: Young Sherlock <xiayh17@gmail.com>
Date: 2026-03-01 01:21:04 +0800
Commit message:

 refactor: replace fanyi with aisdk and add provider support in interpret
Package: clusterProfiler
Commit: cb324d449f255df8abd37e1330638761be23aad4
Author: Young Sherlock <xiayh17@gmail.com>
Date: 2026-03-01 01:20:56 +0800
Commit message:

 chore: update ignore files for LLM config
Package: SIMLR
Commit: b7cc0ade8d562cdc42595b50ef625d129ab046f0
Author: Luca De Sano <luca.desano@gmail.com>
Date: 2026-04-01 13:12:38 +0200
Commit message:

 update to 1.37.1
Package: TRONCO
Commit: 56ebe57f4c17c6123a7037956d7033caaa4ec25e
Author: Luca De Sano <luca.desano@gmail.com>
Date: 2026-04-01 12:57:04 +0200
Commit message:

 update to 2.43.1
Package: phylobar
Commit: 30e99be52e61b5674a5720f869a0a7f12a39dae0
Author: Kris Sankaran <sankaran.kris@gmail.com>
Date: 2026-04-01 11:22:23 +0100
Commit message:

 add utils import about download
Package: Rarr
Commit: 99df17a307d26a4cb479ad022c13b3a8e904fc1b
Author: Hugo Gruson <git@hugogruson.fr>
Date: 2026-04-01 12:14:35 +0200
Commit message:

 Add some additional info in design vignette
Package: Rarr
Commit: e786e2bfe9506295e38f7b2b6b7d0f999edd522e
Author: Hugo Gruson <git@hugogruson.fr>
Date: 2026-03-31 17:29:17 +0200
Commit message:

 Add fixme for unicode bytes encode
Package: phylobar
Commit: 5aae1c4e44b3f85bf78b41409df240dbaddc198b
Author: Kris Sankaran <sankaran.kris@gmail.com>
Date: 2026-04-01 11:06:17 +0100
Commit message:

 Merge pull request #1 from mkdiro-O/devel

Remove MicrobiomeStat dependecy
Package: phylobar
Commit: de9a58378ccad1b39ee43cac5fe0f9aca14eca96
Author: Kris Sankaran <sankaran.kris@gmail.com>
Date: 2026-04-01 11:02:53 +0100
Commit message:

 update package version
Package: phylobar
Commit: 3929005b8c72cc61849bfaf208d6ac8c6fd2c22e
Author: Kris Sankaran <sankaran.kris@gmail.com>
Date: 2026-04-01 11:02:13 +0100
Commit message:

 add test and rebuild docs
Package: phylobar
Commit: d5f8b6de2a8962f5c20458a0774eb574e6249916
Author: Kris Sankaran <sankaran.kris@gmail.com>
Date: 2026-04-01 11:02:01 +0100
Commit message:

 update vignette and description to reflect removed dependency
Package: phylobar
Commit: 566ba0575462d7e4048eda25dd01954134ff6974
Author: Kris Sankaran <sankaran.kris@gmail.com>
Date: 2026-04-01 11:01:38 +0100
Commit message:

 define a deseq normalization function, to remove MicrobiomeStat dependency
Package: rexposome
Commit: 4282f36f14abd52570d710151d5611af5c4bcf48
Author: Xavier Escribà Montagut <xavier.escriba.montagut@gmail.com>
Date: 2026-04-01 11:35:26 +0200
Commit message:

 bump version (devel)
Package: rexposome
Commit: 7f9ffddcd9d10a15e6cece1402e3f719b1eafb27
Author: Xavier Escribà Montagut <xavier.escriba.montagut@gmail.com>
Date: 2026-04-01 11:35:10 +0200
Commit message:

 Merge branch 'master' into devel
Package: rexposome
Commit: 142cc1a94257ee14461e95b7ab69de51b4712a3d
Author: Xavier Escribà Montagut <xavier.escriba.montagut@gmail.com>
Date: 2026-04-01 11:26:05 +0200
Commit message:

 bump version
Package: rexposome
Commit: a4b4a2c888252a15e3d3d504262aa0fc1affdd81
Author: Xavier Escribà Montagut <xavier.escriba.montagut@gmail.com>
Date: 2026-04-01 11:24:00 +0200
Commit message:

 fix: remove pryr dependency

pryr is out of cran
Package: VISTA
Commit: bfb83647c8b0d4b40e05cb4f48e7a6c8648accd8
Author: Chirag Parsania <chirag.parsania@gmail.com>
Date: 2026-04-01 17:33:27 +1100
Commit message:

 Increment version number to 0.99.4
Package: VISTA
Commit: c3c19fd77f0b8111f669eed100cc4db1dbb2deec
Author: Chirag Parsania <chirag.parsania@gmail.com>
Date: 2026-04-01 17:31:30 +1100
Commit message:

 Add runnable examples and clean BiocCheck documentation warnings
Package: EnrichDO
Commit: ebc1cbfd018d75a32734b80f95b13677f49aaa44
Author: CHENGliang!@#123 <liangcheng@hrbmu.edu.cn>
Date: 2026-04-01 13:54:51 +0800
Commit message:

 v1.5.1
Package: EnrichDO
Commit: b6e63a1a86ddac91827568d556c8c5b11a401c9b
Author: CHENGliang!@#123 <liangcheng@hrbmu.edu.cn>
Date: 2026-04-01 13:49:03 +0800
Commit message:

 v1.6
Package: EnrichDO
Commit: 4b1f82fd257bb3b195df4e8b5790bc1efc8f897e
Author: liang cheng <liangcheng@hrbmu.edu.cn>
Date: 2026-04-01 10:41:30 +0800
Commit message:

 Delete .idea directory
Package: EnrichDO
Commit: 7bedb9ec4fed1f39cb279766cead957a5f789f7e
Author: liangcheng-hrbmu <liangcheng@hrbmu.edu.cn>
Date: 2026-03-31 22:42:18 +0800
Commit message:

 v 1.6.0
Package: MetaboDynamics
Commit: 4a19faed796f8a9d5d2006684fa40e865acec5b2
Author: Katja Danielzik <katja.danielzik@uni-due.de>
Date: 2026-04-01 06:58:13 +0200
Commit message:

 polishing vignette and readme
Package: CyTOFpower
Commit: 43535638005ba00159434fcde06d5c603b748544
Author: Andreas Gschwind <andreas.gschwind@stanford.edu>
Date: 2026-03-31 21:42:17 -0700
Commit message:

 Increment the devel branch package version to 1.17.1
Package: alabaster.base
Commit: 5424d3b3138a53e9fe8689e3d65d59316e2fb001
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2026-04-01 15:41:03 +1100
Commit message:

 Fixed the date to the current year, d'oh.
Package: CyTOFpower
Commit: 3899dd41666c2716ae8b2da45c0447f8804b09b6
Author: Andreas Gschwind <andreas.gschwind@stanford.edu>
Date: 2026-03-31 21:36:10 -0700
Commit message:

 change email address
Package: CyTOFpower
Commit: 5589a45706aacefe427c0c00ddaf59599e476dd4
Author: Andreas Gschwind <andreas.gschwind@stanford.edu>
Date: 2026-03-31 21:35:26 -0700
Commit message:

 Run GLMM model - expect known warning from mbest dependency
Package: Harman
Commit: 857a365eae0d14e9b8e8d5c6b2b50630a65ad67a
Author: Jason Ross <jason.ross@csiro.au>
Date: 2026-04-01 15:30:19 +1100
Commit message:

 Fix invalid template constructor syntax for C++20 compatibility

Replace CFactorials(size_t maxN) with CFactorials(size_t maxN)
in CMapSelectKFromN.h. Older toolchains accepted this, but current
Bioconductor Linux builds under g++ 13 / C++20 fail to parse it.
 </pre>
    </div>
  
    

      Package: SeqArray

      Commit: ff7f27ea6c0ce7e83aa01009b768a81a6f9bad5b

      Author:  Xiuwen Zheng <zhengxwen@gmail.com> 

      Date: 2026-03-31 23:22:18 -0500

      Commit message:


	  
		
 update seqGDS2VCF()
 

    

  
    

      Package: tidybulk

      Commit: 264714cf59d0bfad234edb6c5794b0268a80282b

      Author:  Stefano Mangiola <mangiolastefano@gmail.com> 

      Date: 2026-04-01 11:40:47 +1030

      Commit message:


	  
		
 Merge pull request #338 from tidyomics/fix-ubuntu-actions

Update rworkflows.yml to conditionally run telemetry based on OS conf… 

    

  
    

      Package: tidybulk

      Commit: e9578f60e34659b1793c56f056e1bebad2b7f67d

      Author:  Stefano Mangiola <mangiolastefano@gmail.com> 

      Date: 2026-04-01 10:12:37 +1030

      Commit message:


	  
		
 Add fastmatch to DESCRIPTION suggests
 

    

  
    

      Package: tidybulk

      Commit: 4c3c87880bb40b077883cd1ee3c96a2db1482eab

      Author:  Stefano Mangiola <mangiolastefano@gmail.com> 

      Date: 2026-03-18 20:42:31 +1030

      Commit message:


	  
		
 Update rworkflows.yml to switch Bioconductor version from release to devel and adjust Docker container accordingly.
 

    

  
    

      Package: tidybulk

      Commit: 7a39ca56cce0fc0b95e05c1a55bde07603695f7e

      Author:  Stefano Mangiola <mangiolastefano@gmail.com> 

      Date: 2026-03-18 20:17:46 +1030

      Commit message:


	  
		
 Update rworkflows.yml to switch Bioconductor version from devel to release and adjust Docker container accordingly.
 

    

  
    

      Package: tidybulk

      Commit: 1ce0fd38de9690fdda88d50692367483c9c8442e

      Author:  Stefano Mangiola <mangiolastefano@gmail.com> 

      Date: 2026-03-18 19:28:04 +1030

      Commit message:


	  
		
 Update rworkflows.yml to conditionally run telemetry based on OS configuration
 

    

  
    

      Package: tidybulk

      Commit: ed808f65e7c2ffb5aa12a9a79aea1d4bb489177a

      Author:  Stefano Mangiola <mangiolastefano@gmail.com> 

      Date: 2026-03-17 20:06:21 +1030

      Commit message:


	  
		
 Merge pull request #336 from tidyomics/fix/identify-abundant-null-rownames

Enhance tests for identify_abundant and keep_abundant functions to ha… 

    

  
    

      Package: tidybulk

      Commit: a1deeaa682e5eaed578cdf16bd90dfd3007d5d00

      Author:  Stefano Mangiola <mangiolastefano@gmail.com> 

      Date: 2026-03-17 17:33:17 +1030

      Commit message:


	  
		
 version UP 

    

  
    

      Package: tidybulk

      Commit: 6e49d6837b40cbbbda77e0a36f1d42636237559b

      Author:  Stefano Mangiola <mangiolastefano@gmail.com> 

      Date: 2026-03-17 16:20:54 +1030

      Commit message:


	  
		
 Merge branch 'master' into fix/identify-abundant-null-rownames 

    

  
    

      Package: tidybulk

      Commit: 6e3e9df85ae3e65fff9129c502bd7c0b0304dea5

      Author:  Stefano Mangiola <mangiolastefano@gmail.com> 

      Date: 2026-03-17 16:19:24 +1030

      Commit message:


	  
		
 Enhance tests for identify_abundant and keep_abundant functions to handle NULL rownames in SummarizedExperiment. Updated documentation comments for clarity.
 

    

  
    

      Package: tidybulk

      Commit: 59f8c24d94170ca61c0bd2f47e8089397c3ae779

      Author:  Stefano Mangiola <mangiolastefano@gmail.com> 

      Date: 2026-03-17 16:09:44 +1030

      Commit message:


	  
		
 version UP 

    

  
    

      Package: tidybulk

      Commit: 39e6aca78c8d46073457dd3672bd52bbff84510b

      Author:  Stefano Mangiola <mangiolastefano@gmail.com> 

      Date: 2026-03-17 16:07:47 +1030

      Commit message:


	  
		
 Revert "Refactor identify_abundant function to streamline logic for determining abundant features. Updated checks to use rowData instead of colData and simplified the process of identifying features to keep. Removed unnecessary imports and improved code clarity."

This reverts commit eeee8456794c6afe44a0557e00d1b0c5edf4073d.
 

    

  
    

      Package: tidybulk

      Commit: eeee8456794c6afe44a0557e00d1b0c5edf4073d

      Author:  Stefano Mangiola <mangiolastefano@gmail.com> 

      Date: 2026-03-17 16:03:24 +1030

      Commit message:


	  
		
 Refactor identify_abundant function to streamline logic for determining abundant features. Updated checks to use rowData instead of colData and simplified the process of identifying features to keep. Removed unnecessary imports and improved code clarity.
 

    

  
    

      Package: tidybulk

      Commit: dac39174b3359068ad13633973e25839b326149f

      Author:  Stefano Mangiola <mangiolastefano@gmail.com> 

      Date: 2025-11-12 10:02:44 +1030

      Commit message:


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

    

  
    

      Package: tidybulk

      Commit: 8c311d74ef3512e9d843b2e41560138938383671

      Author:  Stefano Mangiola <mangiolastefano@gmail.com> 

      Date: 2025-11-12 10:01:52 +1030

      Commit message:


	  
		
 version UP
 

    

  
    

      Package: VISTA

      Commit: 1bf1d88163cfab7905675b4c3e9ea241fa8d873f

      Author:  Chirag Parsania <chirag.parsania@gmail.com> 

      Date: 2026-04-01 14:21:05 +1100

      Commit message:


	  
		
 Increment version number to 0.99.3
 

    

  
    

      Package: VISTA

      Commit: c0407d02c912923b8fdf755d701af8e307ce57b7

      Author:  Chirag Parsania <chirag.parsania@gmail.com> 

      Date: 2026-04-01 12:20:53 +1100

      Commit message:


	  
		
 Refine benchmark docs and harden benchmark payload handling
 

    

  
    

      Package: VISTA

      Commit: 1d746b34998225284ab1098cc9d9b769d4e9b54b

      Author:  Chirag Parsania <chirag.parsania@gmail.com> 

      Date: 2026-03-31 16:16:21 +1100

      Commit message:


	  
		
 fix docs
 

    

  
    

      Package: VISTA

      Commit: 4d14234e60ed54123e0b8b1690876fb3eaefaf7f

      Author:  Chirag Parsania <chirag.parsania@gmail.com> 

      Date: 2026-03-31 15:47:14 +1100

      Commit message:


	  
		
 Align expression plot APIs and trim slow documentation examples

- align get_expression_violinplot() with the current expression plot argument set
- align get_expression_lineplot() with the same API while preserving compatibility aliases
- add regression tests to keep expression plot signatures in sync
- reduce slow example runtime by moving heavy enrichment/report examples to dontrun
- simplify selected plot examples and regenerate Rd files
 

    

  
    

      Package: alabaster.base

      Commit: 1e19f0eeff82ec13b85f086c571ac160c9d356ad

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

      Date: 2026-04-01 14:16:13 +1100

      Commit message:


	  
		
 Updated the vendored copy of comservatory.
 

    

  
    

      Package: octad

      Commit: 8fc16041df05249786a17a2ea1be490e8656505a

      Author:  Lionir <eygen.chekalin@gmail.com> 

      Date: 2026-03-31 18:28:59 -0700

      Commit message:


	  
		
 dependency update
 

    

  
    

      Package: PlinkMatrix

      Commit: 48d689a039c5d4cf70ce1852129d680684fcf443

      Author:  vjcitn <stvjc@channing.harvard.edu> 

      Date: 2026-03-31 18:59:11 -0400

      Commit message:


	  
		
 trying to scotch BiocCheck warnings
 

    

  
    

      Package: MSstatsBioNet

      Commit: a26e6fb303e4844f60e8b88fbef5d77ee8193b89

      Author:  tonywu1999 <wu.anthon@northeastern.edu> 

      Date: 2026-03-31 17:50:34 -0400

      Commit message:


	  
		
 fix quoted bug (#89) 

    

  
    

      Package: HumanRetinaLRSData

      Commit: e3942cd5836a5f08a8e9e8c8160e08453d42b101

      Author:  Sowmya Parthiban <sparthi1@jh.edu> 

      Date: 2026-03-31 17:47:44 -0400

      Commit message:


	  
		
 Address Bioconductor reviewer comments (v0.99.5)

  - DESCRIPTION: expand description, add URL/BugReports, remove LazyData,
    bump R requirement to 4.6.0, remove unused dplyr from Suggests
  - R/zzz.R: remove .onLoad, validate osf_file_name against local
    metadata.csv (no internet needed), switch data storage to flat CSV
    files, add importFrom utils/BiocFileCache
  - R/make-data.R: update load_object() calls to use base names (no .rds)
  -                                  ing section, remove inline
    plot_pca function definition, wrap lines to 80 chars
 

    

  
    

      Package: BiocAzul

      Commit: 0ba9f0fa3f9e62db93b223419a767f56df21c436

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2026-03-31 17:39:35 -0400

      Commit message:


	  
		
 version bump 0.99.33
 

    

  
    

      Package: BiocAzul

      Commit: 1a195882b4b69542afefe048ddfbe20b72eed3f4

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2026-03-31 17:39:29 -0400

      Commit message:


	  
		
 remove authenticate = FALSE
 

    

  
    

      Package: rnaseqGene

      Commit: 044b3d0bfed4ac398fb5b5cb915da3198bf3251a

      Author:  Mike Love <mikelove@users.noreply.github.com> 

      Date: 2026-03-31 16:46:12 -0400

      Commit message:


	  
		
 fixes #6
 

    

  
    

      Package: LRDE

      Commit: a87820ce20a661af22858f49a4415e6c3fec1c54

      Author:  Ziyang Liu <jacobleo773@gmail.com> 

      Date: 2026-03-31 13:35:59 -0700

      Commit message:


	  
		
 Update DESCRIPTION
 

    

  
    

      Package: ontoProc2

      Commit: d1544e5b589538cac9234b08e3338d544144ed93

      Author:  vjcitn <stvjc@channing.harvard.edu> 

      Date: 2026-03-31 16:21:25 -0400

      Commit message:


	  
		
 deal with datatable
 

    

  
    

      Package: PlinkMatrix

      Commit: 90adf6515a28a65fc59d5342f02f50c7a00fb4f5

      Author:  vjcitn <stvjc@channing.harvard.edu> 

      Date: 2026-03-31 16:19:16 -0400

      Commit message:


	  
		
 bump version and deal with decode_bed example request
 

    

  
    

      Package: ontoProc2

      Commit: 5135ef827ec14993248184beab6ae5ec794059cb

      Author:  vjcitn <stvjc@channing.harvard.edu> 

      Date: 2026-03-31 16:02:29 -0400

      Commit message:


	  
		
 block some chunks
 

    

  
    

      Package: LRDE

      Commit: 16d7b0599466db2521c40a345e16e9db4e9a4fba

      Author:  Ziyang Liu <jacobleo773@gmail.com> 

      Date: 2026-03-31 12:38:34 -0700

      Commit message:


	  
		
 Update DESCRIPTION
 

    

  
    

      Package: punKEGGer

      Commit: c1268f1dfcc0ad2c82b0d9e30bec93b2df95e209

      Author:  gdj <gdeanda@inmegen.edu.mx> 

      Date: 2026-03-31 13:27:31 -0600

      Commit message:


	  
		
 changed name of plotting function to plot_kegg_graph to avoid collisions with other BioC packages
 

    

  
    

      Package: punKEGGer

      Commit: f2fb4cd2a96476718e1f32fb338c17ea2d787d12

      Author:  gdj <gdeanda@inmegen.edu.mx> 

      Date: 2026-03-31 13:26:04 -0600

      Commit message:


	  
		
 removed ggkegg references
 

    

  
    

      Package: punKEGGer

      Commit: bd6420ca3caa0124e18c05ead21f177cbdb96315

      Author:  gdj <gdeanda@inmegen.edu.mx> 

      Date: 2026-03-31 12:17:52 -0600

      Commit message:


	  
		
 added function to fetch pathways via KEGGREST
 

    

  
    

      Package: SparseArray

      Commit: 020902af16965daeee15c5176f33d6f53ad22697

      Author:  Hervé Pagès <hpages.on.github@gmail.com> 

      Date: 2026-03-31 12:26:45 -0700

      Commit message:


	  
		
 Also avoid use of R_UnboundValue (thanks to Luke Tierney for the guidance)
 

    

  
    

      Package: LRDE

      Commit: 26fe64169a18908850c6d7b42d248ba6827285d4

      Author:  ziyang773 <jacobleo773@gmail.com> 

      Date: 2026-03-31 11:20:48 -0700

      Commit message:


	  
		
 Update .gitignore
 

    

  
    

      Package: LRDE

      Commit: 8517a89e30e4da898350ed8769fe788187a3b2cc

      Author:  ziyang773 <jacobleo773@gmail.com> 

      Date: 2026-03-31 11:15:41 -0700

      Commit message:


	  
		
 Remove Rproj
 

    

  
    

      Package: ontoProc2

      Commit: 4c486732a482334b2738a8395f5e432c10cb546e

      Author:  vjcitn <stvjc@channing.harvard.edu> 

      Date: 2026-03-31 14:12:14 -0400

      Commit message:


	  
		
 avoid requiring the protein ontology download
 

    

  
    

      Package: SparseArray

      Commit: 65383c02f986832b1416c6ad39da800d8ced05df

      Author:  Hervé Pagès <hpages.on.github@gmail.com> 

      Date: 2026-03-31 11:38:20 -0700

      Commit message:


	  
		
 SparseArray 1.11.13: Use R_getVar() instead of findVar() when R >= 4.6.0
 

    

  
    

      Package: scToppR

      Commit: b89b5609e34ce0935477ceaeba6a9486a99d5179

      Author:  Bryan Granger <grangerb@musc.edu> 

      Date: 2026-03-31 14:34:36 -0400

      Commit message:


	  
		
 version bump
 

    

  
    

      Package: mzR

      Commit: f768fca73394745cda47f3bc949971b95af0414b

      Author:  Steffen Neumann <sneumann@ipb-halle.de> 

      Date: 2026-03-22 17:42:54 +0100

      Commit message:


	  
		
 try a hack for MacOS Compilation in GH actions
 

    

  
    

      Package: scToppR

      Commit: f69e01e535a0a060d93b0f4b98fa2aefbe98bd7c

      Author:  Bryan Granger <grangerb@musc.edu> 

      Date: 2026-03-31 14:31:42 -0400

      Commit message:


	  
		
 addToppData function
 

    

  
    

      Package: GSVA

      Commit: 28aaf0ea9a5864ba67680c0812ef9faa36d20f0c

      Author:  Robert Castelo <robert.castelo@upf.edu> 

      Date: 2026-03-31 20:01:46 +0200

      Commit message:


	  
		
 Further code reorganization and cleaning
 

    

  
    

      Package: scToppR

      Commit: 141d1266498e7e8769a11013c240e90b9ea00d44

      Author:  Bryan Granger <grangerb@musc.edu> 

      Date: 2026-03-31 13:57:15 -0400

      Commit message:


	  
		
 add SE methods
 

    

  
    

      Package: scToppR

      Commit: a2cedb3afd880e8e97aff13de87f54e1a62a6526

      Author:  Bryan Granger <grangerb@musc.edu> 

      Date: 2026-01-15 12:25:12 -0500

      Commit message:


	  
		
 version bump
 

    

  
    

      Package: ClustIRR

      Commit: 466988092d8de2c5f40a139e337eb69f3df0aa15

      Author:  snaketron <snaketron@users.noreply.github.com> 

      Date: 2026-03-31 19:49:01 +0200

      Commit message:


	  
		
 Merge pull request #57 from snaketron/devel

Devel 

    

  
    

      Package: ClustIRR

      Commit: 088b2939ac247e195b8f6487c2040fc1c139b568

      Author:  snaketron <simo.kitanovski@proton.me> 

      Date: 2026-03-31 19:47:32 +0200

      Commit message:


	  
		
 future remove, 1:10 -> seq_len
 

    

  
    

      Package: ClustIRR

      Commit: d1a58c030f91c01be5b903390d1fdd01a86f13da

      Author:  snaketron <simo.kitanovski@proton.me> 

      Date: 2026-03-31 19:46:54 +0200

      Commit message:


	  
		
 remove futures
 

    

  
    

      Package: ClustIRR

      Commit: 507396dc906dacf5603f5ac878517fc769c4f67c

      Author:  snaketron <simo.kitanovski@proton.me> 

      Date: 2026-03-31 19:46:38 +0200

      Commit message:


	  
		
 bump, gglogo -> ggseqlogo
 

    

  
    

      Package: ClustIRR

      Commit: c19beffecb63a2ca16ebf9135c1ad2ffc5f91065

      Author:  snaketron <snaketron@users.noreply.github.com> 

      Date: 2026-03-31 00:02:20 +0200

      Commit message:


	  
		
 Merge pull request #56 from snaketron/devel

Devel 

    

  
    

      Package: ClustIRR

      Commit: f2bbc46d069c95131a2fcf3f9610871610730f19

      Author:  snaketron <simo.kitanovski@proton.me> 

      Date: 2026-03-31 00:01:19 +0200

      Commit message:


	  
		
 adaptation to fix devel check
 

    

  
    

      Package: ClustIRR

      Commit: 4099fe369485fc02a2651325c8012fad10c2be30

      Author:  snaketron <simo.kitanovski@proton.me> 

      Date: 2026-03-31 00:00:59 +0200

      Commit message:


	  
		
 new way of importing blaster and gglogo breaks devel
 

    

  
    

      Package: ClustIRR

      Commit: 27015871dfbd920a7423cc9f7e90fc1132ea0ca1

      Author:  snaketron <simo.kitanovski@proton.me> 

      Date: 2026-03-30 23:59:43 +0200

      Commit message:


	  
		
 correct imports
 

    

  
    

      Package: ClustIRR

      Commit: 4a0be3e67087629acac98d05869e3fd20279277f

      Author:  snaketron <simo.kitanovski@proton.me> 

      Date: 2026-03-30 23:59:34 +0200

      Commit message:


	  
		
 bump
 

    

  
    

      Package: visiumStitched

      Commit: 9d5b25b1e7ac4cc2112b412a8dcb51d29c0b2b99

      Author:  lcolladotor <lcolladotor@gmail.com> 

      Date: 2026-03-31 13:53:33 -0400

      Commit message:


	  
		
 Update GHA workflow; likely don't need to compile pkgconfig anymore on macOS
 

    

  
    

      Package: TREG

      Commit: 8161ab6c1683f8f3c9c3775d9f60c9150a747df4

      Author:  lcolladotor <lcolladotor@gmail.com> 

      Date: 2026-03-31 13:49:13 -0400

      Commit message:


	  
		
 Update GHA workflow
 

    

  
    

      Package: smokingMouse

      Commit: 22c6710900ea8691b892b80b50b70c608590958d

      Author:  lcolladotor <lcolladotor@gmail.com> 

      Date: 2026-03-31 13:47:00 -0400

      Commit message:


	  
		
 Update GHA workflow
 

    

  
    

      Package: qsvaR

      Commit: 21c225dd233c3775625e8aee2b8621e8506e39ee

      Author:  lcolladotor <lcolladotor@gmail.com> 

      Date: 2026-03-31 13:44:11 -0400

      Commit message:


	  
		
 Update GHA workflow
 

    

  
    

      Package: DeconvoBuddies

      Commit: c24741c1a229635c8dfc344a2fb1b0c573cc95b0

      Author:  lcolladotor <lcolladotor@gmail.com> 

      Date: 2026-03-31 13:40:22 -0400

      Commit message:


	  
		
 Update GHA workflow; likely don't need to compile pkgconfig anymore on macOS
 

    

  
    

      Package: regionReport

      Commit: e125ed92ea086fe7cfe64c071e99554c574ed0e5

      Author:  lcolladotor <lcolladotor@gmail.com> 

      Date: 2026-03-31 13:36:13 -0400

      Commit message:


	  
		
 Update GHA workflow
 

    

  
    

      Package: recountWorkflow

      Commit: 7888de85cf3c613d1593452f79088657485344dd

      Author:  lcolladotor <lcolladotor@gmail.com> 

      Date: 2026-03-31 13:32:22 -0400

      Commit message:


	  
		
 Update GHA workflow
 

    

  
    

      Package: recount3

      Commit: 0f6161ff392cf83df969a52971d2020f761b1217

      Author:  lcolladotor <lcolladotor@gmail.com> 

      Date: 2026-03-31 13:28:57 -0400

      Commit message:


	  
		
 Update GHA workflow
 

    

  
    

      Package: recount

      Commit: ee0517c04054bd4983be8b2504fd52d78cf50b47

      Author:  lcolladotor <lcolladotor@gmail.com> 

      Date: 2026-03-31 13:28:11 -0400

      Commit message:


	  
		
 Update GHA workflow
 

    

  
    

      Package: megadepth

      Commit: ae6706185351e0d5d28f0b21cbc0edf7d4a32491

      Author:  lcolladotor <lcolladotor@gmail.com> 

      Date: 2026-03-31 13:27:10 -0400

      Commit message:


	  
		
 Update GHA workflow
 

    

  
    

      Package: GenomicState

      Commit: 6c702390e4cfda846d0ed2be9cfba8f0d4e1edd0

      Author:  lcolladotor <lcolladotor@gmail.com> 

      Date: 2026-03-31 13:26:02 -0400

      Commit message:


	  
		
 Update GHA workflow
 

    

  
    

      Package: derfinderPlot

      Commit: 0ae7b7d7a5bc4a9da8bd6c29afb51172c906948a

      Author:  lcolladotor <lcolladotor@gmail.com> 

      Date: 2026-03-31 13:24:52 -0400

      Commit message:


	  
		
 Update GHA workflow
 

    

  
    

      Package: derfinderData

      Commit: 9cfcdf73fdc49c2317181c82571680b5d42a2019

      Author:  lcolladotor <lcolladotor@gmail.com> 

      Date: 2026-03-31 13:23:56 -0400

      Commit message:


	  
		
 Update GHA workflow
 

    

  
    

      Package: derfinderHelper

      Commit: 9c62cf19165538aaecbd87b7e1de4d80bf00c3c9

      Author:  lcolladotor <lcolladotor@gmail.com> 

      Date: 2026-03-31 13:22:35 -0400

      Commit message:


	  
		
 Update GHA workflow
 

    

  
    

      Package: regutools

      Commit: 327f7aa2ea9bb1096523dd8b9f435a19f7bc63fc

      Author:  lcolladotor <lcolladotor@gmail.com> 

      Date: 2026-03-31 13:15:13 -0400

      Commit message:


	  
		
 Update GHA workflow
 

    

  
    

      Package: derfinder

      Commit: 38d7a03c2f39137f65b714b00e5dbf659571a586

      Author:  lcolladotor <lcolladotor@gmail.com> 

      Date: 2026-03-31 13:13:32 -0400

      Commit message:


	  
		
 Update GHA workflow
 

    

  
    

      Package: goatea

      Commit: 4552cce94206ed1febe7068933d0ef6f6ede298e

      Author:  Maurits Unkel <mauritsunkel@gmail.com> 

      Date: 2026-03-31 18:26:48 +0200

      Commit message:


	  
		
 Fix Nebbiolo vignette build error Pandoc 99
 

    

  
    

      Package: recount3

      Commit: ef7b80aefb3e59888a04588945cc353f920c9576

      Author:  lcolladotor <lcolladotor@gmail.com> 

      Date: 2026-03-31 12:19:47 -0400

      Commit message:


	  
		
 fix alphabetical ordering of dependencies / citations
 

    

  
    

      Package: DeMixT

      Commit: 990c252e729ee0904f23880b46922af01d0cad8a

      Author:  wwylab <wwang7@mdanderson.org> 

      Date: 2026-03-31 10:56:43 -0500

      Commit message:


	  
		
 Fix OpenMP conditional compilation in DeMixNB.c for Mac compatibility
 

    

  
    

      Package: spatialLIBD

      Commit: e4921b4778d90466974249ff6795617275a717c6

      Author:  gpertea <geo.pertea@gmail.com> 

      Date: 2026-03-26 19:19:03 -0400

      Commit message:


	  
		
 Add top-level license for sponsor readiness
 

    

  
    

      Package: smokingMouse

      Commit: aec1013e3f3353effb76903a446f6f1b6522811e

      Author:  lcolladotor <lcolladotor@gmail.com> 

      Date: 2026-03-31 11:51:30 -0400

      Commit message:


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

    

  
    

      Package: smokingMouse

      Commit: c4dbd8a2ed2d38e5207753839faeb78080a49878

      Author:  daianna21 <glezdaianna@gmail.com> 

      Date: 2025-09-09 00:49:37 +0100

      Commit message:


	  
		
 Update fig in README
 

    

  
    

      Package: DeconvoBuddies

      Commit: 6e817491d8cca53663786bfa42cfe8f30d274786

      Author:  gpertea <geo.pertea@gmail.com> 

      Date: 2026-03-26 19:19:03 -0400

      Commit message:


	  
		
 Clean sponsor-facing repository metadata
 

    

  
    

      Package: recount3

      Commit: 5849cb558c30ffe8697284f1c9719f8cbf39f5ab

      Author:  lcolladotor <lcolladotor@gmail.com> 

      Date: 2026-03-31 11:45:50 -0400

      Commit message:


	  
		
 v1.21.1 -- use lobstr
 

    

  
    

      Package: recount3

      Commit: 0cb305924b932450e5d75f25c24254b15b4db47a

      Author:  lcolladotor <lcolladotor@gmail.com> 

      Date: 2026-03-31 11:43:58 -0400

      Commit message:


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

    

  
    

      Package: recount3

      Commit: 55898d1f6081fdfcefc5bfca2142e482f77c6b20

      Author:  gpertea <geo.pertea@gmail.com> 

      Date: 2026-03-26 20:06:08 -0400

      Commit message:


	  
		
 Replace pryr with lobstr in docs and vignette
 

    

  
    

      Package: recount3

      Commit: a2e0cd318ae0400675e0e6af5360cd1b8fedfa25

      Author:  gpertea <geo.pertea@gmail.com> 

      Date: 2026-03-26 19:19:03 -0400

      Commit message:


	  
		
 Add top-level license for sponsor readiness
 

    

  
    

      Package: GSVA

      Commit: 7dc5111b96a91a3e56b609ffe564ac585ed2aa67

      Author:  Robert Castelo <robert.castelo@upf.edu> 

      Date: 2026-03-31 17:43:45 +0200

      Commit message:


	  
		
 Code reorganization and cleaning
 

    

  
    

      Package: Pedixplorer

      Commit: d742c935be5b801cf6cc3b70ac07051441300f95

      Author:  Louis Le Nézet <58640615+LouisLeNezet@users.noreply.github.com> 

      Date: 2026-03-31 17:34:09 +0200

      Commit message:


	  
		
 Fix `circfun()` issue (#40)

* Fix circfun

* Add environment

* Bump version

* Update test

* Replace dplyr pipe

* Bump version

* Update releases pkgdown

* Fix lint 

    

  
    

      Package: ZarrArray

      Commit: c92038ea7902886d51a13436157267c34c213849

      Author:  Hervé Pagès <hpages.on.github@gmail.com> 

      Date: 2026-03-31 07:06:06 -0700

      Commit message:


	  
		
 add vignette chunk labels
 

    

  
    

      Package: DelayedArray

      Commit: f0d27f42253a6619277bec38dbc3f54dff002a2a

      Author:  Hervé Pagès <hpages.on.github@gmail.com> 

      Date: 2026-03-31 06:52:51 -0700

      Commit message:


	  
		
 DelayedArray 0.37.1: Remove all C code (not used and not needed)
 

    

  
    

      Package: GExPipe

      Commit: 0b4864589d0fe42dc5f14dc0070a2a8798a1cfa8

      Author:  SAFA RAFIQUE <safa.sandhu@gmail.com> 

      Date: 2026-03-31 18:42:47 +0500

      Commit message:


	  
		
 Prepare 0.99.5 Bioconductor resubmission.

Bump package version to 0.99.5, update NEWS with reviewer-facing fixes, remove CITATION until a DOI is available, and include current code/style updates to improve SPB/BiocCheck readiness.

Made-with: Cursor
 

    

  
    

      Package: Rarr

      Commit: 8e117188d469a53c1dfc721e8c1a8aa8d1c31387

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-03-31 14:35:14 +0200

      Commit message:


	  
		
 Gitignore benchmarks folder
 

    

  
    

      Package: Rarr

      Commit: c340401e0171142fc2d7de2e69638388be97d98d

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-03-31 14:34:13 +0200

      Commit message:


	  
		
 Move function definition to match calling order
 

    

  
    

      Package: Rarr

      Commit: c0dabbd468d70c804e4a84e6b2855254351eadc4

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-03-31 14:32:42 +0200

      Commit message:


	  
		
 Simplify if by naming boolean var
 

    

  
    

      Package: GenomicCoordinates

      Commit: f4f7d9bc08d4d178bfae642c7055e24ad61e51ad

      Author:  js2264 <jacquesserizay@gmail.com> 

      Date: 2026-03-31 15:16:07 +0200

      Commit message:


	  
		
 bump to 0.99.3
 

    

  
    

      Package: GenomicCoordinates

      Commit: e0fc95e1d2f8a2e748d2b4b9095779a1c4ae0c2f

      Author:  js2264 <jacquesserizay@gmail.com> 

      Date: 2026-03-31 15:15:56 +0200

      Commit message:


	  
		
 fix: import Seqinfo (2)
 

    

  
    

      Package: GenomicCoordinates

      Commit: ab65901dcb158fc16fe2a9ade781432d996d8ffb

      Author:  js2264 <jacquesserizay@gmail.com> 

      Date: 2026-03-31 15:09:03 +0200

      Commit message:


	  
		
 bump to 0.99.2
 

    

  
    

      Package: GenomicCoordinates

      Commit: b8da12c54c735229649eb64c384bb40c3c789829

      Author:  js2264 <jacquesserizay@gmail.com> 

      Date: 2026-03-31 15:07:48 +0200

      Commit message:


	  
		
 fix: import Seqinfo
 

    

  
    

      Package: GenomicCoordinates

      Commit: b4f91a329a9ddeb95d28c095ffda3c0aefb5e346

      Author:  js2264 <jacquesserizay@gmail.com> 

      Date: 2026-03-31 14:56:53 +0200

      Commit message:


	  
		
 doc: update
 

    

  
    

      Package: GenomicCoordinates

      Commit: ec2d7d893be336deac88f63707d468f07c4fcd5f

      Author:  js2264 <jacquesserizay@gmail.com> 

      Date: 2026-03-31 14:54:37 +0200

      Commit message:


	  
		
 fix: no negative start coordinate allowed
 

    

  
    

      Package: GenomicCoordinates

      Commit: 50d031dbef1c800805acf5dbcebcc95f8606881f

      Author:  js2264 <jacquesserizay@gmail.com> 

      Date: 2026-03-31 14:54:23 +0200

      Commit message:


	  
		
 fix: remove suppressWarnings
 

    

  
    

      Package: GenomicCoordinates

      Commit: 0fca0a64d56c5f7fe57fa9984e7e495f3267bc9b

      Author:  js2264 <jacquesserizay@gmail.com> 

      Date: 2026-03-31 14:52:58 +0200

      Commit message:


	  
		
 lint
 

    

  
    

      Package: GenomicCoordinates

      Commit: 28e99b43b3631b0bd91382b0c4f97eaf7e78aa9f

      Author:  js2264 <jacquesserizay@gmail.com> 

      Date: 2026-03-31 14:51:18 +0200

      Commit message:


	  
		
 refactor: sapply -> vapply
 

    

  
    

      Package: seqpac

      Commit: 6dafa303ce850ae64351eaa30613b648e59c35fb

      Author:  AlessoGozzo <alego91@liu.se> 

      Date: 2026-03-31 14:58:40 +0200

      Commit message:


	  
		
 ggplot deprecated language
 

    

  
    

      Package: seqpac

      Commit: 738df53310992bcccca6c6a1aa16edc92e37e5f3

      Author:  Alessandro Gozzo <alego91@liu.se> 

      Date: 2026-03-31 14:49:22 +0200

      Commit message:


	  
		
 Merge pull request #54 from OestLab/Dev_31032026

Fix deprecated ggplot2 language 

    

  
    

      Package: seqpac

      Commit: bd803b80b458a8ab336ff41062cce0301bbfe9b9

      Author:  AlessoGozzo <alego91@liu.se> 

      Date: 2026-03-31 10:35:48 +0200

      Commit message:


	  
		
 Fix deprecated ggplot2 language
 

    

  
    

      Package: ontoProc2

      Commit: c58c3dfe5135e759388e2d0027f1a62b21425a7d

      Author:  vjcitn <stvjc@channing.harvard.edu> 

      Date: 2026-03-31 08:28:29 -0400

      Commit message:


	  
		
 adding vignette
 

    

  
    

      Package: ontoProc2

      Commit: 41820925be0f4da830ceecaba67cd92041b676fd

      Author:  vjcitn <stvjc@channing.harvard.edu> 

      Date: 2026-03-30 20:45:19 -0400

      Commit message:


	  
		
 responding to BiocCheck
 

    

  
    

      Package: ontoProc2

      Commit: 8f8ae7ad8bd22b49748a2811e508285f3219d02b

      Author:  vjcitn <stvjc@channing.harvard.edu> 

      Date: 2026-03-25 06:17:33 -0400

      Commit message:


	  
		
 updated pkgdown
 

    

  
    

      Package: ontoProc2

      Commit: 1cb74b814f6cc117a19190fcff65b7914065ab17

      Author:  vjcitn <stvjc@channing.harvard.edu> 

      Date: 2026-03-25 06:14:12 -0400

      Commit message:


	  
		
 take care of data statement for tag2cn
 

    

  
    

      Package: ontoProc2

      Commit: 9c962ffd6b18c1a1552863650cab1d513d78c5ca

      Author:  vjcitn <stvjc@channing.harvard.edu> 

      Date: 2026-03-25 06:00:26 -0400

      Commit message:


	  
		
 add a vignette on cell-protein relations
 

    

  
    

      Package: ontoProc2

      Commit: ede32dacb96bfaebd6f133d6c85a79d7371dca24

      Author:  vjcitn <stvjc@channing.harvard.edu> 

      Date: 2026-03-24 14:55:10 -0400

      Commit message:


	  
		
 identifier maps for CL and phrases
 

    

  
    

      Package: ontoProc2

      Commit: 2ec698f5376bf0ba41f754bf2d59630445cad779

      Author:  vjcitn <stvjc@channing.harvard.edu> 

      Date: 2026-03-24 14:52:53 -0400

      Commit message:


	  
		
 added CL/PR interaction functions
 

    

  
    

      Package: PlinkMatrix

      Commit: aaf4a64337a7105ec20c68c11e76c85aea457ff6

      Author:  vjcitn <stvjc@channing.harvard.edu> 

      Date: 2026-03-30 19:17:23 -0400

      Commit message:


	  
		
 bumping version
 

    

  
    

      Package: PlinkMatrix

      Commit: 91e10e8181bd706c12a4f3b246edc8ff0fc853df

      Author:  vjcitn <stvjc@channing.harvard.edu> 

      Date: 2026-03-30 19:17:02 -0400

      Commit message:


	  
		
 remove a BiocCheck error
 

    

  
    

      Package: PlinkMatrix

      Commit: de3d10781e2d394d57a9bfa92f1a06adc44f84fa

      Author:  vjcitn <stvjc@channing.harvard.edu> 

      Date: 2026-03-30 10:45:49 -0400

      Commit message:


	  
		
 respond to BiocCheck
 

    

  
    

      Package: GExPipe

      Commit: 3a150dede8a8c89831d2fe3e71a0ffa87da82235

      Author:  SAFA RAFIQUE <safa.sandhu@gmail.com> 

      Date: 2026-03-31 17:13:31 +0500

      Commit message:


	  
		
 Update app navigation and pipeline summary step
 

    

  
    

      Package: GExPipe

      Commit: 90070d167ea738a242e150b16ddc3031e7a512d4

      Author:  SAFA RAFIQUE <safa.sandhu@gmail.com> 

      Date: 2026-03-31 16:30:19 +0500

      Commit message:


	  
		
 Address Bioconductor review checks and R 4.6 compatibility
 

    

  
    

      Package: GExPipe

      Commit: 6ec5a59d6b65fe1425a28d6e9b3e8dd28585fccb

      Author:  SAFA RAFIQUE <safa.sandhu@gmail.com> 

      Date: 2026-03-31 16:27:38 +0500

      Commit message:


	  
		
 Address Bioconductor review checks and R 4.6 compatibility
 

    

  
    

      Package: betterChromVAR

      Commit: b0ff1db6ba666bdd998cbb9d67165e3b91810dc0

      Author:  plger <pl.germain@gmail.com> 

      Date: 2026-03-31 13:03:03 +0200

      Commit message:


	  
		
 updated doc, re-enabled flbias
 

    

  
    

      Package: betterChromVAR

      Commit: 82b93523c3089c0535eeebd6af392e76114dc876

      Author:  plger <pl.germain@gmail.com> 

      Date: 2026-03-31 13:02:20 +0200

      Commit message:


	  
		
 fixed typo
 

    

  
    

      Package: betterChromVAR

      Commit: f5b000b94ea379d8521ba43f05f0ac9ec6a745ab

      Author:  plger <pl.germain@gmail.com> 

      Date: 2026-03-31 12:29:03 +0200

      Commit message:


	  
		
 fixed bugs I'd just introduced, updated doc
 

    

  
    

      Package: betterChromVAR

      Commit: cf143dd724f774505ed2d4ee6b48b1efb0f53f2e

      Author:  plger <pl.germain@gmail.com> 

      Date: 2026-03-31 11:12:04 +0200

      Commit message:


	  
		
 fixed wrong dimension!
 

    

  
    

      Package: MetaboDynamics

      Commit: 9e25c04018fadbb77eedde3df320ffa2c60b5281

      Author:  Katja Danielzik <katja.danielzik@stud.uni-due.de> 

      Date: 2026-03-31 10:58:51 +0200

      Commit message:


	  
		
 bug fixes
 

    

  
    

      Package: dnaEPICO

      Commit: 8ac388e21f0de0aae6505edf1ad70bbb3d5e5d46

      Author:  Paul Ruiz <ruizpint@qut.edu.au> 

      Date: 2026-03-31 18:57:34 +1000

      Commit message:


	  
		
 Bioconductor Site support email 0.99.9
 

    

  
    

      Package: GSVA

      Commit: d65b071a238034aa05e77240bb5f19b0b1bb11f4

      Author:  Robert Castelo <robert.castelo@upf.edu> 

      Date: 2026-03-31 10:41:26 +0200

      Commit message:


	  
		
 Bump version
 

    

  
    

      Package: GSVA

      Commit: 5f92d269a781fb41b8ba8d2d217f8963ef56842e

      Author:  Robert Castelo <robert.castelo@upf.edu> 

      Date: 2026-03-31 10:41:11 +0200

      Commit message:


	  
		
 Removed non-API calls from C code
 

    

  
    

      Package: jvecfor

      Commit: 636fde0485a8a1896a8c35155c5d47076fadd6a1

      Author:  Anestis Gkanogiannis <ganoyan@gmail.com> 

      Date: 2026-03-31 06:33:40 +0200

      Commit message:


	  
		
 Retry building due to "Support Site: HTTP 504"
 

    

  
    

      Package: qpgraph

      Commit: 8666fca33ca8997440616e387e1535392b863061

      Author:  Robert Castelo <robert.castelo@upf.edu> 

      Date: 2026-03-31 10:31:03 +0200

      Commit message:


	  
		
 Bump version
 

    

  
    

      Package: DOTSeq

      Commit: 2aad0f4572fa8f902b4694939d005ba23f7e975b

      Author:  lcscs12345 <lcscs12345@gmail.com> 

      Date: 2026-03-31 13:12:37 +0800

      Commit message:


	  
		
 fix CITATION
 

    

  
    

      Package: ZarrArray

      Commit: 29718247a9c30a853765a535c7772ba74e2f285d

      Author:  Hervé Pagès <hpages.on.github@gmail.com> 

      Date: 2026-03-30 22:04:31 -0700

      Commit message:


	  
		
 ZarrArray 0.99.1: Complete documentation and improve test coverage
 

    

  
    

      Package: jvecfor

      Commit: 2f22bd665ddd81978a5d297758aa2edbe446ec3b

      Author:  Anestis Gkanogiannis <ganoyan@gmail.com> 

      Date: 2026-03-31 06:17:11 +0200

      Commit message:


	  
		
 Fix NOTES
 

    

  
    

      Package: epiRomics

      Commit: 48f9b8dd208ad85bda31a78ce507349a074122c4

      Author:  Alex M. Mawla <ammawla@ucdavis.edu> 

      Date: 2026-03-30 21:14:02 -0700

      Commit message:


	  
		
 bump version to 0.99.2 to trigger Bioconductor rebuild
 

    

  
    

      Package: jvecfor

      Commit: 7eeb5252d2581d544fb4e0246b456739c01f0008

      Author:  Anestis Gkanogiannis <ganoyan@gmail.com> 

      Date: 2026-03-31 06:05:11 +0200

      Commit message:


	  
		
 Bump version to 0.99.4 and update NEWS; remove obsolete NEWS.Rd file
 

    

  
    

      Package: jvecfor

      Commit: 0951277d778432e5cf068ad49c6984fa88699ef3

      Author:  Anestis Gkanogiannis <ganoyan@gmail.com> 

      Date: 2026-03-31 05:47:57 +0200

      Commit message:


	  
		
 Adapt BiocNeighbors integration to 2.5.4 API (Bioc 3.23)
 

    

  
    

      Package: epiRomics

      Commit: d2f42ab61e1596e69b3410ce12b55316ea487ce9

      Author:  Alex M. Mawla <ammawla@ucdavis.edu> 

      Date: 2026-03-30 19:16:25 -0700

      Commit message:


	  
		
 feat: prepare epiRomics v0.99.1 for Bioconductor submission

- Add synthetic data test suite (380+ tests with concrete expected values)
- Remove all 9 deprecated functions, Gviz/lifecycle dependencies
- Refactor all functions to 50-line Bioconductor limit
- Fix all lines to 80-character limit
- Expose hard-coded values as parameters (genome-aware filter, BigWig scaling, visualization colors)
- Optimize performance (base::Map, .detect_cores, remove dead code)
- Fix roxygen2 fused blocks, regenerate NAMESPACE and man pages
- Bump version to 0.99.1, R >= 4.5.0
- R CMD check: 0 errors, 0 warnings, 0 notes
- BiocCheck: 0 errors, 0 warnings
 

    

  
    

      Package: cytofQC

      Commit: d6548dbdd13ac19bcb1aed0a4b30be88d340f4b0

      Author:  jillbo1000 <jflundell@gmail.com> 

      Date: 2026-03-30 23:09:01 -0400

      Commit message:


	  
		
 remove hrbrthemes
 

    

  
    

      Package: cytofQC

      Commit: 195a08163cad62d91f4769b4303890296a123f47

      Author:  jillbo1000 <jflundell@gmail.com> 

      Date: 2026-03-30 23:05:09 -0400

      Commit message:


	  
		
 remove hrbrthemes
 

    

  
    

      Package: GBScleanR

      Commit: afbbc07a9b2cd1d6eadbbcf83252b9944f8e578d

      Author:  tomoyukif <f.tomoyuki@okayama-u.ac.jp> 

      Date: 2026-03-31 12:05:21 +0900

      Commit message:


	  
		
 minor update
 

    

  
    

      Package: jvecfor

      Commit: 95301a098013cf6f9368b7e12b2d6f45081b57e0

      Author:  Anestis Gkanogiannis <ganoyan@gmail.com> 

      Date: 2026-03-31 04:49:30 +0200

      Commit message:


	  
		
 Address Bioconductor reviewer comments
 - Add JvecforParam/JvecforIndex S4 classes for BiocNeighbors BNPARAM drop-in integration (scran, scater, etc.)
 - Support sparse matrices natively via MatrixMarket format in Java backend, avoiding R-side densification of large dgCMatrix inputs
 - Replace TSV serialization with binary format for dense matrices
 - Switch from system2() to processx::run() for process management
 - Rewrite jvecfor_setup() to use tools::R_user_dir() instead of modifying read-only inst/java/
 - Expand test coverage from 70.9% to 85.5%
 - Add vignette sections for error=TRUE chunks and BNPARAM usage
 

    

  
    

      Package: GBScleanR

      Commit: 6481c672ef9169d1e0af8f228de1f074e4265bfe

      Author:  tomoyukif <f.tomoyuki@okayama-u.ac.jp> 

      Date: 2026-03-31 11:40:25 +0900

      Commit message:


	  
		
 minor update
 

    

  
    

      Package: octad

      Commit: e95feee8a549224bf593a3c81b7de14a8728bfd1

      Author:  Lionir <eygen.chekalin@gmail.com> 

      Date: 2026-03-30 18:22:46 -0700

      Commit message:


	  
		
 fixed dplyr id removal
 

    

  
    

      Package: octad

      Commit: 7e40a9dc40e379005e0e923a4d4b4a783b7077c4

      Author:  Lionir <eygen.chekalin@gmail.com> 

      Date: 2026-03-30 18:22:12 -0700

      Commit message:


	  
		
 fixed dplyr id removal
 

    

  
    

      Package: octad

      Commit: 849635403619e2846862760fa95b8761f0293f93

      Author:  Lionir <eygen.chekalin@gmail.com> 

      Date: 2026-03-30 18:21:52 -0700

      Commit message:


	  
		
 fixed dplyr id removal
 

    

  
    

      Package: octad

      Commit: 299d7254acbb98fa1feab08dc45b5c5164d3ffdc

      Author:  Lionir <eygen.chekalin@gmail.com> 

      Date: 2026-03-30 18:21:36 -0700

      Commit message:


	  
		
 fixed dplyr id removal
 

    

  
    

      Package: cytofQC

      Commit: cd4aa20fa418476808f98796260a80d6a049fba5

      Author:  jillbo1000 <jflundell@gmail.com> 

      Date: 2026-03-30 21:13:22 -0400

      Commit message:


	  
		
 remove hrbrthemes
 

    

  
    

      Package: cytofQC

      Commit: 6882f39d60b9d39d081d756c2cd0891d6abf54bb

      Author:  jillbo1000 <jflundell@gmail.com> 

      Date: 2026-02-09 18:56:45 -0500

      Commit message:


	  
		
 remove hrbrthemes
 

    

  
    

      Package: cytofQC

      Commit: d5007c22faff88720e58d976d166a986f0b039cb

      Author:  jillbo1000 <jflundell@gmail.com> 

      Date: 2026-02-09 18:31:07 -0500

      Commit message:


	  
		
 remove hrbrthemes package
 

    

  
    

      Package: cytofQC

      Commit: 2b7b70b58f6060c7820f2872799f74f21ac06c87

      Author:  jillbo1000 <jflundell@gmail.com> 

      Date: 2026-01-20 00:02:36 -0500

      Commit message:


	  
		
 new check
 

    

  
    

      Package: RFGeneRank

      Commit: fe40a7ea57dcf073d07b66afdd45e6c986da0b0f

      Author:  Abdulaziz Albeshri <a.z.a1410@hotmail.com> 

      Date: 2026-03-31 03:26:46 +0300

      Commit message:


	  
		
 Trigger Bioconductor rebuild
 

    

  
    

      Package: dnaEPICO

      Commit: 92a5b1ba03e74d0bbb2fb2558c98a4ea8e24bc42

      Author:  Paul Ruiz <ruizpint@qut.edu.au> 

      Date: 2026-03-31 09:29:48 +1000

      Commit message:


	  
		
 Bioconductor changes in test_that and Vignette 0.99.8
 

    

  
    

      Package: CONCERTDR

      Commit: b8c36d5a37b8a5636c1b0795fe0eca6c7662a008

      Author:  zeratulhx <1814737900@qq.com> 

      Date: 2026-03-31 09:18:33 +1100

      Commit message:


	  
		
 mailing list
 

    

  
    

      Package: CONCERTDR

      Commit: f71f47e236287bddd02572b7d2833ce58173894f

      Author:  zeratulhx <1814737900@qq.com> 

      Date: 2026-03-31 09:07:02 +1100

      Commit message:


	  
		
 mailing list
 

    

  
    

      Package: qpgraph

      Commit: 7256150c5de783bfb1cd255a2c23cea91772f4be

      Author:  Robert Castelo <robert.castelo@upf.edu> 

      Date: 2026-03-31 00:02:36 +0200

      Commit message:


	  
		
 Removed non-API calls from C code
 

    

  
    

      Package: RFGeneRank

      Commit: f67138d735219ee517f3f4db815a3d9035381120

      Author:  Abdulaziz Albeshri <a.z.a1410@hotmail.com> 

      Date: 2026-03-31 00:24:40 +0300

      Commit message:


	  
		
 Trigger rebuild (no functional changes)
 

    

  
    

      Package: Rarr

      Commit: 5554838b483840de902ca163d9334ccdc9bfd21a

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-03-30 23:10:05 +0200

      Commit message:


	  
		
 Add note about potential future optimization
 

    

  
    

      Package: Rarr

      Commit: 178b5bd1474fd289b80df4ee4c6bbb0c61e57796

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-03-30 20:43:44 +0200

      Commit message:


	  
		
 Move some compressor codec to codec arch
 

    

  
    

      Package: Rarr

      Commit: 4c03ed079dee4dca4791df6f581b17425ea8a704

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-03-30 18:42:28 +0200

      Commit message:


	  
		
 Start using R release for benchmarks again
 

    

  
    

      Package: Rarr

      Commit: 83b06437ed66aa4c8b42389fe6c8f32232b662eb

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-03-30 18:24:53 +0200

      Commit message:


	  
		
 Remove unnecessary isFALSE
 

    

  
    

      Package: Rarr

      Commit: 0f2cf192094b55d752ab0158973a90f8882d3257

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-03-30 18:22:25 +0200

      Commit message:


	  
		
 Move nchar default to function signature
 

    

  
    

      Package: Rarr

      Commit: a89b0ce4ac098c562b2f2166d4d661b63171e0dd

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-03-30 18:15:48 +0200

      Commit message:


	  
		
 Remove outdated nolint comments
 

    

  
    

      Package: Rarr

      Commit: 91a869cc8da7ab53ec247af8c91e14c105bf0788

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-03-30 18:09:38 +0200

      Commit message:


	  
		
 Bump version
 

    

  
    

      Package: Rarr

      Commit: a2e3233ce3b7b771e0edccd56c69b1b917740bd5

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-03-30 18:12:08 +0200

      Commit message:


	  
		
 Avoid dummy assignment
 

    

  
    

      Package: Rarr

      Commit: 40ad36499db554926fb005ba046a36cb49c86481

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-03-30 18:05:34 +0200

      Commit message:


	  
		
 Harmonize bytes-array codec signatures
 

    

  
    

      Package: Rarr

      Commit: a14c1b571c9308bc3a8949016e453b1a4964399d

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-03-30 18:02:01 +0200

      Commit message:


	  
		
 Run more benchmarks
 

    

  
    

      Package: Rarr

      Commit: df1689f424aba17fc3c33ae60b4013bfd5de04ac

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-03-30 18:01:55 +0200

      Commit message:


	  
		
 Handle bytes codec config in .configure_codecs()
 

    

  
    

      Package: RFGeneRank

      Commit: 3ffbe96390231cccb8ff15d0503509e017e422ae

      Author:  Abdulaziz Albeshri <a.z.a1410@hotmail.com> 

      Date: 2026-03-31 00:02:27 +0300

      Commit message:


	  
		
 Address reviewer comments: update to R >= 4.6, improve tests, documentation, and code compliance
 

    

  
    

      Package: DeMixT

      Commit: 60bac21ee9a7e8e21467ff02cfc882f8a1c60bf4

      Author:  wwylab <wwang7@mdanderson.org> 

      Date: 2026-03-30 15:21:41 -0500

      Commit message:


	  
		
 Fix calloc size_t cast warning in DeMixT.c
 

    

  
    

      Package: ClustIRR

      Commit: 45bd57ce87b937c36d3493cf845ddea03ef1be35

      Author:  snaketron <snaketron@users.noreply.github.com> 

      Date: 2026-03-30 20:32:36 +0200

      Commit message:


	  
		
 Merge pull request #55 from snaketron/devel

Devel 

    

  
    

      Package: ClustIRR

      Commit: 6d902349d029296bd457b8f5778ffbfe6a0523ab

      Author:  snaketron <simo.kitanovski@proton.me> 

      Date: 2026-03-30 20:29:23 +0200

      Commit message:


	  
		
 bugfixes and vignette sorting for next release
 

    

  
    

      Package: ClustIRR

      Commit: e2f8025ce39ead39cd00e1008c37fb259399448e

      Author:  snaketron <simo.kitanovski@proton.me> 

      Date: 2026-03-30 20:28:44 +0200

      Commit message:


	  
		
 version bump
 

    

  
    

      Package: ClustIRR

      Commit: be77e834808b1456fd5256eba023a83e4ccff92c

      Author:  snaketron <snaketron@users.noreply.github.com> 

      Date: 2026-02-27 00:33:13 +0100

      Commit message:


	  
		
 Merge pull request #51 from snaketron/devel

speedup in CS comp 

    

  
    

      Package: ClustIRR

      Commit: bb81635d0e0a69e1b157696e3afe3deb91de6230

      Author:  snaketron <simo.kitanovski@proton.me> 

      Date: 2026-02-27 00:31:26 +0100

      Commit message:


	  
		
 speedup in CS comp
 

    

  
    

      Package: ClustIRR

      Commit: 383b30bb373135b2b2d3c8369fe2adc8f302efe1

      Author:  snaketron <snaketron@users.noreply.github.com> 

      Date: 2026-02-23 11:29:14 +0100

      Commit message:


	  
		
 Merge pull request #50 from snaketron/devel

minor fix 

    

  
    

      Package: ClustIRR

      Commit: 0c61f5eb276de0d1b5b1edb1a2b890fba403f296

      Author:  snaketron <simo.kitanovski@proton.me> 

      Date: 2026-02-23 11:24:37 +0100

      Commit message:


	  
		
 minor fix
 

    

  
    

      Package: ClustIRR

      Commit: 9969c73b44bbabda31a429c4ed3d16752ab5616e

      Author:  snaketron <snaketron@users.noreply.github.com> 

      Date: 2026-02-23 11:03:59 +0100

      Commit message:


	  
		
 Merge pull request #48 from snaketron/feat_save_graph

Feature: Save interactive graphs + small patch (cdr3 NA handling for double chain samples) 

    

  
    

      Package: ClustIRR

      Commit: 18ab8c9ebd73605d64526615411b35ef182c2f99

      Author:  snaketron <snaketron@users.noreply.github.com> 

      Date: 2026-02-23 11:03:38 +0100

      Commit message:


	  
		
 Merge branch 'main' into feat_save_graph 

    

  
    

      Package: ClustIRR

      Commit: 9aa3e98109697cea70b5fa4858f96eff518e7bd0

      Author:  snaketron <snaketron@users.noreply.github.com> 

      Date: 2026-02-23 10:59:37 +0100

      Commit message:


	  
		
 Merge pull request #49 from snaketron/devel

NRADs based comparison 

    

  
    

      Package: ClustIRR

      Commit: c8898563403ae071b3db393642ffce4b5d6c4932

      Author:  snaketron <simo.kitanovski@proton.me> 

      Date: 2026-02-23 10:56:51 +0100

      Commit message:


	  
		
 NRADs based comparison
 

    

  
    

      Package: ClustIRR

      Commit: 9c9b90707cae2e5c27a185b9951b9cf1781bc971

      Author:  kaozkai <freibeuter69@freenet.de> 

      Date: 2026-02-19 18:24:07 +0100

      Commit message:


	  
		
 - updated example in man
 

    

  
    

      Package: ClustIRR

      Commit: b6ef9b4c31b51998f929eb60d2c6ae78d33fe67f

      Author:  kaozkai <freibeuter69@freenet.de> 

      Date: 2026-02-19 18:20:02 +0100

      Commit message:


	  
		
 - updated manual for save_interactive_graph()
 

    

  
    

      Package: ClustIRR

      Commit: dbf8a8743c58d1a758a0a9a28474d1d59d19e589

      Author:  kaozkai <freibeuter69@freenet.de> 

      Date: 2026-02-19 18:08:35 +0100

      Commit message:


	  
		
 - patched get_clust() function to return NULL instead of stopping for samples with two chains, where one chain contains only NA
- added tests for the patch
- updated parameter names in tests for save_interactive_graph()
 

    

  
    

      Package: ClustIRR

      Commit: 8b7de0343244b92510fb33caedc2e40c603be1de

      Author:  kaozkai <freibeuter69@freenet.de> 

      Date: 2026-02-18 12:57:59 +0100

      Commit message:


	  
		
 - updated export name
 

    

  
    

      Package: ClustIRR

      Commit: 0651cf4ab047f72b87109d01320eb61cc7709225

      Author:  kaozkai <freibeuter69@freenet.de> 

      Date: 2026-02-18 12:50:03 +0100

      Commit message:


	  
		
 - renamed save_graph() to save_interactive_graph()
- added checks to save_interactive_graph()
- moved htmlwidgets from "Imports" to "Suggests" to decrease package dependencies
- added test-save_interactive_graph
- removed version increment to avoid clash (better done upon merging, anyway)
 

    

  
    

      Package: ClustIRR

      Commit: 20c302609a17dd62703e77b6840f056d0f587ada

      Author:  kaozkai <freibeuter69@freenet.de> 

      Date: 2026-02-17 18:37:41 +0100

      Commit message:


	  
		
 - Added save_graph() feature for graph export of interactive visNetwork graph
- Added short vignette for new feature
- Minor change: Added newline at end of DESCRIPTION
- Version push to 1.9.16
 

    

  
    

      Package: ClustIRR

      Commit: 839ba3543224d7911947783a6181b5195c6ce5d8

      Author:  snaketron <snaketron@users.noreply.github.com> 

      Date: 2026-02-17 12:27:42 +0100

      Commit message:


	  
		
 Merge pull request #47 from snaketron/devel

inproper merge 

    

  
    

      Package: cellmig

      Commit: ee2392ea7a56d0ddd00192a01e0ed57cdc891b5f

      Author:  snaketron <simo.kitanovski@proton.me> 

      Date: 2026-03-30 20:11:56 +0200

      Commit message:


	  
		
 suppress warnings when testing get_dose_response_profile temporarily. This will ensure tests pass. Warnings are produced by ggtree and its interaction with ggplot2 -> issue created ggtree will have to solve this
 

    

  
    

      Package: cellmig

      Commit: a398e3cf2c8d3c186d8fc3d4efefa897a94e66ed

      Author:  snaketron <simo.kitanovski@proton.me> 

      Date: 2026-03-30 20:10:24 +0200

      Commit message:


	  
		
 news before relase
 

    

  
    

      Package: cellmig

      Commit: 96de33b5a76e4762bdd3612dfd5365e4fbd6d7d1

      Author:  snaketron <simo.kitanovski@proton.me> 

      Date: 2026-03-30 20:10:16 +0200

      Commit message:


	  
		
 version bump
 

    

  
    

      Package: cellmig

      Commit: 99bb4bbfbc695604d0b6e7f8bc8a15bbf539f12b

      Author:  snaketron <snaketron@users.noreply.github.com> 

      Date: 2026-02-03 15:55:35 +0100

      Commit message:


	  
		
 Merge pull request #3 from snaketron/devel

warning removed 

    

  
    

      Package: cellmig

      Commit: ff77c5ca9c6ce40928c2cb12ecc529e7f8d0b00c

      Author:  snaketron <snaketron@users.noreply.github.com> 

      Date: 2026-02-03 15:13:13 +0100

      Commit message:


	  
		
 Merge pull request #2 from snaketron/devel

bugfree version 

    

  
    

      Package: scPassport

      Commit: 2297a74d284c0fd631376e4a94b1a3eec0c5eb52

      Author:  Kacar <skacar@iu.edu> 

      Date: 2026-03-30 12:45:28 -0400

      Commit message:


	  
		
 Fix: reduce eval=FALSE vignette chunks, bump version to 0.99.2
 

    

  
    

      Package: scPassport

      Commit: 6129e2a838dca7d279bd408e4612a457d8b6f567

      Author:  Kacar <skacar@iu.edu> 

      Date: 2026-03-30 12:04:08 -0400

      Commit message:


	  
		
 Fix: remove compiled .o files, fix vignette eval=FALSE, remove CITATION, bump version to 0.99.1
 

    

  
    

      Package: CrcBiomeScreen

      Commit: 5994253f2df9018a1409efcf57a91b5996108072

      Author:  Chronostasis <ngzh5554@leeds.ac.uk> 

      Date: 2026-03-30 16:07:16 +0100

      Commit message:


	  
		
 Prepare package for Bioconductor submission

- Fixed R CMD check and BiocCheck issues
- Temporarily disabled XGBoost due to compatibility issues with caret
- Updated documentation and examples to ensure reproducibility
- Replaced direct S4 slot access with accessor functions
- Cleaned up unused files and commented code
- Updated NEWS.md
 

    

  
    

      Package: CrcBiomeScreen

      Commit: b757e7f9f5392d16162ef21979a063a647a54d12

      Author:  Chronostasis <ngzh5554@leeds.ac.uk> 

      Date: 2026-03-11 12:59:04 +0000

      Commit message:


	  
		
 Check the update of bioconductor.
 

    

  
    

      Package: CrcBiomeScreen

      Commit: 8c64c4ae03a27731684c4105b0af42d7a18f665d

      Author:  Chronostasis <ngzh5554@leeds.ac.uk> 

      Date: 2026-03-11 12:58:41 +0000

      Commit message:


	  
		
 Check the update for bioconductor.
 

    

  
    

      Package: Rarr

      Commit: bca935c5c5a8c171062229971f22f6ed2efaaeda

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-03-30 17:44:54 +0200

      Commit message:


	  
		
 Fix design vignette title
 

    

  
    

      Package: MSstatsPTM

      Commit: c2f697df19fab6fedb76a8bcf3cc12c41bec796c

      Author:  tonywu1999 <wu.anthon@northeastern.edu> 

      Date: 2026-03-30 11:32:53 -0400

      Commit message:


	  
		
 Update package version to 2.13.1

Bump version number from 2.13.0 to 2.13.1 in DESCRIPTION file. 

    

  
    

      Package: MSstatsPTM

      Commit: 886797774fcd0ecc8260b9fcb22bd15cafda4da1

      Author:  tonywu1999 <wu.anthon@northeastern.edu> 

      Date: 2026-03-30 11:32:26 -0400

      Commit message:


	  
		
 Revert "deprecation(groupComparisonPTM): Deprecate data.type parameter (#124)" (#126)

This reverts commit 0630b4346704ebebd20241cc0d1a7c27f225337b. 

    

  
    

      Package: MSstatsPTM

      Commit: 0f49cc2656e3c1a6ea4999ee6879b06e0c9b03a3

      Author:  tonywu1999 <wu.anthon@northeastern.edu> 

      Date: 2026-02-25 21:40:54 -0500

      Commit message:


	  
		
 feat(diann): Enable DIANN 2.0 for DIANNtoMSstatsPTMFormat (#125)

 

    

  
    

      Package: ClonalSim

      Commit: 94c8348e067ea091dddab4472e58500a03b72d55

      Author:  Gabriele Bucci <bucci.g@gmail.com> 

      Date: 2026-03-30 16:47:21 +0200

      Commit message:


	  
		
 Merge pull request #13 from gbucci/claude/update-clonalsim-r-requirement-bgw5b

Fix Bioconductor reviewer feedback (v0.99.3) 

    

  
    

      Package: ClonalSim

      Commit: 1d7ee48b18babd6c455fd3f90ef58933bb9bcdbe

      Author:  Claude <noreply@anthropic.com> 

      Date: 2026-03-30 14:32:03 +0000

      Commit message:


	  
		
 Fix Bioconductor reviewer feedback (v0.99.5)

- Remove \dontrun{} from all man page examples (toVCF, toDataFrame,
  toPyClone, toSciClone, plot method) — replaced with runnable
  tempfile()-based examples per Bioconductor guidelines
- Fix vignette export blocks: removed eval=FALSE, now use tempfile()
  so examples run during build
- Bump version 0.99.4 → 0.99.5 to trigger new Bioconductor build

https://claude.ai/code/session_01HTMph1dUaKMNLDDbsCJqTw
 

    

  
    

      Package: Rarr

      Commit: e92d26c9d4abf77b33fb04d23a4bbd9382519c52

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-03-30 16:05:42 +0200

      Commit message:


	  
		
 Run smaller benchmark
 

    

  
    

      Package: Rarr

      Commit: 701b7c65b2e9dd1fb81939dd7c1a3670975d68d4

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-03-30 15:54:15 +0200

      Commit message:


	  
		
 Bump version
 

    

  
    

      Package: Rarr

      Commit: 291e738061c89a46d026444b6ce1cbc9ff36080b

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-03-30 15:54:01 +0200

      Commit message:


	  
		
 Run devtools::document()
 

    

  
    

      Package: Rarr

      Commit: 76837e9129464aff6d02c2671f6d428cb028c98e

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-03-30 15:53:47 +0200

      Commit message:


	  
		
 Mention dimension_names field in NEWS
 

    

  
    

      Package: Rarr

      Commit: 2b7f5acef55e94df3df0add55feb860c7c232489

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-03-30 15:43:46 +0200

      Commit message:


	  
		
 Add initial design vignette
 

    

  
    

      Package: Rarr

      Commit: 3f4161c65728cc88e46716d91e8afebe1cbfdaa2

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-03-30 15:03:45 +0200

      Commit message:


	  
		
 Allow reading & writing dimension names
 

    

  
    

      Package: imcRtools

      Commit: 7891b53c4bcf184a498eb75f6ef915230abcf84a

      Author:  Lasse Meyer <73339780+lassedochreden@users.noreply.github.com> 

      Date: 2026-03-30 13:32:46 +0200

      Commit message:


	  
		
 Merge pull request #146 from BodenmillerGroup/devel_LM

Update function pages for interaction testing 

    

  
    

      Package: imcRtools

      Commit: 7df886dba86acbc76c73a632661362d0ae8ca3fb

      Author:  lassedochreden <lasse.meyer@uzh.ch> 

      Date: 2026-03-30 11:03:30 +0200

      Commit message:


	  
		
 news and version
 

    

  
    

      Package: imcRtools

      Commit: 2c3b05060cbbd23dcc14435f72b07fff04475f6f

      Author:  lassedochreden <lasse.meyer@uzh.ch> 

      Date: 2026-03-30 10:23:16 +0200

      Commit message:


	  
		
 typo
 

    

  
    

      Package: imcRtools

      Commit: e0f58c0a2e0a0c272de45abcb2b8d73dd47893e0

      Author:  lassedochreden <lasse.meyer@uzh.ch> 

      Date: 2026-03-26 15:36:55 +0100

      Commit message:


	  
		
 update function page
 

    

  
    

      Package: imcRtools

      Commit: 2b30126d55de2511cd0d0ea7dc261534e4c7e54f

      Author:  SchulzDan <shooltz@gmx.de> 

      Date: 2026-01-06 08:39:48 +0100

      Commit message:


	  
		
 removed setup-bioconductor... lines
 

    

  
    

      Package: imcRtools

      Commit: 54bf1d520a38a676171cde0d976daf17d2e86355

      Author:  SchulzDan <shooltz@gmx.de> 

      Date: 2026-01-06 08:25:54 +0100

      Commit message:


	  
		
 updated yaml for devel workflow
 

    

  
    

      Package: MsQuality

      Commit: 7a883367e4bb61b2154693177096fdd45a7caa43

      Author:  Thomas Naake <thomasnaake@googlemail.com> 

      Date: 2026-03-30 15:11:50 +0200

      Commit message:


	  
		
 Update DESCRIPTION
 

    

  
    

      Package: MsQuality

      Commit: a48581b9ea385023b1d6ef052dbbfbc6b108f2cf

      Author:  Thomas Naake <thomasnaake@googlemail.com> 

      Date: 2026-03-30 14:42:51 +0200

      Commit message:


	  
		
 use again old file
 

    

  
    

      Package: MsQuality

      Commit: 0da5fbabccfb884f63411d54c9c86fce001fbd39

      Author:  Thomas Naake <thomasnaake@googlemail.com> 

      Date: 2026-03-27 23:10:59 +0100

      Commit message:


	  
		
 Update check-bioc.yml
 

    

  
    

      Package: MsQuality

      Commit: e50372c526480ca59498bc859f011bc1c6491bf7

      Author:  Thomas Naake <thomasnaake@googlemail.com> 

      Date: 2026-03-27 23:07:20 +0100

      Commit message:


	  
		
 Update check-bioc.yml
 

    

  
    

      Package: MsQuality

      Commit: bdf66ba289870e3abfecccbdae3262b4c0013fd4

      Author:  Thomas Naake <thomasnaake@googlemail.com> 

      Date: 2026-03-27 23:06:48 +0100

      Commit message:


	  
		
 Update check-bioc.yml
 

    

  
    

      Package: MsQuality

      Commit: e1b527a5c22c0633dc79c8a5e7546c6caa8dd643

      Author:  Thomas Naake <thomasnaake@googlemail.com> 

      Date: 2026-03-27 23:05:49 +0100

      Commit message:


	  
		
 Update check-bioc.yml
 

    

  
    

      Package: MsQuality

      Commit: ce31ef6fc89f268ad2e9eeca1421b5eedf536e43

      Author:  Thomas Naake <thomasnaake@googlemail.com> 

      Date: 2026-03-27 22:57:01 +0100

      Commit message:


	  
		
 Update check-bioc.yml
 

    

  
    

      Package: MsQuality

      Commit: 540da08ff74df9904228c509ac57ea58c740b813

      Author:  Thomas Naake <thomasnaake@googlemail.com> 

      Date: 2026-03-27 22:55:58 +0100

      Commit message:


	  
		
 Update check-bioc.yml
 

    

  
    

      Package: MsQuality

      Commit: 246b9580f655fc165c1bc097a5c48b01e4f09c56

      Author:  Thomas Naake <thomasnaake@googlemail.com> 

      Date: 2026-03-27 22:46:57 +0100

      Commit message:


	  
		
 Update check-bioc.yml
 

    

  
    

      Package: MsQuality

      Commit: 1ea15dd623bde108ac65bb108e617ec9ff87ef4e

      Author:  Thomas Naake <thomasnaake@googlemail.com> 

      Date: 2026-03-27 22:42:48 +0100

      Commit message:


	  
		
 Update check-bioc.yml
 

    

  
    

      Package: MsQuality

      Commit: 90f015337210f43ac4596c00195d9dd5e69c27ed

      Author:  Thomas Naake <thomasnaake@googlemail.com> 

      Date: 2026-03-27 22:40:01 +0100

      Commit message:


	  
		
 Update check-bioc.yml
 

    

  
    

      Package: MsQuality

      Commit: 83f07e16b1259ded4cd3976fae82b5cd94a46f69

      Author:  Thomas Naake <thomasnaake@googlemail.com> 

      Date: 2026-03-27 22:35:26 +0100

      Commit message:


	  
		
 Update check-bioc.yml
 

    

  
    

      Package: MsQuality

      Commit: 4e7278871a286bcc5d7a570cad5818f534007a30

      Author:  Thomas Naake <thomasnaake@googlemail.com> 

      Date: 2026-03-27 22:33:37 +0100

      Commit message:


	  
		
 Update check-bioc.yml
 

    

  
    

      Package: MsQuality

      Commit: dba6e670367af4df48bbaa4e86b325a1b28b3c93

      Author:  Thomas Naake <thomasnaake@googlemail.com> 

      Date: 2026-03-27 22:27:38 +0100

      Commit message:


	  
		
 Update check-bioc.yml
 

    

  
    

      Package: MsQuality

      Commit: c248fc0cdb24dc565d023b992ec983ef06cb8163

      Author:  Thomas Naake <thomasnaake@googlemail.com> 

      Date: 2026-03-27 22:19:01 +0100

      Commit message:


	  
		
 Update check-bioc.yml
 

    

  
    

      Package: MsQuality

      Commit: dd4624f30ad1d1b106d6ce925767d7decb51d035

      Author:  Thomas Naake <thomasnaake@googlemail.com> 

      Date: 2026-03-27 22:16:08 +0100

      Commit message:


	  
		
 Update check-bioc.yml
 

    

  
    

      Package: MsQuality

      Commit: c418efc62cff31fa86b864ab96cc45f484862fbb

      Author:  Thomas Naake <thomasnaake@googlemail.com> 

      Date: 2026-03-27 22:14:48 +0100

      Commit message:


	  
		
 Update check-bioc.yml
 

    

  
    

      Package: MsQuality

      Commit: fab3019d212850fcbff287031d6e9591f0a6ef42

      Author:  Thomas Naake <thomasnaake@googlemail.com> 

      Date: 2026-03-27 22:13:51 +0100

      Commit message:


	  
		
 Update check-bioc.yml
 

    

  
    

      Package: MsQuality

      Commit: 4f563912d57b817cbe23018bd99e1f1846febb47

      Author:  Thomas Naake <thomasnaake@googlemail.com> 

      Date: 2026-03-27 22:11:40 +0100

      Commit message:


	  
		
 Update check-bioc.yml
 

    

  
    

      Package: MsQuality

      Commit: 71217eb069ea3cbd7eae4085fc926ba0016f1751

      Author:  Thomas Naake <thomasnaake@googlemail.com> 

      Date: 2026-03-27 22:08:25 +0100

      Commit message:


	  
		
 Update check-bioc.yml
 

    

  
    

      Package: MsQuality

      Commit: d9d36e910816a54fe783ac79c8cde8fb190b892a

      Author:  Thomas Naake <thomasnaake@googlemail.com> 

      Date: 2026-03-27 22:06:10 +0100

      Commit message:


	  
		
 Update check-bioc.yml
 

    

  
    

      Package: MsQuality

      Commit: 3251165252a9ec782b527f43df16fcdc30d480e0

      Author:  Thomas Naake <thomasnaake@googlemail.com> 

      Date: 2026-03-27 21:43:00 +0100

      Commit message:


	  
		
 Update check-bioc.yml
 

    

  
    

      Package: MsQuality

      Commit: 180d259baf5ccd03a836c07a00b054c06856501c

      Author:  Thomas Naake <thomasnaake@googlemail.com> 

      Date: 2026-03-27 21:30:42 +0100

      Commit message:


	  
		
 Update check-bioc.yml
 

    

  
    

      Package: MsQuality

      Commit: 021569af4447ba540388b2f4e002c59bb7e16934

      Author:  Thomas Naake <thomasnaake@googlemail.com> 

      Date: 2026-03-27 21:21:52 +0100

      Commit message:


	  
		
 Update check-bioc.yml
 

    

  
    

      Package: MsQuality

      Commit: 95aabd6ef396577678cc37070f57ff9743e6589d

      Author:  Thomas Naake <thomasnaake@googlemail.com> 

      Date: 2026-03-27 21:15:47 +0100

      Commit message:


	  
		
 Update check-bioc.yml
 

    

  
    

      Package: MsQuality

      Commit: ae53bbe0a90e3f9d8b875060806e8f26e3c281eb

      Author:  Thomas Naake <thomasnaake@googlemail.com> 

      Date: 2026-03-26 22:22:39 +0100

      Commit message:


	  
		
 Update MsQuality.Rmd
 

    

  
    

      Package: MsQuality

      Commit: 247f1405d1c9f097bc39dcbb87026b2337df4c1f

      Author:  Thomas Naake <thomasnaake@googlemail.com> 

      Date: 2026-03-26 22:21:04 +0100

      Commit message:


	  
		
 Delete function_Spectra_metrics.R.bak
 

    

  
    

      Package: MsQuality

      Commit: fae76e39c42b149f308d2a63c0da4acddd63c300

      Author:  Thomas Naake <thomasnaake@gmx.de> 

      Date: 2026-03-26 22:13:31 +0100

      Commit message:


	  
		
 Merge pull request #18 from philouail/Chromatograms

Implementing Chromatograms-based metrics calculations.  

    

  
    

      Package: MsQuality

      Commit: d63d64b39b2bbc6bafe5d4748d4101c05afd0f8f

      Author:  Philippine Louail <127301965+philouail@users.noreply.github.com> 

      Date: 2026-03-23 10:31:59 +0100

      Commit message:


	  
		
 Fix Thomas comments
 

    

  
    

      Package: MsQuality

      Commit: 8d13ef4da35cb78b027d83081b0b582e023ee297

      Author:  Philippine Louail <127301965+philouail@users.noreply.github.com> 

      Date: 2026-03-13 14:32:22 +0100

      Commit message:


	  
		
 Update signalToNoiseRatio.Rd
 

    

  
    

      Package: MsQuality

      Commit: 2d57628e9ad543ce37c5fb23a60fa50022814b54

      Author:  Philippine Louail <127301965+philouail@users.noreply.github.com> 

      Date: 2026-03-13 14:32:19 +0100

      Commit message:


	  
		
 refactro: overlap of parameter name
 

    

  
    

      Package: MsQuality

      Commit: 454ba759aaeb69137c304bd2394cd49c0b7b5373

      Author:  Philippine Louail <127301965+philouail@users.noreply.github.com> 

      Date: 2026-03-11 15:44:51 +0100

      Commit message:


	  
		
 fix extra lines
 

    

  
    

      Package: MsQuality

      Commit: a0d5b65419cb72cc3aa6eff74fb42ecf3d07e8ce

      Author:  Philippine Louail <127301965+philouail@users.noreply.github.com> 

      Date: 2026-03-11 15:44:37 +0100

      Commit message:


	  
		
 fix class evaluation
 

    

  
    

      Package: MsQuality

      Commit: 09aa4aba02def77df5423cf69ec4e416c7104251

      Author:  Philippine Louail <127301965+philouail@users.noreply.github.com> 

      Date: 2026-03-11 15:14:28 +0100

      Commit message:


	  
		
 remove unwanted files
 

    

  
    

      Package: MsQuality

      Commit: 048457f8da940dca5c91a63daf8a08c66c4fb167

      Author:  Philippine Louail <127301965+philouail@users.noreply.github.com> 

      Date: 2026-03-11 14:40:56 +0100

      Commit message:


	  
		
 Fix Thomas comments
 

    

  
    

      Package: MsQuality

      Commit: 6edb0a18eb4f89d74b9b930c38e57c11ab30332d

      Author:  Philippine Louail <127301965+philouail@users.noreply.github.com> 

      Date: 2026-03-03 15:18:42 +0100

      Commit message:


	  
		
 Update test_function_calculateMetrics_from_Spectra.R
 

    

  
    

      Package: MsQuality

      Commit: b6f771956354a8dc43afcc1e9e0e4f564c21e1f3

      Author:  Philippine Louail <127301965+philouail@users.noreply.github.com> 

      Date: 2026-03-03 15:18:27 +0100

      Commit message:


	  
		
 Merge branch 'devel' into Chromatograms
 

    

  
    

      Package: MsQuality

      Commit: 1180be0a00163e8e72b0a0aea839c150c4e98d9a

      Author:  Philippine Louail <127301965+philouail@users.noreply.github.com> 

      Date: 2026-02-18 12:05:41 +0100

      Commit message:


	  
		
 fix main branch conflict/updates.
 

    

  
    

      Package: MsQuality

      Commit: 2a3ac53fa4cfba3cde08ef6f9c880ed78cf289b4

      Author:  Philippine Louail <127301965+philouail@users.noreply.github.com> 

      Date: 2026-02-18 12:04:10 +0100

      Commit message:


	  
		
 Merge branch 'devel' into Chromatograms
 

    

  
    

      Package: MsQuality

      Commit: 2e07b0e80d749a8c30b460e49f3d6ab249541324

      Author:  Philippine Louail <127301965+philouail@users.noreply.github.com> 

      Date: 2026-02-12 10:14:36 +0100

      Commit message:


	  
		
 fix version dependency
 

    

  
    

      Package: MsQuality

      Commit: 1f4925b8cbaf446d4353823c5104836be6724238

      Author:  Philippine Louail <127301965+philouail@users.noreply.github.com> 

      Date: 2026-02-11 16:03:38 +0100

      Commit message:


	  
		
 refactor peak boundary and add prominence metric
 

    

  
    

      Package: MsQuality

      Commit: d41ed221dde66611df0f699e1b1f66e6432f1f58

      Author:  Philippine Louail <127301965+philouail@users.noreply.github.com> 

      Date: 2026-02-10 16:12:38 +0100

      Commit message:


	  
		
 peakBoundary, peakWidth, peakBeta implemented
 

    

  
    

      Package: MsQuality

      Commit: c83c4cc0016e5b13deff39793b17d703b532f3df

      Author:  Philippine Louail <127301965+philouail@users.noreply.github.com> 

      Date: 2026-02-09 17:19:42 +0100

      Commit message:


	  
		
 refactor:  metric redundancy
 

    

  
    

      Package: MsQuality

      Commit: 1efd0042797a6b50a468280bb6dbe7be434a928d

      Author:  Philippine Louail <127301965+philouail@users.noreply.github.com> 

      Date: 2026-02-09 10:49:24 +0100

      Commit message:


	  
		
 fix roxygen
 

    

  
    

      Package: MsQuality

      Commit: 06f3964653629ef3ef50ca943ff43a69709104a4

      Author:  Philippine Louail <127301965+philouail@users.noreply.github.com> 

      Date: 2026-02-06 13:46:42 +0100

      Commit message:


	  
		
 Update function_Chromatograms_metrics.R
 

    

  
    

      Package: MsQuality

      Commit: cf1691db7a08b63ca6695f56a872f86b5a23b603

      Author:  Philippine Louail <127301965+philouail@users.noreply.github.com> 

      Date: 2026-02-05 15:29:44 +0100

      Commit message:


	  
		
 refactor peakCount to add na.rm parameter
 

    

  
    

      Package: MsQuality

      Commit: c348129cb8f7a5a2663a75cbbf00629ab5c2acce

      Author:  Philippine Louail <127301965+philouail@users.noreply.github.com> 

      Date: 2026-02-04 17:51:58 +0100

      Commit message:


	  
		
 Update function_Chromatograms_metrics.R
 

    

  
    

      Package: MsQuality

      Commit: b3205f6864a4522e371d35b0c0aa11ef7210ff8e

      Author:  Philippine Louail <127301965+philouail@users.noreply.github.com> 

      Date: 2026-02-04 17:51:51 +0100

      Commit message:


	  
		
 remove unwanted metrics
 

    

  
    

      Package: MsQuality

      Commit: 675bca5fbc7215325616e74a9a8991c3097bba2d

      Author:  Philippine Louail <127301965+philouail@users.noreply.github.com> 

      Date: 2026-01-26 21:23:29 +0100

      Commit message:


	  
		
 refactor: fix some documentation
 

    

  
    

      Package: MsQuality

      Commit: 6fa3309a75c215edc32d3c0f781d677d6f0366ed

      Author:  Philippine Louail <127301965+philouail@users.noreply.github.com> 

      Date: 2026-01-26 21:04:15 +0100

      Commit message:


	  
		
 refactor: change mroe function to generic, and write method dispatch
 

    

  
    

      Package: MsQuality

      Commit: f5dc3aab57a8bb2232298ae955f075552e7a3805

      Author:  Philippine Louail <127301965+philouail@users.noreply.github.com> 

      Date: 2026-01-26 18:27:03 +0100

      Commit message:


	  
		
 feat: Implementation of chromatograms metrics
 

    

  
    

      Package: Rarr

      Commit: c8b39f07452f45b953335143d54fae66505e357f

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-03-30 14:29:52 +0200

      Commit message:


	  
		
 Bump version
 

    

  
    

      Package: Rarr

      Commit: dbccb31abab6c54506406e4986fa42cc23971669

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-03-30 14:29:37 +0200

      Commit message:


	  
		
 Remove outdated nuance from features vignette
 

    

  
    

      Package: Rarr

      Commit: 6ffdaebc80c4e09970026c27bc69904b060116f2

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-03-30 14:28:53 +0200

      Commit message:


	  
		
 Mention possibility to write v3 in NEWS
 

    

  
    

      Package: Rarr

      Commit: 69505a75c040a28ede511ce3ae6f7025413df827

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-03-30 14:15:18 +0200

      Commit message:


	  
		
 Remove custom fields and tweaks before writing metadata
 

    

  
    

      Package: Rarr

      Commit: d38ab0a56684991f235f573cdbef5a369a9b47a5

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-03-30 14:08:34 +0200

      Commit message:


	  
		
 Fix extra nesting in compressors
 

    

  
    

      Package: Rarr

      Commit: a2c1ee4b41434e4c42abf42236a327b5c7abce77

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-03-30 13:54:13 +0200

      Commit message:


	  
		
 Fix write_zarr_attributes() version guess
 

    

  
    

      Package: Rarr

      Commit: 7b4d876582e56fea23d1827a97d48b98dd54c7c9

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-03-30 13:23:15 +0200

      Commit message:


	  
		
 Add version check in write_zarr_attributes()
 

    

  
    

      Package: Rarr

      Commit: 994c4eedb8a5861f71704c3a6db6ea5bfae0d4bf

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-03-30 12:33:58 +0200

      Commit message:


	  
		
 Deal with non-existent zarr.json or metadata
 

    

  
    

      Package: Rarr

      Commit: 76d10ac30d064737741e12f92371931828e0e18b

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-03-30 12:11:29 +0200

      Commit message:


	  
		
 Document new "zarr_version" argument
 

    

  
    

      Package: Rarr

      Commit: 8b366d252b80008b61da4f331394eb83ecfdda47

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-03-30 11:49:41 +0200

      Commit message:


	  
		
 Set empty endian value to NA when reading v3
 

    

  
    

      Package: Rarr

      Commit: 7d5616ca46f1b9184d4b48924327c1120609f11b

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-03-11 23:54:41 +0100

      Commit message:


	  
		
 Fix bytes codec v3 conversion
 

    

  
    

      Package: Rarr

      Commit: 8dde99f7fa31ee4835d15db21a34e2cbd8444151

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-03-11 16:15:32 +0100

      Commit message:


	  
		
 Add option to return silently when no attribute file exists
 

    

  
    

      Package: Rarr

      Commit: dd4e71eba7b49df61d5d544e74cdeaaf136144ae

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-03-11 16:02:09 +0100

      Commit message:


	  
		
 Fix edge case data_type / fill_value mismatch test
 

    

  
    

      Package: Rarr

      Commit: ad86c6c8dee75f22e178f1abb0689442bfc782dc

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-03-11 15:31:59 +0100

      Commit message:


	  
		
 Update tests for new v3 default
 

    

  
    

      Package: Rarr

      Commit: cbab2eaaba5b9ed30d8eae017ed71098d6a1fef2

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-03-11 15:20:57 +0100

      Commit message:


	  
		
 Update dimension_separator default
 

    

  
    

      Package: Rarr

      Commit: 87a9cebf28d22d31cae230c036cd9b5e77d13376

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-03-09 17:18:07 +0100

      Commit message:


	  
		
 Support zarr_version in write_zarr_attributes()
 

    

  
    

      Package: Rarr

      Commit: c0bc701839627af8b83b94b744b7242f082b3806

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-03-09 16:55:34 +0100

      Commit message:


	  
		
 Add API to write v3 array directly
 

    

  
    

      Package: Rarr

      Commit: 854408c3b78984700d98e52eb4f9ff589daa9e78

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-03-28 13:19:30 +0100

      Commit message:


	  
		
 Add note about supported stores
 

    

  
    

      Package: seqpac

      Commit: ee922be1e7141246ab5f4131835a5838e7633e5e

      Author:  AlessoGozzo <alego91@liu.se> 

      Date: 2026-03-30 14:55:58 +0200

      Commit message:


	  
		
 Update Description
 

    

  
    

      Package: seqpac

      Commit: 4ceb3b325c9fc1b6881df3b2e7425564f927114f

      Author:  AlessoGozzo <alego91@liu.se> 

      Date: 2026-03-30 12:38:08 +0200

      Commit message:


	  
		
 Update dependencies
 

    

  
    

      Package: seqpac

      Commit: 02e064680b2595a3de8dc76c02d2707d41300f9f

      Author:  Signe Isacson (prev. Skog) <signe.skog@liu.se> 

      Date: 2026-03-30 08:58:48 +0300

      Commit message:


	  
		
 Merge pull request #53 from OestLab/Dev_11_03_26

Dev 11 03 26 to master 

    

  
    

      Package: seqpac

      Commit: 3f0bc885beabe07655a5407ca44c740cc946001a

      Author:  Anna Asratian <annas44@liu.se> 

      Date: 2026-03-25 15:40:54 +0100

      Commit message:


	  
		
 Explanation and examples for make_conv and PAC_analyze. In addition, some text has been updated.
 

    

  
    

      Package: seqpac

      Commit: 0b3fb648000d34dcce2af7e3d94d471194ee18f2

      Author:  lovisaor <lovisa.orkenby@liu.se> 

      Date: 2026-03-24 10:06:29 +0100

      Commit message:


	  
		
 Fixed the pheno target option to allow a one sample group to be annotated in plot (style=="pheno").

Details:
if rtio > 0.4 and is not numeric;
col<-as.factor(col).

if rtio > 0.4 and numeric;
col will be numeric as before
 

    

  
    

      Package: seqpac

      Commit: a1419dd1c6edc8d7c1a99705021493f38fc976d2

      Author:  lovisaor <lovisa.orkenby@liu.se> 

      Date: 2026-03-23 11:44:27 +0100

      Commit message:


	  
		
 Removed ginnards::move_layers
 

    

  
    

      Package: seqpac

      Commit: b18a256e5af021d45ce1aa1ecf381ec59da01cd3

      Author:  Anna Asratian <annas44@liu.se> 

      Date: 2026-03-20 23:24:17 +0100

      Commit message:


	  
		
 Minor update with text corrections.
 

    

  
    

      Package: seqpac

      Commit: 858777e2335c52a0c334d7f8db7cbcf8b76dda7a

      Author:  Signe Isacson (prev. Skog) <signe.skog@liu.se> 

      Date: 2026-03-16 09:49:19 +0200

      Commit message:


	  
		
 Ensuring safer null removal

refining prior push to make remoal of null entries safer 

    

  
    

      Package: seqpac

      Commit: b66540f329f6d4c7b10c8aa19607052c2f54ddd4

      Author:  AlessoGozzo <alego91@liu.se> 

      Date: 2026-03-12 11:18:08 +0100

      Commit message:


	  
		
 Fix ggplot language and plotting parameters
 

    

  
    

      Package: seqpac

      Commit: 7ab3955a3d72cd5d0870156ed49bb5804b3092bd

      Author:  AlessoGozzo <alego91@liu.se> 

      Date: 2026-03-11 14:55:04 +0100

      Commit message:


	  
		
 ggplot update
 

    

  
    

      Package: seqpac

      Commit: b4ff43be71976c0f8e997b45d24ff94ba2aaac41

      Author:  AlessoGozzo <alego91@liu.se> 

      Date: 2026-03-11 14:49:11 +0100

      Commit message:


	  
		
 Update ggplot2
 

    

  
    

      Package: seqpac

      Commit: 6841728c407ff5a7be02fd82eb7c95f09c1b0b99

      Author:  AlessoGozzo <alego91@liu.se> 

      Date: 2026-03-11 14:30:20 +0100

      Commit message:


	  
		
 Adjusted message"Script terminated by user.
 

    

  
    

      Package: seqpac

      Commit: e346ef756e327a44b912a68277b1a6ccf1e1ef6a

      Author:  AlessoGozzo <alego91@liu.se> 

      Date: 2026-03-11 14:00:26 +0100

      Commit message:


	  
		
 Adjusted x axis scale and deprecated ggplot language
 

    

  
    

      Package: seqpac

      Commit: 2289f172d884b9b92f144957769929ab43a2f928

      Author:  Signe Isacson (prev. Skog) <signe.skog@liu.se> 

      Date: 2026-03-11 10:53:38 +0200

      Commit message:


	  
		
 Remove null entries from map in tRNA_class.R

Removing null entries from the map object if present, so tRNA_class does not break 

    

  
    

      Package: seqpac

      Commit: 4fa84acfc4d555f8735f84ffeccb6cb1aaf22592

      Author:  AlessoGozzo <alego91@liu.se> 

      Date: 2026-03-11 09:12:57 +0100

      Commit message:


	  
		
 Fixed Pheno_target selection, deprecated language ggplot2 and return plot_grid
 

    

  
    

      Package: seqpac

      Commit: da18d9387e6614b0dbe7db187f8555dd3d85005b

      Author:  AlessoGozzo <alego91@liu.se> 

      Date: 2026-03-11 09:08:01 +0100

      Commit message:


	  
		
 Fixed Pheno_target selection, deprecated language ggplot2 and return plot_grid
 

    

  
    

      Package: seqpac

      Commit: fe6f6cd22619c7beb51562734c2bb125a5a4d242

      Author:  Signe Isacson (prev. Skog) <signe.skog@liu.se> 

      Date: 2025-09-30 10:19:54 +0200

      Commit message:


	  
		
 Update DESCRIPTION 

    

  
    

      Package: seqpac

      Commit: 7aae517716d41f6dffdae4755f48eb4875fb4784

      Author:  Signe Isacson (prev. Skog) <signe.skog@liu.se> 

      Date: 2025-09-30 10:13:27 +0200

      Commit message:


	  
		
 Update DESCRIPTION 

    

  
    

      Package: seqpac

      Commit: c88d413b730db5c5c4f4a4da54f7670dc727e4d1

      Author:  Signe Isacson (prev. Skog) <signe.skog@liu.se> 

      Date: 2025-09-30 09:31:15 +0200

      Commit message:


	  
		
 Update DESCRIPTION

version control 

    

  
    

      Package: VISTA

      Commit: 1c2f0fb425219e8ab18611959087e694ba463b15

      Author:  Chirag Parsania <chirag.parsania@gmail.com> 

      Date: 2026-03-30 23:53:13 +1100

      Commit message:


	  
		
 Increment version number to 0.99.2
 

    

  
    

      Package: VISTA

      Commit: d2d5865e1b6688628f0c67685d14a9d25ecfcfad

      Author:  Chirag Parsania <chirag.parsania@gmail.com> 

      Date: 2026-03-30 23:51:51 +1100

      Commit message:


	  
		
 Reduce check runtime with precomputed examples and lighter docs
 

    

  
    

      Package: betterChromVAR

      Commit: c7728123799129a6ee795a251012a1c2eaedcf34

      Author:  plger <pl.germain@gmail.com> 

      Date: 2026-03-30 14:20:38 +0200

      Commit message:


	  
		
 missing imports...
 

    

  
    

      Package: betterChromVAR

      Commit: e764fa54e60defa1a7955f9bcf0791dee3fb95c4

      Author:  plger <pl.germain@gmail.com> 

      Date: 2026-03-30 13:56:48 +0200

      Commit message:


	  
		
 updated doc
 

    

  
    

      Package: betterChromVAR

      Commit: 04559577299340746baad4ecd9b4d28dd0b58432

      Author:  plger <pl.germain@gmail.com> 

      Date: 2026-03-30 13:47:21 +0200

      Commit message:


	  
		
 avoided an import
 

    

  
    

      Package: betterChromVAR

      Commit: 063c15043868c084f164c075f386a82669d64fcf

      Author:  plger <pl.germain@gmail.com> 

      Date: 2026-03-29 16:26:22 +0200

      Commit message:


	  
		
 support for dgeMatrix
 

    

  
    

      Package: betterChromVAR

      Commit: 7d3a9a6bf3b94d20b660c6397bcd3f2bcc0da0c5

      Author:  plger <pl.germain@gmail.com> 

      Date: 2026-03-29 16:04:24 +0200

      Commit message:


	  
		
 clarified dummy data output
 

    

  
    

      Package: betterChromVAR

      Commit: 7f57fe19f937d0eaffe9971470314e82b30e49d8

      Author:  plger <pl.germain@gmail.com> 

      Date: 2026-03-29 16:02:59 +0200

      Commit message:


	  
		
 support GRanges input
 

    

  
    

      Package: betterChromVAR

      Commit: 013a39fa36d12288e9e61b0e4a141739f97255e9

      Author:  plger <pl.germain@gmail.com> 

      Date: 2026-03-29 15:55:24 +0200

      Commit message:


	  
		
 added internal var passthrough option
 

    

  
    

      Package: betterChromVAR

      Commit: 7ac21c56c7930b091a9cadf415a1ccd8217d856d

      Author:  plger <pl.germain@gmail.com> 

      Date: 2026-03-28 15:42:22 +0100

      Commit message:


	  
		
 added qsmooth option
 

    

  
    

      Package: betterChromVAR

      Commit: 56494216d3e988e2078aa254208c212c58d7624e

      Author:  plger <pl.germain@gmail.com> 

      Date: 2026-03-28 15:42:12 +0100

      Commit message:


	  
		
 added some info
 

    

  
    

      Package: partCNV

      Commit: 4b328efd9bf27626c0e3a5f4817c67f4a3825f43

      Author:  lshep <lori.shepherd@roswellpark.org> 

      Date: 2026-03-30 08:21:21 -0400

      Commit message:


	  
		
 Deprecated
 

    

  
    

      Package: kissDE

      Commit: 268347fc71bd1dfe0f22798018886ef39b47422f

      Author:  Aurélie Siberchicot <aurelie.siberchicot@univ-lyon1.fr> 

      Date: 2026-03-30 13:30:04 +0200

      Commit message:


	  
		
 Update the R-CMD-check workflow
 

    

  
    

      Package: kissDE

      Commit: 22659d3676832c6d1b78f6963580271a846a2693

      Author:  Aurélie Siberchicot <aurelie.siberchicot@univ-lyon1.fr> 

      Date: 2026-03-30 13:10:48 +0200

      Commit message:


	  
		
 Update the R-CMD-check workflow
 

    

  
    

      Package: kissDE

      Commit: 58a7f09f1d3eded20e6b5af2148808bd5f731951

      Author:  Aurélie Siberchicot <aurelie.siberchicot@univ-lyon1.fr> 

      Date: 2026-03-30 12:25:59 +0200

      Commit message:


	  
		
 Update the R-CMD-check workflow: correct a misprint in the last commit
 

    

  
    

      Package: kissDE

      Commit: 2ef55a1d3db62965941649e094d11e93a71704d0

      Author:  Aurélie Siberchicot <aurelie.siberchicot@univ-lyon1.fr> 

      Date: 2026-03-30 12:24:16 +0200

      Commit message:


	  
		
 Update the R-CMD-check workflow
 

    

  
    

      Package: kissDE

      Commit: fd8e8a7ebfcaf05b3ae72c80dcf11d4f014534e8

      Author:  Aurélie Siberchicot <aurelie.siberchicot@univ-lyon1.fr> 

      Date: 2026-03-30 12:24:02 +0200

      Commit message:


	  
		
 Add a WORDLIST file
 

    

  
    

      Package: kissDE

      Commit: d3c83773c2b0df6b2d6f138b1ae11babba275079

      Author:  Aurélie Siberchicot <aurelie.siberchicot@univ-lyon1.fr> 

      Date: 2026-03-30 11:15:43 +0200

      Commit message:


	  
		
 Update the latex configuration in the vignette
 

    

  
    

      Package: kissDE

      Commit: 02bee2c96dcc69ae983cca77373e6a8af4d10176

      Author:  Aurélie Siberchicot <aurelie.siberchicot@univ-lyon1.fr> 

      Date: 2026-03-27 16:14:56 +0100

      Commit message:


	  
		
 Update the gitignore file
 

    

  
    

      Package: kissDE

      Commit: 56cabea557933a3b019c6245411c4a7011be17c0

      Author:  Aurélie Siberchicot <aurelie.siberchicot@univ-lyon1.fr> 

      Date: 2026-03-27 16:14:46 +0100

      Commit message:


	  
		
 Update the vignette: update formula
 

    

  
    

      Package: kissDE

      Commit: 36de2c288b9faeb2516f0ec26faa146e7b2ade56

      Author:  Aurélie Siberchicot <aurelie.siberchicot@univ-lyon1.fr> 

      Date: 2026-03-27 15:36:06 +0100

      Commit message:


	  
		
 Update the R-CMD-check workflow
 

    

  
    

      Package: kissDE

      Commit: c5b533439bb113989ec6f64f7148440a80541165

      Author:  Aurélie Siberchicot <aurelie.siberchicot@univ-lyon1.fr> 

      Date: 2026-03-27 15:31:14 +0100

      Commit message:


	  
		
 Update the R-CMD-check workflow
 

    

  
    

      Package: kissDE

      Commit: ec3cac7ad88b284caf2271168ec4af7bfa9f824c

      Author:  Aurélie Siberchicot <aurelie.siberchicot@univ-lyon1.fr> 

      Date: 2026-03-27 15:20:38 +0100

      Commit message:


	  
		
 Update the R-CMD-check workflow
 

    

  
    

      Package: kissDE

      Commit: 6e2e77e6dadc1844fbe3c4a8c9580f90d54b2a69

      Author:  Aurélie Siberchicot <aurelie.siberchicot@univ-lyon1.fr> 

      Date: 2026-03-27 09:18:33 +0100

      Commit message:


	  
		
 Update the R-CMD-check workflow
 

    

  
    

      Package: kissDE

      Commit: 6a5ab3c436e86f1e233db8e2db6ba645c6cc780d

      Author:  Aurélie Siberchicot <aurelie.siberchicot@univ-lyon1.fr> 

      Date: 2026-03-27 08:42:28 +0100

      Commit message:


	  
		
 Update the R-CMD-check workflow
 

    

  
    

      Package: kissDE

      Commit: 4aeab635e2bc1ca5ce23781e33e3b1a91555ab20

      Author:  Aurélie Siberchicot <aurelie.siberchicot@univ-lyon1.fr> 

      Date: 2026-03-26 18:10:53 +0100

      Commit message:


	  
		
 Update R-CMD-check workflow
 

    

  
    

      Package: kissDE

      Commit: 9245cf8894508a4c442d3db8ddff4cd3d36438ef

      Author:  Aurélie Siberchicot <aurelie.siberchicot@univ-lyon1.fr> 

      Date: 2026-03-26 18:05:29 +0100

      Commit message:


	  
		
 Update the R-CMD-check workflow
 

    

  
    

      Package: kissDE

      Commit: dd6b8817d42b8a064628798b553d81a6898b251d

      Author:  Aurélie Siberchicot <aurelie.siberchicot@univ-lyon1.fr> 

      Date: 2026-03-26 16:26:55 +0100

      Commit message:


	  
		
 Remove the rnw vignette
 

    

  
    

      Package: kissDE

      Commit: ba31ee4b54ff9723ca4e9636b3a965c53c9f6abb

      Author:  Aurélie Siberchicot <aurelie.siberchicot@univ-lyon1.fr> 

      Date: 2026-03-26 16:26:42 +0100

      Commit message:


	  
		
 Update some misprints in the quarto vignette
 

    

  
    

      Package: kissDE

      Commit: eb1a3524f1f37aee4fe89eaceecc7fb4c38c3604

      Author:  Aurélie Siberchicot <aurelie.siberchicot@univ-lyon1.fr> 

      Date: 2026-03-26 16:26:21 +0100

      Commit message:


	  
		
 Add 'quarto' in the 'Suggests' field in DESCRIPTION
 

    

  
    

      Package: kissDE

      Commit: 4dd5b3a0bd43c2b9423826b38c7dc444502dc863

      Author:  Aurélie Siberchicot <aurelie.siberchicot@univ-lyon1.fr> 

      Date: 2026-03-26 16:25:51 +0100

      Commit message:


	  
		
 Update Rbuildignore and gitignore files
 

    

  
    

      Package: rols

      Commit: da27ab6cf0ea530cdef967bc2fc75a2a1f9edf9e

      Author:  lshep <lori.shepherd@roswellpark.org> 

      Date: 2026-03-30 07:35:31 -0400

      Commit message:


	  
		
 maintainer requested deprecation
 

    

  
    

      Package: beadarray

      Commit: 7dd13bdf588979ea9f73e785f358fccb6f4adee9

      Author:  lshep <lori.shepherd@roswellpark.org> 

      Date: 2026-03-30 07:26:28 -0400

      Commit message:


	  
		
 Undeprecate
 

    

  
    

      Package: DOTSeq

      Commit: faf2de8b63dedfd23f1b77f487d5d5d10bb9088a

      Author:  lcscs12345 <lcscs12345@gmail.com> 

      Date: 2026-03-30 16:42:10 +0800

      Commit message:


	  
		
 edit title
 

    

  
    

      Package: MetaboDynamics

      Commit: 7932279f86e2587f61777aac651b8b2c9e412a31

      Author:  Katja Danielzik <katja.danielzik@uni-due.de> 

      Date: 2026-03-30 10:07:59 +0200

      Commit message:


	  
		
 version bump
 

    

  
    

      Package: MetaboDynamics

      Commit: fdd6a1af337ae967e94b89d94642273c23420b8f

      Author:  Katja Danielzik <katja.danielzik@uni-due.de> 

      Date: 2026-03-30 10:07:08 +0200

      Commit message:


	  
		
 version bump
 

    

  
    

      Package: LimROTS

      Commit: 70089ba59f96452d0432249014752560cdac084b

      Author:  Ali Youssef <aliali.mostafa99@gmail.com> 

      Date: 2026-03-30 10:49:55 +0300

      Commit message:


	  
		
 Bump the version
 

    

  
    

      Package: LimROTS

      Commit: 318544aa7b15d276db3d0631ca50e3867789739f

      Author:  Ali Youssef <aliali.mostafa99@gmail.com> 

      Date: 2026-03-30 10:48:45 +0300

      Commit message:


	  
		
 fix LimROTS Survival test
 

    

  
    

      Package: LimROTS

      Commit: 73a96fc08272daeefb5bcec205e90a22b43ddbba

      Author:  Ali Youssef <aliali.mostafa99@gmail.com> 

      Date: 2026-03-30 10:10:52 +0300

      Commit message:


	  
		
 fix LimROTS Survival
 

    

  
    

      Package: DOTSeq

      Commit: 26258dd7331968870064f8aab31eaec3bcb41877

      Author:  lcscs12345 <lcscs12345@gmail.com> 

      Date: 2026-03-30 13:10:09 +0800

      Commit message:


	  
		
 add ORCID
 

    

  
    

      Package: DOTSeq

      Commit: 266ada8d31265e459d49166ca35e5dee2f9b24ba

      Author:  lcscs12345 <lcscs12345@gmail.com> 

      Date: 2026-03-30 12:41:24 +0800

      Commit message:


	  
		
 update CITATION and NEWS
 

    

  
    

      Package: SparseArray

      Commit: 10f009ac4ddd790fda77d6f1b33ffdd4b7c473a9

      Author:  Hervé Pagès <hpages.on.github@gmail.com> 

      Date: 2026-03-29 19:23:15 -0700

      Commit message:


	  
		
 SparseArray 1.11.12: Fix col/rowMedians() methods for SparseArray objects

See issue #25
 

    

  
    

      Package: DOTSeq

      Commit: e1b905eb74c3e3d8a52c859f2aa61f8b94eb72b8

      Author:  lcscs12345 <lcscs12345@gmail.com> 

      Date: 2026-03-30 10:22:16 +0800

      Commit message:


	  
		
 update CITATION and NEWS
 

    

  
    

      Package: DOTSeq

      Commit: 33d997e9a2951ecb66c79446b3fbe9e8ec1a6337

      Author:  lcscs12345 <lcscs12345@gmail.com> 

      Date: 2026-03-20 15:14:14 +0800

      Commit message:


	  
		
 add citation
 

    

  
    

      Package: LimROTS

      Commit: 1efe75024bef753a33410034d4cba6f243cd29db

      Author:  Ali Youssef <aliali.mostafa99@gmail.com> 

      Date: 2026-03-30 01:06:05 +0300

      Commit message:


	  
		
 fix Imports and and Bump the version
 

    

  
    

      Package: MetaboDynamics

      Commit: ff8291260fcbe57946dfea53df65b9845a5801dc

      Author:  Katja Danielzik <katja.danielzik@uni-due.de> 

      Date: 2026-03-29 19:17:43 +0200

      Commit message:


	  
		
 version bump
 

    

  
    

      Package: MetaboDynamics

      Commit: 7952009b362aed4cc0cc76581678452fb2aecd91

      Author:  Katja Danielzik <katja.danielzik@uni-due.de> 

      Date: 2026-03-29 17:55:45 +0200

      Commit message:


	  
		
 bug fixes for "raw_plus_count" models
 

    

  
    

      Package: amplican

      Commit: cfb4175fa52521f371fa9ca32d793a704032c3a3

      Author:  JokingHero <kornel.labun@gmail.com> 

      Date: 2026-03-29 15:59:09 +0200

      Commit message:


	  
		
 data.table speedups
 

    

  
    

      Package: amplican

      Commit: 34dc580507ddc36700ad8cc8ab50d609bc8e30bf

      Author:  JokingHero <kornel.labun@gmail.com> 

      Date: 2026-03-29 11:52:13 +0200

      Commit message:


	  
		
 aplican can now restart from temp files
 

    

  
    

      Package: DeMixT

      Commit: c881df7e1d8331345571e054809d82b981f81b5d

      Author:  wwylab <wwang7@mdanderson.org> 

      Date: 2026-03-29 00:09:47 -0500

      Commit message:


	  
		
 Add pre-built vignettes to inst/doc
 

    

  
    

      Package: DeMixT

      Commit: 8b16a3645e97d6a9cc06e888d00294c970870f8f

      Author:  wwylab <wwang7@mdanderson.org> 

      Date: 2026-03-28 23:57:28 -0500

      Commit message:


	  
		
 Keep inst/doc directory for vignette installation
 

    

  
    

      Package: MultiAssayExperiment

      Commit: 2e22d1fcdd4f722d59e857f8ec9e8a4b350db361

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2026-03-28 16:45:09 -0400

      Commit message:


	  
		
 fix typo in NEWS.md
 

    

  
    

      Package: MultiAssayExperiment

      Commit: e89caba5c76e021878618eaa19419bcafe1dc656

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2026-03-28 16:30:39 -0400

      Commit message:


	  
		
 version bump 1.37.4
 

    

  
    

      Package: MultiAssayExperiment

      Commit: 2c99344b4b8cb50e34cc55ab059f0579688f9716

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2026-03-28 16:25:22 -0400

      Commit message:


	  
		
 update NEWS.md
 

    

  
    

      Package: MultiAssayExperiment

      Commit: e94850d546a2e75dd14895cd9832afb1687e64ef

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2026-03-28 16:14:52 -0400

      Commit message:


	  
		
 use factor in smap for unit test
 

    

  
    

      Package: MultiAssayExperiment

      Commit: 5388577c5d7d23272e9935d92066fcc807869d36

      Author:  Patrick Aboyoun <aboyoun.patrick@gene.com> 

      Date: 2026-03-28 09:40:17 -0700

      Commit message:


	  
		
 fix getWithColData row order mismatch in append mode
When mode=append, existing (experiment colData) and leftovers (MAE colData)
had incompatible row orderings, causing patient metadata to be assigned to
wrong samples. Fix uses sampleMap to properly align rows before cbind.
Reported by James Bonaffini. Includes regression test.
 

    

  
    

      Package: MultiAssayExperiment

      Commit: f97bb1b4b71d97df7d1c2d1986641c41ce414114

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2026-03-25 11:18:40 -0400

      Commit message:


	  
		
 replace pr_check.yml with ci.yml GHA
 

    

  
    

      Package: HilbertVisGUI

      Commit: fa901786ec5e726336d029fa3b62b2f021be672d

      Author:  Simon Anders <sanders@fs.tum.de> 

      Date: 2026-03-28 15:12:41 +0100

      Commit message:


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

    

  
    

      Package: HilbertVisGUI

      Commit: ea91d2404d201c888b354f58cf6063c8e51196ef

      Author:  Simon Anders <sanders@fs.tum.de> 

      Date: 2026-03-28 15:01:52 +0100

      Commit message:


	  
		
 replaced old hack to protect R objects from GC with R_PreserveObject/R_ReleaseObject
 

    

  
    

      Package: HilbertVisGUI

      Commit: 2f6a5d72488517775852d92ca0446db6ac3e3d20

      Author:  Simon Anders <sanders@fs.tum.de> 

      Date: 2026-03-28 15:01:30 +0100

      Commit message:


	  
		
 bumped version number
 

    

  
    

      Package: CATS

      Commit: 6812dc3604746354ef55be437836942e1ab31232

      Author:  guldenolgun <32208882+guldenolgun@users.noreply.github.com> 

      Date: 2026-03-28 15:53:52 +0300

      Commit message:


	  
		
 update
 

    

  
    

      Package: COTAN

      Commit: 3b79cc3d8320c1b4fe83f9954d443131ca266e14

      Author:  Marco Fantozzi <57561972+trinetra75@users.noreply.github.com> 

      Date: 2026-03-19 10:12:28 +0100

      Commit message:


	  
		
 Solved vignette and tests issues (#137)

- Fixed bug in converter to SCE in cases when genes (or cells)
meta-data was empty

- Fixed issues with test-plots.py

- Removed calculation of COEX from the UT vingette 

    

  
    

      Package: QUBIC

      Commit: f1c26b45e2e8fa20fd2294434c46e4f63d33b198

      Author:  zy26 <zy26@users.noreply.github.com> 

      Date: 2026-03-28 14:20:07 +0800

      Commit message:


	  
		
 Bump version
 

    

  
    

      Package: QUBIC

      Commit: 85065a11192b7b122246b37c4b640c00b244806e

      Author:  zy26 <zy26@users.noreply.github.com> 

      Date: 2026-03-28 14:19:13 +0800

      Commit message:


	  
		
 Update NEWS.Rd
 

    

  
    

      Package: QUBIC

      Commit: 5eaf25f42d9ca1b21cba90e03d0020a47710a3bb

      Author:  zy26 <zy26@users.noreply.github.com> 

      Date: 2026-03-28 14:37:16 +0800

      Commit message:


	  
		
 Fix biclust compatibility and package docs
 

    

  
    

      Package: phylobar

      Commit: 460373b06d31805d3cae2b2b4bc491298309372d

      Author:  Kris Sankaran <sankaran.kris@gmail.com> 

      Date: 2026-03-27 23:37:31 -0500

      Commit message:


	  
		
 bump package version
 

    

  
    

      Package: phylobar

      Commit: b61d476b52d9162c57cc333581d4553b597d32eb

      Author:  Kris Sankaran <sankaran.kris@gmail.com> 

      Date: 2026-03-27 23:36:48 -0500

      Commit message:


	  
		
 remove docs during package review
 

    

  
    

      Package: phylobar

      Commit: 1a3991e162c8532672bb8107dcbfbff971d0211f

      Author:  Kris Sankaran <sankaran.kris@gmail.com> 

      Date: 2026-03-27 23:35:44 -0500

      Commit message:


	  
		
 Merge remote-tracking branch 'upstream/devel'
 

    

  
    

      Package: phylobar

      Commit: d69ae55fcea8701297e998a72c39dd907750cc98

      Author:  Kris Sankaran <sankaran.kris@gmail.com> 

      Date: 2026-03-27 23:33:33 -0500

      Commit message:


	  
		
 remove lupine from taxonomies article
 

    

  
    

      Package: phylobar

      Commit: 4fc3a6ceeeb49985e42c19cf15980e877f111c66

      Author:  mkdiro-O <mkuo22@wisc.edu> 

      Date: 2026-03-03 18:49:44 -0600

      Commit message:


	  
		
 remove _pkgdown.yml
 

    

  
    

      Package: phylobar

      Commit: 31d660327add478a11f8b6082e78b766e2e4508d

      Author:  mkdiro-O <mkuo22@wisc.edu> 

      Date: 2026-03-03 14:00:34 -0600

      Commit message:


	  
		
 update vignettes
 

    

  
    

      Package: LimROTS

      Commit: 65345d2f46c12694f8f2256ce1648410c2fecdb5

      Author:  Ali Youssef <aliali.mostafa99@gmail.com> 

      Date: 2026-03-28 00:07:08 +0200

      Commit message:


	  
		
 fix version
 

    

  
    

      Package: LimROTS

      Commit: 21d094054e280fc1d09b1cedd8adc434299121dd

      Author:  Ali Youssef <aliali.mostafa99@gmail.com> 

      Date: 2026-03-28 00:05:14 +0200

      Commit message:


	  
		
 update NEWS
 

    

  
    

      Package: LimROTS

      Commit: dd7e446f2a8aa13614ff7a57e5afd49547b2c0d5

      Author:  Ali Youssef <aliali.mostafa99@gmail.com> 

      Date: 2026-03-28 00:02:41 +0200

      Commit message:


	  
		
 bump the version
 

    

  
    

      Package: LimROTS

      Commit: 6031ac46e4a0c6e8afebcc7089c637b0acb118fa

      Author:  Ali Youssef <aliali.mostafa99@gmail.com> 

      Date: 2026-03-27 23:52:12 +0200

      Commit message:


	  
		
 add bootstrapSamples_limRots_cox
 

    

  
    

      Package: LimROTS

      Commit: ca8c3402c0fa018cabc3d92411e2d3248bfefe44

      Author:  Ali Youssef <aliali.mostafa99@gmail.com> 

      Date: 2026-03-27 23:50:03 +0200

      Commit message:


	  
		
 adding examples to LimROTS_survival
 

    

  
    

      Package: LimROTS

      Commit: 9de79cae722de3ff161d35f51249f17d5226bd0a

      Author:  Ali Youssef <aliali.mostafa99@gmail.com> 

      Date: 2026-03-27 23:46:40 +0200

      Commit message:


	  
		
 fix SanityChecK
 

    

  
    

      Package: LimROTS

      Commit: fa9d6fcac6397ffa4b385315292c2d56a6b1909f

      Author:  Ali Youssef <aliali.mostafa99@gmail.com> 

      Date: 2026-03-27 23:44:52 +0200

      Commit message:


	  
		
 survival to Check_SummarizedExperiment
 

    

  
    

      Package: LimROTS

      Commit: 982dcaa283048e0f4be74c26b0087ca5882c3a41

      Author:  Ali Youssef <aliali.mostafa99@gmail.com> 

      Date: 2026-03-27 23:40:13 +0200

      Commit message:


	  
		
 survival to SanityCheck
 

    

  
    

      Package: LimROTS

      Commit: 7667c84c3a84ce02294b983bc146b252336be74a

      Author:  Ali Youssef <aliali.mostafa99@gmail.com> 

      Date: 2026-03-27 22:53:20 +0200

      Commit message:


	  
		
 Adding assay.type to SanityCheck
 

    

  
    

      Package: LimROTS

      Commit: ff89db4df528916aff543331cd92d8f9d9613b64

      Author:  Ali Youssef <aliali.mostafa99@gmail.com> 

      Date: 2026-03-27 22:50:22 +0200

      Commit message:


	  
		
 Adding assay.type to Check_SummarizedExperiment
 

    

  
    

      Package: gutenTAG

      Commit: ae3898c039d2921df78aa16a3eed6f2090eaeb64

      Author:  John Abbey <john@dqbm-nbm-joab.local> 

      Date: 2026-03-27 22:43:35 +0100

      Commit message:


	  
		
 fix anndata warning
 

    

  
    

      Package: fastRanges

      Commit: 8e74a3015a32ce586861a8c568e2a834de9057fa

      Author:  Chirag Parsania <chirag.parsania@gmail.com> 

      Date: 2026-03-28 07:08:39 +1100

      Commit message:


	  
		
 Increment version number to 0.99.2
 

    

  
    

      Package: fastRanges

      Commit: a4d16a8316722f7704132b21d1ac88c9e4a87273

      Author:  Chirag Parsania <chirag.parsania@gmail.com> 

      Date: 2026-03-28 06:56:54 +1100

      Commit message:


	  
		
 github workflow error fixed
 

    

  
    

      Package: fastRanges

      Commit: b553407de0c7512efc2e2e108fe72b7a095b34a0

      Author:  Chirag Parsania <chirag.parsania@gmail.com> 

      Date: 2026-03-28 06:47:06 +1100

      Commit message:


	  
		
 Stop tracking reviewer benchmark snapshots
 

    

  
    

      Package: matter

      Commit: ad7756ef7158b0bc88a86f0317890a918ef1c61c

      Author:  Kylie Bemis <k.bemis@northeastern.edu> 

      Date: 2026-03-27 15:32:31 -0400

      Commit message:


	  
		
 v2.13.4 remove STRING_PTR from C code
 

    

  
    

      Package: matter

      Commit: 4278f9ceb06d7cfd4c96e610977e63bc5774029a

      Author:  Kylie Bemis <k.bemis@northeastern.edu> 

      Date: 2026-03-27 15:26:10 -0400

      Commit message:


	  
		
 rm STRING_PTR and character vector bsearch support (for now)
 

    

  
    

      Package: MotifPeeker

      Commit: 035f003ed8bebd9f731ca58d755ee12383cea7b4

      Author:  HDash <16350928+HDash@users.noreply.github.com> 

      Date: 2026-03-27 16:23:38 +0000

      Commit message:


	  
		
 Update citation in README
 

    

  
    

      Package: MotifPeeker

      Commit: b4edd161ddabe5cbe198e9f5fb94a037a035da1b

      Author:  Hiranyamaya (Hiru) Dash <16350928+HDash@users.noreply.github.com> 

      Date: 2026-03-27 16:18:28 +0000

      Commit message:


	  
		
 Merge pull request #13 from neurogenomics/peak-score

Update citation and adjust bootstrapping population size 

    

  
    

      Package: MotifPeeker

      Commit: 6e8d038641a70cd040067e3acc826836ec649f72

      Author:  HDash <16350928+HDash@users.noreply.github.com> 

      Date: 2026-02-19 15:38:20 +0000

      Commit message:


	  
		
 Update CITATION

Biorxiv -> Bioinformatics Advances
 

    

  
    

      Package: MotifPeeker

      Commit: 34b27c3dd1d0b9556084069bed549aa771e99ed7

      Author:  HDash <16350928+HDash@users.noreply.github.com> 

      Date: 2026-02-19 15:29:14 +0000

      Commit message:


	  
		
 Bound maximum bootstrapping population size
 

    

  
    

      Package: vsn

      Commit: 3ee872b304d920079f65cd3113794411d805d15f

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-03-27 14:22:05 +0100

      Commit message:


	  
		
 Copy logo from BiocStickers
 

    

  
    

      Package: scuttle

      Commit: d10b51fc0d9de5d2fa0f85a659076b35c63e979b

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

      Date: 2026-03-27 22:37:55 +1100

      Commit message:


	  
		
 Updated NEWS file.
 

    

  
    

      Package: scuttle

      Commit: a997286ba778f33b74087cdfcd4a69f58fba730c

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

      Date: 2026-03-27 22:35:56 +1100

      Commit message:


	  
		
 Replace all beachmat3 references with the tatami API. (#37)

This also involves stripping out the beachmat *BlockApply functions in favor of
directly using DelayedArray::blockApply; should be equally inefficient but it
also shouldn't matter as most of the affected functions will be deprecated
anyway in favor of equivalents in scrapper.

We improve the downsampling algorithm by using R's rhyper() function for each
count. This should be much faster because we do not have to iterate up to the
count value for each non-zero count. We also simplify the R function by always
returning a SVT_SparseMatrix, rather than forcing block processing to dump the
results into a DelayedArrayRealizationSink.

For the linear model fitting, we add support for multi-threading, because we
can. For other C++ functions, we'll be throwing them out at some point so
there's no point fleshing it out too much. 

    

  
    

      Package: gutenTAG

      Commit: 03b8b54af7d146d1ec9a03ae03cfcb2577e2e7af

      Author:  John Abbey <john@dqbm-nbm-joab.local> 

      Date: 2026-03-27 12:36:16 +0100

      Commit message:


	  
		
 add package name to watched tags
 

    

  
    

      Package: gutenTAG

      Commit: 9dc9ad95491b94f0f49ee2aca829b8ec53fd343f

      Author:  John Abbey <john@dqbm-nbm-joab.local> 

      Date: 2026-03-27 12:14:07 +0100

      Commit message:


	  
		
 add maintainer email to support site
 

    

  
    

      Package: famat

      Commit: 449de54b299006f6f65e3b84c160cf897e64d49b

      Author:  MathieuCharlesINRAE <mathieu.charles@inrae.fr> 

      Date: 2026-03-27 11:22:29 +0100

      Commit message:


	  
		
 Fix merge conflict >>>>> in code and bump version to 1.21.4
 

    

  
    

      Package: broadSeq

      Commit: 2f25887569987152db6b0cb5c0245910cade0556

      Author:  vondorishi <rishi.dasroy@gmail.com> 

      Date: 2026-03-27 10:44:53 +0200

      Commit message:


	  
		
 version bump in devel
 

    

  
    

      Package: broadSeq

      Commit: a7a4e28a9a330990e5c92e3c65d5d71fb7b3221e

      Author:  vondorishi <rishi.dasroy@gmail.com> 

      Date: 2026-03-27 10:43:37 +0200

      Commit message:


	  
		
 bug fix: noiseq factor
 

    

  
    

      Package: MetaProViz

      Commit: 47b21756866ef16c9dca25d930016a224ff830a6

      Author:  Christina Schmidt <christina.schmidt1@outlook.de> 

      Date: 2026-03-27 09:09:49 +0100

      Commit message:


	  
		
 Bump version: 3.99.40 → 3.99.50
 

    

  
    

      Package: MetaProViz

      Commit: 45784ad6542a2bee8ff0ec715c9b54d7e79b570f

      Author:  jannikfranken <jannik8513@gmailcom> 

      Date: 2026-03-26 18:37:35 +0100

      Commit message:


	  
		
 OmnipathR dependency version update and docs rebuild
 

    

  
    

      Package: MetaProViz

      Commit: f2a4d57cbdf6841e62939cdedb875ac4fd345780

      Author:  jannikfranken <jannik8513@gmailcom> 

      Date: 2026-03-26 18:36:46 +0100

      Commit message:


	  
		
 included seed id compatibility test in traverse_ids()
 

    

  
    

      Package: MetaProViz

      Commit: 1b6f20a1226803db6fa25282d022e1ee21a9c2a7

      Author:  deeenes <turei.denes@gmail.com> 

      Date: 2026-03-25 22:19:59 +0100

      Commit message:


	  
		
 Update OmnipathR function names after reactome/wikipathways refactor

- get_reactome -> reactome_chebi (param species -> organism)
- get_wikipathways_metabolites_sparql -> wikipathways_metabolites_sparql
  (param species -> organism)

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
 

    

  
    

      Package: MetaProViz

      Commit: 02b559048ab8bd5f26c495800a73d94dbf8aa50c

      Author:  Jannik Franken <jannik8513@gmailcom> 

      Date: 2026-03-25 17:15:32 +0100

      Commit message:


	  
		
 update OmnipathR version
 

    

  
    

      Package: MetaProViz

      Commit: 1ad882a0a6845df9acacf446acbefd0dd36faf95

      Author:  Jannik Franken <jannik8513@gmailcom> 

      Date: 2026-03-25 14:16:28 +0100

      Commit message:


	  
		
 added OmnipathR devel install to github actions
 

    

  
    

      Package: MetaProViz

      Commit: a0b24990d3b0b92ec27cfa24f0687490cca52a4a

      Author:  Jannik Franken <jannik8513@gmailcom> 

      Date: 2026-03-25 13:46:29 +0100

      Commit message:


	  
		
 updated OmnipathR required version
 

    

  
    

      Package: MetaProViz

      Commit: 9ba71d515c69ec63395e844d44e06d201044ba58

      Author:  Christina Schmidt <christina.schmidt1@outlook.de> 

      Date: 2026-03-25 12:48:42 +0100

      Commit message:


	  
		
 Update tissue_meta.rda
 

    

  
    

      Package: MetaProViz

      Commit: 328b9d2e139ac9517ff8eecb515d73d5fa2fde7f

      Author:  Christina Schmidt <christina.schmidt1@outlook.de> 

      Date: 2026-03-25 09:30:53 +0100

      Commit message:


	  
		
 update tissue meta to include the fixed pubchem IDs. See ExampleData branch for detailed code
 

    

  
    

      Package: MetaProViz

      Commit: d26dfb95aff48e045dab19b9895ab3ecc9ff6bb3

      Author:  jannikfranken <jannik8513@gmailcom> 

      Date: 2026-03-24 15:40:52 +0100

      Commit message:


	  
		
 enabled CAS number in translate_id()
 

    

  
    

      Package: MetaProViz

      Commit: 1c1a8a8e723774a06d83d937d3e628c5ef65fda8

      Author:  jannikfranken <jannik8513@gmailcom> 

      Date: 2026-03-24 14:49:17 +0100

      Commit message:


	  
		
 added new function metsigdb_macdb
 

    

  
    

      Package: MetaProViz

      Commit: 5bbc437983e1e24b7f0337b0f0afec78edad71cc

      Author:  jannikfranken <jannik8513@gmailcom> 

      Date: 2026-03-24 14:48:51 +0100

      Commit message:


	  
		
 typo
 

    

  
    

      Package: MetaProViz

      Commit: 0d4ad9565ba649f350d8bd061f6a58e4ae4e0b4c

      Author:  jannikfranken <jannik8513@gmailcom> 

      Date: 2026-03-24 14:48:29 +0100

      Commit message:


	  
		
 typo
 

    

  
    

      Package: MetaProViz

      Commit: a767ac43f2cbc68200413efb6dce5c555a9e7c59

      Author:  jannikfranken <jannik8513@gmailcom> 

      Date: 2026-03-24 14:47:33 +0100

      Commit message:


	  
		
 added new atoms to exclusion_metabolites
 

    

  
    

      Package: fastRanges

      Commit: 4baaecc27b0743aea744e875e7ac11e0b6076793

      Author:  Chirag Parsania <chirag.parsania@gmail.com> 

      Date: 2026-03-27 16:06:40 +1100

      Commit message:


	  
		
 update gitignore
 

    

  
    

      Package: fastRanges

      Commit: 6212b7d25d4309775297f1f1963bc7de4682d154

      Author:  Chirag Parsania <chirag.parsania@gmail.com> 

      Date: 2026-03-27 16:02:04 +1100

      Commit message:


	  
		
 Merge branch 'reviewer-fixes'
 

    

  
    

      Package: fastRanges

      Commit: 8eabea6681e20e54b85684150e30fad6ea7a9497

      Author:  Chirag Parsania <chirag.parsania@gmail.com> 

      Date: 2026-03-27 15:55:47 +1100

      Commit message:


	  
		
 Update gitignore rules
 

    

  
    

      Package: fastRanges

      Commit: 4c3fe69e8c5ab873889dcc6ded51a01eaf7e9d84

      Author:  Chirag Parsania <chirag.parsania@gmail.com> 

      Date: 2026-03-27 15:43:02 +1100

      Commit message:


	  
		
 Increment version number to 0.99.1
 

    

  
    

      Package: fastRanges

      Commit: 838cced56449403252612894249ce99b30d95c7d

      Author:  Chirag Parsania <chirag.parsania@gmail.com> 

      Date: 2026-03-27 15:36:41 +1100

      Commit message:


	  
		
 run bioc reviewer benchmark 05
 

    

  
    

      Package: fastRanges

      Commit: 7f2fcf16e3c046ce7a909a08948e955d805ca745

      Author:  Chirag Parsania <chirag.parsania@gmail.com> 

      Date: 2026-03-27 11:49:25 +1100

      Commit message:


	  
		
 Address reviewer compatibility and documentation issues

Improve edge-case handling, and vignette docs

Add select support
 

    

  
    

      Package: Rsubread

      Commit: caff6fb6adb833fbf1dd5c08199fd6462d9cad7a

      Author:  Yang Liao (Monash University) <yliao@m3s105.massive.org.au> 

      Date: 2026-03-27 16:05:09 +1100

      Commit message:


	  
		
 fixed a bug of softclipping in cellCOunts
 

    

  
    

      Package: RBPSpecificity

      Commit: 08837fd1d351cc89c6eaf99f8156c1a90b157bd2

      Author:  SoonYi <55300935+S00NYI@users.noreply.github.com> 

      Date: 2026-03-27 00:18:00 -0400

      Commit message:


	  
		
 Fix plotMS->plotVS in tests, bump version to 0.99.3
 

    

  
    

      Package: RBPSpecificity

      Commit: 0ed0ca9d25620af90501ece992b2d7bcf5868ccd

      Author:  SoonYi <55300935+S00NYI@users.noreply.github.com> 

      Date: 2026-03-27 00:03:33 -0400

      Commit message:


	  
		
 Fix BOM in test-VS.R, bump version to 0.99.2
 

    

  
    

      Package: RBPSpecificity

      Commit: b57c821c6d4ab647d32511e294d319d70ecaaf14

      Author:  SoonYi <55300935+S00NYI@users.noreply.github.com> 

      Date: 2026-03-25 16:56:52 -0400

      Commit message:


	  
		
 Bump version to 0.99.1
 

    

  
    

      Package: RBPSpecificity

      Commit: 9b203cc06afb517a3ae0d02555f7fa60bc4eccb1

      Author:  SoonYi <55300935+S00NYI@users.noreply.github.com> 

      Date: 2026-03-20 21:59:03 -0400

      Commit message:


	  
		
 Update README.md
 

    

  
    

      Package: RBPSpecificity

      Commit: 83f283c0f63efe4dfa097bd8a71096643e1994e9

      Author:  SoonYi <55300935+S00NYI@users.noreply.github.com> 

      Date: 2026-03-20 21:45:45 -0400

      Commit message:


	  
		
 Update NAMESPACE
 

    

  
    

      Package: RBPSpecificity

      Commit: a6f4a77aac98bfe25b9b297adc3df41e2ae6bae2

      Author:  SoonYi <55300935+S00NYI@users.noreply.github.com> 

      Date: 2026-03-20 21:22:18 -0400

      Commit message:


	  
		
 Merge branch 'main' of https://github.com/S00NYI/RBPSpecificity
 

    

  
    

      Package: RBPSpecificity

      Commit: 83df0c1680f6b2197e3ac4051d8aa8c0a321aa39

      Author:  SoonYi <55300935+S00NYI@users.noreply.github.com> 

      Date: 2026-03-20 21:22:15 -0400

      Commit message:


	  
		
 Updating terminology

Mutational Sensitivity has been changed to Variation Sensitivity
 

    

  
    

      Package: RBPSpecificity

      Commit: 8b121b3a5b5651aa356918d1f8e646b8f15eac7e

      Author:  SoonYi <55300935+S00NYI@users.noreply.github.com> 

      Date: 2026-03-09 13:57:58 -0400

      Commit message:


	  
		
 Fix Bioconductor build: untrack .Rproj, add test deps to Suggests
 

    

  
    

      Package: amplican

      Commit: 9cde37c438ccb3c208ccdbf825b0949dca9049b0

      Author:  JokingHero <kornel.labun@gmail.com> 

      Date: 2026-03-26 23:38:15 +0100

      Commit message:


	  
		
 pass checks
 

    

  
    

      Package: amplican

      Commit: de810fc03cf544a533fa4d19f0ccd2d2241cb8da

      Author:  JokingHero <kornel.labun@gmail.com> 

      Date: 2026-03-26 22:35:16 +0100

      Commit message:


	  
		
 let ampliCan rip with speed
 

    

  
    

      Package: TCGAutils

      Commit: f96f424b61d2c7af105499d91cdcfed6d26569e2

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2026-03-26 17:34:38 -0400

      Commit message:


	  
		
 version bump 1.31.5
 

    

  
    

      Package: TCGAutils

      Commit: de549e27b41ca4dc39a36f6e72bb9ddf4ef9d881

      Author:  Marcel Ramos Pérez <LiNk-NY@users.noreply.github.com> 

      Date: 2026-03-26 16:43:16 -0400

      Commit message:


	  
		
 Add missing fnd entries to Authors@R in DESCRIPTION (#39) 

    

  
  


</div>

</div>