Registration Open for EuroBioC2025:
European Bioconductor Conference!

Menu

Source Code & Build Reports:

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

Development Version

Bioconductor packages under development:

Bioconductor has moved to GIT for contributed packages; the subversion logs are no longer active.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

GIT Logs

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

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

Package: CytoGLMM
Commit: 88567319176d0a0b606ce636d873c052c1417854
Author: ChristofSeiler <christof.seiler@gmail.com>
Date: 2025-07-14 19:59:36 +0200
Commit message:

 pkg mbest is back on CRAN

revert back changes removing function cytoglmm
Package: CytoGLMM
Commit: b535e61daa9b8fa78f567d9ec2581b7ed6a62acf
Author: ChristofSeiler <christof.seiler@gmail.com>
Date: 2025-07-14 19:34:26 +0200
Commit message:

 Merge remote-tracking branch 'upstream/devel' into devel
Package: CytoGLMM
Commit: 7217faf7c071b978055f18f67b6cc6f555a8144a
Author: ChristofSeiler <christof.seiler@gmail.com>
Date: 2025-07-14 19:24:38 +0200
Commit message:

 Revert "mbest package is back on CRAN again"

This reverts commit 8a7f71973924e14fafb718a9d84fd14ef9d7d8ad.
Package: CytoGLMM
Commit: 8a7f71973924e14fafb718a9d84fd14ef9d7d8ad
Author: ChristofSeiler <christof.seiler@gmail.com>
Date: 2025-07-14 19:23:33 +0200
Commit message:

 mbest package is back on CRAN again
Package: CytoGLMM
Commit: 156f0cf622bfd07dfb10e50fc83ef6e2154bc2df
Author: ChristofSeiler <christof.seiler@gmail.com>
Date: 2025-07-14 19:21:37 +0200
Commit message:

 Revert "removed mbest pkg"

This reverts commit d8f1c695d3c6c1e456aa2742854c1ff8929a2190.
Package: raer
Commit: b4e6968d238fb9fea162a66187d8206436bf2070
Author: Kent Riemondy <kent.riemondy@gmail.com>
Date: 2025-07-14 11:51:03 -0600
Commit message:

 update docs and fix import of GenomeInfoDb
Package: raer
Commit: a01535ca14f5a23cb9ed1862298d6c952fd6108c
Author: Kent Riemondy <kent.riemondy@gmail.com>
Date: 2025-07-14 06:45:42 -0600
Commit message:

 Merge remote-tracking branch 'upstream/devel' into devel
Package: raer
Commit: c11452f490f9d008e0ffc48f7d2008e8d3bac540
Author: Jay Hesselberth <jay.hesselberth@gmail.com>
Date: 2025-03-09 12:00:12 -0600
Commit message:

 Add air config files
Package: raer
Commit: ec005f8fdc03ad50bf55c9a73714fa4ab753441c
Author: Jay Hesselberth <jay.hesselberth@cuanschutz.edu>
Date: 2025-03-08 08:36:48 -0700
Commit message:

 Reformat with air (#123)
Package: BiocBaseUtils
Commit: ff01b1f01e1e838a62dc40f5570be9b7c10c7db9
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-07-14 13:12:23 -0400
Commit message:

 version bump 1.11.2
Package: BiocBaseUtils
Commit: 544a4d17e1f6c93f9b61b4fd62a1d271062d3cb9
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-07-14 13:12:17 -0400
Commit message:

 update unit test to changes in checkInstalled
Package: ELViS
Commit: 8f3ffe4dd4aae7c2e803b59281147e81790a0a4d
Author: jlee307@uthsc.edu <jlee307@login2.cn.isaac.utk.edu>
Date: 2025-07-14 12:39:27 -0400
Commit message:

 bug fix
Package: hiAnnotator
Commit: e641ca17d3f5d0cf1f221a8ca526a7d875c66a13
Author: lshep <lori.shepherd@roswellpark.org>
Date: 2025-07-14 12:36:23 -0400
Commit message:

 User requested deprecation
Package: proActiv
Commit: 1ed6022f1e51519f45a9ddfbad142c523136d703
Author: jleechung <joseph.lee@u.nus.edu>
Date: 2025-07-14 17:34:20 +0100
Commit message:

 Import GenomeInfoDbData
Package: TFEA.ChIP
Commit: 758108e832796207c8d76f25912fb61007fb2230
Author: yosra <yosraberrouayel@gmail.com>
Date: 2025-07-14 16:39:02 +0200
Commit message:

 added meta
Package: TFEA.ChIP
Commit: 8782227fc65bcfbb6c003466a8803d2b2e123678
Author: yosra <yosraberrouayel@gmail.com>
Date: 2025-07-09 11:33:45 +0200
Commit message:

 bump v
Package: TFEA.ChIP
Commit: 7631dc676984e99cab45cbed2d1150164cc7ce36
Author: yosra <yosraberrouayel@gmail.com>
Date: 2025-07-09 11:07:52 +0200
Commit message:

 fixed vignette
Package: MSstatsPTM
Commit: 243a336d99aa51b2e26817e3eb64711c52f28bc3
Author: tonywu1999 <wu.anthon@northeastern.edu>
Date: 2025-07-14 09:56:27 -0400
Commit message:

 version bump
Package: MSstatsPTM
Commit: 9eead60afd0281746a181fce13811ff57108a675
Author: tonywu1999 <wu.anthon@northeastern.edu>
Date: 2025-07-14 09:53:19 -0400
Commit message:

 fix(maxQuant): Remove unmodified peptides from PTM dataset (#116)
Package: MungeSumstats
Commit: 23e3b70226d001b4612adad7a92cb58e0f3eed3c
Author: Al-Murphy <alanmurph94@hotmail.com>
Date: 2025-07-14 08:49:05 -0400
Commit message:

 Bug fix long tests ieugwasr
Package: GladiaTOX
Commit: 35786620d0f6ce63a795e1b640a5c97f44782768
Author: scanopm
Date: 2025-07-14 14:33:15 +0200
Commit message:

 Bump version
</div>
Package: Chromatograms
Commit: 9a1758f00a77d96d6ef1fb10b2690bf7fbb03a45
Author: Philippine Louail <127301965+philouail@users.noreply.github.com>
Date: 2025-07-14 14:10:13 +0200
Commit message:

 Comments from Bioconductor submission
Package: GladiaTOX
Commit: 2fe9fa9a57edb5a01a1d98d45de58c63a293864a
Author: scanopm
Date: 2025-07-14 13:07:27 +0200
Commit message:

 Merge branch 'master' into devel
</div>
Package: GladiaTOX
Commit: 01c63a48494ccbeeaaa4a3b638d1866de1e85f69
Author: scanopm <Stephane.Cano@pmi.com>
Date: 2025-07-14 10:52:34 +0200
Commit message:

 Bump version
Package: GladiaTOX
Commit: a2558aad6bc8a097852bc581f7849c5830261e3e
Author: Stephane Cano <17638797+scanopm@users.noreply.github.com>
Date: 2025-07-14 08:44:44 +0200
Commit message:

 Merge pull request #4 from MichaelChirico/patch-1

Add URL to DESCRIPTION
Package: GladiaTOX
Commit: 95569575153c2a2df1dbb215832a484e1a1fec4c
Author: Michael Chirico <chiricom@google.com>
Date: 2025-07-11 10:56:14 -0700
Commit message:

 Add URL to DESCRIPTION
Package: GladiaTOX
Commit: 2833f371ff1e63e20da8e0e31c0b8118b036b852
Author: Sylvain Gubian <sylvain.gubian@pmi.com>
Date: 2023-08-25 16:55:27 +0200
Commit message:

 Merge pull request #3 from martin-g/replace-RMySQL-with-RMariaDB

Replace RMySQL with RMariaDB
Package: GladiaTOX
Commit: b0cd73256a361697a1bce4bda1053dbf9e4cf5e2
Author: Martin Tzvetanov Grigorov <mgrigorov@apache.org>
Date: 2023-08-15 13:34:23 +0300
Commit message:

 Replace RMySQL with RMariaDB

As per https://github.com/r-dbi/RMySQL#rmysql: NOTE: this package is being phased out in favor of the new RMariaDB package.

Bump the version to 1.12.0

Signed-off-by: Martin Tzvetanov Grigorov <mgrigorov@apache.org>
Package: GladiaTOX
Commit: 3b36a05017bd67d54a1610f945e0281c7e24918b
Author: scano <Stephane.Cano@pmi.com>
Date: 2022-04-07 13:44:54 +0200
Commit message:

 fix masked arg
Package: GladiaTOX
Commit: 694e0325c0686ef990915aa112abe7845a8668bf
Author: scano <Stephane.Cano@pmi.com>
Date: 2022-04-01 09:15:08 +0200
Commit message:

 Add missing documentation
Package: DuplexDiscovereR
Commit: 2d055bde5103e9099bbb3a004a7b12668bd74ca0
Author: EgorS <egorsemenchenko@gmail.com>
Date: 2025-07-14 11:12:47 +0200
Commit message:

 added roxygen doc for the new args
Package: SingleR
Commit: 0823a7bf4a119a41e75719cc32cd34300bf03680
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2025-07-13 23:16:42 -0700
Commit message:

 Bump to trigger recompilation for new C++ libraries.
Package: scrapper
Commit: 3924f5b630bc4c65d28ab5a6e5b5ad385a7b05bf
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2025-07-13 23:16:08 -0700
Commit message:

 Bump to trigger recompilation for new C++ libraries.
Package: beachmat.tiledb
Commit: c0c20e1d4ebac8aa5bd59e882a141f9fa850438a
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2025-07-13 22:24:42 -0700
Commit message:

 Namespace fixed-width types for standards-compliance.
Package: beachmat.tiledb
Commit: 20cfa38943b3f834b93634d0dd509fbafa2ccb63
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2025-07-13 22:19:22 -0700
Commit message:

 Merge remote-tracking branch 'upstream/devel'
Package: beachmat.tiledb
Commit: 51d92094f8e6c694300afd14ee85917c9cdcb0e0
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2025-01-06 10:35:10 -0800
Commit message:

 Added BBS badges to the README.
Package: beachmat.hdf5
Commit: 80e7ae65cb5ac71b7b759356d0236540cbe56a7b
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2025-07-13 18:33:57 -0700
Commit message:

 Use more appropriate integer types in the C++ code.

Also include the required standard headers and namespace fixed-width types.
Package: beachmat
Commit: 6cf7450fff8cc7599b7d10d5d5e403bc95ec2b5a
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2025-07-13 18:19:54 -0700
Commit message:

 Updates for the latest tatami library.

The biggest change is the use of a interface for the delayed isometric
operations, which streamlines compilation by avoiding redundancy.

Also some minor fixes to include standard headers, avoid integer overflow.
Package: assorthead
Commit: ae0ac1926770110e6a6977ec1aeded7c6f9fdf5d
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2025-07-13 18:33:03 -0700
Commit message:

 Updated versions of the vendored tatami libraries.

This also requires updates to libscran libraries for scrapper to build.
Package: QTLExperiment
Commit: 38de9a9a7b0c90b878e4ad4d371cce47c1928429
Author: dunstone-a <amelia.dunstone@gmail.com>
Date: 2025-07-14 14:29:44 +1000
Commit message:

 Update NEWS and version bump
Package: multistateQTL
Commit: eef556dbb2bb73c8e944f1d47656e7c2f5d43d44
Author: dunstone-a <amelia.dunstone@gmail.com>
Date: 2025-07-14 14:27:18 +1000
Commit message:

 Updated NEWS and version bump
Package: multistateQTL
Commit: 1f0a24b7d2d544376c1900cf470cb4376c8bba0b
Author: dunstone-a <amelia.dunstone@gmail.com>
Date: 2025-07-14 14:04:03 +1000
Commit message:

 Update testing to work with upcoming ggplot2 update
- Related to ggplot2 major update 4.0.0.
- Changed expect_equal() with class() to the new ggplot2::is_ggplot()
Package: QTLExperiment
Commit: eb50d428c1aa8d428558324916af060bbbb24b4b
Author: dunstone-a <amelia.dunstone@gmail.com>
Date: 2025-07-14 13:59:32 +1000
Commit message:

 Merge branch 'devel' of https://gitlab.svi.edu.au/biocellgen-public/qtlexperiment into devel
Package: QTLExperiment
Commit: 191f0b8199708f985603c3201325075b5ac8bd4e
Author: dunstone-a <amelia.dunstone@gmail.com>
Date: 2025-07-14 13:58:46 +1000
Commit message:

 Update to subsetting
- Make subset a generic function
- Typo in rowData documentation
- Trying to remove warnings in subsetting documentation
Package: QTLExperiment
Commit: a792069924792f705cdf007d641a1c40187d2fd4
Author: Amelia Dunstone <amelia.dunstone@svi.edu.au>
Date: 2025-05-27 16:22:14 +1000
Commit message:

 Delete .gitlab-ci.yml
Package: QTLExperiment
Commit: ea52732dd7dd5619e47900aa9b842e1ccd7f54ef
Author: Amelia Dunstone <amelia.dunstone@svi.edu.au>
Date: 2025-05-27 16:20:18 +1000
Commit message:

 Update .gitlab-ci.yml file
Package: QTLExperiment
Commit: c9858e187632511a24402d043cfecb22cc74f5e2
Author: Amelia Dunstone <amelia.dunstone@svi.edu.au>
Date: 2025-05-27 16:17:04 +1000
Commit message:

 Update .gitlab-ci.yml file
Package: QTLExperiment
Commit: 43e6119b2ce7971446373711b3e1953ee64b1863
Author: Amelia Dunstone <amelia.dunstone@svi.edu.au>
Date: 2025-05-27 16:16:22 +1000
Commit message:

 Update .gitlab-ci.yml file
Package: QTLExperiment
Commit: dacd8e50c6247bf9b385c79b8dc979171ef8f51e
Author: Amelia Dunstone <amelia.dunstone@svi.edu.au>
Date: 2025-05-27 16:11:00 +1000
Commit message:

 Update .gitlab-ci.yml file
Package: QTLExperiment
Commit: 6524779805910898221199df5c6870d923333388
Author: Amelia Dunstone <amelia.dunstone@svi.edu.au>
Date: 2025-05-27 15:59:12 +1000
Commit message:

 Update .gitlab-ci.yml file
Package: MerfishData
Commit: 321ff75fe7973f5aa47635707e11844f8e048c60
Author: lgeistlinger <ludwig.geistlinger@gmail.com>
Date: 2025-07-13 19:51:56 -0400
Commit message:

 fix SpatialExperiment example
Package: CPSM
Commit: 372c80eb378f0b02d3e6d80653233d14d3792837
Author: Harpreet Kaur <hks04180@gmail.com>
Date: 2025-07-13 17:59:42 -0400
Commit message:

 Updated vignettes/CPSM.Rmd to change the date
Package: CPSM
Commit: 571cde66b3087fadb33f287985d9a03f99b5d2df
Author: Harpreet Kaur <hks04180@gmail.com>
Date: 2025-07-13 17:53:33 -0400
Commit message:

 Merge save-1.1.3-changes into devel, resolved conflicts
Package: CPSM
Commit: f9e15a35bab752cdc31a25c708e736cb7bac3c70
Author: Harpreet Kaur <hks04180@gmail.com>
Date: 2025-07-13 17:48:18 -0400
Commit message:

  Updated R/km_overlay_plot_f.R to improve figure; updated R/MTLR_pred_model_f.R  to make a corection;  updated  DESCRIPTION to update contributor and data license ;  Bump version to 1.1.3
Package: CPSM
Commit: 40b13076b0b771a8e3abfda2a4a77769c654093a
Author: Harpreet Kaur <hks04180@gmail.com>
Date: 2025-07-13 17:44:24 -0400
Commit message:

  Updated R/km_overlay_plot_f.R to improve figure; updated R/MTLR_pred_model_f.R  to make a corection;  updated  DESCRIPTION to update contributor and data license ;  Bump version to 1.1.3
Package: CPSM
Commit: 43007dfe4e11349de6fe45170c3470bcdfa305a0
Author: Harpreet Kaur <hks04180@gmail.com>
Date: 2025-07-13 17:28:14 -0400
Commit message:

  Updated R/km_overlay_plot_f.R to improve figure; updated  DESCRIPTION to update contributor and data license ;  Bump version to 1.1.3
Package: CPSM
Commit: 3e08166935b3247acfad4712f63817aca642a06d
Author: Harpreet Kaur <hks04180@gmail.com>
Date: 2025-07-13 17:20:35 -0400
Commit message:

 Work in progress: save local changes before rebase
Package: CPSM
Commit: 1fe64fa5961b0f481d784338fc25495c9b462de4
Author: Harpreet Kaur <hks04180@gmail.com>
Date: 2025-07-13 17:11:02 -0400
Commit message:

 Move CC0 license to inst/licenses to avoid R loading error
Package: CPSM
Commit: f8b074e84e5f5f75e09656e21652b1313af0b398
Author: Harpreet Kaur <hks04180@gmail.com>
Date: 2025-07-13 17:01:59 -0400
Commit message:

  Updated R/km_overlay_plot_f.R to improve figure; updated  DESCRIPTION to update contributor and data license ;  Bump version to 1.1.3
Package: CPSM
Commit: 486ed41b668ef0a6a96d73924c4bfb693195e7fa
Author: Harpreet kaur <46756503+hks5august@users.noreply.github.com>
Date: 2025-07-11 10:20:50 -0400
Commit message:

 Add files via upload
Package: CPSM
Commit: ae023d94ecedc7fd0093d8e82435e43752bf3160
Author: Harpreet Kaur <hks04180@gmail.com>
Date: 2025-07-09 14:01:09 -0400
Commit message:

 Update km_overlay_plot_f.R  function and documentation, DESCRIPTION, NEWS.md vignettes/CPSM.Rmd , version bumped to 1.1.3
Package: CPSM
Commit: eff8e6c499b7bd610135c9acc2abb08eeb883632
Author: Harpreet Kaur <hks04180@gmail.com>
Date: 2025-07-09 13:33:18 -0400
Commit message:

 Update km_overlay_plot_f.R  function and documentation, DESCRIPTION, NEWS.md vignettes/CPSM.Rmd
Package: CPSM
Commit: 72181bd3ed8c8f1071661141623ac200b62a9e3e
Author: Harpreet Kaur <hks04180@gmail.com>
Date: 2025-07-09 13:32:17 -0400
Commit message:

 Update km_overlay_plot_f.R  function and documentation, DESCRIPTION, NEWS.md vignettes/CPSM.Rmd
Package: CPSM
Commit: f9ffdaf685db48124f0e9efc8c45cf3c61aa119f
Author: Harpreet Kaur <hks04180@gmail.com>
Date: 2025-07-01 13:46:52 -0400
Commit message:

 Update R/km_overlay_plot_f.R file to improve image
Package: CPSM
Commit: ae9d6810c0e135b17a1246d0d5d7649b3759c2ce
Author: Harpreet kaur <46756503+hks5august@users.noreply.github.com>
Date: 2025-05-05 13:16:52 -0400
Commit message:

 Update README.md
Package: CPSM
Commit: b2626007fb119c630170589a957dd5fb2748f811
Author: Harpreet kaur <46756503+hks5august@users.noreply.github.com>
Date: 2025-05-05 13:16:24 -0400
Commit message:

 Update README.md
Package: CPSM
Commit: a413701cda77105e34ae40e024c3a965b34f0ebf
Author: Harpreet kaur <46756503+hks5august@users.noreply.github.com>
Date: 2025-05-05 13:15:02 -0400
Commit message:

 Update README.md
Package: CPSM
Commit: c83e2fe030a2c13aa6deaaad33ea5926bcd92b8b
Author: Harpreet kaur <46756503+hks5august@users.noreply.github.com>
Date: 2025-05-05 13:11:37 -0400
Commit message:

 Update README.md
Package: CPSM
Commit: edfefe0dc25a5afb3227e41956d108a8c10e1f5a
Author: Harpreet kaur <46756503+hks5august@users.noreply.github.com>
Date: 2025-05-05 13:11:15 -0400
Commit message:

 Update README.md
Package: CPSM
Commit: d7247a01d0585ed9ea99099e0bd1f9cc22e82584
Author: Harpreet kaur <46756503+hks5august@users.noreply.github.com>
Date: 2025-05-01 19:30:59 -0400
Commit message:

 Add files via upload
Package: CPSM
Commit: 30933eb8fe3fe8af75e11258aba371a75bb747dd
Author: Harpreet kaur <46756503+hks5august@users.noreply.github.com>
Date: 2025-04-29 10:46:34 -0400
Commit message:

 Update CPSM.Rmd
Package: CPSM
Commit: 945559261813c96dc3d916825da6e3ef9e15e880
Author: Harpreet kaur <46756503+hks5august@users.noreply.github.com>
Date: 2025-04-29 10:28:43 -0400
Commit message:

 Update CPSM.Rmd
Package: CPSM
Commit: bc708256c2a68fab78b8e969a48a158b5178fcbe
Author: Harpreet kaur <46756503+hks5august@users.noreply.github.com>
Date: 2025-04-29 10:27:59 -0400
Commit message:

 Update CPSM.Rmd
Package: CPSM
Commit: 6ef45f14c833a09bd107bc07f0a09134564e373b
Author: Harpreet kaur <46756503+hks5august@users.noreply.github.com>
Date: 2025-04-28 19:06:13 -0400
Commit message:

 Update README.md
Package: CPSM
Commit: e92e787e934a68c3d7b969eaceea860ff9d04209
Author: Harpreet kaur <46756503+hks5august@users.noreply.github.com>
Date: 2025-04-26 21:49:06 -0400
Commit message:

 Add files via upload
Package: CPSM
Commit: 29db77cd2708de171563d594ed9d54b620a2eddf
Author: Harpreet kaur <46756503+hks5august@users.noreply.github.com>
Date: 2025-04-25 14:01:07 -0400
Commit message:

 Update README.md
Package: CPSM
Commit: fe0dd0f2643d4c7d123336763b7cc29533d07935
Author: Harpreet kaur <46756503+hks5august@users.noreply.github.com>
Date: 2025-04-25 13:59:22 -0400
Commit message:

 Add files via upload
Package: CPSM
Commit: 900b2c42e1ea72ede3066b2151c19cf411d2ea15
Author: Harpreet kaur <46756503+hks5august@users.noreply.github.com>
Date: 2025-04-25 13:47:40 -0400
Commit message:

 Update .gitignore
Package: CPSM
Commit: abf5949a2e208ecdb157e99c53f9e32e461f174d
Author: Harpreet kaur <46756503+hks5august@users.noreply.github.com>
Date: 2025-04-25 13:46:45 -0400
Commit message:

 Update DESCRIPTION
Package: CPSM
Commit: 30ffe9576f233ea06a4ac977c63808dc21b3afae
Author: Harpreet kaur <46756503+hks5august@users.noreply.github.com>
Date: 2025-04-25 08:34:31 -0400
Commit message:

 Update CPSM.Rmd
Package: CPSM
Commit: b185800229e33200ccafe2059bff0502f80f3ca6
Author: Harpreet kaur <46756503+hks5august@users.noreply.github.com>
Date: 2025-04-25 01:47:20 -0400
Commit message:

 Update DESCRIPTION
Package: CPSM
Commit: a77c3e79c3b423f1c52c6cdc25e9a07f62849244
Author: Harpreet kaur <46756503+hks5august@users.noreply.github.com>
Date: 2025-04-24 22:20:02 -0400
Commit message:

 Add files via upload
Package: CPSM
Commit: 4e1bd98e68bc45cc59875cdc3406353f934cfdf3
Author: Harpreet kaur <46756503+hks5august@users.noreply.github.com>
Date: 2025-04-24 22:19:09 -0400
Commit message:

 Add files via upload
Package: CPSM
Commit: ea1381cbfae91720cbfffab34c871de26df668ef
Author: Harpreet kaur <46756503+hks5august@users.noreply.github.com>
Date: 2025-04-24 22:18:50 -0400
Commit message:

 Add files via upload
Package: CPSM
Commit: 6f4e584f2687827f661bf04c018d8b892dc7f7fe
Author: Harpreet kaur <46756503+hks5august@users.noreply.github.com>
Date: 2025-04-24 22:18:23 -0400
Commit message:

 Add files via upload
Package: CPSM
Commit: 605dc2b486a46327d52514a349e2dfdb0ce55314
Author: Harpreet kaur <46756503+hks5august@users.noreply.github.com>
Date: 2025-04-24 22:17:59 -0400
Commit message:

 Add files via upload
Package: CPSM
Commit: 2270dbd3d8b6de8492532b723c907aa6cbf80dd7
Author: Harpreet kaur <46756503+hks5august@users.noreply.github.com>
Date: 2025-04-24 22:16:57 -0400
Commit message:

 Update README.md
Package: CPSM
Commit: 841e69b7b66a38e9f62231686dd977bf46185994
Author: Harpreet kaur <46756503+hks5august@users.noreply.github.com>
Date: 2025-04-24 22:15:20 -0400
Commit message:

 Add files via upload
Package: CPSM
Commit: 7fba21890278ed299e5af9c5d1e6245c0740f662
Author: Harpreet kaur <46756503+hks5august@users.noreply.github.com>
Date: 2025-04-24 22:13:55 -0400
Commit message:

 Add files via upload
Package: CPSM
Commit: 7b42e2b345108c72c92f73b097bfb2d0473eb4e4
Author: Harpreet kaur <46756503+hks5august@users.noreply.github.com>
Date: 2025-04-16 15:46:12 -0400
Commit message:

 Update DESCRIPTION
Package: CPSM
Commit: 2addcd7854ba72f26744ae33dda4fa3e57ea3bfb
Author: Harpreet kaur <46756503+hks5august@users.noreply.github.com>
Date: 2025-03-11 20:54:11 -0400
Commit message:

 Add files via upload
Package: CPSM
Commit: 03741fef23f812d77b69223b0731acdf9eb6ba4f
Author: Harpreet kaur <46756503+hks5august@users.noreply.github.com>
Date: 2025-03-01 14:09:03 -0500
Commit message:

 Add files via upload
Package: CPSM
Commit: caeec335910d92411e1c8a8edee7e8ca8c72b238
Author: Harpreet kaur <46756503+hks5august@users.noreply.github.com>
Date: 2025-03-01 13:24:34 -0500
Commit message:

 Delete tests/testthat/Rplots.pdf
Package: CPSM
Commit: 589be70c0ea0b79c8f4dd8a45ef1353e2a86c25c
Author: Harpreet kaur <46756503+hks5august@users.noreply.github.com>
Date: 2025-03-01 13:14:33 -0500
Commit message:

 Add files via upload
Package: CPSM
Commit: e18323a055ec4038873df67f166e766d7059776b
Author: Harpreet kaur <46756503+hks5august@users.noreply.github.com>
Date: 2025-03-01 13:13:38 -0500
Commit message:

 Add files via upload
Package: CPSM
Commit: cc161468e6bd76dcb3106bd7fc4970cbf8098c09
Author: Harpreet kaur <46756503+hks5august@users.noreply.github.com>
Date: 2025-03-01 12:50:01 -0500
Commit message:

 Update README.md
Package: CPSM
Commit: 9ad498bfd861ee15d951229c7faea179619b057e
Author: Harpreet kaur <46756503+hks5august@users.noreply.github.com>
Date: 2025-03-01 12:48:50 -0500
Commit message:

 Update README.md
Package: CPSM
Commit: 8b8832bea835cdf6d6855a6389ac6896a49fe6d9
Author: Harpreet kaur <46756503+hks5august@users.noreply.github.com>
Date: 2025-03-01 12:45:09 -0500
Commit message:

 Add files via upload
Package: CPSM
Commit: eda169e6a332c9a76f36c40a93a76879ea300097
Author: Harpreet kaur <46756503+hks5august@users.noreply.github.com>
Date: 2025-02-28 13:54:07 -0500
Commit message:

 Add files via upload
Package: CPSM
Commit: f3e3a070293f3f3bb8032bf18186056f01aec1ca
Author: Harpreet kaur <46756503+hks5august@users.noreply.github.com>
Date: 2025-02-24 14:39:15 -0500
Commit message:

 Delete CPSM.Rproj
Package: CPSM
Commit: 8f061efedef581b8893d187a7bec48a5e4910dc7
Author: Harpreet kaur <46756503+hks5august@users.noreply.github.com>
Date: 2025-02-16 14:05:02 -0500
Commit message:

 Update .gitignore
Package: CPSM
Commit: 9beff0b4b4dc8df645da94ddbfe4979e2c359cf5
Author: Harpreet kaur <46756503+hks5august@users.noreply.github.com>
Date: 2025-02-16 13:58:21 -0500
Commit message:

 Update README.md
Package: CPSM
Commit: 2ccddd7718c327fe3ee68aa26db0ba749ed8c9a8
Author: Harpreet kaur <46756503+hks5august@users.noreply.github.com>
Date: 2025-02-16 13:55:58 -0500
Commit message:

 Add files via upload
Package: CPSM
Commit: 267fc8bba5b9a0a796ed2bf9fa27194f66729d4d
Author: Harpreet kaur <46756503+hks5august@users.noreply.github.com>
Date: 2025-01-23 14:05:24 -0500
Commit message:

 Update DESCRIPTION
Package: CATALYST
Commit: 0262c36926dc0723d5286ac346d793183a179c0b
Author: HelenaLC <helena@crowell.eu>
Date: 2025-07-13 15:49:24 +0200
Commit message:

 ver bump
Package: CATALYST
Commit: ec583f61a5e74e22b4888f242cd83296090e575c
Author: HelenaLC <helena@crowell.eu>
Date: 2025-07-13 15:25:52 +0200
Commit message:

 ggplot2 goes S7-related fixes
Package: CATALYST
Commit: 090f6443985b4285c6bebc0589fc57f3e4ae566b
Author: HelenaLC <helena@crowell.eu>
Date: 2025-07-13 14:47:57 +0200
Commit message:

 ggplot2 goes S7-related fixes
Package: cn.farms
Commit: b3efc79d98212f2ffc8c51b80668750de540090c
Author: mitterec <a.mitterecker@gmail.com>
Date: 2025-07-13 00:46:51 +0200
Commit message:

 Bump version number
Package: enrichplot
Commit: ae61a6fe932763eaceb6a75815b97c10c24ae815
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2025-07-12 23:40:13 +0800
Commit message:

 fixed R check, #325
Package: enrichplot
Commit: f763729016e8687d12bfca29d1af31ff913169d7
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2025-07-12 23:06:11 +0800
Commit message:

 Merge branch 'devel' of github.com:YuLab-SMU/enrichplot into devel
Package: enrichplot
Commit: e7e597ff6022a02b75c30e9c08539b80cf6afc07
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2025-07-12 23:04:33 +0800
Commit message:

 new parameters in treeplot
Package: enrichplot
Commit: a07f4ec8bfa0b3df59baa3de0acc55913f2bb6ae
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2025-07-12 23:03:06 +0800
Commit message:

 more flexible to transform color scale and allows overwrite previous setting, #316
Package: enrichplot
Commit: 6ab14d286b6103685cd2f3928340430e85a933e6
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2025-07-12 22:49:38 +0800
Commit message:

 Merge pull request #321 from davorvr/devel

Fix BP ontology check
Package: enrichplot
Commit: 058cdef0b06ca50ddccf4e5d6e8ee25cee6bc39e
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2025-07-12 22:26:20 +0800
Commit message:

 Merge pull request #316 from ThomasKAtkins/color_transform

Added log transformation argument for color scale
Package: enrichplot
Commit: 6ef62ff50ac6605a42e12364e139da04b37dd5f3
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2025-07-12 22:26:06 +0800
Commit message:

 Update utilities.R

restore color scheme
Package: enrichplot
Commit: 6604348bd95c618d9ac4e8d2a9793ae302d7a3f8
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2025-07-12 22:20:12 +0800
Commit message:

 Merge pull request #323 from NastiaSkuba/patch-1

Update treeplot.R
Package: enrichplot
Commit: c20bedea2dfdc8fe9ce21d1182ccff231b5007c3
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2025-07-12 22:17:34 +0800
Commit message:

 Merge pull request #325 from SciLiciumTheo/master

Add support for different leave/tip and clade font size in treeplot.R
Package: enrichplot
Commit: cde28158eece925392f4cd04758d2a8c6b598363
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2025-07-12 17:45:28 +0800
Commit message:

 new parameters in `gseaplot2()`, #774
Package: enrichplot
Commit: 788f49da0bbe13ddb7c5346f3761f768ac7326d4
Author: SciLiciumTheo <101104633+SciLiciumTheo@users.noreply.github.com>
Date: 2025-06-11 12:19:37 +0200
Commit message:

 FIX treeplot.R linting
Package: enrichplot
Commit: 3ca4aa94305335e1c515d9a7a61d2cdf36aba178
Author: SciLiciumTheo <101104633+SciLiciumTheo@users.noreply.github.com>
Date: 2025-06-11 12:16:56 +0200
Commit message:

 FEAT treeplot.R add support for different font size for leaves and clades

After https://github.com/YuLab-SMU/enrichplot/issues/324
Package: enrichplot
Commit: 20f09f7bf93704b0f93cb3f4d65833e8269f8ff0
Author: Nastia <84533119+NastiaSkuba@users.noreply.github.com>
Date: 2025-06-04 19:20:01 +0200
Commit message:

 Update treeplot.R

This change solves the problem of inconsistent simplified labels for treeplot. Now, the roots and cluster_color are in same order.
Package: enrichplot
Commit: 4ddf63a86f05856863d68d858b49ce2a53b070d2
Author: Davor Virag <42250444+davorvr@users.noreply.github.com>
Date: 2025-05-19 22:16:40 +0200
Commit message:

 Fix BP ontology check

BF -> BP typo fix
Package: enrichplot
Commit: 48b95e2c573e2cb4398ae0d74a2d497d621be264
Author: ThomasKAtkins <32600420+ThomasKAtkins@users.noreply.github.com>
Date: 2025-03-26 14:29:18 -0400
Commit message:

 Added log transformation argument for color scale
Package: OmnipathR
Commit: ee6fdf167b4f9ec181781d2113f79cf680c82a4b
Author: deeenes <turei.denes@gmail.com>
Date: 2025-07-12 14:36:56 +0200
Commit message:

 Bump version: 3.17.0 → 3.17.1
Package: OmnipathR
Commit: 623655b34649a538d1def163053469451ea1822e
Author: deeenes <turei.denes@gmail.com>
Date: 2025-07-12 14:36:52 +0200
Commit message:

 propagate bioc version bump to `bump2version`
Package: OmnipathR
Commit: a72383e532c3cbb81a6deaf38d00530570e64aa8
Author: deeenes <turei.denes@gmail.com>
Date: 2025-07-12 14:35:43 +0200
Commit message:

 Merge branch 'devel' of git.bioconductor.org:packages/OmnipathR into devel
Package: OmnipathR
Commit: 02b2582018051ef07173b1ef717a93374256eca4
Author: deeenes <turei.denes@gmail.com>
Date: 2025-05-22 13:00:44 +0200
Commit message:

 `metalinks`: moved from `figshare` to `rescued.omnipathdb.org`
Package: openPrimeR
Commit: 8e59976cd8f4cf5fb21ee834a0ac55512114f86a
Author: Matthias Doering <matthias-doering@gmx.de>
Date: 2025-07-12 11:57:47 +0200
Commit message:

 version bump
Package: openPrimeR
Commit: 0c6f767945ec499eefc83747e3aecaaa24e4ebee
Author: Matthias Doering <matthias-doering@gmx.de>
Date: 2025-07-12 11:57:26 +0200
Commit message:

 Merge remote-tracking branch 'bioc/devel' into devel
Package: openPrimeR
Commit: 1994e5e0379cb080bce277aae8685b0fbfd208fe
Author: Matthias Doering <matthias-doering@gmx.de>
Date: 2025-07-12 11:54:53 +0200
Commit message:

 fix strsplit error when reading fasta file for R4.5

strsplit had extraneous argument
Package: cn.farms
Commit: f8ac600a0aca88e515cba7e7791ca73c9241baf4
Author: mitterec <a.mitterecker@gmail.com>
Date: 2025-07-12 00:00:14 +0200
Commit message:

 Fix error with Calloc
Package: SpatialOmicsOverlay
Commit: 33cf5fb0fc60f931ba8af017c65fa4788be5444e
Author: Maddy Griswold <mgriswold@nanostring.com>
Date: 2025-07-11 11:39:29 -0600
Commit message:

 update to bioc version
Package: SpatialOmicsOverlay
Commit: 69260f76ada78adac8256aeb20cedbdc2ca4fa72
Author: Maddy Griswold <40255151+maddygriz@users.noreply.github.com>
Date: 2025-05-19 09:33:20 -0600
Commit message:

 Update to Bruker signature
Package: SpatialOmicsOverlay
Commit: 534b0b4928d540328ce296aa771ed90f2c3b3b92
Author: Maddy Griswold <40255151+maddygriz@users.noreply.github.com>
Date: 2025-05-12 09:18:54 -0600
Commit message:

 Merge pull request #60 from Nanostring-Biostats/PI25

cache resources
Package: SpatialOmicsOverlay
Commit: d89db3982924ce0e99f09c40e1355179ad4751f4
Author: Maddy Griswold <mgriswold@nanostring.com>
Date: 2025-04-29 19:39:54 +0000
Commit message:

 cache resources
Package: SpatialOmicsOverlay
Commit: 3cabce1ae6bf8c1b686af38e22cf60f6ea1c8fb9
Author: Maddy Griswold <40255151+maddygriz@users.noreply.github.com>
Date: 2024-12-16 10:54:37 -0700
Commit message:

 update to bruker support email
Package: GeoMxWorkflows
Commit: 0844c8d5055aac6b3c5716c62082b9c10417c9f1
Author: Maddy Griswold <mgriswold@nanostring.com>
Date: 2025-07-11 11:34:52 -0600
Commit message:

 update to bioc version
Package: GeoMxWorkflows
Commit: b4780a28378fa99e9f60ba3b0db35a8ed9f0a736
Author: Maddy Griswold <40255151+maddygriz@users.noreply.github.com>
Date: 2025-07-11 11:33:33 -0600
Commit message:

 Merge pull request #34 from Nanostring-Biostats/fixTypo

fix typo
Package: GeoMxWorkflows
Commit: de5e42e0afb93e475c8a66c7ff6ecd2c406738db
Author: Maddy Griswold <mgriswold@nanostring.com>
Date: 2025-07-11 10:28:08 -0600
Commit message:

 Merge remote-tracking branch 'upstream/devel'
Package: GeoMxWorkflows
Commit: 42686e6aac11fb1fbf54985390a880de1baf9fc0
Author: Maddy Griswold <mgriswold@nanostring.com>
Date: 2025-06-19 21:30:12 +0000
Commit message:

 fix typo
Package: GeoMxWorkflows
Commit: 5a5249b6db344c4ad618d965213deaa0ba5c82cb
Author: Maddy Griswold <40255151+maddygriz@users.noreply.github.com>
Date: 2025-05-19 09:40:42 -0600
Commit message:

 Update to Bruker signature
Package: GeoMxWorkflows
Commit: d6d8e63559b806d268764c081d6f3d4841608de6
Author: Maddy Griswold <40255151+maddygriz@users.noreply.github.com>
Date: 2024-12-16 11:05:56 -0700
Commit message:

 update to bruker support email
Package: ggtree
Commit: 1444d4d77f1275b0ac0981d8ee649551b6b5cb9e
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2025-07-12 00:45:38 +0800
Commit message:

 compatible with ggplot2 v4.0.0
Package: ggtree
Commit: 8371532a9032b2aa55c11d6d21d61f24409233c6
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2025-07-12 00:31:16 +0800
Commit message:

 Merge pull request #657 from xiangpin/master

consistency with upcoming ggplot2 version
Package: ggtree
Commit: 1193ff86154ff3482d9e34605f35ed8a1befcef0
Author: xiangpin <xshuangbin@163.com>
Date: 2025-07-11 15:43:19 +0800
Commit message:

 using is_waiver codes avoid error when using old ggplot2 version
Package: ggtree
Commit: aca415cb843d3d77617fcd14615d836bdcf6faca
Author: xiangpin <xshuangbin@163.com>
Date: 2025-06-26 14:35:39 +0800
Commit message:

 avoid the error that could not find function is.waive
Package: ggtree
Commit: 88dc31bbd61e73460cb2d1c29a57bd77ec26966c
Author: xiangpin <xshuangbin@163.com>
Date: 2025-06-20 19:51:51 +0800
Commit message:

 Merge branch 'master' of https://github.com/xiangpin/ggtree
Package: ggtree
Commit: 1adac1dd1124fff7fd70a8f585629c8c517dbf2c
Author: xiangpin <xshuangbin@163.com>
Date: 2025-06-20 19:47:34 +0800
Commit message:

 consistency with upcoming ggplot2 version
Package: ggtree
Commit: 2b366a1c3cebb4e2ff7008be26c48291f7b73d66
Author: xiangpin <xshuangbin@163.com>
Date: 2025-06-20 18:10:24 +0800
Commit message:

 consistency with upcoming ggplot2 version
Package: ggtree
Commit: 7b5e5ee1447549d500ef07c30f1c6183ef8f1319
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2025-04-17 09:39:31 +0800
Commit message:

 update bioc version
Package: BiocPkgTools
Commit: eb8199ff7423d0936bb65b5be989df5983f20e9e
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-07-11 12:43:26 -0400
Commit message:

 version bump 1.27.7
Package: BiocPkgTools
Commit: 0064c71ea0db54b2aa867aedc1868483b54e2405
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-07-11 12:14:21 -0400
Commit message:

 use |> pipes
Package: BiocPkgTools
Commit: 3c26f12bf306fef8462404548fc460d99862833e
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-07-11 12:14:03 -0400
Commit message:

 use <- assignment
Package: BiocPkgTools
Commit: f5a0bce254e2d8e61572f66f432c3a0cabdbd731
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-07-11 12:09:14 -0400
Commit message:

 use igraph >= 2.0.0

- is_igraph
- graph_from_graphnel
Package: gDRimport
Commit: fd3c2c1696806db80d5d2f149bdef3223a31db68
Author: Bartek <32614650+bczech@users.noreply.github.com>
Date: 2025-07-11 17:45:05 +0200
Commit message:

 Merge pull request #105 from gdrplatform/GDR-3061

Gdr 3061
Package: gDRimport
Commit: ebf85b0849745b7fda17b9a8f49461164575c2d8
Author: Bartek Czech <bartosz.w.czech@gmail.com>
Date: 2025-07-11 17:12:58 +0200
Commit message:

 refactor: update duration logic
Package: gDRimport
Commit: 90529f4e02264c29316e4e39f40a36a0b3abe680
Author: Bartek Czech <bartosz.w.czech@gmail.com>
Date: 2025-07-11 16:39:01 +0200
Commit message:

 chore: bump version and update NEWS.md
Package: gDRimport
Commit: e7dd3a2df1ac98e929d8e13fd210f309e0cdd3d1
Author: Bartek Czech <bartosz.w.czech@gmail.com>
Date: 2025-07-11 16:38:46 +0200
Commit message:

 refactor: restore run managing
Package: gDRimport
Commit: c2008fd3eac0b440340ea5695b69a5f5878d4af7
Author: bczech <bartosz.czech@contractors.roche.com>
Date: 2025-07-10 09:10:27 -0700
Commit message:

 chore: bump version and update NEWS.md
Package: gDRimport
Commit: a4468f8ad344bb2981f69baaf52f329e1fd9ac6c
Author: bczech <bartosz.czech@contractors.roche.com>
Date: 2025-07-10 09:10:23 -0700
Commit message:

 refactor: update logic
Package: gDRimport
Commit: c721f6824a2a2eebb6283a6f7831d19b2146ac69
Author: Bartek <32614650+bczech@users.noreply.github.com>
Date: 2025-05-15 12:36:25 +0200
Commit message:

 Merge pull request #104 from gdrplatform/GDR-2986

Gdr 2986
Package: gDRimport
Commit: 3f9360dc81acb79be9b09dfe0464c7cb1dff9a32
Author: Bartek Czech <bartosz.w.czech@gmail.com>
Date: 2025-05-15 09:05:55 +0200
Commit message:

 chore: bump version and update NEWS.md
Package: gDRimport
Commit: 4ea1fdf591a99c2d1cca830f65f80816afa48326
Author: Bartek Czech <bartosz.w.czech@gmail.com>
Date: 2025-05-15 09:05:50 +0200
Commit message:

 refactor: extend code to support public PRISM data
Package: geomeTriD
Commit: d0eeb39ed96e898ad7cb5ce5f14e24a39b427584
Author: Jianhong Ou <jou@JNXKY095H1.local>
Date: 2025-07-11 11:43:16 -0400
Commit message:

 add samescale button.
Package: EBSeq
Commit: 58baae75ef8a9caa7bef8984e9c50963158af775
Author: Stat <87042085+KINGofBTC@users.noreply.github.com>
Date: 2025-07-11 23:43:46 +0800
Commit message:

 clear indent
Package: SpaceTrooper
Commit: 0c53a9c3b0e1b992f8d952d6e62f914e9b4b182a
Author: Dario <dario.righelli@gmail.com>
Date: 2025-07-11 17:17:01 +0200
Commit message:

 ver bump
Package: SpaceTrooper
Commit: 6c2584c1df3b144ecc5dae6cc791a0eefd6c407f
Author: Dario <dario.righelli@gmail.com>
Date: 2025-07-11 17:16:41 +0200
Commit message:

 fixing lambda doc
Package: ROTS
Commit: f9e54732b370cadc0c9a08074ef462ca319d901e
Author: Tomi Suomi <tomi.suomi@utu.fi>
Date: 2025-07-11 18:12:53 +0300
Commit message:

 Bump version
Package: ROTS
Commit: bc5f52ff0801d87152ccef9ca400f063cc0c0070
Author: Tomi Suomi <tomi.suomi@utu.fi>
Date: 2025-07-11 18:12:24 +0300
Commit message:

 Update documentation
Package: ROTS
Commit: 006839e4c9f9dfb60d9127b3b7a83da19bbf6573
Author: Tomi Suomi <tomi.suomi@utu.fi>
Date: 2025-07-11 18:05:12 +0300
Commit message:

 Check for fixed parameters
Package: ROTS
Commit: df448353c3c25aa185dda8a8f0b66c2de514d3f4
Author: Tomi Suomi <tomi.suomi@utu.fi>
Date: 2025-07-11 18:04:23 +0300
Commit message:

 Add fixed parameter support for lm and lme
Package: SpaceTrooper
Commit: 3eea093cfa36781f7b9313bb04e3e4d2fa44cf1b
Author: Dario <dario.righelli@gmail.com>
Date: 2025-07-11 16:43:31 +0200
Commit message:

 bumping version
Package: SpaceTrooper
Commit: efa7b9ccd0499c20f4943b3b2750b04be2f59bc6
Author: Dario <dario.righelli@gmail.com>
Date: 2025-07-11 16:38:12 +0200
Commit message:

 fixing some warnings/notes
Package: SpaceTrooper
Commit: 524672608ceb1b24c965edfc6f87a1ad6684ecb2
Author: Dario <dario.righelli@gmail.com>
Date: 2025-07-11 16:18:01 +0200
Commit message:

 removing empty spaces
Package: DuplexDiscovereR
Commit: 16328fbffa0753f1ddb78bef684affd452c5efdd
Author: EgorS <egorsemenchenko@gmail.com>
Date: 2025-07-11 16:04:11 +0200
Commit message:

 quick fix of the if statement in pipeline exec. If counts df were not provided, pvalues were triggered anyway
Package: ChIPpeakAnno
Commit: b1cad5fe377bdf5091a2f3d06f085be884453fc4
Author: Jianhong Ou <jou@JNXKY095H1.local>
Date: 2025-07-11 09:55:39 -0400
Commit message:

 fix an issue in genomicElementDistribution when convert seqlevelsStyle.
Package: ChemmineOB
Commit: 5877b52fc3827ecd9dca6e4d9fd188f8ac9f5c82
Author: khoran <khoran@cs.ucr.edu>
Date: 2025-07-11 06:35:23 -0700
Commit message:

 missed some bits while re-adding zlibbioc, neded for windows
Package: BgeeCall
Commit: aafd4da866299d50246515831cfd4012731d0449
Author: Julien Wollbrett <julien.wollbrett@unil.ch>
Date: 2025-07-11 15:13:33 +0200
Commit message:

 solve test error caused by txdbmaker dependency issue
Package: scifer
Commit: 42512968877eae88ceaa48d283c9ccd6aabc2f65
Author: Rodrigo Arcoverde <rodrigo.arcoverdi@gmail.com>
Date: 2025-07-11 15:04:38 +0200
Commit message:

 Checks for conda installation

Ensures conda is installed before proceeding with the igblast environment creation. This prevents errors when conda is not already available on the system.
Package: scifer
Commit: 9942e265461b5f284ae293bd8aeac1b4f3bedfdf
Author: Rodrigo Arcoverde <rodrigo.arcoverdi@gmail.com>
Date: 2025-07-11 15:04:23 +0200
Commit message:

 Fix warning from biostrings/pwalign

Excludes `compareStrings` function from the imported Biostrings package in NAMESPACE.
This prevents potential conflicts or namespace pollution, as the function is likely not needed and may clash with other definitions.
Package: BgeeCall
Commit: 66d22c549184583e510a1efc90e8f8323d458757
Author: Julien Wollbrett <julien.wollbrett@unil.ch>
Date: 2025-07-11 14:57:42 +0200
Commit message:

 2nd round solving warnings/notes for bioconductor release
Package: amplican
Commit: 48e5f7d4655598b94aa66643aca5570ea0782969
Author: JokingHero <kornel.labun@gmail.com>
Date: 2025-07-11 14:07:29 +0200
Commit message:

 make primer detection more robust and way faster
Package: BgeeCall
Commit: 958692b374cebce352d47522c815c35f6c2f642e
Author: Julien Wollbrett <julien.wollbrett@unil.ch>
Date: 2025-07-11 14:00:24 +0200
Commit message:

 solve warning issues from bioconductor build
Package: BgeeCall
Commit: 27ae75b5191f991bbb2b9bf73f538542f8a827d6
Author: Julien Wollbrett <julien.wollbrett@unil.ch>
Date: 2025-07-11 13:53:49 +0200
Commit message:

 update documentation and imports
Package: broadSeq
Commit: 0ee75b2c98f855ababd4d86136d136684271b47c
Author: vondorishi <rishi.dasroy@gmail.com>
Date: 2025-07-11 14:42:34 +0300
Commit message:

 version bump
Package: broadSeq
Commit: 0e7e9e1f9da66e4dae0d2156518149cb31e6b974
Author: vondorishi <rishi.dasroy@gmail.com>
Date: 2025-07-11 14:42:20 +0300
Commit message:

 By default EBseq does not produce signed FC, adding that to column 'signedRealFC'
Package: rawDiag
Commit: 5b52b292a95735a09f015b22aa9d1e8d4037c2b9
Author: Christian Panse <cp@fgcz.ethz.ch>
Date: 2025-07-11 08:00:47 +0200
Commit message:

 version bump 1.5.2
Package: rawDiag
Commit: dd8c4b1df290ee2b3098791547e3aed90716810f
Author: Christian Panse <cp@fgcz.ethz.ch>
Date: 2025-07-11 08:00:12 +0200
Commit message:

 Merge branch 'devel' of git.bioconductor.org:packages/rawDiag into devel
Package: rawDiag
Commit: 3a76e565fbe18547ff15d719ebc51e1b729fa77e
Author: Christian Panse <cp@fgcz.ethz.ch>
Date: 2025-07-11 07:59:39 +0200
Commit message:

 choose TIC and BPC 1st
Package: MetabolomicsPipeline
Commit: 664aca066bd9d6c26099ca81c10fc9afa28270fa
Author: joelparkeruofa <joelparker@arizona.edu>
Date: 2025-07-10 16:54:08 -0700
Commit message:

 updating camel casing for test
Package: MetabolomicsPipeline
Commit: 9ab56f8500a93374654491e741af31ae0fea77ad
Author: joelparkeruofa <joelparker@arizona.edu>
Date: 2025-07-10 16:53:25 -0700
Commit message:

 Updating tests with camel casing
Package: MetabolomicsPipeline
Commit: 8c1ae00fa679b7c18d4d645dfea08de156dd51ca
Author: joelparkeruofa <joelparker@arizona.edu>
Date: 2025-07-10 15:45:06 -0700
Commit message:

 updating subpathwayAnalysis to include treatment pvalue
Package: AnVILGCP
Commit: b6b0c4bda0de334dcc714a9115544b0d57b28e20
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-07-10 17:26:33 -0400
Commit message:

 version bump 1.3.6
Package: AnVILGCP
Commit: 9e6a71e8cd92c0c671b1dd9923de5e07d344c6bf
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-07-10 17:26:28 -0400
Commit message:

 add GCPtools >= 0.99.1 dependency
Package: AnVILGCP
Commit: b511099cc004353d1a2cfeacfde7deeabee448c1
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-07-10 17:13:40 -0400
Commit message:

 use gsutil_sh_quote exported from GCPtools
Package: AnVILGCP
Commit: 1d42c30f994b77f425e56052280b05c6cce9ad0b
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-07-10 17:13:19 -0400
Commit message:

 use exported gsutil_is_uri from GCPtools
Package: AnVILGCP
Commit: ddaa06c77e07cbb01b64e0639537048dc4f32ce8
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-07-10 17:12:44 -0400
Commit message:

 remove test_gcloud_sdk.R
Package: AnVILGCP
Commit: 039653f9bd85a0379b058afd040bb00a10476d05
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-07-10 17:12:14 -0400
Commit message:

 deprecate gsutil functions
Package: GCPtools
Commit: 6190486a13ac302e068aad42d7cc7bf77911e67a
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-07-10 17:23:57 -0400
Commit message:

 version bump 0.99.1
Package: GCPtools
Commit: bf310539eb0edb8b1d9e0beae647ec6bc4fa75cc
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-07-10 17:20:02 -0400
Commit message:

 add test_gcloud_sdk.R
Package: GCPtools
Commit: bdd7665511372ae503a56a9256c7cf10ed343152
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-07-10 17:19:05 -0400
Commit message:

 add test_gsutil.R
Package: GCPtools
Commit: c366ce6851470dcfd38f034dd8599047a9996908
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-07-10 17:17:55 -0400
Commit message:

 export gsutil_is_uri
Package: GCPtools
Commit: 60d5a51e7a9f360d3b66e6c36f1f7e910d5fc66c
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-07-10 17:17:21 -0400
Commit message:

 export gsutil_sh_quote
Package: AnVIL
Commit: c53c254d0a652b5bf60d010032677ca902176f29
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-07-10 16:31:13 -0400
Commit message:

 version bump 1.21.7
Package: AnVIL
Commit: 77537957ebab95a656febd41307a1a15a14530e5
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-07-10 16:24:16 -0400
Commit message:

 update Dockstore version 1.17.0
Package: AnVIL
Commit: 32c52f78c2c671057eb0126075cde5a001f2638a
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-07-10 16:30:53 -0400
Commit message:

 version bump 1.21.6
Package: AnVIL
Commit: 046e10f04c027af28c0eea4032dc5d6275bab8de
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-07-10 16:23:59 -0400
Commit message:

 import checkInstalled for avworkflow_gadget
Package: AnVIL
Commit: e3062342f21ff4cdade5d15a775f5dc65fece2a3
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-07-10 16:23:38 -0400
Commit message:

 use gcloud_access_token from GCPtools
Package: AnVILGCP
Commit: aa5f87ac47f824f7a84b7df5b8325a50b66cf98c
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-07-10 16:00:25 -0400
Commit message:

 version bump 1.3.5
Package: AnVILGCP
Commit: 3a257b4db217d08b94276d77e7b6ccfc1ae2d455
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-07-10 15:59:34 -0400
Commit message:

 version bump 1.3.4
Package: AnVILGCP
Commit: 0df2fa20f4bd494f1c3feb9c912e1a915ceb30d6
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-07-10 15:59:26 -0400
Commit message:

 add interactive() condition to examples
Package: AnVILGCP
Commit: 4254e7f0f692c6052d4892e42e0cbeeb2598fbe4
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-07-10 15:59:02 -0400
Commit message:

 use functions from GCPtools directly
Package: AnVILGCP
Commit: 22240046d74bd3b4854213110ad0cfe39b707d2a
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-07-10 15:58:11 -0400
Commit message:

 deprecate gcloud utilities and import from GCPtools
Package: CPSM
Commit: cb65e3c5973534c958224bf03a2e3009f8e73ce6
Author: Harpreet Kaur <hks04180@gmail.com>
Date: 2025-07-10 15:26:09 -0400
Commit message:

 Update km_overlay_plot_f.R function to improve figure
Package: RaggedExperiment
Commit: 4cb9ce7518ddda891309a239ba5af84b3bb64055
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-07-10 14:19:28 -0400
Commit message:

 version bump 1.33.7
Package: RaggedExperiment
Commit: 956b071e538af4d55d20d9b11c7586ee95abd2a2
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-07-10 14:19:22 -0400
Commit message:

 roxygen package Rd update
Package: RaggedExperiment
Commit: 1a997f8542f9f8dde0c5a671b71bf69081a11a71
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-07-10 14:19:09 -0400
Commit message:

 move chunk options to code chunk body
Package: RaggedExperiment
Commit: ff60b8f4a54f73b7d7853632144fca0fa94aad9f
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-07-10 13:55:39 -0400
Commit message:

 version bump 1.33.6
Package: RaggedExperiment
Commit: ad5aeb963a9264a0750dafd366cac4807a06e038
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-07-10 13:55:27 -0400
Commit message:

 remove long link
Package: RaggedExperiment
Commit: 04eac2a9aeeeeccb4ab7c69127db9e37fd007836
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-07-10 13:55:13 -0400
Commit message:

 minor update indentation
Package: RaggedExperiment
Commit: 02c3e0ca7381ebbd74658ebc6d1aa0c840fdac29
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-07-10 13:42:20 -0400
Commit message:

 remove extra space in vignette
Package: RaggedExperiment
Commit: a2b9dd656b87a4f89db43d8e369165b61fe8760f
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-07-10 13:42:08 -0400
Commit message:

 update R version for Bioc version
Package: RaggedExperiment
Commit: bb5f156f586314cc92f5c79ed137eb11ba931d81
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-07-10 13:40:31 -0400
Commit message:

 version bump 1.33.5
Package: RaggedExperiment
Commit: 60d7945a66e18d809ac1e270b6519ec324974484
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-07-10 13:40:28 -0400
Commit message:

 remove random backslash
Package: gg4way
Commit: 7ae4e96a0f3c7fd79c9023cc3a4aa984b2688575
Author: Ben Laufer <laufer.benjamin@gene.com>
Date: 2025-07-10 10:31:37 -0700
Commit message:

 Version bump to 1.7.1
Package: gg4way
Commit: 4c06d40d9c5a761e35c8cf165f20ace6c868b68a
Author: Ben Laufer <laufer.benjamin@gene.com>
Date: 2025-07-10 10:28:27 -0700
Commit message:

 Updates for new major version of ggplot2
Package: RaggedExperiment
Commit: d1ebde4130b53dd0e506f1ecf35832dd3f163f2e
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-07-10 13:31:26 -0400
Commit message:

 version bump 1.33.4
Package: RaggedExperiment
Commit: 48810f539e9187f2bcb32dcc54a6b44f37563bd3
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-07-10 13:30:50 -0400
Commit message:

 update NEWS.md
Package: RaggedExperiment
Commit: 04df595aff0e204338e2b074d4f67613a2cdd3d8
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-07-10 13:28:10 -0400
Commit message:

 PRs to devel only
Package: RaggedExperiment
Commit: f3fdb7394d2de82a974f3f4f2f1598981cc28715
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-07-10 13:27:49 -0400
Commit message:

 use BiocStyle::Biocpkg in inline vignette text
Package: RaggedExperiment
Commit: 2f82ac0fb231968c99c25fcdbe528e2373be7aae
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-07-10 13:27:23 -0400
Commit message:

 add chunk labels to vignettes
Package: scDotPlot
Commit: 4db1f01a64c98b2c09638498df24d006b89c44f7
Author: Ben Laufer <laufer.benjamin@gene.com>
Date: 2025-07-10 10:22:39 -0700
Commit message:

 Version bump to 1.3.1
Package: scDotPlot
Commit: 3996b83eef3c6360c08528ea54609c09fca31ccc
Author: Ben Laufer <laufer.benjamin@gene.com>
Date: 2025-07-10 10:15:59 -0700
Commit message:

 Updates for new major version of ggplot2
Package: asuri
Commit: 64b8b2522ffaa8bc3d6126d35c8f9e265773e699
Author: aberral <aberralgonzalez@gmail.com>
Date: 2025-07-10 15:01:54 +0200
Commit message:

 man fix for missing \value
Package: asuri
Commit: e7941b5a2c78fc922fbf2a66caf0cd640d57c5f0
Author: aberral <aberralgonzalez@gmail.com>
Date: 2025-07-10 14:37:39 +0200
Commit message:

 bump version
Package: asuri
Commit: cf9a8612c5ee55a3bd481bb1f12041f56d4744ac
Author: aberral <aberralgonzalez@gmail.com>
Date: 2025-07-10 14:34:23 +0200
Commit message:

  man fix
Package: asuri
Commit: ecc1e90591c41da49141a01e940003e69edd4c08
Author: aberral <aberralgonzalez@gmail.com>
Date: 2025-07-10 14:02:33 +0200
Commit message:

 man fix
Package: asuri
Commit: a6cca459f3a6dabb3687e32885e814e8d979fcfe
Author: aberral <aberralgonzalez@gmail.com>
Date: 2025-07-10 11:17:35 +0200
Commit message:

 man fix
Package: bsseq
Commit: c673ef9e5bab4f950d42634881a12e2abc25f485
Author: Peter Hickey <peter.hickey@gmail.com>
Date: 2025-07-10 16:20:18 +1000
Commit message:

 Merge remote-tracking branch 'github/devel' into devel
Package: bsseq
Commit: 87281013747fe86a99502e05e28f78bcd7e25b0a
Author: Kasper Daniel Hansen <kasperdanielhansen@gmail.com>
Date: 2025-05-05 07:52:09 -0400
Commit message:

 clearing multiple missing links in man pages
Package: broadSeq
Commit: c8f969c052090e4c19b65a4302296dc7af8696a4
Author: vondorishi <rishi.dasroy@gmail.com>
Date: 2025-07-10 09:07:08 +0300
Commit message:

 version bump
Package: broadSeq
Commit: ba54a56b7bbf080be7f5ce2149fdf1599a866508
Author: vondorishi <rishi.dasroy@gmail.com>
Date: 2025-07-10 09:06:54 +0300
Commit message:

 fixinf DELocal contrast
Package: sccomp
Commit: 2ef5a77fdba9603e2bebe7777c9ea0d04e789ff4
Author: Stefano Mangiola <mangiolastefano@gmail.com>
Date: 2025-07-09 21:59:55 +0930
Commit message:

 Merge pull request #210 from MangiolaLaboratory/fix-converge-metrics-for-random-effect

Fix converge metrics for random effect
Package: sccomp
Commit: ee0ba6bf1c7ef4430d2bf0c8d0169f18f4401e0b
Author: Stefano Mangiola <mangiolastefano@gmail.com>
Date: 2025-07-09 20:56:53 +0930
Commit message:

 add convergence on random
Package: sccomp
Commit: a27b6d7030f409c7a5648c18db22aac121d56d7e
Author: Stefano Mangiola <mangiolastefano@gmail.com>
Date: 2025-07-09 20:23:35 +0930
Commit message:

 Add tests for convergence metrics in fixed and random effects models

- Introduced a new test file to validate the availability of convergence metrics for fixed effects while ensuring that random effects do not have these metrics.
- Implemented tests for both composition and variability parameters, confirming the expected behavior of convergence metrics across different model specifications.
- Included summary output for clarity on test results.
Package: sccomp
Commit: f74b32c1c605b7b571881954aca029250225bc3c
Author: Stefano Mangiola <mangiolastefano@gmail.com>
Date: 2025-07-06 15:51:49 +0930
Commit message:

 update introduction with mixed linear models
Package: sccomp
Commit: 1ca46b8883f76413b2f049eb09b5a64e403dfe52
Author: Stefano Mangiola <mangiolastefano@gmail.com>
Date: 2025-06-30 17:54:05 +0930
Commit message:

 Merge pull request #208 from MangiolaLaboratory/FDR-plot-messaging

Fdr plot messaging
Package: sccomp
Commit: 4fdb0291345b2bb94eb2e601241bbcaef9a5cffa
Author: Stefano Mangiola <mangiolastefano@gmail.com>
Date: 2025-06-30 17:07:51 +0930
Commit message:

 Merge branch 'FDR-plot-messaging' of https://github.com/MangiolaLaboratory/sccomp into FDR-plot-messaging
Package: sccomp
Commit: f95df5d48f5224f0f990f3d94b5b4b17da12c1be
Author: Stefano Mangiola <mangiolastefano@gmail.com>
Date: 2025-06-30 15:32:08 +0930
Commit message:

 fix tests and docs
Package: sccomp
Commit: cea81fb179b8be0b31060c7a1579ba42ea045aca
Author: Stefano Mangiola <mangiolastefano@gmail.com>
Date: 2025-06-27 18:33:09 -0400
Commit message:

 Enhance plotting functions with significance_statistic parameter

- Added a new parameter `significance_statistic` to `plot_1D_intervals` and `plot_2D_intervals` functions, allowing users to specify which statistic to highlight (default is "FDR").
- Updated the logic in both functions to handle the new parameter and adjust color coding based on the selected statistic.
- Enhanced documentation to reflect the changes and added tests to ensure functionality for both `significance_statistic` and `show_fdr_message` parameters.
Package: sccomp
Commit: 6b2df36a23ff274a9730749d68511beeddff700b
Author: Stefano Mangiola <mangiolastefano@gmail.com>
Date: 2025-06-27 18:04:29 -0400
Commit message:

 Add show_fdr_message parameter to plotting functions

- Introduced a new logical parameter `show_fdr_message` in `plot_1D_intervals` and `plot_2D_intervals` functions to control the display of the Bayesian FDR interpretation message on the plots. Default is set to TRUE.
- Updated documentation for both functions to include the new parameter.
- Added tests to verify the functionality of the `show_fdr_message` parameter in both plotting functions.
Package: sccomp
Commit: 1cc2345f9c16236e2a6d047a43aab6386e56f89c
Author: Stefano Mangiola <mangiolastefano@gmail.com>
Date: 2025-06-30 17:07:08 +0930
Commit message:

 Merge pull request #209 from MangiolaLaboratory/patch-30-jun-fix-tests

Refactor tests for replicate_data to handle X_random_effect_unseen
Package: sccomp
Commit: 028dc55cff0fa3847c7e32e2c40fccb94d0cde0f
Author: Stefano Mangiola <mangiolastefano@gmail.com>
Date: 2025-06-30 16:13:36 +0930
Commit message:

 Refactor tests for replicate_data to handle X_random_effect_unseen

- Updated tests to check the number of columns in X_random_effect_unseen, ensuring it is empty when new_data is NULL.
- Removed redundant checks and print statements related to NA columns and sums in X_random_effect_unseen.
- Enhanced robustness of tests by ensuring checks for group values are only performed when applicable.
Package: sccomp
Commit: 766299d92ccfdefcdd4b694992dc7a70d20a3aa1
Author: Stefano Mangiola <mangiolastefano@gmail.com>
Date: 2025-06-30 15:32:08 +0930
Commit message:

 fix tests and docs
Package: sccomp
Commit: 7d560e1d22c87af2a4447da1fe6b5faf5576d861
Author: Stefano Mangiola <mangiolastefano@gmail.com>
Date: 2025-06-27 18:33:09 -0400
Commit message:

 Enhance plotting functions with significance_statistic parameter

- Added a new parameter `significance_statistic` to `plot_1D_intervals` and `plot_2D_intervals` functions, allowing users to specify which statistic to highlight (default is "FDR").
- Updated the logic in both functions to handle the new parameter and adjust color coding based on the selected statistic.
- Enhanced documentation to reflect the changes and added tests to ensure functionality for both `significance_statistic` and `show_fdr_message` parameters.
Package: sccomp
Commit: 28eff81536742251efc8032e5f82f09e3ef10a49
Author: Stefano Mangiola <mangiolastefano@gmail.com>
Date: 2025-06-27 18:04:29 -0400
Commit message:

 Add show_fdr_message parameter to plotting functions

- Introduced a new logical parameter `show_fdr_message` in `plot_1D_intervals` and `plot_2D_intervals` functions to control the display of the Bayesian FDR interpretation message on the plots. Default is set to TRUE.
- Updated documentation for both functions to include the new parameter.
- Added tests to verify the functionality of the `show_fdr_message` parameter in both plotting functions.
Package: sccomp
Commit: 4e21d30a21ef887d9a10b5d11904237951941370
Author: Stefano Mangiola <mangiolastefano@gmail.com>
Date: 2025-06-27 13:56:17 -0400
Commit message:

 version UP
Package: sccomp
Commit: 0557f6776a5899f56db5fc899ae89df367c40d51
Author: Stefano Mangiola <mangiolastefano@gmail.com>
Date: 2025-06-27 13:55:43 -0400
Commit message:

 Merge pull request #207 from MangiolaLaboratory/add-robust-prediction

Enhance sccomp_predict and summary_to_tibble functions to support rob…
Package: sccomp
Commit: 3cfd38b298f226b0c7efa0bc3f2bdc56c1410fa3
Author: Stefano Mangiola <mangiolastefano@gmail.com>
Date: 2025-06-20 13:53:17 +1000
Commit message:

 Enhance sccomp_predict and summary_to_tibble functions to support robust statistics

- Added a new parameter `robust` to `sccomp_predict` and `summary_to_tibble` functions to allow users to choose between classical and robust statistics for summary calculations.
- Updated documentation to reflect the new `robust` parameter and its implications on the output.
- Modified the prediction logic to return median and median absolute deviation when `robust` is set to TRUE.
- Added tests to ensure robust predictions return expected columns and values.
Package: sccomp
Commit: dcc5b0e2265873c9d87e278c47ab0b392d016e02
Author: Stefano Mangiola <mangiolastefano@gmail.com>
Date: 2025-06-18 12:29:36 +1000
Commit message:

 Merge pull request #205 from MangiolaLaboratory/deprecate-function-name

deprecate remove variation for remove effects
Package: sccomp
Commit: 16e605802d9257c677a3f6bd100037084a6897f5
Author: Stefano Mangiola <mangiolastefano@gmail.com>
Date: 2025-06-12 22:01:26 +0930
Commit message:

 Merge pull request #206 from MangiolaLaboratory/fix-average-effect-for-complex-designs

Enhance NA handling in complex interaction design matrix
Package: sccomp
Commit: c34533b3a7561f4b98c04638a3cc4d8cb8891c53
Author: stemangiola <mangiolastefano@gmail.com>
Date: 2025-06-12 21:56:27 +1000
Commit message:

 fix for unnodelled random effect combinations
Package: sccomp
Commit: 45a7bc43262f2a8a89b77d624598ab27d0ef1fa9
Author: Stefano Mangiola <mangiolastefano@gmail.com>
Date: 2025-06-12 18:54:50 +0930
Commit message:

 Fixed design matrix with rownames
Package: sccomp
Commit: 75a4f7b9f381b6163dffca8666c3ec4cff5c35f3
Author: Stefano Mangiola <mangiolastefano@gmail.com>
Date: 2025-06-12 18:33:08 +0930
Commit message:

 Solve CHECK

Refactor NAMESPACE and utilities for NA handling

- Removed export of `calculate_na_fraction_contribution` as it is no longer needed.
- Updated NAMESPACE to include new imports from `dplyr` and `tidyr` for enhanced data manipulation.
- Added necessary imports in `utilities.R` to support new functionality.
- Deleted outdated documentation for `calculate_na_fraction_contribution`.
- Updated tests to skip certain commands for compatibility with new changes.
Package: sccomp
Commit: f1005dde0020b0dce98dc00c13249ac0134770d3
Author: Stefano Mangiola <mangiolastefano@gmail.com>
Date: 2025-06-12 17:49:32 +0930
Commit message:

 Update version to 2.1.9 and enhance NA handling in design matrix

- Bump package version in DESCRIPTION file.
- Introduce `calculate_na_fraction_contribution` function to compute contributions of NA values in design matrices.
- Add `handle_missing_values` function to standardize NA handling for categorical and numeric variables.
- Update NAMESPACE to export new functions and import necessary dependencies.
- Add documentation for new functions and enhance existing tests to cover NA scenarios in design matrices.
Package: sccomp
Commit: 1572df3b1f108cff86c89f906def452924a8fff8
Author: Stefano Mangiola <mangiolastefano@gmail.com>
Date: 2025-06-11 00:09:01 +0930
Commit message:

 Merge branch 'master' into deprecate-function-name
Package: sccomp
Commit: 59d95507bb23202763b623a7723424fe4e7e2039
Author: Stefano Mangiola <mangiolastefano@gmail.com>
Date: 2025-06-11 00:08:25 +0930
Commit message:

 Deprecate `sccomp_remove_unwanted_variation` function and update documentation to direct users to `sccomp_remove_unwanted_effects`. Added new Rd file for documentation and clarified usage examples.
Package: sccomp
Commit: 20c589379fe189a002f25525e1ffc9da2c337e4c
Author: Stefano Mangiola <mangiolastefano@gmail.com>
Date: 2025-06-10 23:52:33 +0930
Commit message:

 Remove redundant import of `%$%` from `magrittr` in NAMESPACE file for clarity and consistency.
Package: sccomp
Commit: ef3af36bc699447124a22e51961e03c00afd5a55
Author: Stefano Mangiola <mangiolastefano@gmail.com>
Date: 2025-06-10 23:41:15 +0930
Commit message:

 Merge branch 'deprecate-function-name' of https://github.com/MangiolaLaboratory/sccomp into deprecate-function-name
Package: sccomp
Commit: 1f1becacdf148cc0cf53119a56794a33ab4a7e75
Author: Stefano Mangiola <mangiolastefano@gmail.com>
Date: 2025-06-10 23:40:42 +0930
Commit message:

 Update version to 1.99.20 and deprecate sccomp_remove_unwanted_variation function in favor of sccomp_remove_unwanted_effects. Added tests to ensure deprecation warning and result consistency between the two functions.
Package: sccomp
Commit: c18187b3e2385423dc2f40d33c4cfde791891a39
Author: Stefano Mangiola <mangiolastefano@gmail.com>
Date: 2025-06-10 20:34:15 +0930
Commit message:

 deprecate remove variation for remove effects
Package: sccomp
Commit: cb705be9cfeca518d01b52ec4e417ae6e1fae4ae
Author: Stefano Mangiola <mangiolastefano@gmail.com>
Date: 2025-06-10 23:40:42 +0930
Commit message:

 Update version to 1.99.20 and deprecate sccomp_remove_unwanted_variation function in favor of sccomp_remove_unwanted_effects. Added tests to ensure deprecation warning and result consistency between the two functions.
Package: sccomp
Commit: 0f591beda9117b0bdd65266ae269e1d88b04c8ff
Author: Stefano Mangiola <mangiolastefano@gmail.com>
Date: 2025-06-10 20:34:15 +0930
Commit message:

 deprecate remove variation for remove effects
Package: MetabolomicsPipeline
Commit: c88f0c4db617a644d22e28bc96eb9c08110a2f59
Author: joelparkeruofa <joelparker@arizona.edu>
Date: 2025-07-09 16:48:09 -0700
Commit message:

 changing subpathway_boxplots to camel casing
Package: crisprScore
Commit: 0e5cd772e7d3a1ffefb673cd1190f148eb6920a8
Author: Jean-Philippe Fortin <fortin946@gmail.com>
Date: 2025-07-09 20:10:44 +0200
Commit message:

 Should pass check
Package: crisprScore
Commit: a3c73041cdc210ea8396a15f24dc4b993fc09eed
Author: Jean-Philippe Fortin <fortin946@gmail.com>
Date: 2025-06-20 16:20:52 +0200
Commit message:

 Merge branch 'devel' into fixBasilisk
Package: crisprScore
Commit: 06ce8a04151bce33f173790f683daa6361cb2bf5
Author: Jean-Philippe Fortin <fortin946@gmail.com>
Date: 2025-06-20 16:19:41 +0200
Commit message:

 Merge pull request #21 from mzhibo/devel

Fix conda channel priority for Azimuth/RuleSet3; update tutorial typos
Package: crisprScore
Commit: cd111c7fc0b50ea3ac60c527041a4c4c2d45cdba
Author: Jean-Philippe Fortin <fortin946@gmail.com>
Date: 2025-06-20 16:11:05 +0200
Commit message:

 Removed activateenv
Package: crisprScore
Commit: 1cdd97aff3c1e9bfae8ae659b8d181addfc7f551
Author: mzhibo <32151277+mzhibo@users.noreply.github.com>
Date: 2025-04-24 13:26:17 -0700
Commit message:

 Update crisprScore.Rmd
Package: crisprScore
Commit: d255647ee6cafefad09322c8ffaf935d87f03d26
Author: mzhibo <32151277+mzhibo@users.noreply.github.com>
Date: 2025-04-24 12:34:11 -0700
Commit message:

 Update basilisk.R on conda channel priority for RuleSet3 env setup

conda-forge ahead of bioconda to avoid biopython installation error due to strict repo priority
Package: crisprScore
Commit: 9ee76799f862a561330eb73bd3b986e390387588
Author: mzhibo <32151277+mzhibo@users.noreply.github.com>
Date: 2025-04-24 11:55:55 -0700
Commit message:

 Update basilisk.R on conda channel priority for azimuth env setup

put conda-forge before bioconda to allow biopython=1.74 to be correctly installed
Package: scifer
Commit: 65e452e154aee6a946f6388c59788ccef747bc88
Author: Rodrigo Arcoverde <rodrigo.arcoverdi@gmail.com>
Date: 2025-07-09 18:39:24 +0200
Commit message:

 Refactors igblast wrapper for improved reliability

Migrates the igblast wrapper to use `basilisk.utils` for environment creation, enhancing robustness across different platforms. The new basilisk package now only works with pure python environments (aka pip packages), so packages only available in conda, such as igblast, could not use it anymore.
Removes the dedicated `basilisk.R` file, simplifying the codebase.
Improves error handling and input validation for database and fasta file paths, providing clearer messages to the user.
Updates the igblast function to be compatible with various operating systems.
Package: asuri
Commit: dfc1b3f73546b706cddd1e765198252509a280ff
Author: aberral <aberralgonzalez@gmail.com>
Date: 2025-07-09 18:39:08 +0200
Commit message:

 watched tags added
Package: asuri
Commit: 88ea4d94752514df1bc023e2f9bdfcaa15289273
Author: aberral <aberralgonzalez@gmail.com>
Date: 2025-07-09 18:25:36 +0200
Commit message:

 mail fix
Package: asuri
Commit: c457fdcc03bdd808aaed03707891ca4b5b0f3732
Author: aberral <aberralgonzalez@gmail.com>
Date: 2025-07-09 18:14:26 +0200
Commit message:

 mail fix
Package: asuri
Commit: 8b6ed50abbe80dcdd77ca439db44d9aaa108e575
Author: aberral <aberralgonzalez@gmail.com>
Date: 2025-07-09 18:03:05 +0200
Commit message:

 mail and note fixes
Package: BiocCheck
Commit: ca3623d11404c2b76d60be3dbd22a08eb1dcc9c7
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-07-09 12:00:32 -0400
Commit message:

 version bump 1.45.8
Package: BiocCheck
Commit: e1467aff01da23151e3188eac4dfec74be490a89
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-07-09 12:00:19 -0400
Commit message:

 update NEWS
Package: BiocCheck
Commit: 792ac4a1cba071dfe43f2d6f9650893b137fd70d
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-06-23 12:22:37 -0400
Commit message:

 skip class and internal keyword docs
Package: RnBeads
Commit: 512a55553918a57da2cf3b76de28895b223ee665
Author: Michael Scherer <michael.scherer@dkfz.de>
Date: 2025-07-09 19:58:21 +0200
Commit message:

 Merge branch 'devel' of git.bioconductor.org:packages/RnBeads
Package: RnBeads
Commit: 2d5ece613b1da19b095047eda2208eb1de6de9c4
Author: Michael Scherer <michael.scherer@dkfz.de>
Date: 2025-07-09 19:56:59 +0200
Commit message:

 Small fix for reporting SNP probes EPICv1 vs EPICv2
Package: RnBeads
Commit: c46dc3b65edea865d3785d11b6024958269cda74
Author: Scherer <m261r@b370-worker01.dkfz-heidelberg.de>
Date: 2025-05-28 15:37:29 +0200
Commit message:

 Added reshape to Depends
Package: asuri
Commit: 5163d574d572a628e152d08a1999db2391bf37d0
Author: aberral <aberralgonzalez@gmail.com>
Date: 2025-07-09 17:46:37 +0200
Commit message:

 version bump
Package: asuri
Commit: acfa1e8674bb97af0ede1ac4729e6ccff281a3db
Author: aberral <aberralgonzalez@gmail.com>
Date: 2025-07-09 17:46:15 +0200
Commit message:

 final fixes for reduced time
- examples fixed with rda
- simplified vignette
- added rd doc for new rda files
Package: rawrr
Commit: 004a953fcfd4a3d064de51f7a2846e291b4488ac
Author: Christian Panse <cp@fgcz.ethz.ch>
Date: 2025-07-09 14:48:53 +0200
Commit message:

 roxygen2::roxygenize() cosmetics
Package: rawrr
Commit: af17adeec182f9aa3ba2f8ff33b1a4d8a801b29c
Author: Christian Panse <cp@fgcz.ethz.ch>
Date: 2025-07-09 14:41:49 +0200
Commit message:

 #92 pass stderr and stdout to system2 call
Package: CENTREprecomputed
Commit: 036ab444f79e6b5c8225cf8401688f8203102cc0
Author: saral98 <sarl98@mi.fu-berlin.de>
Date: 2025-07-09 13:24:06 +0200
Commit message:

 bump up version 0.99.1
Package: CENTREprecomputed
Commit: 97ad349e6d7ecbc53b07f13fdc1bfeba8f3981f3
Author: saral98 <sarl98@mi.fu-berlin.de>
Date: 2025-07-09 13:22:33 +0200
Commit message:

 bump down version
Package: CENTREprecomputed
Commit: 4e986966ca7fdbfb138a6abf95901c7aee3ae2e8
Author: saral98 <sarl98@mi.fu-berlin.de>
Date: 2025-07-09 13:11:54 +0200
Commit message:

 bump up to version 0.99.1
Package: CENTREprecomputed
Commit: ea3a9a47ccba2ffd1a6c0e23a6f26beb30eac360
Author: saral98 <sarl98@mi.fu-berlin.de>
Date: 2025-07-08 17:54:17 +0200
Commit message:

 make package buildable on bioc-submission
Package: scafari
Commit: 3386fb64084f99a7f3fe40f0c0433c6bdb8c3f92
Author: swind <swind@uni-muenster.de>
Date: 2025-07-09 13:11:58 +0200
Commit message:

 raise version
Package: scafari
Commit: 8d3bd1b85a9011c86258475fc662c44cc5a4121d
Author: swind <swind@uni-muenster.de>
Date: 2025-07-09 13:08:35 +0200
Commit message:

 update test
Package: asuri
Commit: 903c6c9d157c855d23a28ac972c5504b3eba6c69
Author: aberral <aberralgonzalez@gmail.com>
Date: 2025-07-09 11:55:22 +0200
Commit message:

 reduced time fix
Package: asuri
Commit: ded3a75aafd1fa3cb0a1a1dc0b61db167e0c7914
Author: aberral <aberralgonzalez@gmail.com>
Date: 2025-07-08 13:09:02 +0200
Commit message:

 Fix to reduce RCMD build time
Package: SpectriPy
Commit: c9c77abf8083c2627655808f61148d0fb646d560
Author: jorainer <johannes.rainer@gmail.com>
Date: 2025-07-09 11:51:15 +0200
Commit message:

 fix: update NAMESPACE
Package: DuplexDiscovereR
Commit: 5376917aa56f973aef251d477b98d8740268d0dd
Author: Egors01 <yegor.smb@gmail.com>
Date: 2025-07-09 11:38:06 +0200
Commit message:

 Merge branch 'bioc_devel'
Package: DuplexDiscovereR
Commit: d6efb448f8eff1658437c1885409f1eb61d8c3da
Author: Egors01 <yegor.smb@gmail.com>
Date: 2025-07-09 11:30:39 +0200
Commit message:

 update NEWS.md
Package: DuplexDiscovereR
Commit: 48a1fa78bb059a02d5ce342f4cda1761589fd5b1
Author: Egors01 <yegor.smb@gmail.com>
Date: 2025-07-09 11:08:19 +0200
Commit message:

 merge current dev into bioc_dev
Package: DuplexDiscovereR
Commit: 1247af914a974361b9c6dfdff7fc7f3966f2941a
Author: Egors01 <yegor.smb@gmail.com>
Date: 2025-07-09 10:47:47 +0200
Commit message:

 version update according to the current bioconductor versioning
Package: DuplexDiscovereR
Commit: 4771b137809c3f373f9f5f75996e6e4b2a54df58
Author: EgorS <egorsemenchenko@gmail.com>
Date: 2025-07-04 11:57:20 +0200
Commit message:

 NEWS and version update
Package: DuplexDiscovereR
Commit: af80b0db553b0baff8fb28790cdaef3e29a2e51b
Author: Egors01 <38434635+Egors01@users.noreply.github.com>
Date: 2025-07-04 11:52:10 +0200
Commit message:

 Merge pull request #14 from Egors01/dev

Dev
Package: DuplexDiscovereR
Commit: 06a077a8c6c5fc51a5bc67131868c8566c017694
Author: EgorS <egorsemenchenko@gmail.com>
Date: 2025-07-04 11:39:19 +0200
Commit message:

 added anno_gr_keys argument passing for feature annotation when whole pipeline is executed
Package: DuplexDiscovereR
Commit: bf4d786c3d4d561aac000abd109b408c6ba15f6c
Author: Egors01 <egors01@yandex.ru>
Date: 2025-06-19 12:17:42 +0200
Commit message:

 added option to skip pvalue calculation
Package: DuplexDiscovereR
Commit: 162c89c07e3d1759174327ee0fa99d58ba1396bc
Author: Egors01 <egors01@yandex.ru>
Date: 2025-05-27 16:28:27 +0200
Commit message:

 fixed some stuff after merge: 1) arg min_len  2) too high node threshold for the collapse similar
Package: DuplexDiscovereR
Commit: 78e760b0d8fdaed1e5c0ba344183b7e90ec6a654
Author: Egors01 <egors01@yandex.ru>
Date: 2025-05-27 15:41:28 +0200
Commit message:

 Merge remote-tracking branch 'origin/bioc_currect' into feature/trimming
Package: DuplexDiscovereR
Commit: 47f270183c53e794123bbb28a82a908fb30d09f1
Author: Semenchenko <esemenc@cl-meyer16.mdc-berlin.net>
Date: 2025-01-07 10:29:07 +0100
Commit message:

 local old version for paper
Package: DuplexDiscovereR
Commit: 42f0c1a4521468ada92d44c59222e51ef11db47f
Author: EgorS <Egor.Semenchenko@mdc-berlin.de>
Date: 2024-08-13 16:53:35 +0200
Commit message:

 sj feature added
Package: DuplexDiscovereR
Commit: 3f860bb62cf8aa8e972b2b1dc696bbc77f031f36
Author: EgorS <Egor.Semenchenko@mdc-berlin.de>
Date: 2024-06-13 11:20:00 +0200
Commit message:

 splicejnc strict added
Package: scafari
Commit: a0fed5bb13fbcb4fe264a807f805213637325941
Author: swind <swind@uni-muenster.de>
Date: 2025-07-09 11:37:56 +0200
Commit message:

 raise version
Package: scafari
Commit: 12c5a4daef09dfa48fdd2a2b83323c7c6b451d34
Author: swind <swind@uni-muenster.de>
Date: 2025-07-09 11:36:48 +0200
Commit message:

 version issue
Package: scafari
Commit: 609606bec25ce605602e6aa3a0ac8226e0ddf1d7
Author: swind <swind@uni-muenster.de>
Date: 2025-07-09 11:22:55 +0200
Commit message:

 update man pages
Package: scafari
Commit: 9d5318a03b84d66767eb57662dff62493315933d
Author: swind <swind@uni-muenster.de>
Date: 2025-07-09 11:22:32 +0200
Commit message:

 update man pages
Package: multistateQTL
Commit: 15228988dc34349f6e1bfc7628543ef10f08a64a
Author: dunstone-a <amelia.dunstone@gmail.com>
Date: 2025-07-09 19:29:40 +1000
Commit message:

 Move data.table to 'Imports'
Package: scafari
Commit: 9cbce3c15e9dd5fc94ae30e7bf25b0c92604fdce
Author: swind <swind@uni-muenster.de>
Date: 2025-07-09 10:54:20 +0200
Commit message:

 raise version to 6
Package: scafari
Commit: 304e94952a9be56a47a094ae08dff9a592072bfb
Author: swind <swind@uni-muenster.de>
Date: 2025-07-09 10:32:02 +0200
Commit message:

 raise version
Package: scafari
Commit: 863de9446f98114ce8721ef82447ad5d3f0d9b2a
Author: swind <swind@uni-muenster.de>
Date: 2025-07-09 10:28:27 +0200
Commit message:

 only add line
Package: scafari
Commit: d8e6bbcad79274fc6246d8530f453b795dfa98c7
Author: swind <swind@uni-muenster.de>
Date: 2025-07-09 10:28:12 +0200
Commit message:

 update norm test
Package: scafari
Commit: 3c6350c1b9c1b374fdb51b07434a64e490842554
Author: swind <swind@uni-muenster.de>
Date: 2025-07-09 10:03:50 +0200
Commit message:

 fix normalizeRC test
Package: SpectriPy
Commit: 47ba84d1b54422ad55ee651eb357cd1909b2d73a
Author: jorainer <johannes.rainer@gmail.com>
Date: 2025-07-09 09:33:13 +0200
Commit message:

 fix: add tryCatch to Python loading to print config
Package: SpectriPy
Commit: 8dfc12ebb309b63763bb8bfd4d89c739bb02452d
Author: jorainer <johannes.rainer@gmail.com>
Date: 2025-07-09 09:21:05 +0200
Commit message:

 refactor: replace msdata by MsDataHub
Package: scafari
Commit: e4f478f3b016967ce31f9dec4faf3949342035b1
Author: swind <swind@uni-muenster.de>
Date: 2025-07-09 09:14:21 +0200
Commit message:

 raise version
Package: scafari
Commit: 962d24c9ce8b3d6161ef733c5f32552a4a304e34
Author: swind <swind@uni-muenster.de>
Date: 2025-07-09 08:50:17 +0200
Commit message:

 rm one of the double depends
Package: scafari
Commit: 4a7a4488a2983e47d7bd98f2d4609530bc9c46f9
Author: swind <swind@uni-muenster.de>
Date: 2025-07-09 08:49:51 +0200
Commit message:

 rm one of the double R depends

Merge remote-tracking branch 'upstream/devel'
# Bitte geben Sie eine Commit-Beschreibung ein, um zu erklären, warum dieser
# Merge erforderlich ist, insbesondere wenn es einen aktualisierten
# Upstream-Branch mit einem Thema-Branch zusammenführt.
#
# Zeilen, die mit '#' beginnen, werden ignoriert,
# und eine leere Beschreibung bricht den Commit ab.
Package: scafari
Commit: 406bc53fd8ca1f29b9d584f2a462ad83a12bbd37
Author: swind <swind@uni-muenster.de>
Date: 2025-07-09 08:34:14 +0200
Commit message:

 add more tests
Package: scafari
Commit: 4a8bf286f52bb474f86aa0b28abe576f7e5aec2e
Author: swind <swind@uni-muenster.de>
Date: 2025-07-09 08:33:56 +0200
Commit message:

 add testdata and data acquisition description
Package: scafari
Commit: ded9f66a8705c2e41501d564d905576b011d5442
Author: swind <swind@uni-muenster.de>
Date: 2025-07-09 08:33:10 +0200
Commit message:

 add _PACKAGE
Package: scafari
Commit: daf0926fb4804db507cb1d393f729922382b3212
Author: swind <swind@uni-muenster.de>
Date: 2025-07-09 08:31:06 +0200
Commit message:

 biocstyle vignette with correct indent
Package: scafari
Commit: f582e5562942970c5313140eb0d3fdfedc41aba6
Author: swind <swind@uni-muenster.de>
Date: 2025-07-09 08:30:36 +0200
Commit message:

 paste in stop error handling
Package: scafari
Commit: 8fc089f88710c4e6f70b5f06e3877f809960eae6
Author: swind <swind@uni-muenster.de>
Date: 2025-07-09 08:29:34 +0200
Commit message:

 version to 3, change to Bioc install
Package: scafari
Commit: da8d59ddb6b7882062eb7e0a62fd05920527d5a9
Author: swind <swind@uni-muenster.de>
Date: 2025-07-08 16:41:53 +0200
Commit message:

 fix line breaks, error handling and add files for testing
Package: scafari
Commit: 342614a885906bc4fed9bc79e3c09c7c6f329859
Author: swind <swind@uni-muenster.de>
Date: 2025-07-08 16:39:48 +0200
Commit message:

 fix line breaks and error handling
Package: scafari
Commit: adde3cc35277faa610b36c985bbb95daea9c5d72
Author: swind <swind@uni-muenster.de>
Date: 2025-07-08 16:39:08 +0200
Commit message:

 add content
Package: scafari
Commit: 14f328ac8c766b14bb815e2308247c8dfaa75512
Author: swind <swind@uni-muenster.de>
Date: 2025-07-08 16:38:51 +0200
Commit message:

 reformat, remove hidden fct from export
Package: scafari
Commit: bf82fa104a41e5c2fbf908bd120a3a7463fbacf1
Author: swind <swind@uni-muenster.de>
Date: 2025-07-07 10:23:21 +0200
Commit message:

 document data acquisition
Package: scafari
Commit: 81fa89ee5098fa833c53218ad2ca5510f9464264
Author: swind <swind@uni-muenster.de>
Date: 2025-07-07 09:10:28 +0200
Commit message:

 fix typo
Package: scafari
Commit: ffa1301a5407b3d4a57ca0821ec1c9fcf0112eb9
Author: swind <swind@uni-muenster.de>
Date: 2025-07-06 20:08:08 +0200
Commit message:

 fix = assignements and 1:2 to seq
Package: scafari
Commit: 31bb3f52430800aa655b0220fb930746ea3f2b4c
Author: swind <swind@uni-muenster.de>
Date: 2025-07-06 19:55:13 +0200
Commit message:

 rm print
Package: scafari
Commit: 14f3a1a59bdb6e391ea282c534d84011dfe554e6
Author: swind <swind@uni-muenster.de>
Date: 2025-07-06 19:53:53 +0200
Commit message:

 rm print
Package: splatter
Commit: 230eec3d0d6d16f94df77b280fe70ac9714a7ed5
Author: Luke Zappia <lazappi@users.noreply.github.com>
Date: 2025-07-08 21:04:15 +0200
Commit message:

 Update NEWS and bump version
Package: splatter
Commit: c49f484751f995bf771c7d1c15eccbf7fb7eea76
Author: Luke Zappia <lazappi@users.noreply.github.com>
Date: 2025-07-08 21:02:03 +0200
Commit message:

 Fix documentation links
Package: splatter
Commit: ad02e55c6e5069a75a7113b92fcc0e01f1bff380
Author: Luke Zappia <lazappi@users.noreply.github.com>
Date: 2025-07-08 21:01:01 +0200
Commit message:

 Fix inst/NEWS.Rd formatting
Package: cellxgenedp
Commit: fc61bdfe7a67844b6c89354d924affa3ab1006a7
Author: Martin Morgan <mtmorgan.xyz@gmail.com>
Date: 2025-07-08 13:23:02 -0400
Commit message:

 do not unlist 'facet' columns when constructing tibbles

- fixes bug introduced when all 'organism' dataset entries have a
  single organism
Package: immunogenViewer
Commit: 3a07d7924aa724538e22f167797fac802fac9cba
Author: Waury <kwy700@login3.cm.cluster>
Date: 2025-07-08 18:40:11 +0200
Commit message:

 Version bump
Package: immunogenViewer
Commit: 0a814794bdea5f5a1b5b67eee712859ab59b4053
Author: Waury <kwy700@login3.cm.cluster>
Date: 2025-07-08 18:21:18 +0200
Commit message:

 Merge remote-tracking branch 'origin/main' into devel
Package: immunogenViewer
Commit: 039fd544301dcaf89cf7f3fcc2e8f68a0ea3317c
Author: Katharina Waury <47524923+kathiwaury@users.noreply.github.com>
Date: 2025-07-08 18:13:54 +0200
Commit message:

 Removed PredictProtein features
Package: BiocBaseUtils
Commit: f61c0e1d9ad6e6336ae248a6d4e92d93e7f9a8da
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-07-08 11:36:10 -0400
Commit message:

 update NEWS.md
Package: BiocBaseUtils
Commit: 0cc24a13cf27bc376000926f0b55642b7b9a7e63
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-07-08 11:31:24 -0400
Commit message:

 version bump 1.11.1
Package: BiocBaseUtils
Commit: c8ad63cff998e7a3d02e4b4758ee6b7a2e6be9e7
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-07-08 11:31:14 -0400
Commit message:

 add pkgs to error output in checkInstalled
Package: BiocBaseUtils
Commit: 40693d5d27eb365286d9f50feda7956b669ecc2e
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-07-08 11:30:58 -0400
Commit message:

 update lifeCycle examples
Package: ChemmineOB
Commit: 41a61277ee6bea2584f3df6c785f1e32e2a6cb18
Author: khoran <khoran@cs.ucr.edu>
Date: 2025-07-08 08:20:54 -0700
Commit message:

 re-add dependance for zlibbioc to windows build, as it seems to not build otherwise
Package: rawrr
Commit: 02c1b11bdf773ae71b30dc1953cdb60013e6b478
Author: Christian Panse <cp@fgcz.ethz.ch>
Date: 2025-07-08 15:09:38 +0200
Commit message:

 #92 add stdout and stderr to system2
Package: proActiv
Commit: b882c5c43273946decd313369bfeb640f46b4f81
Author: jleechung <joseph.lee@u.nus.edu>
Date: 2025-07-08 13:57:57 +0100
Commit message:

 Update annotation seqinfo class with GenomeInfoDb
Package: proActiv
Commit: f5afd3ddf0430b7090469b6899e89a9b68adcf6c
Author: jleechung <joseph.lee@u.nus.edu>
Date: 2025-07-08 13:15:42 +0100
Commit message:

 Merge remote-tracking branch 'upstream/devel' into devel
Package: proActiv
Commit: 11623e558b9a799d63da1da5d4ed0fe9917d6ae4
Author: Joseph Lee <joseph.lee@u.nus.edu>
Date: 2022-01-24 16:17:35 +0800
Commit message:

 Merge pull request #37 from lu000016/master

fix a typo in doc
Package: proActiv
Commit: 14ba4142e202f0749830e872cb41f5c8fe2791e0
Author: Xiaotong Lu <lu000016@hi129-060.hi.umn.edu>
Date: 2022-01-20 19:38:13 -0600
Commit message:

 fix a typo in doc

error is found in (### Creating a Promoter Annotation object)

"annotation" -> "annotations"
Package: ProteinGymR
Commit: 9d2cbe1ea1cf12c686855461d5ecf39fd3e7b769
Author: tram-nguyen-n <tram_nguyen@hms.harvard.edu>
Date: 2025-07-08 12:10:37 +0000
Commit message:

 bumped version
Package: ProteinGymR
Commit: dfb6cd7aaff886c1fea7620ebcac3b243aa62e0c
Author: Tram Nguyen <tram_nguyen@hms.harvard.edu>
Date: 2025-07-08 08:07:15 -0400
Commit message:

 Merge pull request #48 from ccb-hms/RELEASE_3_21

fix vignette typos
Package: ProteinGymR
Commit: 2d2dc25c89b8de808494309d8673dff86f3ec69f
Author: Tram Nguyen <tram_nguyen@hms.harvard.edu>
Date: 2025-07-08 08:06:48 -0400
Commit message:

 Merge branch 'devel' into RELEASE_3_21
Package: ProteinGymR
Commit: aaf4a8d1b564382244b7035a5b53cb8a450ee88f
Author: tram-nguyen-n <tram_nguyen@hms.harvard.edu>
Date: 2025-07-08 12:05:20 +0000
Commit message:

 fixed typos
Package: ProteinGymR
Commit: 601e135f6ce8c8dbd2d84334802a6c1c0f5e3475
Author: tram-nguyen-n <tram_nguyen@hms.harvard.edu>
Date: 2025-07-07 21:08:32 +0000
Commit message:

 bumped version
Package: ProteinGymR
Commit: 2d47ce8c6b972c6ee26222d8f7dbcc9bb53f2b00
Author: tram-nguyen-n <tram_nguyen@hms.harvard.edu>
Date: 2025-07-07 21:08:06 +0000
Commit message:

 -fixed zeroshot heatmap scaling
-vignette edits

Merge remote-tracking branch 'origin/devel' into RELEASE_3_21

# Conflicts:
#	DESCRIPTION
Package: ProteinGymR
Commit: 0b34428e52ebe03090abce719813d5eb5be2e5c0
Author: tram-nguyen-n <tram_nguyen@hms.harvard.edu>
Date: 2025-06-02 14:54:58 +0000
Commit message:

 bump version for RELEASE
Package: velociraptor
Commit: 7b11f27fecda81927d8a097823138b93ae6e7577
Author: Kevin Rue-Albrecht <kevinrue67@gmail.com>
Date: 2025-07-08 13:09:03 +0100
Commit message:

 Merge remote-tracking branch 'upstream/devel' into devel
Package: velociraptor
Commit: 89fb8cc1b361672a47365d70dcd2773b891579a9
Author: Kevin Rue-Albrecht <kevinrue67@gmail.com>
Date: 2025-07-08 13:06:20 +0100
Commit message:

 Fixes needed for Bioconductor 3.22 release (#99)

* bump x.y.z version to even y prior to creation of RELEASE_3_20 branch

* bump x.y.z version to odd y following creation of RELEASE_3_20 branch

* 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

* import OS detecting functions from basilisk

* update bioc version in github action

* switch r version to use

* add news and description

* reset windows environment

* Update basilisk.R

* Update basilisk.R

* Update basilisk.R

* Update test-plotting.R

* fix example

* last move away from basilisk.utils

* try pinning 'scvelo==0.3.3' for all three os

* switch github action macos runner to match BBS (macos-arm 13)

* fix conditions to match all macOS runners

* fetch R version appropriate version of units for macos

* downgrade llvm to last know version supported by llvmlite

* remove extra steps apparently not needed for macos runners

---------

Co-authored-by: J Wokaty <jennifer.wokaty@sph.cuny.edu>
Co-authored-by: A Wokaty <andres.wokaty@sph.cuny.edu>
Co-authored-by: Kevin Rue <kevinrue@users.noreply.github.com>
Package: asuri
Commit: 705528a47c491fe85f28dd888519a3aecc2f990d
Author: aberral <aberralgonzalez@gmail.com>
Date: 2025-07-08 11:59:18 +0200
Commit message:

 initial fixes
- CMD ERRORS
- VIGNETTE FIX
Package: PoDCall
Commit: 10b9db7a62469760792dce7953a4524b9aa65f7d
Author: Hans Petter Brodal <hanspbr@uio.no>
Date: 2025-07-08 10:44:33 +0200
Commit message:

 Fixed conflicts in version change
Package: PoDCall
Commit: ea07dc95f0f964057d2d664aec77cf6181899272
Author: Hans Petter Brodal <hanspbr@uio.no>
Date: 2025-07-08 10:38:27 +0200
Commit message:

 Added alternative way to set threshold for instances when it would otherwise be returned as NA. Bumped version.
Package: GenVisR
Commit: 6b022978f0e8876c712b478f3fb5ab99a947bc56
Author: zlskidmore <zlskidmore@gmail.com>
Date: 2025-07-07 19:57:40 -0500
Commit message:

 formally deprecate all vdiffr functions, and attempt to work around data.table melt and dcast issues
Package: MetabolomicsPipeline
Commit: edf925863fd53829dd53daccb0a4e62a72f33b04
Author: joelparkeruofa <joelparker@arizona.edu>
Date: 2025-07-07 15:57:15 -0700
Commit message:

 updating to camel casing
Package: GEOquery
Commit: c9f0784e31b14aa7b0872e250452f5fa60830c75
Author: Sean Davis <seandavi@gmail.com>
Date: 2025-07-07 15:26:32 -0700
Commit message:

 version bump
Package: GEOquery
Commit: 547d01fdea84901bc657b54b2c476b46eb3c33eb
Author: Sean Davis <seandavi@gmail.com>
Date: 2025-07-07 15:25:35 -0700
Commit message:

 Merge branch 'devel' of git.bioconductor.org:packages/GEOquery into devel
Package: GEOquery
Commit: c83c5ab5fd3f3af99e80c228503043624a1dbe58
Author: Sean Davis <seandavi@gmail.com>
Date: 2025-07-07 15:21:00 -0700
Commit message:

 Merge branch 'main' into devel
Package: GEOquery
Commit: 974828c6f3a54a639bf15cd0ad8c94beacf799bc
Author: Sean Davis <seandavi@gmail.com>
Date: 2025-07-07 15:17:53 -0700
Commit message:

 bug fix in rna-seq handling

When GEO processes RNA-seq data, they drop samples
that do not meet QC criteria. This results in a
mismatch between the sample information in the
GSE and the quantifications that GEO produces. This
fix just matches the names to limit to only those
samples with quantification available.
Package: GEOquery
Commit: ed73c1a3a6208b5723d75aa65f3da02f77f809b4
Author: Sean Davis <seandavi@gmail.com>
Date: 2024-11-08 10:30:31 -0500
Commit message:

 Add citation.cff
Package: mia
Commit: 95ee8b1c13c7699f405b20569c80d4df6a23a5dd
Author: Tuomas Borman <60338854+TuomasBorman@users.noreply.github.com>
Date: 2025-07-08 00:09:54 +0300
Commit message:

 Fix unit tests (#747)
Package: ProteinGymR
Commit: d45bfad5383730cebd159f1cb950cd897453877e
Author: tram-nguyen-n <tram_nguyen@hms.harvard.edu>
Date: 2025-07-07 21:10:19 +0000
Commit message:

 bumped version
Package: ProteinGymR
Commit: 6e7aa2eab35edff9bccbb347111f7fe8c10f3a45
Author: tram-nguyen-n <tram_nguyen@hms.harvard.edu>
Date: 2025-07-07 21:00:24 +0000
Commit message:

 fixed numbering typo
Package: ProteinGymR
Commit: 91c6100db7f249d8332df6ab1dde3520f9c5ccde
Author: tram-nguyen-n <tram_nguyen@hms.harvard.edu>
Date: 2025-07-07 20:59:56 +0000
Commit message:

 edits to visualization vignette
Package: ProteinGymR
Commit: 487e8f138ed4a40f958f69f321db49bd35ee8b3c
Author: tram-nguyen-n <tram_nguyen@hms.harvard.edu>
Date: 2025-06-18 14:54:55 -0400
Commit message:

 bug fix for model heatmap scaling
Package: ProteinGymR
Commit: 17eef1b7fa25a4ddb51a9e31694c9348e9a67129
Author: tram-nguyen-n <tram_nguyen@hms.harvard.edu>
Date: 2025-06-18 11:49:19 -0400
Commit message:

 polish up data vignette
Package: fgsea
Commit: d6f1670c60bbc48ad1a95f98dc52921ec98d2542
Author: Alexey Sergushichev <alsergbox@gmail.com>
Date: 2025-07-07 15:59:21 -0500
Commit message:

 version bump
Package: fgsea
Commit: 8e64800f60cc1bcf9466cec5e743e4d981fb32e8
Author: Alexey Sergushichev <alsergbox@gmail.com>
Date: 2025-07-07 13:11:46 -0500
Commit message:

 specify name of msigdbr arguments
Package: NanoStringNCTools
Commit: 6c5e9350a8d3217c09685ed5e1215c6a0a348928
Author: Maddy Griswold <mgriswold@nanostring.com>
Date: 2025-07-07 12:32:39 -0600
Commit message:

 dev version
Package: NanoStringNCTools
Commit: 5c9db853f986c701ac2f13cd616c937558d03b64
Author: Griswold <Madison.Griswold@bruker.com>
Date: 2025-07-07 12:11:12 -0600
Commit message:

 version merge
Package: NanoStringNCTools
Commit: f318d38b803015b11b2b1b608911aed6a6503588
Author: Maddy Griswold <40255151+maddygriz@users.noreply.github.com>
Date: 2025-07-07 12:08:04 -0600
Commit message:

 update to bioc version
Package: NanoStringNCTools
Commit: cbec1b3b1f2f8856aef5a7288388b4b87918df03
Author: Griswold <Madison.Griswold@bruker.com>
Date: 2025-07-07 11:56:44 -0600
Commit message:

 Merge remote-tracking branch 'upstream/devel'
Package: NanoStringNCTools
Commit: 8da0197d2e6f4527730b511537d9ff93800a7c78
Author: Maddy Griswold <40255151+maddygriz@users.noreply.github.com>
Date: 2025-07-07 11:08:00 -0600
Commit message:

 Merge pull request #40 from Nanostring-Biostats/envBug

Environments cannot be NULL
Package: NanoStringNCTools
Commit: a3f442e4306fab00ad84a7c2d06d15f0cfee0737
Author: Maddy Griswold <40255151+maddygriz@users.noreply.github.com>
Date: 2025-05-19 09:36:06 -0600
Commit message:

 Update to Bruker signature
Package: NanoStringNCTools
Commit: 955c8db46305766ee5664edf564e5ddb8a8052f5
Author: Maddy Griswold <mgriswold@nanostring.com>
Date: 2025-04-30 19:44:27 +0000
Commit message:

 new environment
Package: NanoStringNCTools
Commit: b18f4949bd65862ef27a1a38f87ed7b5d83e26ca
Author: Maddy Griswold <40255151+maddygriz@users.noreply.github.com>
Date: 2024-12-16 11:05:24 -0700
Commit message:

 update to bruker support email
Package: immunotation
Commit: 6def00b68d74700129af030bd3a2f994d4f10f27
Author: lshep <lori.shepherd@roswellpark.org>
Date: 2025-07-07 13:08:19 -0400
Commit message:

 Deprecated
 - unresponsive
 - email bounced
Package: qckitfastq
Commit: 6157afcc7596d5b1f442040f8886beea24be24aa
Author: lshep <lori.shepherd@roswellpark.org>
Date: 2025-07-07 12:54:41 -0400
Commit message:

 Deprecated
- unresponsive
Package: ELViS
Commit: 24a63cbf47ca7afdada036e19a6693d9576a8f77
Author: jlee307@uthsc.edu <jlee307@login2.cn.isaac.utk.edu>
Date: 2025-07-07 12:46:37 -0400
Commit message:

 bug fix
Package: XNAString
Commit: b20a70bf7d0f54b41ebd11f5b38fccdcc6a65e14
Author: lshep <lori.shepherd@roswellpark.org>
Date: 2025-07-07 12:39:25 -0400
Commit message:

 Deprecation

 - unresponsive
 - emails bounced
Package: Rfastp
Commit: 7b7ac5f4326296235dcd7251fbe2a847c2bb64d1
Author: lshep <lori.shepherd@roswellpark.org>
Date: 2025-07-07 12:36:36 -0400
Commit message:

 Deprecate

 - unresponsive
Package: MADSEQ
Commit: dbdc7a667792aa2aa0df8e0ac3132e9e13507c56
Author: lshep <lori.shepherd@roswellpark.org>
Date: 2025-07-07 12:29:00 -0400
Commit message:

 Deprecated

  - unresponsive
Package: Harshlight
Commit: 5d2eb5d3803237823196d597301ed86ff6645f8e
Author: lshep <lori.shepherd@roswellpark.org>
Date: 2025-07-07 12:24:28 -0400
Commit message:

 Deprecated

 - unresponsive
 - email bounced
Package: DeeDeeExperiment
Commit: 5e9ba2bfc6898b18bde19a947422063e595da33e
Author: Najla Abassi <abassi.nejla96@gmail.com>
Date: 2025-07-07 16:44:31 +0200
Commit message:

 updating the news and version bump 0.99.1
Package: vsclust
Commit: 900f4303639e10a90e70fed989138bbefdfaf229
Author: veitveit <veits@bmb.sdu.dk>
Date: 2025-07-07 10:15:51 +0200
Commit message:

 versioning
Package: vsclust
Commit: 54c3047400be2b97c4ba54bcf561036d90022139
Author: veitveit <veits@bmb.sdu.dk>
Date: 2025-07-07 10:15:08 +0200
Commit message:

 fixes for bioconductor
Package: vsclust
Commit: b38c29c5a9f7e850d7eb9f8dbc3986da2f5d6064
Author: veitveit <veits@bmb.sdu.dk>
Date: 2025-07-07 10:14:58 +0200
Commit message:

 fixes for bioconductor
Package: SpectriPy
Commit: 2422daf5583c89b82a84dacc5e2acb5b0440e4b5
Author: jorainer <johannes.rainer@gmail.com>
Date: 2025-07-07 09:32:34 +0200
Commit message:

 refactor: force immediate loading of Python libraries
Package: SpectriPy
Commit: 31c783304662e199ac796e637288f8e95efb7cec
Author: jorainer <johannes.rainer@gmail.com>
Date: 2025-07-04 16:02:37 +0200
Commit message:

 docs: update/fix installation instructions

- Update the README pointing to the new configuration.
- Update the installation instruction vignette.
Package: BgeeCall
Commit: bd5e591be69aeafd9950333f740c22c2651984ae
Author: Julien Wollbrett <julien.wollbrett@unil.ch>
Date: 2025-07-07 09:30:26 +0200
Commit message:

 add last missing dependencies
Package: AlphaMissenseR
Commit: 66a10dcf61a33648b22da86df21a3f9596562ecc
Author: Martin Morgan <mtmorgan.xyz@gmail.com>
Date: 2025-07-06 18:44:43 -0400
Commit message:

 Merge branch 'ccb-hms-devel' into devel
Package: AlphaMissenseR
Commit: cc85322f3d8731212ed6d2e37be44cd1107d1b32
Author: tram-nguyen-n <tram_nguyen@hms.harvard.edu>
Date: 2025-06-30 15:55:20 +0000
Commit message:

 bump version
Package: AlphaMissenseR
Commit: 2b7636d7ca335575fcf06edb8eb554ab26fb3e0c
Author: tram-nguyen-n <tram_nguyen@hms.harvard.edu>
Date: 2025-06-30 15:55:02 +0000
Commit message:

 require GenomicRanges duckdb >= 1.3.1
Package: epistasisGA
Commit: 94dbf1e1a8d4585e2d2e8b8092fa43c1f31bfbd2
Author: mnodzenski <michael.nodzenski@gmail.com>
Date: 2025-07-06 14:40:40 -0400
Commit message:

 bump version number to build E-GADGETS update
Package: epistasisGA
Commit: 72dee36a931af0efe45226bfff2c5969c9bd992f
Author: mnodzenski <michael.nodzenski@gmail.com>
Date: 2023-02-15 16:00:27 -0500
Commit message:

 Updated version of E-GADGETS with new nomination procedure for risk alleles and permuting exposure in the standardization step.
Package: epistasisGA
Commit: 5646bd125b573953960e8f509f3055f20c1070fd
Author: Michael Nodzenski <michael.nodzenski@gmail.com>
Date: 2025-07-06 13:24:12 -0400
Commit message:

 Merge pull request #2 from SciomeLLC/dev

Vignette modifications and bug fix for missing data preprocessing
Package: epistasisGA
Commit: aed48a4eec3e4998862d39f80617832987d96b02
Author: sciome-bot <software.tools@sciome.com>
Date: 2024-06-25 16:23:40 -0400
Commit message:

 Merge branch 'master' of github-sciome-bot:SciomeLLC/epistasisGA into dev
Package: epistasisGA
Commit: 824630703e9d7ced09d0b21df697c8339b14fa9a
Author: sciome-bot <software.tools@sciome.com>
Date: 2024-06-25 16:22:53 -0400
Commit message:

 fixing bug in missing data preprocessing
Package: epistasisGA
Commit: 5481a6ebc435929fafe3d7449a5e840d30a7c5f0
Author: sciome-bot <software.tools@sciome.com>
Date: 2024-03-27 10:28:27 -0400
Commit message:

 Modifying vignette to clarify global permutation tests vs. not. fleshing out information on SNPs in the same LD block.
Package: epistasisGA
Commit: 47b4d305def824a72a5481235c613355a39bf903
Author: Taylor Petty <Taylor.Petty@sciome.com>
Date: 2024-03-15 11:54:22 -0400
Commit message:

 Final change to markdown -- change from David and Clare
Package: epistasisGA
Commit: bbb85cbcdc1f0139a059247882c26ed4bf79fcd6
Author: Taylor Petty <Taylor.Petty@sciome.com>
Date: 2024-03-13 16:29:31 -0400
Commit message:

 remove explanation of why external data, per David's suggestion
Package: epistasisGA
Commit: 1696b9fe400bde5cc45aa4c7d50b14128a13ab85
Author: Taylor Petty <Taylor.Petty@sciome.com>
Date: 2024-03-13 11:38:17 -0400
Commit message:

 Minor additions from Clare
Package: epistasisGA
Commit: 026fe9faa0d6a37cc98eb28d1283f405312c760f
Author: Taylor Petty <Taylor.Petty@sciome.com>
Date: 2024-03-12 15:03:57 -0400
Commit message:

 fleshing out information on SNPs in the same LD block
Package: epistasisGA
Commit: 93eb8f09d174b1faf999e609be089d67105594a2
Author: Taylor Petty <Taylor.Petty@sciome.com>
Date: 2024-03-12 13:23:03 -0400
Commit message:

 Modifying vignette to clarify global permutation tests vs. not
Package: epialleleR
Commit: a330d040243300ef86cea9bce2fde1fd09442e58
Author: Oleksii.Nikolaienko <oleksii.nikolaienko@uib.no>
Date: 2025-07-06 13:52:13 +0200
Commit message:

 fix documentation crosslinks
Package: epialleleR
Commit: 6e0a1af34aee2afe29f177a2aaa53946920b0f33
Author: Oleksii.Nikolaienko <oleksii.nikolaienko@uib.no>
Date: 2025-07-06 13:31:29 +0200
Commit message:

 GenomeInfoDb to Seqinfo
Package: epialleleR
Commit: d92bd1ae217adcc83890a0855d6c85c01a5fee96
Author: Oleksii.Nikolaienko <oleksii.nikolaienko@uib.no>
Date: 2025-07-05 20:52:30 +0200
Commit message:

 fresh check
Package: ramr
Commit: 87b137fc8656d351572a96c03cfb195d816985e1
Author: Oleksii.Nikolaienko <oleksii.nikolaienko@uib.no>
Date: 2025-07-06 13:03:47 +0200
Commit message:

 GenomeInfoDb to Seqinfo
Package: ramr
Commit: 8bba30d48def5e7f855c979a097980c0f5258c90
Author: Oleksii.Nikolaienko <oleksii.nikolaienko@uib.no>
Date: 2025-07-05 21:24:19 +0200
Commit message:

 fresh check
Package: Aerith
Commit: 39ba1fa008d94a43f6e30d32c7497acce744ed94
Author: xyz1396 <1074082710@qq.com>
Date: 2025-07-06 02:19:30 -0500
Commit message:

 bump version
Package: Aerith
Commit: a74cebba9cfa4fecebce9b1133378a073cdf295d
Author: xyz1396 <1074082710@qq.com>
Date: 2025-07-06 02:13:21 -0500
Commit message:

 Merge updates for .gitignore, plotPSMs.R, readScans.cpp, and test_scorePSM.R from dev branch for fix R CMD check error
Package: stPipe
Commit: 7dc40c0913618f23c23de7e45d37f3b75dfffd3c
Author: YangXuuu <xuyang1121wws@gmail.com>
Date: 2025-07-05 18:22:32 +1000
Commit message:

 Version update and adressing warnings.
Package: Coralysis
Commit: 216b175ffc5c13a1c8648847ff02af87be6eea98
Author: antonioggsousa <antonioggsousa@gmail.com>
Date: 2025-07-05 10:05:20 +0300
Commit message:

 Testing Coralysis logo rendenring size
Package: Coralysis
Commit: 818194e80e7b711fa9a229959fbcd95267855496
Author: antonioggsousa <antonioggsousa@gmail.com>
Date: 2025-07-05 10:02:18 +0300
Commit message:

 Testing Coralysis logo rendenring size
Package: Coralysis
Commit: b28a0ce63bbf6901beae987148a836a82b57a535
Author: antonioggsousa <antonioggsousa@gmail.com>
Date: 2025-07-04 16:27:49 +0300
Commit message:

 Testing Coralysis logo rendenring size
Package: Coralysis
Commit: ae73f69d1f369b84e28f171012114dd9d17f18e8
Author: antonioggsousa <antonioggsousa@gmail.com>
Date: 2025-07-04 16:21:47 +0300
Commit message:

 Testing Coralysis logo rendenring size
Package: Coralysis
Commit: 109f1548a0a7bc0409a74bd81b29621bd8779cc3
Author: antonioggsousa <antonioggsousa@gmail.com>
Date: 2025-07-04 16:20:37 +0300
Commit message:

 Testing Coralysis logo rendenring size
Package: Coralysis
Commit: 8ebee30ae086adf2f590eda0d6931af5f1235f7c
Author: antonioggsousa <antonioggsousa@gmail.com>
Date: 2025-07-04 16:18:27 +0300
Commit message:

 Testing Coralysis logo rendenring size
Package: gdsfmt
Commit: ff1082fbad07defaab2f8c6a3a42861811b4f26a
Author: Xiuwen Zheng <zhengxwen@gmail.com>
Date: 2025-07-05 00:12:34 -0500
Commit message:

 fast appending
Package: SeqArray
Commit: 309bc2316bf5c92a7ac6cad92f44f79fa0341330
Author: Xiuwen Zheng <zhengxwen@gmail.com>
Date: 2025-07-05 00:00:02 -0500
Commit message:

 parallel seqDigest()
Package: edgeR
Commit: 26fba820320d7ebb7ae7e609955c1af0af7663bb
Author: Gordon Smyth <smyth@wehi.edu.au>
Date: 2025-07-05 11:29:48 +1000
Commit message:

 edgeR 4.7.3
- New function catchOarfish.
- New argument `path` for catchRSEM.
Package: ontoProc
Commit: 9763147bd1d33db87b5922f7e34eaa52daa0cc8e
Author: vjcitn <stvjc@channing.harvard.edu>
Date: 2025-07-04 14:12:23 -0400
Commit message:

 improve formalize function
Package: GenomicScores
Commit: dd870d995f25a7c51a67c51cc6fb74dd0e728f22
Author: Robert Castelo <robert.castelo@upf.edu>
Date: 2025-07-04 19:23:05 +0200
Commit message:

 Fixed GHA workflow for release
Package: GenomicScores
Commit: 149d977e1fa73025a0766516bc5c3f1f56603bd2
Author: Robert Castelo <robert.castelo@upf.edu>
Date: 2025-07-04 18:47:52 +0200
Commit message:

 Fixed coverage badge in README
Package: GenomicScores
Commit: fea1c6bd9b51b301b7c4392032fe4f9a8aa69360
Author: Robert Castelo <robert.castelo@upf.edu>
Date: 2025-07-04 18:26:06 +0200
Commit message:

 Added workflow_dispatch to GHA workflow
Package: GenomicScores
Commit: b325af1a3d77b4349a59a67f605e8f819c97e097
Author: Robert Castelo <robert.castelo@upf.edu>
Date: 2025-07-04 18:13:41 +0200
Commit message:

 Bump version
Package: GenomicScores
Commit: 18d6ddccf6bd26ddae84c355f47869afdf6ad9e7
Author: Robert Castelo <robert.castelo@upf.edu>
Date: 2025-07-04 18:13:27 +0200
Commit message:

 Fixed resources metadata and documentation problems
Package: Coralysis
Commit: a0a11eb2943d210284fedc984085d14091511e2e
Author: antonioggsousa <antonioggsousa@gmail.com>
Date: 2025-07-04 16:10:53 +0300
Commit message:

 Add funding
Package: Coralysis
Commit: d15ef6e5ae2d33eac340bd7c525bdb65b27a3b27
Author: antonioggsousa <antonioggsousa@gmail.com>
Date: 2025-07-04 13:46:37 +0300
Commit message:

 Fix formatting issues
Package: Coralysis
Commit: bb46cb52ab6f8b1c731899e7bc470ea3d333352c
Author: antonioggsousa <antonioggsousa@gmail.com>
Date: 2025-07-04 13:28:26 +0300
Commit message:

 Updating the README.md file
Package: Coralysis
Commit: f97606fdaf7c6e79f6fa5205a8469f8ff79439a7
Author: Antonio Goncalves de Sousa <aggode@node03.novalocal>
Date: 2025-06-27 10:14:20 +0300
Commit message:

 Fixing alias name typo
Package: ontoProc
Commit: e962d95c605de3ec1f5585dc6f5938774aa181e1
Author: vjcitn <stvjc@channing.harvard.edu>
Date: 2025-07-04 06:31:55 -0400
Commit message:

 add the demonstration mapping with ellmer
Package: stPipe
Commit: fb2ff37f286ebda232a4cab3a1e446ad1624e14c
Author: YangXuuu <xuyang1121wws@gmail.com>
Date: 2025-07-04 17:44:21 +1000
Commit message:

 Version update.
Package: stPipe
Commit: 98246b5469f138f29541a9aea476c640ec184593
Author: YangXuuu <xuyang1121wws@gmail.com>
Date: 2025-07-04 17:43:59 +1000
Commit message:

 Rename progressbar.
Package: stPipe
Commit: 5c5ec2143e829afddd866dc5eddc12c2e1fdf5d1
Author: YangXuuu <xuyang1121wws@gmail.com>
Date: 2025-07-04 17:38:44 +1000
Commit message:

 Replace cout with Rcpp::Rcout.
Package: SpectriPy
Commit: 9d639a666c107ef9816f7e3ddde1ccd27f0180c3
Author: jorainer <johannes.rainer@gmail.com>
Date: 2025-07-04 09:24:13 +0200
Commit message:

 docs: add labels to vignette code chunks
Package: stPipe
Commit: 89a4b6dd5cd41ecebfe026787278f1967bdc31ff
Author: YangXuuu <xuyang1121wws@gmail.com>
Date: 2025-07-04 17:34:58 +1000
Commit message:

 Replace << endl; with + n;.
Package: SpectriPy
Commit: 05f30dbb32c0f51fa228bc67fc55c2888f3295f0
Author: jorainer <johannes.rainer@gmail.com>
Date: 2025-07-03 09:14:21 +0200
Commit message:

 ci: set RETICULATE_PYTHON_ENV to .Rprofile for macOS
Package: SpectriPy
Commit: 661c1f77191eb5ef3d90f641b00b4148d2e0fb46
Author: jorainer <johannes.rainer@gmail.com>
Date: 2025-07-03 08:24:16 +0200
Commit message:

 ci: use RETICULATE_PYTHON_ENV on macOS
Package: SpectriPy
Commit: ed4f98bd7460ca3c7502a50b3f06376866674f81
Author: jorainer <johannes.rainer@gmail.com>
Date: 2025-07-03 07:50:56 +0200
Commit message:

 ci: next try to fix macOS GHA
Package: SpectriPy
Commit: faaac109090d4cbb8a9ce488c646f1a979651490
Author: jorainer <johannes.rainer@gmail.com>
Date: 2025-07-02 15:05:08 +0200
Commit message:

 ci: create full virtualenv for macOS
Package: SpectriPy
Commit: 68bed8e8326949e8114a18dcb564142174b82837
Author: jorainer <johannes.rainer@gmail.com>
Date: 2025-07-02 14:43:48 +0200
Commit message:

 ci: create a virtual env for macOS
Package: SpectriPy
Commit: 323d1d602e4f9ddb53e68e23986f3b8b770e8743
Author: jorainer <johannes.rainer@gmail.com>
Date: 2025-07-02 14:15:49 +0200
Commit message:

 ci: remove forced installation of reticulate on macOS
Package: SpectriPy
Commit: cdd4f74599140a7ee3d40119785e69e95eac99c5
Author: jorainer <johannes.rainer@gmail.com>
Date: 2025-07-02 11:03:03 +0200
Commit message:

 refactor: use py_require instead of manual library installation

- Change to the new suggested `py_require()` functions from *reticulate* (issue
  #81).
Package: SpectriPy
Commit: aa7104b0106a763eda4cfa6747c14d965f3dd121
Author: jorainer <johannes.rainer@gmail.com>
Date: 2025-06-13 11:45:16 +0200
Commit message:

 ci: install Python through reticulate on macOS
Package: SpectriPy
Commit: daab62bb647eea0c0994177d3d01b53ddded927f
Author: jorainer <johannes.rainer@gmail.com>
Date: 2025-06-13 10:34:50 +0200
Commit message:

 ci: use dependencies = TRUE
Package: SpectriPy
Commit: 51625b4dd95fd06d328f647f1006dfd2644f1b66
Author: jorainer <johannes.rainer@gmail.com>
Date: 2025-06-13 08:10:15 +0200
Commit message:

 ci: disable package caching on linux
Package: SpectriPy
Commit: 1f49f1ed19471c5c61ba249421efe9dc30c0949c
Author: jorainer <johannes.rainer@gmail.com>
Date: 2025-06-13 07:42:48 +0200
Commit message:

 ci: macOS install python with brew
Package: SpectriPy
Commit: 83b7e9eacdeb0d5750873d10432580a39eb6b5c0
Author: jorainer <johannes.rainer@gmail.com>
Date: 2025-06-13 07:36:05 +0200
Commit message:

 ci: macOS install pyenv
Package: SpectriPy
Commit: d6067836e43c01dd00bb3953007c2b4c0d9d3607
Author: jorainer <johannes.rainer@gmail.com>
Date: 2025-06-13 07:26:25 +0200
Commit message:

 ci: use reticulate to install Python on macOS
Package: SpectriPy
Commit: 70bd26ca649455daee01a48eea4c0283fbf3bfe6
Author: jorainer <johannes.rainer@gmail.com>
Date: 2025-06-12 17:18:29 +0200
Commit message:

 ci: only install required and imported packages
Package: stPipe
Commit: 6e85cda5cfbb0e2814841bd5e17df19e894cb14d
Author: YangXuuu <xuyang1121wws@gmail.com>
Date: 2025-07-04 16:57:17 +1000
Commit message:

 Remove std::cout.
Package: stPipe
Commit: ee9d4b5d1bbddc463e5408f9e6717e25d2921875
Author: YangXuuu <xuyang1121wws@gmail.com>
Date: 2025-07-04 15:53:25 +1000
Commit message:

 Modifiy codes based on the reviewer's comments.
Package: FlexAssays
Commit: a2ac72f175d6bce4127756c9a7351b44c83aa03e
Author: ycli1995 <ycli1995@outlook.com>
Date: 2025-07-04 11:48:18 +0800
Commit message:

 Bump version to 0.99.5
* Fix ORCID
Package: FlexAssays
Commit: 787a068e01a7b1b409b5821b6723244f53bf84ef
Author: ycli1995 <ycli1995@outlook.com>
Date: 2025-07-04 11:34:36 +0800
Commit message:

 Bump version to 0.99.4
* Fix a stupid bug in DESCRIPTION
Package: FlexAssays
Commit: 67f071153be3475f4ee475422cb07e32c5628c6e
Author: ycli1995 <ycli1995@outlook.com>
Date: 2025-07-04 11:29:26 +0800
Commit message:

 Bump version to 0.99.3
* Fix WARNING and some of NOTES for bioconductor checking
Package: FlexAssays
Commit: 12a79bae1eaacf89ce5b0e805a33bbb0edb534d4
Author: ycli1995 <ycli1995@outlook.com>
Date: 2025-07-04 10:48:16 +0800
Commit message:

 Bump version to 0.99.2
* fix ERROR for `SVT_SparseArray`
Package: FlexAssays
Commit: 8676b1d269649a6141a51e85eb133ea834eaee87
Author: ycli1995 <ycli1995@outlook.com>
Date: 2025-07-04 10:29:48 +0800
Commit message:

 Bump version to 0.99.1
Package: XeniumIO
Commit: 94e988c170a91a576ddb9c32ef1d3d302019539d
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-07-03 16:58:11 -0400
Commit message:

 version bump 1.1.3
Package: XeniumIO
Commit: a7516775c1b54f9d0239de82f54171855763fb17
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-07-03 16:58:09 -0400
Commit message:

 remove rtype arg from bfcdownload
Package: MetabolomicsPipeline
Commit: 7948947c62835a21b3f6974ec0c34d0bef5fc5dd
Author: joelparkeruofa <joelparker@arizona.edu>
Date: 2025-07-03 14:08:23 -0500
Commit message:

 updating vignette
Package: MetabolomicsPipeline
Commit: e75a429dfa176a16ccde5d4e9e304c8a9a722849
Author: joelparkeruofa <joelparker@arizona.edu>
Date: 2025-07-03 14:05:55 -0500
Commit message:

 allowing messages to be true
Package: MetabolomicsPipeline
Commit: 698efd2bae32a10ac8f872676ab4c3f070857ec7
Author: joelparkeruofa <joelparker@arizona.edu>
Date: 2025-07-03 13:58:52 -0500
Commit message:

 updating documentation to not encourage users to use T/F
Package: MetabolomicsPipeline
Commit: 9ab52bb4437d9c3a6d09f7f3f959a88e892d8002
Author: joelparkeruofa <joelparker@arizona.edu>
Date: 2025-07-03 13:37:05 -0500
Commit message:

 adding magick dependency
Package: SingleMoleculeFootprinting
Commit: a208a9b73fdf38c6b81db3b018962a89bd74d98f
Author: GuidoBarzaghi <guidobarzaghi@gmail.com>
Date: 2025-07-03 17:39:57 +0200
Commit message:

 Addressed Reviewers #1 comments
Package: enrichmet
Commit: 9d5f20643a27bfb13b481fcbc5aa831fc350781d
Author: Yonatan2627 <yaayalew@gmail.com>
Date: 2025-07-03 10:52:57 -0400
Commit message:

 Bump version to 0.99.2
Package: DeconvoBuddies
Commit: 819ba70a8cee3a71cd9744299805321fd20daae7
Author: lahuuki <lahuuki@gmail.com>
Date: 2025-07-03 10:20:19 -0400
Commit message:

 Bump version
Package: DeconvoBuddies
Commit: 17f23d6a2cdc3e0b88b94943ef89586df723c43c
Author: lahuuki <lahuuki@gmail.com>
Date: 2025-07-03 10:19:06 -0400
Commit message:

 Merge branch 'devel' of github.com:LieberInstitute/DeconvoBuddies into devel
Package: DeconvoBuddies
Commit: 274d52c512b70003d0342083ddbdc6bb1e6af396
Author: lahuuki <lahuuki@gmail.com>
Date: 2025-07-03 10:18:16 -0400
Commit message:

 Add documentation for plot_type param
Package: DeconvoBuddies
Commit: 859b0be079704277480412acf74143a2e34c889a
Author: lahuuki <lahuuki@gmail.com>
Date: 2025-07-03 10:17:57 -0400
Commit message:

 Add option to plot a boxplot or violin plot with "plot_type"
Package: BgeeCall
Commit: bb6f2924480a3bddb8fc6791680a60130d33e1c3
Author: Julien Wollbrett <julien.wollbrett@unil.ch>
Date: 2025-07-03 14:50:17 +0200
Commit message:

 update dependencies
Package: org.Hbacteriophora.eg.db
Commit: 36e89ee003bad7609ac6e2d292e208fc57828f01
Author: kabilanbio <kabilan151414@gmail.com>
Date: 2025-07-03 16:50:26 +0530
Commit message:

 Resolve merge conflict in .gitignore and complete merge
Package: org.Hbacteriophora.eg.db
Commit: b0b5027e2aedd9cbaadcb5277aab807a993bde65
Author: KABILAN S <kabilan151414@gmail.com>
Date: 2025-07-03 14:58:26 +0530
Commit message:

 version bump
Package: org.Hbacteriophora.eg.db
Commit: a72c5b0a8b1c9245c5930b1d7aa021959274624e
Author: kabilanbio <kabilan151414@gmail.com>
Date: 2025-07-02 02:37:02 +0530
Commit message:

 latest_changes
Package: org.Hbacteriophora.eg.db
Commit: 17d9bbad48a3279f1df8ac3c6ef0e7da80d0ab1f
Author: kabilanbio <kabilan151414@gmail.com>
Date: 2025-07-01 18:00:30 +0530
Commit message:

 New Description
Package: org.Hbacteriophora.eg.db
Commit: f39f50d5340e835a6f081866df793a1be72d8165
Author: kabilanbio <kabilan151414@gmail.com>
Date: 2025-07-01 17:59:13 +0530
Commit message:

 Ignore RStudio project files
Package: org.Hbacteriophora.eg.db
Commit: 4851a38a997803200ce1ca459aa34d0ef065ea22
Author: kabilanbio <kabilan151414@gmail.com>
Date: 2025-07-01 15:28:11 +0530
Commit message:

 Remove .Rproj file as per BiocCheck requirement
Package: org.Hbacteriophora.eg.db
Commit: 4c4f89d816c919202801c208f9b4dc2aa307313d
Author: kabilanbio <kabilan151414@gmail.com>
Date: 2025-07-03 16:37:05 +0530
Commit message:

 Save changes to .gitignore and .Rproj before switching branches
Package: EventPointer
Commit: 0a34adb9b15d205e711f1fdc90c3481307d4a0be
Author: JFerrer-B <jafhernandez@tecnun.es>
Date: 2025-07-03 13:00:26 +0200
Commit message:

 citation of new version of EventPointer
Package: cBioPortalData
Commit: 28ec34054b440f2e3d51e0bfda877917b67d25e8
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-07-02 16:34:20 -0400
Commit message:

 version bump 2.21.4

</div> </div>