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Package: biomaRt
Commit: 22f4d9f8d41e0e69628f83a2e2fbf990fd2fbf2c
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-09-20 12:17:25 +0200
Commit message:

 Run devtools::document()
Package: biomaRt
Commit: 05fc4fcda0237b8d311f2c2e4d441815b39ce553
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-09-20 12:17:08 +0200
Commit message:

 Fix typo
Package: biomaRt
Commit: 50a27d2cf0659fedfd5c1ff91700af6243bb2db1
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-09-20 12:15:50 +0200
Commit message:

 Bump version number
Package: biomaRt
Commit: f7e293327cf49ac7fd582cd18724dc9de21bb42c
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-09-20 12:15:37 +0200
Commit message:

 Run devtools::document()
Package: biomaRt
Commit: 00fe87925153441624776ebe69bb73b8a9387723
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-09-20 12:15:18 +0200
Commit message:

 Run desc::desc_normalize()
Package: biomaRt
Commit: 0477cbe04b8408c4a3d150238eb393e65d4ed4c0
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-09-20 12:14:37 +0200
Commit message:

 Remove URL with lapsed domain name
Package: biomaRt
Commit: c36f7587bf504c047eb58fb35acb61bce2c39c4b
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-09-19 18:26:20 +0200
Commit message:

 Set Hugo as maintainer
Package: SETA
Commit: ca704e39a9f22e503c0cac2ae58ab404c619c075
Author: kylekimler <kylejkimler@gmail.com>
Date: 2025-09-19 18:10:45 -0400
Commit message:

 bioconductor review
Package: tidyexposomics
Commit: 16aeeb297c324c42a40ece5750aa55df46110f18
Author: BioNomad <jlaird1@binghamton.edu>
Date: 2025-09-19 17:34:41 -0400
Commit message:

 tracking/testing updates
Package: SETA
Commit: eb94bab2923f9c3950339c3a9089f0bb32ac9b2e
Author: kylekimler <kylejkimler@gmail.com>
Date: 2025-09-19 17:27:51 -0400
Commit message:

 bioconductor review 3
Package: MSstatsLiP
Commit: 4e6b3a7d665f37d530588962b4f77b5b4d2d0cd1
Author: tonywu1999 <anthonywu92@gmail.com>
Date: 2025-09-19 17:13:22 -0400
Commit message:

 Update package version to 1.15.2

Bump version from 1.15.1 to 1.15.2 in DESCRIPTION file.
Package: MSstatsLiP
Commit: 0a4cb7946e4ce7a35a18226b0ef15484926a909f
Author: tonywu1999 <anthonywu92@gmail.com>
Date: 2025-09-19 15:59:50 -0400
Commit message:

 tests(pcaPlot): Add barwidth to pcaplot to remove warnings
Package: MSstatsLiP
Commit: 20ef0018d6fac4e1520f6ec369914409cea05c9d
Author: tonywu1999 <wu.anthon@northeastern.edu>
Date: 2025-09-19 15:25:19 -0400
Commit message:

 tests(pcaPlot): Add barwidth to pcaplot to remove warnings
Package: MSstatsPTM
Commit: d2558b78d6847d3b9bf703dfb666f8d7a4c41cf2
Author: tonywu1999 <wu.anthon@northeastern.edu>
Date: 2025-09-19 17:11:16 -0400
Commit message:

 Update package version to 2.11.5
Package: MSstatsPTM
Commit: eaedc0d317d49ac6bc17173529fcca93cd058e8c
Author: tonywu1999 <wu.anthon@northeastern.edu>
Date: 2025-09-19 16:00:59 -0400
Commit message:

 fix(dataProcessPlotsPTM, groupComparisonPlotsPTM): Migrate away from deprecated functions for ggplot (#120)
Package: MSstatsPTM
Commit: 16c54eb570132ffe092c54db27a3e26af1d4dcea
Author: tonywu1999 <wu.anthon@northeastern.edu>
Date: 2025-09-17 10:14:31 -0400
Commit message:

 docs(fragpipe): Modify vignettes to include global profiling run example (#119)
Package: SETA
Commit: b77967536e673a8c3d85b2bb5aad805ef694dcc7
Author: kylekimler <kylejkimler@gmail.com>
Date: 2025-09-19 17:09:21 -0400
Commit message:

 bioconductor review 3
Package: Pirat
Commit: 879affc0b767e86e50974c3068fbe3a3ea236977
Author: Lucas Etourneau <lucas.etourneau@berkeley.edu>
Date: 2025-09-19 12:24:52 -0700
Commit message:

 Rm cpuonly
Package: rtracklayer
Commit: 56d4984581a89f801afb00773d86f2a4abcf75b2
Author: Michael Lawrence <michafla@gene.com>
Date: 2025-09-19 09:21:52 -0700
Commit message:

 Merge pull request #137 from CPOS-HPC/devel

Add additional check to handle older libcurl
Package: rtracklayer
Commit: 010d1c0caf0d7452ffcf545f4f500780fe6ff6e7
Author: Emik <phoenix0919mik@gmail.com>
Date: 2025-09-19 14:10:09 +0800
Commit message:

 Merge branch 'lawremi:devel' into devel
Package: rtracklayer
Commit: 1d981ce5989c7b73c3c8ab7a94ea29cd178a1c20
Author: Emik <phoenix0919mik@gmail.com>
Date: 2025-04-11 20:09:05 +0800
Commit message:

 Merge branch 'lawremi:devel' into devel
Package: rtracklayer
Commit: 9c59a9ba3c9ad95b088cdf73b354c08a35d14285
Author: Emik <phoenix0919mik@gmail.com>
Date: 2025-03-08 22:28:44 +0800
Commit message:

 Merge branch 'lawremi:devel' into devel
Package: rtracklayer
Commit: 414b3d0564239316075654bb31e02c621acbc69a
Author: Phoenix Emik <phoenix0919mik@gmail.com>
Date: 2025-03-04 11:14:35 +0800
Commit message:

 Add check to handle older libcurl
Package: CSOA
Commit: c31b17a312ff91cdf1e34a8bd497baa56bfb56ed
Author: andrei-stoica26 <andreistoica@foxmail.com>
Date: 2025-09-20 00:11:24 +0800
Commit message:

 Fixed plotting function tests
Package: iModMix
Commit: 30fc00f04f13171124370990cf9a0405e6ef4323
Author: Isis Narvaez-Bandera <isis.narvaez@upr.edu>
Date: 2025-09-19 10:52:59 -0400
Commit message:

 full corplot
Package: iModMix
Commit: 6eafd768bfc7ea160f2d8a468c15c654627b42f3
Author: Isis Narvaez-Bandera <isis.narvaez@upr.edu>
Date: 2025-09-18 15:54:42 -0400
Commit message:

 move app.R and Docker
Package: iModMix
Commit: 82174af5faffeaf3a5747d7384c7912ccfe14635
Author: Isis Narvaez-Bandera <isis.narvaez@upr.edu>
Date: 2025-09-15 14:06:10 -0400
Commit message:

 2.99
Package: curatedMetagenomicData
Commit: e5b5f83fb46a28e61a25546bf0d70c2bc0e39d4d
Author: Levi Waldron <lwaldron.research@gmail.com>
Date: 2025-07-18 03:53:05 -0400
Commit message:

 Merge pull request #319 from shbrief/master

Example analysis using harmonized metadata
Package: curatedMetagenomicData
Commit: f383cef193325e3647de59b6477d1ac58570c653
Author: Sehyun Oh <shbrief@gmail.com>
Date: 2025-06-05 23:31:59 -0400
Commit message:

 Updates following the reviewer's suggestions
Package: curatedMetagenomicData
Commit: e77007c870ee42864dc6ab80e4eb54008eb0d303
Author: Sehyun Oh <shbrief@hotmail.com>
Date: 2025-05-22 21:56:36 -0400
Commit message:

 version bump
Package: curatedMetagenomicData
Commit: 5aa172ab2a91c45f52f9cc5a394d342eab960b29
Author: Sehyun Oh <shbrief@hotmail.com>
Date: 2025-05-22 21:56:20 -0400
Commit message:

 add authors who updated the vignette
Package: curatedMetagenomicData
Commit: 6613f06ffb88e3236e6c1ff5532120809ddae8b9
Author: Sehyun Oh <shbrief@hotmail.com>
Date: 2025-05-22 15:34:39 -0400
Commit message:

 updated vignette
Package: curatedMetagenomicData
Commit: cade2aa811bcae6085e22ad82669dbb73b825b5e
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-04-21 16:11:15 -0400
Commit message:

 add flatly bootswatch
Package: curatedMetagenomicData
Commit: 8bfb7f14fd5879495c71a06b747ad4cd322e636f
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-04-21 13:48:58 -0400
Commit message:

 renovate GHA
Package: spicyR
Commit: 21dfb33aae3b1c26dde144830d0b6db7372bab8d
Author: ellispatrick <ellis.patrick@sydney.edu.au>
Date: 2025-09-19 23:46:22 +1000
Commit message:

 commented out survival bubble plot and added message
Package: spicyR
Commit: fe47ce5ee644c542057b5e5163cfc30865fd8f62
Author: ellispatrick <ellis.patrick@sydney.edu.au>
Date: 2025-09-19 20:34:12 +1000
Commit message:

 linewidth
Package: RiboCrypt
Commit: e669838cb3ffcfa927456451dd26066729a86aa8
Author: m-swirski <michal.swirski@student.uw.edu.pl>
Date: 2025-09-19 12:52:30 +0000
Commit message:

 merge from master
Package: RiboCrypt
Commit: a77c5a303fbe38c4eb866a6d6acbc3235239cddb
Author: Roleren <hauken_heyken@hotmail.com>
Date: 2025-09-19 13:12:46 +0200
Commit message:

 Improved DEG plot
Package: RiboCrypt
Commit: 30127ae4561c86684b176db221f2af2d59f5d4d7
Author: Roleren <hauken_heyken@hotmail.com>
Date: 2025-09-18 16:12:16 +0200
Commit message:

 Preparing for bioc push
Package: RiboCrypt
Commit: e72c5ed346efa650abf7d74caa363656c94efc0b
Author: Roleren <hauken_heyken@hotmail.com>
Date: 2025-09-16 14:35:06 +0200
Commit message:

 Improved tutorial
Package: RiboCrypt
Commit: 5a573d6a3a8259e30e7e8ea435de4b61b8976cf3
Author: Roleren <hauken_heyken@hotmail.com>
Date: 2025-09-16 14:04:14 +0200
Commit message:

 Added url copy for unique argument
Package: RiboCrypt
Commit: 19aa2f7bc5fe417a0d4cbd6f2a659424413d1dcc
Author: Roleren <hauken_heyken@hotmail.com>
Date: 2025-09-16 13:05:05 +0200
Commit message:

 another bug libraries_string_split fixed
Package: RiboCrypt
Commit: d2d4385fdb6dd9b298b8b0033054b1aadc884082
Author: Roleren <hauken_heyken@hotmail.com>
Date: 2025-09-16 13:00:27 +0200
Commit message:

 Small na fix bug
Package: RiboCrypt
Commit: c164465658b6158867d7d634260fd4fab49bd5cd
Author: Roleren <hauken_heyken@hotmail.com>
Date: 2025-09-16 12:56:37 +0200
Commit message:

 Small bugfix analysis page
Package: RiboCrypt
Commit: 6cda0f5feb757392d92e502652a159051c7f9b75
Author: Roleren <hauken_heyken@hotmail.com>
Date: 2025-09-16 12:43:29 +0200
Commit message:

 Fixed sharing bug and added unique alignments flag
Package: RiboCrypt
Commit: 91dcd6f17512cf703decf743066d438d9236b25a
Author: Roleren <hauken_heyken@hotmail.com>
Date: 2025-09-13 01:04:00 +0200
Commit message:

 Fixed bug for not plotting on start when gene was not changed from url
Package: RiboCrypt
Commit: a75814456a0ace4bf9202dc7b9ac0c646cb22f8f
Author: Roleren <hauken_heyken@hotmail.com>
Date: 2025-09-13 00:44:25 +0200
Commit message:

 Complete rewrite of launching of Ribocrypt and url API behavoir
Package: RiboCrypt
Commit: efde47738893ce4c0fd8cca432fe14ec81c00db4
Author: Roleren <hauken_heyken@hotmail.com>
Date: 2025-09-09 11:53:04 +0200
Commit message:

 Small fix to megabrowser metamotif
Package: RiboCrypt
Commit: ea8090a082a5e74c1fe842583e8949dd9ad88bdb
Author: Roleren <hauken_heyken@hotmail.com>
Date: 2025-08-27 14:40:34 +0200
Commit message:

 Fixed x axis bug and added svg export for codon plot
Package: RiboCrypt
Commit: 90a3bcd8194fb1af52355e4a8ea980402716a197
Author: Roleren <hauken_heyken@hotmail.com>
Date: 2025-08-19 14:33:44 +0200
Commit message:

 Safer translon table load for IDs
Package: RiboCrypt
Commit: 41b7b128e66cfb5ea8d86300b2b608fc20db48f0
Author: Roleren <hauken_heyken@hotmail.com>
Date: 2025-08-19 12:38:48 +0200
Commit message:

 Added peptide view in translon table
Package: RiboCrypt
Commit: 6f1b9dfddca0ad285f2bac138e2161336d8b3781
Author: Roleren <hauken_heyken@hotmail.com>
Date: 2025-08-19 00:12:31 +0200
Commit message:

 Added support for peptide structure render of translons
Package: RiboCrypt
Commit: 5f3cd578a7b95865477a33968294595ec9e0c878
Author: Roleren <hauken_heyken@hotmail.com>
Date: 2025-08-14 15:54:27 +0200
Commit message:

 Fixed megabrowser min count settings being null and failing
Package: RiboCrypt
Commit: 407e93005bb81ce5c654104ef0b862d380c588d3
Author: Roleren <hauken_heyken@hotmail.com>
Date: 2025-08-11 14:58:24 +0200
Commit message:

 Added mapability track
Package: RiboCrypt
Commit: d99b5bacd995d80fda5b28defb279fe50e3c139b
Author: Roleren <hauken_heyken@hotmail.com>
Date: 2025-08-09 00:53:09 +0200
Commit message:

 Added support for collections in browser, max 200 libs
Package: RiboCrypt
Commit: 9074576864108eb6deffcb7d063414d27876e36d
Author: Roleren <hauken_heyken@hotmail.com>
Date: 2025-08-08 23:28:23 +0200
Commit message:

 Improved default exps used
Package: RiboCrypt
Commit: ce513ac3aa2ac05bed9fdacfd83d33dee93e2a03
Author: Roleren <hauken_heyken@hotmail.com>
Date: 2025-08-08 21:59:39 +0200
Commit message:

 Exp box is now server side
Package: procoil
Commit: 25a668ca9c90b38a436d718572b2021d2fcec88a
Author: UBod <ulrich@bodenhofer.com>
Date: 2025-09-19 13:44:55 +0200
Commit message:

 Update of Authors@R in DESCRIPTION; version number bumped to 2.37.1
Package: podkat
Commit: af07a5d7f92f286a34e7b993642c0fe21cf5f532
Author: UBod <ulrich@bodenhofer.com>
Date: 2025-09-19 13:35:34 +0200
Commit message:

 Updated DESCRIPTION; version number bumped to 1.41.1
Package: msa
Commit: f99034dfc5e5376a7227a8b1ffd1f61513516701
Author: UBod <ulrich@bodenhofer.com>
Date: 2025-09-19 13:20:43 +0200
Commit message:

 Removed some files from version controL
Package: ORFik
Commit: 91fe5a24a821d2fc17b54f2e90bf3c9feadf20c2
Author: Roleren <hauken_heyken@hotmail.com>
Date: 2025-09-19 13:15:59 +0200
Commit message:

 Merge branch 'master' into devel
Package: ORFik
Commit: 819776f3019c145a5a5b2a74801a710b81dbf277
Author: Roleren <hauken_heyken@hotmail.com>
Date: 2025-09-19 13:15:41 +0200
Commit message:

 bump version, new bioc push
Package: ORFik
Commit: 35fc3ca55caacb1363598b128322ccace0794085
Author: Roleren <hauken_heyken@hotmail.com>
Date: 2025-09-19 13:15:11 +0200
Commit message:

 Improved docs
Package: ORFik
Commit: bf74671ea1b4ffcdf9d94f06bd5879de49195b73
Author: Roleren <hauken_heyken@hotmail.com>
Date: 2025-09-19 12:34:54 +0200
Commit message:

 improved DEG models
Package: msa
Commit: 2b38f632a0eb5725c3482ec666f7ab574c123f0e
Author: UBod <ulrich@bodenhofer.com>
Date: 2025-09-19 13:11:14 +0200
Commit message:

 Further update in DESCRIPTION
Package: immunotation
Commit: f7d28f1e4649204e990fb11bc372cde39d3c0770
Author: Katharina Imkeller <ag.imkeller@gmail.com>
Date: 2025-09-19 13:07:55 +0200
Commit message:

 update email maintainer by merge with release branch
Package: immunotation
Commit: 92372f91a4f9d7bd2f75549a42cf5e9ab98e093c
Author: Katharina Imkeller <ag.imkeller@gmail.com>
Date: 2025-09-19 13:05:11 +0200
Commit message:

 update email maintainer
Package: immunotation
Commit: 67890ee01e584d58e6c7f45985b21e65327b93d4
Author: Katharina Imkeller <ag.imkeller@gmail.com>
Date: 2025-08-27 16:11:48 +0200
Commit message:

 release version correction
Package: immunotation
Commit: 54401f6b17c3ad1b8b5d4a033268505cff13e817
Author: Katharina Imkeller <ag.imkeller@gmail.com>
Date: 2025-08-27 16:09:25 +0200
Commit message:

 fix decoding check
Package: kebabs
Commit: fd08123c56322dc71e3f4ce2044ccea69b8fb4a8
Author: UBod <ulrich@bodenhofer.com>
Date: 2025-09-19 12:55:49 +0200
Commit message:

 Update of Authors@R in DESCRIPTION; version number bumped to 1.43.1
Package: msa
Commit: 944c5a5399d39f9905ec25e75ec0c8466bcaeea9
Author: UBod <ulrich@bodenhofer.com>
Date: 2025-09-19 11:08:00 +0200
Commit message:

 fix of OpenMP integration; version number bumped to 1.41.3
Package: biomaRt
Commit: 7ce8dafc423b9abb78b73c932b0a76f8ac0c3333
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-09-19 10:05:47 +0200
Commit message:

 Bump version
Package: biomaRt
Commit: 0e0d9000323af25b6b8686808f62e5eb0797c22b
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-09-19 09:50:56 +0200
Commit message:

 Reduce nesting in findGenomeName()
Package: biomaRt
Commit: 83c74f746bfcd6e25524bc7b46e4c4257090a14c
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-09-19 09:41:58 +0200
Commit message:

 Fix misplaced parenthesis
Package: tidyexposomics
Commit: c2d7a15f9729026b85bbc95b0c992a6266fed96d
Author: BioNomad <jlaird1@binghamton.edu>
Date: 2025-09-18 18:04:59 -0400
Commit message:

 removing deprecated functions
Package: scRNAseqApp
Commit: 8d1289425e332eaccdd419404bb184be54db47d2
Author: Jianhong Ou <jianhong.ou@gmail.com>
Date: 2025-09-18 16:45:21 -0400
Commit message:

 Add zoom in for plot.
Package: Rtpca
Commit: 2872d594f6d8c49caf81b893de7e52fc8f506e57
Author: Nils Kurzawa <nilskurzawa@Mac.fritz.box>
Date: 2025-09-18 21:18:24 +0200
Commit message:

 fixed test error
Package: tidyexposomics
Commit: 6054bfa15dd39485c42f227c5d7aa3efa80fbb39
Author: BioNomad <jlaird1@binghamton.edu>
Date: 2025-09-18 15:13:50 -0400
Commit message:

 namespace fixes
Package: signeR
Commit: 6916ef7e1399836adbb9612ad395d61f13bffa6f
Author: Renan Valieris <renan.valieris@accamargo.org.br>
Date: 2025-09-18 15:39:56 -0300
Commit message:

 maintenance stuff
Package: S4Vectors
Commit: f2afb3e3b35d3b4f97a1d6122f65160d09d4de58
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2025-09-18 11:05:43 -0700
Commit message:

 S4Vectors 0.47.2: Replace C callable new_DataFrame with new_DFrame
Package: ggbio
Commit: 23b9ab1988fbc67756ae1af293303fa3a690353b
Author: Michael Lawrence <lawremi@gmail.com>
Date: 2025-09-18 09:46:37 -0700
Commit message:

 correct at least one place where we send facets= to facet_grid, fixes #173
Package: ggbio
Commit: f78696508d1487a36049a127772df72faef24637
Author: Michael Lawrence <lawremi@gmail.com>
Date: 2025-09-16 12:52:43 -0700
Commit message:

 replace at least some of the instances of size to linewidth when specifying line aesthetics
Package: ggbio
Commit: bd80e74149d2a9007117c758cb3f81e579af8102
Author: Michael Lawrence <lawremi@gmail.com>
Date: 2025-09-18 09:46:17 -0700
Commit message:

 use margin_auto() to pass margins to element_text()
Package: ggbio
Commit: 8711a67a59e893f1f5723488ecbd690965e12472
Author: Michael Lawrence <lawremi@gmail.com>
Date: 2025-09-18 09:45:29 -0700
Commit message:

 support the new S7 classes from ggplot2, fixes #175

still need to fix the deprecation warnings
Package: ggbio
Commit: 15def7bb5fd5d3c3d98c91e8f289085cb2304ef0
Author: AtaJadidAhari <atajadidahari@gmail.com>
Date: 2025-09-18 18:29:12 +0200
Commit message:

 Fix github action workflow  (#177)

* use r-lib actions setup-r & setup-r-dependencies

* Update R-CMD-check-and-coverage.yaml

* simplify gha workflow
Package: ggbio
Commit: ba410303fa24d97fd0486d95217dfdd17031667b
Author: AtaJadidAhari <atajadidahari@gmail.com>
Date: 2025-09-17 13:42:23 +0200
Commit message:

 update gha checkout and cache versions
Package: ggbio
Commit: 119b824416c5346f0aca14f323e725639dd97034
Author: Sanchit Saini <sanchitsaini14@gmail.com>
Date: 2025-08-06 00:48:43 +0530
Commit message:

 Safely register classes as S4 with `setOldClass` checks and removed options class
Package: ggbio
Commit: 7d7e0229138f918832f31450d65c05c06f2415f7
Author: Teun van den Brand <tahvdbrand@gmail.com>
Date: 2025-07-03 10:47:54 +0200
Commit message:

 include S7 class in OldClass definition
Package: ggbio
Commit: 77d5d4712705717af783a0acf0e12ee8183470c2
Author: Teun van den Brand <tahvdbrand@gmail.com>
Date: 2025-07-03 10:42:18 +0200
Commit message:

 fix examples with misdirected mapping
Package: ggbio
Commit: 008a4bc0e2bebca2024684dfab025f0d06a32a10
Author: Teun van den Brand <tahvdbrand@gmail.com>
Date: 2025-07-03 09:10:53 +0200
Commit message:

 replace `aes_string()`
Package: ggbio
Commit: 59f752f114c64535c7c1e82c302843dfb329bfeb
Author: Teun van den Brand <tahvdbrand@gmail.com>
Date: 2025-07-02 17:57:24 +0200
Commit message:

 fix examples. These .Rd files need to be edited manually, do they predate roxygen??
Package: ggbio
Commit: 0ca7eb6de9eb64605143685fb63351f83131402a
Author: Teun van den Brand <tahvdbrand@gmail.com>
Date: 2025-07-02 17:41:52 +0200
Commit message:

 don't use removed `cunion()`
Package: ggbio
Commit: 5fee390021d3c332c60474c103687f816309735e
Author: Teun van den Brand <tahvdbrand@gmail.com>
Date: 2025-07-02 17:36:53 +0200
Commit message:

 `guide_legend(bycol)` is/was not an argument
Package: ggbio
Commit: 38d3525750638c43c3084ecdc1a68600b0761863
Author: Teun van den Brand <tahvdbrand@gmail.com>
Date: 2025-07-02 17:36:09 +0200
Commit message:

 replace internal function
Package: ggbio
Commit: fa510d4562d9a864f744b8d8b2033b402c3fd7d5
Author: Teun van den Brand <tahvdbrand@gmail.com>
Date: 2025-07-02 17:30:12 +0200
Commit message:

 additional instances of `facet_grid(facets)`
Package: ggbio
Commit: a2f46c3ed5d454ef28dd657ff76150699e34275f
Author: Teun van den Brand <tahvdbrand@gmail.com>
Date: 2025-07-02 16:27:03 +0200
Commit message:

 fix partial match
Package: ggbio
Commit: 7f22fc004568ad8d895c742826ddd190fe9a838a
Author: Teun van den Brand <tahvdbrand@gmail.com>
Date: 2025-07-02 16:12:35 +0200
Commit message:

 fix deprecated `element_line(size)`
Package: ggbio
Commit: 5086c5ce2a242ce8bf8ff47875f89878895a6bd5
Author: Teun van den Brand <tahvdbrand@gmail.com>
Date: 2025-07-02 15:39:51 +0200
Commit message:

 tiptoe around defunct `facet_grid(facets)`
Package: ggbio
Commit: 6b18ff06433f62d59371dd09deddd337b5be2387
Author: Teun van den Brand <tahvdbrand@gmail.com>
Date: 2025-07-02 14:25:20 +0200
Commit message:

 use `ggplot::margin()` instead of `grid::unit()`
Package: RFLOMICS
Commit: ff4ba40f17efc627a967bbc67abbe73f7238926a
Author: Nadia Bessoltane-Bentahar <nadia.bessoltane@inra.fr>
Date: 2025-09-18 16:37:45 +0200
Commit message:

 resolve conflicts
Package: RFLOMICS
Commit: d97ff4acf7768213e9b86e592117b50755c0d1f1
Author: HULOT Audrey <audrey.hulot@inrae.fr>
Date: 2025-08-04 16:10:41 +0200
Commit message:

 removed EnhancedVolcanoPlot, replaced by 'just' a ggplot2 volcano.
Package: RFLOMICS
Commit: 460352b2c9d3cae3c756f3cdd720c7a930304d58
Author: Nadia Bessoltane-Bentahar <nadia.bessoltane@inra.fr>
Date: 2025-09-16 14:56:55 +0200
Commit message:

 Bump version to 1.1.4
Package: RFLOMICS
Commit: a46b2b1c68ef1a1c12d8e5d5566f6d31a2efdcad
Author: Nadia Bessoltane-Bentahar <nadia.bessoltane@inra.fr>
Date: 2025-09-16 14:52:13 +0200
Commit message:

 Debug the reactivity of the data analysis summary module.
    Improve the interpretability of the plotAnnotSummary.
Package: RFLOMICS
Commit: 922344b072a629a5817ed3984a90674893c8155f
Author: Nadia Bessoltane-Bentahar <nadia.bessoltane@inra.fr>
Date: 2025-09-16 10:56:30 +0200
Commit message:

 Debug the reactivity of the data analysis summary module.
Improve the interpretability of the plotAnnotSummary.
Package: RFLOMICS
Commit: 3b97a9787e07108c3b2352647a8d5d6b8c961609
Author: Nadia Bessoltane-Bentahar <nadia.bessoltane@inra.fr>
Date: 2025-09-16 10:54:39 +0200
Commit message:

 Debug the reactivity of the data analysis summary module.
Improve the interpretability of the plotAnnotSummary.
Package: RFLOMICS
Commit: 9e33b1b04171995abcf11a02b2f716fed0f63ab7
Author: Nadia Bessoltane-Bentahar <nadia.bessoltane@inra.fr>
Date: 2025-09-05 09:52:16 +0200
Commit message:

 debug: update diff summary
Package: RFLOMICS
Commit: 7d13880de632003c1cfb7e6c3894c58826449d43
Author: HULOT Audrey <audrey.hulot@inrae.fr>
Date: 2025-09-16 10:38:33 +0200
Commit message:

 changed ways of testing ggplot2 objects
Package: RFLOMICS
Commit: 7c1955dcf2f1359b790e026a8137f4277b23df33
Author: HULOT Audrey <audrey.hulot@inrae.fr>
Date: 2025-09-16 10:26:19 +0200
Commit message:

 some changes in tests (error in checking ggplot type)
Package: RFLOMICS
Commit: 7544b4d95c48112d519bf5b0c6186806a396e9a4
Author: HULOT Audrey <audrey.hulot@inrae.fr>
Date: 2025-09-09 15:44:50 +0200
Commit message:

 #11 fix domain in plotEnrichComp for command line vignette (failed check)
Package: RFLOMICS
Commit: 43759e2a08d1a1d3319654c3fec316b51e3a78e1
Author: HULOT Audrey <audrey.hulot@inrae.fr>
Date: 2025-09-09 15:44:04 +0200
Commit message:

 fix matrixType in test (log2FC not available anymore)
Package: RFLOMICS
Commit: 07f88e7b86bd0b05c906d7651fa6a7a53a2ec0f8
Author: HULOT Audrey <audrey.hulot@inrae.fr>
Date: 2025-09-09 15:43:36 +0200
Commit message:

 complete.cases -> completeCases arg in help for plotOverview()
Package: RFLOMICS
Commit: b1393253151ab7ef4ae9b41a6aaf3dcd8b4aea8f
Author: HULOT Audrey <audrey.hulot@inrae.fr>
Date: 2025-09-09 15:43:11 +0200
Commit message:

 bump version
Package: RFLOMICS
Commit: ca670fc325ed5de601a29482b3d5524a4a905905
Author: HULOT Audrey <audrey.hulot@inrae.fr>
Date: 2025-09-03 08:08:53 +0200
Commit message:

 added args in plotDataOverview (raw and complete cases) and added the Samples overview in mixOmics output
Package: RFLOMICS
Commit: fb27e9e9158fc6c730afe8ff055c58214863e67b
Author: HULOT Audrey <audrey.hulot@inrae.fr>
Date: 2025-09-02 16:28:57 +0200
Commit message:

 #10 overviews plot are now adequately displayed with removed samples in omics summary and data integration overview. MixOmics displays only the complete cases.
Package: RFLOMICS
Commit: fddb762cd2ba25f3b89f15a961a695de80194e9b
Author: HULOT Audrey <audrey.hulot@inrae.fr>
Date: 2025-09-02 15:18:19 +0200
Commit message:

 #9 removed dataset names in the ORA comparaison, transpose the matrix and increase window size.
Package: RFLOMICS
Commit: 09b11c7932fafd55e418df72abe96192cd417b54
Author: HULOT Audrey <audrey.hulot@inrae.fr>
Date: 2025-08-13 15:23:24 +0200
Commit message:

 modified enrichcomp module so that the size of the output window can be 1000 px.
Package: RFLOMICS
Commit: aae75b874f5b2ff12d45f6063921ae8df471045f
Author: HULOT Audrey <audrey.hulot@inrae.fr>
Date: 2025-08-13 15:22:45 +0200
Commit message:

 modified import
Package: RFLOMICS
Commit: 72ad8401d5c478cdae9139f60c277334b1db6a54
Author: HULOT Audrey <audrey.hulot@inrae.fr>
Date: 2025-08-13 15:22:33 +0200
Commit message:

 need import from complexheatmap
Package: RFLOMICS
Commit: 6aa3e9a74e94c79f9c37deff391b04e2f3173caa
Author: HULOT Audrey <audrey.hulot@inrae.fr>
Date: 2025-08-13 11:34:21 +0200
Commit message:

 added interactive output for enrichment comparison
Package: RFLOMICS
Commit: 6cccb6c464c2327000e3d6a7626ed597080612e8
Author: HULOT Audrey <audrey.hulot@inrae.fr>
Date: 2025-08-13 11:34:03 +0200
Commit message:

 changed tabset name
Package: RFLOMICS
Commit: 246b7aa7290052bc36e90ee6fdba6bc09b1cccf7
Author: HULOT Audrey <audrey.hulot@inrae.fr>
Date: 2025-08-13 11:33:48 +0200
Commit message:

 modified heatmap for enrichment comparisons (now it's ggplot) + adapt  title to have pvalue cutoff in it
Package: RFLOMICS
Commit: 44ec82732203e7f5ae67a105a481cda2737d6f09
Author: HULOT Audrey <audrey.hulot@inrae.fr>
Date: 2025-08-13 11:30:56 +0200
Commit message:

 bump
Package: RFLOMICS
Commit: 30a4c7d4e28478ed56845d82b907382387d69a97
Author: HULOT Audrey <audrey.hulot@inrae.fr>
Date: 2025-08-12 13:22:25 +0200
Commit message:

 comparison will not show anymore when only one contrast is selected.
Package: RFLOMICS
Commit: ac1244f19bee0f7ddd37dc33fe538376e92d75d6
Author: HULOT Audrey <audrey.hulot@inrae.fr>
Date: 2025-08-12 11:16:52 +0200
Commit message:

 typos and cleaning + greyed button when user cannot select anything
Package: RFLOMICS
Commit: d859fc3ee730b7f357294564f039babbddf42f64
Author: HULOT Audrey <audrey.hulot@inrae.fr>
Date: 2025-08-12 11:15:49 +0200
Commit message:

 added some imported functions
Package: RFLOMICS
Commit: 5d699dd5f6014ec99a21fe2f3b7fd7d57df78e76
Author: HULOT Audrey <audrey.hulot@inrae.fr>
Date: 2025-08-04 17:59:09 +0200
Commit message:

 remove interactive argument
Package: RFLOMICS
Commit: 7975e9522a0ce21e1b34c056ee5ced3f4535c353
Author: HULOT Audrey <audrey.hulot@inrae.fr>
Date: 2025-08-04 16:13:42 +0200
Commit message:

 added plotly dependecy
Package: RFLOMICS
Commit: 2028ad98be7de1b684e2d2fd0815f0ff53da2ec3
Author: HULOT Audrey <audrey.hulot@inrae.fr>
Date: 2025-08-04 16:10:41 +0200
Commit message:

 removed EnhancedVolcanoPlot, replaced by 'just' a ggplot2 volcano.
Package: RFLOMICS
Commit: e70d1ea96b79b3b77b16787c57499a379be814f1
Author: HULOT Audrey <audrey.hulot@inrae.fr>
Date: 2025-08-04 14:16:12 +0200
Commit message:

 added plotly version of dotplot and heatplot in enrichment module
Package: RFLOMICS
Commit: c3aec8dcc987e5033ff06073302084d8c97791dd
Author: HULOT Audrey <audrey.hulot@inrae.fr>
Date: 2025-08-04 14:15:31 +0200
Commit message:

 add interactive argument
Package: RFLOMICS
Commit: 8c67749b13ed21bf823203ec581ccd6aac80ddc5
Author: HULOT Audrey <audrey.hulot@inrae.fr>
Date: 2025-08-04 14:15:18 +0200
Commit message:

 added interactive argument in plotclusterProfiler
Package: RFLOMICS
Commit: 58c9f5eb6eefb3996927f91fe7f792d89c969de6
Author: HULOT Audrey <audrey.hulot@inrae.fr>
Date: 2025-08-04 14:14:43 +0200
Commit message:

 changed example in annotation (wrong arguments)
Package: RFLOMICS
Commit: b9a781dc47b600fba9f2550667b06dc3ff03a9e8
Author: HULOT Audrey <audrey.hulot@inrae.fr>
Date: 2025-07-31 11:19:46 +0200
Commit message:

 #3 changed the warning message Dialog window.
Package: RFLOMICS
Commit: f6ca87aaa2994380c1e90d489778012e92efe4d0
Author: HULOT Audrey <audrey.hulot@inrae.fr>
Date: 2025-07-31 10:48:11 +0200
Commit message:

 fixed warning activated even with 0 length message.
Package: RFLOMICS
Commit: a54df38ce56093cce236b78c34605d40b27b7267
Author: HULOT Audrey <audrey.hulot@inrae.fr>
Date: 2025-07-31 09:01:02 +0200
Commit message:

 #3 Change stop to warning in RNAseq check, round values if needed
Package: RFLOMICS
Commit: c656b4dc859b8b754b6161e29c4ada1a183e1d83
Author: Nadia Bessoltane-Bentahar <nadia.bessoltane@inra.fr>
Date: 2025-05-16 09:03:14 +0200
Commit message:

 allow 50 rep for interface
Package: RFLOMICS
Commit: f7b4dd6e0e8bf8d8a58be8e366fc4e49e8ca80e7
Author: Nadia Bessoltane-Bentahar <nadia.bessoltane@inra.fr>
Date: 2025-05-14 13:24:30 +0200
Commit message:

 accept negative values in data but not in count data
Package: ORFik
Commit: 66245282b2424b48de6db101b25a18cf50cf15b4
Author: Roleren <hauken_heyken@hotmail.com>
Date: 2025-09-18 16:20:58 +0200
Commit message:

 Merge branch 'master' into devel
Package: ORFik
Commit: 390b0fc95ddbebbee3654adcb1920f9436213172
Author: Roleren <hauken_heyken@hotmail.com>
Date: 2025-09-18 16:20:46 +0200
Commit message:

 bump version
Package: ORFik
Commit: 6faab3df706c54bdde5496ee4b9360006888350a
Author: Roleren <hauken_heyken@hotmail.com>
Date: 2025-09-18 16:20:22 +0200
Commit message:

 removed non ascii
Package: ORFik
Commit: 80e9346004d5739dfcbc97b048f2d7bd294781c0
Author: Roleren <hauken_heyken@hotmail.com>
Date: 2025-09-18 16:15:52 +0200
Commit message:

 Merge branch 'master' into devel
Package: ORFik
Commit: 092d8b02d09cf7db262cce8e1ac066f2148b3ee9
Author: Roleren <hauken_heyken@hotmail.com>
Date: 2025-09-18 16:15:21 +0200
Commit message:

 small bugfix difexp
Package: ORFik
Commit: d9817e0007882b396066ca3ef07d9a5df2601069
Author: Roleren <hauken_heyken@hotmail.com>
Date: 2025-09-18 16:01:12 +0200
Commit message:

 small update to uniqueMappers
Package: ORFik
Commit: 4bbd8536300733015980a21b92f271d81e09bdf0
Author: Roleren <hauken_heyken@hotmail.com>
Date: 2025-09-18 15:49:45 +0200
Commit message:

 Prepare to push to bioc
Package: ORFik
Commit: a7a8250465149eb82adb8897e8200cc11def1ef7
Author: Roleren <hauken_heyken@hotmail.com>
Date: 2025-09-15 14:00:08 +0200
Commit message:

 Improved unique mappers for default filepath
Package: ORFik
Commit: ec1705e92872747a00469105072feca9c443714e
Author: Roleren <hauken_heyken@hotmail.com>
Date: 2025-09-13 00:55:04 +0200
Commit message:

 Improved getGAlignments from data.table
Package: ORFik
Commit: 7e1e6be1dedf353a06b19bb79ad64083a2bcb73e
Author: Roleren <hauken_heyken@hotmail.com>
Date: 2025-09-09 15:49:09 +0200
Commit message:

 fixed bug libFolder
Package: ORFik
Commit: 5d5e02aead551a66edab0f43077221fb4df5b235
Author: Roleren <hauken_heyken@hotmail.com>
Date: 2025-09-09 15:04:15 +0200
Commit message:

 Added unique mapper docs
Package: ORFik
Commit: 90234ef35258fe2ff710cbb5e6c5646f112db046
Author: Roleren <hauken_heyken@hotmail.com>
Date: 2025-09-09 14:18:09 +0200
Commit message:

 Added unique mappers syntax to ORFik
Package: ORFik
Commit: 4837644d218420be67a8d6c90d79b6e3cbe8ee85
Author: Roleren <hauken_heyken@hotmail.com>
Date: 2025-09-05 12:02:23 +0200
Commit message:

 Fixed bug normalize_dt merge
Package: ORFik
Commit: e8d9d97c62ff58c3b1c71b0825e2aefcbcffb5a2
Author: Roleren <hauken_heyken@hotmail.com>
Date: 2025-09-04 15:28:55 +0200
Commit message:

 Documentation mergelibs
Package: ORFik
Commit: eb7fe409b20cae7a3d98452dd9f1644abd415df3
Author: Roleren <hauken_heyken@hotmail.com>
Date: 2025-09-04 12:30:54 +0200
Commit message:

 Improved version of ofst merging
Package: ORFik
Commit: 84d872e9c5814d7c2c4f01e9032fb1ab04ac1b50
Author: Roleren <hauken_heyken@hotmail.com>
Date: 2025-09-03 15:07:24 +0200
Commit message:

 Fixed numeric to integer conversion mergeLibs
Package: ORFik
Commit: a2fa4829cae954ca56681aa8911fb41cc5a2f6ea
Author: Roleren <hauken_heyken@hotmail.com>
Date: 2025-09-03 14:53:22 +0200
Commit message:

 bugfix mergeLibs
Package: ORFik
Commit: 002495b6067bcf745ff648be2f3d95f5d1d3c3b0
Author: Roleren <hauken_heyken@hotmail.com>
Date: 2025-09-03 14:44:57 +0200
Commit message:

 Fixed bug list.experiments
Package: ORFik
Commit: 19cc9b9e4e3c30d81457836c4e9dd6c81bd3d7bb
Author: Roleren <hauken_heyken@hotmail.com>
Date: 2025-09-03 14:26:21 +0200
Commit message:

 Bugfix for seqnames mergeLibs
Package: ORFik
Commit: 75c49a3f41b15b4a5b4ad2d2aea2a90c3ef2ec19
Author: Roleren <hauken_heyken@hotmail.com>
Date: 2025-09-03 13:45:36 +0200
Commit message:

 Fixed bug in mergeLibs
Package: ORFik
Commit: d11950aab4265d5ea8b51ab4af8c945d81821162
Author: Roleren <hauken_heyken@hotmail.com>
Date: 2025-09-02 12:36:40 +0200
Commit message:

 Small improvement to list.experiments
Package: ORFik
Commit: 21032c7c2c37527545690533c04787082ea6812d
Author: Roleren <hauken_heyken@hotmail.com>
Date: 2025-09-02 12:21:47 +0200
Commit message:

 Improved list.experiments more
Package: ORFik
Commit: 17e3252994621323e2a250adab2eb07c14ccf697
Author: Roleren <hauken_heyken@hotmail.com>
Date: 2025-09-02 12:03:31 +0200
Commit message:

 Improved run time of list.experiments
Package: ORFik
Commit: e7261fd5dd0fe96bee678809a5950c450fb221c7
Author: Roleren <hauken_heyken@hotmail.com>
Date: 2025-08-27 13:22:04 +0200
Commit message:

 Added more docs
Package: ORFik
Commit: 1098d4d508033ed6eaed6f83cd80896cd1caef56
Author: Roleren <hauken_heyken@hotmail.com>
Date: 2025-08-27 13:19:13 +0200
Commit message:

 Improved bamVarName
Package: ORFik
Commit: b99b8309f64b0fbdbaf0062922c193fe90a3342d
Author: Roleren <hauken_heyken@hotmail.com>
Date: 2025-08-18 22:27:41 +0200
Commit message:

 Added as.character for GRangesList
Package: ORFik
Commit: b8543e64224a278866f133df470a222f61d53230
Author: Roleren <hauken_heyken@hotmail.com>
Date: 2025-08-18 21:52:58 +0200
Commit message:

 Added makeGRangesListFromCharacter function
Package: ORFik
Commit: d8ca6ebe16128c167e350fc73ccb6d9202b5de33
Author: Roleren <hauken_heyken@hotmail.com>
Date: 2025-08-18 13:30:13 +0200
Commit message:

 Removed 150nt period from check in detectRibosomeShifts
Package: ORFik
Commit: dfbb3048db067bad18c14ed5b82145f4b61006e9
Author: Roleren <hauken_heyken@hotmail.com>
Date: 2025-08-15 14:30:09 +0200
Commit message:

 Fixed bug negative strand mega fst
Package: ORFik
Commit: 29dee90caed8792b68097e621c43e4ada09b4cf6
Author: Roleren <hauken_heyken@hotmail.com>
Date: 2025-08-14 15:32:50 +0200
Commit message:

 Improved countTable_regions
Package: ORFik
Commit: 5976c934fdf2014f384f4ab5c9ee5be8fd207c3c
Author: Roleren <hauken_heyken@hotmail.com>
Date: 2025-08-14 11:30:31 +0200
Commit message:

 Improved countTable functions
Package: ORFik
Commit: d8ee82f79fbad5836a90647b89eab56f51cd279a
Author: Roleren <hauken_heyken@hotmail.com>
Date: 2025-08-13 12:50:27 +0200
Commit message:

 fixed bug shifting table
Package: ORFik
Commit: 92bfe2680ce166c9556b2eca4d86ba564f798357
Author: Roleren <hauken_heyken@hotmail.com>
Date: 2025-08-13 12:26:50 +0200
Commit message:

 Added support for shift table subset
Package: ORFik
Commit: ffcee16b4f5793a5f9109160ab84d3b79ef1490e
Author: Roleren <hauken_heyken@hotmail.com>
Date: 2025-08-11 15:23:11 +0200
Commit message:

 Fixed bug for bigwig load on minus strand
Package: ORFik
Commit: db1c962385a77298e24cdfbc47606b83316d155f
Author: Roleren <hauken_heyken@hotmail.com>
Date: 2025-08-08 10:41:32 +0200
Commit message:

 bigwig supports numeric
Package: ORFik
Commit: d172d1351c9561253c1d14632edaac92bce2738f
Author: Roleren <hauken_heyken@hotmail.com>
Date: 2025-08-07 15:25:15 +0200
Commit message:

 Fixed ncORF prediction bug
Package: ORFik
Commit: 6a55b571f9a9d77e05b679ab45f6e440aa9157c2
Author: Roleren <hauken_heyken@hotmail.com>
Date: 2025-08-07 13:56:53 +0200
Commit message:

 Added support to predict ncORF type
Package: Chromatograms
Commit: d785cf9b4986e5839cf5bad4870be471572b87fe
Author: Philippine Louail <philippine.louail@outlook.com>
Date: 2025-09-18 15:52:16 +0200
Commit message:

 Merge pull request #39 from rformassspectrometry/jomain

Thanks Johannes, let|s see if that fixes the build on Bioconductor
docs: add dependencies to Vignette
Package: Chromatograms
Commit: c1185b892c6750de73eca010056746eb491d499e
Author: Johannes Rainer <johannes.rainer@gmail.com>
Date: 2025-09-18 15:38:36 +0200
Commit message:

 fix: update the editorconfig to avoid final newlines to be deleted
Package: Chromatograms
Commit: c42248a6cc1a156c3a878769d2e0b88b72b1e5e7
Author: Johannes Rainer <johannes.rainer@gmail.com>
Date: 2025-09-18 15:28:19 +0200
Commit message:

 docs: add dependencies to Vignette
Package: MIRit
Commit: a9cb805beceb7935ab7d956091fee60b29644f29
Author: jacopo-ronchi <jacopo.ronchi@unimib.it>
Date: 2025-09-18 10:25:47 +0000
Commit message:

 version bump in devel after bug fix
Package: MIRit
Commit: c5089d8a8eb68e26c303baf6fe2f31165b5046af
Author: jacopo-ronchi <jacopo.ronchi@unimib.it>
Date: 2025-09-18 10:19:57 +0000
Commit message:

 bug fix: fixing the structure of the miRTarBase table both in devel and release.
Package: asuri
Commit: 4c9f55e8604718306f171e551581e070d166f721
Author: aberral <aberralgonzalez@gmail.com>
Date: 2025-09-18 10:41:13 +0200
Commit message:

 bioccheck fix base man page
version bump
Package: immunoClust
Commit: 9098b87f771296315754dd7d0e69804fe041c2d0
Author: Till Sörensen <till-antoni.soerensen@charite.de>
Date: 2025-09-18 09:52:53 +0200
Commit message:

 remove check warnings
Package: spicyR
Commit: 24c1974f74d1d2de8774ee2c9e24ac831604253f
Author: ellispatrick <ellis.patrick@sydney.edu.au>
Date: 2025-09-18 14:25:41 +1000
Commit message:

 Fix unit test precision
Package: SeqArray
Commit: 358028c7640ce42c170dcdedd8a439c39ab0d193
Author: Xiuwen Zheng <zhengxwen@gmail.com>
Date: 2025-09-17 20:42:49 -0500
Commit message:

 update seqApply() & seqBlockApply()
Package: TPP2D
Commit: ab2b00c0d0f12ba4959cfbce8af262f14d24bf33
Author: Nils Kurzawa <nilskurzawa@Mac.fritz.box>
Date: 2025-09-17 21:54:17 +0200
Commit message:

 version bump
Package: TPP2D
Commit: 3025f01e8f493e21afe703ac63df57c991fc2503
Author: Nils Kurzawa <nilskurzawa@Mac.fritz.box>
Date: 2025-09-17 21:48:51 +0200
Commit message:

 fixed test warnings and errors
Package: asuri
Commit: fb832bc44f45a75de0f9578f24a50fe322c1c0e1
Author: aberral <aberralgonzalez@gmail.com>
Date: 2025-09-17 19:00:00 +0200
Commit message:

 version bump
Package: asuri
Commit: ba7936c85a0846d3a731975669730c212cd646fb
Author: aberral <aberralgonzalez@gmail.com>
Date: 2025-09-17 18:59:14 +0200
Commit message:

 bioccheck fixes
Package: asuri
Commit: afae28baed51aeff51fd13a9217565cce9408894
Author: aberral <aberralgonzalez@gmail.com>
Date: 2025-09-17 18:26:24 +0200
Commit message:

 bot fixes
Package: masstools
Commit: 4b06cfff2316a321f6c5948a3b65d2a3ae42675d
Author: chain-buds <bspchemy@gmail.com>
Date: 2025-09-17 23:31:01 +0800
Commit message:

 Merge branch 'dev' of https://github.com/chain-buds/masstools into dev
Package: masstools
Commit: 48e0234743e416f6af549dc279e73c18befbf081
Author: chain-buds <bspchemy@gmail.com>
Date: 2025-09-17 23:28:52 +0800
Commit message:

 20250917-bioc-submission-debug
Package: masstools
Commit: a452e47b460f44fcf0fa37af99591d6847a00312
Author: chain-buds <bspchemy@gmail.com>
Date: 2025-09-17 23:27:45 +0800
Commit message:

 20250917-bioc-submission-debug
Package: ProteinGymR
Commit: 9c2d8c6e784811db6809cada5c86d8ad6612c8a9
Author: tram-nguyen-n <tram_nguyen@hms.harvard.edu>
Date: 2025-09-17 15:19:16 +0000
Commit message:

 bump devel
Package: ProteinGymR
Commit: 8e262d815985eb333eccd385fe1023e5ba48267f
Author: tram-nguyen-n <tram_nguyen@hms.harvard.edu>
Date: 2025-09-17 15:18:53 +0000
Commit message:

 require specific version of gghalves
Package: tidyexposomics
Commit: 40b529b76e75262579d2ee31ad5692b87ac9ce18
Author: BioNomad <jlaird1@binghamton.edu>
Date: 2025-09-17 11:13:56 -0400
Commit message:

 namespace fixes
Package: markeR
Commit: c9aaf4e359783f2b647cbd4e53ec8c3e0e253246
Author: Rita Silva <ritamtbsilva@gmail.com>
Date: 2025-09-17 16:08:53 +0100
Commit message:

 Minor fix in `.onAttach()`
Package: motifTestR
Commit: fbf0e927eefdf2809377454dd65d304fd305ee69
Author: Stevie Ped <stephen.pederson.au@gmail.com>
Date: 2025-09-18 00:27:54 +0930
Commit message:

 Merged with upstream
Package: motifTestR
Commit: 1e723dbb6743b9ddabf57f12f1a9c7acf14cdc8c
Author: Stevie Ped <stephen.pederson.au@gmail.com>
Date: 2025-09-18 00:20:17 +0930
Commit message:

 Update .gitignore
Package: motifTestR
Commit: cb80d745fda364b5720c398f0aa7eae4832a37d6
Author: Stevie Ped <stephen.pederson.au@gmail.com>
Date: 2025-09-17 23:16:28 +0930
Commit message:

 Reinstated extraChIPs
Package: motifTestR
Commit: 3c94e1d9d073494a88ec70feeb7675d934e348a8
Author: Stevie Ped <stephen.pederson.au@gmail.com>
Date: 2025-09-17 23:05:48 +0930
Commit message:

 Deleted CoplexUpset & extraChIPs from Suggests
Package: motifTestR
Commit: 7f4ab538f1ffe8f0f7aae8e323788714f438d641
Author: Stevie Ped <stephen.pederson.au@gmail.com>
Date: 2025-09-17 22:45:04 +0930
Commit message:

 Fixed Seqinfo import
Package: motifTestR
Commit: e0f9a1b20d52804fbcca47e1b4162af2f37f5f37
Author: Stevie Ped <stephen.pederson.au@gmail.com>
Date: 2025-09-17 22:12:54 +0930
Commit message:

 Bugfix after ggplot2 4.0.0
Package: motifTestR
Commit: 9aae344839a47c43e36ffc4e8cb6f24eae7be0fa
Author: Stevie Ped <stephen.pederson.au@gmail.com>
Date: 2025-07-11 23:25:21 +0930
Commit message:

 Updated ggplot2 version
Package: motifTestR
Commit: cb8ce583612738e306a16022f5a795765e064f0a
Author: Stevie Ped <stephen.pederson.au@gmail.com>
Date: 2025-06-21 00:18:45 +0930
Commit message:

 Updated tests for new ggplot2. Vignette fails (ComplexUpset error)
Package: motifTestR
Commit: 605085819cf1dcc3c6d8a83f3841cde7b51cc91e
Author: Stevie Ped <stephen.pederson.au@gmail.com>
Date: 2025-04-22 17:14:43 +0930
Commit message:

 Moved pkgdown to gh-actions
Package: motifTestR
Commit: 332e49bcb1f4bf7676ea692bdf8c126089c04c09
Author: Stevie Ped <stephen.pederson.au@gmail.com>
Date: 2025-04-22 02:04:47 +0930
Commit message:

 Updated pkgdown
Package: motifTestR
Commit: 265bb5f6dbdc18610b91598276f63818ddf417e1
Author: Stevie Ped <stephen.pederson.au@gmail.com>
Date: 2025-04-22 01:17:04 +0930
Commit message:

 Added simMultiMotifs
Package: markeR
Commit: 5c66613103eeccb79d2bc06a254bb47afbd335e2
Author: Rita Silva <ritamtbsilva@gmail.com>
Date: 2025-09-17 15:40:10 +0100
Commit message:

 Update NEWS.md
Package: markeR
Commit: 6181d5d527ab96661f7174c39822e470d2ad3e69
Author: Rita Silva <ritamtbsilva@gmail.com>
Date: 2025-09-17 15:29:08 +0100
Commit message:

 minor changes
Package: markeR
Commit: 22ff53151b0eee797bbf50517c9ef0b8fcdca23e
Author: Rita Silva <ritamtbsilva@gmail.com>
Date: 2025-09-17 14:38:48 +0100
Commit message:

 add warning on ggplot
Package: markeR
Commit: ffd0abe2fbd4de5abf3cbc5f64a4804dcc9a57ba
Author: Rita Silva <ritamtbsilva@gmail.com>
Date: 2025-09-17 14:34:40 +0100
Commit message:

 ensure compatibility with  ggplot2 <= 3.5.2
Package: markeR
Commit: 677dd4ed2cef4d1577afc998aaa3bdf27f2955ff
Author: Rita Silva <ritamtbsilva@gmail.com>
Date: 2025-09-17 14:29:58 +0100
Commit message:

 update vignette
Package: markeR
Commit: 4dcf7b99afb1d9ba6faf9caaa2532e9c3a1c593c
Author: Rita Silva <ritamtbsilva@gmail.com>
Date: 2025-09-17 14:29:51 +0100
Commit message:

 changes in gene set similarity function (cold / warm colors, limits, etc)
Package: markeR
Commit: 36d499e752994d9a701eb00f1b003cae1d924a31
Author: Rita Silva <ritamtbsilva@gmail.com>
Date: 2025-09-17 14:29:14 +0100
Commit message:

 number sims for fpr = 100
Package: markeR
Commit: 31a68645471221cd16f3b72cfc7c94f4a34c9fe0
Author: Rita Silva <ritamtbsilva@gmail.com>
Date: 2025-09-17 14:28:54 +0100
Commit message:

 changes in data documentation
Package: markeR
Commit: e8816357410a478d9fd8309036338ccca921b318
Author: Rita Silva <ritamtbsilva@gmail.com>
Date: 2025-09-12 18:12:02 +0100
Commit message:

 add BiocStyle to Suggests
Package: markeR
Commit: 6d3f1488b4a8381ab6e1825ccb7f99b2b1092fd4
Author: Rita Silva <ritamtbsilva@gmail.com>
Date: 2025-09-12 17:37:20 +0100
Commit message:

 usage data
Package: markeR
Commit: 791e61ecea532f59955e00f300459004157891e6
Author: Rita Silva <ritamtbsilva@gmail.com>
Date: 2025-09-12 17:37:12 +0100
Commit message:

 marker vignette v1
Package: biomaRt
Commit: 0a059d89b10350782a5af9a379b0a3a554b4b0be
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-09-17 12:17:46 +0200
Commit message:

 Document change
Package: biomaRt
Commit: 21d25fdce4c301d987bf48c7190e14a8e5ee5950
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-09-17 12:06:34 +0200
Commit message:

 Bump patch version
Package: biomaRt
Commit: c77acff2828f1155acbb906f057c05e5cfc6d9d2
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-09-16 15:59:40 +0200
Commit message:

 Replace for loop by sprintf() in exportFASTA()
Package: biomaRt
Commit: 91c31d9c146adbce4f5558bafa726baed5321f69
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-09-17 12:04:32 +0200
Commit message:

 Add snapshot tests for exportFASTA()
Package: rawrr
Commit: a6c7dff8de6490d884a779de7aa4b61fd765b91f
Author: Christian Panse <cp@fgcz.ethz.ch>
Date: 2025-09-17 11:45:49 +0200
Commit message:

 #93
Package: rawrr
Commit: 6869214b7820cb47fd1652910661427d8e30597f
Author: Christian Panse <cp@fgcz.ethz.ch>
Date: 2025-09-17 11:40:51 +0200
Commit message:

 Merge branch 'devel' of git.bioconductor.org:packages/rawrr into devel
Package: rawrr
Commit: 002e7ef02a2198937ce67693f2155f11bfec3834
Author: Christian Panse <cp@fgcz.ethz.ch>
Date: 2025-09-17 11:36:36 +0200
Commit message:

 fix #94
Package: rawrr
Commit: 5af233337ef016063ab50583e3564e95c3b2067c
Author: Christian Panse <cp@fgcz.ethz.ch>
Date: 2025-09-17 11:36:36 +0200
Commit message:

 solve isse #94
Package: BASiCS
Commit: a6635d4b063e8397774ee86cf470ce9e59400ac4
Author: Catalina Vallejos <catalina.vallejos@ed.ac.uk>
Date: 2025-09-17 09:48:21 +0100
Commit message:

 version 2.21.1 (2025-09-17)

- Updates divide and conquer approach to use an effect size as a metric to
decide whether the partions are balanced (instead of a p-value)
- Minor typos and technical fixes
Package: BASiCS
Commit: b25e73045bda3ea263700cec9c56c61e31e63227
Author: Catalina Vallejos <catalina.vallejos@ed.ac.uk>
Date: 2025-09-17 09:44:49 +0100
Commit message:

 Update version
Package: BASiCS
Commit: d51eefb18fd04327efa26dbfb62328ec536756d4
Author: Catalina Vallejos <catalina.vallejos@ed.ac.uk>
Date: 2025-09-17 09:42:47 +0100
Commit message:

 Merge remote-tracking branch 'upstream/devel' into devel
Package: BASiCS
Commit: 0c23f0add6b492c62905de25137442fd7808574e
Author: Catalina Vallejos <catalina.vallejos@ed.ac.uk>
Date: 2025-09-17 09:39:05 +0100
Commit message:

 Update DESCRIPTION
Package: BASiCS
Commit: 8de506dc0abfb9194c7ca418cef281acbc40afd6
Author: Catalina Vallejos <cata.vallejos.m@gmail.com>
Date: 2025-09-16 11:22:15 +0100
Commit message:

 Update README.md
Package: BASiCS
Commit: f8f7a714c63c86f38eac176dd14f2a526b80fd86
Author: Catalina Vallejos <cata.vallejos.m@gmail.com>
Date: 2025-09-08 16:51:30 +0300
Commit message:

 Merge pull request #285 from catavallejos/use-eta-not-alpha

Use eta squared for threshold, not alpha
Package: BASiCS
Commit: 456bbacc4c8e6b8472a5ec031102c1a96b080a03
Author: Alan O'Callaghan <alan.ocallaghan@outlook.com>
Date: 2025-09-08 14:15:43 +0100
Commit message:

 Technical fixes
Package: BASiCS
Commit: 03001904ef745ad03dd5d0b631b7a68aa4078bb7
Author: Alan O'Callaghan <alan.ocallaghan@outlook.com>
Date: 2025-04-30 15:57:24 +0100
Commit message:

 Update utils_DivideAndConquer.R
Package: BASiCS
Commit: 49186bda2c5e410a87c9dd8e19d20310c97e5465
Author: Alan O'Callaghan <alan.ocallaghan@outlook.com>
Date: 2025-04-23 11:41:48 +0100
Commit message:

 Fix tests
Package: BASiCS
Commit: e405856ffe97a2c92dcf8ad3b22d6e87f3ee1933
Author: Alan O'Callaghan <alan.ocallaghan@outlook.com>
Date: 2025-04-23 11:27:01 +0100
Commit message:

 Typo
Package: BASiCS
Commit: 8f0de51625ae0d7413119d2e8ef30d3475713c57
Author: Alan O'Callaghan <alan.ocallaghan@outlook.com>
Date: 2025-04-22 11:54:15 +0100
Commit message:

 Merge branch 'use-eta-not-alpha' of github.com:catavallejos/BASiCS into use-eta-not-alpha
Package: BASiCS
Commit: 3fdee37feadf2e6693ec9b41e0b6e26d4d58a931
Author: Alan O'Callaghan <alan.ocallaghan@outlook.com>
Date: 2025-04-22 11:54:04 +0100
Commit message:

 Redock and fix arg passing
Package: BASiCS
Commit: 02dea20155bb81fc8b2757d12ddbedf7dcb92a09
Author: Alan O'Callaghan <alan.ocallaghan@outlook.com>
Date: 2025-04-22 11:46:47 +0100
Commit message:

 Update DESCRIPTION
Package: BASiCS
Commit: 7d40d70d3e69e9b1f1624ebe3514598f9ce036d3
Author: Alan O'Callaghan <alan.ocallaghan@outlook.com>
Date: 2025-04-22 10:50:29 +0100
Commit message:

 typo
Package: BASiCS
Commit: 2bf0d68f72334bec7c686ff7f7bf127446bd8f5e
Author: Alan O'Callaghan <alan.ocallaghan@outlook.com>
Date: 2025-04-22 10:35:46 +0100
Commit message:

 Use eta squared for threshold, not alpha
Package: asuri
Commit: 4dcc0701a061378c84aadbd48f0808fd73fc4271
Author: aberral <aberralgonzalez@gmail.com>
Date: 2025-09-17 09:58:18 +0200
Commit message:

 v bump
Package: asuri
Commit: 49262b38a814888a1dc1fab2ec825ed90b6d4c76
Author: aberral <aberralgonzalez@gmail.com>
Date: 2025-09-16 17:46:07 +0200
Commit message:

 minor fixes
Package: asuri
Commit: 384abbb0d9b7d7ed5a76e235ffbd35508a005eec
Author: aberral <aberralgonzalez@gmail.com>
Date: 2025-09-16 11:18:53 +0200
Commit message:

 minor fixes
Package: asuri
Commit: 36de9eac6aa9d0d8f69c88440f8d0bfc4b783be0
Author: aberral <aberralgonzalez@gmail.com>
Date: 2025-09-12 15:09:04 +0200
Commit message:

 fix readme
Package: asuri
Commit: 03bf4b7c107ae85c482d16983a95e40d11c04bc7
Author: aberral <aberralgonzalez@gmail.com>
Date: 2025-09-12 15:06:15 +0200
Commit message:

 Fixes for bioconductor reviewer
* Readme updated
* Namespace generated via roxygen
* Man pages added
* Plot functions accesible to end user
* Data inconsistencies fixed
* Vignette fixed
Package: sitePath
Commit: 9ca37dc0ce8066d30bb1a70a41d682346cee95bb
Author: Chengyang Ji <chengyang.ji12@alumni.xjtlu.edu.cn>
Date: 2025-09-17 07:28:13 +0000
Commit message:

 Wait for ggtree to fix geom_tiplab(); GeomText returns non vector variable so commented out
Package: sitePath
Commit: 297869ab27fd837072083f6151f879b996499f19
Author: Chengyang Ji <chengyang.ji12@alumni.xjtlu.edu.cn>
Date: 2025-09-17 05:16:44 +0000
Commit message:

 Merge remote-tracking branch 'upstream/devel'
Package: sitePath
Commit: e8e9d188413225a29fb6cb08948dacb4e75f6900
Author: Chengyang Ji <chengyang.ji12@alumni.xjtlu.edu.cn>
Date: 2022-09-26 07:48:32 +0000
Commit message:

 Fixes in file path and web link
Package: sitePath
Commit: 2cb976408327937fde47568910d614d4a9465e74
Author: Chengyang Ji <chengyang.ji12@alumni.xjtlu.edu.cn>
Date: 2022-09-26 07:11:30 +0000
Commit message:

 Move figures to man/figures; Update DESCRIPTION and README
Package: sitePath
Commit: d9c9a20bd78d23f398b8d4e41993699e7b73ecc6
Author: Chengyang Ji <chengyang.ji12@alumni.xjtlu.edu.cn>
Date: 2022-09-26 03:31:16 +0000
Commit message:

 Update READMED and GHA
Package: sitePath
Commit: d1a67bdd862e2b19cd6220d1e59f4ba3b4ce2012
Author: Chengyang Ji <chengyang.ji12@alumni.xjtlu.edu.cn>
Date: 2022-09-21 09:34:27 +0000
Commit message:

 biocthis version 1.7.0 generated GHA
Package: ggtree
Commit: 58b3c7cd7a3191a3d45f0160d7dca8d7d6fd28ff
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2025-09-17 14:33:48 +0800
Commit message:

 pkg version
Package: ggtree
Commit: a614dd034032a02d9f80c48dc0b8463778bfda37
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2025-09-16 16:32:42 +0800
Commit message:

 update docs
Package: ggtree
Commit: b9fb75348411eb158f63c7fa3f3f5a88688d5a46
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2025-09-16 16:20:37 +0800
Commit message:

 Merge pull request #662 from xiangpin/rm_iggtree

rm iggtree package
Package: ggtree
Commit: 67de915aa45a7e559ed253fba0d3f94789a774a8
Author: xiangpin <xshuangbin@163.com>
Date: 2025-08-26 17:45:09 +0800
Commit message:

 use internal interactive geom
Package: ggtree
Commit: 1a116a8f6ea3a024788f39ae4fe2139df2c6694b
Author: xiangpin <xshuangbin@163.com>
Date: 2025-08-11 19:54:51 +0800
Commit message:

 using aes instead of aes_string
Package: ggtree
Commit: 865e6716949a1c1c6b6c139407a3259c4160d2a6
Author: xiangpin <xshuangbin@163.com>
Date: 2025-08-07 17:14:12 +0800
Commit message:

 using GeomInteractive* layer from iggtree
Package: ggtree
Commit: b5de02120e5508cec242ccf0b338a007206117b6
Author: xiangpin <xshuangbin@163.com>
Date: 2025-08-07 12:18:00 +0800
Commit message:

 fixed warnings by aes_
Package: ggtree
Commit: cdd540122084007390b901a355fee2e7b2601bcd
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2025-07-13 17:35:20 +0800
Commit message:

 update docs
Package: ggtree
Commit: dbe297aafad557f5ea025d040e25ae81e176c181
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2025-07-13 17:30:46 +0800
Commit message:

 Merge pull request #631 from yasche/fix-issue-626

Added support for XStringSet in msaplot
Package: ggtree
Commit: a71071810e47c3183f1336de7cfedf596e3e62a7
Author: yasche <yannikschermer@googlemail.com>
Date: 2024-09-13 08:19:34 +0200
Commit message:

 Added support for XStringSet in msaplot
Package: MicrobiotaProcess
Commit: dde7a83f06a2c69d1332fdf9c959b943cbd825d0
Author: xiangpin <xshuangbin@163.com>
Date: 2025-09-17 14:24:41 +0800
Commit message:

 bump version
Package: MicrobiotaProcess
Commit: c99fa6e163f8fa7739b240b32cb9cca0c86078ce
Author: xiangpin <xshuangbin@163.com>
Date: 2025-07-01 21:24:35 +0800
Commit message:

 Compatibility with ggplot2 > 3.5.2
Package: MicrobiotaProcess
Commit: 1034039344ced2e0f7c4ddbe6805523cbd04a81f
Author: xiangpin <xshuangbin@163.com>
Date: 2025-04-17 16:59:57 +0800
Commit message:

 bioc3.21 release
Package: MicrobiotaProcess
Commit: 7479b3fd8aeec0688c8b7bccf7acd9ec31facfe1
Author: xiangpin <xshuangbin@163.com>
Date: 2025-04-17 16:51:08 +0800
Commit message:

 Merge remote-tracking branch 'upstream/devel'
Package: MicrobiotaProcess
Commit: a2caa6bd17f07996b6c5afcd9b933890ed57c4b2
Author: xiangpin <xshuangbin@163.com>
Date: 2024-11-04 17:47:55 +0800
Commit message:

 Bioconductor 3.20 release
Package: biomaRt
Commit: 3b5a9f9bc324ba9f9c40c43b752daabc0d58414c
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-09-16 16:29:00 +0200
Commit message:

 Bump version
Package: biomaRt
Commit: f8b71c26c1c5f5726cdd2629af837b30cec042c4
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-09-16 16:28:52 +0200
Commit message:

 Document change to testthat edition 3
Package: biomaRt
Commit: b37c660e601ee9f0889845f395db2eeee6e7f8dd
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-09-16 16:26:59 +0200
Commit message:

 Use testthat v3
Package: biomaRt
Commit: 98b7170a28f730061e24b045ac2130a5dccb298b
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-09-16 15:42:48 +0200
Commit message:

 Bump version
Package: biomaRt
Commit: c19430d893925e2318bb9126e661bcb89216038e
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-09-16 15:41:55 +0200
Commit message:

 Document change in examples
Package: biomaRt
Commit: b509e74eebe65ba8cfc02f33e7f5166ce3d65725
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-09-16 15:40:26 +0200
Commit message:

 Replace "ensembl" with "ENSEMBL_MART_ENSEMBL" for consistency with listMarts()

Fix #133
Package: biomaRt
Commit: 68bf69bfd661d3afd4fac1b2a9f5c51ef28bb75f
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-09-16 15:28:52 +0200
Commit message:

 Fix getLDS() example

Related to #61
Package: biomaRt
Commit: 7d11a191d8021fedeee5244d1db35e275d4defe2
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-09-16 15:00:15 +0200
Commit message:

 Fix partial matching warning
Package: biomaRt
Commit: 451ce5d2ce858453bcbcb3b29ef75e156a3da1a1
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-09-16 14:54:20 +0200
Commit message:

 Fix plantmart useEnsemblGenomes()

Related to #58
Package: biomaRt
Commit: 6ae656822c3738fa9ace4cfcb34623ccf2132705
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-09-16 14:52:44 +0200
Commit message:

 Fix exportFASTA() example
Package: biomaRt
Commit: cb94be47be9b74ea253685fcd86539b390f3ffc9
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-09-16 14:11:15 +0200
Commit message:

 Use exampleIf to run examples conditionally
Package: biomaRt
Commit: cf29d6a30439e9351beb54b3be233c1e6c4879e2
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-09-05 22:10:53 +0200
Commit message:

 Bump patch version
Package: biomaRt
Commit: f8de77c24d709815cf7186721e390d2bba95e677
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-09-05 22:10:37 +0200
Commit message:

 Document removal of https arg
Package: biomaRt
Commit: 3faa14a8057b5482b983b8178fd7af468434f8cf
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-09-05 22:04:18 +0200
Commit message:

 Force HTTPS scheme while cleaning Ensembl URL
Package: biomaRt
Commit: 4180c7bb5047ac88220e85e6b5236e75359a87c8
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-09-05 22:01:37 +0200
Commit message:

 Simplify https regex
Package: biomaRt
Commit: 552bac9281b1923780c5ec857274dfed84a3ba89
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-09-05 22:01:11 +0200
Commit message:

 Remove deprecated https argument
Package: biomaRt
Commit: e2fe8036646d1c84794d0ed0f7f07c7dd3ee16c6
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-09-08 12:49:00 +0200
Commit message:

 Fix generics formatting manually
Package: biomaRt
Commit: 79b3dac7fd9c449352438b6cd5d5b13f736a1892
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-09-08 12:48:50 +0200
Commit message:

 Tell air to ignore setGeneric()
Package: biomaRt
Commit: 646fd91311107bdfee8ee8844051e177ad81664f
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-09-06 11:37:53 +0200
Commit message:

 Remove regex remnants from startsWith() call
Package: biomaRt
Commit: c90eeee81368909bde3e7ba525dec5f0395ca1ac
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-09-08 10:39:06 +0200
Commit message:

 Remove unused variable
Package: biomaRt
Commit: ca98a51741556a73769325ec19f8925c0c532c88
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-09-06 11:21:40 +0200
Commit message:

 Avoid manually handling connection in read.table()
Package: biomaRt
Commit: 68e7db4db71d059d656258462e9b2df4bf7da845
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-09-06 11:19:45 +0200
Commit message:

 Mark one additional regex as fixed
Package: biomaRt
Commit: 85931616d4f33ef24921fb74fbfbab52f9659f5d
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-09-05 18:59:59 +0200
Commit message:

 Remove static variable from loop condition
Package: spatialLIBD
Commit: 40da043d0235e01a12a7f52a0b367d3850bad9e8
Author: lcolladotor <lcolladotor@gmail.com>
Date: 2025-09-16 20:46:54 -0400
Commit message:

 v1.21.6 -- merged and close #115
Package: spatialLIBD
Commit: f5a1ca75a196313025d4154f67767b0dd01fed9a
Author: lcolladotor <lcolladotor@gmail.com>
Date: 2025-09-16 20:44:21 -0400
Commit message:

 Fix some comments, from #115
Package: spatialLIBD
Commit: 427a62151d83d6ea9d1085130152b19165b2c887
Author: lcolladotor <lcolladotor@gmail.com>
Date: 2025-09-16 20:42:46 -0400
Commit message:

 Auto-formatted code with Air
Package: spatialLIBD
Commit: 44d886a85038c20ad2d9417e9c409ad9ba3d9220
Author: lcolladotor <lcolladotor@gmail.com>
Date: 2025-09-16 20:42:04 -0400
Commit message:

 Auto-formatted code with Air
Package: spatialLIBD
Commit: 2e260c469b1bba62c6effa3db60fc028c5646a5b
Author: Leonardo Collado-Torres <lcolladotor@gmail.com>
Date: 2025-09-16 20:41:26 -0400
Commit message:

 Merge pull request #115 from LieberInstitute/reg_pb_add_gene_search

Automatically add gene_search col to rowData of pseudobulked data
Package: spatialLIBD
Commit: 95dd3a1f03a7ead013aef5f88e1983efbfa84c0f
Author: lahuuki <lahuuki@gmail.com>
Date: 2025-09-10 12:22:16 -0400
Commit message:

 If gene_name and gene_id are in rowData, add gene_search as defined in check_sce_layer
Package: spatialLIBD
Commit: d547858f8a373620ece408df84dfbe2163ed3455
Author: lcolladotor <lcolladotor@gmail.com>
Date: 2025-09-16 20:27:01 -0400
Commit message:

 Auto-reformatted some files with Air
Package: spatialLIBD
Commit: 910497195987e09ebef745437056a09b53c7a464
Author: lcolladotor <lcolladotor@gmail.com>
Date: 2025-09-16 20:26:07 -0400
Commit message:

 Fix this unit test now with ggplot2 v4.0.0 in mind

See https://www.tidyverse.org/blog/2025/09/ggplot2-4-0-0/ for details about ggplot2's update

```R
 > class(vis_gene(spe, geneid = c("sum_umi", rownames(spe)[1])))
[1] "ggplot2::ggplot" "ggplot"          "ggplot2::gg"     "S7_object"       "gg"
```
Package: Pirat
Commit: dce8fe3742d3ca1262b926989cee8c7f77c3b683
Author: Lucas Etourneau <lucas.etourneau@berkeley.edu>
Date: 2025-09-16 17:23:29 -0700
Commit message:

 Version cpuonly
Package: tidyexposomics
Commit: 314f0d01065885141a63023d8746d16377a38cdf
Author: BioNomad <jlaird1@binghamton.edu>
Date: 2025-09-16 17:52:09 -0400
Commit message:

 removing git-lfs filter
Package: tidyexposomics
Commit: 95bf41bb3551c8221de98fadbf531a13a2bd7006
Author: BioNomad <jlaird1@binghamton.edu>
Date: 2025-09-16 17:46:28 -0400
Commit message:

 timeout fixes and network function updates
Package: ImageArray
Commit: 632baf374c675f5500dc880915c4dce69324dfb1
Author: Artur-man <artur-man@hotmail.com>
Date: 2025-09-16 23:46:51 +0200
Commit message:

 bump version
Package: ImageArray
Commit: e41e3ac0ac9647f503d0d9f47ce4dd8c1761bb76
Author: Artür Manukyan <artur-man@hotmail.com>
Date: 2025-09-16 13:54:05 +0200
Commit message:

 Merge pull request #29 from Artur-man/devel

bump version, fix .gitignore
Package: ImageArray
Commit: d9577f5c7c30d8e7a6facfa87bb120e2d6a32f99
Author: Artur-man <artur-man@hotmail.com>
Date: 2025-09-16 13:46:11 +0200
Commit message:

 bump version
Package: ImageArray
Commit: 75698b6cc260920c95e752287359418977d57d3c
Author: Artur-man <artur-man@hotmail.com>
Date: 2025-09-15 20:55:42 +0200
Commit message:

 update gitignore
Package: anglemania
Commit: 7f7a9c5962af8f5b1b6ed3f088b775d0bb3df241
Author: kollo97 <aaron.kollo@gmail.com>
Date: 2025-09-16 21:13:10 +0200
Commit message:

 Bioc minor revisions
Package: MetaboDynamics
Commit: 9a7e2281b6ebe1d5ef34e8bfad03c48b435bfdac
Author: ada697e <katja.danielzik@uni-due.de>
Date: 2025-09-16 20:05:54 +0200
Commit message:

 bug fixes
Package: MetaboDynamics
Commit: 399433c604d0b0ade95c51191754b9c86a8e3142
Author: ada697e <katja.danielzik@uni-due.de>
Date: 2025-09-16 19:10:23 +0200
Commit message:

 updated figure titles and readme figures
Package: MetaboDynamics
Commit: 60f3c9baa1d2694807aa319740e5bf2e16293198
Author: ada697e <katja.danielzik@uni-due.de>
Date: 2025-09-11 17:48:30 +0200
Commit message:

 Merge branch 'devel' of github.com:KatjaDanielzik/MetaboDynamics into devel
Package: MetaboDynamics
Commit: 8c744c2a97eb2f43638b7274ab4ef9de9cf72250
Author: ada697e <katja.danielzik@uni-due.de>
Date: 2025-09-11 17:47:53 +0200
Commit message:

 dynamics_model
Package: affycoretools
Commit: 34fce494eb90b4fd317c82195202c55ec049ed52
Author: Jim MacDonald <jmacdon@uw.edu>
Date: 2025-09-16 09:12:27 -0700
Commit message:

 Change to doGlimma to account for partial NA coefficients.
Package: metaboliteIDmapping
Commit: a6a6bf68a30713a22c1adf0d6a9537a064f23c9b
Author: Sebastian Canzler <sebastian.canzler@ufz.de>
Date: 2025-09-16 17:14:40 +0200
Commit message:

 Version bump devel.
Package: metaboliteIDmapping
Commit: 1ea64e1264c87fc658a7bdba1392d6f87751ee1b
Author: Sebastian Canzler <sebastian.canzler@ufz.de>
Date: 2025-09-16 17:14:09 +0200
Commit message:

 Add BiocStyle to DESCRIPTION
Package: CoGAPS
Commit: b480cd10bdee19feb137a5e9f3fd8587abe3909f
Author: dimalvovs <dmitrijs.lvovs@gmail.com>
Date: 2025-09-16 09:46:38 -0400
Commit message:

 bump version
Package: CoGAPS
Commit: 0fb5c4f42b886243ea80ff285520c2c421933d2e
Author: dimalvovs <dmitrijs.lvovs@gmail.com>
Date: 2025-09-16 09:41:08 -0400
Commit message:

 Nextflow (#145)

* bump x.y.z version to even y prior to creation of RELEASE_3_21 branch

* bump x.y.z version to odd y following creation of RELEASE_3_21 branch

* init cirro config

* move config so cirro can find it

* update preprocess.py

* update and mv main.nf

* update cirro to newer format

* update example pipeline

* update params

* update resources

* make nsets < than cpus

* update to sparse

* run on 10k iterations 5,10,15,20 patterns

* report every 100 steps

* example to run on disco HPC

* make it process_long and no distributed

* filter top 5K genes

* update params

* rm Seurat::NormalizeData step

* configure cirro inputs

* debug cirro inputs

* debug cirro inputs

* debug cirro inputs

* allow comma separated string for npatterns

* update docs for nextflow mode

* update nextflow instructions

* update npatterns in cirro

* split preprocess from CoGAPS

* refactor, increase RAM

* use sparseMatrixStats for var estimation

* point to nexflow container, improve proprocessing

* debug channel composition

* increase cpus as filtering reduced RAM footprint

* pin to CoGAPS 3.21.5 due to broken distributed="single-cell"

* fix stitchTogether, close #146

* add DistributedCoGAPS tests

* Update nextflow.config

Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>

* add Distributed_CoGAPS tests

* Update main.nf

Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>

* Update main.nf

Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>

* Update nextflow.config

Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>

---------

Co-authored-by: A Wokaty <andres.wokaty@sph.cuny.edu>
Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>
Package: CoGAPS
Commit: a1a03c23b6c372b369ddbcd5b05218bf45e94a4e
Author: dimalvovs <dmitrijs.lvovs@gmail.com>
Date: 2025-07-09 14:00:59 -0400
Commit message:

 Nextflow (#144)

* init cirro config

* move config so cirro can find it

* update preprocess.py

* update and mv main.nf

* update cirro to newer format

* update example pipeline

* update params

* update resources

* make nsets < than cpus

* update to sparse

* run on 10k iterations 5,10,15,20 patterns

* report every 100 steps

* example to run on disco HPC

* make it process_long and no distributed

* filter top 5K genes

* update params

* rm Seurat::NormalizeData step

* configure cirro inputs

* debug cirro inputs

* debug cirro inputs

* debug cirro inputs

* allow comma separated string for npatterns

* update docs for nextflow mode

* update nextflow instructions

* update npatterns in cirro
Package: CoGAPS
Commit: 930515c04bb9d8dde2054fe217ab567b4a390ef1
Author: dimalvovs <dlvovs1@jh.edu>
Date: 2025-04-30 13:41:39 -0400
Commit message:

 Merge pull request #143 from FertigLab/142-an-example-of-running-in-nextflow

add example for running in nextflow, close #142

- merging as reviewer hit the wrong button and intended to approve
Package: CoGAPS
Commit: 1f3187e535311e1ad25320de4a8d1a35fc9c80e8
Author: dimalvovs <dmitrijs.lvovs@gmail.com>
Date: 2025-04-28 11:31:41 -0400
Commit message:

 add example for running in nextflow, close #142
Package: Ibex
Commit: 2b46df65458ad69d562a747c71ca76ebf71a6425
Author: theHumanBorch <ncborch@gmail.com>
Date: 2025-09-16 08:33:35 -0500
Commit message:

 Merge branch 'main' into devel

Adding onload call
Package: Ibex
Commit: ebf8f33156e58325e2eb89839b5258fe068d0e1e
Author: theHumanBorch <ncborch@gmail.com>
Date: 2025-09-16 08:33:11 -0500
Commit message:

 Merge pull request #23 from BorchLab/OnLoad

onload lock
Package: Ibex
Commit: 77f9c4b9df149bc332aad3a8b027672751c9a919
Author: theHumanBorch <ncborch@gmail.com>
Date: 2025-09-16 08:17:02 -0500
Commit message:

 onload lock
Package: epigraHMM
Commit: 4d03bb7b0f5d18b9731edceaa64aa101d17d784f
Author: Pedro Baldoni <26856909+plbaldoni@users.noreply.github.com>
Date: 2025-09-15 17:35:46 -0400
Commit message:

 version bump in devel
Package: epigraHMM
Commit: 2b87d82e4e7c7c44b09b91d60ebbc0abc3560a39
Author: Pedro Baldoni <26856909+plbaldoni@users.noreply.github.com>
Date: 2025-09-15 17:33:58 -0400
Commit message:

 bug fix: fix class check
Package: ExpressionAtlas
Commit: ff253c4985e3a44cfca4a189f61104c4a0cbfeba
Author: Anil Thanki <thanki.anil@gmail.com>
Date: 2025-09-16 14:06:07 +0100
Commit message:

 Bump version to 2.1.1 and adds new maintainer
Package: ExpressionAtlas
Commit: f0d7fa2c29c6156998b5a8e7d8501924e8cbdba6
Author: Anil Thanki <thanki.anil@gmail.com>
Date: 2025-09-08 17:02:28 +0100
Commit message:

 Merge pull request #18 from ebi-gene-expression-group/master-rel-3-20_patch

Modify package date and author roles
Package: ExpressionAtlas
Commit: 884974142e208b403449d1460fe9894a82e66699
Author: Anil Thanki <thanki.anil@gmail.com>
Date: 2025-09-08 17:00:32 +0100
Commit message:

 Apply suggestions from code review

Co-authored-by: Pedro Madrigal <8195212+pmb59@users.noreply.github.com>
Package: ExpressionAtlas
Commit: 150f739366d4854498fc0b32fa6d04f474975bd6
Author: Anil Thanki <thanki.anil@gmail.com>
Date: 2025-09-01 15:42:02 +0100
Commit message:

 Bump version from 1.99.6 to 2.1.0
Package: ExpressionAtlas
Commit: 03b3938e136c1180efcf12b1f90eb6bb28ec9959
Author: Anil Thanki <thanki.anil@gmail.com>
Date: 2025-09-01 15:10:29 +0100
Commit message:

 Update DESCRIPTION

Co-authored-by: Pedro Madrigal <8195212+pmb59@users.noreply.github.com>
Package: ExpressionAtlas
Commit: 685aba839be25ccfbb62eb151bb45fd6b784cb18
Author: Anil Thanki <thanki.anil@gmail.com>
Date: 2025-09-01 14:37:43 +0100
Commit message:

 Modify package date and author roles
Package: Ibex
Commit: 6087a8b01378dc8972d997808c59ef933e2e2c89
Author: theHumanBorch <ncborch@gmail.com>
Date: 2025-09-16 06:56:42 -0500
Commit message:

 Merge branch 'main' into devel
Editing package per reviewer requests
Package: Ibex
Commit: 3b060024f1270c5967d2c8a75a24e6e4f50b80ad
Author: theHumanBorch <ncborch@gmail.com>
Date: 2025-09-16 06:55:46 -0500
Commit message:

 Merge pull request #22 from BorchLab/bioconductor-review

bioc Review
Package: Ibex
Commit: cd4d6ac58909ca618c3c83b56a4996c579787128
Author: theHumanBorch <ncborch@gmail.com>
Date: 2025-09-16 06:41:12 -0500
Commit message:

 bioc Review

* Deprecated `quietBCRgenes()`
* Converted `Ibex.matrix()` to `Ibex_matrix()`
* Added Install Instructions for BioCondcutor on README and Vignette
* Removed references to Keras3 Installation
* Removed LazyData TRUE statement
Package: Ibex
Commit: b907835587aabc1f39e95fc0881b704d479217c5
Author: theHumanBorch <ncborch@gmail.com>
Date: 2025-09-15 12:28:51 -0500
Commit message:

 Delete .trigger_build
Package: Ibex
Commit: 01a5fe3d809410cbea6071fe7c79473d970fd45a
Author: theHumanBorch <ncborch@gmail.com>
Date: 2025-08-18 05:21:18 -0500
Commit message:

 Update README.md
Package: Ibex
Commit: b92c700d07fe54c2c1557ab58f11a9e9ddce6e83
Author: theHumanBorch <ncborch@gmail.com>
Date: 2025-08-18 03:11:19 -0500
Commit message:

 Update ibex_hex.png
Package: looking4clusters
Commit: dcc36e3a9ab27da8aa6c16f7ebaa6cd08842c7f4
Author: BioinfoUSAL <bioinfo@usal.es>
Date: 2025-09-16 13:21:45 +0200
Commit message:

 plot method removed
Package: SwarnSeq
Commit: feb029534ccb8b2e014682a56b1bfa10fc72c026
Author: Samarendra Das <samarendra.das@icar.org.in>
Date: 2025-09-16 14:13:08 +0530
Commit message:

 Update package version
Package: ggtreeExtra
Commit: e44a79f43b6a59b19414319c0ac3036753a103bd
Author: xiangpin <xshuangbin@163.com>
Date: 2025-09-16 16:22:53 +0800
Commit message:

 bump version
Package: ggtreeExtra
Commit: a144fdf86bce089b6a256b6e6faca90d97b5aaf0
Author: xiangpin <xshuangbin@163.com>
Date: 2025-08-11 19:22:50 +0800
Commit message:

 export the original name of y in mapping
Package: ggtreeExtra
Commit: fadeb15ddee632b2b19334b757a4698eeb4747a8
Author: xiangpin <xshuangbin@163.com>
Date: 2025-07-02 15:52:21 +0800
Commit message:

 Merge remote-tracking branch 'origin/master'
Package: ggtreeExtra
Commit: 0344d2ed5237836400549c6838bdf3f683672b57
Author: xiangpin <xshuangbin@163.com>
Date: 2025-07-02 15:52:15 +0800
Commit message:

 using aes instead of aes_ or aes_string
Package: ggtreeExtra
Commit: 6526747c77f8a4acbb6c7703706e8b378e2ba0b0
Author: xiangpin <xshuangbin@163.com>
Date: 2025-06-26 14:40:45 +0800
Commit message:

 be compatible with new ggplot2 (>3.5.2)
Package: ggtreeExtra
Commit: 7015f46ca9156c5e088f99a8f2b9d209ff2090de
Author: xiangpin <xshuangbin@163.com>
Date: 2025-04-17 16:59:03 +0800
Commit message:

 bioc3.21 release
Package: ggtreeExtra
Commit: c481a027f7a08bfa7c67b47269e59f27e751a785
Author: xiangpin <xshuangbin@163.com>
Date: 2025-04-17 16:56:07 +0800
Commit message:

 Merge remote-tracking branch 'upstream/devel'
Package: ggtreeExtra
Commit: 6de952d3a2809752010d3ab8cceeb7b508c072ab
Author: xiangpin <xshuangbin@163.com>
Date: 2024-11-04 17:47:07 +0800
Commit message:

 Bioconductor 2.0 released
Package: ggtreeExtra
Commit: b9982b89f76f6627caa934e0637f055b8597e6e8
Author: xiangpin <xshuangbin@163.com>
Date: 2024-11-04 17:45:34 +0800
Commit message:

 Merge remote-tracking branch 'upstream/devel'
Package: ggtreeExtra
Commit: 2b6fdcc9f11901734ebf5d3da5c6ffe322be3f13
Author: xiangpin <xshuangbin@163.com>
Date: 2024-07-11 14:25:38 +0800
Commit message:

 to be better compatible with dendrogram layout
Package: ggtreeExtra
Commit: fe1e13893e813004602b126f28767635cd1a2ed5
Author: xiangpin <xshuangbin@163.com>
Date: 2024-05-14 18:06:12 +0800
Commit message:

 bump version and update news
Package: ggtreeExtra
Commit: 76d6869addc3e99ce1e919c738a3a7074a361277
Author: xiangpin <xshuangbin@163.com>
Date: 2024-04-12 14:49:20 +0800
Commit message:

 bump version
Package: ggtreeExtra
Commit: 7aff3d725344fe1170ba1950cd7843bfb640d59d
Author: xiangpin <xshuangbin@163.com>
Date: 2024-04-12 14:16:33 +0800
Commit message:

 update rd
Package: ggtreeExtra
Commit: 49a129c5ca90f99afe9ec486368547a8f356be17
Author: xiangpin <xshuangbin@163.com>
Date: 2024-01-10 11:08:52 +0800
Commit message:

 Merge remote-tracking branch 'upstream/devel'
Package: ggtreeExtra
Commit: db5a26c1618e0d6bae29883689b208e39a181ee0
Author: xiangpin <xshuangbin@163.com>
Date: 2023-08-03 15:26:59 +0800
Commit message:

 update version
Package: ggtreeExtra
Commit: 221b2853e9e414665e0d9c754f5bac62165da9ab
Author: xiangpin <xshuangbin@163.com>
Date: 2023-08-03 15:26:18 +0800
Commit message:

 update citation format
Package: ggtreeExtra
Commit: e1de32465fe066aa6c87d1a6abcdf30f243ae7f9
Author: xiangpin <xshuangbin@163.com>
Date: 2023-05-04 10:11:30 +0800
Commit message:

 new version released with bioconductor 3.17
Package: tidybulk
Commit: 6eafc1e32c7c44c5fbbfb7f88cf93a56fa12200a
Author: Stefano Mangiola <mangiolastefano@gmail.com>
Date: 2025-09-16 17:36:04 +0930
Commit message:

 Merge branch 'master' of https://github.com/stemangiola/tidybulk
Package: tidybulk
Commit: 881bf0ebd7c5080d334d92f443e67d0bf441a1aa
Author: Stefano Mangiola <mangiolastefano@gmail.com>
Date: 2025-09-16 17:35:34 +0930
Commit message:

 Update package version and RoxygenNote; enhance tests for SummarizedExperiment functionality

- Bumped package version to 1.99.4 and updated RoxygenNote to 7.3.3.
- Improved tests for SummarizedExperiment methods to ensure multiplier values are positive and finite, and that the number of unique multipliers is reasonable.
- Added checks for the existence and validity of key columns in differential abundance tests, ensuring logFC, P-values, and FDR values are within expected ranges.
Package: tidybulk
Commit: 574b8f7c970a97c2327674dff51b9ca02573e0e5
Author: Stefano Mangiola <mangiolastefano@gmail.com>
Date: 2025-09-15 11:16:00 +0930
Commit message:

 Update README.md
Package: SwarnSeq
Commit: 3a65114d15b387ae68265046ca12d716cd658cba
Author: Samarendra Das <samarendra.das@icar.org.in>
Date: 2025-09-16 12:15:09 +0530
Commit message:

 First version change
Package: omicsGMF
Commit: d65f2094ae4928d756cac67038de79e55e25c207
Author: Alexandre Segers <alexandre.segers@ugent.be>
Date: 2025-09-16 08:44:19 +0200
Commit message:

 update README
Package: omicsGMF
Commit: f3e208860debf68b5ab7bafbc9c27c1ab376bb9c
Author: Alexandre Segers <alexandre.segers@ugent.be>
Date: 2025-09-16 08:30:37 +0200
Commit message:

 version bump
Package: omicsGMF
Commit: e82c0d7043fe286b97b92c346552c511ace355c9
Author: Alexandre Segers <alexandre.segers@ugent.be>
Date: 2025-03-28 16:08:07 +0100
Commit message:

 update README
Package: sccomp
Commit: b70ae15f43ec64d403d3c7a03994ed56912d073e
Author: Stefano Mangiola <mangiolastefano@gmail.com>
Date: 2025-08-19 21:27:50 +0930
Commit message:

 Add test script for sccomp issue #229

This commit introduces a new R script that tests the resolution of the reframe/full_join error related to issue #229. The script loads a toy dataset, runs the analysis pipeline, and confirms that the bug is resolved, providing a clear message upon completion.
Package: sccomp
Commit: b9f62302fc54bca23266bd70dc0828b02e73dfeb
Author: Stefano Mangiola <mangiolastefano@gmail.com>
Date: 2025-07-21 20:55:47 +0930
Commit message:

 Merge pull request #223 from MangiolaLaboratory/improve-validation-messages

Improve error handling and clarity. Updated parameter handling to use…
Package: sccomp
Commit: 09288de8ab5fd8c6037b6b284ac8ecc8dc26a330
Author: Stefano Mangiola <mangiolastefano@gmail.com>
Date: 2025-07-21 14:43:24 +0930
Commit message:

 Merge pull request #222 from MangiolaLaboratory/custom-cache-directory

Add cache_stan_model parameter to relevant functions and update docum…
Package: sccomp
Commit: 2ba0c5c1e9664e98a2f2c1b2cdea633c0f45aa50
Author: Stefano Mangiola <mangiolastefano@gmail.com>
Date: 2025-07-21 12:32:45 +0930
Commit message:

 fixed documentation
Package: sccomp
Commit: 33b5072361208ac6e6d518fb5159aa227e8b1431
Author: Stefano Mangiola <mangiolastefano@gmail.com>
Date: 2025-07-20 10:32:56 +0930
Commit message:

 Update R/validation.R use seq_len

Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>
Package: sccomp
Commit: b91a0661ed3628144945926a61322e647bada84b
Author: Stefano Mangiola <mangiolastefano@gmail.com>
Date: 2025-07-20 10:09:29 +0930
Commit message:

 Import additional dplyr functions in validation and NAMESPACE files. Added n_distinct and all_of to enhance data processing capabilities.
Package: sccomp
Commit: aa44abd370a199986d71cc471d0ea11a4377ddad
Author: Stefano Mangiola <mangiolastefano@gmail.com>
Date: 2025-07-20 10:05:18 +0930
Commit message:

 Enhance validation functions by importing additional dplyr functions and refining data processing steps. Added group_by and summarise imports, and improved handling of factor variables in check_sample_consistency_of_factors function.
Package: sccomp
Commit: 49574b41ea46a607c93d35263eb9b496aa352f46
Author: Stefano Mangiola <mangiolastefano@gmail.com>
Date: 2025-07-19 16:04:38 +0930
Commit message:

 version UP
Package: sccomp
Commit: 44a1a85af47e4d83b286beea9458ab00fb935b36
Author: Stefano Mangiola <mangiolastefano@gmail.com>
Date: 2025-07-19 16:03:41 +0930
Commit message:

 version UP
Package: sccomp
Commit: da70833ebeb99e474a3da2c481ab6dfaf0313c0f
Author: Stefano Mangiola <mangiolastefano@gmail.com>
Date: 2025-07-19 16:01:54 +0930
Commit message:

 Improve error handling and clarity. Updated parameter handling to use quosures and enhanced the error message for inconsistent factor values across samples.
Package: sccomp
Commit: 16fbb8bb5ac5858e4c24245dd9f0d845efc1c06e
Author: Stefano Mangiola <mangiolastefano@gmail.com>
Date: 2025-07-19 15:23:02 +0930
Commit message:

 Add cache_stan_model parameter to relevant functions and update documentation

Introduced a new parameter, cache_stan_model, to functions including sccomp_estimate, sccomp_replicate, simulate_data, and sccomp_remove_outliers. This parameter specifies the cache directory for compiled Stan models, ensuring version isolation. Updated documentation and tests to reflect these changes, ensuring proper functionality and default settings.
Package: sccomp
Commit: 12beb07c50b651797900c3f5a43c1d45e4311a2a
Author: Stefano Mangiola <mangiolastefano@gmail.com>
Date: 2025-07-19 11:54:30 +0930
Commit message:

 fix vb_iterative
Package: sccomp
Commit: c6f6a8c2fa8aee5392152fda2edb27f4e7857689
Author: Stefano Mangiola <mangiolastefano@gmail.com>
Date: 2025-07-18 16:19:05 +0930
Commit message:

 Update README and vignettes with new figures, correct figure paths, and enhance documentation clarity. Added new images for improved visualization and adjusted parameter handling in plots.
Package: sccomp
Commit: be0135baa2eb1286282911ffe673f38b4685e68e
Author: Stefano Mangiola <mangiolastefano@gmail.com>
Date: 2025-07-18 09:38:16 +0930
Commit message:

 Change figures to relative path
Package: sccomp
Commit: b3a0d7ce8cc24d089310da33e0967cadc6ef2f5b
Author: Stefano Mangiola <mangiolastefano@gmail.com>
Date: 2025-07-17 21:44:30 +0930
Commit message:

 Refactor README and plotting functions to enhance clarity and consistency. Updated figure paths, removed obsolete images, and improved parameter handling in plots. Added new figures for better visualization in documentation.
Package: sccomp
Commit: fe366fddce03bec56e13806326a79e7345af1806
Author: Stefano Mangiola <mangiolastefano@gmail.com>
Date: 2025-07-17 18:48:55 +0930
Commit message:

 Refactor README and plotting functions for clarity and consistency. Updated table formatting in README, improved plot caption handling, and refined boxplot aesthetics. Adjusted parameter levels in 2D plots for better visualization.
Package: sccomp
Commit: 1ee45d587131ab776eceb37757f8d1967344f58e
Author: Stefano Mangiola <mangiolastefano@gmail.com>
Date: 2025-07-17 12:37:42 +0930
Commit message:

 Merge pull request #219 from MangiolaLaboratory/fix-README-figure-paths

update paths
Package: sccomp
Commit: a59c15135a47501fc45c60535d7217ae43097c3a
Author: Stefano Mangiola <mangiolastefano@gmail.com>
Date: 2025-07-17 12:36:01 +0930
Commit message:

 Update figure paths in README and vignettes, removing obsolete images and ensuring consistency in image rendering. Adjusted documentation for clarity and improved user experience.
Package: sccomp
Commit: 81d31e0d1af20e13272cc237df2f51e3db7e1350
Author: Stefano Mangiola <mangiolastefano@gmail.com>
Date: 2025-07-17 11:44:30 +0930
Commit message:

 Corrected figure paths, and refined image rendering logic in RMarkdown. Enhanced documentation for better user experience.
Package: sccomp
Commit: 235db702baea00aa60ff287ec510909ae1b2a54b
Author: Stefano Mangiola <mangiolastefano@gmail.com>
Date: 2025-07-17 01:06:04 +0930
Commit message:

 update paths
Package: SwarnSeq
Commit: 61a3d3219183b039a53bade3c610887418258548
Author: Samarendra Das <samarendra.das@icar.org.in>
Date: 2025-09-16 11:36:45 +0530
Commit message:

 Remove first warning
Package: methylInheritance
Commit: 8bce9e0bb9a865846ee2aadf776d8b7e755f325b
Author: adeschen <adeschen@hotmail.com>
Date: 2025-09-16 00:37:04 -0400
Commit message:

 Update package version to 1.33.1
Package: methylInheritance
Commit: 7be30267061fad5d82fb47d453f11940cda09f63
Author: adeschen <adeschen@hotmail.com>
Date: 2025-09-16 00:17:14 -0400
Commit message:

 Update doc
Package: methylInheritance
Commit: 5fe7c8b78f436de23b8d375cb86b015dee0ac660
Author: adeschen <adeschen@hotmail.com>
Date: 2025-09-16 00:15:41 -0400
Commit message:

 Update doc
Package: methylInheritance
Commit: 7c668743ada2d56cb8aca34b70789f5af29303c5
Author: Astrid Deschênes <adeschen@users.noreply.github.com>
Date: 2025-09-16 00:03:29 -0400
Commit message:

 Merge pull request #19 from adeschen/adeschen-patch-1

Update check-bioc.yml
Package: methylInheritance
Commit: 5a99560d1175663346c9d9bd48d9b1c6caa11695
Author: Astrid Deschênes <adeschen@users.noreply.github.com>
Date: 2025-09-16 00:02:50 -0400
Commit message:

 Update check-bioc.yml
Package: methylInheritance
Commit: 24a6d842507cacf9182ce2f707619c058ebf6a42
Author: adeschen <adeschen@hotmail.com>
Date: 2025-09-15 23:59:10 -0400
Commit message:

 Update github action
Package: methylInheritance
Commit: 0f51649850d349c18b86fb537dcc87fe4c36f220
Author: adeschen <adeschen@hotmail.com>
Date: 2025-09-15 23:56:17 -0400
Commit message:

 Update github action
Package: methylInheritance
Commit: c3790e20c1b0ce4cfe9fa6daa66c7b7dfe8affa1
Author: adeschen <adeschen@hotmail.com>
Date: 2025-09-15 23:55:23 -0400
Commit message:

 Update github action
Package: methylInheritance
Commit: b1f4269ccb7f53842d33fe40773bb19dc018d932
Author: adeschen <adeschen@hotmail.com>
Date: 2025-09-15 23:54:31 -0400
Commit message:

 Update github action
Package: methylInheritance
Commit: 5550b733a2b8c07202f6e5c1dab9ad7c3efe993f
Author: adeschen <adeschen@hotmail.com>
Date: 2025-09-15 23:52:32 -0400
Commit message:

 Update doc for demoForTransgenerationalAnalysis dataset
Package: methylInheritance
Commit: 829a1468b31beaaabae3e98a518a5bccc49cb846
Author: adeschen <adeschen@hotmail.com>
Date: 2025-09-15 23:26:00 -0400
Commit message:

 Update github action
Package: methylInheritance
Commit: 43f8772bcb9cd6346c1917f8d98296f4001abdc5
Author: adeschen <adeschen@hotmail.com>
Date: 2025-09-15 23:24:59 -0400
Commit message:

 Update github action
Package: methylInheritance
Commit: b120837a5717490b30dd0d21aae14f88babc0260
Author: adeschen <adeschen@hotmail.com>
Date: 2025-09-15 23:24:01 -0400
Commit message:

 Update github action
Package: methylInheritance
Commit: 8499da7f23936bb763950135dfcd4aecd7bbecf8
Author: adeschen <adeschen@hotmail.com>
Date: 2025-09-15 23:20:21 -0400
Commit message:

 Update github action
Package: methylInheritance
Commit: 44405da554473a7843cfc9b3c993712b0ba04be1
Author: adeschen <adeschen@hotmail.com>
Date: 2025-09-15 23:15:41 -0400
Commit message:

 Update github action
Package: methylInheritance
Commit: e60293cce0a9c0a2b391aa0732749789db490188
Author: adeschen <adeschen@hotmail.com>
Date: 2025-09-15 23:14:42 -0400
Commit message:

 Update runOnePermutationOnAllGenerations() doc
Package: methylInheritance
Commit: a5daeb215ba682042c1ace6b294ab78b6dcfcfca
Author: adeschen <adeschen@hotmail.com>
Date: 2025-09-15 23:07:43 -0400
Commit message:

 Update doc for readInterGenerationResults()
Package: methylInheritance
Commit: be0c2610fa88d342fcab1e2919eea04a112a9e1d
Author: adeschen <adeschen@hotmail.com>
Date: 2025-09-15 22:01:46 -0400
Commit message:

 Update github action
Package: methylInheritance
Commit: 7eeef55c78d82382d9872c06e67ffe578c85ada8
Author: adeschen <adeschen@hotmail.com>
Date: 2025-09-15 22:01:28 -0400
Commit message:

 Update doc vor saveIneterGenrationResults()
Package: methylInheritance
Commit: 3fd5d59db6fb69a7123ed119d94701d5d0b12967
Author: adeschen <adeschen@hotmail.com>
Date: 2025-09-15 21:26:45 -0400
Commit message:

 Update items in doc
Package: methylInheritance
Commit: d3b43af4bd964d52e9af1118ef37523848879861
Author: adeschen <adeschen@hotmail.com>
Date: 2025-09-15 21:23:28 -0400
Commit message:

 Update items in doc
Package: methylInheritance
Commit: 4f1e67dff228ecb0cbc00e632bdd8efca9120016
Author: adeschen <adeschen@hotmail.com>
Date: 2025-09-15 21:09:25 -0400
Commit message:

 Update github action
Package: methylInheritance
Commit: 0e8550c980409d1eaf423b0e98decf80f89085c0
Author: adeschen <adeschen@hotmail.com>
Date: 2025-09-15 21:08:00 -0400
Commit message:

 Update github action
Package: methylInheritance
Commit: b453fed39661e6981853dc0bc451b929e21ea3ad
Author: adeschen <adeschen@hotmail.com>
Date: 2025-09-15 21:02:45 -0400
Commit message:

 Update github action
Package: methylInheritance
Commit: 8f4cc2312464c69cdf65022c03d277e58704c584
Author: adeschen <adeschen@hotmail.com>
Date: 2025-09-15 21:01:27 -0400
Commit message:

 Update github action
Package: methylInheritance
Commit: 3b7b9a366bdb751b55ef761c857e1333ce2f3c6b
Author: adeschen <adeschen@hotmail.com>
Date: 2025-09-15 20:59:07 -0400
Commit message:

 Update github action
Package: methylInheritance
Commit: 1125526a936aa917b9a621b84da90a3c006ced0a
Author: adeschen <adeschen@hotmail.com>
Date: 2025-09-15 20:55:54 -0400
Commit message:

 Update github action
Package: methylInheritance
Commit: fb7df384996d8a62df7a2efc931ad31817ba8afa
Author: adeschen <adeschen@hotmail.com>
Date: 2025-09-15 20:47:36 -0400
Commit message:

 Update github action
Package: methylInheritance
Commit: de613d0d160ddf3b8ed349711ef397d4d14d79fd
Author: adeschen <adeschen@hotmail.com>
Date: 2025-09-15 20:41:43 -0400
Commit message:

 Update github action
Package: methylInheritance
Commit: fae5e2171a5ba4710b2b46252c405948d023014b
Author: adeschen <adeschen@hotmail.com>
Date: 2025-09-15 20:39:14 -0400
Commit message:

 Update github action
Package: methylInheritance
Commit: 5e932d17bcad13167298a1f14dbb982206ec450f
Author: adeschen <adeschen@hotmail.com>
Date: 2025-09-15 20:38:10 -0400
Commit message:

 Update github action
Package: methylInheritance
Commit: c7cf218da2c87edb66ede9b47ba9efe5fbeeef35
Author: adeschen <adeschen@hotmail.com>
Date: 2025-09-15 20:34:41 -0400
Commit message:

 Update github action
Package: methylInheritance
Commit: 0aad8807bc4a230f16b0d05ba5767d09ab71e18e
Author: adeschen <adeschen@hotmail.com>
Date: 2025-09-15 20:31:29 -0400
Commit message:

 Update code to remove ggplot2 error and update doc
Package: methylInheritance
Commit: 469f5a1ec7a66bc6f5503cfafff4258e0cbf5af9
Author: adeschen <adeschen@hotmail.com>
Date: 2025-09-15 18:16:51 -0400
Commit message:

 Merge remote-tracking branch 'upstream/devel'
Package: methylInheritance
Commit: 257421cbb02cee26364e6f9f661af0604313e0c3
Author: Astrid Deschênes <adeschen@users.noreply.github.com>
Date: 2021-04-19 11:22:11 -0400
Commit message:

 Update cache in check-bioc.yml
Package: methylInheritance
Commit: a082ccc428cf10610ad04b15f5ca7b73094388cc
Author: Astrid Deschenes <adeschen@hotmail.com>
Date: 2021-04-07 19:40:18 -0400
Commit message:

 Add github action bioc-check
Package: methylInheritance
Commit: 71a2022e0f3059c0f08325b7896a1f4c97003714
Author: Astrid Deschenes <adeschen@hotmail.com>
Date: 2021-04-07 19:39:02 -0400
Commit message:

 Remove space around = when using named arguments in functions
Package: IRanges
Commit: 3bb03070ab2467c49910ea9d2abe3676780c5753
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2025-09-15 21:35:29 -0700
Commit message:

 IRanges 2.43.2: Some clarification in nearest()'s documentation
Package: Voyager
Commit: 7cd5ab1ab88493d75ddeff20e086e4446b2759dc
Author: Lambda Moses <dlu2@caltech.edu>
Date: 2025-09-15 22:18:05 -0400
Commit message:

 Merge branch 'devel' of git.bioconductor.org:packages/Voyager into devel
Package: Voyager
Commit: d45c1c94d0d33f3ba824389c12c020a2c6247984
Author: Lambda Moses <dlu2@caltech.edu>
Date: 2025-09-15 17:08:19 -0400
Commit message:

 tiledb version
Package: Voyager
Commit: 105b8e52e9b3de0a924a2dbeed7ed814275514f8
Author: Lambda Moses <dlu2@caltech.edu>
Date: 2025-09-15 17:07:53 -0400
Commit message:

 Deal with ggpot2 update
Package: Voyager
Commit: a19b6eae8ad5b2ffea706d79759f2e45ec1e309a
Author: Lambda Moses <dlu2@caltech.edu>
Date: 2025-09-15 17:02:03 -0400
Commit message:

 Updated documentation
Package: ggkegg
Commit: df43afa68f68bdae45541e83e62eeef52afef09b
Author: noriakis <nori@hgc.jp>
Date: 2025-09-16 10:11:43 +0900
Commit message:

 v1.7.1 in devel
Package: ggkegg
Commit: 67004b8b20aebac25412c83ef715657781ddcd37
Author: noriakis <nori@hgc.jp>
Date: 2025-09-16 10:10:30 +0900
Commit message:

 avoid linetype aes
Package: ggsc
Commit: a648db4bee20d61d1d984c0a4268fe1b6fd141d9
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2025-07-02 12:02:00 +0800
Commit message:

 compatible with ggplot2 v>3.5.2
Package: ggsc
Commit: f2061775656f70b1783b0ded54d87fe7db4fd7f2
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2025-07-02 11:44:30 +0800
Commit message:

 Merge pull request #40 from xiangpin/master

Compatibility with new ggplot2 > 3.5.2
Package: ggsc
Commit: 8f5cf0200952e6e74cc550979010081a5709ad00
Author: xiangpin <xshuangbin@163.com>
Date: 2025-07-01 14:50:24 +0800
Commit message:

 Compatibility with ggplot2 4.0.0
Package: ggsc
Commit: 09a61fb9bcf09be19a75e6f2cce1e9aefd11b5b9
Author: xiangpin <xshuangbin@163.com>
Date: 2025-07-01 14:49:11 +0800
Commit message:

 supporting pie chart when reduction is specified
Package: ggsc
Commit: 36b63c5bde23378cd636603722950632230d0fb8
Author: xushuangbin <xshuangbin@163.com>
Date: 2025-05-28 12:01:31 +0800
Commit message:

 Merge remote-tracking branch 'upstream/devel'
Package: ggsc
Commit: 42bbe18c4308fada7895932662392a64e21375c8
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2025-04-17 10:05:44 +0800
Commit message:

 update bioc version
Package: ggsc
Commit: cff6139f757f9977e93117d713020e7c168651fc
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2025-04-17 10:05:40 +0800
Commit message:

 Merge remote-tracking branch 'upstream/devel' into devel
Package: ggsc
Commit: 9bd39f4a0ec7ca65ac4f8406a7f485cb40733fe1
Author: xiangpin <xshuangbin@163.com>
Date: 2024-12-18 11:44:24 +0800
Commit message:

 Merge remote-tracking branch 'upstream/devel'
Package: ggsc
Commit: d1616cf111f9085ac068cb83e051cc13a0afabd3
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2024-10-30 14:53:57 +0800
Commit message:

 update bioc version
Package: ggsc
Commit: f72150a9dbe8db1338dea5ec4d9862678db04108
Author: xiangpin <xshuangbin@163.com>
Date: 2024-10-14 20:15:33 +0800
Commit message:

 adjust levels of features
Package: ggsc
Commit: 593cf47b882f5444520882494b3bf91031a14174
Author: xiangpin <xshuangbin@163.com>
Date: 2024-09-29 17:03:42 +0800
Commit message:

 Merge remote-tracking branch 'upstream/devel'
Package: ggsc
Commit: 8b80818a1aeae2e377fa2819b6ef520479e8666d
Author: xiangpin <xshuangbin@163.com>
Date: 2024-09-29 17:03:32 +0800
Commit message:

 Merge remote-tracking branch 'origin/master'
Package: ggsc
Commit: 038910e201612f87522b02fe5b6ca8e8c4bfd739
Author: xiangpin <xshuangbin@163.com>
Date: 2024-08-30 15:14:44 +0800
Commit message:

 Merge remote-tracking branch 'origin/master'
Package: SETA
Commit: a4503cc6a21dfa45dad25150816b189b5a51f083
Author: kylekimler <kylejkimler@gmail.com>
Date: 2025-09-15 19:19:43 -0400
Commit message:

 bioconductor review
Package: SETA
Commit: a3d44869ef4542de995f646bd1583c75ca0267c6
Author: kylekimler <kylejkimler@gmail.com>
Date: 2025-09-15 15:48:15 -0400
Commit message:

 bioconductor review
Package: BioNERO
Commit: 4f3bb9cd82445545511e40ce9ce249d3f4189155
Author: almeidasilvaf <fabricio_almeidasilva@hotmail.com>
Date: 2025-09-15 22:10:39 +0200
Commit message:

 Version bump in devel
Package: BioNERO
Commit: b4a2ff81c5e2db25fe7720cea932e9e89cb37b27
Author: almeidasilvaf <fabricio_almeidasilva@hotmail.com>
Date: 2025-09-15 22:10:16 +0200
Commit message:

 Updated ggplot unit tests
Package: BUSpaRse
Commit: d0c6bbde26a16df8acb5f952dcf7d530b86aa073
Author: Lambda Moses <dlu2@caltech.edu>
Date: 2025-09-15 15:35:34 -0400
Commit message:

 Version bump
Package: BUSpaRse
Commit: 252b61a65d44faa847f3eb99457bb4dd411f69f6
Author: Lambda Moses <dlu2@caltech.edu>
Date: 2025-09-15 15:33:26 -0400
Commit message:

 Version 99 is no longer in the archive
Package: smoothclust
Commit: bccbce4576b63bac34b3e6b682309eaf22f0314d
Author: Lukas Weber <lmweb012@gmail.com>
Date: 2025-09-15 15:26:25 -0400
Commit message:

 runtime optimizations for metric function
Package: smoothclust
Commit: ac71d8476577f01ffa520f17dc8fc63f6082e6ef
Author: Lukas Weber <lmweb012@gmail.com>
Date: 2025-09-15 15:11:57 -0400
Commit message:

 runtime optimizations for kernel and knn methods
Package: smoothclust
Commit: f250437b5454c17b48d51780989f53a5cad42b44
Author: Lukas Weber <lmweb012@gmail.com>
Date: 2025-09-15 13:57:50 -0400
Commit message:

 GHA fix for SPE superclass ExpData error
Package: immReferent
Commit: c0e17f99939d1c08dff546068bdb72d902e3bae0
Author: theHumanBorch <ncborch@gmail.com>
Date: 2025-09-15 13:24:04 -0500
Commit message:

 0.99.4
Package: ChIPDBData
Commit: e6258fea5b75651024f06cd7107218d0b52596dd
Author: yosra <yosraberrouayel@gmail.com>
Date: 2025-09-15 19:50:41 +0200
Commit message:

 corrected bump v in NEWS
Package: Bioc.gff
Commit: ff146d42fcfb89950bfe0107ff9b13a76bf68ea4
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-09-15 13:30:58 -0400
Commit message:

 version bump 0.99.16
Package: Bioc.gff
Commit: d2d6d8d6c19f7b0c0996c17685606d51ae860e25
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-09-15 13:30:49 -0400
Commit message:

 rename gff_remote to gff_local in vignette
Package: smoothclust
Commit: be5c65b8f953ae559de13e3f73b11f13d7b7b323
Author: Lukas Weber <lmweb012@gmail.com>
Date: 2025-09-15 13:30:04 -0400
Commit message:

 runtime optimizations for uniform method
Package: SummarizedExperiment
Commit: 95336904bd0441c585d17e5b4645e14bb8c63161
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2025-09-15 10:27:14 -0700
Commit message:

 SummarizedExperiment 1.39.2: Requires GenomicRanges >= 1.61.4
Package: immReferent
Commit: 343c0af40fecbe219b8c1efe9be632a6107fbe0f
Author: theHumanBorch <ncborch@gmail.com>
Date: 2025-09-15 12:20:35 -0500
Commit message:

 0.99.3 bump
Package: GenomicRanges
Commit: 635c45880dceb86204735486e0e414b7a60dafd7
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2025-09-15 10:17:47 -0700
Commit message:

 update unit tests
Package: GenomicRanges
Commit: f640e0bdfe373f0351f60925a857a013c29d42a3
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2025-09-15 10:13:49 -0700
Commit message:

 GenomicRanges 1.61.4: Small internal renaming

Rename internal helper .find_core_GRanges_cols() to
find_core_GRanges_cols().
Package: GenomeInfoDb
Commit: 4f3c737f819fc780a43c54fb9a74d0e1443665b6
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2025-09-12 23:39:58 -0700
Commit message:

 GenomeInfoDb 1.45.11: Fix getChromInfoFromNCBI("Pan_troglodytes-2.1.4")

In September 2025, someone modified the NCBI assembly report for
Pan_troglodytes-2.1.4 (GCF_000001515.5). Among other things, they
added a duplicated entry for chromosome 21 (RefSeqAccn NC_006488.2),
and this addition broke getChromInfoFromNCBI("Pan_troglodytes-2.1.4").
This commit repairs getChromInfoFromNCBI() by dropping the NC_006488.2
row. The idea is to keep the original chromosome 21 because it has a
length that is equal to the length of chr21 in UCSC genome panTro4.

Also, it seems that, as part of the September 2025 changes to
GCF_000001515.5, some sequences were renamed, with the consequence
that test_switching_Seqinfo_to_RefSeq_style() now fails on panTro4.
So this commit also excludes panTro4 from this test.

Finally, downloading GCF_000001515.5_Pan_troglodytes-2.1.4_genomic.fna.gz
with BSgenomeForge::downloadGenomicSequencesFromNCBI("GCF_000001515.5")
reveals that the RefSeq accessions in the FASTA file differ from those
in the NCBI assembly report for thousands of sequences!

So overall the situation with GCF_000001515.5 is not looking good to say
the least.
Package: smoothclust
Commit: 70446a03902e511be69f72e379fa57e571423bcd
Author: Lukas Weber <lmweb012@gmail.com>
Date: 2025-09-15 12:35:23 -0400
Commit message:

 version bump to test build
Package: smoothclust
Commit: 0b458e34d704750f96f870459256a343c4d6e58f
Author: Lukas Weber <lmweb012@gmail.com>
Date: 2025-09-15 12:34:40 -0400
Commit message:

 text updates
Package: UniProt.ws
Commit: 0d308fa4f65b37e041e7a4c8a4aa4b1a63990516
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-09-15 12:27:52 -0400
Commit message:

 version bump 2.49.4
Package: UniProt.ws
Commit: 2293156a2e20f9f716835b7a88db8a4ca848228c
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-09-15 12:27:46 -0400
Commit message:

 check for only TRUE value from bfcneedsupdate
Package: ELViS
Commit: a8349a411cca614af445a12195d27e80b2876970
Author: jlee307@uthsc.edu <jlee307@clr0737.cn.isaac.utk.edu>
Date: 2025-09-15 12:15:40 -0400
Commit message:

 Minor bug fix in test script
Package: masstools
Commit: 482180971b397ca5754c067814e2b639c75e9380
Author: ShunPeng Bai <100484992+chain-buds@users.noreply.github.com>
Date: 2025-09-04 19:03:53 +0800
Commit message:

 Merge pull request #11 from chain-buds/dev

delete openwd, setwd_project, install_fastgit, get_project_wd function
Package: masstools
Commit: 2f454c188dc098636d354319abe5c84db7ee7361
Author: chain-buds <bspchemy@gmail.com>
Date: 2025-09-04 18:36:35 +0800
Commit message:

 delete four funcitons
Package: masstools
Commit: 7448c9a67582f34b461753aa67ff542c752737b3
Author: ShunPeng Bai <100484992+chain-buds@users.noreply.github.com>
Date: 2025-09-04 16:56:05 +0800
Commit message:

 Merge branch 'tidymass:main' into main
Package: masstools
Commit: 083725840fe7f75b5d28d8272a7af819b46fdde8
Author: chain-buds <bspchemy@gmail.com>
Date: 2025-08-23 14:57:14 +0800
Commit message:

 comment three unused functions
Package: masstools
Commit: 3868054684b7cb0dcc95895fc75ac7febf4954fc
Author: Ejo <yijiang@Ejos-MacBook-Pro.local>
Date: 2025-08-14 20:47:17 +0800
Commit message:

 update readme
Package: masstools
Commit: c205e08b6ea754907f32c68986ed337b558242bb
Author: Ejo <yijiang@Ejos-MacBook-Pro.local>
Date: 2025-08-14 20:30:00 +0800
Commit message:

 update date
Package: masstools
Commit: e4ea73de9cf29bb61d436c113a80a6bf4a497218
Author: ShunPeng Bai <100484992+chain-buds@users.noreply.github.com>
Date: 2025-08-08 21:03:52 +0800
Commit message:

 Merge pull request #9 from chain-buds/main

reply the requirments from reviewer
Package: masstools
Commit: 1d878eede35323a15e19d7b6258652d50ed33871
Author: chain-buds <bspchemy@gmail.com>
Date: 2025-08-08 21:01:45 +0800
Commit message:

 delete pkgdown, and modify the introduction, and add the scripts
Package: masstools
Commit: 7d89ec9ab4bc2d5e7db83c2ed3b5e3d0ca7f7dba
Author: chain-buds <bspchemy@gmail.com>
Date: 2025-07-25 20:38:56 +0800
Commit message:

 Merge branch 'main' of https://github.com/chain-buds/masstools
Package: masstools
Commit: c098b5db96438bc327a779ed2dcbb010d3509385
Author: chain-buds <bspchemy@gmail.com>
Date: 2025-07-25 20:38:40 +0800
Commit message:

 update
Package: masstools
Commit: d62abfd72f6d071b2f411eabed24213b0bd44889
Author: ShunPeng Bai <100484992+chain-buds@users.noreply.github.com>
Date: 2025-07-25 18:05:11 +0800
Commit message:

 Merge branch 'tidymass:main' into main
Package: masstools
Commit: 3341dfc44707f61c456489f45efca87679613eb7
Author: chain-buds <bspchemy@gmail.com>
Date: 2025-07-25 18:04:39 +0800
Commit message:

 update
Package: masstools
Commit: b7a2eb485d0d2d75f65ba89b1ad7363ea16e5cd3
Author: ShunPeng Bai <100484992+chain-buds@users.noreply.github.com>
Date: 2025-07-25 15:00:45 +0800
Commit message:

 Merge pull request #7 from chain-buds/main

delete cre role of xiaotao
Package: masstools
Commit: b1a629ebf2b186c48140fe2dddc18d0d374344b6
Author: chain-buds <bspchemy@gmail.com>
Date: 2025-07-25 14:58:50 +0800
Commit message:

 Merge branch 'main' of https://github.com/chain-buds/masstools
Package: masstools
Commit: a4f8f306b44d5820138a2ca3ebd650bd8cb7fbc2
Author: chain-buds <bspchemy@gmail.com>
Date: 2025-07-25 14:58:40 +0800
Commit message:

 delete cre role of xiaotao
Package: masstools
Commit: 769310d8babb9e7bb250fa332a46d3fe073f0e7a
Author: ShunPeng Bai <100484992+chain-buds@users.noreply.github.com>
Date: 2025-07-25 13:43:22 +0800
Commit message:

 Merge pull request #6 from chain-buds/main

add bai shunpeng to maintainer
Package: masstools
Commit: 5f7359fc0051f90fb76e41e5466b9d361ba076dc
Author: ShunPeng Bai <100484992+chain-buds@users.noreply.github.com>
Date: 2025-07-25 13:42:09 +0800
Commit message:

 Merge branch 'tidymass:main' into main
Package: masstools
Commit: 06ddc60291d43beb779ffc31a6000814643cdbc2
Author: chain-buds <bspchemy@gmail.com>
Date: 2025-07-25 13:41:19 +0800
Commit message:

 add bai shunpeng to maintainer
Package: masstools
Commit: 20c31ab84669378520f8f13a28ae55025027ce8c
Author: ShunPeng Bai <100484992+chain-buds@users.noreply.github.com>
Date: 2025-07-25 13:01:55 +0800
Commit message:

 Merge pull request #5 from chain-buds/main

fix version to requirement of Bioc
Package: masstools
Commit: ab78c050e23b177686dc13003c31c5bca4844054
Author: chain-buds <bspchemy@gmail.com>
Date: 2025-07-25 10:46:38 +0800
Commit message:

 Merge branch 'main' of https://github.com/chain-buds/masstools
Package: masstools
Commit: b70c3631e208e5431affe56c69ddaa2c7e77aec1
Author: chain-buds <bspchemy@gmail.com>
Date: 2025-07-25 10:46:09 +0800
Commit message:

 fix version to requirement of bioc
Package: masstools
Commit: f5f50ceec53f4c5bbc682a8f64d1e4506ce70db5
Author: Xiaotao Shen <shenxt1990@outlook.com>
Date: 2025-07-16 22:16:15 +0800
Commit message:

 Merge pull request #4 from chain-buds/main

fully checked
Package: masstools
Commit: 6a434126e4eed64b92b9041e9647b404aa716c67
Author: chain-buds <bspchemy@gmail.com>
Date: 2025-07-16 22:02:06 +0800
Commit message:

 full checked
Package: masstools
Commit: 931812a4c8a25294641e2277c2cf9ffc8386d71f
Author: jaspershen <shenxt1990@163.com>
Date: 2025-02-25 06:35:33 +0800
Commit message:

 add new functions
Package: masstools
Commit: 25b851580b54dff6c0f4c6431c18016790f9bc25
Author: jaspershen <shenxt1990@163.com>
Date: 2024-12-03 17:45:41 +0800
Commit message:

 fix bugs
Package: masstools
Commit: 8015641126a75fef506a29c7b0dd10819aebf496
Author: jaspershen <shenxt1990@163.com>
Date: 2024-02-07 11:27:11 -0800
Commit message:

 fix bugs
Package: masstools
Commit: 0b0474a84e302f97d7e4ba4dbe0d326e17ead91c
Author: Xiaotao Shen <shenxt1990@outlook.com>
Date: 2024-02-07 11:18:52 -0800
Commit message:

 Merge pull request #3 from amason30/main

add RTINMINUTES per massTools issue #2
Package: masstools
Commit: ff45e8fc8680ffd72689a23d60161adcf5a9b6b5
Author: amason30 <masonar@umich.edu>
Date: 2024-02-07 14:13:07 -0500
Commit message:

 add RTINMINUTES
Package: masstools
Commit: 95a6b2b9fd22b942d6fa511398b47b8cc2614d22
Author: jaspershen <shenxt1990@163.com>
Date: 2023-10-01 09:37:46 -0700
Commit message:

 update webiste
Package: masstools
Commit: d77a10e19b083637f3b7439eff5a07521aa302a3
Author: jaspershen <shenxt1990@163.com>
Date: 2023-09-30 20:32:28 -0700
Commit message:

 update
Package: masstools
Commit: c0dbcb4179af3ced7954ea9b610b8aed836ef8a9
Author: jaspershen <shenxt1990@163.com>
Date: 2023-09-30 19:48:12 -0700
Commit message:

 update
Package: masstools
Commit: 908eb6ad6c16cf69e618ac037f542e742456a3c0
Author: jaspershen <shenxt1990@163.com>
Date: 2023-09-30 19:34:16 -0700
Commit message:

 update documents
Package: masstools
Commit: 41417df352219954db714017f8d4d2603fe5ffd7
Author: jaspershen <shenxt1990@163.com>
Date: 2023-09-29 11:06:28 -0700
Commit message:

 update
Package: masstools
Commit: b3c73bcf9130048f0deabfb3ca2205cafc5a9fbe
Author: jaspershen <shenxt1990@163.com>
Date: 2023-04-28 22:51:27 -0700
Commit message:

 update
Package: masstools
Commit: 40d6e373e4ef986d000ac111e5a96b12d861e2b0
Author: jaspershen <shenxt1990@163.com>
Date: 2023-04-24 08:54:32 -0700
Commit message:

 update for license
Package: masstools
Commit: 146f222b67358da00b68a671d18877c0c736214d
Author: jaspershen <shenxt1990@163.com>
Date: 2023-04-23 15:15:24 -0700
Commit message:

 fix bugs according to cran reviewer
Package: masstools
Commit: 5cc8aabd17cea8728e7866607e74174287cb5493
Author: jaspershen <shenxt1990@163.com>
Date: 2023-04-22 01:47:22 -0700
Commit message:

 fix bug
Package: masstools
Commit: c4c59056621e504f007279a3588853f8f5f3760d
Author: jaspershen <shenxt1990@163.com>
Date: 2023-04-22 00:52:09 -0700
Commit message:

 fix bugs
Package: masstools
Commit: ad7219732372173d034b6ac36aa3323375fe98c6
Author: jaspershen <shenxt1990@163.com>
Date: 2022-09-21 13:22:13 -0700
Commit message:

 update