Bioconductor 3.23 Release Schedule

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

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Bioconductor has moved to GIT for contributed packages; the subversion logs are no longer active.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

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Package: NanoMethViz
Commit: 899e3110e01598a4578a3366e7ad0199f0a3c6df
Author: shians <registertonysu@gmail.com>
Date: 2026-03-26 13:20:08 +1100
Commit message:

 Version bump
Package: NanoMethViz
Commit: a87d87896b025d847c9ba6538c7ee296ea2a4cab
Author: shians <registertonysu@gmail.com>
Date: 2026-03-26 13:18:56 +1100
Commit message:

 Removed DSS suggestion
Package: NanoMethViz
Commit: 1f31b13e89c6baa10a3105e677462fa8e6965dea
Author: shians <registertonysu@gmail.com>
Date: 2026-03-26 13:18:30 +1100
Commit message:

 Fixed potential negative coordinate
Package: NanoMethViz
Commit: b7c4b81354c6b4e293c6b696e73050bf7bd5073c
Author: shians <registertonysu@gmail.com>
Date: 2026-03-26 13:17:58 +1100
Commit message:

 Changed assignment operator
Package: NanoMethViz
Commit: 07cc80c34fd91bcf7ac49a7c9b200dc56ccc3014
Author: shians <registertonysu@gmail.com>
Date: 2026-02-24 16:51:59 +1100
Commit message:

 Added comments
Package: NanoMethViz
Commit: 3472d481d453cda96636e96456f0246ccaccf605
Author: shians <registertonysu@gmail.com>
Date: 2026-02-24 16:23:33 +1100
Commit message:

 Version bump to v3.7.2
Package: NanoMethViz
Commit: c84e5ce95d72a88e09911af43feac6648f05a4ba
Author: shians <registertonysu@gmail.com>
Date: 2026-02-24 16:22:22 +1100
Commit message:

 Added sorting to heatmap
Package: NanoMethViz
Commit: a03245116638c701e4a841aa152742bd800cc139
Author: shians <registertonysu@gmail.com>
Date: 2026-02-24 14:36:25 +1100
Commit message:

 Refactored duplicated code
Package: NanoMethViz
Commit: d4ed262d118061c3cfcf7456fb7c861786bc7d10
Author: shians <registertonysu@gmail.com>
Date: 2026-02-24 10:54:43 +1100
Commit message:

 Updated REAMDE
Package: NanoMethViz
Commit: 3053b2d9f873fbece5c534d2832b45e8c378bab8
Author: shians <registertonysu@gmail.com>
Date: 2026-02-12 14:31:17 +1100
Commit message:

 Updated README
Package: chopsticks
Commit: 06c2564c70953022b18d6ea24529328b21ea3dcb
Author: Hin-Tak Leung <htl10@users.sourceforge.net>
Date: 2026-03-26 01:28:43 +0000
Commit message:

 Fixes for non-API calls in R 4.6

s/R_data_class\((.+), FALSE\)/R_class\(\1\)/
s/IS_S4_OBJECT\((.+)\)/Rf_isS4\(\1\)/
s/SET_S4_OBJECT\((.+)\)/Rf_asS4\(\1, TRUE, 0\)/
Package: Seqtometry
Commit: b5415062087ec23ec807ff0ee9f8031330accc46
Author: Robert Kousnetsov <robert.kousnetsov@health.slu.edu>
Date: 2026-03-25 19:47:58 -0500
Commit message:

 Update for v0.99.3
Package: postNet
Commit: 186cacd82a616cfc3a733be6726cbabfdaa0e0fd
Author: Krzysztof Szkop <krzysztof.szkop@gmail.com>
Date: 2026-03-25 22:06:09 +0000
Commit message:

 KS
Package: postNet
Commit: 36aa299d044c0e3e2f820df1b1b1c63a9c05dd96
Author: Krzysztof Szkop <krzysztof.szkop@gmail.com>
Date: 2026-03-25 21:48:14 +0000
Commit message:

 KS
Package: muscat
Commit: 017b290b414212c357e184d17edcca27f4302ace
Author: HelenaLC <helena@crowell.eu>
Date: 2026-03-24 00:26:54 +0100
Commit message:

 make gha use r dev
Package: muscat
Commit: 6463410fe3c8b2d9ede2cc82f5f250ca5bd3b8fe
Author: HelenaLC <helena@crowell.eu>
Date: 2026-03-24 00:14:16 +0100
Commit message:

 update GHA
Package: muscat
Commit: af1edb8d072f529df24f57bf4038b84ab081f0c5
Author: HelenaLC <helena@crowell.eu>
Date: 2026-03-08 14:02:13 +0100
Commit message:

 track changes
Package: muscat
Commit: eff48034c5bb74ec6004fb322d5422e18c2b212e
Author: HelenaLC <helena@crowell.eu>
Date: 2026-03-08 11:20:41 +0100
Commit message:

 fix #102
Package: muscat
Commit: e9bd6c6a4d5f00327667af2d1c8c6c6a084b857d
Author: HelenaLC <helena@crowell.eu>
Date: 2026-03-08 11:18:17 +0100
Commit message:

 fix #102
Package: muscat
Commit: a36f58455cf4cb58a878b1e999c303f51e9a754f
Author: HelenaLC <helena@crowell.eu>
Date: 2026-03-08 10:09:04 +0100
Commit message:

 use requireNamespace instead of require
Package: muscat
Commit: e0b25a9555e584565dad6bdd197c4ffdcbae9b4e
Author: HelenaLC <helena@crowell.eu>
Date: 2026-03-08 10:07:47 +0100
Commit message:

 import utils::tail
Package: muscat
Commit: da31ff63c8ae53894e9d3a3cc6b9e6e5b1b23b99
Author: HelenaLC <helena@crowell.eu>
Date: 2026-03-08 10:07:41 +0100
Commit message:

 import utils::tail
Package: muscat
Commit: 3072b6b6519c2884d480d9e6f7046d255593b97c
Author: HelenaLC <helena@crowell.eu>
Date: 2026-03-08 10:07:31 +0100
Commit message:

 fix typo
Package: muscat
Commit: 4cb630959bbeba6035c08c973b0d35bea2927b8e
Author: HelenaLC <helena@crowell.eu>
Date: 2026-03-08 09:29:58 +0100
Commit message:

 fix unit test
Package: muscat
Commit: f4345b5dc1188daaf09d778cda1c4456a6299566
Author: HelenaLC <helena@crowell.eu>
Date: 2026-03-08 09:23:53 +0100
Commit message:

 update Gilis citation
Package: muscat
Commit: 82375ab300c620be6743b6f59a389cbfe31b85cf
Author: HelenaLC <helena@crowell.eu>
Date: 2026-03-08 09:18:42 +0100
Commit message:

 omit cowplot in favor of patchwor
Package: muscat
Commit: befe78f94282ae079a06d5f19717deda61deb4bf
Author: HelenaLC <helena@crowell.eu>
Date: 2026-03-08 08:56:01 +0100
Commit message:

 update GHA
Package: muscat
Commit: 7e2eea4a363997bb37f1b4154226c57b56fea7f3
Author: HelenaLC <helena@crowell.eu>
Date: 2026-03-08 08:55:43 +0100
Commit message:

 .split_cells unit test
Package: muscat
Commit: aaf37b1b15e2a8e59976b144b7a192aff99f605a
Author: HelenaLC <helena@crowell.eu>
Date: 2026-03-07 20:10:27 +0100
Commit message:

 fix ut
Package: muscat
Commit: 9684dafb3de063cf3ac6d291f200fd8fa52249aa
Author: HelenaLC <helena@crowell.eu>
Date: 2026-03-07 19:58:47 +0100
Commit message:

 move DESeq2 to Suggests:
Package: muscat
Commit: 115c339142515386bf985516ed37eae4d3961b19
Author: HelenaLC <helena@crowell.eu>
Date: 2026-03-07 19:34:28 +0100
Commit message:

 omit data.table and purrr from Imports:; sctransform to Suggests:
Package: muscat
Commit: 9f8473ce101bc0def841e06e1fdb5506ae6a512d
Author: HelenaLC <helena@crowell.eu>
Date: 2026-03-06 15:15:15 +0100
Commit message:

 rnm edgeR::calcNormFactors to normLibSizes
Package: postNet
Commit: db70e34beb896952e9cc4b9bfdb7811698cee8e7
Author: Krzysztof Szkop <krzysztof.szkop@gmail.com>
Date: 2026-03-25 19:57:27 +0000
Commit message:

 KS
Package: postNet
Commit: 14b1cd72fe36affffed6dc1bc22fc84c2940cda9
Author: Krzysztof Szkop <krzysztof.szkop@gmail.com>
Date: 2026-03-25 19:40:35 +0000
Commit message:

 KS
Package: postNet
Commit: 007da9073a43574a5408e61f7d4dcfd35b4a51a7
Author: Krzysztof Szkop <krzysztof.szkop@gmail.com>
Date: 2026-03-25 19:25:18 +0000
Commit message:

 KS
Package: postNet
Commit: 954c3392963bb38053c07c330889be4a79e73519
Author: Krzysztof Szkop <krzysztof.szkop@gmail.com>
Date: 2026-03-25 19:11:40 +0000
Commit message:

 KS
Package: OmnipathR
Commit: b4e61a5281c0c4c7b23f33097a516dce2a00361a
Author: deeenes <turei.denes@gmail.com>
Date: 2026-03-25 19:11:52 +0100
Commit message:

 Bump version: 3.19.11 → 3.19.12
Package: OmnipathR
Commit: 3f1f6aeff871e1a1ef032d2fc4e580c5598fb471
Author: deeenes <turei.denes@gmail.com>
Date: 2026-03-25 19:10:41 +0100
Commit message:

 Handle empty URL in omnipath_cache_key and missing SBML in metatlas

omnipath_cache_key now returns character(0) when given an empty URL
vector instead of crashing in pmap with size mismatch. Also guard
against missing SBML files in metabolic_atlas_model — some models
have no SBML file, causing an empty url_param that propagated to the
cache key computation.

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
Package: OmnipathR
Commit: f163c4bfcf70c6412fa9df7fb39c4edc6bf475cb
Author: deeenes <turei.denes@gmail.com>
Date: 2026-03-25 19:00:44 +0100
Commit message:

 docs rebuild
Package: OmnipathR
Commit: 6dc41920550fc8ba229539d892d09273c4c38e74
Author: deeenes <turei.denes@gmail.com>
Date: 2026-03-25 18:56:09 +0100
Commit message:

 Refactor reactome.R and wikipathways.R

- Remove `get_` prefix from all function names:
  get_reactome_pathway_relations -> reactome_pathway_relations
  get_reactome_pathways -> reactome_pathways
  get_pathway_participants -> reactome_chebi_pathways
  get_reactome -> reactome_chebi
  get_wikipathways_pathways -> wikipathways_pathways
  get_wikipathways -> wikipathways_metabolites
  get_wikipathways_metabolites_sparql -> wikipathways_metabolites_sparql
  get_metabolite_pathway_table -> wikipathways_metabolite_table

- Replace custom species handling (normalize_reactome_species,
  reactome_species_table) with taxonomy.R integration: use latin_name()
  for organism resolution and a simple named vector for Reactome codes;
  rename `species` parameter to `organism` for consistency

- Tidyverse style: continuous pipes with %<>%, eliminate unnecessary
  intermediate variables, replace toupper/trimws/gsub/grepl with
  stringr equivalents, replace lapply/vapply with purrr, replace
  write.csv with readr::write_csv, integer L suffixes

- Replace cat/flush.console/print with progress::progress_bar and
  logger::log_warn in the GPML parsing loop

- Add NSE vs R CMD check workarounds (NULL assignments)
- Add file headers matching package convention
- Remove dead code (commented-out devel httr2 blocks, Sys.sleep)
- Single implicit return at function end
- Use .data$column for filter() to avoid NSE ambiguity

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
Package: OmnipathR
Commit: d1821e400d0eaf3a7e6b4666a585dda925233634
Author: deeenes <turei.denes@gmail.com>
Date: 2026-03-25 16:50:41 +0100
Commit message:

 Bump version: 3.19.10 → 3.19.11
Package: OmnipathR
Commit: 2871a638733191d251fad86a3ad6a3e161270a31
Author: deeenes <turei.denes@gmail.com>
Date: 2026-03-25 16:50:35 +0100
Commit message:

 include `metatlas_sbml` (created earlier, was only missing from git repo)
Package: postNet
Commit: 07c3d4959b53b8fd7d3ca7ed037fb954e697e77c
Author: Krzysztof Szkop <krzysztof.szkop@gmail.com>
Date: 2026-03-25 18:09:08 +0000
Commit message:

 KS
Package: hipathia
Commit: 2281546aa185b77b04f54f44575abeee88335aab
Author: Marta Hidalgo <marta.hidalgo@outlook.es>
Date: 2026-03-25 18:53:27 +0100
Commit message:

 updating devel to Zenodo
Package: hipathia
Commit: 38da92cc9fa9bc9c585890d1fb4e3768619f670c
Author: Marta R. Hidalgo <marta.hidalgo@outlook.es>
Date: 2026-03-25 18:35:21 +0100
Commit message:

 adding man get_file file
Package: hipathia
Commit: 550cdc9500a54d851de08db92f3aa945edf09add
Author: Marta R. Hidalgo <marta.hidalgo@outlook.es>
Date: 2026-03-25 18:33:05 +0100
Commit message:

 adapting to download files from Zenodo
Package: hipathia
Commit: 65ad8d5fd793e06aa415849dff9c21e53ee242b7
Author: Marta Hidalgo <marta.hidalgo@outlook.es>
Date: 2026-03-20 15:11:59 +0100
Commit message:

 bumping to version 3.11.1
Package: hipathia
Commit: 77efc2b1a90d4b6558dfa3dfacd446c60d0420ef
Author: Marta Hidalgo <marta.hidalgo@outlook.es>
Date: 2026-03-20 15:11:32 +0100
Commit message:

 updating to hpAnnot version 3
Package: hipathia
Commit: ee26bd1b8bacccd517c8798fed2f316e2ccf9ef9
Author: A Wokaty <andres.wokaty@sph.cuny.edu>
Date: 2025-10-29 10:44:56 -0400
Commit message:

 bump x.y.z version to odd y following creation of RELEASE_3_22 branch
Package: hipathia
Commit: 0f5a9281f5378c1214311cbc7e582dfec265c590
Author: A Wokaty <andres.wokaty@sph.cuny.edu>
Date: 2025-10-29 10:44:56 -0400
Commit message:

 bump x.y.z version to even y prior to creation of RELEASE_3_22 branch
Package: hipathia
Commit: 20a20d03954668847609f506aef5ceba5cf29d6f
Author: Marta R. Hidalgo <marta.hidalgo@outlook.es>
Date: 2025-09-29 22:50:15 +0200
Commit message:

 commenting figures in vignette
Package: hipathia
Commit: 4b6c9cf6503f62c18139f00b26345eaf0eaa71d6
Author: Marta Hidalgo <marta.hidalgo@outlook.es>
Date: 2025-09-25 20:58:05 +0200
Commit message:

 Merge remote-tracking branch 'upstream/devel'
Package: hipathia
Commit: 99eb11deec74d48f91fb1bc7415513d78ec3bcd2
Author: Marta R. Hidalgo <marta.hidalgo@outlook.es>
Date: 2023-05-22 11:40:47 +0200
Commit message:

 changing plotVisGraphDE output options
Package: postNet
Commit: fa1020192ce629f1953704ee41a4b47ef7689eb6
Author: Krzysztof Szkop <krzysztof.szkop@gmail.com>
Date: 2026-03-25 17:57:37 +0000
Commit message:

 KS
Package: postNet
Commit: 365275110abefdcf3756a147a7d2a48463944560
Author: Krzysztof Szkop <krzysztof.szkop@gmail.com>
Date: 2026-03-25 17:45:26 +0000
Commit message:

 KS
Package: postNet
Commit: 863c093c9cafe4178019e749ce7a7f422d2386af
Author: Krzysztof Szkop <krzysztof.szkop@gmail.com>
Date: 2026-03-25 17:44:55 +0000
Commit message:

 KS
Package: postNet
Commit: ea70362ff4d83bd72d0833749ebd012f55739327
Author: Krzysztof Szkop <krzysztof.szkop@gmail.com>
Date: 2026-03-25 17:27:29 +0000
Commit message:

 KS
Package: wiggleplotr
Commit: d0fc81f9000f5aec0eeb83fa466291822a4791c2
Author: Kaur Alasoo <kauralasoo@gmail.com>
Date: 2026-03-25 19:25:32 +0200
Commit message:

 Update DESCRIPTION
Package: RNAshapeQC
Commit: fefca97a9bd7f46e3dc050e80e37d69894abb704
Author: Miyeon Yeon <sqr.yeon@gmail.com>
Date: 2026-03-25 12:16:42 -0500
Commit message:

 Fix a syntax error in norm_pileup.gene function (Bioconductor/Contributions#4054)
Package: PolySTest
Commit: 1327884eb61d0f1962be11126a2470ae42d68335
Author: veitveit <veits@bmb.sdu.dk>
Date: 2026-03-20 16:58:27 +0100
Commit message:

 simple fix of documentation
Package: XAItest
Commit: 5a750fa41311818a5f96a0ea30ea5f00f910f875
Author: gui <ghislain.fievet@gmail.com>
Date: 2026-03-25 17:50:19 +0100
Commit message:

 Fix addSimThresh example and show namespace import
Package: RNAshapeQC
Commit: 336f98f3bc675944a9bf86ee69f4c68c644fb996
Author: Miyeon Yeon <sqr.yeon@gmail.com>
Date: 2026-03-25 11:48:59 -0500
Commit message:

 Update norm_pileup.gene function to use nCores directly (Bioconductor/Contributions#4054)
Package: OMA
Commit: 404b3d213a46b957c6b7d86dab928d69ccfb4c84
Author: Tuomas Borman <60338854+TuomasBorman@users.noreply.github.com>
Date: 2026-03-25 18:46:20 +0200
Commit message:

 Change license to CC BY 4.0
Package: kissDE
Commit: 31e6a40fc9f89ee3ff7a895de549c05362764a25
Author: Aurélie Siberchicot <aurelie.siberchicot@univ-lyon1.fr>
Date: 2026-03-25 17:35:20 +0100
Commit message:

 Add a quarto vignette
Package: kissDE
Commit: 7c272dae574995d6ab10da80f9713ce834d161ba
Author: Aurélie Siberchicot <aurelie.siberchicot@univ-lyon1.fr>
Date: 2026-03-25 17:33:09 +0100
Commit message:

 Correct misprint in DESCRIPTION
Package: kissDE
Commit: b86eba20c8ab3b439425d8f29050e09a2c1f827b
Author: Aurélie Siberchicot <aurelie.siberchicot@univ-lyon1.fr>
Date: 2026-03-24 10:32:11 +0100
Commit message:

 Replace the '=' sign by the '<-' one to assign a value to a variable
Package: kissDE
Commit: 3bca9ade864cbd361c3b50d225e1ee25052e05c9
Author: Aurélie Siberchicot <aurelie.siberchicot@univ-lyon1.fr>
Date: 2026-03-24 10:31:35 +0100
Commit message:

 Correct the 'stop' calling (without 'paste')
Package: kissDE
Commit: 2781224b47fc00680f1cfd7e089823429e55eac7
Author: Aurélie Siberchicot <aurelie.siberchicot@univ-lyon1.fr>
Date: 2026-03-24 10:31:04 +0100
Commit message:

 Add the ORCID of the maintainer
Package: biocViews
Commit: 39e7c59bef4d6be5517138dfd270a09a4b9d4480
Author: A Wokaty <awokaty@users.noreply.github.com>
Date: 2026-03-25 12:06:15 -0400
Commit message:

 Bump version to 1.79.4
Package: biocViews
Commit: 2d315d48c7eb97fffc07e362e639eece7ab44702
Author: jwokaty <jwokaty@users.noreply.github.com>
Date: 2026-03-25 12:05:13 -0400
Commit message:

 Merge pull request #25 from Bioconductor/unsupportedpackages

Add Config/Bioconductor/UnsupportedPlatforms
Package: biocViews
Commit: 8f9b228833a6154cb0287334173e9b755fca59ca
Author: A Wokaty <awokaty@users.noreply.github.com>
Date: 2026-03-25 11:57:44 -0400
Commit message:

 Add Config/Bioconductor/UnsupportedPlatforms
Package: arrayQualityMetrics
Commit: b77a5bc756813aad1a63fe6e429033ce39a4cdca
Author: Hugo Gruson <git@hugogruson.fr>
Date: 2026-03-25 15:47:02 +0100
Commit message:

 Bump version
Package: arrayQualityMetrics
Commit: b73f11c5998ece3cd28d63505ec87e798af5e740
Author: Hugo Gruson <git@hugogruson.fr>
Date: 2026-03-25 15:49:05 +0100
Commit message:

 Remove class(x) == occurrence
Package: arrayQualityMetrics
Commit: c3867afc03ffce6c53c8a1ddee5507904eaceabf
Author: Hugo Gruson <git@hugogruson.fr>
Date: 2026-03-25 15:48:47 +0100
Commit message:

 Switch CITATION to bibentry()
Package: arrayQualityMetrics
Commit: 330f658cb95fd1ce76dcac2ffb7f0daf75081caa
Author: Hugo Gruson <git@hugogruson.fr>
Date: 2026-03-25 15:46:37 +0100
Commit message:

 Switch to Authors@R in DESCRIPTION
Package: arrayQualityMetrics
Commit: 526700d58a6b0796504ebc6da1a810547c64c5f6
Author: Hugo Gruson <git@hugogruson.fr>
Date: 2026-03-25 15:45:03 +0100
Commit message:

 Convert arrayQualityMetrics from Rmd to Rnw
Package: arrayQualityMetrics
Commit: 42b1ec1f2a4124139f38a449e1f370856b88b365
Author: Hugo Gruson <git@hugogruson.fr>
Date: 2026-03-25 15:09:34 +0100
Commit message:

 Convert aqm vignette from Rnw to Rmd
Package: VisiumIO
Commit: 989b6eba6767cb9ce4cfa49c651b3ee07f9f4b37
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2026-03-25 11:01:31 -0400
Commit message:

 version bump 1.7.7
Package: VisiumIO
Commit: c52f70d28b5c7508dd0b76ed71be1af3269961a3
Author: Marcel Ramos Pérez <LiNk-NY@users.noreply.github.com>
Date: 2026-03-24 20:34:27 +0000
Commit message:

 Add missing fnd entries to Authors@R in DESCRIPTION
Package: VisiumIO
Commit: 9c7fa8e1f504fc69d9ec041d83017aa656f9dea5
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2026-03-24 16:38:47 -0400
Commit message:

 replace pr_check.yml with ci.yml GHA
Package: TENxIO
Commit: ca832808404725ac54f5daf7ef732f9b4e060254
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2026-03-25 10:58:46 -0400
Commit message:

 version bump 1.13.4
Package: TENxIO
Commit: 152ba99e439dd36cdbb26ecd7ae68410f199ec2c
Author: Marcel Ramos Pérez <LiNk-NY@users.noreply.github.com>
Date: 2026-03-24 20:34:33 +0000
Commit message:

 Add missing fnd entries to Authors@R in DESCRIPTION
Package: TENxIO
Commit: 1e19056840081bea3b70279a32bbbb7b52fad546
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2026-03-24 16:46:10 -0400
Commit message:

 replace pr_check.yml with ci.yml GHA
Package: betterChromVAR
Commit: 58b74cab61363f2cf49eda322fe25e437eb50ff5
Author: plger <pl.germain@gmail.com>
Date: 2026-03-25 14:17:04 +0100
Commit message:

 ensure that example data doesn't have rows of zeroes...
Package: betterChromVAR
Commit: bf215609aeae549e531b1b6607177e1190e87814
Author: plger <pl.germain@gmail.com>
Date: 2026-03-25 13:53:01 +0100
Commit message:

 better description
Package: PinPath
Commit: 24d7a11e75d9694bd668196de8ff558be349a87c
Author: Jarno Koetsier <jarno.koetsier@gmail.com>
Date: 2026-03-25 14:06:19 +0100
Commit message:

 Bump package version
Package: PinPath
Commit: ddd7f934249200302ce43a116b0dd4286eed320f
Author: Jarno Koetsier <jarno.koetsier@gmail.com>
Date: 2026-03-25 14:05:59 +0100
Commit message:

 Typo fixes in website
Package: PinPath
Commit: 5305025e497eea8b3949e3616452e9c87b914d69
Author: Jarno Koetsier <jarno.koetsier@gmail.com>
Date: 2026-03-25 14:05:35 +0100
Commit message:

 update documentation
Package: looplook
Commit: f16c250e6856bbec3c895528b83581186a2aee50
Author: Ying Zhang <12207129@zju.edu.cn>
Date: 2026-03-25 21:04:37 +0800
Commit message:

 Bump version to 0.99.8 to re-trigger build due to server network timeout
Package: betterChromVAR
Commit: 32f978d8a40e5dbea31985a4ed181dcdd3c37029
Author: plger <pl.germain@gmail.com>
Date: 2026-03-25 13:49:18 +0100
Commit message:

 version bump
Package: betterChromVAR
Commit: eb07c32af2cec8e48129798cce811ee3c29d32b5
Author: plger <pl.germain@gmail.com>
Date: 2026-03-24 18:11:26 +0100
Commit message:

 version bump
Package: looplook
Commit: a2079de801a915200070beb40200979579a44288
Author: Ying Zhang <12207129@zju.edu.cn>
Date: 2026-03-25 19:42:51 +0800
Commit message:

 Update documentation to remove unicode geq completely and clean Git
Package: OmnipathR
Commit: 45d96664ca0c5cbb9ae91dd8321973226932d0c8
Author: deeenes <turei.denes@gmail.com>
Date: 2026-03-25 12:34:45 +0100
Commit message:

 Bump version: 3.19.9 → 3.19.10
Package: OmnipathR
Commit: 9be17fb70e1116ca211187d01c55562ed99ff778
Author: deeenes <turei.denes@gmail.com>
Date: 2026-03-25 11:51:01 +0100
Commit message:

 Document .slow_doctest usage in AGENTS.md

Explains correct placement (function body, not @examples), why it
must not be exported, and the pattern for nested slow-doctest functions.

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
Package: OmnipathR
Commit: c32fa776efd10db8d4d44ba15e27ab930d7f8560
Author: deeenes <turei.denes@gmail.com>
Date: 2026-03-25 11:50:52 +0100
Commit message:

 Regenerate NAMESPACE and man pages

Remove .slow_doctest export, update Rd files for reactome and
wikipathways functions.

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
Package: OmnipathR
Commit: 1f7f9fb25b182119fb0d0789da367865e5f2a9ea
Author: deeenes <turei.denes@gmail.com>
Date: 2026-03-25 11:50:43 +0100
Commit message:

 Move .slow_doctest() from @examples to function body

.slow_doctest() was placed in @examples blocks in reactome.R and
wikipathways.R, but it must be the first line of the function body
so it can make the calling function return early on build servers.
In @examples it fails because the function is not exported. Also
reverts the export added in the previous commit.

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
Package: OmnipathR
Commit: 6dfb7611706dfe301587383c3066b3980d1e8cfd
Author: deeenes <turei.denes@gmail.com>
Date: 2026-03-25 09:48:50 +0100
Commit message:

 Export .slow_doctest so R CMD check can find it in examples

.slow_doctest() is used in @examples across 30+ functions to skip
slow doctests on build servers, but was marked @noRd and not exported,
causing "could not find function" errors during R CMD check.

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
Package: OmnipathR
Commit: 86fa702fc0ce5f79bab16447f41eac32e0e8b405
Author: deeenes <turei.denes@gmail.com>
Date: 2026-03-24 14:45:56 +0100
Commit message:

 Fix return() inside magrittr pipe in biomart_query buildserver path

return() doesn't work inside a {} block within a magrittr pipe chain
-- it errors with "no function to return from". Restructured the error
handling to break the pipe before the error check, so return() is at
the function's top level.

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
Package: OmnipathR
Commit: 86e81183048386893ba88aba63d971fb14eb142f
Author: jannikfranken <Jannik8513@gmail.com>
Date: 2026-03-24 11:01:48 +0100
Commit message:

 corrected single_gpml fetch
Package: OMA
Commit: 11d78d4b8a5d90369da5318a979979797df81992
Author: Tuomas Borman <60338854+TuomasBorman@users.noreply.github.com>
Date: 2026-03-25 12:57:40 +0200
Commit message:

 Fix Bioc build (#850)
Package: looplook
Commit: b269509b675259902e0fe9f1ffa9a96329346587
Author: Ying Zhang <12207129@zju.edu.cn>
Date: 2026-03-25 18:54:07 +0800
Commit message:

 Fix Unicode, bump version to 0.99.6, and remove Rproj
Package: Rarr
Commit: f10eb15996e74fce0b863232ae594b71d3f17559
Author: Hugo Gruson <git@hugogruson.fr>
Date: 2026-03-25 11:24:36 +0100
Commit message:

 Use custom function instead of R.utils::extract() (#130)
Package: MsBackendMetaboLights
Commit: d606a8fecb7fc12f850426cc98c96fcc1cc3f133
Author: Johannes Rainer <5506112+jorainer@users.noreply.github.com>
Date: 2026-03-25 11:35:10 +0100
Commit message:

 Merge pull request #14 from rformassspectrometry/jomain

feat: add MetaboLights utility functions
Package: MsBackendMetaboLights
Commit: c282c896030f5df24719b7ab102d7acd682bcbb1
Author: Johannes Rainer <johannes.rainer@gmail.com>
Date: 2026-03-24 15:38:17 +0100
Commit message:

 feat: add MetaboLights utility functions

- Add utility functions to retrieve metadata information from
  MetaboLights. These were taken, and modified, from MsIO.
- Add a section to the vignette describing their use.
Package: MsBackendMetaboLights
Commit: 8721da3267ff8d62ba1fe67e9f538bc93ceea0ad
Author: Johannes Rainer <5506112+jorainer@users.noreply.github.com>
Date: 2026-03-03 07:16:48 +0100
Commit message:

 Merge pull request #13 from rformassspectrometry/jomain

Jomain
Package: MsBackendMetaboLights
Commit: ea462688c16500e4aaac73441eb8a9035a51d3f5
Author: Johannes Rainer <johannes.rainer@gmail.com>
Date: 2026-03-02 15:37:37 +0100
Commit message:

 Reformat DESCRIPTION
Package: MsBackendMetaboLights
Commit: 2b8ce9d40719a91e6b5d435af1f7a25dcee97d21
Author: Johannes Rainer <johannes.rainer@gmail.com>
Date: 2026-02-05 08:09:28 +0100
Commit message:

 ci: drop installation of the msdata package
Package: limpa
Commit: 7c1482726dd4004bc04fb54cfc2e7d10b494a6e4
Author: Gordon Smyth <smyth@wehi.edu.au>
Date: 2026-03-25 21:21:38 +1100
Commit message:

 limpa 1.3.10
- New function plotAveVsMis().
- dpcCN() now uses a systematic rather than a random sample of rows.
- Rename argument `sample.column` to `run.column` in EListFromLongFormatFile(), readDIANN() and readSpectronaut().
- Use of `base::is.unsorted` for more efficient checking of whether proteins are already sorted in two functions.
Package: limpa
Commit: 4ac14bfde69a11240133a40323ac5b3faf488193
Author: Gordon Smyth <smyth@wehi.edu.au>
Date: 2026-03-25 21:16:32 +1100
Commit message:

 limpa 1.3.9
- plotPeptides() now allows users to set the x and y axis labels, same as plotProtein().
Package: LimROTS
Commit: b141d052a45cd90e55e03d6f17b2cb05f8b40e84
Author: Ali Youssef <aliali.mostafa99@gmail.com>
Date: 2026-03-25 12:01:24 +0200
Commit message:

 Update the README file and bump the version.
Package: queeems
Commit: 4e793c1d5fce05ac7dbf1be52464083d1f19bebc
Author: thsadiq <hassan.t.sadiq@gmail.com>
Date: 2026-03-25 11:37:03 +0200
Commit message:

 Final touch for Bioc pre-view process
Package: looplook
Commit: 55dce7b0903faab1a187595ff70d7e881dec6586
Author: Ying Zhang <12207129@zju.edu.cn>
Date: 2026-03-25 17:31:18 +0800
Commit message:

 Update looplook.Rmd and bump version to 0.99.5
Package: queeems
Commit: 3267393e176ef9ef6b686bdb46fd57cecc534a46
Author: thsadiq <hassan.t.sadiq@gmail.com>
Date: 2026-03-25 10:43:54 +0200
Commit message:

 Fine-tuned coding syntax
Package: looplook
Commit: 454ef043025193b38effc802e21a1b239917f4bc
Author: Ying Zhang <12207129@zju.edu.cn>
Date: 2026-03-25 11:27:04 +0800
Commit message:

 remove BiocCheck
Package: looplook
Commit: da642b61f9b8849aede4e66b98e90c809057b14e
Author: Ying Zhang <12207129@zju.edu.cn>
Date: 2026-03-25 11:17:07 +0800
Commit message:

 Pass all BiocCheck and R CMD check locally with optimized runtimes
Package: looplook
Commit: eba52c444111ccf789e4eb8422948d357cc8cebe
Author: Ying Zhang <12207129@zju.edu.cn>
Date: 2026-03-25 09:44:49 +0800
Commit message:

 Remove .DS_Store files to pass BiocCheck
Package: PinPath
Commit: a9e82e91c735485622fbf2cde5f0614ffc5a8ba1
Author: Jarno Koetsier <jarno.koetsier@gmail.com>
Date: 2026-03-25 08:10:48 +0100
Commit message:

 empty commit to trigger new build
Package: spatialFDA
Commit: e70d8210bc46c36616c0ec596ac272631a9c0ec4
Author: mjemons <martin.emons@gmail.com>
Date: 2026-03-25 07:30:02 +0100
Commit message:

 fix to old naming and backward compatibility
Package: DenoIST
Commit: 5a33eb8e4f9af228d28aced346c9dc526460d328
Author: Aaron Kwok <akwok@svi.edu.au>
Date: 2026-03-17 18:25:00 +1100
Commit message:

 fixed critical bug in neighbour offset calculation
Package: atacInferCnv
Commit: 18275eae8308a9a84d61ff7c022d44adfa8d97d8
Author: Konstantin Okonechnikov <k.okonechnikov@gmail.com>
Date: 2026-03-25 06:57:41 +0100
Commit message:

 Biconductor fixes: documentation
Package: assorthead
Commit: 7c091ad4f942723ad56c10208eb4c9b7cd76ea4a
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2026-03-25 14:51:22 +1100
Commit message:

 Updated the vendored kaori library.
Package: assorthead
Commit: d86dd3ead0cc3b4d5d8d2def08186a4cf7639494
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2026-03-25 13:29:38 +1100
Commit message:

 Updated almost all libraries that depend on byteme.
Package: assorthead
Commit: bc8c381a87691760dff58dce35b0104abfede57a
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2026-03-13 22:20:24 +1100
Commit message:

 Added headers for tatami_mtx.
Package: alabaster.base
Commit: eaf14753e24fc70e17b7b07e83fdc593dcc623ba
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2026-03-25 14:09:40 +1100
Commit message:

 Bugfix for linking error message in cloneFile().
Package: postNet
Commit: e279dd10680d3fe94fa9f52fe11dc7e7f70a91b5
Author: Krzysztof Szkop <krzysztof.szkop@gmail.com>
Date: 2026-03-24 23:41:40 +0000
Commit message:

 KS
Package: postNet
Commit: 2da6c97330c79242bc03a7ec78d2414c8b5c4eef
Author: Krzysztof Szkop <krzysztof.szkop@gmail.com>
Date: 2026-03-24 23:08:50 +0000
Commit message:

 KS
Package: postNet
Commit: 625505cb4daf80092b4ba3beaee161a36b8bd7f6
Author: Krzysztof Szkop <krzysztof.szkop@gmail.com>
Date: 2026-03-24 23:06:27 +0000
Commit message:

 KS
Package: gCrisprTools
Commit: cc6b147887df44d7189bcf1c2452f3d25d61066a
Author: Russell Bainer <bainerr@eikontx.com>
Date: 2026-03-24 15:39:10 -0700
Commit message:

 update the date in desc
Package: LimROTS
Commit: f56714ec441f35703e9a3d8527323116bb4b62bb
Author: Ali Youssef <aliali.mostafa99@gmail.com>
Date: 2026-03-24 23:28:15 +0200
Commit message:

 bump version and update NEWS
Package: LimROTS
Commit: 08ddbb56944604899edfe5004920b6ed1eb0fc22
Author: Ali Youssef <aliali.mostafa99@gmail.com>
Date: 2026-03-24 23:19:03 +0200
Commit message:

 Add full Cox analysis function supporting final fit method
Package: LimROTS
Commit: 75aa82a45975ab7fb7bc6d5aad38a458d28be3d8
Author: Ali Youssef <aliali.mostafa99@gmail.com>
Date: 2026-03-24 23:14:47 +0200
Commit message:

 Add full Cox analysis function supporting both permutation and bootstrap methods
Package: LimROTS
Commit: abc3d6818ca748b311764efa2798be00b32cd22d
Author: Ali Youssef <aliali.mostafa99@gmail.com>
Date: 2026-03-24 22:58:42 +0200
Commit message:

 Add survival parameter to SanityChecK
Package: LimROTS
Commit: f021e6329ce72383e7d70e79e6da6dbc36477f67
Author: Ali Youssef <aliali.mostafa99@gmail.com>
Date: 2026-03-24 22:52:48 +0200
Commit message:

 Parallel processing handling function for LimROTS survival
Package: LimROTS
Commit: 201480be5fe976c2ce4c93e15e4ad7149109d0b0
Author: Ali Youssef <aliali.mostafa99@gmail.com>
Date: 2026-03-24 22:50:20 +0200
Commit message:

 The main Function for the LimROTS survival analysis
Package: LimROTS
Commit: fb63cd17bef71d2363a454f838a46f138133e775
Author: Ali Youssef <aliali.mostafa99@gmail.com>
Date: 2026-03-24 22:37:55 +0200
Commit message:

 Add survival parameter to Check_SummarizedExperiment
Package: atacInferCnv
Commit: 6e82e71c854850d8b9afa15aabeb49ebbf28d78a
Author: Konstantin Okonechnikov <k.okonechnikov@gmail.com>
Date: 2026-03-24 21:30:48 +0100
Commit message:

 Minor fixes for Bioc
Package: atacInferCnv
Commit: b0442871a0fee06ef6e25b8cb121256013dd1d9b
Author: Konstantin Okonechnikov <k.okonechnikov@gmail.com>
Date: 2026-03-23 14:34:34 +0100
Commit message:

 Fix issues for Bioconductor with infercnv object return
Package: LimROTS
Commit: e24ab6ff624b0e76e0de7af8466c5e524b4a3903
Author: Ali Youssef <aliali.mostafa99@gmail.com>
Date: 2026-03-24 22:29:46 +0200
Commit message:

 Version bump
Package: LimROTS
Commit: 5d91af6c6532f87299fd8b3d8e9f5742c5e6c772
Author: Ali Youssef <aliali.mostafa99@gmail.com>
Date: 2026-03-24 11:53:15 +0200
Commit message:

 Merge pull request #34 from raivo-otus/feat/assay-selection
Package: LimROTS
Commit: 1397f5d628c6bb347a0a1121aed43568e8eaa9e0
Author: raivo-otus <rasmus.hindstrom@utu.fi>
Date: 2026-03-22 11:08:00 +0200
Commit message:

 update documentation
Package: LimROTS
Commit: 45bb8650d7e81bddb3e54db8d8d03030290c4705
Author: raivo-otus <rasmus.hindstrom@utu.fi>
Date: 2026-03-22 11:07:39 +0200
Commit message:

 fix
Package: LimROTS
Commit: e4d9db05b978ae1c28e5e8a40ce10460d28dd65c
Author: raivo-otus <rasmus.hindstrom@utu.fi>
Date: 2026-03-22 11:03:30 +0200
Commit message:

 Add contributor
Package: LimROTS
Commit: 81d071cd7eeca3d8309eff683754d714db15afa1
Author: raivo-otus <rasmus.hindstrom@utu.fi>
Date: 2026-03-22 10:55:47 +0200
Commit message:

 Add assay selection and unit tests
Package: XeniumIO
Commit: e0aec231676795286735d4b4afe276cc33765ee4
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2026-03-24 16:19:51 -0400
Commit message:

 version bump 1.3.3
Package: XeniumIO
Commit: abba11ded50ca385a08b0f1b4566c9ac7af6f69b
Author: Marcel Ramos Pérez <LiNk-NY@users.noreply.github.com>
Date: 2026-03-24 16:19:14 -0400
Commit message:

 Add missing funder entries to Authors@R in DESCRIPTION (#3)
Package: XeniumIO
Commit: 07df9f83ed834e71a9fde38369b21c8010b52bfb
Author: Copilot <198982749+Copilot@users.noreply.github.com>
Date: 2026-03-24 15:37:01 -0400
Commit message:

 Adopt centralized reusable workflow from waldronlab/.github (#4)

* Replace pr_check.yml with ci.yml caller for central reusable workflow

Co-authored-by: LiNk-NY <4392950+LiNk-NY@users.noreply.github.com>
Agent-Logs-Url: https://github.com/waldronlab/XeniumIO/sessions/b988f50a-06c4-425d-b1fc-d93ae75b57ae

---------

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>
Package: MultiAssayExperiment
Commit: e2ff26c19761c83e094c619832aa1f2f66b47105
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2026-03-24 13:54:38 -0400
Commit message:

 version bump 1.37.3
Package: MultiAssayExperiment
Commit: e88e5f887e7a91612ef95d390c7c7f918ca84c3e
Author: Marcel Ramos Pérez <LiNk-NY@users.noreply.github.com>
Date: 2026-03-24 13:38:09 -0400
Commit message:

 Add missing funder entries to Authors@R in DESCRIPTION (#345)
Package: MultiAssayExperiment
Commit: d6a700d4f2127cb4705afa2f09e4180f8ab03c5e
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2026-03-24 11:34:01 -0400
Commit message:

 update GHA pr_check.yml
Package: RBedMethyl
Commit: da9e02f4bb0b320aee409cceb1fa599983446285
Author: vaslem <vaslemonidis@hotmail.com>
Date: 2026-03-24 18:02:56 +0100
Commit message:

 Made BSseq an Import, so that coercion works in all cases
Package: RBedMethyl
Commit: 03a30b6995dba730b3fc4dc5f56775c5c9ec589a
Author: vaslem <vaslemonidis@hotmail.com>
Date: 2026-02-19 12:57:02 +0100
Commit message:

 Update vignette to clarify usage of subsetByRegion with bracketing index system
Package: RBedMethyl
Commit: 4686fb2952e999bee8ca83420cccb02278761f3e
Author: vaslem <vaslemonidis@hotmail.com>
Date: 2026-02-19 12:55:47 +0100
Commit message:

 Rename filterCoverage to filterByCoverage for consistency and update documentation and examples accordingly.
Package: RBedMethyl
Commit: c4a96678b4db0d1cd84b6aa4be043b5cb067b5e4
Author: vaslem <vaslemonidis@hotmail.com>
Date: 2026-02-19 12:49:37 +0100
Commit message:

 Remove .lintr file and add it to .gitignore
Package: RBedMethyl
Commit: aeb0441abe183d0b1e7540226eb2570fa9382e5a
Author: vaslem <vaslemonidis@hotmail.com>
Date: 2026-02-19 12:48:44 +0100
Commit message:

 Add new vignette for ONT-scale workflows with RBedMethyl and remove old vignette
Package: PinPath
Commit: 317db40018b79b6485c1bd06326790e738e2bc6e
Author: Jarno Koetsier <jarno.koetsier@gmail.com>
Date: 2026-03-24 17:17:36 +0100
Commit message:

 file location of output files explicitely indicated in tutorials
Package: Rarr
Commit: 23d7350fa8c7716afc3a1afa983b1db678135685
Author: Hugo Gruson <git@hugogruson.fr>
Date: 2026-03-24 13:59:39 +0100
Commit message:

 Check for chunk existence early
Package: Rarr
Commit: 0b3488729fcc7213399faa2835ee9131a13a0c1e
Author: Hugo Gruson <git@hugogruson.fr>
Date: 2026-03-23 18:57:00 +0100
Commit message:

 Use faster str2lang() function
Package: AnnotationGx
Commit: dc8d14d4414ddd1dc64d66df2afddf79a1e032fe
Author: mtran <mtran256@uwo.ca>
Date: 2026-03-24 09:20:15 -0400
Commit message:

 docs: set BHK as maintainer
Package: parati
Commit: 0efd43c6397ce53a631d3724f895b8aa52cf193a
Author: liangyong1991 <496187474@qq.com>
Date: 2026-03-24 21:19:30 +0800
Commit message:

 Modified DESCRIPTION, R/io_helpers.R and R/io_vcf.R
Package: MetaProViz
Commit: d317f242e3bfa7eec5691dc9f44fca3693b69ed5
Author: Jannik Franken <jannik8513@gmailcom>
Date: 2026-03-23 18:32:58 +0100
Commit message:

 added metabolite exclusion to make_gene_metab_set
Package: MetaProViz
Commit: 0927b689ffe9f579f0a90bc74f5f3b948bcaae48
Author: Jannik Franken <jannik8513@gmailcom>
Date: 2026-03-23 16:48:34 +0100
Commit message:

 re-ran documentation
Package: MetaProViz
Commit: 80e74bd91419b695d202b59e1b2493c1c73aef8d
Author: Jannik Franken <jannik8513@gmailcom>
Date: 2026-03-23 16:29:42 +0100
Commit message:

 removed metsigdb_wikipathways example
Package: MetaProViz
Commit: f68bec066eb538088eef969c049d550884022c15
Author: Christina Schmidt <christina.schmidt1@outlook.de>
Date: 2026-03-23 16:05:10 +0100
Commit message:

 Changed Overview Figure to graphical abstract of preprint
Package: MetaProViz
Commit: edfc6188afd7a48fe165caac594732da5c8cdf0e
Author: Christina Schmidt <christina.schmidt1@outlook.de>
Date: 2026-03-23 16:02:21 +0100
Commit message:

 Added Bioconductor install to readme and vignettes
Package: MetaProViz
Commit: f9d093661ce652d287efbaf20eca5d3b26bd4815
Author: Christina Schmidt <christina.schmidt1@outlook.de>
Date: 2026-03-23 15:47:09 +0100
Commit message:

 PNG assets are no longer forcibly excluded in package-build contexts
Package: MetaProViz
Commit: 66bd469a8c6c71218e8def9703b93b9036c447bd
Author: Christina Schmidt <christina.schmidt1@outlook.de>
Date: 2026-03-23 15:44:55 +0100
Commit message:

 Disabling crop avoids magick-dependent post-processing on builders lacking magick (should fix warnings on Bioconductor build)
Package: MetaProViz
Commit: b3e36b9e2c89eaebbf948acbb91a01c603c84ea8
Author: Christina Schmidt <christina.schmidt1@outlook.de>
Date: 2026-03-23 15:44:23 +0100
Commit message:

 Removed reliance on figure path, to fix display on .io pages
Package: MetaProViz
Commit: 8ce8ad9e679c1dac27a7c20bbf1734df591ca967
Author: Jannik Franken <jannik8513@gmailcom>
Date: 2026-03-23 13:21:32 +0100
Commit message:

 cleaned op exclusion metabolites
Package: MetaProViz
Commit: 41f74f5565408466c39356b0e6993049913eaf4e
Author: Jannik Franken <jannik8513@gmailcom>
Date: 2026-03-23 13:20:25 +0100
Commit message:

 included traverse_ids function
Package: MetaProViz
Commit: da0a50ffb3ebb2fa004dd0864f4ca2ae7c18f219
Author: jannikfranken <jannik8513@gmailcom>
Date: 2026-03-19 17:41:02 +0100
Commit message:

 re-wrote metsigdb to enable removal of non-wanted metabolites across IDs
Package: MetaProViz
Commit: 4a63125b2b291938a24607039a610231919e2188
Author: Jannik Franken <jannik8513@gmailcom>
Date: 2026-03-19 16:28:51 +0100
Commit message:

 added force install OmnipathR devel
Package: MetaProViz
Commit: e2e93265a16ef6327733d314006570409e44ce47
Author: jannikfranken <jannik8513@gmailcom>
Date: 2026-03-19 16:06:49 +0100
Commit message:

 update OmnipathR version
Package: MetaProViz
Commit: 2595a3eb0a64fdbe23795147f3b16cd1da18d401
Author: Jannik Franken <jannik8513@gmailcom>
Date: 2026-03-19 14:54:11 +0100
Commit message:

 test after new OmnipathR changes
Package: MetaProViz
Commit: 5adf399245f57bc80da85cba71801a5a83380246
Author: Christina Schmidt <christina.schmidt1@outlook.de>
Date: 2026-03-19 13:55:38 +0100
Commit message:

 Remove image from quick-start.Rmd

Removed image tag from quick-start documentation.
Package: MetaProViz
Commit: 4e84d6b7717a9a9f42913cb09765ad7d93900fb2
Author: Jannik Franken <jannik8513@gmailcom>
Date: 2026-03-04 10:21:51 +0000
Commit message:

 added NSE workaround for variables to address RCMD check NOTE
Package: MetaProViz
Commit: dd6959fe27ab41f6512b3c3f561dfd159600d46d
Author: Jannik Franken <jannik8513@gmailcom>
Date: 2026-03-04 10:07:41 +0000
Commit message:

 fixed OmnipathR new function dependencies and imports
Package: MetaProViz
Commit: 313a4e7af2a29807a99c0a7e8718bda8c6dafa86
Author: Jannik Franken <jannik8513@gmailcom>
Date: 2026-03-03 17:01:37 +0000
Commit message:

 Merge branch 'devel' of https://github.com/saezlab/MetaProViz into devel
Package: MetaProViz
Commit: a25eaf080268ba3505b0bd9b882f389308372f65
Author: Jannik Franken <jannik8513@gmailcom>
Date: 2026-03-03 17:01:32 +0000
Commit message:

 added metsigdb_reactome and metsigdb_wikipathways
Package: parati
Commit: 7756497153fa9652ba27c63430031395e636916c
Author: liangyong1991 <496187474@qq.com>
Date: 2026-03-24 19:46:57 +0800
Commit message:

 Remove vcf_to_plink.R and address reviewer comments
Package: EWCE
Commit: 4d035dafb98f280480fde7c5fff2615e1fcd66bb
Author: HDash <16350928+HDash@users.noreply.github.com>
Date: 2026-03-18 11:54:31 +0000
Commit message:

 fix get_exp_data_for_bootstrapped_genes docs

Clarify the placeholder documentation and align the documented arguments with the function signature so generated Rd stays valid. Also include a small run_DGE test correction by coercing level2annot to a factor.
Package: EWCE
Commit: 089369e0ad9001b5549f27269f1ba73246747795
Author: HDash <16350928+HDash@users.noreply.github.com>
Date: 2026-03-17 14:32:42 +0000
Commit message:

 bug fix species validation sentinel handling
Package: EWCE
Commit: 8d432eb929a62dd21876430426930b3b771d42f3
Author: HDash <16350928+HDash@users.noreply.github.com>
Date: 2026-03-17 14:12:15 +0000
Commit message:

 version bump in devel
Package: EWCE
Commit: a8186ca059902797eb64fd023971b7933f960041
Author: HDash <16350928+HDash@users.noreply.github.com>
Date: 2026-03-17 14:12:15 +0000
Commit message:

 bug fix bootstrap input validation
Package: GEOmetadb
Commit: 958a0811940b4177d1e1ac7b1894836e9b51564f
Author: Zhu <zhujack@nci-02219617-m.verizon.net>
Date: 2026-03-24 07:13:54 -0400
Commit message:

 Use tbl instead of src_sqlite in  vignettes/GEOmetadb.Rmd
Package: postNet
Commit: 2578b24c5bf7610265aa812cdf540f54cfd88cc9
Author: Krzysztof Szkop <krzysztof.szkop@gmail.com>
Date: 2026-03-24 10:55:47 +0000
Commit message:

 KS
Package: sosta
Commit: cc0428117469d9d9eae1efa0ef424a083a5b1aa3
Author: sgunz <samuel.gunz@uzh.ch>
Date: 2026-03-24 09:33:27 +0100
Commit message:

 moved all GHA to check-bioc
Package: sosta
Commit: d41efabe0a4a0f60effc3cd63578dfba20c918e1
Author: sgunz <samuel.gunz@uzh.ch>
Date: 2026-03-24 09:12:09 +0100
Commit message:

 add bioc GHA
Package: sosta
Commit: 62a20e7eededd6c8108b40e287d2694f077c5173
Author: Samuel Gunz <samuel.gunz@uzh.ch>
Date: 2026-03-23 10:21:38 +0100
Commit message:

 Different changes related to `sosta` revision (#18)

* improved threshold detection; more simulation args

* added distance to fov boundary calculation to vignette

* shapeMetrics assertion and FOV border

* added manuals, updated version and different files
Package: XAItest
Commit: 64c37aad751b2e142e6230e9595230ce816568b8
Author: gui <ghislain.fievet@gmail.com>
Date: 2026-03-24 08:30:37 +0100
Commit message:

 Bump version and fix documentation warnings
Package: cellNexus
Commit: 938e238b65101f6ebf702fa6bee99d0601058d95
Author: Mengyuan Shen <129487421+myushen@users.noreply.github.com>
Date: 2026-03-24 16:31:05 +1100
Commit message:

 Merge pull request #96 from myushen/bioconductor

Fix newline formatting and update metadata handling
Package: cellNexus
Commit: 450a07b2c15207e6a2eab95316d3474e3c1c2035
Author: myushen <mengyuan.shen@outlook.com>
Date: 2026-03-24 12:27:54 +1100
Commit message:

 version bump
Package: cellNexus
Commit: 8dd9102b8136aca30177ddb12c5c0d9c03c0e2e0
Author: myushen <mengyuan.shen@outlook.com>
Date: 2026-03-23 16:54:48 +1100
Commit message:

 use sample data unit test
Package: cellNexus
Commit: e7c81ce34d71dd6c72c086f4f961b888153a9d48
Author: myushen <mengyuan.shen@outlook.com>
Date: 2026-03-23 15:46:02 +1100
Commit message:

 get_metadata by default grabs cellnexus meta
Package: cellNexus
Commit: 449ba6f161a48cf59f8ad044fa0e0d19a0732026
Author: myushen <mengyuan.shen@outlook.com>
Date: 2026-03-23 12:50:00 +1100
Commit message:

 remove dev/. newline after each pipe
Package: cellNexus
Commit: 64b8c20adb25b3daf1c45779583d293bd1504a86
Author: stemangiola <mangiolastefano@gmail.com>
Date: 2026-03-21 17:49:57 +1100
Commit message:

 update website Rbuildignore
Package: cellNexus
Commit: 3c79d21c24fff45e6277a45d35915385127212a2
Author: stemangiola <mangiolastefano@gmail.com>
Date: 2026-03-21 17:49:24 +1100
Commit message:

 update website renv
Package: BamScale
Commit: 1666311e0cc5ba906077e5b5c8b8e1ba3f4cf9d8
Author: Chirag Parsania <chirag.parsania@gmail.com>
Date: 2026-03-24 16:43:45 +1100
Commit message:

 Increment version number to 0.99.7
Package: BamScale
Commit: 4d09145cc90c1e1abfb5ee8fd48b7ed84f9a440c
Author: Chirag Parsania <chirag.parsania@gmail.com>
Date: 2026-03-24 16:43:25 +1100
Commit message:

 Polish benchmark docs, pkgdown article, and readme
Package: BamScale
Commit: 2fbd3df4cb5896d8ecd6ab632cfceb94e0cc832a
Author: Chirag Parsania <chirag.parsania@gmail.com>
Date: 2026-03-24 15:56:32 +1100
Commit message:

 Merge branch 'perf/recover-hotpath'
Package: BamScale
Commit: d26ddc4dc2962d965b1f48423cd7b992b1e0894d
Author: Chirag Parsania <chirag.parsania@gmail.com>
Date: 2026-03-24 15:55:15 +1100
Commit message:

 update gitignore
Package: BamScale
Commit: 8942a248e3c498a043d556cf73527faf29a7771d
Author: Chirag Parsania <chirag.parsania@gmail.com>
Date: 2026-03-24 15:52:28 +1100
Commit message:

 Finalize benchmark reports and manuscript result runs
Package: BamScale
Commit: 9a27bad3eb9d4b417d3a105031721987db7b5813
Author: Chirag Parsania <chirag.parsania@gmail.com>
Date: 2026-03-24 15:49:55 +1100
Commit message:

 Restore qname/cigar hot path for benchmark-critical workloads
Package: SingleCellExperiment
Commit: f781efae4ec160ff109f4b53b47d39e41469e536
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2026-03-24 15:30:43 +1100
Commit message:

 Force row/colPairs to return sparse matrices in triplet form.

This counteracts a change to Matrix defaults to align with our documentation.
Package: dnaEPICO
Commit: 9b3a557297fbe1cfe550b9440b8757b8eed3d552
Author: Paul Ruiz <ruizpint@qut.edu.au>
Date: 2026-03-24 14:56:10 +1000
Commit message:

 Bioconductor changes in test_that 0.99.7
Package: dnaEPICO
Commit: a97d731a5eab97d8e58be50c528341126c2ceada
Author: Paul Ruiz <ruizpint@qut.edu.au>
Date: 2026-03-24 14:51:52 +1000
Commit message:

 Bioconductor changes in test_that 0.99.7
Package: dnaEPICO
Commit: be5c3b53bbfa7418bc522faaa131437ad9c9ee24
Author: Paul Ruiz <ruizpint@qut.edu.au>
Date: 2026-03-24 14:08:32 +1000
Commit message:

 Bioconductor full test version 0.99.6
Package: dnaEPICO
Commit: 572aa109bb5b4f50b8a3c397b858f9b5d4607d18
Author: Paul Ruiz <ruizpint@qut.edu.au>
Date: 2026-03-24 14:05:08 +1000
Commit message:

 Bioconductor reduce check time 0.99.6
Package: dnaEPICO
Commit: 1087001ad5debea32e4bcccf545844f0f42abe9a
Author: Paul Ruiz <ruizpint@qut.edu.au>
Date: 2026-03-24 13:22:07 +1000
Commit message:

 Bioconductor reduce check time 0.99.5
Package: dnaEPICO
Commit: b7f260cecff8b271c7a4b9a9cf779964549eedc1
Author: Paul Ruiz <ruizpint@qut.edu.au>
Date: 2026-03-24 12:51:56 +1000
Commit message:

 Bioconductor reduce check time 0.99.4
Package: dnaEPICO
Commit: 2dd9546c35ee158191d0cb6a72901f845d6137e8
Author: Paul Ruiz <ruizpint@qut.edu.au>
Date: 2026-03-24 12:33:25 +1000
Commit message:

 Bioconductor reduce check time 0.99.3
Package: VISTA
Commit: be96afc7e6154a051f9c4f653cb0d2661cedeb2d
Author: Chirag Parsania <chirag.parsania@gmail.com>
Date: 2026-03-24 13:02:13 +1100
Commit message:

 version increment to 0.99.1
Package: VISTA
Commit: 153b856f3bb32c21660ff320b3e9f04cc16c40a0
Author: Chirag Parsania <chirag.parsania@gmail.com>
Date: 2026-03-24 13:00:35 +1100
Commit message:

 Fix Rd Unicode and remove tracked build clutter
Package: VISTA
Commit: 32cb1b53851b31b773dfcc74d40ee6774ed016db
Author: Chirag Parsania <chirag.parsania@gmail.com>
Date: 2026-03-24 12:56:34 +1100
Commit message:

 Fix Gviz plotting edge cases and clean Bioc check artifacts
Package: dnaEPICO
Commit: 0d80f4b92cddf489e59144bf508139a7baaa992c
Author: Paul Ruiz <ruizpint@qut.edu.au>
Date: 2026-03-24 11:01:47 +1000
Commit message:

 Bioconductor reduce check time 0.99.2
Package: dnaEPICO
Commit: 927d40b47122c07a0305b708741a2026749e1876
Author: Paul Ruiz <ruizpint@qut.edu.au>
Date: 2026-03-24 10:23:09 +1000
Commit message:

 Bioconductor warnings and errors
Package: OmnipathR
Commit: a2c4f00a70d9a2f25a1fd0b055add58bb26491f4
Author: deeenes <turei.denes@gmail.com>
Date: 2026-03-23 20:21:55 +0100
Commit message:

 Bump version: 3.19.8 → 3.19.9
Package: OmnipathR
Commit: 4e099350d01199a45633b59f243854cd5f260c7d
Author: deeenes <turei.denes@gmail.com>
Date: 2026-03-23 20:21:49 +0100
Commit message:

 Merge branch 'devel' of github.com:saezlab/OmnipathR into devel
Package: OmnipathR
Commit: c8cd4692267a07ca16315016dc1decd8c1eae820
Author: jannikfranken <Jannik8513@gmail.com>
Date: 2026-03-23 17:05:37 +0100
Commit message:

 added MacDB metabolite-cancer associations function
Package: OmnipathR
Commit: a4acb4c33e4298edd6d1a2c2303806e43cf07c0c
Author: jannikfranken <Jannik8513@gmail.com>
Date: 2026-03-19 14:48:43 +0100
Commit message:

 use OmnipathR downloader everywhere
Package: OmnipathR
Commit: 6e188b237a1d3aca0692c6cfc471d099b4cf36d3
Author: jannikfranken <Jannik8513@gmail.com>
Date: 2026-03-17 17:46:36 +0100
Commit message:

 Bump version: 3.19.7 → 3.19.8
Package: OmnipathR
Commit: 4e7460b27218e83ca6cfcfd3b04ccb42162ed069
Author: jannikfranken <Jannik8513@gmail.com>
Date: 2026-03-17 17:38:11 +0100
Commit message:

 finalised code structure, added comments
Package: OmnipathR
Commit: ce8796f5a0e3746b01cc88bc5c0106ac2515b11b
Author: jannikfranken <Jannik8513@gmail.com>
Date: 2026-03-05 12:42:39 +0000
Commit message:

 refactoring wikipathways sparql function to fit OmnipathR structure and coding style
Package: OmnipathR
Commit: b8ff8f633917f64db2cac227e0e8e1259ff63e74
Author: jannikfranken <Jannik8513@gmail.com>
Date: 2026-03-05 12:42:08 +0000
Commit message:

 added Saezverse and OmnipathR subdir to AGENTS.md
Package: OmnipathR
Commit: 96389d93d6012329a7cb2aee8232bbe5f3ca3d96
Author: jannikfranken <Jannik8513@gmail.com>
Date: 2026-03-04 14:22:03 +0000
Commit message:

 enabled multi-species query for wikipathways and re-ran documentation
Package: OmnipathR
Commit: 7d40e9dc5ecf8c18b07bdb1295a71e738800291b
Author: deeenes <turei.denes@gmail.com>
Date: 2026-03-23 20:16:31 +0100
Commit message:

 Bump version: 3.19.7 → 3.19.8
Package: OmnipathR
Commit: 15fb7be76732d027ee1dcda319e876004cd968cd
Author: deeenes <turei.denes@gmail.com>
Date: 2026-03-23 19:43:09 +0100
Commit message:

 On buildservers, return empty tibble on BioMart failure instead of error

When running on Bioconductor or OmniPath build servers, BioMart
errors now emit a warning and return an empty data frame with the
correct columns, so build & check doesn't fail due to temporary
third-party API outages.

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
Package: OmnipathR
Commit: 0454531c974682eb46d12542072a5b3ab6149673
Author: deeenes <turei.denes@gmail.com>
Date: 2026-03-23 19:33:55 +0100
Commit message:

 Add cache system vignette

Documents data structures (records, versions, keys), core operations
(save, load, search, remove), cleanup functions, key generation, and
the locking mechanism.

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
Package: OmnipathR
Commit: a21a05f348be09d47c5395c51c4fa17073e8b14d
Author: deeenes <turei.denes@gmail.com>
Date: 2026-03-23 19:33:48 +0100
Commit message:

 Add unit tests for the cache system

51 tests covering cache key generation, save/load round-trips,
removal by key/URL, search, cleanup, version filtering, and status
updates. Tests use temporary cache directories to avoid interfering
with the user's real cache.

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
Package: OmnipathR
Commit: af2c04af66c520b8efee18ce21aef3e49d2683e4
Author: deeenes <turei.denes@gmail.com>
Date: 2026-03-23 19:21:50 +0100
Commit message:

 Fix omnipath_cache_remove wiping entire cache on single key removal

When removing a cache entry by key or URL without version filtering,
the map over omnipath_cache_keep_versions was called with status=NULL,
causing statuses %in% NULL to evaluate to FALSE for all versions in
all remaining records. This effectively wiped the entire cache instead
of just the targeted entry. The fix skips version filtering when no
version filter parameters are provided.

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
Package: OmnipathR
Commit: 026bf343615fc86f7df5fd8abba02ee3ef223564
Author: deeenes <turei.denes@gmail.com>
Date: 2026-03-23 19:12:42 +0100
Commit message:

 Handle BioMart error responses gracefully in biomart_query

When Ensembl BioMart returns a server error (e.g. database
connection failure) instead of data, the response is now detected,
removed from cache, and a clear error is raised. Previously, the
error text was returned as a 1-column data frame, causing a
cryptic set_names() failure downstream.

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
Package: OmnipathR
Commit: d305f1f5d4ee004436ad7c5395bacb033f026e3f
Author: deeenes <turei.denes@gmail.com>
Date: 2026-03-23 19:12:27 +0100
Commit message:

 Remove stray top-level SPARQL call in wikipathways.R

The call `get_wikipathways_metabolites_sparql()` at file scope
caused a network request at package load time, breaking load_all()
and package installation when the WikiPathways SPARQL endpoint
was unavailable.

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
Package: recoup
Commit: 6ef1a7ad563090a5cf0a04e1954b2711b6b67f49
Author: Panagiotis Moulos <pmoulos@gmail.com>
Date: 2026-03-23 18:33:02 +0000
Commit message:

 Fixed 1 warning
Package: SpliceImpactR
Commit: 25ae9d13179e33be609b6479fb62d4c7432328eb
Author: Zachary Wakefield <zachpwakefield@gmail.com>
Date: 2026-03-23 11:58:30 -0600
Commit message:

 Merge branch 'main' into devel
"v bump again"
Package: SpliceImpactR
Commit: 5436813f56606af40cc33e917f2b8fb75bb90c12
Author: Zachary Wakefield <zachpwakefield@gmail.com>
Date: 2026-03-23 11:54:15 -0600
Commit message:

 fixed rcmd issue
Package: SpliceImpactR
Commit: 97a3b687c5be267f36d9725268294fca238fbd9f
Author: Zachary Wakefield <zachpwakefield@gmail.com>
Date: 2026-03-23 11:18:10 -0600
Commit message:

 Merge branch 'main' into devel
Comprehensive update to address reviews
Package: SpliceImpactR
Commit: 4e655f362235ea2a3272fd7cc7dda0fd7ddf7ca0
Author: Zachary Wakefield <zachpwakefield@gmail.com>
Date: 2026-03-23 11:05:30 -0600
Commit message:

 version bump p2
Package: SpliceImpactR
Commit: 66307909675ef6533287ba4e1300c612c5d865e1
Author: Zachary Wakefield <zachpwakefield@gmail.com>
Date: 2026-03-23 11:04:31 -0600
Commit message:

 version bump
Package: SpliceImpactR
Commit: ff2e32ec05fa75965d06bf089178e985ff3e24e7
Author: Zachary Wakefield <zachpwakefield@gmail.com>
Date: 2026-03-23 10:59:17 -0600
Commit message:

 follow up commits to address example and various other issues
Package: SpliceImpactR
Commit: bbfa0295ad86ce50e57d0f8364289af4ce7c43c2
Author: Zachary Wakefield <zachpwakefield@gmail.com>
Date: 2026-03-17 00:26:50 -0600
Commit message:

 complete update, S4, caching, etc
Package: SpliceImpactR
Commit: efea06f6caa40781967a8346a4e03d82095dfa6c
Author: Zachary Wakefield <zachpwakefield@gmail.com>
Date: 2026-03-04 12:05:07 -0500
Commit message:

 started S4 conversion, wrapper gives out S4 and many accession fxns for S4 summarizedexperiment
Package: SpliceImpactR
Commit: 663c7e4e1611414dcd82adc6dd5a520783a30129
Author: Zachary Wakefield <zachpwakefield@gmail.com>
Date: 2026-03-04 00:19:17 -0500
Commit message:

 slight add to vignette and readme
Package: SpliceImpactR
Commit: d7015c74f5312627ed0f7efb0e688d9203868838
Author: Zachary Wakefield <zachpwakefield@gmail.com>
Date: 2026-03-03 16:58:41 -0500
Commit message:

 reworked output data frame to be more interpretable, S4 coming. Plus removed upset plots because they were useless
Package: SpliceImpactR
Commit: 577e3a8577aa2f39f82fcfb7a7cf9b28fe816507
Author: Zachary Wakefield <zachpwakefield@gmail.com>
Date: 2026-03-03 12:30:55 -0500
Commit message:

 fixed transcript_type bug and added trans/prot viz to readme
Package: SpliceImpactR
Commit: fdf37137a051daca7a2638de03aa7c66341a2a63
Author: Zachary Wakefield <zachpwakefield@gmail.com>
Date: 2026-03-02 11:21:12 -0500
Commit message:

 readme updates
Package: SpliceImpactR
Commit: 44bcee9d399e68f5df3dee27f488c3bee4ca59f2
Author: Zachary Wakefield <zachpwakefield@gmail.com>
Date: 2026-03-02 10:29:52 -0500
Commit message:

 added transcript/protein visualization, fixed protein coding protocol in matching, updated protein feature test sets
Package: SpliceImpactR
Commit: 7055e101bb28fc5ed602c54ce4d412cf4fb95997
Author: Zachary Wakefield <zachpwakefield@gmail.com>
Date: 2026-02-04 14:02:59 -0500
Commit message:

 updated exon class pref for A3SS and A5SS to reflect more accurate placements
Package: SpliceImpactR
Commit: ae17cc20e3778d6337aa78a994f6409e80e8c0ea
Author: Zachary Wakefield <zachpwakefield@gmail.com>
Date: 2026-02-04 12:38:22 -0500
Commit message:

 uncommented the accident
Package: SpliceImpactR
Commit: 7a03ed90729bb79f35fa35c946b305e851b8fba4
Author: Zachary Wakefield <zachpwakefield@gmail.com>
Date: 2026-02-04 10:59:24 -0500
Commit message:

 roxygenized
Package: SpliceImpactR
Commit: 39be7d467d3e5d565d9e175b8ecd75c6f5c3624d
Author: Zachary Wakefield <zachpwakefield@gmail.com>
Date: 2026-02-04 10:56:13 -0500
Commit message:

 add non combine to protein features as default
Package: SpliceImpactR
Commit: 489168d2f55eee4b6a95b1e25e49fa50cf29ecfb
Author: Zachary Wakefield <zachpwakefield@gmail.com>
Date: 2026-02-03 22:31:58 -0500
Commit message:

 another one
Package: SpliceImpactR
Commit: fd9f03842aee3859fd108244784743c1d21b8596
Author: Zachary Wakefield <zachpwakefield@gmail.com>
Date: 2026-02-03 17:55:55 -0500
Commit message:

 another one in Rd
Package: SpliceImpactR
Commit: 4e301e60184faa85c5e2d13afae87fe85de1f6b0
Author: Zachary Wakefield <zachpwakefield@gmail.com>
Date: 2026-02-03 17:54:33 -0500
Commit message:

 fix linear motif Rd
Package: SpliceImpactR
Commit: efec677faf71a0bac379349af2d05f7835422f6b
Author: Zachary Wakefield <zachpwakefield@gmail.com>
Date: 2026-02-03 17:17:55 -0500
Commit message:

 Full update to ppi operations
Package: SpliceImpactR
Commit: 11cf6282bec27c910ff13f46cf7889d779ca6751
Author: Zachary Wakefield <zachpwakefield@gmail.com>
Date: 2026-01-07 12:18:58 -0500
Commit message:

 get_domains checks now for full protein overlap in AS as well as ATE
Package: SpliceImpactR
Commit: 9ad9060f4428316f68633da72de89c01747d3927
Author: Zachary Wakefield <zachpwakefield@gmail.com>
Date: 2025-12-29 15:24:42 -0500
Commit message:

 added individual event probe fix to filter on form
Package: SpliceImpactR
Commit: e305d03d18670d9777bb2a0b7ac1a3c25ff4393d
Author: Zachary Wakefield <zachpwakefield@gmail.com>
Date: 2025-12-16 16:44:27 -0500
Commit message:

 added individual event probe
Package: SpliceImpactR
Commit: 516b32d4ed7af3f1c1dd6d6cfafc21060103dd91
Author: Zachary Wakefield <zachpwakefield@gmail.com>
Date: 2025-12-16 11:07:17 -0500
Commit message:

 more readme updates
Package: SpliceImpactR
Commit: c3a5e98dc63d4118f1a34b1e560b33ac85d94d9d
Author: Zachary Wakefield <zachpwakefield@gmail.com>
Date: 2025-12-16 10:57:06 -0500
Commit message:

 small readme change
Package: SpliceImpactR
Commit: fb16607c67a0f7b880d6befedf55a0fef2f09b28
Author: Zachary Wakefield <zachpwakefield@gmail.com>
Date: 2025-12-16 10:55:18 -0500
Commit message:

 readme fix
Package: SpliceImpactR
Commit: 236ab07c5c1ca6ea7ba1e26da907e881fe721b21
Author: Zachary Wakefield <zachpwakefield@gmail.com>
Date: 2025-12-11 15:48:04 -0500
Commit message:

 version -> release
Package: SpliceImpactR
Commit: b5b285130ee293adcd82ef22b4813691e4ff4ef8
Author: Zachary Wakefield <zachpwakefield@gmail.com>
Date: 2025-12-11 14:43:13 -0500
Commit message:

 change default to event_max and clean GeneID in precalc ds
Package: SpliceImpactR
Commit: 744425a0c9a8e70b879b2ec0e72990e0f35f1ab8
Author: Zachary Wakefield <zachpwakefield@gmail.com>
Date: 2025-12-09 16:17:36 -0500
Commit message:

 Add option for AFE/ALE zero-filling strategy
Package: SpliceImpactR
Commit: ed331969d8f4cd53bc4b2c0642959fd0b1f5d294
Author: Zachary Wakefield <zachpwakefield@gmail.com>
Date: 2025-11-17 17:54:06 -0500
Commit message:

 psuedocount for size factor calc added to avoid explosion
Package: SpliceImpactR
Commit: 015ebc0c3e137b50adb0bb22c53ea16e8daf076f
Author: Zachary Wakefield <zachpwakefield@gmail.com>
Date: 2025-11-17 13:21:07 -0500
Commit message:

 corrected check for exons in coding regions in frame shift check by requiring both transcript and exon in annotations
Package: BiocPkgDash
Commit: 3650cbdcd4c65c9c37006e4e9a10d204a56ef2d9
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2026-03-23 13:14:34 -0400
Commit message:

 update README.md
Package: BiocPkgDash
Commit: 29b63f2783150c355d245596d490e7ac1093afb9
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2026-03-23 13:11:01 -0400
Commit message:

 version bump 0.99.49
Package: BiocPkgDash
Commit: bfd150cc1d8f7226217c85e122f6b5cd306b57a4
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2026-03-23 13:10:48 -0400
Commit message:

 add note regarding BiocFileCache caching
Package: kissDE
Commit: 722172dd7d65d39b6896cd578b0bd10e33e3bd9b
Author: Aurélie Siberchicot <aurelie.siberchicot@univ-lyon1.fr>
Date: 2026-03-23 17:30:41 +0100
Commit message:

 Update the duplicated chunk names in the vignette
Package: kissDE
Commit: d6a8254dc9cb3358fd3192f460db13440335c531
Author: Aurélie Siberchicot <aurelie.siberchicot@univ-lyon1.fr>
Date: 2026-03-23 17:18:57 +0100
Commit message:

 T/F values become TRUE/FALSE
Package: kissDE
Commit: 03ba9022ef52b346b146083367d5ee46d340e52c
Author: Aurélie Siberchicot <aurelie.siberchicot@univ-lyon1.fr>
Date: 2026-03-23 16:49:27 +0100
Commit message:

 Correct the use of 'aes' from ggplot2 ('aes_string' is now deprecated) and also call the '.data' object from rlang
Package: kissDE
Commit: 525d84413cc0589c8f56ea88548e98583c6d0996
Author: Aurélie Siberchicot <aurelie.siberchicot@univ-lyon1.fr>
Date: 2026-03-17 17:36:05 +0100
Commit message:

 Update the checking workflow
Package: PTMods
Commit: 19e3a936220d114bc9c66dedcca6df0717b0a36b
Author: GuillaumeDeflandre <potamoidef@gmail.com>
Date: 2026-03-23 16:25:52 +0100
Commit message:

 docs: bump version to 0.99.3
Package: PTMods
Commit: fb6589ee3fbe4080f7799d287fcad485e73be320
Author: GuillaumeDeflandre <potamoidef@gmail.com>
Date: 2026-03-23 15:40:39 +0100
Commit message:

 docs: add Enhances PSMatch in DESCRIPTION file
Package: PTMods
Commit: 15848d736772b97ef25112e50672418b8e763286
Author: Guillaume Deflandre <37773040+guideflandre@users.noreply.github.com>
Date: 2026-03-23 15:31:33 +0100
Commit message:

 Fix formatting in README.md for suggested packages
Package: PTMods
Commit: ee90548202799397d2a574dbd5d8372b31972d39
Author: Laurent Gatto <laurent.gatto@gmail.com>
Date: 2026-03-23 10:20:50 +0100
Commit message:

 Merge pull request #20 from rformassspectrometry/addModifications

Add modifications (fixed and variable) as well as useful PTM utils
Package: PTMods
Commit: 69a7b4c292e5f69e8561e4be78c7c43e48ff1dfd
Author: GuillaumeDeflandre <potamoidef@gmail.com>
Date: 2026-03-23 09:59:05 +0100
Commit message:

 docs: see previous commit
Package: PTMods
Commit: 54a5a22557deac0406b503d0655c9e459a482de6
Author: GuillaumeDeflandre <potamoidef@gmail.com>
Date: 2026-03-23 09:58:53 +0100
Commit message:

 docs: corrected reference to other functions in addModifications
Package: PTMods
Commit: fc579e4e4faf51162866d05082b9c4ba0c71977e
Author: GuillaumeDeflandre <potamoidef@gmail.com>
Date: 2026-02-26 15:52:53 +0100
Commit message:

 Tests: edit test for addModifications
Package: PTMods
Commit: 64562fcd881d5be81eebfa7b301f992faad75036
Author: GuillaumeDeflandre <potamoidef@gmail.com>
Date: 2026-02-26 15:45:07 +0100
Commit message:

 Docs: add vignette documentation for the new modifications functions
Package: PTMods
Commit: 2637e62ee9f3d73cc17151b5e83dce6d4db317bb
Author: GuillaumeDeflandre <potamoidef@gmail.com>
Date: 2026-02-25 16:45:28 +0100
Commit message:

 Feat: also match to deltaMass when no sign is give
Package: PTMods
Commit: 3d8900346d6021b6c1007816b9c385f71bd42568
Author: GuillaumeDeflandre <potamoidef@gmail.com>
Date: 2026-02-25 16:29:08 +0100
Commit message:

 Docs: do not report a warning when converting from deltaMass to deltaMass
Package: PTMods
Commit: 11ba20c56a14e34e21b15a7e0afe6587944072df
Author: GuillaumeDeflandre <potamoidef@gmail.com>
Date: 2026-02-25 12:04:42 +0100
Commit message:

 Feat: added fixed/variable modification functions amongst other PTM utils

The once complex calculateFragments that depended on variable and fixed
modifications parameters is now transferred to PTMods. Multiple
functions exist, mainly the split of fixed and variable modifications is
most important here. Additionally, any annotation style is accepted and
preserved.
Package: jvecfor
Commit: ff61f80ebe6d1a3053074a2e30c14879aeb86190
Author: Anestis Gkanogiannis <ganoyan@gmail.com>
Date: 2026-03-23 15:28:28 +0100
Commit message:

 Bump package version to 0.99.1
Package: jvecfor
Commit: 2f1884a9a35aeb3899b2b1b01c638798e62cb6cd
Author: Anestis Gkanogiannis <ganoyan@gmail.com>
Date: 2026-03-23 15:27:41 +0100
Commit message:

 Remove Makefile and Maven wrapper properties; add package to Watched Tags
Package: miaViz
Commit: 032ed913876d1e1df55feeacc604a8a8fd498ede
Author: Tuomas Borman <60338854+TuomasBorman@users.noreply.github.com>
Date: 2026-03-23 14:53:31 +0200
Commit message:

 Option to select number of columns/rows in plotBoxplot (#223)
Package: miaViz
Commit: 95ce5510256200b6192edd55a0e6d9113d57016f
Author: raivo-otus <56149499+raivo-otus@users.noreply.github.com>
Date: 2026-03-10 12:03:15 +0200
Commit message:

 Refix tree loadings (#217)

Co-authored-by: Tuomas Borman <60338854+TuomasBorman@users.noreply.github.com>
Co-authored-by: Muluh <127390183+0xMuluh@users.noreply.github.com>
Co-authored-by: Tuomas Borman <tvborm@utu.fi>
Package: scConform
Commit: db853e59f491b57c2844c724b2daac052da7fef4
Author: Daniela Corbetta <Corbettadaniela@gmail.com>
Date: 2026-03-20 17:05:48 +0100
Commit message:

 Merge pull request #19 from ccb-hms/main

up
Package: scConform
Commit: 863333d97911017685e9e61875a3ea8d39e68354
Author: Daniela Corbetta <Corbettadaniela@gmail.com>
Date: 2026-03-20 17:02:04 +0100
Commit message:

 Update CI workflow to use only devel configurations

Removed old configurations for various OS releases and added new configurations for development versions on Ubuntu, macOS, and Windows.
Package: scConform
Commit: d372107edf3d24dff62d2b24cc41584f2c78fb58
Author: DanielaCorbetta <corbettadaniela@gmail.com>
Date: 2026-03-20 16:44:33 +0100
Commit message:

 Merge branch 'devel'
Package: scConform
Commit: d199b162b9b994fd46393d25ad05ed4f99e501ba
Author: DanielaCorbetta <corbettadaniela@gmail.com>
Date: 2026-03-20 16:34:03 +0100
Commit message:

 Bump version to 0.99.4
Package: scConform
Commit: 7121657c25e379bed0bfb559b1957813def382cc
Author: DanielaCorbetta <corbettadaniela@gmail.com>
Date: 2026-03-20 16:09:15 +0100
Commit message:

 Address Bioconductor review comments

- Updated DESCRIPTION (R >= 4.6.0, biocViews, Authors)
- Cleaned NAMESPACE with selective imports
- Improved vignette installation and references
- Refactored functions to avoid growing objects in loops
- Updated roxygen documentation (markdown, clearer params)
- Fixed plotResult() and graphical argument forwarding
- Prevented Rplots.pdf generation in tests
Package: scConform
Commit: 51d0cd06d28f35199cfc07a514cba357fe4a90fd
Author: Daniela Corbetta <Corbettadaniela@gmail.com>
Date: 2026-03-05 14:23:53 +0100
Commit message:

 Merge pull request #18 from ccb-hms/devel

Devel
Package: vsn
Commit: 07b2ea564ded316633c8644007664b54585fcd26
Author: Hugo Gruson <git@hugogruson.fr>
Date: 2026-03-23 11:02:18 +0100
Commit message:

 Bump version
Package: vsn
Commit: efadc5e5dd0d4ed068174f7dd17061fe9eb2afd5
Author: Hugo Gruson <git@hugogruson.fr>
Date: 2026-03-23 10:57:40 +0100
Commit message:

 Convert last vignette to Rmd
Package: GEOmetadb
Commit: 9da5309b04dd9ccc439649ca0ff0ec2d846a234c
Author: Zhu <zhujack@nci-02219617-m.verizon.net>
Date: 2026-03-22 20:15:36 -0400
Commit message:

 Replaced src_sqlite with tbl in line 285 of vignettes/GEOmetadb.Rmd and bump the version to 1.73.1.
Package: GEOmetadb
Commit: 4abbfd93367be1c30bcd6b559749155602f046f0
Author: Zhu <zhujack@nci-02219617-m.verizon.net>
Date: 2026-03-22 20:14:09 -0400
Commit message:

 Replaced src_sqlite with tbl in line 285 of vignettes/GEOmetadb.Rmd and bump the version to 1.75.0.
Package: signatureSearch
Commit: 3c678914caffeb5406dfd1539fc63dc6fd580f1c
Author: brendangongol <bgong001@ucr.edu>
Date: 2026-03-22 11:51:56 -0700
Commit message:

 addressing warning messages
Package: signatureSearch
Commit: 302b268c862df4b5a8303909f4301678cf7d915c
Author: brendangongol <bgong001@ucr.edu>
Date: 2026-03-22 10:54:56 -0700
Commit message:

 addressing warning messages
Package: Qtlizer
Commit: 57c816716ddcf86a41545ff876932f0c8a442d78
Author: Matthias Munz <matthias.munz@gmx.de>
Date: 2026-03-22 17:25:28 +0100
Commit message:

 Bump version in devel
Package: Qtlizer
Commit: 4b007687e8e2418647cc0b3595f8bbfbe543ffd8
Author: Matthias Munz <matthias.munz@gmx.de>
Date: 2026-03-22 17:25:10 +0100
Commit message:

 Update zzz.R
Package: sitadela
Commit: e8967ae27a43e2fd40eb1e81d45e6ac90c2ab7a4
Author: Panagiotis Moulos <pmoulos@gmail.com>
Date: 2026-03-22 15:43:48 +0000
Commit message:

 Temporary fix Ensembl issues, add mm39
Package: sitadela
Commit: 2279e403d58cbc5b602df807ec032f5a8ce9abd7
Author: Panagiotis Moulos <pmoulos@gmail.com>
Date: 2026-03-22 09:53:45 +0000
Commit message:

 Merge branch 'devel' of git.bioconductor.org:packages/sitadela into devel
Package: sitadela
Commit: e6b4fc539edd3ce005f80d27e11860514fde207e
Author: Panagiotis Moulos <panos@prisma-1.elixir.grnet.lan>
Date: 2026-03-18 16:35:54 +0000
Commit message:

 Temporary changes towards UCSC fixes and mm39 support
Package: QFeatures
Commit: e3806418a6cc746db279c89d8da1d54a277c310f
Author: Laurent Gatto <lgatto@protonmail.ch>
Date: 2026-03-22 15:09:45 +0100
Commit message:

 add link to contrib and CoC
Package: DECIPHER
Commit: bedfd211e76f161a74a17f508c98c9a5cf0289bb
Author: Erik Wright <sixfoot10@Eriks-MacBook-Pro-2.local>
Date: 2026-03-22 07:58:53 -0500
Commit message:

 Small changes to Treeline.

 Committer: Erik Wright <Erik.Wright@bcm.edu>
 Changes to be committed:
	modified:   DESCRIPTION
	modified:   R/DetectRepeats.R
	modified:   R/InferDemography.R
	modified:   R/Treeline.R
	modified:   man/Add2DB.Rd
	modified:   man/AdjustAlignment.Rd
	modified:   man/AlignDB.Rd
	modified:   man/AlignPairs.Rd
	modified:   man/AlignProfiles.Rd
	modified:   man/AlignSeqs.Rd
	modified:   man/AlignSynteny.Rd
	modified:   man/AlignTranslation.Rd
	modified:   man/AmplifyDNA.Rd
	modified:   man/Array2Matrix.Rd
	modified:   man/BrowseDB.Rd
	modified:   man/BrowseSeqs.Rd
	modified:   man/CalculateEfficiencyArray.Rd
	modified:   man/CalculateEfficiencyFISH.Rd
	modified:   man/CalculateEfficiencyPCR.Rd
	modified:   man/Clusterize.Rd
	modified:   man/Codec.Rd
	modified:   man/ConsensusSequence.Rd
	modified:   man/Cophenetic.Rd
	modified:   man/CorrectFrameshifts.Rd
	modified:   man/CreateChimeras.Rd
	modified:   man/DB2Seqs.Rd
	modified:   man/DECIPHER-package.Rd
	modified:   man/DesignArray.Rd
	modified:   man/DesignPrimers.Rd
	modified:   man/DesignProbes.Rd
	modified:   man/DesignSignatures.Rd
	modified:   man/DetectRepeats.Rd
	modified:   man/DigestDNA.Rd
	modified:   man/Disambiguate.Rd
	modified:   man/DistanceMatrix.Rd
	modified:   man/ExtractGenes.Rd
	modified:   man/FindChimeras.Rd
	modified:   man/FindGenes.Rd
	modified:   man/FindNonCoding.Rd
	modified:   man/FindSynteny.Rd
	modified:   man/FormGroups.Rd
	modified:   man/Genes-class.Rd
	modified:   man/IdConsensus.Rd
	modified:   man/IdLengths.Rd
	modified:   man/IdTaxa.Rd
	modified:   man/IdentifyByRank.Rd
	modified:   man/IndexSeqs.Rd
	modified:   man/InferDemography.Rd
	modified:   man/InferRecombination.Rd
	modified:   man/InferSelection.Rd
	modified:   man/InvertedIndex-class.Rd
	modified:   man/LearnNonCoding.Rd
	modified:   man/LearnTaxa.Rd
	modified:   man/MapCharacters.Rd
	modified:   man/MaskAlignment.Rd
	modified:   man/MeltDNA.Rd
	modified:   man/NonCoding-class.Rd
	modified:   man/OrientNucleotides.Rd
	modified:   man/PredictDBN.Rd
	modified:   man/PredictHEC.Rd
	modified:   man/ReadDendrogram.Rd
	modified:   man/RemoveGaps.Rd
	modified:   man/ScoreAlignment.Rd
	modified:   man/SearchDB.Rd
	modified:   man/SearchIndex.Rd
	modified:   man/Seqs2DB.Rd
	modified:   man/StaggerAlignment.Rd
	modified:   man/Synteny-class.Rd
	modified:   man/Taxa-class.Rd
	modified:   man/TerminalChar.Rd
	modified:   man/TileSeqs.Rd
	modified:   man/Treeline.Rd
	modified:   man/TrimDNA.Rd
	modified:   man/WriteDendrogram.Rd
	modified:   man/WriteGenes.Rd
	modified:   src/ClusterME.c
	modified:   src/DECIPHER.h
	modified:   src/R_init_decipher.c
	modified:   src/Search.c
	modified:   vignettes/GrowingTrees.Rnw
	modified:   vignettes/PopulationGenetics.Rnw
Package: XAItest
Commit: d1935a1e0f2f1ac112d3f8da62bbd31b4857c071
Author: gui <ghislain.fievet@gmail.com>
Date: 2026-03-22 08:18:19 +0100
Commit message:

 Add XAI Triad citation
Package: spatialFDA
Commit: e57aeef9bae41cc77457ded683848e059feee6ce
Author: Martin Emons <55688661+mjemons@users.noreply.github.com>
Date: 2026-03-22 11:43:47 +0100
Commit message:

 Robust covariance estimation with sandwich estimators (#22)

* implemented AR1 penalty and SW estimators

* NA handling in ACF calculation

* implemented constant offset per image

* varying image intercept

* go back to constant offste

* implemented gamm4 fits, removed ridge penalty

* improvements in summary output

* interaction effect of sample and image intercept

* constant random interaction

* constant image and smooth patient effect

* nested mixed effect

* constant image intercept and smooth sample one

* change to bam and fix errors

* enable gamm4 fit

* interaction random effect

* non-nested REs

* add ridgepenalty back

* functionalGam class and clipping of p-values in [0,1]

* implemented new SW from FS

* removed ridge penalty and new naming of SW correction

* removed image intercept and adapted plotting

* changed defaults

* added discrete = TRUE as default

* bug fix when no curves are calculated - added test for this

* adjusted vignettes to new code

* remove mgcv from suggests

* changed assertion on weights

* updated news and description
Package: esATAC
Commit: f884d0fbfa61963a08efbcb5699e31a9c5c4e333
Author: Zheng Wei <wzweizheng@qq.com>
Date: 2026-03-21 23:26:00 -0700
Commit message:

 version bump
Package: esATAC
Commit: e24aa7634f3fdee48048d26be195afca33959ba3
Author: Zheng Wei <wzweizheng@qq.com>
Date: 2026-03-21 23:25:22 -0700
Commit message:

 fix makeTxDbFromUCSC issue
Package: RNAshapeQC
Commit: 1a58458dcd14da63d58be263536137607d890c92
Author: Miyeon Yeon <sqr.yeon@gmail.com>
Date: 2026-03-21 11:13:24 -0500
Commit message:

 Update vignette and functions to Bioconductor style (Bioconductor/Contributions#4054)
Package: recoup
Commit: 2449cd4d988cd463e3d9876b1fab114627198a33
Author: Panagiotis Moulos <pmoulos@gmail.com>
Date: 2026-03-21 13:56:40 +0000
Commit message:

 Added mm39 to args, fixed NAMESPACE
Package: Rarr
Commit: ac946308c80b7f62df9d254ac9f4d2a9ec99b87d
Author: Hugo Gruson <git@hugogruson.fr>
Date: 2026-03-21 14:51:39 +0100
Commit message:

 Run devtools::document()
Package: recoup
Commit: fbd5da641cce48ffdef60d17ad7c403be1287aaf
Author: Panagiotis Moulos <pmoulos@gmail.com>
Date: 2026-03-21 13:36:56 +0000
Commit message:

 Temporary fix Ensembl issues, add mm39, equcab3
Package: Rarr
Commit: 15fbae8e8acd71d278bdcbe55ddbe7f9ea72c406
Author: Hugo Gruson <git@hugogruson.fr>
Date: 2026-03-21 13:42:22 +0100
Commit message:

 Remove unused function
Package: Rarr
Commit: 5f502f359b07d806e7572647ae64ed16bb9d0ef3
Author: Hugo Gruson <git@hugogruson.fr>
Date: 2026-03-18 08:57:16 +0100
Commit message:

 Bump version
Package: Rarr
Commit: 6445cab297c70e7a28a56bda810722fbc9dac43c
Author: Hugo Gruson <git@hugogruson.fr>
Date: 2026-03-18 08:57:09 +0100
Commit message:

 Add package load benchmark
Package: Rarr
Commit: 557f73e39e88daf7021468a66ce8755e597bc0d3
Author: Hugo Gruson <git@hugogruson.fr>
Date: 2026-03-18 08:55:26 +0100
Commit message:

 Mention const change in NEWS
Package: Rarr
Commit: ac4ce922d6085b633d57bdf4ebf97a31b38ebc8c
Author: Hugo Gruson <git@hugogruson.fr>
Date: 2026-03-17 19:46:44 +0100
Commit message:

 Remove unnecessary RAW() casting
Package: Rarr
Commit: cecfbebf591b32e071987fe19e09ef5b3e625dbc
Author: Hugo Gruson <git@hugogruson.fr>
Date: 2026-03-17 16:30:37 +0100
Commit message:

 Use const where appropriate in C code
Package: Rarr
Commit: 2cc5812e2fd1fef6a10b8e0e4f8fb617969bf45b
Author: Hugo Gruson <git@hugogruson.fr>
Date: 2026-03-16 20:37:58 +0100
Commit message:

 Make cli wrapper slightly faster
Package: metaseqR2
Commit: 055a11623162908254326fdd889d1d528cd40efb
Author: Panagiotis Moulos <pmoulos@gmail.com>
Date: 2026-03-21 12:23:54 +0000
Commit message:

 Temporary fix Ensembl issues, add mm39, equcab3
Package: iClusterPlus
Commit: 954aabde7ed69942d3e85f56ef845339b4ef6cb0
Author: qianxing.mo <qianxing.mo@moffitt.org>
Date: 2026-03-20 15:34:31 -0400
Commit message:

 change Integrative clustering to iCluster for consistency in Tutorial_iCluster2b_singleCell.Rmd
Package: omicsViewer
Commit: bfd7dd713e1312070e1fd61361b8c1c86df226bd
Author: Chen Meng <mengchen18@gmail.com>
Date: 2026-03-20 18:43:34 +0100
Commit message:

 feat: complete snapshot status save/restore for all modules

- Fix na2null crash on vector inputs during snapshot restore
  (is.na on vector + || requires scalar logical)
- Add status save/restore for ORA triselector selection
- Add status save/restore for PTM motif triselector selection
- Add Bees/Curve plot type save/restore in feature_general
- Include cor heatmap and dynamic heatmap status in data space return
- Restore feature/sample selection from snapshots in L0_module_app
- Fix WebGL detection timing (shiny:connected vs document.ready)
- Wrap PTM/ORA status in tryCatch for modules without data

Bump version to 1.15.4.

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
Package: omicsViewer
Commit: ac050cb6c9cd2aa6be13322b3fa3dc5e594cb900
Author: Chen Meng <mengchen18@gmail.com>
Date: 2026-03-20 16:58:21 +0100
Commit message:

 fix: scatter plot regression line crash on NA/Inf and WebGL fallback

- Replace !is.na() filter with is.finite() to also exclude Inf/-Inf
  values that cause lm() and cor.test() to fail
- Use cleaned df$x/df$y in cor.test() instead of raw input vectors
- Move toWebGL() from plotly_scatter() into renderPlotly with
  browser-side WebGL detection, falling back to standard plotly
  when WebGL is not supported
- Add CLAUDE.md with developer notes

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
Package: DMRsegaldata
Commit: 8a7ee2dc0eebcc5deb12ba647b526b20922c4c91
Author: vaslem <vaslemonidis@hotmail.com>
Date: 2026-03-20 18:21:20 +0100
Commit message:

 Bump package version to 0.99.6 in DESCRIPTION and documentation
Package: DMRsegaldata
Commit: 0df93a023b1a4511dcbfabe079b115b28373db2f
Author: vaslem <vaslemonidis@hotmail.com>
Date: 2026-03-20 18:12:26 +0100
Commit message:

 Add ExperimentHub to package dependencies in DESCRIPTION to conform with at least one Bioconductor dependency
Package: DMRsegaldata
Commit: 62d1e9b900e83fb2f90fc54f5ab4bceb855fb15e
Author: vaslem <vaslemonidis@hotmail.com>
Date: 2026-03-20 18:07:24 +0100
Commit message:

 Extended the /dontrun in the example
Package: DMRsegaldata
Commit: 4eb3c0a8308b739a0f5f4dc11b7058c28772edb2
Author: vaslem <vaslemonidis@hotmail.com>
Date: 2026-03-20 18:02:20 +0100
Commit message:

 Updated tags on bioconductor site
Package: DMRsegaldata
Commit: b9cca4bce3ebb2ec5774fe65f8ea55db18e890c8
Author: vaslem <vaslemonidis@hotmail.com>
Date: 2026-03-20 17:55:23 +0100
Commit message:

 Removed future package and updatd pattern matching in .Rbuildignore
Package: DMRsegaldata
Commit: 42a42969298bd9a8f77ba006bafe4ecd0e4ce5bc
Author: vaslem <vaslemonidis@hotmail.com>
Date: 2026-03-20 17:39:57 +0100
Commit message:

 Minor fixes, regarding formatting
Package: DMRsegaldata
Commit: 803dc488ac430dba7c6fe6c3d8bc96c0415b829d
Author: vaslem <vaslemonidis@hotmail.com>
Date: 2026-03-02 17:53:27 +0100
Commit message:

 Update .Rbuildignore to include .lintr and data directories
Package: DMRsegaldata
Commit: 99cac17fbcc8502efe722a849031ec1fc5779c4f
Author: vaslem <vaslemonidis@hotmail.com>
Date: 2026-03-02 17:48:47 +0100
Commit message:

 Update .gitignore to include .lintr and remove .lintr file; modify make-data.R to delete temporary files after data download
Package: DMRsegaldata
Commit: 63f3066af51baf8c320e360145842e43b650e004
Author: vaslem <vaslemonidis@hotmail.com>
Date: 2026-03-02 17:40:52 +0100
Commit message:

 Update .gitignore to exclude the parent directory of Rcheck
Package: DMRsegaldata
Commit: f1aa9238cb7e5eb04fc54acc0171af50dd4a1efa
Author: vaslem <vaslemonidis@hotmail.com>
Date: 2026-03-02 17:39:20 +0100
Commit message:

 Fix .gitignore to correctly include DMRsegaldata.Rcheck directory
Package: signatureSearch
Commit: 971fc48def05c1bf9cf803dced46c6e6df5d624c
Author: brendangongol <brengong@gmail.com>
Date: 2026-03-20 08:53:47 -0700
Commit message:

 Addresseing warning messages
Package: Chromatograms
Commit: 4bd208631edc0b5e14b80968dbd834e4dace05a9
Author: Philippine Louail <philippine.louail@outlook.com>
Date: 2026-03-20 16:27:07 +0100
Commit message:

 Merge pull request #49 from rformassspectrometry/phili

feat: add peakBoundary()
Package: Chromatograms
Commit: fc438cb648165c5147ab43b6034b8685b943cd6e
Author: Philippine Louail <127301965+philouail@users.noreply.github.com>
Date: 2026-03-20 16:09:53 +0100
Commit message:

 fix: use valleys()
Package: Chromatograms
Commit: f6943b3560cb0061888b015a16265b16ca98edbc
Author: Philippine Louail <127301965+philouail@users.noreply.github.com>
Date: 2026-03-20 15:07:59 +0100
Commit message:

 feat: add peakBoundary()
Package: scater
Commit: ec4264a15da1ab41fb2173d1093e87644b2760ca
Author: Alan O'Callaghan <alan.ocallaghan@outlook.com>
Date: 2026-03-20 15:06:29 +0000
Commit message:

 Relax tests and import stats::quantile
Package: hipathia
Commit: b9c057b309479c921bde971f57ad770e412fa1d9
Author: Marta Hidalgo <marta.hidalgo@outlook.es>
Date: 2026-03-20 15:15:53 +0100
Commit message:

 Merge branch 'master' into devel
Package: hipathia
Commit: 9c238198099c38bdfbe006099b096f942d47e3e5
Author: Marta Hidalgo <marta.hidalgo@outlook.es>
Date: 2026-03-20 15:11:59 +0100
Commit message:

 bumping to version 3.11.1
Package: hipathia
Commit: 849d00930f0f51f533ed5dee7921608c90f1a219
Author: Marta Hidalgo <marta.hidalgo@outlook.es>
Date: 2026-03-20 15:11:32 +0100
Commit message:

 updating to hpAnnot version 3
Package: hipathia
Commit: 7486aceacc5e06077a391207dac200174095f4c3
Author: Marta R. Hidalgo <marta.hidalgo@outlook.es>
Date: 2025-09-29 22:50:15 +0200
Commit message:

 commenting figures in vignette
Package: hipathia
Commit: adde3c8da719e6c9481603aabf024e97d96c297d
Author: Marta R. Hidalgo <marta.hidalgo@outlook.es>
Date: 2023-05-22 11:40:47 +0200
Commit message:

 changing plotVisGraphDE output options
Package: hipathia
Commit: d2b7516af93967f2bf08142ab4045939c8a724a0
Author: Marta R. Hidalgo <marta.hidalgo@outlook.es>
Date: 2025-09-29 22:50:15 +0200
Commit message:

 commenting figures in vignette
Package: hipathia
Commit: e95649fa5b1cbbc6cf5406a72b272830328e85e4
Author: Marta R. Hidalgo <marta.hidalgo@outlook.es>
Date: 2023-05-22 11:40:47 +0200
Commit message:

 changing plotVisGraphDE output options
Package: cellNexus
Commit: 67ef23be5cc59104a07a5ece88623c7baeb3dea8
Author: Mengyuan Shen <129487421+myushen@users.noreply.github.com>
Date: 2026-03-20 21:48:05 +1100
Commit message:

 Merge pull request #95 from myushen/bioconductor

get_metadata grabs populated columns only
Package: cellNexus
Commit: 557c01760cf579ba3db413fe6b80788864353fad
Author: myushen <mengyuan.shen@outlook.com>
Date: 2026-03-20 21:25:47 +1100
Commit message:

 version up
Package: cellNexus
Commit: f1e05db9297f27c5f5e1a582e2617d4cb9a3e02c
Author: myushen <mengyuan.shen@outlook.com>
Date: 2026-03-20 21:06:02 +1100
Commit message:

 Merge branch 'master' into bioconductor
merge master
Package: cellNexus
Commit: 496a0ba02ae83513558f4c4714a5410908a7b074
Author: myushen <mengyuan.shen@outlook.com>
Date: 2026-03-20 20:34:36 +1100
Commit message:

 update docs
Package: cellNexus
Commit: ff8943c51bb8c630fc187181d5a94dbc3bb00eb2
Author: myushen <mengyuan.shen@outlook.com>
Date: 2026-03-20 17:22:33 +1100
Commit message:

 get_metadata only returns cellnexus annotations. join_census_table append census annotations
Package: cellNexus
Commit: 98d083bd23e1dc5728d4db9573bebc872e9c8887
Author: myushen <mengyuan.shen@outlook.com>
Date: 2026-03-20 16:22:25 +1100
Commit message:

 pull from master, solve conflicts

Merge branch 'master' into bioconductor

# Conflicts:
#	NAMESPACE
#	R/data.R
#	R/metadata.R
#	R/utils.R
#	R/zzz.R
#	README.md
#	man/duckdb_read_parquet.Rd
#	man/get_metacell.Rd
#	man/get_metadata.Rd
#	man/keep_updated_metadata.Rd
#	tests/testthat/test-query.R
Package: cellNexus
Commit: 031aa8f232c89a3252e9c4a1c8d76e570384eb00
Author: myushen <mengyuan.shen@outlook.com>
Date: 2026-03-20 16:08:40 +1100
Commit message:

 put metacell function as internal. every man page should have example. every internal should not generate Rd
Package: cellNexus
Commit: c4ee3d5ae0016da8abd9f7e627803e010ecfff3a
Author: Stefano Mangiola <mangiolastefano@gmail.com>
Date: 2026-03-20 13:48:17 +1030
Commit message:

 update renv for website
Package: cellNexus
Commit: 825113b29248663cbff090744f26f8ceae7c8488
Author: Mengyuan Shen <129487421+myushen@users.noreply.github.com>
Date: 2026-03-20 12:44:01 +1100
Commit message:

 Merge pull request #91 from myushen/master

update deployment manifest
Package: cellNexus
Commit: 0c0bdf1a4f8bf00713d77433cebf0b20eccbe41c
Author: myushen <mengyuan.shen@outlook.com>
Date: 2026-03-20 12:25:07 +1100
Commit message:

 use org name
Package: cellNexus
Commit: 464f22052a3580ef99250f4bca0e5cbe869c7bfe
Author: myushen <mengyuan.shen@outlook.com>
Date: 2026-03-20 11:29:12 +1100
Commit message:

 version bump
Package: cellNexus
Commit: 7fd0ce70d3df5863508790313a3100f1ea6cabc7
Author: myushen <mengyuan.shen@outlook.com>
Date: 2026-03-20 10:40:23 +1100
Commit message:

 fix deployment manifest and url
Package: goatea
Commit: f0ceaf50d6457ec65d23534a8192638430f82836
Author: Maurits Unkel <mauritsunkel@gmail.com>
Date: 2026-03-20 11:39:39 +0100
Commit message:

 Fix clusterProfiler::enricher(universe = NULL) to universe = as.character(all_genes_background) for mv to enrichit package
Package: Chromatograms
Commit: 95cb9d4c381797854d427ae051a2db6c7d97b525
Author: Philippine Louail <philippine.louail@outlook.com>
Date: 2026-03-13 14:33:15 +0100
Commit message:

 Merge pull request #48 from rformassspectrometry/phili

refactor: efficiency update for data access and .process_peaks_data()
Package: Chromatograms
Commit: 6c8ea54a44639c60ea5e19b7b64cce2902af5ec3
Author: Philippine Louail <127301965+philouail@users.noreply.github.com>
Date: 2026-03-13 14:13:13 +0100
Commit message:

 force data.table install
Package: Chromatograms
Commit: b150a1d1baded8a97e473f6ac65db20de43a3745
Author: Philippine Louail <127301965+philouail@users.noreply.github.com>
Date: 2026-03-13 14:10:44 +0100
Commit message:

 fix cache
Package: Chromatograms
Commit: 641a3f9f7a789829d91babf71078ace14e8a9554
Author: Philippine Louail <127301965+philouail@users.noreply.github.com>
Date: 2026-03-13 13:57:54 +0100
Commit message:

 refactor small codes parts based on jo's comments
Package: Chromatograms
Commit: 3c231d39cf9228d399fe98713e073a0663032767
Author: Philippine Louail <127301965+philouail@users.noreply.github.com>
Date: 2026-03-11 18:29:31 +0100
Commit message:

 Code clean and fix based on jo comments
Package: Chromatograms
Commit: 1f81de2ee8dc6358564bde367ca8a9c995ac0594
Author: Philippine Louail <127301965+philouail@users.noreply.github.com>
Date: 2026-03-10 12:09:28 +0100
Commit message:

 Update helpers.R
Package: Chromatograms
Commit: 61446a113c792e13085e153808f9f9ab8c4fb4f2
Author: Philippine Louail <127301965+philouail@users.noreply.github.com>
Date: 2026-03-10 12:05:52 +0100
Commit message:

 efficiency update
Package: Chromatograms
Commit: 52783acc934c44fe11117a50758f32b5270d37fc
Author: Philippine Louail <philippine.louail@outlook.com>
Date: 2026-03-05 14:25:26 +0100
Commit message:

 Merge pull request #46 from rformassspectrometry/phili

feature c() and filterEmptyChromatograms() methods.
Package: Chromatograms
Commit: 8acc80f88e88a592107cd75febc3db9f0e235c6c
Author: Philippine Louail <127301965+philouail@users.noreply.github.com>
Date: 2026-03-05 13:44:35 +0100
Commit message:

 feature: add filterEmptyChromatograms()
Package: Chromatograms
Commit: 6f7b0c3c3913841be31e69be40dd065e553bc2af
Author: Philippine Louail <127301965+philouail@users.noreply.github.com>
Date: 2026-02-26 14:50:37 +0100
Commit message:

 feature: concatenate and extrapolation
Package: Chromatograms
Commit: d3219c2e4c789fe0a5a6b1543d013483051e575b
Author: Philippine Louail <127301965+philouail@users.noreply.github.com>
Date: 2026-02-05 16:44:04 +0100
Commit message:

 refactor: order or returned peaksData for chromBackendSpectra
Package: imageTCGAutils
Commit: 57ea13cfd704a5009aa5b59ca80e11712c0f7f0c
Author: billila <ilaria.billato@studenti.unipd.it>
Date: 2026-03-20 10:59:06 +0100
Commit message:

 version bump 0.99.21
Package: imageTCGAutils
Commit: 8f19b143dbed7870cb59a82ccf752dc055143bd0
Author: billila <ilaria.billato@studenti.unipd.it>
Date: 2026-03-20 10:56:52 +0100
Commit message:

 add remotes package for GHA
Package: scECODA
Commit: 35c1068aa375c567eb40efed17c75ea850fc0d08
Author: halterc <chalterbio@gmail.com>
Date: 2026-03-20 10:19:45 +0100
Commit message:

 Version bump
Package: scECODA
Commit: 9b26caa4f9fd7456dcd8e0a25d9d0fb5ed210c9a
Author: halterc <chalterbio@gmail.com>
Date: 2026-03-20 10:19:38 +0100
Commit message:

 plot_pca: changed anosim_parallel = 1 (default) (update documentation)
Package: msdata
Commit: 9e1a3d5e1e76dcf0c430b3cda6a34975a39c7974
Author: Laurent Gatto <lgatto@protonmail.ch>
Date: 2026-03-20 09:46:56 +0100
Commit message:

 remove files
Package: SeqArray
Commit: 3f3d0dcef37096a9c1277b992171a023ecdd8755
Author: Xiuwen Zheng <zhengxwen@gmail.com>
Date: 2026-03-19 22:56:44 -0500
Commit message:

 new 'ploidy' in seqVCF2GDS()
Package: SpiecEasi
Commit: e1a8004db8ce30707ad5a39555ad7a72c19aa0b2
Author: Zachary Kurtz <zdkurtz@gmail.com>
Date: 2026-03-19 20:32:21 -0400
Commit message:

 bump patch
Package: SpiecEasi
Commit: a596224f0931a7f1a8867cd0a950122fc759158e
Author: Zachary Kurtz <zdkurtz@gmail.com>
Date: 2026-03-19 20:27:59 -0400
Commit message:

 fix parallel vignette for Windows builds
Package: glmSparseNet
Commit: 29cbab5ffcbf58317fa1f598af7c3d3abafdb50f
Author: André Veríssimo <211358+averissimo@users.noreply.github.com>
Date: 2026-03-20 00:09:47 +0000
Commit message:

 fix: linter errors
Package: OmicsMLRepoR
Commit: b9df1d6ff0899a1d14de9c2eb4ebe6bf46c33016
Author: Sehyun Oh <shbrief@gmail.com>
Date: 2026-03-19 20:06:31 -0400
Commit message:

 version bump
Package: OmicsMLRepoR
Commit: 868c8afec42af172dbb390a6b64263513f21fbec
Author: Sehyun Oh <shbrief@gmail.com>
Date: 2026-03-19 20:03:50 -0400
Commit message:

 Merge branch 'devel' of https://github.com/shbrief/OmicsMLRepoR into devel
Package: OmicsMLRepoR
Commit: 53cec52550ff5720a7d13927474765696c8f2657
Author: Sehyun Oh <shbrief@gmail.com>
Date: 2026-03-19 19:53:06 -0400
Commit message:

 remove synonym search test due to inconsistency in OLS
Package: OmicsMLRepoR
Commit: 83e3f857fdd2cc6a7d20cd48152ae4cdfa86a8ff
Author: Sehyun Oh <shbrief@gmail.com>
Date: 2026-03-13 11:24:08 -0400
Commit message:

 version bump
Package: OmicsMLRepoR
Commit: a11ed795393cdaeffc32406f2915aaa43ce5c3f9
Author: Sehyun Oh <shbrief@gmail.com>
Date: 2026-02-02 12:26:07 -0500
Commit message:

 version bump
Package: OmicsMLRepoR
Commit: db4405a61700c558209303deae0a545e1d6c6b92
Author: Sehyun Oh <shbrief@gmail.com>
Date: 2026-03-13 11:13:21 -0400
Commit message:

 version bump
Package: OmicsMLRepoR
Commit: b2c43a51051a6dece8e0cc3dcf1ca7878c3cb9e6
Author: Sehyun Oh <shbrief@gmail.com>
Date: 2026-03-13 11:13:11 -0400
Commit message:

 update rols API endpoint
Package: OmicsMLRepoR
Commit: 1edeb0349a20d28e39f8e8905a2b7a5f2f07f703
Author: Sehyun Oh <shbrief@gmail.com>
Date: 2026-03-04 09:15:38 -0500
Commit message:

 Fix bfcdownload() parameter name and version bump

Use 'rid' instead of 'rids' in bfcdownload() call to fix
vignette build error: "!missing(rid) is not TRUE"

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
Package: OmicsMLRepoR
Commit: 232810b540054488d6b75492c56971a8ce46dbdc
Author: Sehyun Oh <shbrief@gmail.com>
Date: 2026-02-11 16:09:36 -0500
Commit message:

 version bump
Package: OmicsMLRepoR
Commit: 1ea55b06b3315f6470be2b920ad25b13960721d3
Author: Sehyun Oh <shbrief@gmail.com>
Date: 2026-02-11 16:09:12 -0500
Commit message:

 Stop tracking test vignettes
Package: OmicsMLRepoR
Commit: e578f8cbe7b4989cabeb55569e2534adb34bb941
Author: Sehyun Oh <shbrief@gmail.com>
Date: 2026-02-02 12:24:32 -0500
Commit message:

 version bump
Package: clusterExperiment
Commit: 884dd90fbfe99d7a9dcf73370c9958f19b155280
Author: Elizabeth Purdom <epurdom@stat.berkeley.edu>
Date: 2026-03-19 14:14:25 -0700
Commit message:

 bump up version
Package: clusterExperiment
Commit: 794d20ed2ae109c404bca7433b3677dacb3dff8a
Author: Elizabeth Purdom <epurdom@stat.berkeley.edu>
Date: 2026-03-19 14:10:40 -0700
Commit message:

 fix malformed \item braces in makeConsensus docs

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
Package: clusterExperiment
Commit: d7b065941a35e427519f4129117df40996f2d231
Author: Elizabeth Purdom <epurdom@stat.berkeley.edu>
Date: 2026-03-19 14:08:20 -0700
Commit message:

 fix \itemize -> \describe in getClusterIndex docs

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
Package: imageFeatureTCGA
Commit: 9cf2e5a1b17f54e3c2ca04f8a8211861418f51eb
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2026-03-19 17:11:57 -0400
Commit message:

 version bump 0.99.65
Package: imageFeatureTCGA
Commit: ef730cc8a5c7d94cd4fc5c77b98c73acec922861
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2026-03-19 17:11:54 -0400
Commit message:

 fill locals vector only for those not cached and redownloaded
Package: imageFeatureTCGA
Commit: fe56701c52d31b2a971e1b1fa3e1f5690e4f503d
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2026-03-19 17:10:44 -0400
Commit message:

 create urls_to_download vector for clarity
Package: imageFeatureTCGA
Commit: 43db360a26e6b6f568b7b17a37addb4a79990ec9
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2026-03-19 17:09:10 -0400
Commit message:

 use .move_file to fallback to file.copy when file.rename fails
Package: imageFeatureTCGA
Commit: 168e9f37f53c47c41fec9b846e7086d466296bc6
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2026-03-19 16:04:40 -0400
Commit message:

 version bump 0.99.64
Package: imageFeatureTCGA
Commit: cd99343e61a864404b322dc4508464ff891ac915
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2026-03-19 16:04:31 -0400
Commit message:

 minor clean up
Package: imageFeatureTCGA
Commit: 81b7a8bf2f77476cd1fe04f42c9444204cf2a5f3
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2026-03-19 16:04:20 -0400
Commit message:

 combine base URLs for catalog and resources
Package: glmSparseNet
Commit: e861615408415e80822b2d69ff2e718c87bf5421
Author: André Veríssimo <211358+averissimo@users.noreply.github.com>
Date: 2026-03-19 19:08:31 +0000
Commit message:

 fix: message from logger not being caught
Package: HiCool
Commit: 0f6ba8e9a37edd9faa559085a53d34dbcb811bc4
Author: js2264 <jacquesserizay@gmail.com>
Date: 2026-03-19 18:54:03 +0100
Commit message:

 bump to 1.11.3
Package: HiCool
Commit: 00b3f6f9d4e1174950b17cabcef1711b813132a5
Author: Jacques <jacquesserizay@gmail.com>
Date: 2026-03-19 18:48:57 +0100
Commit message:

 fix: set KMP_DUPLICATE_LIB_OK to TRUE to prevent double-init of OpenMP runtime
Package: imageTCGAutils
Commit: 79cb7dd2e1538ef301f74e683713e2cbbac09e0a
Author: billila <ilaria.billato@studenti.unipd.it>
Date: 2026-03-19 18:03:40 +0100
Commit message:

 version bump 0.99.20
Package: imageTCGAutils
Commit: 3d6d8e0420a19303fc9cbd200b49ab2109fb499d
Author: billila <ilaria.billato@studenti.unipd.it>
Date: 2026-03-19 17:59:00 +0100
Commit message:

 restructure matchHoverNetToTiles function
Package: RCX
Commit: ee9b8612d3d99fe0d5dc67d2ddf2fd3eb9917465
Author: Florian J. Auer <florian.auer@informatik.uni-augsburg.de>
Date: 2026-03-19 17:23:34 +0100
Commit message:

 fix: toIgraph now can handle edgeless networks
Package: RCX
Commit: a3f7bf366055194b53f4bbf52aa1fe305fd2027a
Author: Florian J. Auer <florian.auer@informatik.uni-augsburg.de>
Date: 2026-03-19 17:20:41 +0100
Commit message:

 fix: toIgraph now can handle edgeless networks
Package: RCX
Commit: 2f3da7746c81188d728593418c76d1dc659d8d99
Author: Florian J. Auer <florian.auer@informatik.uni-augsburg.de>
Date: 2026-03-19 17:13:59 +0100
Commit message:

 fix: toIgraph now can handle edgeless networks
Package: RCX
Commit: 6cdc2411cb122611631364f8e040c92183e63e6a
Author: Florian J. Auer <florian.auer@informatik.uni-augsburg.de>
Date: 2026-01-20 13:11:19 +0100
Commit message:

 Fix: cyGroups follows a different naming structure in the JSON export. Updated the export function accordingly. Also the CyGroup ids have to be present in RCX object, a check for those references has been added.
Package: BiocPkgDash
Commit: 61a14a0db6bb3b717e34ae2c75f788d082109eb2
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2026-03-19 11:01:38 -0400
Commit message:

 version bump 0.99.48
Package: BiocPkgDash
Commit: f2425db690da6bb1451daf2a4498e64c3fe36a5c
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2026-03-18 18:17:35 -0400
Commit message:

 conditionally show or hide the content with is_email_provided()
Package: scECODA
Commit: 0edd3f5bf353d482a1c42b54ba65f366fac3b14c
Author: halterc <chalterbio@gmail.com>
Date: 2026-03-19 15:13:21 +0100
Commit message:

 Version bump
Package: scECODA
Commit: 50fd402ab5761af69ca44f4345f6d9b298238dec
Author: halterc <chalterbio@gmail.com>
Date: 2026-03-19 15:11:50 +0100
Commit message:

 Merge branch 'main' of https://github.com/carmonalab/scECODA
Package: scECODA
Commit: 025871e19dda47be9e3cec473102cc2397704000
Author: halterc <chalterbio@gmail.com>
Date: 2026-03-19 15:10:02 +0100
Commit message:

 plot_pca: changed anosim_parallel = 1 (default)
Package: scECODA
Commit: 2298172ce3f8996a486e419c8c9dfc4da4c381a3
Author: halterc <chalterbio@gmail.com>
Date: 2026-03-19 15:10:02 +0100
Commit message:

 plot_pca: changed anosim_parallel = 1 (default)
Package: variancePartition
Commit: 16e114ff973d966d1d8ad74a9218b67c74022585
Author: Gabriel Hoffman <gabriel.hoffman@gmail.com>
Date: 2026-03-19 09:20:03 -0400
Commit message:

 1.41.5
Package: variancePartition
Commit: 15d79e68c62bc65d39516e650cf34883ade5547e
Author: Gabriel Hoffman <gabriel.hoffman@gmail.com>
Date: 2026-03-19 09:18:00 -0400
Commit message:

 1.41.4
Package: CAGEfightR
Commit: 26802e1fe0485fd60abd7280a627a30befb3ad1d
Author: Malte Thodberg <maltethodberg@gmail.com>
Date: 2026-03-19 12:22:35 +0100
Commit message:

 Removed pryr dependency and replaced it with lobstr and purrr. Updated DESCRIPTION in the process.
Package: CompoundDb
Commit: 7daa5754dffffde823e42268a9bd3dc6a1a9ddd8
Author: Johannes Rainer <5506112+jorainer@users.noreply.github.com>
Date: 2026-03-19 09:10:35 +0100
Commit message:

 Merge pull request #124 from rformassspectrometry/jomain

fix: support filling missing spectra variables in HMDB import
Package: CompoundDb
Commit: 268d02823fdc49b194dc95945e944eb1e4be4e24
Author: Johannes Rainer <johannes.rainer@gmail.com>
Date: 2026-03-19 08:57:37 +0100
Commit message:

 fix: support filling missing spectra variables in HMDB import
Package: MetaboAnnotation
Commit: 34e5ba4bdeb5d2fe021dac40d50bbfbadd566c8d
Author: Johannes Rainer <5506112+jorainer@users.noreply.github.com>
Date: 2026-03-19 09:10:28 +0100
Commit message:

 Merge pull request #131 from rformassspectrometry/jomain

refactor: use rbindlistWithRownames
Package: MetaboAnnotation
Commit: b9e5ea16f6201e72173df382b2b5566e2f54f909
Author: Johannes Rainer <johannes.rainer@gmail.com>
Date: 2026-03-19 08:51:17 +0100
Commit message:

 fix: addMatches allows filling
Package: MetaboAnnotation
Commit: f0ac37c2f24fb73c35a9268d16b177a2c2e1aa1e
Author: Johannes Rainer <johannes.rainer@gmail.com>
Date: 2026-03-19 07:26:40 +0100
Commit message:

 ci: fix namespace and use R devel
Package: MetaboAnnotation
Commit: 04b81666020fc043406f57f779603096071c22de
Author: Johannes Rainer <johannes.rainer@gmail.com>
Date: 2026-03-18 15:33:16 +0100
Commit message:

 refactor: use rbindlistWithRownames
Package: SMTrackR
Commit: 6533c78358a13e2e84a7527aa842b4aff9138669
Author: satyanarayan-rao <satyanarayan.rao@cuanschutz.edu>
Date: 2026-03-19 13:13:53 +0530
Commit message:

 added BiocStyle in Imports and Suggests
Package: cellNexus
Commit: ad1fdbc6b893161ee1d6591fa5a8cc65190905be
Author: Mengyuan Shen <129487421+myushen@users.noreply.github.com>
Date: 2026-03-19 16:02:06 +1100
Commit message:

 Merge pull request #90 from myushen/master

Load RShiny data correctly and show vignettes output
Package: cellNexus
Commit: b8519ace0b14f49bfcb3edd6b68613ee135bd329
Author: Mengyuan Shen <mengyuan.shen@outlook.com>
Date: 2026-03-19 15:40:09 +1100
Commit message:

 Update query builder assay selection box
Solve conflicts, rebase
Package: cellNexus
Commit: b0daa74cffae975dbeceeababfd1cb20193cbe87
Author: myushen <mengyuan.shen@outlook.com>
Date: 2026-03-19 15:24:30 +1100
Commit message:

 dependency
Package: cellNexus
Commit: c7af92ba895055bd70f973ebe7efecd138bf6fb6
Author: myushen <mengyuan.shen@outlook.com>
Date: 2026-03-19 15:16:13 +1100
Commit message:

 show vignettes output. load rshiny data correctly
Package: cellNexus
Commit: 913b749c8c69ba9421892a59b4ea112093db48f0
Author: Mengyuan Shen <129487421+myushen@users.noreply.github.com>
Date: 2026-03-19 14:02:47 +1100
Commit message:

 Merge pull request #63 from myushen/read_files_progress_bar

Read files progress bar
Package: cellNexus
Commit: 31ac8e2b182ce3bb15c21cfcfd51d039b89a6110
Author: myushen <mengyuan.shen@outlook.com>
Date: 2026-03-19 12:32:23 +1100
Commit message:

 Merge master and solve conflicts. Add progress bar for reading each assay

Merge branch 'master' into read_files_progress_bar

# Conflicts:
#	DESCRIPTION
#	R/counts.R
#	dev/split_census_anndata_base_on_sample_id.R
Package: cellNexus
Commit: e0d1542823a0919ace61029b791f6ec6622f9f7f
Author: myushen <mengyuan.shen@outlook.com>
Date: 2026-03-19 11:09:01 +1100
Commit message:

 update vignettes
Package: cellNexus
Commit: 4091432e26cc5d4395acf647abb5a73877fff9e5
Author: myushen <mengyuan.shen@outlook.com>
Date: 2026-03-19 09:59:03 +1100
Commit message:

 fix warning messages in check
Package: cellNexus
Commit: 0c7ba62188073a8a426450752c11a4a15df184d2
Author: myushen <mengyuan.shen@outlook.com>
Date: 2026-03-18 17:00:23 +1100
Commit message:

 merge devel

Merge branch 'devel'

# Conflicts:
#	DESCRIPTION
#	NAMESPACE
#	R/counts.R
#	R/data.R
#	R/interface_app.R
#	R/metadata.R
#	R/utils.R
#	dev/5_unify_and_update_sce_metadata.R
#	man/create_interface_app.Rd
#	man/get_SingleCellExperiment.Rd
#	man/get_metadata.Rd
#	man/get_metadata_url.Rd
#	man/get_pseudobulk.Rd
#	man/get_seurat.Rd
#	man/get_single_cell_experiment.Rd
#	vignettes/cellNexus.Rmd
Package: cellNexus
Commit: b9bc93bf4644597fadcba5e5d2c8f550547fd26d
Author: myushen <mengyuan.shen@outlook.com>
Date: 2026-03-18 13:04:10 +1100
Commit message:

 Merge branch 'master' of https://github.com/myushen/cellNexus
Package: cellNexus
Commit: c40ff7e814a73d6d7d802c49270e48fbf4c5ec68
Author: Stefano Mangiola <mangiolastefano@gmail.com>
Date: 2026-03-17 18:16:13 +1030
Commit message:

 Merge pull request #89 from MangiolaLaboratory/pseudobulk-SE

Update version to 0.99.10; enhance get_pseudobulk() with as_Summarize…
Package: cellNexus
Commit: ac3e896dde6057ac0699d5bfce5349175ff6bbf0
Author: Stefano Mangiola <mangiolastefano@gmail.com>
Date: 2026-03-17 17:36:16 +1030
Commit message:

 Potential fix for pull request finding

Co-authored-by: Copilot Autofix powered by AI <175728472+Copilot@users.noreply.github.com>
Package: cellNexus
Commit: 6ba57e8656abff68c6955ee009651a44a4c06855
Author: Stefano Mangiola <mangiolastefano@gmail.com>
Date: 2026-03-17 17:23:04 +1030
Commit message:

 Update version to 0.99.10; enhance get_pseudobulk() with as_SummarizedExperiment parameter to optionally return a SummarizedExperiment while preserving feature rownames. Add corresponding tests.
Package: cellNexus
Commit: d250a3ba5199f4ec83110817b08f2f918e16b87b
Author: myushen <mengyuan.shen@outlook.com>
Date: 2026-03-17 17:29:48 +1100
Commit message:

 merge solve conflict
Package: cellNexus
Commit: 7b09f7ec05a503483a1f39050be3dab0ee1c0c1b
Author: myushen <mengyuan.shen@outlook.com>
Date: 2026-03-13 14:17:47 +1100
Commit message:

 update data release
Package: cellNexus
Commit: f0b6f6944a8c54dfcc38e388ff27ee9ffe51ebbe
Author: Mengyuan Shen <129487421+myushen@users.noreply.github.com>
Date: 2026-03-17 17:15:58 +1100
Commit message:

 Merge pull request #86 from myushen/bioconductor

Bioconductor
Package: cellNexus
Commit: 1639e03d5f4a4a787793ef40a574e45c13694908
Author: myushen <mengyuan.shen@outlook.com>
Date: 2026-03-17 16:17:57 +1100
Commit message:

 version bump
Package: cellNexus
Commit: d7ec13c11a6772937173c5c7df9a611ed35505af
Author: Mengyuan Shen <129487421+myushen@users.noreply.github.com>
Date: 2026-03-17 15:46:26 +1100
Commit message:

 Merge branch 'master' into bioconductor
Package: cellNexus
Commit: 51dddf2f80103181adf70146e2f961bb8f8b436e
Author: Mengyuan Shen <129487421+myushen@users.noreply.github.com>
Date: 2026-03-17 15:33:02 +1100
Commit message:

 Merge pull request #85 from j-andrews7/app_updates

App updates
Package: cellNexus
Commit: 11af7021476ec38cfbed255e3e42f333e4449f5c
Author: Mengyuan Shen <mengyuan.shen@outlook.com>
Date: 2026-03-17 15:19:02 +1100
Commit message:

 rclipboard dep issue, try remove
Package: cellNexus
Commit: 725d9f6c94ff9f43036cba0b8e3883f178566fce
Author: Mengyuan Shen <mengyuan.shen@outlook.com>
Date: 2026-03-17 13:51:15 +1100
Commit message:

 suggest rclipboard
Package: cellNexus
Commit: 87f38756392a703c40df79220af24b2a4ee0f139
Author: Mengyuan Shen <mengyuan.shen@outlook.com>
Date: 2026-03-17 11:45:47 +1100
Commit message:

 sync_assay_file to download files without relying on reading metadata
Package: cellNexus
Commit: f118dca360ad2de67f3c43998444ec17a3a3a282
Author: myushen <mengyuan.shen@outlook.com>
Date: 2026-03-17 09:47:20 +1100
Commit message:

 Stop tracking dev scripts, ignore dev/
Package: cellNexus
Commit: 6fcc3ac2a9dd7414ee37e6542d5d89636bcf027c
Author: myushen <mengyuan.shen@outlook.com>
Date: 2026-03-17 09:38:09 +1100
Commit message:

 update metadata release version
Package: cellNexus
Commit: ba769372169555fb35727859c8fbbf63a8b58571
Author: Mengyuan Shen <mengyuan.shen@outlook.com>
Date: 2026-03-16 18:25:35 +1100
Commit message:

 fix = to <-; use zellkonverter::writeH5AD for internal save anndata function
Package: cellNexus
Commit: 06f2b789b9ded296d06e345461daadee2bb57a5e
Author: myushen <mengyuan.shen@outlook.com>
Date: 2026-03-16 16:36:53 +1100
Commit message:

 Merge branch 'bioconductor' of https://github.com/myushen/cellNexus into bioconductor
Package: cellNexus
Commit: 4b698bec365720300e20fc1d9cef5d19468a89a9
Author: myushen <mengyuan.shen@outlook.com>
Date: 2026-03-16 16:35:57 +1100
Commit message:

 update system requirement
Package: cellNexus
Commit: e0611caad5ec2b190d971d94b96e486eac68e974
Author: Mengyuan Shen <mengyuan.shen@outlook.com>
Date: 2026-03-16 16:35:10 +1100
Commit message:

 refactor get_sce, get_pseudobulk, get_metacell. avoid code repetition
Package: cellNexus
Commit: 95f63308c340147f9a6536bee64d4c943b7cc5f2
Author: Mengyuan Shen <mengyuan.shen@outlook.com>
Date: 2026-03-16 16:34:44 +1100
Commit message:

 systemrequire
Package: cellNexus
Commit: da5d32d2d145ad8b40303038ac53bf084bfacba3
Author: myushen <mengyuan.shen@outlook.com>
Date: 2026-03-13 14:17:47 +1100
Commit message:

 update data release
Package: cellNexus
Commit: ce8c6535da36bf44c16ef621413f60d5a514c08c
Author: myushen <mengyuan.shen@outlook.com>
Date: 2026-03-09 17:20:33 +1100
Commit message:

 merge from master

Merge branch 'master' into bioconductor

# Conflicts:
#	R/counts.R
#	R/utils.R
#	man/get_pseudobulk.Rd
#	man/save_sce_as_h5ad.Rd
Package: cellNexus
Commit: 465f79eb932b57119220e5ad66e748b12c47577e
Author: myushen <mengyuan.shen@outlook.com>
Date: 2026-03-09 17:16:34 +1100
Commit message:

 update:
get_metacell() to use numeric internally.
get_sce() converts numeric to character to slice anndata.
save_sce inherit ... from `anndataR`
Package: cellNexus
Commit: b6e3ae9d3ccb050face829eb19711e020470d798
Author: myushen <mengyuan.shen@outlook.com>
Date: 2026-03-03 17:25:39 +1100
Commit message:

 remove internal functions Rds. add unit test for get_CPM()
Package: cellNexus
Commit: 2b96918de911722764ec22bd4f309ab78702fcb4
Author: myushen <mengyuan.shen@outlook.com>
Date: 2026-03-03 15:42:39 +1100
Commit message:

 fix write_h5ad
Package: cellNexus
Commit: a8748fd33e4368efd9c09f5432944bdf760b0946
Author: myushen <mengyuan.shen@outlook.com>
Date: 2026-03-03 15:37:07 +1100
Commit message:

 fix check warnings and errors
Package: cellNexus
Commit: fc3f83d3dc43aac9160e3ed7d751c8e51913911e
Author: Mengyuan Shen <mengyuan.shen@outlook.com>
Date: 2026-02-27 17:52:08 +1100
Commit message:

 fix check warnings and errors
Package: cellNexus
Commit: dd4bd96c3074b32e8abd8b935fc4c92d32971835
Author: myushen <mengyuan.shen@outlook.com>
Date: 2026-02-27 17:36:10 +1100
Commit message:

 import zellkonverter
Package: cellNexus
Commit: c57d3dd9c277ee6371bccb30a103ed5c6940c961
Author: Mengyuan Shen <mengyuan.shen@outlook.com>
Date: 2026-02-27 16:26:11 +1100
Commit message:

 tags consistency for noRd and internal
Package: cellNexus
Commit: 9869643dc921c53834e40949aa7291237f83e98c
Author: Mengyuan Shen <mengyuan.shen@outlook.com>
Date: 2026-02-27 16:02:24 +1100
Commit message:

 remove , refactor directly in
Package: cellNexus
Commit: cabee9a4c55691c8f7f76bb4acfefcc8606ce36f
Author: Mengyuan Shen <mengyuan.shen@outlook.com>
Date: 2026-02-27 15:17:07 +1100
Commit message:

 rename read_parquet to avoid package function conflict
Package: cellNexus
Commit: 801cb2d958988be6acbea67ec0ffe209d1b14653
Author: Mengyuan Shen <mengyuan.shen@outlook.com>
Date: 2026-02-27 14:57:59 +1100
Commit message:

 update readability section
Package: cellNexus
Commit: 73382a4f15715992ae74891bce7a97c608978a29
Author: Mengyuan Shen <mengyuan.shen@outlook.com>
Date: 2026-02-27 14:39:16 +1100
Commit message:

 update syntax, no cat
Package: cellNexus
Commit: c0e100cc37ed012598af775d9e4fead529d9e9c1
Author: Mengyuan Shen <mengyuan.shen@outlook.com>
Date: 2026-02-27 14:35:03 +1100
Commit message:

 package unit test coverage to 71%
Package: cellNexus
Commit: 962b6fb90614b4d5f5dabd0722b7d7ae07350d45
Author: Mengyuan Shen <129487421+myushen@users.noreply.github.com>
Date: 2026-02-27 10:44:51 +1100
Commit message:

 Merge pull request #87 from myushen/cell_communication

Cell communication
Package: cellNexus
Commit: b9d5b9d315f200e0a482d48409cc3ce3801fbf9f
Author: myushen <mengyuan.shen@outlook.com>
Date: 2026-02-27 10:27:54 +1100
Commit message:

 fix check warning
Package: cellNexus
Commit: 6adfb028ced454e008c2b1b4c9de1c6c6ad060df
Author: Mengyuan Shen <mengyuan.shen@outlook.com>
Date: 2026-02-26 17:48:13 +1100
Commit message:

 out consistency..
Package: cellNexus
Commit: 476915fd7cf6573abb6729a3be5bbee492033bfc
Author: Mengyuan Shen <mengyuan.shen@outlook.com>
Date: 2026-02-26 17:47:53 +1100
Commit message:

 man pages have runnable examples
Package: cellNexus
Commit: fee86ecee63f78580cdd55eee927e0e62e538ae7
Author: Mengyuan Shen <mengyuan.shen@outlook.com>
Date: 2026-02-26 16:55:49 +1100
Commit message:

 vignette uses biocstyle, and has a table of contents
Package: cellNexus
Commit: af082515ff73668db5b3aacb7e3637ef72fd2e43
Author: Mengyuan Shen <mengyuan.shen@outlook.com>
Date: 2026-02-26 16:42:21 +1100
Commit message:

 update NEWS and CITATION
Package: cellNexus
Commit: 36efc050b5bfd9d624c4793ea07821f90630e270
Author: Mengyuan Shen <mengyuan.shen@outlook.com>
Date: 2026-02-26 16:36:01 +1100
Commit message:

 Add NEWS.md
Package: cellNexus
Commit: 16c4768b093e3fa40ab37a62d5d2951c34e1b00a
Author: myushen <mengyuan.shen@outlook.com>
Date: 2026-02-26 16:11:17 +1100
Commit message:

 enable sct in get_SCE
Package: cellNexus
Commit: 28dd294e1620421403e7a2449869d09dc3c961e8
Author: myushen <mengyuan.shen@outlook.com>
Date: 2026-02-26 16:08:48 +1100
Commit message:

 update documentation and sct assay
Package: cellNexus
Commit: 6a38c4dd3596b4a3359fdcf2cc122b1d7b3c20ea
Author: myushen <mengyuan.shen@outlook.com>
Date: 2026-02-26 14:53:49 +1100
Commit message:

 remove import_SCE(). its in cellnexuscloud package
Package: cellNexus
Commit: a9706297b37d285f9e77cfb45eebe058c2958244
Author: myushen <mengyuan.shen@outlook.com>
Date: 2026-02-26 14:35:51 +1100
Commit message:

 calling internal data using data(...)
Package: cellNexus
Commit: ce07f1f96de61c036fc5d295d0c2daa200c0c770
Author: myushen <mengyuan.shen@outlook.com>
Date: 2026-02-25 17:08:04 +1100
Commit message:

 dont use assertthat, update readme
Package: cellNexus
Commit: 91e5dcf3fcdc8f12c93d856016fc20cbd3e9b828
Author: myushen <mengyuan.shen@outlook.com>
Date: 2026-02-25 16:51:17 +1100
Commit message:

 update author list
Package: cellNexus
Commit: fd21a0295efb8f9f08a611314d9afb0a52c6c96f
Author: myushen <mengyuan.shen@outlook.com>
Date: 2026-02-24 17:10:17 +1100
Commit message:

 address: LazyData,Depends, Imports, Suggests, Enhances fields
Package: cellNexus
Commit: 22f8ef509abc3c1503692d22d00b32b4bc9946d4
Author: myushen <mengyuan.shen@outlook.com>
Date: 2026-02-24 13:04:20 +1100
Commit message:

 avoid check warning
Package: cellNexus
Commit: 2a5b4ed2aa5ba640395e015ded0f8f9be5e2c170
Author: myushen <mengyuan.shen@outlook.com>
Date: 2026-02-24 11:22:38 +1100
Commit message:

 Merge branch 'master' of https://github.com/myushen/cellNexus
pull from remote
Package: cellNexus
Commit: ec43a7449f2fe61610ba5634ab9ef5c1ae1ee53a
Author: myushen <mengyuan.shen@outlook.com>
Date: 2026-02-24 11:18:57 +1100
Commit message:

 loads dplyr internally when calling cellNexus
Package: cellNexus
Commit: 240e1a0df1912f093ac6a82172f74a7113263aa6
Author: myushen <mengyuan.shen@outlook.com>
Date: 2026-02-24 11:13:17 +1100
Commit message:

 better split. cellnexus_metadata only contains curated columns. census_metadata contains CELLxGENE columns. metacell_metadata has all metacell related columns.
Package: cellNexus
Commit: bc5a05316f56e4ee37497162164fe87d85fd8cc1
Author: Jared Andrews <jared.andrews07@gmail.com>
Date: 2026-02-22 18:59:23 -0600
Commit message:

 Update manifest.json
Package: cellNexus
Commit: 9f6a192f8a978ac498abc2a6f2ac48fce0604ce5
Author: Jared Andrews <jared.andrews07@gmail.com>
Date: 2026-02-22 18:44:05 -0600
Commit message:

 app ui updates
Package: cellNexus
Commit: 4b253e6f344f443ac2f1ff99211786c462f8bdb3
Author: Jared Andrews <jared.andrews07@gmail.com>
Date: 2026-02-22 17:42:45 -0600
Commit message:

 Update manifest.json
Package: cellNexus
Commit: f904fe9fcc47cfc5434f94380906f8f0fd6e3256
Author: Jared Andrews <jared.andrews07@gmail.com>
Date: 2026-02-22 17:39:45 -0600
Commit message:

 allow app return as list for deployment
Package: cellNexus
Commit: e612b827888b3ff5136f64a1b7bc2ca2b6d74d8c
Author: Jared Andrews <jared.andrews07@gmail.com>
Date: 2026-02-22 17:18:51 -0600
Commit message:

 Update manifest.json
Package: cellNexus
Commit: 620e2f76db33a4d2d46fc8e4ca74244e3950062c
Author: Jared Andrews <jared.andrews07@gmail.com>
Date: 2026-02-22 17:11:55 -0600
Commit message:

 fix a few `check` notes
Package: cellNexus
Commit: 77de57769e567380a93baa5c67281d60283a910c
Author: Jared Andrews <jared.andrews07@gmail.com>
Date: 2026-02-22 14:08:53 -0600
Commit message:

 Update manifest.json
Package: cellNexus
Commit: 17b7182b5de950242d61dc97c2b9ec2c1e9bf991
Author: Jared Andrews <jared.andrews07@gmail.com>
Date: 2026-02-22 14:06:03 -0600
Commit message:

 cleaner data loading for app deployment
Package: cellNexus
Commit: a69586051dcd05232dcd8739374d7212f8476e18
Author: Jared Andrews <jared.andrews07@gmail.com>
Date: 2026-02-22 12:42:54 -0600
Commit message:

 Update manifest.json
Package: cellNexus
Commit: 9e7cfe3f38c4845b89fb8e13a89720ef202602ad
Author: Jared Andrews <jared.andrews07@gmail.com>
Date: 2026-02-22 12:27:38 -0600
Commit message:

 more proper data storage
Package: cellNexus
Commit: 6d7deee7a7f5393b5c2022f43c86f7bae8c50e7d
Author: Jared Andrews <jared.andrews07@gmail.com>
Date: 2026-02-22 11:51:37 -0600
Commit message:

 Update manifest.json
Package: cellNexus
Commit: 49941b02e9aff5b15f6e1f630c72f550523f6156
Author: Jared Andrews <jared.andrews07@gmail.com>
Date: 2026-02-22 04:36:29 -0600
Commit message:

 Update manifest.json
Package: cellNexus
Commit: 621dfbde078945038380690f7ebd90aff3b3bcac
Author: Jared Andrews <jared.andrews07@gmail.com>
Date: 2026-02-22 04:27:29 -0600
Commit message:

 Update manifest.json
Package: cellNexus
Commit: 0ac3aed35edcaaac79eb165270f834adbf34b7a3
Author: Jared Andrews <jared.andrews07@gmail.com>
Date: 2026-02-22 04:23:46 -0600
Commit message:

 app manifest for publishing
Package: cellNexus
Commit: ac024d59d11a683ac2f3d161b5e0d8af7e5ca86f
Author: Jared Andrews <jared.andrews07@gmail.com>
Date: 2026-02-22 04:14:49 -0600
Commit message:

 parallelize downloads
Package: cellNexus
Commit: 6ff3fc65381d0a9072940d0b45ac3caddee23d89
Author: Jared Andrews <jared.andrews07@gmail.com>
Date: 2026-02-22 03:38:17 -0600
Commit message:

 add python query block
Package: cellNexus
Commit: 0379ad5a3a3ae75e8e05c290661663c2e85dc29b
Author: Jared Andrews <jared.andrews07@gmail.com>
Date: 2026-02-22 02:57:23 -0600
Commit message:

 Create app.r
Package: cellNexus
Commit: b5346a6c5d4002b4d0a354e33100948b1e46bc62
Author: Jared Andrews <jared.andrews07@gmail.com>
Date: 2026-02-20 23:37:18 -0600
Commit message:

 Merge branch 'MangiolaLaboratory:master' into app_updates
Package: cellNexus
Commit: df7da2a24c6149dac10c08ee8c71476a84e277bf
Author: Stefano Mangiola <mangiolastefano@gmail.com>
Date: 2026-02-20 10:29:49 +0100
Commit message:

 Merge pull request #84 from MangiolaLaboratory/website

Change image alignment in index.md from center to left for better lay…
Package: cellNexus
Commit: fa24d57b4429bf32a1336e7bbfaf827115f5a1e7
Author: Stefano Mangiola <mangiolastefano@gmail.com>
Date: 2026-02-20 10:28:55 +0100
Commit message:

 Change image alignment in index.md from center to left for better layout consistency
Package: cellNexus
Commit: 2ed14cf15a01067f06cc0395fb30e03906ab7078
Author: Stefano Mangiola <mangiolastefano@gmail.com>
Date: 2026-02-20 09:44:54 +0100
Commit message:

 Merge pull request #83 from MangiolaLaboratory/website

Update image styling in index.md for improved responsiveness
Package: cellNexus
Commit: e494caa4642ae12392f27ed3fa822838bdff98ff
Author: Stefano Mangiola <mangiolastefano@gmail.com>
Date: 2026-02-20 09:28:57 +0100
Commit message:

 Update image styling in index.md for improved responsiveness
Package: cellNexus
Commit: 9f76b860cf984618452841a9daa5ed2a3e6cf60c
Author: Stefano Mangiola <mangiolastefano@gmail.com>
Date: 2026-02-19 18:56:07 +0100
Commit message:

 Merge pull request #82 from MangiolaLaboratory/website

Update image path in index.md for documentation consistency