Bioconductor 3.22 Released

Menu

Source Code & Build Reports:

Source code is stored in Git. Software packages are built and checked nightly.

Development Version

Bioconductor packages under development:

Bioconductor has moved to GIT for contributed packages; the subversion logs are no longer active. The following are the git logs.

GIT Logs

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

This list is also available as an RSS feed (devel branch), and RSS feed (release branch)

Package: BulkSignalR
Commit: e236c5a672c11179cd6849c10309823429230d15
Author: jcolinge <65902924+jcolinge@users.noreply.github.com>
Date: 2025-11-08 23:09:36 +0100
Commit message:

 bug-fix: multtest does not work with len 1 vectors
Package: basilisk.utils
Commit: 863ddfbb45c346e458764d3fb57802ba77b07ba9
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2025-11-09 08:33:51 +1100
Commit message:

 Commented on the naming situation in the vignette.
Package: GSVA
Commit: 51b250c28b4b2b80b1e480d16a7c7009b8bec37c
Author: Robert Castelo <robert.castelo@upf.edu>
Date: 2025-11-08 19:12:38 +0100
Commit message:

 Bump version
Package: GSVA
Commit: 5c5fb30bce9feee0e9988855eb7761db727d3a13
Author: Robert Castelo <robert.castelo@upf.edu>
Date: 2025-11-08 19:12:15 +0100
Commit message:

 Fix in kcdf="Gaussian" when input is SparseArray
Package: SingleCellSignalR
Commit: 926b6b567118158543b51741aa21f4a1c53d943e
Author: jcolinge <65902924+jcolinge@users.noreply.github.com>
Date: 2025-11-08 18:13:31 +0100
Commit message:

 bug-fix: syntax error in message()
Package: SingleCellSignalR
Commit: e427e35f9ead3db8eba6eb210ded0ccb9b8a2306
Author: jcolinge <65902924+jcolinge@users.noreply.github.com>
Date: 2025-11-08 17:50:50 +0100
Commit message:

 syntax error in message()
Package: SparseArray
Commit: 45142ef19371007d50ea723ddb3527dd3ebb2fea
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2025-11-08 01:29:02 -0800
Commit message:

 start refactoring C-level helper subassign_leaf_by_OPBuf()
Package: SparseArray
Commit: 0fa8490006d8d89715b57255a3ef24137cb4e863
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2025-11-07 22:05:39 -0800
Commit message:

 more improvements to internal helper .subassign_SVT_with_Rarray()
Package: crisprDesign
Commit: afa77b0961499c0f7b5e87b8e5dcc6006e19d432
Author: Jean-Philippe Fortin <fortin946@gmail.com>
Date: 2025-11-07 14:00:14 -0800
Commit message:

 Merged news
Package: crisprDesign
Commit: 9d8923b8f1b7af9811dac905a55df7d757f7d3ce
Author: Jean-Philippe Fortin <fortin946@gmail.com>
Date: 2025-11-07 13:59:01 -0800
Commit message:

 Added more annotation columns to addEditedAlleles
Package: crisprDesign
Commit: 30c99479f710a898ff6b0e24e0d0cfc11603e61c
Author: Jean-Philippe Fortin <fortin946@gmail.com>
Date: 2025-11-07 12:05:59 -0800
Commit message:

 Added aa changes column
Package: crisprDesign
Commit: e512a93960f543552628e12cb24c10838ebdf573
Author: Jean-Philippe Fortin <fortin946@gmail.com>
Date: 2025-11-05 15:50:23 -0800
Commit message:

 Fixed .addAminoAcids
Package: crisprDesign
Commit: ab013fff6a41e3b84e20e5e63e50a403133c1b44
Author: Jean-Philippe Fortin <fortin946@gmail.com>
Date: 2025-11-05 09:54:48 -0800
Commit message:

 Done with the be vignette
Package: crisprDesign
Commit: f8b4ffaf9cf02275aa54b0b3231005e8d05a9b72
Author: Jean-Philippe Fortin <fortin946@gmail.com>
Date: 2025-11-05 09:53:56 -0800
Commit message:

 Updated gitignore
Package: crisprDesign
Commit: cd79f12415bf0aa5ff3cd9b09008728ecfbc43ca
Author: Jean-Philippe Fortin <fortin946@gmail.com>
Date: 2025-11-05 09:30:52 -0800
Commit message:

 Fixed scoring one more time
Package: crisprDesign
Commit: b0c65bf4275531e8f7424508b362dc6c892351f7
Author: Jean-Philippe Fortin <fortin946@gmail.com>
Date: 2025-11-04 19:06:57 -0800
Commit message:

 Finalized new variant calling algorithm
Package: crisprDesign
Commit: f251158351d27a6138fcff0faac59026ca542012
Author: Jean-Philippe Fortin <fortin946@gmail.com>
Date: 2025-11-04 10:29:14 -0800
Commit message:

 Added maxVariantScore back
Package: crisprDesign
Commit: c792e561a60948d17ea4046c7b5ffd6027949ef3
Author: Jean-Philippe Fortin <fortin946@gmail.com>
Date: 2025-11-03 15:00:15 -0800
Commit message:

 Simplified the editing algo
Package: crisprDesign
Commit: fc94df1559fa31b66bccc23e3fc4fda299596ac0
Author: Jean-Philippe Fortin <fortin946@gmail.com>
Date: 2025-10-31 12:13:07 -0700
Commit message:

 Dealing with unassigned
Package: crisprDesign
Commit: a690ab62fed4ab1d0a283de6a09436a6626bf091
Author: Jean-Philippe Fortin <fortin946@gmail.com>
Date: 2025-10-31 11:25:54 -0700
Commit message:

 Adding amino acids for non-editing alelles
Package: crisprDesign
Commit: cbc2ea7a13ba7875d9780628605275bf55f8b247
Author: Jean-Philippe Fortin <fortin946@gmail.com>
Date: 2025-10-30 16:38:56 -0700
Commit message:

 Added aa position to editedAlleles
Package: crisprDesign
Commit: 6e255356f05fd37d313453eb4674029727ecc2f6
Author: Jean-Philippe Fortin <fortin946@gmail.com>
Date: 2025-10-30 15:59:37 -0700
Commit message:

 Added position information to editedAlleles
Package: crisprDesign
Commit: c4c33a6be17f4c730d41354bea73f7b0d03bd976
Author: Jean-Philippe Fortin <fortin946@gmail.com>
Date: 2025-10-30 15:09:16 -0700
Commit message:

 Done
Package: crisprDesign
Commit: c956a94039d1354ae8407612bef009c5e5227d99
Author: Jean-Philippe Fortin <fortin946@gmail.com>
Date: 2025-10-30 10:10:21 -0700
Commit message:

 Removed missenseMargin
Package: crisprDesign
Commit: b70fb06e57e0236594e0c6de0dc04aba9947159c
Author: Jean-Philippe Fortin <fortin946@gmail.com>
Date: 2025-10-29 11:18:39 -0700
Commit message:

 Added no editing category
Package: crisprDesign
Commit: b9b8a33de5e89ee2a0ed791999fb8b5df453bc7e
Author: Jean-Philippe Fortin <fortin946@gmail.com>
Date: 2025-10-29 11:10:14 -0700
Commit message:

 Fixed editedAlleles accessor function unlisting option
Package: crisprDesign
Commit: a954d5708eeab6817ba65b6b2e03074d0b2d7ee2
Author: Jean-Philippe Fortin <fortin946@gmail.com>
Date: 2025-10-28 10:18:02 -0700
Commit message:

 Added splice junction call for BE
Package: crisprDesign
Commit: 5f14e7346aec0cedf7ff958dcbba86f277dd5da8
Author: Jean-Philippe Fortin <fortin946@gmail.com>
Date: 2025-10-27 21:08:49 -0700
Commit message:

 Done with the missense
Package: crisprDesign
Commit: 5738cbf38fbfa8ca56fd6891ada66a0ead456070
Author: Jean-Philippe Fortin <fortin946@gmail.com>
Date: 2025-10-27 18:43:34 -0700
Commit message:

 Added a few modifications to the allele calling
Package: lefser
Commit: ffb1ed63daa7a5f75e80b820032b22cb691e1313
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-11-07 15:43:02 -0500
Commit message:

 version bump 1.21.1
Package: lefser
Commit: b6127082808619eefb081659c2b98bffc6043099
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-11-07 15:45:34 -0500
Commit message:

 add label.font.color to vignette
Package: lefser
Commit: f897658cd8d6c3120b6970b26bb28d3683cee2d1
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-11-07 15:45:17 -0500
Commit message:

 update NEWS.md
Package: lefser
Commit: 94dfba8e6b3a34e0ff07e79f1bc4d3025dc840fe
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-11-07 15:20:09 -0500
Commit message:

 fix color argument defaults

- improve .selectPalette
Package: lefser
Commit: 11857b7c528c5efc267088ca90041d14a405b521
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-11-07 14:30:43 -0500
Commit message:

 fix code and doc formatting
Package: lefser
Commit: 2c3d96b90e6670539ff5b55a9f006caca14a0674
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-11-07 14:25:07 -0500
Commit message:

 add label.font.color and ... to lefserPlot
Package: lefser
Commit: d7b1cefab8d7768b660b94b3b97a4232e8a34418
Author: Copilot <198982749+Copilot@users.noreply.github.com>
Date: 2025-11-07 14:09:43 -0500
Commit message:

 Add label.font.face parameter to lefserPlot() for text formatting control (#90)

* Add label.font.face parameter to lefserPlot function

Co-authored-by: LiNk-NY <4392950+LiNk-NY@users.noreply.github.com>

* Add input validation for label.font.face and fix typo

Co-authored-by: LiNk-NY <4392950+LiNk-NY@users.noreply.github.com>

* use match.arg

* update docs

* update unit test

* update NEWS

---------

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Co-authored-by: LiNk-NY <4392950+LiNk-NY@users.noreply.github.com>
Co-authored-by: LiNk-NY <marcel.ramos@sph.cuny.edu>
Package: SparseArray
Commit: c445d0d8ea452af99f3bbcb84676c47eeae0658b
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2025-11-07 11:46:58 -0800
Commit message:

 more improvements to internal helper .subassign_SVT_with_Rarray()
Package: cBioPortalData
Commit: 0773368269dee2904f8c571c853281ca20f676b6
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-11-07 13:23:07 -0500
Commit message:

 version bump 2.23.2
Package: cBioPortalData
Commit: ae577da66f949aed81ca0c39d1dc9076e4c767f5
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-11-07 13:21:15 -0500
Commit message:

 bug fix: remove resourceCounts from API response
Package: MetaScope
Commit: d49e047678018638e05ac2266605c31ea1923fad
Author: Sean Lu <seanlu96@gmail.com>
Date: 2025-11-07 11:54:11 -0500
Commit message:

 Resolve merge conflicts
Package: MetaScope
Commit: bca3bbb4963f7f5d3f13dfa4e2285caa65c845ae
Author: Sean Lu <seanlu96@gmail.com>
Date: 2025-11-07 11:43:38 -0500
Commit message:

 checks bug fixes
Package: MetaScope
Commit: cd34616980c01e1fae35c32dc3efd0406941500e
Author: Sean Lu <seanlu96@gmail.com>
Date: 2025-11-07 11:14:55 -0500
Commit message:

 check bug fixes
Package: MetaScope
Commit: 3d4c4ed378b77f9988fdde11ba725d2eee95a1b6
Author: Sean <89270441+seanlu96@users.noreply.github.com>
Date: 2025-10-20 22:55:01 -0400
Commit message:

 Merge pull request #57 from seanlu96/master

chunk update bam
Package: MetaScope
Commit: 0f99183dfb2164cf63deb05e6b2f509697dee9a5
Author: Sean Lu <seanlu96@gmail.com>
Date: 2025-10-20 22:54:20 -0400
Commit message:

 chunk update bam
Package: MetaScope
Commit: d557dbb562f4ee52ca9e2d8c8efc3a5111aec550
Author: Sean <89270441+seanlu96@users.noreply.github.com>
Date: 2025-10-17 19:54:46 -0400
Commit message:

 Merge pull request #56 from seanlu96/master

optimized metablast
Package: MetaScope
Commit: c4d02fb5771be37f3a579f616c8a6e0bc9010725
Author: Sean <89270441+seanlu96@users.noreply.github.com>
Date: 2025-10-17 19:54:19 -0400
Commit message:

 Merge branch 'wejlab:devel' into master
Package: MetaScope
Commit: 36623210f8e6768b89fff038ca6a7a3ffa070055
Author: Sean Lu <seanlu96@gmail.com>
Date: 2025-10-17 19:53:35 -0400
Commit message:

 metablast optimizations
Package: MetaScope
Commit: 886098a5fd8188dd3918fba17718417e13ff3534
Author: Sean <89270441+seanlu96@users.noreply.github.com>
Date: 2025-10-16 14:51:22 -0400
Commit message:

 Merge pull request #55 from seanlu96/master

fixed metablast
Package: MetaScope
Commit: ff13ca697fc7d6b17ba6d1a1cf98718b69ad47b2
Author: Sean Lu <seanlu96@gmail.com>
Date: 2025-10-16 14:50:38 -0400
Commit message:

 fixed metablast
Package: MetaScope
Commit: 354cfc580f9fe7de1f01d577d0590076fa765c7d
Author: Sean <89270441+seanlu96@users.noreply.github.com>
Date: 2025-09-25 11:55:51 -0400
Commit message:

 Merge pull request #54 from seanlu96/master

update run metascope
Package: MetaScope
Commit: a7781ac522ae6867cb4e8d427a0cb487034eef41
Author: Sean <89270441+seanlu96@users.noreply.github.com>
Date: 2025-09-25 11:55:32 -0400
Commit message:

 Merge branch 'wejlab:devel' into master
Package: MetaScope
Commit: 70e44985ee146d01b4fa43e7aae1b47ab0b9cc55
Author: Sean <89270441+seanlu96@users.noreply.github.com>
Date: 2025-09-25 11:55:25 -0400
Commit message:

 Update run_metascope.R

added extra args for align_target
Package: MetaScope
Commit: 608121a4be95d7655e4096deaaf0e26acd8458c1
Author: Sean <89270441+seanlu96@users.noreply.github.com>
Date: 2025-09-24 12:53:37 -0400
Commit message:

 Merge pull request #53 from seanlu96/master

update to generate merged feature tables
Package: MetaScope
Commit: 48fcc2200a7115bcf1992203673f6bd5602765ae
Author: Sean <89270441+seanlu96@users.noreply.github.com>
Date: 2025-09-24 12:52:18 -0400
Commit message:

 Merge branch 'wejlab:devel' into master
Package: MetaScope
Commit: a3d1c718fe649446fbe2471d0b2da7ad35b3b27f
Author: Sean Lu <seanlu96@gmail.com>
Date: 2025-09-24 12:51:50 -0400
Commit message:

 Merge branch 'master' of https://github.com/seanlu96/MetaScope
Package: MetaScope
Commit: 5d93b1e2be6c0a7b5151976481a1b07be57cfdd2
Author: Sean <89270441+seanlu96@users.noreply.github.com>
Date: 2025-09-22 17:04:27 -0400
Commit message:

 added merged feature table output for metascope
Package: MetaScope
Commit: 7ee2a8db86179e0218ff20a471361d429e62a659
Author: Sean <89270441+seanlu96@users.noreply.github.com>
Date: 2025-09-22 17:04:52 -0400
Commit message:

 Merge pull request #52 from seanlu96/master

updates to run_metascope
Package: MetaScope
Commit: 371872fbca868ff63b87a0c4b33c8aa06630f1a0
Author: Sean <89270441+seanlu96@users.noreply.github.com>
Date: 2025-09-22 17:04:27 -0400
Commit message:

 Merge branch 'wejlab:devel' into master
Package: MetaScope
Commit: 831a011d0841cc9339ed2fe87ef25feefa59d45f
Author: Sean Lu <seanlu96@gmail.com>
Date: 2025-09-22 16:32:25 -0400
Commit message:

 run_metascope bug fixes with arguments
Package: MetaScope
Commit: a1562173bf913492b6ba6218f91658c4bed20204
Author: Sean <89270441+seanlu96@users.noreply.github.com>
Date: 2025-09-18 17:30:44 -0400
Commit message:

 Update README.md
Package: MetaScope
Commit: 1d60e6122fd0b0f1aecd7d6d49263c6ef38362fe
Author: Sean Lu <seanlu96@gmail.com>
Date: 2025-09-15 17:06:54 -0400
Commit message:

 bug fixes
Package: MetaScope
Commit: 54f8e6a0402863398d489a0421fe93f008bedc17
Author: Sean Lu <seanlu96@gmail.com>
Date: 2025-09-15 16:34:44 -0400
Commit message:

 added wrapper function for full metascope 16S
Package: MetaScope
Commit: face9eb7577f12edc845f08a7fb893fc5c1997fb
Author: Sean <89270441+seanlu96@users.noreply.github.com>
Date: 2025-09-15 09:52:59 -0400
Commit message:

 Merge pull request #51 from seanlu96/master

bug fixes with download_refseq
Package: MetaScope
Commit: 426dfa7fa87a867807025e7d197c0177375efa33
Author: Sean Lu <seanlu96@gmail.com>
Date: 2025-09-05 13:43:26 -0400
Commit message:

 bug fixes
Package: MetaScope
Commit: 445bf96b6d8c9833a502376485ce0752fc7449ff
Author: Sean <89270441+seanlu96@users.noreply.github.com>
Date: 2025-08-25 20:00:53 -0400
Commit message:

 Merge pull request #50 from technophilic03/devel

Added metascope_inspect function as a wrapper to bowtie2-inspect
Package: MetaScope
Commit: d5daa5a8cb28ef05331c3c6f086a27d978e5eb3d
Author: technophilic03 <leng@bu.edu>
Date: 2025-08-25 12:54:03 -0400
Commit message:

 Roxygen updates for metascope_inspect
Package: MetaScope
Commit: 76491985d2ac2c16a62f480016e8b76988320605
Author: technophilic03 <leng@bu.edu>
Date: 2025-08-25 12:53:10 -0400
Commit message:

 Added bowtie2 inspect scripts to inst/ folder
Package: MetaScope
Commit: 835a2fcaaa6800bb99f47140d5541cd68a1e7760
Author: technophilic03 <leng@bu.edu>
Date: 2025-08-25 12:52:02 -0400
Commit message:

 Added metascope-inspect as a bowtie2-inspect wrapper
Package: GSVA
Commit: da6381b67ab5f664e767cecca96284fd867425e0
Author: Robert Castelo <robert.castelo@upf.edu>
Date: 2025-11-07 17:46:40 +0100
Commit message:

 Bump version
Package: GSVA
Commit: 8adda3da3de4b9d1d60f965fcae8bc05a205723d
Author: Robert Castelo <robert.castelo@upf.edu>
Date: 2025-11-07 17:46:16 +0100
Commit message:

 Fix on the parallel scanning of nonzero constant rows
Package: Aerith
Commit: 5365565e471a2127ceb413ee125f625399ada945
Author: xyz1396 <1074082710@qq.com>
Date: 2025-11-04 17:09:34 -0600
Commit message:

 bump version
Package: Aerith
Commit: 6f12a2d4d094cb5f96c6719c899ef69d9878f15c
Author: xyz1396 <1074082710@qq.com>
Date: 2025-11-04 17:02:43 -0600
Commit message:

 fix citation
Package: Aerith
Commit: 32401f615cfd317f58a0c44b0e4fa2a3c9feb38a
Author: xyz1396 <1074082710@qq.com>
Date: 2025-11-04 12:20:21 -0600
Commit message:

 add citation
Package: Aerith
Commit: b05a8898f0c8f4c6d1bcadaace5a7aa6056d9af2
Author: xyz1396 <1074082710@qq.com>
Date: 2025-11-04 11:52:24 -0600
Commit message:

 merge from upstream
Package: GenomicDataCommons
Commit: 06edbb7fba904aabeba8992bbc0047a02f49ddf8
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-11-07 11:02:31 -0500
Commit message:

 version bump 1.35.1
Package: GenomicDataCommons
Commit: b1b5b8f10c78b0355982edcbf010e4d5464292de
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-11-07 10:59:16 -0500
Commit message:

 relax tests for exposures element in clinical_data
Package: gatom
Commit: bedd7f8c6922ac1d16df5f2306fdd80d25a601fb
Author: Alexey Sergushichev <alsergbox@gmail.com>
Date: 2025-11-07 10:00:41 -0600
Commit message:

 version bump
Package: gatom
Commit: a881aa354832b6edae955691f1b4f2b5a2f530cf
Author: Alexey Sergushichev <alsergbox@gmail.com>
Date: 2025-11-06 17:57:00 -0600
Commit message:

 switch from GGally/ggnet to ggnetwork
Package: gatom
Commit: dc4790548f3acabc54692d54a54cf6a98ce76c59
Author: Alexey Sergushichev <alsergbox@gmail.com>
Date: 2025-11-06 17:21:20 -0600
Commit message:

 Replace deprecated igraph commands
Package: plyranges
Commit: 40182e800c0abc3d332c327e3dab5c2f364b1223
Author: Mike Love <mikelove@users.noreply.github.com>
Date: 2025-11-07 08:54:55 -0500
Commit message:

 version bump
Package: plyranges
Commit: da1d45606292fd3f79e79a028f0a6b4ed5fe43e3
Author: Stuart Lee <8033857+sa-lee@users.noreply.github.com>
Date: 2025-06-26 13:56:58 +1000
Commit message:

 Merge pull request #115 from sa-lee/devel

fix: update pkgdown.yml with pull and pipe
Package: plyranges
Commit: b4d9bc4415639a06dc0440faa0dbf2cc65f5996c
Author: sa-lee <stuart.andrew.lee@gmail.com>
Date: 2025-06-26 13:56:25 +1000
Commit message:

 fix: update pkgdown.yml with pull and pipe
Package: plyranges
Commit: 0a6f9de212dc38642dbb27e831f791e8de9a58ee
Author: Stuart Lee <8033857+sa-lee@users.noreply.github.com>
Date: 2025-06-26 10:58:17 +1000
Commit message:

 Merge pull request #114 from sa-lee/devel

update pkgdown yml and remove full dplyr import
Package: plyranges
Commit: ac55d420f26fb9eb1d87b715c553978bc9f039a6
Author: sa-lee <stuart.andrew.lee@gmail.com>
Date: 2025-06-26 10:18:17 +1000
Commit message:

 fix: update pkgdown yaml
Package: plyranges
Commit: c312646733f03d0e44d27e8826cab5a9a187770e
Author: sa-lee <stuart.andrew.lee@gmail.com>
Date: 2025-06-26 10:06:52 +1000
Commit message:

 fix: NAMESPACE regression
Package: plyranges
Commit: ef553068942ad635cbcf5f198125bd24949cb7b9
Author: Stuart Lee <8033857+sa-lee@users.noreply.github.com>
Date: 2025-06-26 09:54:06 +1000
Commit message:

 Merge pull request #113 from sa-lee/devel

feat: add pull method, alongside tests and updated documentation
Package: plyranges
Commit: 154e5c3a885cf8fe05a24ffff8116876861edc0d
Author: sa-lee <stuart.andrew.lee@gmail.com>
Date: 2025-06-25 13:30:35 +1000
Commit message:

 fix typo, update note about package dependency updates
Package: plyranges
Commit: dc3e1576bc5c185c2d88772147526132d71de6ee
Author: sa-lee <stuart.andrew.lee@gmail.com>
Date: 2025-06-24 17:18:30 +1000
Commit message:

 fix: tests, remove dplyr warning
Package: plyranges
Commit: 65a1462c52abfe2b68a50e0c8f9ce983dc1e380e
Author: sa-lee <stuart.andrew.lee@gmail.com>
Date: 2025-06-24 16:45:47 +1000
Commit message:

 fix: update imports
Package: plyranges
Commit: a60797b86f05b470fa23e208834d8597075ea7ba
Author: sa-lee <stuart.andrew.lee@gmail.com>
Date: 2025-06-24 16:22:26 +1000
Commit message:

 refactor: fix tests with moving dplyr to Depends
Package: plyranges
Commit: 3622845238c948c4a5207ecd7bb17d590af0859b
Author: sa-lee <stuart.andrew.lee@gmail.com>
Date: 2025-06-24 16:07:50 +1000
Commit message:

 refactor: fix doc issues and R CMD CHECK notes
Package: plyranges
Commit: e41037f912f381965c4ec5424c13682729585178
Author: sa-lee <stuart.andrew.lee@gmail.com>
Date: 2025-06-24 14:55:48 +1000
Commit message:

 feat: add pull method, alongside tests and updated documentation
Package: mCSEAdata
Commit: 679fb795be942a7986902e71199fef45bef41cd4
Author: jordimartorell <jmartorellm@gmail.com>
Date: 2025-11-07 13:33:40 +0100
Commit message:

 Fix documentation
Package: Rarr
Commit: 8d89fed53f6ecbc125c2d2468d4511f92cb745b7
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-11-06 13:37:36 +0100
Commit message:

 Bump version
Package: Rarr
Commit: 19030f8be97d6f1a11a97e7bf829c8a8ac56cfc1
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-11-06 13:37:22 +0100
Commit message:

 Document new data types in NEWS
Package: Rarr
Commit: ad8d60b48330af67abfb51e0560c32228c502cf9
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-11-07 10:38:15 +0100
Commit message:

 Restrict cases where .truncate_overflow() is called
Package: Rarr
Commit: c4c2d105f5b2fa17b47a277ac40e7015e32cdcb1
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-11-06 12:47:17 +0100
Commit message:

 Add tests for writing float32
Package: Rarr
Commit: 2abbcb827f6b2cb986f6ee55e50ddfa13a2eda79
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-10-10 16:20:32 +0200
Commit message:

 Run devtools::document()
Package: Rarr
Commit: 4e19bf4c48cad90d884b0cafb8b7612e0e2fe44d
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-10-10 14:34:32 +0200
Commit message:

 Add warning about overflows in write_zarr_array()
Package: Rarr
Commit: 03429c70794e8953ff94d7900416d9bff2e0871c
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-10-10 14:32:09 +0200
Commit message:

 Add support for writing lower precision integers and floats
Package: Rarr
Commit: a59c6228118e3918ab3c71f0a28e9a4bf800f4ca
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-10-10 14:05:40 +0200
Commit message:

 Ensure portability when writing from big endian machines
Package: Rarr
Commit: 1c7730fb3e5237f176ead0ae570de8b37566389d
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-10-09 17:16:02 +0200
Commit message:

 Fix typo
Package: Rarr
Commit: b03d1293babe87839c17872b7daf76440e0be137
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-10-09 13:11:46 +0200
Commit message:

 Add support for writing boolean arrays
Package: Pirat
Commit: 5cf48c5a78214bb87666c1713b1f468285c589e7
Author: Lucas Etourneau <lucas.etourneau@berkeley.edu>
Date: 2025-11-07 11:38:38 +0100
Commit message:

 change package version
Package: ClusterGVis
Commit: 1386690b7b6e0d5f5aff950bf063d3b1776c8c61
Author: junjunlab <1138976957@qq.com>
Date: 2025-11-07 17:54:53 +0800
Commit message:

 revision 0.99.7 for bioconductor
Package: Pirat
Commit: 04f9055960a90b198f02bc82951d1495a2307975
Author: Lucas Etourneau <38471671+Lucas-Et@users.noreply.github.com>
Date: 2025-11-07 10:15:00 +0100
Commit message:

 Change import from lbfgs to LBFGS
Package: Pirat
Commit: bcaaf8df1f3a2851c1d88011ed091ce2c2116db4
Author: Lucas Etourneau <38471671+Lucas-Et@users.noreply.github.com>
Date: 2025-11-07 10:14:34 +0100
Commit message:

 Rename lbfgs.py to LBFGS.py
Package: MetaProViz
Commit: 1b508251e43f4b83dbd363fec60f42e8da294f91
Author: deeenes <turei.denes@gmail.com>
Date: 2025-11-06 13:02:33 +0100
Commit message:

 Bump version: 3.99.20 → 3.99.21
Package: MetaProViz
Commit: e112b009ea48fb49d6f3652cc29db03600be9fa1
Author: deeenes <turei.denes@gmail.com>
Date: 2025-11-06 13:02:29 +0100
Commit message:

 docs rebuild
Package: MetaProViz
Commit: abc4640971087353d755c09689ee7140f24ca585
Author: deeenes <turei.denes@gmail.com>
Date: 2025-11-06 13:02:20 +0100
Commit message:

 enabled doctests of small infrastructure functions
Package: SparseArray
Commit: f62ecd676181d32bb5bfd939d19459cb33c8dfde
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2025-11-06 23:12:16 -0800
Commit message:

 some improvements to internal helper .subassign_SVT_with_Rarray()
Package: pathlinkR
Commit: b21e90a833bf964feb65453545d4d5208e2c9504
Author: Travis Blimkie <travis.m.blimkie@gmail.com>
Date: 2025-11-06 15:28:12 -0800
Commit message:

 Specified the order of legends in pathnetGGraph.
Package: TCGAutils
Commit: 014a2cf778e06bf0a556f922e712dbba85502088
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-11-06 17:11:08 -0500
Commit message:

 version bump 1.31.1
Package: TCGAutils
Commit: fbdb37b6da94cac0916f3d2c95340b6fc32413dd
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-11-06 17:08:53 -0500
Commit message:

 add BiocFileCache to Suggests
Package: TCGAutils
Commit: 5cd680f7f9ada31c26772cbfdf6b44674ee04e7a
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-11-04 14:58:44 -0500
Commit message:

 add helper functions for mirToRanges reimplementation
Package: TCGAutils
Commit: 7a41ffa865d8978de2fa01023f04e8d12af5d447
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-11-05 17:34:20 -0500
Commit message:

 remove microRNAs import from GenomicFeatures
Package: TCGAutils
Commit: 9da527e3b373af87100930bf934a8bc7b67bcaae
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-11-06 14:12:35 -0500
Commit message:

 consolidate single-use helper functions
Package: TCGAutils
Commit: 913bdf8a130773ee53b982e1a45d21064243c623
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-11-06 14:12:18 -0500
Commit message:

 minor move importFrom directive
Package: TCGAutils
Commit: 061f3f66d5ab6da4fc8f62d5b44914bb6d8ea728
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-11-05 17:54:03 -0500
Commit message:

 RoxygenNote version bump
Package: TCGAutils
Commit: 582ea0b276baaca7ca88d9530e50db25fd1e0baf
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-11-05 17:50:03 -0500
Commit message:

 update internal helpers docs
Package: TCGAutils
Commit: 08ec8c41fd4ed30cf4edface5adc196da66c8094
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-11-05 17:48:32 -0500
Commit message:

 add pattern checks to .isFixable
Package: TCGAutils
Commit: 2449d6717037dad1049e74020be2b3987b3204cd
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-11-05 17:48:08 -0500
Commit message:

 use threshold in .checkHas

- remove default values for pattern
Package: cBioPortalData
Commit: 4222cea8cdc3ecbdef21cd45c5555feb82a1bbf4
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-11-06 15:56:24 -0500
Commit message:

 version bump 2.23.1
Package: cBioPortalData
Commit: a22a512e2d65396379bd9e9204ef147c4895c8be
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-11-06 14:26:12 -0500
Commit message:

 update RoxygenNote version
Package: cBioPortalData
Commit: 295913e0c32adac5d3dc9daa025279c4a8a05efa
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-11-06 14:25:36 -0500
Commit message:

 remove defunct removeDataCache function
Package: AnVILGCP
Commit: aa52d1b463e1759c88e2f86b35aaf301dcc0ef7a
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-11-06 15:38:05 -0500
Commit message:

 version bump 1.5.1
Package: AnVILGCP
Commit: 3aa3a1ac9a6cf9564068e644cff4dded35005be2
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-11-06 14:48:29 -0500
Commit message:

 defunct gcloud functions moved to GCPtools
Package: GSVA
Commit: caee9c927bf39b2765b8bcfb7698fd11daa6f3ff
Author: Robert Castelo <robert.castelo@upf.edu>
Date: 2025-11-06 20:03:56 +0100
Commit message:

 Bump version
Package: GSVA
Commit: 7b31045821184d6d7b9dcc4bbaf876f6741d791b
Author: Robert Castelo <robert.castelo@upf.edu>
Date: 2025-11-06 20:03:33 +0100
Commit message:

 Fixed row filtering
Package: MungeSumstats
Commit: d2204cef0e1dd6e16bfaac9b0a5844d57ada207f
Author: Al-Murphy <alanmurph94@hotmail.com>
Date: 2025-11-06 13:53:48 -0500
Commit message:

 Bug Fix: IEU GWAS download
Package: MungeSumstats
Commit: b687ae342a7f62753d8af98d04645f8230cf2b28
Author: Alan Murphy <62257358+Al-Murphy@users.noreply.github.com>
Date: 2025-11-06 11:50:47 -0500
Commit message:

 Merge pull request #210 from toby-clark4/master

fixed import_sumstats download error
Package: MungeSumstats
Commit: b50471388345e6e87dca1c38db4e78e441d49549
Author: Toby Clark <tobyclark02@outlook.com>
Date: 2025-11-06 15:21:55 +0000
Commit message:

 fixed import_sumstats download error
Package: pathlinkR
Commit: 50ff9054d01f841c58dc76c3c6d2551913aa5a18
Author: Travis Blimkie <travis.m.blimkie@gmail.com>
Date: 2025-11-06 10:21:01 -0800
Commit message:

 Set order of legends in pathwayPlots.
Package: destiny
Commit: 8cc0bffe8ac72989ac6a0511e5aa71132edab632
Author: Philipp A. <flying-sheep@web.de>
Date: 2025-11-06 14:14:03 +0100
Commit message:

 Fix tests (#69)
Package: rhdf5
Commit: 7833404a30303597cdd4d87d815ca9f0d350f05b
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-11-05 15:28:02 +0100
Commit message:

 Bump version
Package: rhdf5
Commit: 4cc3db39d5a4c305fc2822db6978b5a2bf1ec76c
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-11-05 15:24:07 +0100
Commit message:

 Use fct() syntax in vignettes
Package: rhdf5
Commit: 56dbfe9f60e3d0664994a2c35fd51181c95a8cba
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-11-05 14:52:45 +0100
Commit message:

 Use 'returns' consistently instead of 'return'
Package: rhdf5
Commit: 781829d1be3cd31746f1c660ce2bbb7259c3e1f0
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-11-05 14:48:50 +0100
Commit message:

 Fix some typos
Package: rhdf5
Commit: 3688c8dd65b7e80df6ef0f01bc6c980a41cf11fa
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-11-05 14:45:25 +0100
Commit message:

 Improve some roxygen markdown manually
Package: rhdf5
Commit: c9d920e642d2b4305ab9a87e231896b0229229a5
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-11-05 14:21:27 +0100
Commit message:

 Run roxygen2md::roxygen2md()
Package: pmp
Commit: 0f6f235cd57bee78d519afde750e94667add9706
Author: Gavin Rhys Lloyd <grlloyd@users.noreply.github.com>
Date: 2025-11-06 10:39:10 +0000
Commit message:

 version bump and news
Package: pmp
Commit: 2a1b835b8a2b9b4eedfa5eef1aa2c6a05aa73ec2
Author: Gavin Rhys Lloyd <grlloyd@users.noreply.github.com>
Date: 2025-11-06 10:38:10 +0000
Commit message:

 fix broken tests
Package: GSVA
Commit: f164b7c95ffd5a09f01dda701a43f93972596886
Author: Robert Castelo <robert.castelo@upf.edu>
Date: 2025-11-06 08:55:51 +0100
Commit message:

 Fixing recovery from errors found during parallelization
Package: epiSeeker
Commit: 7ac589a2621d09c0f69bab33cc5e136a2cbbef4a
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2025-11-06 10:29:48 +0800
Commit message:

 fixed typo and clean up code
Package: epiSeeker
Commit: 340049b87cc0dfb637d882d0d421855680af7166
Author: liming <limiang929@gmail.com>
Date: 2025-11-05 12:22:03 +0800
Commit message:

 update test for change of txdb version
Package: epiSeeker
Commit: b43656e721db10d577b1b9f970aa42a97b206f65
Author: liming <limiang929@gmail.com>
Date: 2025-10-24 11:01:55 +0800
Commit message:

 update txdb check function
Package: epiSeeker
Commit: 8eb57e579e5d62e69b2ff8b3ae4cf47a645c3fff
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2025-10-15 14:11:32 +0800
Commit message:

 update docs
Package: epiSeeker
Commit: 66906b04fe5f0f5ec82599d3b1ce568b75dbceee
Author: liming <limiang929@gmail.com>
Date: 2025-10-15 12:55:55 +0800
Commit message:

 update env fucntion
Package: MSstatsBioNet
Commit: 5afd016a34a7f9b950c19c1f255266aaacf0514b
Author: tonywu1999 <wu.anthon@northeastern.edu>
Date: 2025-11-05 18:51:59 -0500
Commit message:

 fix(curation): Use matches_hash for statement hash due to string issues (#64)
Package: tximport
Commit: 9bee8fd2a8c997738114f678de5946fd50867275
Author: Mike Love <mikelove@users.noreply.github.com>
Date: 2025-11-05 17:00:34 -0500
Commit message:

 version bump
Package: tximport
Commit: aaad647aa964ad666930cfefff24d30849ba86a2
Author: Mike Love <mikelove@users.noreply.github.com>
Date: 2025-11-05 17:00:20 -0500
Commit message:

 fix bib
Package: leapR
Commit: d721db968a6ad9cdf916630c5d1326fa1a44ebc4
Author: Sara JC Gosline <sara.gosline@pnnl.gov>
Date: 2025-11-05 11:45:33 -0800
Commit message:

 incremented version with updated vignette
Package: leapR
Commit: 1d86d225ac1d36bb5ed4f88f5ab6e02633eeeb0b
Author: Sara JC Gosline <sara.gosline@pnnl.gov>
Date: 2025-11-05 11:12:14 -0800
Commit message:

 updated to add back bioc install
Package: annoLinker
Commit: dd054da0815d8ab991ce0163de4383be4a54fa1b
Author: Jianhong Ou <jianhong.ou@gmail.com>
Date: 2025-11-05 13:18:37 -0500
Commit message:

 bump version.
Package: ShortRead
Commit: ab09a1bb799709f4a94f19860d17be257f38a5de
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2025-11-05 10:00:35 -0800
Commit message:

 ShortRead 1.69.2: Fix trimEnds() method for XStringSet objects

This is a long-standing dormant bug (12+ years) that only gets revealed
now because of a small change in Biostrings::get_seqtype_conversion_lookup()
in Biostrings 2.79.2.
Package: annoLinker
Commit: 347b5a4b11773a944bd0a85190e00ce4aed3362c
Author: Jianhong Ou <jianhong.ou@gmail.com>
Date: 2025-11-05 12:25:20 -0500
Commit message:

 bump the version number.
Package: MSstatsBioNet
Commit: b42471f0c0bafeb3b5fdec0dd083f5cafa0ca667
Author: tonywu1999 <wu.anthon@northeastern.edu>
Date: 2025-11-05 12:12:09 -0500
Commit message:

 feature(visualizeNetworkWithHTML): add edge clicking to URL for regular HTML (#63)
Package: CoSIA
Commit: 3d2338a445fd37eec7f37c92b6673af2f1006707
Author: Amanda Clark <adc0032@auburn.edu>
Date: 2025-11-05 10:45:05 -0600
Commit message:

 version bump 1.11.0 > 1.11.1
Package: CoSIA
Commit: c44b4d08c6a814245d40d07d8a019cc61d0e40a8
Author: Amanda Clark <adc0032@auburn.edu>
Date: 2025-11-05 10:43:54 -0600
Commit message:

 Merge branch 'main' of https://github.com/lasseignelab/CoSIA into devel
update maintainer
Conflicts:
	DESCRIPTION
Package: CoSIA
Commit: f35fea0cde6eb91c00b3dcd9507bd712a90a5d4b
Author: Tonie <148514625+toniecrumley@users.noreply.github.com>
Date: 2025-10-31 09:30:18 -0500
Commit message:

 Update roles and add new person entry

Anthony B. Crumley was added as the maintainer, and Amanda D. Clark was changed to author.
Package: CoSIA
Commit: 70c3935b25504b40e4969588beff70d695605287
Author: Amanda Clark <adc0032@auburn.edu>
Date: 2025-10-08 09:42:33 -0500
Commit message:

 Update DESCRIPTION

version bump with email update
Package: annoLinker
Commit: c881eab57c34df33b7000c22f61b50b0205831fc
Author: Jianhong Ou <jianhong.ou@gmail.com>
Date: 2025-11-05 11:55:38 -0500
Commit message:

 Add the scripts for extdata
Package: annoLinker
Commit: a2b1e8a44b542bcc5b7ddbd18e2c9209c32ac196
Author: Jianhong Ou <jianhong.ou@gmail.com>
Date: 2025-11-05 11:46:47 -0500
Commit message:

 remove .DS_Store file.
Package: rhdf5
Commit: 0f052a90da54f63cf22f0404c4bb6dfce1d50dca
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-11-02 14:35:29 +0100
Commit message:

 Bump version
Package: rhdf5
Commit: dae7b38d4a29f8931b11e01eac04ce4be5cfbd65
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-11-03 09:21:56 +0100
Commit message:

 Make fix_missing() more general
Package: rhdf5
Commit: ce0303255272ce22d026180be949a07dcad04104
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-11-03 09:21:30 +0100
Commit message:

 Add test for passing down missing values
Package: rhdf5
Commit: 7d5adeedaaf53d622c787bda614e0edce2f26beb
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-11-02 14:31:08 +0100
Commit message:

 Use match.arg() on bit64conversion
Package: rhdf5
Commit: 4a782503762fd3bed233a0c71b7833380821f573
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-11-02 14:30:19 +0100
Commit message:

 Differentiate between missing scenarios

Could be missing because omitted or missing passed down from higher in the call stack
Package: rhdf5
Commit: 1d82b444f9ca8e63a393b4cd7717d30009f5cd14
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-11-03 09:24:09 +0100
Commit message:

 Document bit64conversion breaking change in NEWS
Package: rhdf5
Commit: 4165c2c20e139d829938869dc652cc222cc03ec7
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-11-02 12:25:16 +0100
Commit message:

 Add warning about deprecated bit64conversion values
Package: rhdf5
Commit: 9d8f05e1a828b032420066aa30f680379aa8d1dd
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-11-03 16:32:01 +0100
Commit message:

 Fix partial matching
Package: MIRit
Commit: a0208d2fb3053f53f2d2632b95080b1eaf8d5700
Author: jacopo-ronchi <jacopo.ronchi@unimib.it>
Date: 2025-11-05 13:05:07 +0000
Commit message:

 build: version bump to 1.7.1 in the DESCRIPTION file.
Package: MIRit
Commit: b810cdddc63ab8807783d70aca0f96b7e8ee6419
Author: jacopo-ronchi <jacopo.ronchi@unimib.it>
Date: 2025-11-05 13:04:12 +0000
Commit message:

 tests: a fix was included to allow the test involving selected KEGG pathways. This was necessary due to the change of the retrieved pathway graphs.
Package: MIRit
Commit: c1c57015170c37874e518b62732a2472d7ebd035
Author: jacopo-ronchi <jacopo.ronchi@unimib.it>
Date: 2025-11-05 13:02:43 +0000
Commit message:

 build: the README.md file has been updated.
Package: MIRit
Commit: dd1f58db298541efbde0533775203d45044a3ca1
Author: jacopo-ronchi <jacopo.ronchi@unimib.it>
Date: 2025-11-05 13:02:03 +0000
Commit message:

 build: GitHub workflows for automatic R CMD check, coverage test, and pkgdown website deploy have been included.
Package: MIRit
Commit: 7722b790570502b83eca351d45e0c32232e23614
Author: jacopo-ronchi <jacopo.ronchi@unimib.it>
Date: 2025-11-05 13:00:46 +0000
Commit message:

 build: the README.Rmd file is no longer used to maintain the README.md file.
Package: rGREAT
Commit: 36f069a781fccca5af6588d79bf70ac87e144c66
Author: Zuguang Gu <jokergoo@gmail.com>
Date: 2025-11-05 11:00:30 +0100
Commit message:

 merge
Package: rGREAT
Commit: 28bb92233fae0222294529f14e51b1009a3e1ece
Author: Zuguang Gu <jokergoo@gmail.com>
Date: 2025-11-05 10:58:39 +0100
Commit message:

 Merge branch 'master' into devel
Package: rGREAT
Commit: 8ee906da30c61db10553bd07d921cfa5aa991542
Author: Zuguang Gu <jokergoo@gmail.com>
Date: 2025-11-05 10:58:11 +0100
Commit message:

 fix docs
Package: Pirat
Commit: d3c7e09eeda22a2cfef83d1427a8664579bc99e1
Author: Lucas Etourneau <38471671+Lucas-Et@users.noreply.github.com>
Date: 2025-11-05 10:29:51 +0100
Commit message:

 Rename LBFGS.py to lbfgs.py
Package: MetaProViz
Commit: 8442f67b8d5f9f803eda9667198c02f27aa290cf
Author: deeenes <turei.denes@gmail.com>
Date: 2025-11-04 12:57:45 +0100
Commit message:

 Bump version: 3.99.19 → 3.99.20
Package: MetaProViz
Commit: d251227b752ec4aed96c2441aa6cd8e65fd97424
Author: deeenes <turei.denes@gmail.com>
Date: 2025-11-04 12:55:48 +0100
Commit message:

 Bump version: 3.99.18 → 3.99.19
Package: MetaProViz
Commit: 6cbeea84d6211b8257bd4efd9d44907950c00d2a
Author: deeenes <turei.denes@gmail.com>
Date: 2025-11-04 12:55:18 +0100
Commit message:

 Revert "code formatting: break long argument lists"

This reverts commit 06811fcdb5a4cc52185613d4bdf5a2e380ed8f37.
Package: beer
Commit: cbc6d3d4822e6ba5003afd689891876565eacc9b
Author: Athena Chen <achen@gatebio.com>
Date: 2025-11-04 19:02:26 -0500
Commit message:

 Merge pull request #12 from athchen/sync_repos

Sync Bioconductor and local repos
Package: beer
Commit: 34e6c8c948a8682a7e40570da85cf33c9a3fa969
Author: Athena Chen <athena_chen@gatebio.com>
Date: 2025-11-04 17:25:23 -0500
Commit message:

 Add JAGS dependency
Package: beer
Commit: bad3c3f5be10bf10f5367b155a40f570e5687438
Author: Athena Chen <athena_chen@gatebio.com>
Date: 2025-11-04 17:13:19 -0500
Commit message:

 Updated github actions
Package: beer
Commit: 466c473ac4d1b815eb09d2f2976b6c5e847d8302
Author: Athena Chen <athena_chen@gatebio.com>
Date: 2025-11-04 17:01:19 -0500
Commit message:

 Bumped package version to update BioC versioning
Package: beer
Commit: f2542e8ba9efb174766bebb605248ed6fd606ed3
Author: Athena Chen <achen@gatebio.com>
Date: 2025-11-04 16:58:10 -0500
Commit message:

 Merged origin changes into devel
Package: beer
Commit: 2b85b26d0c9f3f4724b5e4735dcfacbb14f9be1a
Author: Athena Chen <athena_chen@gatebio.com>
Date: 2025-11-04 16:38:51 -0500
Commit message:

 Updated roxygen documentation to correctly refer to progressr::progressor instead of progressr::progress
Package: beer
Commit: 6a31209959d885ec592b657de6ffc95388994aeb
Author: Athena Chen <athena_chen@gatebio.com>
Date: 2022-06-30 19:31:11 -0400
Commit message:

 Version bump
Package: beer
Commit: b590edddc45f274a9ef440f2f6f7dd9d968cf19a
Author: Athena Chen <athena_chen@gatebio.com>
Date: 2022-06-30 19:21:45 -0400
Commit message:

 Added MCMC diagnostic plot examples
Package: pathlinkR
Commit: e3eb62051f982e642459e4bf4034912073b77618
Author: Travis Blimkie <travis.m.blimkie@gmail.com>
Date: 2025-11-04 15:59:02 -0800
Commit message:

 pathwayEnrichment results column pathwayName is now a character, not a factor.
Package: MSstatsBioNet
Commit: e265c55af1e47160f332dbef80ce65a599b0b4ab
Author: tonywu1999 <wu.anthon@northeastern.edu>
Date: 2025-11-04 18:44:40 -0500
Commit message:

 feature(export-png): Add functionality to export networks as high quality PNGs (#62)
Package: Aerith
Commit: 3e3c251ba6c0af3b28fb989f89421d0fe6d4930d
Author: xyz1396 <1074082710@qq.com>
Date: 2025-11-04 17:09:34 -0600
Commit message:

 bump version
Package: Aerith
Commit: 256ab4eb07f8e03a223f30e21ff317d18e4ad1fe
Author: xyz1396 <1074082710@qq.com>
Date: 2025-11-04 17:02:43 -0600
Commit message:

 fix citation
Package: MSstatsBioNet
Commit: de9ed82fe974dc16b98ae9915ed512ee470f3f8a
Author: tonywu1999 <wu.anthon@northeastern.edu>
Date: 2025-11-04 18:03:02 -0500
Commit message:

 feature(curation): Add functionality to filter results by curation (#61)
Package: OSTA
Commit: f37c1f6f5b3eab41ebe0ef779a6ddfdb6e4489da
Author: HelenaLC <helena@crowell.eu>
Date: 2025-11-04 19:07:48 +0100
Commit message:

 test new trigger
Package: OSTA
Commit: c5585ab2b1cdc67e4e8b6a4e68805c24cdb637d1
Author: Helena L. Crowell <helena@crowell.eu>
Date: 2025-11-04 19:03:55 +0100
Commit message:

 Merge pull request #244 from almahmoud/new_trigger

New trigger
Package: OSTA
Commit: 6465dd83b6b6ca0959b075ca7852e29253dafcf0
Author: Alexandru Mahmoud <almahmoudresearch@gmail.com>
Date: 2025-11-04 16:58:31 +0100
Commit message:

 Use workflow_run trigger
Package: OSTA
Commit: 38a48257fc6e58c53595b86c25956fa45bd84f1f
Author: Alexandru Mahmoud <almahmoudresearch@gmail.com>
Date: 2025-11-04 16:54:16 +0100
Commit message:

 Ignore DESCRIPTION for biocbook
Package: GSVA
Commit: e01cffe6ef1ce98d275225be618aeedd9b6f7888
Author: Robert Castelo <robert.castelo@upf.edu>
Date: 2025-11-04 21:15:43 +0100
Commit message:

 Bump version
Package: GSVA
Commit: a559517399227463d3c573c5a4ca854067a95edb
Author: Robert Castelo <robert.castelo@upf.edu>
Date: 2025-11-04 21:15:17 +0100
Commit message:

 Several fixes in the code and the documentation
Package: Biostrings
Commit: b15bffbdbe6cb33c456c2989fa45b8f3c8ef1682
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2025-11-04 11:49:55 -0800
Commit message:

 Biostrings 2.79.2: More tweaks to XString/XStringSet comparison methods

o When comparing a BStringSet object with a DNAStringSet or RNAStringSet
  object, the former is no longer coerced to DNAStringSet or RNAStringSet.
  Instead, coercion now happens the other way around, that is, the latter
  now gets coerced to BStringSet. This means that:
  - This comparison can no longer fail. That's because coercion from
    DNAStringSet or RNAStringSet to BStringSet always works (unlike
    coercion in the opposite direction).
  - This comparison is no longer case insensitive.

o Replace all comparison methods between XString objects (13 in total)
  with 3 "Compare" methods.

o Comparison between an XString object and a character vector of
  arbitrary length is now supported.

o Refactor unit test for XString comparisons and extend coverage to all
  supported cases.

o Name unit test files accordingly to their corresponding R/*.R file

o Other minor tweaks to some unit tests.

o Add some missing aliases in various .Rd files.
Package: Biostrings
Commit: ab26c60f48f90b939aa64d7129beca28165aabc3
Author: Aidan Lakshman <30053966+ahl27@users.noreply.github.com>
Date: 2025-11-03 18:37:50 -0500
Commit message:

 fix: XString comparisons

* Updates comparison (==, !=, <=) to make XString objects compare against characters and other XString objects (adapted from XVector PR#6)

* adds testing for XString comparison operators
Package: MultiAssayExperiment
Commit: 908499dd0a4b98597aef375aa751fb8721fcc3a2
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-11-04 13:59:26 -0500
Commit message:

 version bump 1.37.1
Package: MultiAssayExperiment
Commit: c6772d09a984e8369f57528eed79b96e8c41fad0
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-11-04 13:59:20 -0500
Commit message:

 update RoxygenNote version
Package: MultiAssayExperiment
Commit: d80091aae47b553e491f0bed8ab067956cf4aced
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-11-04 13:59:12 -0500
Commit message:

 remove longFormat from package
Package: DOTSeq
Commit: 846f1dedac39a547f4db342ca919d0a28c720dd6
Author: lcscs12345 <lcscs12345@gmail.com>
Date: 2025-11-05 07:52:30 +1300
Commit message:

 add doi
Package: DOTSeq
Commit: 47ee60bb6c225766f394147f6c39c1d14b809d27
Author: lcscs12345 <lcscs12345@gmail.com>
Date: 2025-11-04 19:35:50 +1300
Commit message:

 add doi
Package: Aerith
Commit: 5c503404802a08a0fd28a03faec0777894f5974a
Author: xyz1396 <1074082710@qq.com>
Date: 2025-11-04 12:20:21 -0600
Commit message:

 add citation
Package: DMRcaller
Commit: 5ec5d133ed83e2b1776ab2ca41683cbad80dd11c
Author: nrzabet <r.zabet@qmul.ac.uk>
Date: 2025-11-04 18:15:34 +0000
Commit message:

 fixed bug in filterVMRsONT.R
Package: Aerith
Commit: fb5b4dcb8b4e61cda0d7be55261151f72d5a2504
Author: xyz1396 <1074082710@qq.com>
Date: 2025-11-04 11:52:24 -0600
Commit message:

 merge from upstream
Package: Aerith
Commit: 51cb983b07677508131293d614ff7da7438a01f9
Author: xyz1396 <1074082710@qq.com>
Date: 2025-11-04 11:45:50 -0600
Commit message:

 revise to 4 spaces for line indents, add citation
Package: Aerith
Commit: 0822bed2b3dce360a55c242064abca8b3c11bc78
Author: xyz1396 <1074082710@qq.com>
Date: 2025-11-04 10:36:18 -0600
Commit message:

 refine readme.md under windows, replace @ to slot(), add demo for precursor_peak_calculator_DIY_averagine
Package: Aerith
Commit: daab67b840523d8a06f010a53dc8876dce439064
Author: xyz1396 <1074082710@qq.com>
Date: 2025-10-28 11:35:29 -0500
Commit message:

 fix missing \value sections
Package: Aerith
Commit: 4b7c6e74383de7768a3a2f2cd3e25938d0fdaaa8
Author: xyz1396 <1074082710@qq.com>
Date: 2025-10-27 21:12:42 -0500
Commit message:

 fix missing \value sections
Package: Aerith
Commit: c76491be1ee5ac7da3903c40a8516476ca18f94b
Author: xyz1396 <1074082710@qq.com>
Date: 2025-10-27 02:26:16 -0500
Commit message:

 fix .git files limit error, and Empty or missing \value sections warning
Package: Aerith
Commit: 14be7828634932aa9a271cd192a7481f0bebc07b
Author: xyz1396 <1074082710@qq.com>
Date: 2025-10-23 13:41:31 -0500
Commit message:

 fix compile error on mac
Package: Aerith
Commit: 15b5517161a43614b682857b1ff2647bb730699c
Author: xyz1396 <1074082710@qq.com>
Date: 2025-10-10 03:34:58 -0500
Commit message:

 bump version
Package: Aerith
Commit: d423cb4368f82ca79da370b466315de178beab7a
Author: xyz1396 <1074082710@qq.com>
Date: 2025-10-10 00:10:27 -0500
Commit message:

 add demos to some rcpp function, optimize vignettes
Package: Aerith
Commit: 3cf2424b72aa823f399299f084e2db8a97a538bb
Author: xyz1396 <1074082710@qq.com>
Date: 2025-09-10 02:50:29 -0500
Commit message:

 bump version
Package: Aerith
Commit: 5cd74d768f19b7123a96ca38ffdd034925fdd11d
Author: xyz1396 <1074082710@qq.com>
Date: 2025-09-10 02:14:18 -0500
Commit message:

 revise document of plot-AAspectra
Package: Aerith
Commit: f88e03c1f55fce6d86728f974860b15e739ae091
Author: xyz1396 <1074082710@qq.com>
Date: 2025-09-09 21:08:54 -0500
Commit message:

 Remove configure.sh from tracking
Package: Aerith
Commit: 5d38018e4d0c2d539fea7ed172edc62e0fe75c2e
Author: xyz1396 <1074082710@qq.com>
Date: 2025-09-09 20:56:59 -0500
Commit message:

 revise document of plotAAspectra.R and plotProteinSipPct.R
Package: Aerith
Commit: ead6f5aed064a60e0a165b69d4e57bd2e8f4acbb
Author: xyz1396 <1074082710@qq.com>
Date: 2025-09-09 03:08:12 -0500
Commit message:

 Stop tracking vignettes/.gitignore
Package: Aerith
Commit: a2b62a6647d90678fb25c9084a6aec27dfd81a3e
Author: xyz1396 <1074082710@qq.com>
Date: 2025-09-09 03:04:31 -0500
Commit message:

 Stop tracking .vscode
Package: Aerith
Commit: 51eefb946f5d474fa83125480eaf0cba865d53cf
Author: xyz1396 <1074082710@qq.com>
Date: 2025-09-09 02:59:11 -0500
Commit message:

 Stop tracking .gitignore .Rbuildignore
Package: Aerith
Commit: 20fbafecbc821c3ee382f329c3193d2645d3474b
Author: xyz1396 <1074082710@qq.com>
Date: 2025-09-08 22:20:21 -0500
Commit message:

 change tests using built-in demo files
Package: Aerith
Commit: 2134f96cd01e73690666b3655dce216ba944a98b
Author: xyz1396 <1074082710@qq.com>
Date: 2025-09-08 00:19:45 -0500
Commit message:

 update Score-function-test-of-PSM.Rmd, Theoretic-spectra-generation-of-SIP-labeled-compound.Rmd, Theoretic-spectra-generation-of-SIP-labeled-peptide.Rmd, Visualization-of-SIP-proteomic-result.Rmd. Remove eval=FALSE chunks
Package: Aerith
Commit: 2cbcafad6acad8465de0129619f9bd0b4434b6d0
Author: xyz1396 <1074082710@qq.com>
Date: 2025-09-04 22:41:57 -0500
Commit message:

 update Aerith.Rmd, Input-data-format.Rmd, PSM-annotation-and-visualization.Rmd. Remove eval=FALSE chunks
Package: Aerith
Commit: 1e1b25e9ced78d33a014b5ef6bcb7a757522b8d4
Author: xyz1396 <1074082710@qq.com>
Date: 2025-09-04 02:14:33 -0500
Commit message:

 add filterIsotopicPeaksTopN, set OMP_STACKSIZE = "16M" when init, add parameters for plotMolecularIsotopes
Package: Aerith
Commit: ee0440910e72ede5817e68504b8a8d403731ef8b
Author: xyz1396 <1074082710@qq.com>
Date: 2025-07-16 20:26:39 -0500
Commit message:

 Merge branch 'main' into dev
Package: Aerith
Commit: 2e68fa7d7044a1d73ed2278b7082166e2b67a45d
Author: xyz1396 <1074082710@qq.com>
Date: 2025-07-15 21:48:55 -0500
Commit message:

 bump version
Package: Aerith
Commit: 7b85b0f4af9e78fa5635930fef7cd78852a55d61
Author: xyz1396 <1074082710@qq.com>
Date: 2025-07-15 21:39:12 -0500
Commit message:

 fix cran warnings
Package: Aerith
Commit: 86278f024894870448803ddd12680db66635860f
Author: xyz1396 <1074082710@qq.com>
Date: 2025-07-06 02:19:30 -0500
Commit message:

 bump version
Package: Aerith
Commit: 0561ae7433f60fe118ea521a1cbf204a27d11942
Author: xyz1396 <1074082710@qq.com>
Date: 2025-07-06 02:13:21 -0500
Commit message:

 Merge updates for .gitignore, plotPSMs.R, readScans.cpp, and test_scorePSM.R from dev branch for fix R CMD check error
Package: Aerith
Commit: 3690ddba0ac326da4e96665ee75cfcfd1645c5cb
Author: xyz1396 <1074082710@qq.com>
Date: 2025-07-06 01:26:32 -0500
Commit message:

 fix R CMD check error
Package: Aerith
Commit: 5b7976ae8734baca35afcfd4a58d4ae9291e4f01
Author: xyz1396 <1074082710@qq.com>
Date: 2025-06-13 21:03:37 -0500
Commit message:

 Merge branch 'dev'
Package: Aerith
Commit: 3b76f8694408b2fbe8f83d24677cadf82dd5cc86
Author: xyz1396 <1074082710@qq.com>
Date: 2025-06-13 20:58:52 -0500
Commit message:

 revise vignettes
Package: Aerith
Commit: d0dc7dfd95dc4b576fc4b01004bcc7305334f098
Author: xyz1396 <1074082710@qq.com>
Date: 2025-06-13 19:37:52 -0500
Commit message:

 remove extdata
Package: Aerith
Commit: 505058eb0e3cab829a44a6729a244476cee677bc
Author: xyz1396 <1074082710@qq.com>
Date: 2025-06-13 19:30:19 -0500
Commit message:

 revise vignette from dependent on rmd folder to inst/extdata folder
Package: Aerith
Commit: c094239fa09465c12106fd7cfc23189389a1064d
Author: XYZ(YiXiong) <1074082710@qq.com>
Date: 2025-05-27 00:12:48 -0500
Commit message:

 Update DESCRIPTION with GPL-3.0
Package: Aerith
Commit: 8085436a0b014f996cf5103aa4f73b224b04d9a8
Author: XYZ(YiXiong) <1074082710@qq.com>
Date: 2025-05-27 00:08:39 -0500
Commit message:

 Update LICENSE.md to markdown style
Package: Aerith
Commit: ab690e89d786b1e0b839b81d91bc383068a832ad
Author: XYZ(YiXiong) <1074082710@qq.com>
Date: 2025-05-26 23:58:23 -0500
Commit message:

 Create LICENSE.md
Package: Aerith
Commit: ade1b3c791e178d452a5fc2190286fa046468915
Author: XYZ(YiXiong) <1074082710@qq.com>
Date: 2025-05-26 23:50:59 -0500
Commit message:

 version bump
Package: Aerith
Commit: b923c98738f0f51ffe0007e404f0db74a7ee3157
Author: xyz1396 <1074082710@qq.com>
Date: 2025-05-26 03:32:46 -0500
Commit message:

 fix file path error of plotPSMs function on windows
Package: Aerith
Commit: 3bf7064eeaca157b9e497209792da6e47ece644d
Author: xyz1396 <1074082710@qq.com>
Date: 2025-05-26 01:22:35 -0500
Commit message:

 Add documentation for the exported functions recommended by Bioconductor.
Package: Aerith
Commit: 4e519962b75b9639076842a9cc166b8adef6fb23
Author: xyz1396 <1074082710@qq.com>
Date: 2025-05-21 12:34:01 -0500
Commit message:

 fix warning form BiocCheck::BiocCheck
Package: Aerith
Commit: d73eda880c2f51863845f5ccf614bde36d0aa1bc
Author: xyz1396 <1074082710@qq.com>
Date: 2025-05-21 03:48:21 -0500
Commit message:

 revise for bioconductor submitting
Package: Aerith
Commit: 9a9b4178f1d074bda505a1a3da97506f0b4ea491
Author: xyz1396 <1074082710@qq.com>
Date: 2025-05-05 00:54:50 -0500
Commit message:

 add link parameter for openmp on windows, add suggesting import of mzR and MSnbase
Package: Aerith
Commit: 11af7bb44219f58cb95ccafe83f305ac506fd4f8
Author: xyz1396 <1074082710@qq.com>
Date: 2025-04-16 12:18:51 -0500
Commit message:

 optimize readme
Package: Aerith
Commit: 348d6f2490bb8c62bcfbf4e8d2b0df3f230dce78
Author: xyz1396 <1074082710@qq.com>
Date: 2025-04-16 02:27:37 -0500
Commit message:

 add simplified calculation of WDPscore; revise spectral entropy to consider all peak intensity in real scan
Package: Aerith
Commit: 35f88206f57bfa61ceaa4220989611a9027a4653
Author: xyz1396 <1074082710@qq.com>
Date: 2025-03-11 02:23:32 -0500
Commit message:

 add vignettes for score function and PSMs results visual
Package: Aerith
Commit: 40d7d6cf3938f4f1c2871dc42623ec0ee96085a9
Author: xyz1396 <1074082710@qq.com>
Date: 2025-02-15 01:43:03 -0600
Commit message:

 vignette of PSM-annotation-and-visualization, add line_width and color setting of function plotAAsectra, add MVH score from myrimatch
Package: Aerith
Commit: 36b6fa1451fe43e25a473a764c54b4e27c0b2409
Author: xyz1396 <1074082710@qq.com>
Date: 2025-01-09 12:36:09 -0600
Commit message:

 add vignettes
Package: Aerith
Commit: 1c8b1468bfc1b4259d0212b227d5afc30cc0bde0
Author: xyz1396 <1074082710@qq.com>
Date: 2024-12-24 20:01:26 -0600
Commit message:

 add .vscode folder in track
Package: Aerith
Commit: 77d9974813dc4b7636ac5f83c3a9700586499411
Author: xyz1396 <1074082710@qq.com>
Date: 2024-12-20 02:13:00 -0600
Commit message:

 optimize PSM feature extract speed. add mentocarlo and fft isotope peak generate function
Package: Aerith
Commit: 61a33e8de49f3a42c637e7a733d0d0a434545f37
Author: xyz1396 <1074082710@qq.com>
Date: 2024-11-06 20:02:47 -0600
Commit message:

 refine spe2pepreader, featureextractor, addfunction for reading pepxml file
Package: Aerith
Commit: 516d2205c36ea75d04b08424a438e73e19af6319
Author: xyz1396 <1074082710@qq.com>
Date: 2024-08-13 11:42:42 -0500
Commit message:

 add function for PSM isotopic peaks annotation
Package: Aerith
Commit: 7799545dd5c5e9e2c24f5fb7638dfa3980c83eb4
Author: xyz1396 <1074082710@qq.com>
Date: 2024-06-10 23:37:31 -0500
Commit message:

 delet test.cpp
Package: Aerith
Commit: 02762d7004eeb6d2506bd179bbfcc190173847bf
Author: xyz1396 <1074082710@qq.com>
Date: 2024-06-10 23:24:46 -0500
Commit message:

 add  and 
 </pre>
    </div>
  
    

      Package: Aerith

      Commit: 00d0a3032569b3bd0757f407e655fa9ce0a975ff

      Author:  xyz1396 <1074082710@qq.com> 

      Date: 2024-06-10 23:16:27 -0500

      Commit message:


	  
		
 extract other features from MS1 level of sipros spe2pep file
 

    

  
    

      Package: Aerith

      Commit: 4858d7533a1009e5ac0e5a04b2f4ebbe29b9ab16

      Author:  xyz1396 <1074082710@qq.com> 

      Date: 2024-05-09 00:03:46 -0500

      Commit message:


	  
		
 add extract feature function and move to sipros5 spe2pep format with precursor scannumber
 

    

  
    

      Package: Aerith

      Commit: 09a7bd60e549d3eba0ec3caa41106fbb900dbed4

      Author:  xyz1396 <1074082710@qq.com> 

      Date: 2024-04-23 00:16:07 -0500

      Commit message:


	  
		
 extract isotopic abundance from MS1
 

    

  
    

      Package: Aerith

      Commit: 822cb1e48c98ece0400911943c075d23dd955852

      Author:  xyz1396 <1074082710@qq.com> 

      Date: 2024-04-04 00:19:13 -0500

      Commit message:


	  
		
 update to the FT2 file format of Raxport5 and spe2pep format of Sipros 5
 

    

  
    

      Package: Aerith

      Commit: 2cb46fe672ef2d93e44b774c9e3416c9e3fa91c2

      Author:  xyz1396 <1074082710@qq.com> 

      Date: 2024-01-25 19:19:27 -0600

      Commit message:


	  
		
 improve reading ft file performance
 

    

  
    

      Package: Aerith

      Commit: e5e663da91be042bdf02e328e9e626d8c0439b33

      Author:  xyz1396 <1074082710@qq.com> 

      Date: 2023-11-23 22:22:23 -0600

      Commit message:


	  
		
 for reading .Spe2PepFile
 

    

  
    

      Package: Aerith

      Commit: b17b05879cd28c35da1e6ea2ebc772f49a8e5610

      Author:  xyz1396 <1074082710@qq.com> 

      Date: 2023-04-13 23:25:36 -0500

      Commit message:


	  
		
 add denoise function, refine psm plot function
 

    

  
    

      Package: Aerith

      Commit: b57eb395c5da366d1eb049d05801e1ee758c25de

      Author:  xyz1396 <1074082710@qq.com> 

      Date: 2023-01-08 00:10:20 -0600

      Commit message:


	  
		
 revise read me again
 

    

  
    

      Package: Aerith

      Commit: 6fc28afa592a6a100a454875b3dfe90da519172c

      Author:  xyz1396 <1074082710@qq.com> 

      Date: 2023-01-08 00:09:03 -0600

      Commit message:


	  
		
 revise read me
 

    

  
    

      Package: Aerith

      Commit: effc5a937e8f008714c92cfc56afe19f49018a3a

      Author:  xyz1396 <1074082710@qq.com> 

      Date: 2023-01-06 23:44:59 -0600

      Commit message:


	  
		
 change read me
 

    

  
    

      Package: Aerith

      Commit: a5a7dffb87b6305c422054f0c7cdb1777700b07d

      Author:  xyz1396 <1074082710@qq.com> 

      Date: 2023-01-06 23:42:45 -0600

      Commit message:


	  
		
 upload files
 

    

  
    

      Package: Aerith

      Commit: f3ce4b1be5ea409856d8d1f30b125346f6708377

      Author:  Phase Technician XYZ <1074082710@qq.com> 

      Date: 2023-01-06 22:05:49 -0600

      Commit message:


	  
		
 Initial commit 

    

  
    

      Package: CNVMetrics

      Commit: d592e3d52adb257d07c712cfd387e60022f18ef5

      Author:  adeschen <adeschen@hotmail.com> 

      Date: 2025-11-04 12:21:51 -0500

      Commit message:


	  
		
 Version bump in devel
 

    

  
    

      Package: CNVMetrics

      Commit: 0595e73baa825f9e3e5e16c64bc2836336758d98

      Author:  adeschen <adeschen@hotmail.com> 

      Date: 2025-11-04 12:11:34 -0500

      Commit message:


	  
		
 Merge remote-tracking branch 'upstream/devel'
 

    

  
    

      Package: CNVMetrics

      Commit: aa3731adfc55b9761a4ac53d20a984c1383b794a

      Author:  adeschen <adeschen@hotmail.com> 

      Date: 2025-11-03 19:34:16 -0500

      Commit message:


	  
		
 Update check-bioc
 

    

  
    

      Package: CNVMetrics

      Commit: 4bff88e58071879863a45fd807784924422d5100

      Author:  adeschen <adeschen@hotmail.com> 

      Date: 2025-11-03 19:28:48 -0500

      Commit message:


	  
		
 Update check-bioc
 

    

  
    

      Package: CNVMetrics

      Commit: c3e9b5181e6158c6bde8dc3725ea563682867b26

      Author:  adeschen <adeschen@hotmail.com> 

      Date: 2025-11-03 19:23:00 -0500

      Commit message:


	  
		
 Update test-coverage
 

    

  
    

      Package: CNVMetrics

      Commit: 9b7161a7ce5a6dbf57f748ed22731632717f2756

      Author:  adeschen <adeschen@hotmail.com> 

      Date: 2025-11-03 19:13:59 -0500

      Commit message:


	  
		
 Update check-bioc
 

    

  
    

      Package: CNVMetrics

      Commit: 77ddafcf94f1a4448d12bc28d7a0e28edac947d7

      Author:  adeschen <adeschen@hotmail.com> 

      Date: 2025-11-03 19:10:58 -0500

      Commit message:


	  
		
 Update cehck-bioc
 

    

  
    

      Package: CNVMetrics

      Commit: 85e857eaddf09fb9790bf4ae89399164e95e0d13

      Author:  adeschen <adeschen@hotmail.com> 

      Date: 2025-11-03 18:33:09 -0500

      Commit message:


	  
		
 bug fix: Update itemize sections throughout all documentation
 

    

  
    

      Package: MSstatsBioNet

      Commit: afe0d21e354a4b6323030ed353fe3da15360508d

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

      Date: 2025-11-04 12:01:49 -0500

      Commit message:


	  
		
 version bump

1.3.0 to 1.3.1 

    

  
    

      Package: MSstatsBioNet

      Commit: 135cdea37c5eb40660f977b63f9cdeef9201d1b0

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

      Date: 2025-11-04 11:52:15 -0500

      Commit message:


	  
		
 refactor(getSubnetworkFromIndra): deprecate force_include_proteins parameter in favor of force_include_other (#60)

 

    

  
    

      Package: GSVAdata

      Commit: c11ec1562be901869009054028b935b400dbfb42

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

      Date: 2025-11-04 17:53:49 +0100

      Commit message:


	  
		
 Remove old microarray data from Armstrong et al. (2002) that is not used anymore in the vignette of GSVA and added a dependency on the microarray annotation package hgu95a.db
 

    

  
    

      Package: Pirat

      Commit: 91397bab5f079c18ffb755b8b7b808d3f203a6cf

      Author:  Lucas Etourneau <lucas.etourneau@berkeley.edu> 

      Date: 2025-11-04 17:42:22 +0100

      Commit message:


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

    

  
    

      Package: Pirat

      Commit: 57be4dff76c5f494e72d9fcb897c94a10eb107b6

      Author:  Lucas Etourneau <lucas.etourneau@berkeley.edu> 

      Date: 2025-11-04 12:03:21 +0100

      Commit message:


	  
		
 Adapt to new basilisk
 

    

  
    

      Package: Pirat

      Commit: 8f4540e51d7a44b282ba17c47e9bd5e6fd05520f

      Author:  Lucas Etourneau <lucas.etourneau@berkeley.edu> 

      Date: 2025-11-04 10:58:45 +0100

      Commit message:


	  
		
 Try other python
 

    

  
    

      Package: ChIPseeker

      Commit: be792409cc50ffba769e70aa64aea646f6fe9ffa

      Author:  Guangchuang Yu <guangchuangyu@gmail.com> 

      Date: 2025-11-04 22:26:51 +0800

      Commit message:


	  
		
 bump version
 

    

  
    

      Package: ChIPseeker

      Commit: 5535fab4ee7076f961a4b8eeb7980c63deaf3e9e

      Author:  Guangchuang Yu <guangchuangyu@gmail.com> 

      Date: 2025-11-04 22:19:15 +0800

      Commit message:


	  
		
 Merge pull request #265 from MingLi-929/devel

update test for change of txdb version 

    

  
    

      Package: ChIPseeker

      Commit: 0b85d6dab65e03c8579ca0f37e05e75ef049e8bc

      Author:  liming <limiang929@gmail.com> 

      Date: 2025-11-04 16:24:21 +0800

      Commit message:


	  
		
 update test for change of txdb version
 

    

  
    

      Package: ChIPseeker

      Commit: a073bc5481f6d286be23f2ab696cfee4412cac6a

      Author:  Guangchuang Yu <guangchuangyu@gmail.com> 

      Date: 2025-11-01 14:46:55 +0800

      Commit message:


	  
		
 update bioc version
 

    

  
    

      Package: hammers

      Commit: 2bbd134c65fe4e7808b53a026382239c56688d24

      Author:  andrei-stoica26 <andreistoica@foxmail.com> 

      Date: 2025-11-04 21:28:35 +0800

      Commit message:


	  
		
 Improved examples
 

    

  
    

      Package: CatsCradle

      Commit: 032f58b80ed864814a43e963399c5fb40db966e4

      Author:  AnnaLaddach <annaladdach@gmail.com> 

      Date: 2025-11-04 12:21:19 +0000

      Commit message:


	  
		
 version bump in devel
 

    

  
    

      Package: CatsCradle

      Commit: 5d1c036f63e9be4e1846b51e04337636f47e09f2

      Author:  AnnaLaddach <annaladdach@gmail.com> 

      Date: 2025-11-04 12:06:23 +0000

      Commit message:


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

    

  
    

      Package: CatsCradle

      Commit: 619e425ed75d274cd74f1b997a233744b950256c

      Author:  AnnaLaddach <annaladdach@gmail.com> 

      Date: 2025-11-04 12:04:54 +0000

      Commit message:


	  
		
 Change to exSeuratObj for compatibility with Seurat updates
 

    

  
    

      Package: Rarr

      Commit: 602dac2c347cb959e3df42dd57c32b20ccc7479a

      Author:  Hugo Gruson <10783929+Bisaloo@users.noreply.github.com> 

      Date: 2025-11-04 12:15:56 +0100

      Commit message:


	  
		
 Bump version
 

    

  
    

      Package: Rarr

      Commit: 13a174342cebb0a6d0128ecfbfc1f5ed294a58a5

      Author:  Hugo Gruson <10783929+Bisaloo@users.noreply.github.com> 

      Date: 2025-11-04 12:15:42 +0100

      Commit message:


	  
		
 Document endian news
 

    

  
    

      Package: Rarr

      Commit: 96c804f6dae9a0995917b9dd65f3556dcb394b33

      Author:  Hugo Gruson <10783929+Bisaloo@users.noreply.github.com> 

      Date: 2025-11-04 08:46:14 +0100

      Commit message:


	  
		
 Do not apply endian_codec when writing unicode
 

    

  
    

      Package: Rarr

      Commit: 81d1560505ce1e3977dd61c495642b3e1cd367aa

      Author:  Hugo Gruson <10783929+Bisaloo@users.noreply.github.com> 

      Date: 2025-10-31 19:47:40 +0100

      Commit message:


	  
		
 Make unicode a special case for endian codec
 

    

  
    

      Package: Rarr

      Commit: f5732264a2c280114d9ae135e67a5c1168ed0ca1

      Author:  Hugo Gruson <10783929+Bisaloo@users.noreply.github.com> 

      Date: 2025-10-31 19:47:17 +0100

      Commit message:


	  
		
 Force some readBin() for little endian
 

    

  
    

      Package: Rarr

      Commit: ee35fcbbc55c0d0baed32565d8e13cae5d2ccc62

      Author:  Hugo Gruson <10783929+Bisaloo@users.noreply.github.com> 

      Date: 2025-10-31 12:01:24 +0100

      Commit message:


	  
		
 Move .readVlenUTF8() to read_utils.R
 

    

  
    

      Package: Rarr

      Commit: 686852441740005f560f957ec77a1d6727002c1c

      Author:  Hugo Gruson <10783929+Bisaloo@users.noreply.github.com> 

      Date: 2025-10-28 20:02:19 +0100

      Commit message:


	  
		
 Skip DelayedArray tests on big endian

There is some strange results that hint at compatibility limitations lower in the stack
 

    

  
    

      Package: Rarr

      Commit: bc8e092e91d9242759e490daa1f7088cc815efa0

      Author:  Hugo Gruson <10783929+Bisaloo@users.noreply.github.com> 

      Date: 2025-10-28 17:16:39 +0100

      Commit message:


	  
		
 Implement endian codec
 

    

  
    

      Package: Rarr

      Commit: 640b950507c617588e038b0e7de6567525428182

      Author:  Hugo Gruson <10783929+Bisaloo@users.noreply.github.com> 

      Date: 2025-10-18 16:49:14 +0200

      Commit message:


	  
		
 Bump version
 

    

  
    

      Package: Rarr

      Commit: b59146b1abf4328db2ada524586e2f90008333bb

      Author:  Hugo Gruson <10783929+Bisaloo@users.noreply.github.com> 

      Date: 2025-10-18 16:49:04 +0200

      Commit message:


	  
		
 Mention transpose codec in NEWS
 

    

  
    

      Package: Rarr

      Commit: a93ce346e9bbcb4a1bc35b60e1c43a0c6c347aea

      Author:  Hugo Gruson <10783929+Bisaloo@users.noreply.github.com> 

      Date: 2025-10-31 09:44:44 +0100

      Commit message:


	  
		
 Run devtools::document()
 

    

  
    

      Package: Rarr

      Commit: 68b2dcbd7b1960307d991a2795cd1ea7c8c2f7ef

      Author:  Hugo Gruson <10783929+Bisaloo@users.noreply.github.com> 

      Date: 2025-10-18 16:43:11 +0200

      Commit message:


	  
		
 Test C-ordering roundtrip in both 2D and 3D
 

    

  
    

      Package: Rarr

      Commit: 07574108781297d15e68d7a7f248380ea6adb7a0

      Author:  Hugo Gruson <10783929+Bisaloo@users.noreply.github.com> 

      Date: 2025-10-18 16:42:56 +0200

      Commit message:


	  
		
 Add codec_transpose_decode()
 

    

  
    

      Package: Rarr

      Commit: 4fca3a9e2182740d4eea194acd91b8863745efe8

      Author:  Hugo Gruson <10783929+Bisaloo@users.noreply.github.com> 

      Date: 2025-10-18 16:40:25 +0200

      Commit message:


	  
		
 Add standalone test for codecs
 

    

  
    

      Package: Rarr

      Commit: 6e3a5a72fca981cd27275b320a1bd163ea680c9a

      Author:  Hugo Gruson <10783929+Bisaloo@users.noreply.github.com> 

      Date: 2025-10-17 15:43:35 +0200

      Commit message:


	  
		
 Make tranpose an explicit codec
 

    

  
    

      Package: Rarr

      Commit: c70b915eb15b1296c5dd9dbd3695e4ece0080d09

      Author:  Hugo Gruson <10783929+Bisaloo@users.noreply.github.com> 

      Date: 2025-10-17 16:09:01 +0200

      Commit message:


	  
		
 Add test for fill order in update_zarr_array()
 

    

  
    

      Package: hammers

      Commit: d815d5b4108ab9f61e6e5ca5ae1605aa010b073b

      Author:  andrei-stoica26 <andreistoica@foxmail.com> 

      Date: 2025-11-04 16:35:53 +0800

      Commit message:


	  
		
 Fixed tests
 

    

  
    

      Package: densvis

      Commit: 6d9f4c7441e3e04ad2233dfef1df50a661d8808b

      Author:  Alan O'Callaghan <alan.ocallaghan@outlook.com> 

      Date: 2025-11-04 08:09:39 +0000

      Commit message:


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

    

  
    

      Package: densvis

      Commit: 0d873976e154d3ea5e3a553e5e8617e0fb8ec09c

      Author:  Alan O'Callaghan <alan.ocallaghan@outlook.com> 

      Date: 2025-11-04 08:09:11 +0000

      Commit message:


	  
		
 Bump version
 

    

  
    

      Package: densvis

      Commit: 2876d50ef0a1770b630bccc840cae460aa0f4eea

      Author:  Alan O'Callaghan <alan.ocallaghan@outlook.com> 

      Date: 2025-11-04 08:07:57 +0000

      Commit message:


	  
		
 Merge branch 'devel' of github.com:alanocallaghan/densvis into devel
 

    

  
    

      Package: densvis

      Commit: 37a6b9dfbe6b1be76affcaeb1a3b3b6fa8bba9e3

      Author:  Alan O'Callaghan <alan.ocallaghan@outlook.com> 

      Date: 2025-10-24 05:50:18 +0100

      Commit message:


	  
		
 Update llvmlite version to 0.45.0

See #10 and https://github.com/numba/llvmlite/issues/1290
 

    

  
    

      Package: densvis

      Commit: 39d05b8da177baf5e301e704ff9ec5fb072f4f09

      Author:  Alan O'Callaghan <alan.ocallaghan@outlook.com> 

      Date: 2025-10-24 06:34:15 +0100

      Commit message:


	  
		
 Update package versions in basilisk.R 

    

  
    

      Package: densvis

      Commit: 43f8c237ce75c183927ee6548c69032b42de7301

      Author:  Alan O'Callaghan <alan.ocallaghan@outlook.com> 

      Date: 2025-10-24 06:28:48 +0100

      Commit message:


	  
		
 Update numpy version to 2.3.4 

    

  
    

      Package: densvis

      Commit: 0d409e623dbca2610ee2fc742a3a3d9ed04e905f

      Author:  Alan O'Callaghan <alan.ocallaghan@outlook.com> 

      Date: 2025-10-24 06:05:34 +0100

      Commit message:


	  
		
 Update llvmlite version constraint in basilisk.R 

    

  
    

      Package: densvis

      Commit: 991445075e4f4e6fcca0aa9a0a1e7b509d4ab908

      Author:  Alan O'Callaghan <alan.ocallaghan@outlook.com> 

      Date: 2025-10-24 06:01:10 +0100

      Commit message:


	  
		
 Update package versions for numba and numpy 

    

  
    

      Package: densvis

      Commit: 4eff40ea72964a493003917d9d00088d2d3fa062

      Author:  Alan O'Callaghan <alan.ocallaghan@outlook.com> 

      Date: 2025-10-24 05:50:18 +0100

      Commit message:


	  
		
 Update llvmlite version to 0.45.0

See #10 and https://github.com/numba/llvmlite/issues/1290 

    

  
    

      Package: densvis

      Commit: aa3ee7e0b60b2a9ad6013c61bb61f6140fa1d50a

      Author:  Alan O'Callaghan <alan.ocallaghan@outlook.com> 

      Date: 2025-10-23 15:25:10 +0100

      Commit message:


	  
		
 Merge branch 'devel' of github.com:alanocallaghan/densvis into devel
 

    

  
    

      Package: densvis

      Commit: 61e77f4f7594d3244ebeca026a392b734453bedb

      Author:  Alan O'Callaghan <alan.ocallaghan@outlook.com> 

      Date: 2025-10-23 15:25:06 +0100

      Commit message:


	  
		
 dispatch
 

    

  
    

      Package: MsBackendMetaboLights

      Commit: d9f698a7006cae72f35ccfad830dcd01427967ae

      Author:  Johannes Rainer <5506112+jorainer@users.noreply.github.com> 

      Date: 2025-11-04 08:35:39 +0100

      Commit message:


	  
		
 Merge pull request #12 from rformassspectrometry/jomain

refactor: increase download retries 

    

  
    

      Package: MsBackendMetaboLights

      Commit: 8c857b442c8398f8375c59eeab333880b0701110

      Author:  Johannes Rainer <johannes.rainer@gmail.com> 

      Date: 2025-11-04 07:58:21 +0100

      Commit message:


	  
		
 feat: export retry() function
 

    

  
    

      Package: MsBackendMetaboLights

      Commit: f9a170aae5690225e0f7e65592123685be84ae20

      Author:  Johannes Rainer <johannes.rainer@gmail.com> 

      Date: 2025-11-04 06:42:57 +0100

      Commit message:


	  
		
 fix: fix unit tests based on the changed defaults
 

    

  
    

      Package: MsBackendMetaboLights

      Commit: b12c90dc53b1ec4483c491773beed23bf2039694

      Author:  Johannes Rainer <johannes.rainer@gmail.com> 

      Date: 2025-11-03 16:26:01 +0100

      Commit message:


	  
		
 refactor: increase download retries
 

    

  
    

      Package: OSTA

      Commit: 7d91daa53f8ab1a787db24903fc8630e145ebd82

      Author:  Lukas Weber <lmweb012@gmail.com> 

      Date: 2025-11-04 10:30:41 +0800

      Commit message:


	  
		
 version and date
 

    

  
    

      Package: OSTA

      Commit: b3cba146a32da973cc97280e6cb28507dabe0f2c

      Author:  Lukas Weber <lmweb012@gmail.com> 

      Date: 2025-11-04 10:30:11 +0800

      Commit message:


	  
		
 Merge branch 'sandbox' into devel
 

    

  
    

      Package: OSTA

      Commit: 3974747d5d189b3bafda382c9e8dc0697b64be2e

      Author:  Lukas Weber <lmweb012@gmail.com> 

      Date: 2025-11-04 10:20:09 +0800

      Commit message:


	  
		
 revert version number
 

    

  
    

      Package: OSTA

      Commit: 0e29fb90256df8dc77b2329af7e14c6fb913f4a1

      Author:  Lukas Weber <lmweb012@gmail.com> 

      Date: 2025-11-03 22:23:38 +0800

      Commit message:


	  
		
 Merge pull request #243 from lmweber/timing

runtime recording 

    

  
    

      Package: OSTA

      Commit: b2ae3120b5c36c18fde594a97115b421ce2bbd32

      Author:  HelenaLC <helena@crowell.eu> 

      Date: 2025-11-03 15:04:08 +0100

      Commit message:


	  
		
 use helper-style variable name to stash runtimes
 

    

  
    

      Package: OSTA

      Commit: f8fafcbb5fb2d39f5a4ded75b90421389510fa73

      Author:  HelenaLC <helena@crowell.eu> 

      Date: 2025-11-03 15:01:47 +0100

      Commit message:


	  
		
 v1.0.1
 

    

  
    

      Package: OSTA

      Commit: bbb77163c18f25c277dcd84be1dcf74e798c1f1c

      Author:  HelenaLC <helena@crowell.eu> 

      Date: 2025-11-03 15:00:53 +0100

      Commit message:


	  
		
 uncomment code
 

    

  
    

      Package: OSTA

      Commit: afc9d55e736fd8871c32fc383e4cabe45187ba7e

      Author:  HelenaLC <helena@crowell.eu> 

      Date: 2025-11-03 14:59:48 +0100

      Commit message:


	  
		
 add chunk hooks to record runtimes & print out tabular summary in apx
 

    

  
    

      Package: OSTA

      Commit: 12d7032ca9044cba8039727da4c29a48548f2837

      Author:  HelenaLC <helena@crowell.eu> 

      Date: 2025-11-02 17:22:35 +0100

      Commit message:


	  
		
 omit loading tx files
 

    

  
    

      Package: OSTA

      Commit: 6b7d5af0ee5a16f49ae6f16eaf8843fb768e01dd

      Author:  HelenaLC <helena@crowell.eu> 

      Date: 2025-11-02 14:07:39 +0100

      Commit message:


	  
		
 + imports: scRNAseq
 

    

  
    

      Package: OSTA

      Commit: 6b7553b95983942e2320609509e6e76e164d0bfc

      Author:  Helena L. Crowell <helena@crowell.eu> 

      Date: 2025-11-02 09:14:32 +0100

      Commit message:


	  
		
 img-quality control updates; added img-workflow-cosmx

 

    

  
    

      Package: OSTA

      Commit: e4fa4fc16bf714b9c5a8cbc77fd7ea7b6dc75ebd

      Author:  HelenaLC <helena@crowell.eu> 

      Date: 2025-11-02 09:13:46 +0100

      Commit message:


	  
		
 Merge branch 'sandbox' into cosmx
 

    

  
    

      Package: OSTA

      Commit: 6105e9f9d74d276533b813a729c808449cbe60cc

      Author:  HelenaLC <helena@crowell.eu> 

      Date: 2025-11-02 09:12:21 +0100

      Commit message:


	  
		
 hlc revision
 

    

  
    

      Package: OSTA

      Commit: 653467ecb81606211a9f4a3a639d151dd5d4ff4e

      Author:  HelenaLC <helena@crowell.eu> 

      Date: 2025-11-01 09:14:01 +0100

      Commit message:


	  
		
 omit :::
 

    

  
    

      Package: OSTA

      Commit: 57016a00c10593ec3fda5b8aad67825c591741c0

      Author:  Davide Risso <risso.davide@gmail.com> 

      Date: 2025-10-31 17:36:34 +0100

      Commit message:


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

    

  
    

      Package: OSTA

      Commit: 6d5bd1310a24cab0fb29ef830814fb1a59069069

      Author:  Davide Risso <risso.davide@gmail.com> 

      Date: 2025-10-31 17:33:05 +0100

      Commit message:


	  
		
 Minor changes
 

    

  
    

      Package: OSTA

      Commit: 41b7b1f6cac46078bbc0f9f93aa325f6a06cda21

      Author:  Davide Risso <risso.davide@gmail.com> 

      Date: 2025-10-31 16:58:00 +0100

      Commit message:


	  
		
 Cosmx Workflow
 

    

  
    

      Package: OSTA

      Commit: 1c25ac2cd6c36de77cf4fb74cc3994b994425dac

      Author:  Helena L. Crowell <helena@crowell.eu> 

      Date: 2025-10-31 08:11:57 +0100

      Commit message:


	  
		
 +IF in ind-image-analysis

 

    

  
    

      Package: OSTA

      Commit: 7c62e8d1cbd1023dd069c8600a6f305e4c91f741

      Author:  HelenaLC <helena@crowell.eu> 

      Date: 2025-10-31 08:11:13 +0100

      Commit message:


	  
		
 aesthetic revision to ease readability
 

    

  
    

      Package: OSTA

      Commit: fdc9caecfaba47b50ad1bcbb7726e5b3a3e16f63

      Author:  Davide Risso <risso.davide@gmail.com> 

      Date: 2025-10-29 12:02:50 +0100

      Commit message:


	  
		
 Add details on SpaceTrooper
 

    

  
    

      Package: OSTA

      Commit: 086963fcce528cd2e86063eb8649bbd75fbb2a7e

      Author:  billila <ilaria.billato@studenti.unipd.it> 

      Date: 2025-10-28 16:39:27 +0100

      Commit message:


	  
		
 fix minor
 

    

  
    

      Package: OSTA

      Commit: d736b86642b57efa459bff2c9a01ba4268e9f9fd

      Author:  billila <ilaria.billato@studenti.unipd.it> 

      Date: 2025-10-28 16:36:48 +0100

      Commit message:


	  
		
 fix minor
 

    

  
    

      Package: OSTA

      Commit: 12e6641c8e989c4660b13a7471fb6f51682bf880

      Author:  Davide Risso <risso.davide@gmail.com> 

      Date: 2025-10-27 15:56:45 +0100

      Commit message:


	  
		
 Cosmx workflow
 

    

  
    

      Package: OSTA

      Commit: 26f5ff835571e347cb1f9d33717f6614444771f2

      Author:  Davide Risso <risso.davide@gmail.com> 

      Date: 2025-10-27 15:55:47 +0100

      Commit message:


	  
		
 Merge branch 'sandbox' of github.com:drisso/PrinciplesSTA into sandbox
 

    

  
    

      Package: OSTA

      Commit: cae44658e941b03c1a5dc0ceb55b2723190980d2

      Author:  billila <ilaria.billato@studenti.unipd.it> 

      Date: 2025-10-27 12:40:36 +0100

      Commit message:


	  
		
 add bibliography
 

    

  
    

      Package: OSTA

      Commit: 180cf539d82aa5602bbb6bed02157ad751a608d3

      Author:  Ilaria Billato <78036851+billila@users.noreply.github.com> 

      Date: 2025-10-27 12:03:35 +0100

      Commit message:


	  
		
 Merge branch 'lmweber:devel' into devel
 

    

  
    

      Package: OSTA

      Commit: d78458a5aa9c884c991e0590207abf3d3ca1b086

      Author:  billila <ilaria.billato@studenti.unipd.it> 

      Date: 2025-10-21 11:24:19 +0200

      Commit message:


	  
		
 add immunofluorescence part
 

    

  
    

      Package: OSTA

      Commit: 5e9d61769c3f284e7b17ed381b680ee8150037cf

      Author:  Davide Risso <risso.davide@gmail.com> 

      Date: 2025-10-20 11:04:01 +0200

      Commit message:


	  
		
 SpaceTrooper is now in Bioconductor
 

    

  
    

      Package: DOTSeq

      Commit: a88fe9e5ee8ef2a32a4a5e6b4028a25499b6d2d7

      Author:  lcscs12345 <lcscs12345@gmail.com> 

      Date: 2025-11-04 15:08:36 +1300

      Commit message:


	  
		
 add pasilla
 

    

  
    

      Package: DOTSeq

      Commit: 38e729b6498bd7ae548b62972df9b52b7fdeefd4

      Author:  lcscs12345 <lcscs12345@gmail.com> 

      Date: 2025-11-04 14:54:22 +1300

      Commit message:


	  
		
 add pasilla
 

    

  
    

      Package: DOTSeq

      Commit: 8dee2dc5314eb07e59ab35ab0f96a368c20c1170

      Author:  lcscs12345 <lcscs12345@gmail.com> 

      Date: 2025-11-04 14:25:37 +1300

      Commit message:


	  
		
 add pasilla
 

    

  
    

      Package: DOTSeq

      Commit: bac9a08dfda4e6aa10fd0c11d252ce5fc484fded

      Author:  lcscs12345 <lcscs12345@gmail.com> 

      Date: 2025-11-04 14:19:57 +1300

      Commit message:


	  
		
 add pasilla
 

    

  
    

      Package: PhyloProfile

      Commit: afcd9c43bfc4ac89f1a77c1643b2a23440a7ad37

      Author:  AnnamTran <trvinh@gmail.com> 

      Date: 2025-11-03 23:28:53 +0100

      Commit message:


	  
		
 fixed core gene ident with strain; fixed cus profile with 1000+ genes/taxa
 

    

  
    

      Package: BSgenome

      Commit: c2fc0dbd3c611e8863caa1644e2b38b468a3d230

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

      Date: 2025-11-03 14:15:06 -0800

      Commit message:


	  
		
 BSgenome 1.79.1: Post-release cleanup

Functions BSgenome::forgeMasksFile, BSgenome::forgeSeqFiles,
BSgenome::forgeSeqlengthsRdaFile, BSgenome::forgeSeqlengthsRdsFile,
BSgenome::forgeBSgenomeDataPkg, and BSgenome::forgeMaskedBSgenomeDataPkg
are now formally defunct in BioC 3.23 after being deprecated in BioC 3.22.
 

    

  
    

      Package: DOTSeq

      Commit: 0c199eed545490dbce32176959534c2e0c0c104b

      Author:  lcscs12345 <lcscs12345@gmail.com> 

      Date: 2025-11-04 10:09:31 +1300

      Commit message:


	  
		
 change email
 

    

  
    

      Package: mobileRNA

      Commit: b58cca24d0f89b5500b8778d1b92175892816fd6

      Author:  KJeynesCupper <kejc@illinois.edu> 

      Date: 2025-11-03 11:51:23 -0600

      Commit message:


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

# Conflicts:
#	DESCRIPTION
 

    

  
    

      Package: mobileRNA

      Commit: d30185c3993ed131507a1b3f5cd7246f833d158b

      Author:  KJeynesCupper <kejc@illinois.edu> 

      Date: 2025-11-03 11:45:01 -0600

      Commit message:


	  
		
 VERSION CONTROL
 

    

  
    

      Package: mobileRNA

      Commit: 0d692d29a2803fa31322a797161c77f96c92f205

      Author:  KJeynesCupper <kejc@illinois.edu> 

      Date: 2025-11-03 11:36:01 -0600

      Commit message:


	  
		
 Seqinfo to namespace

Namespace dependency missing from DESCRIPTION Imports/Depends entries: ‘Seqinfo’
 

    

  
    

      Package: smoppix

      Commit: fe4ac0dcb7829d0fe77454f7509b211f49c984b9

      Author:  stijn <stijn.hawinkel@psb.ugent.be> 

      Date: 2025-11-03 18:32:49 +0100

      Commit message:


	  
		
 version chqnge

Merge branch 'devel' of git.bioconductor.org:packages/smoppix
# Please enter a commit message to explain why this merge is necessary,
# especially if it merges an updated upstream into a topic branch.
#
# Lines starting with '#' will be ignored, and an empty message aborts
# the commit.
 

    

  
    

      Package: smoppix

      Commit: 5733e3d48a37a5b664a0588e3532f7c7756560de

      Author:  stijn <stijn.hawinkel@psb.ugent.be> 

      Date: 2025-11-03 18:30:46 +0100

      Commit message:


	  
		
 R version bump
 

    

  
    

      Package: smoppix

      Commit: aa6894c2938bc1847d05eb6c820700f92a53490b

      Author:  stijn <stijn.hawinkel@psb.ugent.be> 

      Date: 2025-11-03 18:20:09 +0100

      Commit message:


	  
		
 Document plotCells
 

    

  
    

      Package: smoppix

      Commit: d724a7f76635d897b072cdd16150154b1b1005ef

      Author:  stijn <stijn.hawinkel@psb.ugent.be> 

      Date: 2025-11-03 17:25:51 +0100

      Commit message:


	  
		
 Remove weird feature number restriction
 

    

  
    

      Package: smoppix

      Commit: c09cb4412cb43e4121236e20e86fa33c69443e60

      Author:  stijn <stijn.hawinkel@psb.ugent.be> 

      Date: 2025-10-27 16:50:57 +0100

      Commit message:


	  
		
 More space for the scale bar
 

    

  
    

      Package: LACHESIS

      Commit: 0cbd1e498faa282f4ec2522ea06ff9a363bed98e

      Author:  VerenaK90 <ve.koerber@web.de> 

      Date: 2025-11-03 15:21:55 +0000

      Commit message:


	  
		
 version bump
 

    

  
    

      Package: eisaR

      Commit: 7a06cdb610f7b6cd6065d1fc0e20c1abbefde352

      Author:  mbstadler <stadler.michael@gmail.com> 

      Date: 2025-11-03 15:29:00 +0100

      Commit message:


	  
		
 skip missing-library tests also on r-universe

Co-authored-by: Charlotte Soneson <charlottesoneson@gmail.com>
Co-authored-by: Michael Stadler <stadler.michael@gmail.com>
 

    

  
    

      Package: MetaProViz

      Commit: 5d2405206e5945f166149fee824d1798fccdd2b3

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

      Date: 2025-11-03 13:15:41 +0100

      Commit message:


	  
		
 nothing
 

    

  
    

      Package: MsBackendSql

      Commit: c6833d3d76cbec02dd3decba0abd43e8736da54b

      Author:  Johannes Rainer <5506112+jorainer@users.noreply.github.com> 

      Date: 2025-11-03 12:57:03 +0100

      Commit message:


	  
		
 Merge pull request #33 from rformassspectrometry/jomain

Ensure peaks are ordered correctly with longForm() and duckdb 

    

  
    

      Package: MsBackendSql

      Commit: 2a72440121346993bf607cf9cd8d22bbcb7b9f4c

      Author:  Johannes Rainer <johannes.rainer@gmail.com> 

      Date: 2025-11-03 11:47:38 +0100

      Commit message:


	  
		
 update version
 

    

  
    

      Package: MsBackendSql

      Commit: 0d4a5ed1a19697b809f670eb594ee628d788140c

      Author:  Johannes Rainer <johannes.rainer@gmail.com> 

      Date: 2025-11-03 11:42:40 +0100

      Commit message:


	  
		
 ci: use devel versions of R
 

    

  
    

      Package: MsBackendSql

      Commit: d63ecc6eced96b231840dea241d4441197f196d1

      Author:  Johannes Rainer <johannes.rainer@gmail.com> 

      Date: 2025-11-03 11:39:40 +0100

      Commit message:


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

    

  
    

      Package: MsBackendSql

      Commit: 085ff671b208fde89c229026b4ffbe8d15399da3

      Author:  Johannes Rainer <johannes.rainer@gmail.com> 

      Date: 2025-11-03 11:37:47 +0100

      Commit message:


	  
		
 refactor: use ORDER BY with JOIN query for duckdb

- For `longForm()` and duckdb backend: include an ORDER BY statement to the
  JOIN query (issue #31).
 

    

  
    

      Package: MsBackendSql

      Commit: 69e8aa564680319b88d820958261179713798923

      Author:  Johannes Rainer <johannes.rainer@gmail.com> 

      Date: 2025-10-30 17:16:23 +0100

      Commit message:


	  
		
 refactor: prepare full duckdb support (issue #31)

- For storage of peaks data in long-form add a peak_id_ database table column
  depending on the database used (e.g. duckdb).
 

    

  
    

      Package: spatialFDA

      Commit: bd8c241aacd70eec883ad5cbea6d3cd804744c87

      Author:  mjemons <martin.emons@gmail.com> 

      Date: 2025-11-03 11:07:08 +0100

      Commit message:


	  
		
 removed scam option added news to all changes so far
 

    

  
    

      Package: spatialFDA

      Commit: a174d57bcb749c1c1c6fa111594d44793ae06ffd

      Author:  mjemons <martin.emons@gmail.com> 

      Date: 2025-11-03 09:28:55 +0100

      Commit message:


	  
		
 merge version Bump
 

    

  
    

      Package: spatialFDA

      Commit: 570ed9e8a3d1785bc6230848fcbcf895682f7e0f

      Author:  mjemons <martin.emons@gmail.com> 

      Date: 2025-10-31 11:31:06 +0100

      Commit message:


	  
		
 Merge branch 'devel' of github.com:mjemons/spatialFDA into devel
merge formula fix and prefit arg passing
 

    

  
    

      Package: spatialFDA

      Commit: e6916ca33e526adec47fc5767fd1c5da8a2b3acf

      Author:  mjemons <martin.emons@gmail.com> 

      Date: 2025-10-31 11:30:10 +0100

      Commit message:


	  
		
 pass arguments to prefit
 

    

  
    

      Package: spatialFDA

      Commit: 2a7217d5929e504f92d8fc41b0ceb4bd9e18e094

      Author:  Martin Emons <55688661+mjemons@users.noreply.github.com> 

      Date: 2025-10-28 16:14:14 +0100

      Commit message:


	  
		
 Merge pull request #21 from mjemons/FixEnvCall

fix environemnt problems 

    

  
    

      Package: spatialFDA

      Commit: f1f50098ac06dd3c50dc4f20804917f9d8bb677c

      Author:  mjemons <martin.emons@gmail.com> 

      Date: 2025-10-28 15:39:05 +0100

      Commit message:


	  
		
 fix environemnt problems
 

    

  
    

      Package: spatialFDA

      Commit: fb7e3bdff11d49a583166ce3b44239ff307b1369

      Author:  mjemons <martin.emons@gmail.com> 

      Date: 2025-10-26 13:44:04 +0100

      Commit message:


	  
		
 option to sqrt transform weights
 

    

  
    

      Package: spatialFDA

      Commit: d6a512ea7b313360080efa48705f64eea5999362

      Author:  mjemons <martin.emons@gmail.com> 

      Date: 2025-10-23 12:58:02 +0200

      Commit message:


	  
		
 changed cutoff calculation
 

    

  
    

      Package: spatialFDA

      Commit: 5789b3c953b4fdc346505c50ecd94c4f51ad2a7a

      Author:  mjemons <martin.emons@gmail.com> 

      Date: 2025-10-22 18:44:34 +0200

      Commit message:


	  
		
 implemented AR1.rho parameter
 

    

  
    

      Package: spatialFDA

      Commit: 59fa04d9d031d17a0cc1b4cdcb806a34d46d74a3

      Author:  mjemons <martin.emons@gmail.com> 

      Date: 2025-10-22 11:20:27 +0200

      Commit message:


	  
		
 implemented shape constraint with scam
 

    

  
    

      Package: spatialFDA

      Commit: 4fb29b64c13d12f4d2cce54fb0a81df683bbb79f

      Author:  mjemons <martin.emons@gmail.com> 

      Date: 2025-10-20 17:51:56 +0200

      Commit message:


	  
		
 remove message statement
 

    

  
    

      Package: spatialFDA

      Commit: 6c6aec9b08b523dbfb2d6aa27b5f7655389414c9

      Author:  mjemons <martin.emons@gmail.com> 

      Date: 2025-10-20 17:48:02 +0200

      Commit message:


	  
		
 fix ID
 

    

  
    

      Package: spatialFDA

      Commit: ad271eee4dc13b25dbea666c7fee7565ef20a945

      Author:  mjemons <martin.emons@gmail.com> 

      Date: 2025-10-20 17:42:57 +0200

      Commit message:


	  
		
 fix call of ID variable
 

    

  
    

      Package: spatialFDA

      Commit: 6f0ae0493bb2eb648ecb512e3f67402807fa1ff1

      Author:  mjemons <martin.emons@gmail.com> 

      Date: 2025-10-20 17:30:40 +0200

      Commit message:


	  
		
 fix Errors in UpperDeltaProb
 

    

  
    

      Package: spatialFDA

      Commit: 1d97e6b0ed5f8a8bcd2c9a0b8a93619340520a60

      Author:  mjemons <martin.emons@gmail.com> 

      Date: 2025-10-20 16:40:41 +0200

      Commit message:


	  
		
 for G functions, add a filtering of the constant 1 part
 

    

  
    

      Package: spatialFDA

      Commit: e107c9d2dae62346733c77149814a1dff4cbc5d3

      Author:  mjemons <martin.emons@gmail.com> 

      Date: 2025-10-16 10:36:27 +0200

      Commit message:


	  
		
 pass H explicitly to the gam
 

    

  
    

      Package: spatialFDA

      Commit: 004a9665455b37ee76bf5808155ebdc04c629001

      Author:  mjemons <martin.emons@gmail.com> 

      Date: 2025-10-16 08:06:41 +0200

      Commit message:


	  
		
 correct dimenions for H with prefit
 

    

  
    

      Package: spatialFDA

      Commit: 6ebc362cac881c98bd19207507045e53562dd8d9

      Author:  mjemons <martin.emons@gmail.com> 

      Date: 2025-10-15 20:52:24 +0200

      Commit message:


	  
		
 add option to define a ridge penalty
 

    

  
    

      Package: spatialFDA

      Commit: 95b67b4bda060fcac067988697129e5a37bed89f

      Author:  mjemons <martin.emons@gmail.com> 

      Date: 2025-10-13 11:30:08 +0200

      Commit message:


	  
		
 bug fix for GAM
 

    

  
    

      Package: alabaster.base

      Commit: 1d97e98f8966c6f7124c7c0114113c0cd584054f

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

      Date: 2025-11-02 23:55:31 -0800

      Commit message:


	  
		
 Set default bit64conversion= argument for updated rhdf5.
 

    

  
    

      Package: SVP

      Commit: e8643518b2e10dc19c90710c95218fd6f68d9320

      Author:  xiangpin <xshuangbin@163.com> 

      Date: 2025-11-03 15:03:04 +0800

      Commit message:


	  
		
 bump version and update news
 

    

  
    

      Package: SVP

      Commit: 1d4c0b14d805ea653f49c0bc12f6c68bcaa72f33

      Author:  xiangpin <xshuangbin@163.com> 

      Date: 2025-06-15 17:13:00 +0800

      Commit message:


	  
		
 bump version
 

    

  
    

      Package: SVP

      Commit: 951bd752e1d1a7c50bcb26a2ab321d2a531f1778

      Author:  xiangpin <xshuangbin@163.com> 

      Date: 2025-06-15 17:11:04 +0800

      Commit message:


	  
		
 update the visualization of plot_lisa_feature
 

    

  
    

      Package: SVP

      Commit: a49b5bf82b1729eb506dbde9b4f8dedc3401ae50

      Author:  xiangpin <xshuangbin@163.com> 

      Date: 2025-06-15 16:28:54 +0800

      Commit message:


	  
		
 Merge branch 'main' into RELEASE_3_21
 

    

  
    

      Package: SVP

      Commit: 795043f6c238032353361c82d613e56245adb696

      Author:  xushuangbin <xshuangbin@163.com> 

      Date: 2025-06-13 19:02:22 +0800

      Commit message:


	  
		
 update knn.k.use arg
 

    

  
    

      Package: SVP

      Commit: 5bbb304924c679fef74e0e64e896f1fe0f7abfee

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

      Date: 2025-05-08 12:30:33 -0400

      Commit message:


	  
		
 Version bump to trigger rebuilding/propagation of Windows and Mac binaries
 

    

  
    

      Package: SVP

      Commit: ecd5f0785ccd0239a037b3a3ac90a335ca34a3e8

      Author:  xushuangbin <xshuangbin@163.com> 

      Date: 2025-04-17 17:06:19 +0800

      Commit message:


	  
		
 bioc3.21 release
 

    

  
    

      Package: sesameData

      Commit: 6ec5de603daa0c31a1eb02765b7f8bb7c3094219

      Author:  Wanding Zhou <zhouwanding@gmail.com> 

      Date: 2025-11-02 20:50:11 -0500

      Commit message:


	  
		
 bump to 1.29.1, updated data using zenodo upload
 

    

  
    

      Package: tidySpatialExperiment

      Commit: 9871264f23563e1a5d8850e4845cc8c6cd3b3ad7

      Author:  William Hutchison <william.8191@fastmail.com> 

      Date: 2025-11-03 11:43:39 +1100

      Commit message:


	  
		
 Version up
 

    

  
    

      Package: tidySpatialExperiment

      Commit: ab73876ae0767bae980c1e2832b4037816fa9ca3

      Author:  William Hutchison <william.8191@fastmail.com> 

      Date: 2025-11-03 11:43:16 +1100

      Commit message:


	  
		
 Merge BioConductor repository version bumps
 

    

  
    

      Package: tidySpatialExperiment

      Commit: fa6d5f3d0645b427c4aa7084db1ef2f577e4e9a8

      Author:  william-hutchison <william.8191@fastmail.com> 

      Date: 2025-11-03 11:37:00 +1100

      Commit message:


	  
		
 Merge pull request #47 from william-hutchison/remove-conflicting-functions

Remove conflicting functions 

    

  
    

      Package: tidySpatialExperiment

      Commit: 069aeb8771c088f7197ac183d05195600db8cc38

      Author:  William Hutchison <william.8191@fastmail.com> 

      Date: 2025-11-03 11:22:02 +1100

      Commit message:


	  
		
 Version up
 

    

  
    

      Package: tidySpatialExperiment

      Commit: 77c2b87bc7d544f92c1398e40fb92c1dfc6cad5f

      Author:  William Hutchison <william.8191@fastmail.com> 

      Date: 2025-11-03 11:21:47 +1100

      Commit message:


	  
		
 Udpate 'bind_cols()' and 'bind_rows()' tests
 

    

  
    

      Package: tidySpatialExperiment

      Commit: 1736874d0451cf19b93d42edbab18cfb7d8f6c25

      Author:  William Hutchison <william.8191@fastmail.com> 

      Date: 2025-11-03 11:15:29 +1100

      Commit message:


	  
		
 Udpate 'bind_cols()' and 'bind_rows()' examples
 

    

  
    

      Package: tidySpatialExperiment

      Commit: b5569de1409f691bb4388fb76a909049a05c81c5

      Author:  William Hutchison <william.8191@fastmail.com> 

      Date: 2025-10-31 17:11:18 +1100

      Commit message:


	  
		
 Version up
 

    

  
    

      Package: tidySpatialExperiment

      Commit: 72509422a37c352fbc2ab33f46a21e9fd0828d6c

      Author:  William Hutchison <william.8191@fastmail.com> 

      Date: 2025-10-31 17:11:00 +1100

      Commit message:


	  
		
 Move ttservice to Depends field
 

    

  
    

      Package: tidySpatialExperiment

      Commit: 540688a56bba7d7782e5d36eb29cddeda1ce4eb1

      Author:  William Hutchison <william.8191@fastmail.com> 

      Date: 2025-10-31 16:33:39 +1100

      Commit message:


	  
		
 Version up
 

    

  
    

      Package: tidySpatialExperiment

      Commit: 66dfb4e59d883ad567ace4397db2eade0b389ac5

      Author:  William Hutchison <william.8191@fastmail.com> 

      Date: 2025-10-31 16:33:24 +1100

      Commit message:


	  
		
 Add missing function import
 

    

  
    

      Package: tidySpatialExperiment

      Commit: 6dfa2a18da90b818b6b46fc2de03a78983e41148

      Author:  William Hutchison <william.8191@fastmail.com> 

      Date: 2025-10-31 16:21:26 +1100

      Commit message:


	  
		
 Remove redefinition of 'bind_cols()' and 'bind_rows()'
 

    

  
    

      Package: tidySpatialExperiment

      Commit: 7261a13bd29b467269aa84fcc8e8a842c96739c8

      Author:  William Hutchison <william.8191@fastmail.com> 

      Date: 2025-10-31 16:09:13 +1100

      Commit message:


	  
		
 Add missing function import
 

    

  
    

      Package: tidySpatialExperiment

      Commit: 83be70103f67dff8f12ce5c5d2fdc9d8181615d3

      Author:  William Hutchison <william.8191@fastmail.com> 

      Date: 2025-10-31 16:04:47 +1100

      Commit message:


	  
		
 Remove unused import
 

    

  
    

      Package: tidySpatialExperiment

      Commit: e0d8f0a68049b82aa752c2235efc3949e39cb381

      Author:  William Hutchison <william.8191@fastmail.com> 

      Date: 2025-10-31 16:00:03 +1100

      Commit message:


	  
		
 Remove redefinition of 'aggregate_cells()'
 

    

  
    

      Package: tidySpatialExperiment

      Commit: e8f82a3f56a33c3843ccb6b37acda1c1f6928b36

      Author:  William Hutchison <william.8191@fastmail.com> 

      Date: 2025-10-31 15:57:16 +1100

      Commit message:


	  
		
 Consolidate unnesting functions
 

    

  
    

      Package: SplicingGraphs

      Commit: 8abbef909f4c249fc62e4aa05c89b3a1fcaefb2d

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

      Date: 2025-11-02 09:50:45 -0800

      Commit message:


	  
		
 drop use of precomputed SplicingGraphs object 'sg_with_reads' in vignette
 

    

  
    

      Package: SplicingGraphs

      Commit: 0f477f251da074de5f54a7072a6f2cb54307089c

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

      Date: 2025-11-02 01:00:36 -0700

      Commit message:


	  
		
 SplicingGraphs 1.51.1: Repair vignette

The latest TxDb.Hsapiens.UCSC.hg19.knownGene (v 3.22.1, based on UCSC
track GENCODE V48lift37) is no longer suitable for the SplicingGraphs
vignette so we've switched to TxDb.Hsapiens.UCSC.hg19.refGene.
 

    

  
    

      Package: clusterProfiler

      Commit: c6e07d0e9c363a5102ca04de419b7d72bf739495

      Author:  Guangchuang Yu <guangchuangyu@gmail.com> 

      Date: 2025-11-01 22:45:20 +0800

      Commit message:


	  
		
 bump version
 

    

  
    

      Package: clusterProfiler

      Commit: 8669269d14d4f948d5975e56e6fb2d44367b885c

      Author:  Guangchuang Yu <guangchuangyu@gmail.com> 

      Date: 2025-11-01 22:43:26 +0800

      Commit message:


	  
		
 bump version
 

    

  
    

      Package: clusterProfiler

      Commit: f0243622a9d885dca2a44bd69383f2a3a76fe4ba

      Author:  Guangchuang Yu <guangchuangyu@gmail.com> 

      Date: 2025-10-30 16:10:09 +0800

      Commit message:


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

    

  
    

      Package: clusterProfiler

      Commit: 3e5d5a4b2ae2a486cbf72b7c2f540e0fbf4f0315

      Author:  Guangchuang Yu <guangchuangyu@gmail.com> 

      Date: 2025-10-30 16:08:35 +0800

      Commit message:


	  
		
 update enrich-pc
 

    

  
    

      Package: clusterProfiler

      Commit: 394892e4ff69fb14fc0d451adfca028fb72a69c3

      Author:  Guangchuang Yu <guangchuangyu@gmail.com> 

      Date: 2025-10-23 21:05:53 +0800

      Commit message:


	  
		
 update
 

    

  
    

      Package: clusterProfiler

      Commit: 39395ce1f997da2f29a5a4b2d92d4d9e72923d53

      Author:  Guangchuang Yu <guangchuangyu@gmail.com> 

      Date: 2025-04-17 09:51:00 +0800

      Commit message:


	  
		
 update bioc version
 

    

  
    

      Package: SwarnSeq

      Commit: 8f1ca0a58c8de9676dcdb81f4bcdc419f271bbc3

      Author:  Samarendra Das <samarendra.das@icar.org.in> 

      Date: 2025-11-01 17:15:27 +0530

      Commit message:


	  
		
 SingleCellExperiment was used in modification.
 

    

  
    

      Package: splatter

      Commit: 646e458e9556ff2feaa712e60e8fa3d88a8ddd93

      Author:  Luke Zappia <lazappi@users.noreply.github.com> 

      Date: 2025-11-01 12:08:53 +0100

      Commit message:


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

* upstream/devel:
  bump x.y.z version to odd y following creation of RELEASE_3_22 branch
 

    

  
    

      Package: splatter

      Commit: 2e75db7706855754b14aeb33586007fe5adc0769

      Author:  Luke Zappia <lazappi@users.noreply.github.com> 

      Date: 2025-11-01 12:05:04 +0100

      Commit message:


	  
		
 Bioconductor 3.22 release
 

    

  
    

      Package: splatter

      Commit: 319c55c6d00007a78c8dd61ac8c815f9d4e68b4e

      Author:  Luke Zappia <lazappi@users.noreply.github.com> 

      Date: 2025-11-01 12:03:18 +0100

      Commit message:


	  
		
 Merge remote-tracking branch 'upstream/RELEASE_3_22' into devel

* upstream/RELEASE_3_22:
  bump x.y.z version to even y prior to creation of RELEASE_3_22 branch
 

    

  
    

      Package: splatter

      Commit: 65286c7789f10c4ebc7f34b0e5a8fdc6616472a2

      Author:  dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> 

      Date: 2025-08-12 07:00:48 +0200

      Commit message:


	  
		
 Bump actions/checkout from 4 to 5 (#182)

Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
 

    

  
    

      Package: splatter

      Commit: 5c03bcf28383ee4fbe9f4eee8e778984ef89bf86

      Author:  Luke Zappia <lazappi@users.noreply.github.com> 

      Date: 2025-07-10 17:47:12 +0200

      Commit message:


	  
		
 Add write permissions to pkgdown workflow
 

    

  
    

      Package: splatter

      Commit: 4e21ebc92774f23139d3ee8e85115141287817f5

      Author:  Luke Zappia <lazappi@users.noreply.github.com> 

      Date: 2025-07-09 21:24:38 +0200

      Commit message:


	  
		
 Update check GHA (#181)

* Update check GHA

* Fix missing biocversion_str in check GHA

* Fix typo in check GHA 

    

  
    

      Package: zellkonverter

      Commit: 38b921d8aa6cf264b9d8140f981cf1dd0f8e0b83

      Author:  Luke Zappia <lazappi@users.noreply.github.com> 

      Date: 2025-11-01 12:21:07 +0100

      Commit message:


	  
		
 Fix version in NEWS
 

    

  
    

      Package: zellkonverter

      Commit: 57b9d7a337d0cad27d4c9b9320425e8e37c73994

      Author:  Luke Zappia <lazappi@users.noreply.github.com> 

      Date: 2025-11-01 12:20:22 +0100

      Commit message:


	  
		
 Bioconductor 3.23 devel
 

    

  
    

      Package: zellkonverter

      Commit: e34e43c8e309fec966d3a46f13207944f6aed68e

      Author:  Luke Zappia <lazappi@users.noreply.github.com> 

      Date: 2025-11-01 12:19:23 +0100

      Commit message:


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

* upstream/devel:
  bump x.y.z version to odd y following creation of RELEASE_3_22 branch
 

    

  
    

      Package: zellkonverter

      Commit: 4a98e5cb1ce541d6182bd1700466b8c8cceca3dd

      Author:  Luke Zappia <lazappi@users.noreply.github.com> 

      Date: 2025-11-01 12:14:25 +0100

      Commit message:


	  
		
 Bioconductor 3.22 release
 

    

  
    

      Package: zellkonverter

      Commit: c357324e8ee9e81b72c88dacb41d90067ea1f785

      Author:  Luke Zappia <lazappi@users.noreply.github.com> 

      Date: 2025-11-01 12:13:20 +0100

      Commit message:


	  
		
 Merge remote-tracking branch 'upstream/RELEASE_3_22' into devel

* upstream/RELEASE_3_22:
  bump x.y.z version to even y prior to creation of RELEASE_3_22 branch
 

    

  
    

      Package: Rsubread

      Commit: 8fedb934b06a7a72aa56a51d4ca0a6ef5f086036

      Author:  Yang Liao (Monash University) <yliao@m3-login2.massive.org.au> 

      Date: 2025-11-01 17:11:35 +1100

      Commit message:


	  
		
 altered cellCounts for testing features
 

    

  
    

      Package: smoothclust

      Commit: 1246c80e932cd1a18dccfa1359c8490b461fa539

      Author:  Lukas Weber <lmweb012@gmail.com> 

      Date: 2025-11-01 10:00:55 +0800

      Commit message:


	  
		
 update GHA
 

    

  
    

      Package: OrganismDbi

      Commit: a63751b6cc056aff02cfdedc1ef981d3317729a0

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

      Date: 2025-10-31 15:33:12 -0700

      Commit message:


	  
		
 OrganismDbi 1.53.2: Post-release cleanup

Argument 'miRBaseBuild' (to functions makeOrganismDbFromUCSC() and
makeOrganismDbFromBiomart()) is now gone after being defunct in
BioC 3.22.

Also arguments 'url' and 'port' are now defunct after being
deprecated in BioC 3.22.
 

    

  
    

      Package: leapR

      Commit: 5e355f7e8d673a5f1cf5bb93909be726bba775d4

      Author:  Sara JC Gosline <sara.gosline@pnnl.gov> 

      Date: 2025-10-31 13:11:57 -0700

      Commit message:


	  
		
 updated documentation
 

    

  
    

      Package: leapR

      Commit: 4cdd6344f88838c68806c35f56bb8083c61b7eec

      Author:  Sara JC Gosline <sara.gosline@pnnl.gov> 

      Date: 2025-10-31 12:44:33 -0700

      Commit message:


	  
		
 made last bits of changes
 

    

  
    

      Package: leapR

      Commit: bd8d9ffeff39c4694c1bab7c8fa90245875a45bc

      Author:  Sara JC Gosline <sara.gosline@pnnl.gov> 

      Date: 2025-10-30 15:42:33 -0700

      Commit message:


	  
		
 updated to account for additional bioC issues

- figured out the seq_len vs seq_along issue
- shortened lines
- added input checking
- fixed typos
- added man page
 

    

  
    

      Package: scrapper

      Commit: 1a313d952522e945e6ef66e342a36d378e3a54a6

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

      Date: 2025-10-31 00:26:44 -0700

      Commit message:


	  
		
 Updated bindings for the latest version of scran_graph_cluster.

Also minor bug fix for creating unweighted graphs.
 

    

  
    

      Package: scrapper

      Commit: d6a9e9e51335abfc3794dd9e7413cc33120e912c

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

      Date: 2025-10-29 15:39:30 -0700

      Commit message:


	  
		
 Updated the ignore file, moved Rigraphlib to LinkingTo.
 

    

  
    

      Package: scrapper

      Commit: 875fd4c9f972eb7807ec54523585560afce7bcf8

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

      Date: 2025-10-29 15:18:17 -0700

      Commit message:


	  
		
 Stripped out the analyze() function from the vignette.

Now that it's been moved to scrapple::analyze.se().
 

    

  
    

      Package: assorthead

      Commit: 16d94c97a39c30c5e6768f44b765c9e40083062f

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

      Date: 2025-10-30 21:01:35 -0700

      Commit message:


	  
		
 Updated vendored copies of raiigraph, scran_graph_cluster.
 

    

  
    

      Package: Rigraphlib

      Commit: 445817dc273b67afbf41d48a0b9a150bc075dec8

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

      Date: 2025-10-30 20:59:58 -0700

      Commit message:


	  
		
 Updated vendored version of igraph to 1.0.0.

Also commit the source code directly instead of storing a tarball, to get
around the BioC Git server's file size limits.
 

    

  
    

      Package: ShortRead

      Commit: c488f2966454c7bd2cadccb96415f3ef97ac3134

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

      Date: 2025-10-31 09:50:57 -0700

      Commit message:


	  
		
 ShortRead 1.69.1: Import pattern() from pwalign instead of Biostrings
 

    

  
    

      Package: GXwasR

      Commit: a56e631c0f0f781be8645062656bd0e792f2fc65

      Author:  Banabithi Bose <banabithi.bose@gmail.com> 

      Date: 2025-10-31 10:03:32 -0500

      Commit message:


	  
		
 Version bumped.
 

    

  
    

      Package: GXwasR

      Commit: 20442b403ef8da8d09d1dd180604692f7511e36a

      Author:  D Mayer <32186106+the-mayer@users.noreply.github.com> 

      Date: 2025-10-31 06:19:33 -0600

      Commit message:


	  
		
 Merge pull request #60 from boseb/misc-bioc

Vignette and Style 

    

  
    

      Package: GXwasR

      Commit: d4fd65bd42b3c6b4b2fcac25a0b02d901524382d

      Author:  David Mayer <david.mayer@cuanschutz.edu> 

      Date: 2025-10-30 08:45:20 -0400

      Commit message:


	  
		
 changes for BiocCheck
- F to FALSE in preimputationQC
- apply biocthis::bioc_style()
 

    

  
    

      Package: bsseq

      Commit: 46b4295329703d0bf694c707c816772bfbf4c037

      Author:  Kasper Daniel Hansen <kasperdanielhansen@gmail.com> 

      Date: 2025-10-31 11:03:21 -0400

      Commit message:


	  
		
 Making read.modkit and read.modbam2bed defunct
 

    

  
    

      Package: bsseq

      Commit: 13d941106f789484620bf16c62feff3d9f877c6c

      Author:  Kasper Daniel Hansen <kasperdanielhansen@gmail.com> 

      Date: 2025-10-31 09:58:40 -0400

      Commit message:


	  
		
 merging from release
 

    

  
    

      Package: bsseq

      Commit: a0f3ce3f5728d805476f0aad9e44a4748323a028

      Author:  Kasper Daniel Hansen <kasperdanielhansen@gmail.com> 

      Date: 2025-10-10 11:25:36 -0400

      Commit message:


	  
		
 getting rid of Travis since we have been using Github Actions for a while
 

    

  
    

      Package: MetaProViz

      Commit: 06811fcdb5a4cc52185613d4bdf5a2e380ed8f37

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

      Date: 2025-10-31 15:22:56 +0100

      Commit message:


	  
		
 code formatting: break long argument lists
 

    

  
    

      Package: MetaProViz

      Commit: 47cc5a9af900ada0782bc9d7e2a58f50facf9e88

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

      Date: 2025-10-31 11:55:36 +0100

      Commit message:


	  
		
 Bump version: 3.99.17 → 3.99.18
 

    

  
    

      Package: MetaProViz

      Commit: da03ed010c71f69526dfac528350166045b15623

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

      Date: 2025-10-31 11:55:33 +0100

      Commit message:


	  
		
 docs rebuild
 

    

  
    

      Package: MetaProViz

      Commit: db946fdfec3526daa164a215d2e4fec045f71529

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

      Date: 2025-10-31 11:54:50 +0100

      Commit message:


	  
		
 moved examples of ID translation functions into `\dontrun` due to 15 min BioC timeout for R CMD check
 

    

  
    

      Package: dmGsea

      Commit: 248aa7cd204a3a7eb4cb6aa0e3138ecc660b9aa3

      Author:  xuz1 <xuz@niehs.nih.gov> 

      Date: 2025-10-31 09:40:12 -0400

      Commit message:


	  
		
 bugfix

Signed-off-by: xuz1 <xuz@niehs.nih.gov>
 

    

  
    

      Package: DESpace

      Commit: 3dbd101c6483dc2e536fc8eced1da63fbdc94e69

      Author:  peicai <peiying.cai@gmail.com> 

      Date: 2025-10-31 13:13:38 +0100

      Commit message:


	  
		
 updated citation
 

    

  
    

      Package: rhdf5

      Commit: 8cd8dc6e82333e4baaa093d59d2f20f6f5586118

      Author:  Hugo Gruson <10783929+Bisaloo@users.noreply.github.com> 

      Date: 2025-10-31 09:46:45 +0100

      Commit message:


	  
		
 Bump version
 

    

  
    

      Package: rhdf5

      Commit: 97e6d85586c8d5a105b6786df227bc3ef0a2ec64

      Author:  Hugo Gruson <10783929+Bisaloo@users.noreply.github.com> 

      Date: 2025-10-31 09:46:29 +0100

      Commit message:


	  
		
 Mention fix in NEWS
 

    

  
    

      Package: rhdf5

      Commit: ca84366af7955b3ae300c53b6b4444b7377cd8f8

      Author:  Hugo Gruson <10783929+Bisaloo@users.noreply.github.com> 

      Date: 2025-10-21 20:15:03 +0200

      Commit message:


	  
		
 Fix orientation on native unsigned int
 

    

  
    

      Package: rhdf5

      Commit: 514f9f1f63d60ce9cc5d6787b07c443b175cf72c

      Author:  Hugo Gruson <10783929+Bisaloo@users.noreply.github.com> 

      Date: 2025-10-21 18:33:23 +0200

      Commit message:


	  
		
 Add regression test for #157
 

    

  
    

      Package: rhdf5

      Commit: 74937b0c7afb6f6dd1b63dda214cc8091a4082f0

      Author:  Hugo Gruson <10783929+Bisaloo@users.noreply.github.com> 

      Date: 2025-10-31 09:14:16 +0100

      Commit message:


	  
		
 Bump version
 

    

  
    

      Package: rhdf5

      Commit: f81b9097ca9da16e43addfd3fdc7299b42153bca

      Author:  Hugo Gruson <10783929+Bisaloo@users.noreply.github.com> 

      Date: 2025-10-31 09:12:57 +0100

      Commit message:


	  
		
 Run devtools::document()
 

    

  
    

      Package: rhdf5

      Commit: 31b7c2e9288835c3cddb386b7bdc4d25bc164070

      Author:  Hugo Gruson <10783929+Bisaloo@users.noreply.github.com> 

      Date: 2025-10-21 15:08:11 +0200

      Commit message:


	  
		
 Use double quotes
 

    

  
    

      Package: rhdf5

      Commit: 7b422fbaf166df85fadb11180ac304d8a4606a5b

      Author:  Hugo Gruson <10783929+Bisaloo@users.noreply.github.com> 

      Date: 2025-10-21 14:33:59 +0200

      Commit message:


	  
		
 Use dedicated ...length() base function where appropriate
 

    

  
    

      Package: rhdf5

      Commit: 0ed9fb9673dd5b7c238241637b9b471022dd4c69

      Author:  Hugo Gruson <10783929+Bisaloo@users.noreply.github.com> 

      Date: 2025-10-21 14:33:33 +0200

      Commit message:


	  
		
 Use dedicated nzchar() base function where appropriate
 

    

  
    

      Package: rhdf5

      Commit: 5ea680b34dbd6cba2bec7fe75e4789e6271c127e

      Author:  Hugo Gruson <10783929+Bisaloo@users.noreply.github.com> 

      Date: 2025-10-21 14:33:02 +0200

      Commit message:


	  
		
 Do not pass functions as characters
 

    

  
    

      Package: rhdf5

      Commit: a32b4a3096ef8d58e0cbaca5bee629e19c5ac53d

      Author:  Hugo Gruson <10783929+Bisaloo@users.noreply.github.com> 

      Date: 2025-10-21 14:06:10 +0200

      Commit message:


	  
		
 Make bit64conversion default explicit
 

    

  
    

      Package: rhdf5

      Commit: 7d7eb9e6ef6e9b706ed477db7f829715986fc67d

      Author:  Hugo Gruson <10783929+Bisaloo@users.noreply.github.com> 

      Date: 2025-10-21 14:05:54 +0200

      Commit message:


	  
		
 Remove unnecessary ifelse()
 

    

  
    

      Package: rhdf5

      Commit: 6040f892c6c9f43dcb85e64949ee5196050bf667

      Author:  Hugo Gruson <10783929+Bisaloo@users.noreply.github.com> 

      Date: 2025-10-21 14:05:40 +0200

      Commit message:


	  
		
 document return
 

    

  
    

      Package: rhdf5

      Commit: 966e5c10ace603fc729d2878f2a0117529ff7e08

      Author:  Hugo Gruson <10783929+Bisaloo@users.noreply.github.com> 

      Date: 2025-10-21 14:04:45 +0200

      Commit message:


	  
		
 Reduce nesting and remove unnecessary parentheses
 

    

  
    

      Package: rhdf5

      Commit: 460149fd55b36ca3637a166d8653d80397337069

      Author:  Hugo Gruson <10783929+Bisaloo@users.noreply.github.com> 

      Date: 2025-10-21 12:46:36 +0200

      Commit message:


	  
		
 Fix some long lines
 

    

  
    

      Package: rhdf5

      Commit: 48148dfa9d4f0a0db2184cab120206c23857c9c3

      Author:  Hugo Gruson <10783929+Bisaloo@users.noreply.github.com> 

      Date: 2025-10-21 12:31:19 +0200

      Commit message:


	  
		
 Fix package name in vignette
 

    

  
    

      Package: rhdf5

      Commit: 3133c72125d4ec5bed648cf507998a60ed288fbf

      Author:  Hugo Gruson <10783929+Bisaloo@users.noreply.github.com> 

      Date: 2025-10-21 11:44:22 +0200

      Commit message:


	  
		
 Remove unused variables
 

    

  
    

      Package: rhdf5

      Commit: ee3e7eb49dcefcda154fa124399655a6e73092fc

      Author:  Hugo Gruson <10783929+Bisaloo@users.noreply.github.com> 

      Date: 2025-10-21 11:35:47 +0200

      Commit message:


	  
		
 Use seq_along() where possible
 

    

  
    

      Package: rhdf5

      Commit: 4be344a10a2954d4482e18fd91ce0a3870a14ebc

      Author:  Hugo Gruson <10783929+Bisaloo@users.noreply.github.com> 

      Date: 2025-10-21 11:32:17 +0200

      Commit message:


	  
		
 Simplify newnames definition
 

    

  
    

      Package: rhdf5

      Commit: 89ea65ea690a2bfc39461f3614c5ed94f9d79076

      Author:  Hugo Gruson <10783929+Bisaloo@users.noreply.github.com> 

      Date: 2025-10-21 11:25:29 +0200

      Commit message:


	  
		
 Remove sapply() where possible
 

    

  
    

      Package: rhdf5

      Commit: 1454dddd24abc35212a589d7abaf42dfb7b362ab

      Author:  Hugo Gruson <10783929+Bisaloo@users.noreply.github.com> 

      Date: 2025-10-21 11:13:06 +0200

      Commit message:


	  
		
 Use shortcircuit boolean operator where appropriate
 

    

  
    

      Package: rhdf5

      Commit: 04d998f8b476e45200c1d200af4f60b00556021c

      Author:  Hugo Gruson <10783929+Bisaloo@users.noreply.github.com> 

      Date: 2025-10-21 11:08:06 +0200

      Commit message:


	  
		
 Use anyNA() where appropriate
 

    

  
    

      Package: rhdf5

      Commit: 8a011597e6910e8f8c40f36a38c585e6712071d1

      Author:  Hugo Gruson <10783929+Bisaloo@users.noreply.github.com> 

      Date: 2025-10-21 10:55:08 +0200

      Commit message:


	  
		
 Setup lintr
 

    

  
    

      Package: rhdf5

      Commit: 425e4616b4ef9d85b50d9e65a2651cb11ac81a36

      Author:  Hugo Gruson <10783929+Bisaloo@users.noreply.github.com> 

      Date: 2025-08-15 15:25:39 +0200

      Commit message:


	  
		
 Fix R CMD check NOTE about method consistency
 

    

  
    

      Package: rhdf5

      Commit: 65a1611cd377311ee5ef150e58df101946d5fc8c

      Author:  Hugo Gruson <10783929+Bisaloo@users.noreply.github.com> 

      Date: 2025-08-15 15:00:48 +0200

      Commit message:


	  
		
 Add curl as a devel dependency

Since it is required for testthat::skip_if_offline()
 

    

  
    

      Package: rhdf5

      Commit: c80c3aebee0a32d0128953b4e529f201bd88edc7

      Author:  Hugo Gruson <10783929+Bisaloo@users.noreply.github.com> 

      Date: 2025-10-30 19:32:59 +0100

      Commit message:


	  
		
 Bump version
 

    

  
    

      Package: rhdf5

      Commit: b8eda3c92e355a8fcc0af994988c9e7bf8ce7a3e

      Author:  Hugo Gruson <10783929+Bisaloo@users.noreply.github.com> 

      Date: 2025-10-24 18:15:03 +0200

      Commit message:


	  
		
 Mark deNBI as funder
 

    

  
    

      Package: rhdf5

      Commit: afba574a116b85d0b5558b8c79b5fe31db12a2bd

      Author:  Hugo Gruson <10783929+Bisaloo@users.noreply.github.com> 

      Date: 2025-10-24 18:12:44 +0200

      Commit message:


	  
		
 Update logo location in README
 

    

  
    

      Package: rhdf5

      Commit: 23c0bf600d50dafcee763f4b6ff11c416afeb45d

      Author:  Hugo Gruson <10783929+Bisaloo@users.noreply.github.com> 

      Date: 2025-10-24 18:12:05 +0200

      Commit message:


	  
		
 Update logo & favicon
 

    

  
    

      Package: rhdf5

      Commit: 8aa529c74586f07b7670fff5ab1117db540d3776

      Author:  Hugo Gruson <10783929+Bisaloo@users.noreply.github.com> 

      Date: 2025-10-24 18:09:55 +0200

      Commit message:


	  
		
 Add pkgdown link to DESCRIPTION
 

    

  
    

      Package: rhdf5

      Commit: 9b6dc3554666736f50f4d91fa0e74246d4a43495

      Author:  Hugo Gruson <10783929+Bisaloo@users.noreply.github.com> 

      Date: 2025-10-24 18:09:24 +0200

      Commit message:


	  
		
 Fix settings
 

    

  
    

      Package: rhdf5

      Commit: c585976b4cd518da14b61c71a9bd61e315744324

      Author:  Hugo Gruson <10783929+Bisaloo@users.noreply.github.com> 

      Date: 2025-10-24 18:08:08 +0200

      Commit message:


	  
		
 Add pkgdown.yaml GHA workflow
 

    

  
    

      Package: rhdf5

      Commit: 8c3c468cb57475a02f9145b91cf3467a8dd9c417

      Author:  Hugo Gruson <10783929+Bisaloo@users.noreply.github.com> 

      Date: 2025-10-24 18:07:45 +0200

      Commit message:


	  
		
 Fix _pkgdown.yml
 

    

  
    

      Package: rhdf5

      Commit: 17e09a5d824cfdcf45d41df79b6c639ee4ada64a

      Author:  Hugo Gruson <10783929+Bisaloo@users.noreply.github.com> 

      Date: 2025-10-24 16:03:04 +0200

      Commit message:


	  
		
 Bump version
 

    

  
  


</div>

</div>