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GIT Logs

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

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Package: Rarr
Commit: 2b5ecfd29f91e015ff148d9d414d5adc1d363488
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-12-05 18:21:18 +0100
Commit message:

 Bump version
Package: Rarr
Commit: 5ed59586e70a7fc6bef9c7f577b604c30d2a5518
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-12-05 18:21:03 +0100
Commit message:

 Remove outdated README note
Package: Rarr
Commit: 3f6f5252d8b8dc3d008298e4e304ef81ab2ecef0
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-12-05 17:36:03 +0100
Commit message:

 Mark .configure_codecs() as internal
Package: Rarr
Commit: 97537ef468e7cdac1593bdd5cb32832e851ebc65
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-12-05 17:35:17 +0100
Commit message:

 Use toString() where relevant
Package: Rarr
Commit: 12688f837e48846d4dca52b92813f73dfc266628
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-12-05 15:57:09 +0100
Commit message:

 Remove outdated TODO comment
Package: Rarr
Commit: a37e401462a78464c9ac605c9c05c93ad48b7343
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-12-05 15:53:53 +0100
Commit message:

 Mark regex as fixed
Package: Rarr
Commit: 62941a449fd9b538aae644587110f3f828c699d0
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-12-05 15:53:31 +0100
Commit message:

 Run devtools::document()
Package: Rarr
Commit: 3cc9fecf4333c4feca623e5903a3bbe1089ce4a9
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-12-05 15:53:21 +0100
Commit message:

 Import back utils::tail
Package: Rarr
Commit: 7629e90506dcb01fbb62fbde0baa3b56578e33bb
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-12-05 15:52:22 +0100
Commit message:

 Simplify lz4 decompression
Package: Rarr
Commit: bf2d2c5335fe64e13f6032bc515e62c342c979ec
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-12-05 15:42:19 +0100
Commit message:

 Support numcodecs lz4
Package: Rarr
Commit: 21987f2036f4e02035e6955137a76a8626076409
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-12-05 10:26:11 +0100
Commit message:

 Remove error about multiple array bytes codec for now
Since we always add the bytes codec during the v2->v3 metadata conversion
Package: Rarr
Commit: 7e0960946b7e6e9ee4081411d7a598e85601d659
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-12-05 10:06:02 +0100
Commit message:

 Fix lazy eval issue
Package: Rarr
Commit: a7e83e692959d284bd1caa36e3a627a0b4241644
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-12-04 23:27:20 +0100
Commit message:

 Move compressors to codec infra
Package: Rarr
Commit: 5b970e13a80562a861f6cddd9fb7ad9d88035a68
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-12-04 19:28:28 +0100
Commit message:

 Group all codec steps together
Package: Rarr
Commit: 38ef050ed8bb56ebb6241e5b7d1262edd134cba0
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-12-04 19:22:46 +0100
Commit message:

 Remove obsolete short circuit in transpose codec

The no-op case is now handled is .configure_codecs() by not configuring this codec
Package: Rarr
Commit: 542305be5ba491b532c86dc8f6a69a05a747fa3b
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-12-04 17:34:30 +0100
Commit message:

 Add read_c_order benchmark test
Package: Rarr
Commit: b972a208aa0e01dd8272493d03c202b6d10fb9f3
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-12-04 17:16:21 +0100
Commit message:

 Test function factory for codecs
Package: Rarr
Commit: 14b950cddc3e685f9b3b4a7331df9cee25f0ba01
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-12-04 16:21:17 +0100
Commit message:

 Fix encode/decode naming for transpose codec
Package: Rarr
Commit: 235673f1dcd2cbe753cf8f1812020ca525425564
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-12-04 16:10:23 +0100
Commit message:

 Move decompression step to codec
Package: Rarr
Commit: cfbf109a01caae35d0d6d21790fc90b49706b12c
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-12-04 15:57:00 +0100
Commit message:

 Use _ instead of - in codec name
Package: Rarr
Commit: 354b8e060a91db60a1c91689ad619744b7ceaccd
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-12-04 15:40:47 +0100
Commit message:

 Rename endian codec to codec_bytes
Package: Rarr
Commit: f2e714e378ff4a0df63010eaa82df08be28b9d83
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-11-11 14:19:27 +0100
Commit message:

 Run devtools::document()
Package: Rarr
Commit: e9ab8647f5360a65ca920885db39a9281dd5bb6f
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-11-11 14:13:10 +0100
Commit message:

 Remove redundant arguments in compress_and_write_chunk()
Package: Rarr
Commit: 9b347f237366cef859fb4dd3521bc2173cbbab13
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-11-11 13:23:10 +0100
Commit message:

 Split codecs in files depending on their type
Package: Rarr
Commit: 1d456593b2792b4c136bb2addb674fd2049d1090
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-11-11 13:17:43 +0100
Commit message:

 Implement vlen_utf8 codec
Package: Rarr
Commit: 7412646e51380aae31b2e6e1ffcefc950deb8bfc
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-11-04 14:14:21 +0100
Commit message:

 Move all codec related steps in .compress_and_write_chunk
Package: Rarr
Commit: 29cad0c9efa05bbecf0414373aa14adc63bc0110
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-12-05 15:30:37 +0100
Commit message:

 Remove commented out unneeded code
Package: scToppR
Commit: f58d6faedad4f21f0ffd0fea5a1daed96b2b9497
Author: Bryan Granger <grangerb@musc.edu>
Date: 2025-12-05 12:17:56 -0500
Commit message:

 Increment version number to 0.99.6
Package: scToppR
Commit: f89a7c8aa472947694f05c945d53d0b1da19fccb
Author: Bryan Granger <grangerb@musc.edu>
Date: 2025-12-05 12:17:28 -0500
Commit message:

 vignette curl issue
Package: scToppR
Commit: 4da7fbbc60fd0b4b3915f220ac67a96deff86f04
Author: Bryan Granger <grangerb@musc.edu>
Date: 2025-12-05 11:43:16 -0500
Commit message:

 styler on gitignore
Package: scToppR
Commit: a73c4e374b5df05f1b32590b09a9725e4f7b0c13
Author: Bryan Granger <grangerb@musc.edu>
Date: 2025-12-04 15:57:06 -0500
Commit message:

 remove cat and print
Package: scToppR
Commit: 40d01e9ac633e4acd43634f9abde514db8e5dac0
Author: Bryan Granger <grangerb@musc.edu>
Date: 2025-12-04 13:46:59 -0500
Commit message:

 R style changes
Package: scToppR
Commit: 350b3fe6c3ba53d6219a532e0045d048ba90d364
Author: Bryan Granger <grangerb@musc.edu>
Date: 2025-12-04 13:29:17 -0500
Commit message:

 Increment version number to 0.99.5
Package: scToppR
Commit: 3b71fc3f114c1143f3dd91ec15d513d99c9fdf80
Author: Bryan Granger <grangerb@musc.edu>
Date: 2025-12-04 13:28:51 -0500
Commit message:

 vignette updates
Package: scToppR
Commit: a5ab752bc59d7a779d6b0b205191b6f8547b83c1
Author: Bryan Granger <grangerb@musc.edu>
Date: 2025-12-04 12:19:45 -0500
Commit message:

 tests for toppplot and toppfun
Package: scToppR
Commit: 33fc8e40d42500d2e791557319b22b6589973cab
Author: Bryan Granger <grangerb@musc.edu>
Date: 2025-10-21 13:12:37 -0400
Commit message:

 vignette updates
Package: scToppR
Commit: 81ce4dc9758ed25ac9f417760243674383e4d1f6
Author: Bryan Granger <grangerb@musc.edu>
Date: 2025-09-08 10:37:45 -0400
Commit message:

 genes from response
Package: TENxIO
Commit: a3eab208fe98aea1e59e7279fda9eeebf4e35203
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-12-05 11:33:03 -0500
Commit message:

 version bump 1.13.2
Package: TENxIO
Commit: eb2dd446fabaf3fdc2e080d2c88810ba3c408893
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-12-05 11:31:59 -0500
Commit message:

 use edition 2 for Darwin
Package: TENxIO
Commit: 140fef218694d0740c2975a77c22764df26fe433
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-12-05 11:12:05 -0500
Commit message:

 version bump 1.13.1
Package: TENxIO
Commit: ac16d1d677e6f29fdcb20e315954641f411cf158
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-12-05 11:12:00 -0500
Commit message:

 update RoxygenNote
Package: TENxIO
Commit: d8c17684c4593df361c9cb6cce05b63ef2397438
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-12-05 11:11:53 -0500
Commit message:

 add chunk labels to vignette
Package: MungeSumstats
Commit: 09b26973b3b85f7a8c3401e9e56012aea09d68c3
Author: Al-Murphy <alanmurph94@hotmail.com>
Date: 2025-12-05 10:53:13 -0500
Commit message:

 Documentation: check_chr()
Package: MetaboAnnotatoR
Commit: f7e076692d1f9e5d64b522da73d1432951d2e8fe
Author: Gomes Da Graca <ggomesda@ic.ac.uk>
Date: 2025-12-05 14:56:24 +0000
Commit message:

 new bump added
Package: MetaboAnnotatoR
Commit: 16ebd28b0c139ef3701d85a65910b270299891bb
Author: Gomes Da Graca <ggomesda@ic.ac.uk>
Date: 2025-12-05 14:51:03 +0000
Commit message:

 example updated to include zenodo data download
Package: DeeDeeExperiment
Commit: c9530246df11bcf8f59d0c145d5c0d7b8c53a489
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2025-12-05 14:11:15 +0100
Commit message:

 version bump, 1.1.2
Package: DeeDeeExperiment
Commit: 75a452b2be029ecf62ef6a5d63476298371f3140
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2025-12-05 14:03:50 +0100
Commit message:

 gentle nag to the companion vignette within the main one
Package: ROTS
Commit: 05e59b2f089dbbea8424c893bf2046a16dbf8acb
Author: Tomi Suomi <tomi.suomi@utu.fi>
Date: 2025-12-05 16:06:10 +0200
Commit message:

 Modify multi-group statistic
Package: immApex
Commit: a9e4f8987750ae921d6b4498c7b0ed913e24eabe
Author: theHumanBorch <ncborch@gmail.com>
Date: 2025-12-05 07:27:33 -0600
Commit message:

 Merge branch 'main' into devel
Package: immApex
Commit: 935529bf716319b93bd832b206964fc08c380981
Author: theHumanBorch <ncborch@gmail.com>
Date: 2025-12-05 07:24:32 -0600
Commit message:

 clarify threshold
Package: DeeDeeExperiment
Commit: 9bbc0eee18361bf69993c673ccf6738369064a5c
Author: Najla Abassi <abassi.nejla96@gmail.com>
Date: 2025-12-05 13:18:59 +0100
Commit message:

 update news
Package: DeeDeeExperiment
Commit: 78c8b9c51365170340797a98a8082f7349b272af
Author: Najla Abassi <112277365+NajlaAbassi@users.noreply.github.com>
Date: 2025-12-05 13:17:28 +0100
Commit message:

 Merge pull request #10 from imbeimainz/dea_limma_wip

DeeDeeExperiment update
Package: DeeDeeExperiment
Commit: 825e42a6880bddfcd5c798d325c874376660eb37
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2025-12-05 13:15:32 +0100
Commit message:

 Merge branch 'devel' into dea_limma_wip
Package: DeeDeeExperiment
Commit: 953d8372e1c9c1eda045c17617d1fbbfa3370e9a
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2025-12-05 12:53:50 +0100
Commit message:

 re-rendering manpages
Package: DeeDeeExperiment
Commit: 1983569f9f28899d2ee60fa8422805d22ea3f53f
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2025-12-05 12:53:43 +0100
Commit message:

 adding a bit more of text to accompany the single-cell vignette
Package: DeeDeeExperiment
Commit: ac7ebd1bbf85de9cac97eb28943e5da54af31fd5
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2025-12-05 12:53:18 +0100
Commit message:

 Lea's name reported correctly in all vignettes
Package: DeeDeeExperiment
Commit: c756782a538db3ba86054bb6b699e6c0aa8d86ae
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2025-12-05 12:53:00 +0100
Commit message:

 typo fixed
Package: DeeDeeExperiment
Commit: b86e3dd2755acbabc32e3bc0ad383b7921cfaeff
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2025-12-05 12:52:51 +0100
Commit message:

 updated Lea's name and email
Package: DeeDeeExperiment
Commit: 4e1f2ac41a5236844b7de8979a5fe13d80f141d2
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2025-12-04 18:03:57 +0100
Commit message:

 version bump, 1.1.1 - even while we wait for the PR to be fully in
Package: DeeDeeExperiment
Commit: 1b3205db95fde5426bb3e44faf568736cbb4fd26
Author: Najla Abassi <abassi.nejla96@gmail.com>
Date: 2025-12-04 17:47:54 +0100
Commit message:

 update warnings in addDEA
Package: DeeDeeExperiment
Commit: af28fce7aeb14e7969f1f95fdf5ea25937cffaaa
Author: Najla Abassi <abassi.nejla96@gmail.com>
Date: 2025-12-04 17:47:29 +0100
Commit message:

 updating description & news
Package: DeeDeeExperiment
Commit: eda649394fcc1dd8e6e48d9822bf15824046c12c
Author: Najla Abassi <abassi.nejla96@gmail.com>
Date: 2025-12-04 17:47:00 +0100
Commit message:

 adding new min-vignette for single-cell
Package: DeeDeeExperiment
Commit: 63782e5738d3271029660cecddffc6736824ba1b
Author: Najla Abassi <abassi.nejla96@gmail.com>
Date: 2025-12-04 17:46:20 +0100
Commit message:

 updating vignette to show how to integrate multi contrast limma results in dde
Package: DeeDeeExperiment
Commit: 1b349a52611cc1ca2df00300ba0f89272c4836a3
Author: Najla Abassi <abassi.nejla96@gmail.com>
Date: 2025-12-04 17:45:30 +0100
Commit message:

 updating dde figure
Package: DeeDeeExperiment
Commit: 4897479125e9c1adffc0ab9eef454ec157516ccf
Author: Najla Abassi <abassi.nejla96@gmail.com>
Date: 2025-12-04 17:45:07 +0100
Commit message:

 update readme
Package: DeeDeeExperiment
Commit: 422e4d18856171117b85bd0acb3e39fc677868e8
Author: Najla Abassi <abassi.nejla96@gmail.com>
Date: 2025-12-04 17:44:52 +0100
Commit message:

 mention muscat in documentation
Package: DeeDeeExperiment
Commit: 57194ad3b3862ce71b580bdb8d55d7a1d8b2302e
Author: Najla Abassi <abassi.nejla96@gmail.com>
Date: 2025-12-04 17:43:31 +0100
Commit message:

 update typos in documentation
Package: DeeDeeExperiment
Commit: c84521f8e18cbdcbcb1a441eef215d67691fcc8c
Author: Najla Abassi <abassi.nejla96@gmail.com>
Date: 2025-12-01 15:34:51 +0100
Commit message:

 update import functions, helpers and methods (mainly addDEA and getDEA) to store the original object in the metadata, while keeping a pointer to link the original object to the corresponding contrasts in the dea slot
Package: DeeDeeExperiment
Commit: c25eb59f8e99bf340945684ec2a882b9e2d82182
Author: Najla Abassi <abassi.nejla96@gmail.com>
Date: 2025-12-01 15:32:10 +0100
Commit message:

 update versions
Package: DeeDeeExperiment
Commit: ec909801923154103a2ce0bced7033bc7720df02
Author: Najla Abassi <abassi.nejla96@gmail.com>
Date: 2025-12-01 15:31:57 +0100
Commit message:

 add news
Package: DeeDeeExperiment
Commit: 31847315dc8fd11c5868cb09896a5e1b19d6aed4
Author: Najla Abassi <abassi.nejla96@gmail.com>
Date: 2025-12-01 15:31:08 +0100
Commit message:

 setting up extra tests
Package: DeeDeeExperiment
Commit: 128cba093fe0aa45d871b2fa3436738058882dbf
Author: Najla Abassi <abassi.nejla96@gmail.com>
Date: 2025-12-01 15:30:26 +0100
Commit message:

 updating constructor function to handle limma objects with multiple contrasts
Package: DeeDeeExperiment
Commit: 473d2535e0021255828d295f9b53f6f1211d5cba
Author: Najla Abassi <abassi.nejla96@gmail.com>
Date: 2025-12-01 15:29:33 +0100
Commit message:

 adding data documentation
Package: DeeDeeExperiment
Commit: b8a09b8f05417a9ce90067d528a757b6b1399b60
Author: Najla Abassi <abassi.nejla96@gmail.com>
Date: 2025-12-01 15:28:58 +0100
Commit message:

 updating namespace
Package: DeeDeeExperiment
Commit: 09705b82ebcdebf4aeac0bd7ab7067b1051fbb2b
Author: Najla Abassi <abassi.nejla96@gmail.com>
Date: 2025-12-01 15:28:09 +0100
Commit message:

 add helper functions to easily integrate data from muscat and MArrayLM with multiple constrasts
Package: DeeDeeExperiment
Commit: 108fdfbaf6b505fb0bbf495020ab2e07d3503a55
Author: Najla Abassi <abassi.nejla96@gmail.com>
Date: 2025-12-01 15:25:48 +0100
Commit message:

 adding toy data for single-cell examples and tests
Package: MsBackendSql
Commit: 2530928a62f5d04936c2cf24c0dae926ee6d4975
Author: Johannes Rainer <5506112+jorainer@users.noreply.github.com>
Date: 2025-12-05 12:34:51 +0100
Commit message:

 Merge pull request #35 from rformassspectrometry/jomain

refactor: tiny performance improvements
Package: MsBackendSql
Commit: 34ad40a9a28217e354271671eae426898b503a06
Author: Johannes Rainer <johannes.rainer@gmail.com>
Date: 2025-12-04 16:52:04 +0100
Commit message:

 refactor: tiny performance improvements

- Pass sorted spectra IDs to the SQL queries.
- Avoid matching and re-ordering of `spectraData()` rows if not required.
Package: MsBackendSql
Commit: f0a2f592fb26b1639cc161dbc11d8c92595ab92d
Author: Johannes Rainer <johannes.rainer@gmail.com>
Date: 2025-11-03 13:04:18 +0100
Commit message:

 Update README
Package: MetaProViz
Commit: 4f8ba622d5e6342bfa3874d3955a8ead5f0492f4
Author: deeenes <turei.denes@gmail.com>
Date: 2025-12-05 11:38:29 +0100
Commit message:

 Bump version: 3.99.30 → 3.99.31
Package: MetaProViz
Commit: 006087cf7b9cb8425a8a8edd73a65cb50c55c075
Author: deeenes <turei.denes@gmail.com>
Date: 2025-12-05 11:38:21 +0100
Commit message:

 removed debugging code for BioC SPB cache persistence issue
Package: LimROTS
Commit: f921fa790848b9dea97812049355b7808c66a055
Author: Ali Youssef <aliali.mostafa99@gmail.com>
Date: 2025-12-05 12:57:11 +0200
Commit message:

 Add copyright statements to R project files
Package: LimROTS
Commit: 748f53242f130acc8e5c27586c1abfd234c66f34
Author: Ali Youssef <aliali.mostafa99@gmail.com>
Date: 2025-12-05 12:55:04 +0200
Commit message:

 Bump version to 1.3.13 in DESCRIPTION file
Package: MetaProViz
Commit: 016d117338b422dc8f7c12a4aee795fad4ccb9b6
Author: deeenes <turei.denes@gmail.com>
Date: 2025-12-04 17:48:41 +0100
Commit message:

 Bump version: 3.99.29 → 3.99.30
Package: MetaProViz
Commit: 7ed4b1041e6aca5e8cf0971a55ee932f22089c6d
Author: deeenes <turei.denes@gmail.com>
Date: 2025-12-04 17:48:00 +0100
Commit message:

 more diagnosticts and solution attempt for cache persistance issue in BioC SPB
Package: MetaboAnnotatoR
Commit: 2303c69b143af8a09beb9f90109166e53eee7aa7
Author: Gomes Da Graca <ggomesda@ic.ac.uk>
Date: 2025-12-05 08:52:01 +0000
Commit message:

 bump added and date updated
Package: MetaboAnnotatoR
Commit: 32bebe5f8e6a170cf083b40874ab405823961996
Author: Gomes Da Graca <ggomesda@ic.ac.uk>
Date: 2025-12-05 08:51:06 +0000
Commit message:

 examples updated
Package: crisprDesign
Commit: 35ace6d68d287a73833b14774a34688b4886530c
Author: Jean-Philippe Fortin <fortin946@gmail.com>
Date: 2025-12-04 20:50:50 -0800
Commit message:

 Added SNP from gRanges input
Package: BatchSVG
Commit: 1a3f7ad9fcaee3289f4d1c5c2b75a798bbcb1687
Author: Kinnary Shah <kinnaryshahh@gmail.com>
Date: 2025-12-04 17:48:47 -0500
Commit message:

 update jacqui name
Package: scRNAseqApp
Commit: 667730965b0f0cea0280935b7401dfdc4d42a3fb
Author: Jianhong Ou <jianhong.ou@gmail.com>
Date: 2025-12-04 17:32:27 -0500
Commit message:

 add download function for lasso.
Package: ClustIRR
Commit: 507d14512bd92c8885308379e0c94ea2920413b5
Author: snaketron <snaketron@users.noreply.github.com>
Date: 2025-12-03 17:58:30 +0100
Commit message:

 Merge pull request #41 from snaketron/devel

Devel
Package: variancePartition
Commit: e3e0d0ae4a75db3f9a1c29104729ac6a23e67544
Author: Gabriel Hoffman <gabriel.hoffman@gmail.com>
Date: 2025-12-04 13:14:55 -0500
Commit message:

 bump version
Package: fgsea
Commit: 4fd674d097bea00307d837e447ed783111cd43eb
Author: Alexey Sergushichev <alsergbox@gmail.com>
Date: 2025-12-04 11:45:21 -0600
Commit message:

 version bump
Package: fgsea
Commit: 9a06694dfc7b54a0a698061a97db15945ede725c
Author: Alexey Sergushichev <alsergbox@gmail.com>
Date: 2025-11-10 11:57:32 -0600
Commit message:

 fix tests after switching to integer stats
Package: fgsea
Commit: 22c4de0b337a4e7d8aaced3121aa73947a271dde
Author: Alexey Sergushichev <alsergbox@gmail.com>
Date: 2025-11-10 10:52:05 -0600
Commit message:

 include cstdint for int64_t
Package: fgsea
Commit: cec35436ac5dfc587e8aaa9b219bfef043cc3597
Author: Alexey Sergushichev <alsergbox@gmail.com>
Date: 2025-11-07 15:40:42 -0600
Commit message:

 version bump
Package: fgsea
Commit: 296d348759cba2f84883958e39597484d27de4fe
Author: Alexey Sergushichev <alsergbox@gmail.com>
Date: 2025-11-07 15:04:12 -0600
Commit message:

 rounding to integers instead of ceiling
Package: fgsea
Commit: 0193cef4a0b6aeb82ce350d5fd8f8949c1e697fe
Author: Alexey Sergushichev <alsergbox@gmail.com>
Date: 2025-11-07 13:29:57 -0600
Commit message:

 gene weights are converted to integers on R's side
Package: fgsea
Commit: 7207d6bf384b154e094110a9529021b1f56f61f7
Author: Alexey Sergushichev <alsergbox@gmail.com>
Date: 2025-11-07 11:15:29 -0600
Commit message:

 adjust double ES to exact score conversion
Package: fgsea
Commit: 3493f7afa4c40861d81c23cfb4e6c80bfe4c9994
Author: Alexey Sergushichev <alsergbox@gmail.com>
Date: 2025-11-05 14:34:00 -0600
Commit message:

 update test for issue-151
Package: fgsea
Commit: 390166fdedeac2fdb7c9275c4e387e0f14e048fc
Author: Alexey Sergushichev <alsergbox@gmail.com>
Date: 2025-11-04 17:43:30 -0600
Commit message:

 Merge master and hash-greater
Package: fgsea
Commit: bc19c01ff2cb04b033b5ec0c854a02abc83b9786
Author: Alexey Sergushichev <alsergbox@gmail.com>
Date: 2025-11-04 17:01:56 -0600
Commit message:

 more accurate formulas
Package: fgsea
Commit: 0767636de71c04027a1d7be1c2ae3e19e9ae3ac6
Author: Alexey Sergushichev <alsergbox@gmail.com>
Date: 2025-05-20 16:10:55 -0500
Commit message:

 wip: hashing to fix #151
Package: STADyUM
Commit: c0a84f538f55e234d7dca15319064511a9e830ab
Author: Rebecca Hassett <hassett@cshl.edu>
Date: 2025-12-04 11:59:57 -0500
Commit message:

 devel version bump
Package: STADyUM
Commit: 357fb35e60fd06fc821948e9c11effef1c4ff038
Author: Rebecca Hassett <hassett@cshl.edu>
Date: 2025-11-25 17:06:05 -0500
Commit message:

 Remove plyranges dependencies
Package: STADyUM
Commit: 7803b32f00d8bba90f40bb20dadc1962ac6ff69f
Author: Rebecca Hassett <hassett@cshl.edu>
Date: 2025-12-04 11:44:15 -0500
Commit message:

 devel version bump
Package: STADyUM
Commit: fba3a6eef0786dbd9c5016cf23b73b0ca969d6a3
Author: Rebecca Hassett <hassett@cshl.edu>
Date: 2025-12-04 11:40:00 -0500
Commit message:

 devel version bump
Package: LimROTS
Commit: 924f28c1cf0ca3fbb7e1827c649bb0673a4d7520
Author: Ali Youssef <aliali.mostafa99@gmail.com>
Date: 2025-12-04 18:30:29 +0200
Commit message:

 Bump version from 1.3.11 to 1.3.12 and update license
Package: LimROTS
Commit: fada8b6b195a36faac0ae46680be4adfcce7d4b9
Author: Ali Youssef <aliali.mostafa99@gmail.com>
Date: 2025-12-04 18:28:16 +0200
Commit message:

 Update LICENSE file with new copyright details
Package: MungeSumstats
Commit: 76542bf957a40fefa97b0690d1711ead59c6edc5
Author: Al-Murphy <alanmurph94@hotmail.com>
Date: 2025-12-04 11:25:06 -0500
Commit message:

 Bug Fix: liftover() fucntionality
Package: MetaboAnnotatoR
Commit: 57a2e763f280d0b0a9decbb3d4a11b8485e44ba1
Author: Gomes Da Graca <ggomesda@ic.ac.uk>
Date: 2025-12-04 15:44:13 +0000
Commit message:

 bump added and date updated
Package: MetaboAnnotatoR
Commit: 0babbe7ad3b1c45ad42fff4d5148f066de921b0a
Author: Gomes Da Graca <ggomesda@ic.ac.uk>
Date: 2025-12-04 15:42:53 +0000
Commit message:

 formatting changes
Package: MetaboAnnotatoR
Commit: 106dfb4e02fd40f0a549ea8dff8cd6426416b46a
Author: Gomes Da Graca <ggomesda@ic.ac.uk>
Date: 2025-12-04 15:42:08 +0000
Commit message:

 example improved
Package: Rarr
Commit: 3b1addca8d935c5fc6a893c442bbda1860ff3d75
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-12-03 20:11:22 +0100
Commit message:

 Bump version
Package: Rarr
Commit: 953189d1c4513586acc92f5acd00e2034f216db1
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-12-04 10:08:22 +0100
Commit message:

 Run devtools::document()
Package: Rarr
Commit: 7c8a73a36d916b94ce6e64461936ff53bc5b45c9
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-12-04 10:06:55 +0100
Commit message:

 Use slightly faster way to paste on matrix rows

``` r
x <- as.matrix(expand.grid(1:10, 1:20, 1:30))

microbenchmark::microbenchmark(
  c(apply(x, 1, paste, collapse = "-")),
  as.vector(apply(x, 1, paste, collapse = "-")),
  unlist(apply(x, 1, paste, collapse = "-", simplify = FALSE)),
  vapply(seq_len(nrow(x)), function(i) paste(x[i, ], collapse = "-"), character(1)),
  check = "identical",
  times = 1e4
)
```

Created on 2025-12-04 with [reprex v2.1.1](https://reprex.tidyverse.org)
Package: Rarr
Commit: afec89f0c02b4a26c5abcd64c49e2e3bc12736c7
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-12-03 20:11:16 +0100
Commit message:

 Mention scalar array reading support in NEWS
Package: Rarr
Commit: bb47f84eed485c2ad3184401f051bcc80377a8c1
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-12-03 19:55:57 +0100
Commit message:

 Harmonize var names between read_ and write_ and create a shared helper
Package: Rarr
Commit: 8095c9dd60761b4878983fd264c30b1bb169e81f
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-12-03 19:53:57 +0100
Commit message:

 Set dim to 1 for scalar case
Package: Rarr
Commit: d8c4c87ba5b8709ed535a30c1628ddfb4a349e0e
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-11-27 10:40:51 +0100
Commit message:

 Add test for scalar
Package: Rarr
Commit: df7a50a14216b093fa8344018bdc207c41e82e52
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-12-03 16:33:16 +0100
Commit message:

 Do not use i as argument in .extract_elements()

Since we can squash 2 args in ones and get more explicit argument name but taking the row directly instead of its index
Package: Rarr
Commit: 585d9b4d3e13a3a99b133e7332931c2fb0fc9d8f
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-12-03 15:26:14 +0100
Commit message:

 Add note about future potential improvement for overhanging chunks
Package: CrcBiomeScreen
Commit: b649f5ff21867681cb57412b203022da56e923d3
Author: Chronostasis <ngzh5554@leeds.ac.uk>
Date: 2025-12-04 14:35:45 +0000
Commit message:

 Fix runnable examples and add watched tag
Package: MetaboAnnotatoR
Commit: fa7c1202427695c39eda03b0bfade9d4a79a1583
Author: Gomes Da Graca <ggomesda@ic.ac.uk>
Date: 2025-12-04 13:35:56 +0000
Commit message:

 version bump added
Package: MetaboAnnotatoR
Commit: 0af900cb546139dd43edf6007d7cba1120ce0840
Author: Gomes Da Graca <ggomesda@ic.ac.uk>
Date: 2025-12-04 12:21:37 +0000
Commit message:

 loop counter corrected
Package: DOtools
Commit: 42d8aae210fe919c55a0308e5cdce35ff64196a3
Author: MarianoRuzJurado <mariani95@gmx.de>
Date: 2025-12-04 15:03:00 +0100
Commit message:

 Merge remote-tracking branch 'upstream/devel' into devel
Package: DOtools
Commit: 559bd4b61f44aed44409e119be022de8349ed3be
Author: MarianoRuzJurado <mariani95@gmx.de>
Date: 2025-12-04 14:58:54 +0100
Commit message:

 -Fix tests
Package: DOtools
Commit: 292f87288d5eaa62568dfccba9ae44140f6ee3f6
Author: MarianoRuzJurado <mariani95@gmx.de>
Date: 2025-12-04 14:49:11 +0100
Commit message:

 -Fixes in DO.Dotplot
-Fixes in DO.Subset
-Fixes in DO.scVI
Package: EventPointer
Commit: 08861cc5e848d8293eef6e24b3fc3d237c52d2c5
Author: JFerrer-B <jafhernandez@tecnun.es>
Date: 2025-12-04 09:57:09 +0100
Commit message:

 replace GenomicFeatures with txdbmaker for TxDb functions in multiple scripts
Package: GenomeInfoDb
Commit: becc410181aabbef4cfff8bb138ccd7003b35f65
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2025-12-03 18:04:41 -0800
Commit message:

 GenomeInfoDb 1.47.2: Make sure list_ftp_dir() works on an empty FTP dir
Package: StabMap
Commit: ce4dd564282d386fdb19bfc9e5e9c260e62de3c6
Author: Shila Ghazanfar <shila.ghazanfar@sydney.edu.au>
Date: 2025-12-04 11:25:27 +1100
Commit message:

 Merge branch 'RELEASE_3_22' nto devel
Package: StabMap
Commit: 3c9726a7fb16801c59dbfafba96d705fd575aa40
Author: Shila Ghazanfar <shila.ghazanfar@sydney.edu.au>
Date: 2025-12-04 00:22:21 +0000
Commit message:

 fix sparse KNN handling and classifyEmbedding test snapshot
Package: tidyexposomics
Commit: a26c0899fbb86f78245745c64fef18a6fcd344fc
Author: BioNomad <jlaird1@binghamton.edu>
Date: 2025-12-03 17:36:09 -0500
Commit message:

 0.99.9 updates
Package: igblastr
Commit: 35a253349094f35cb56327dc85247a766bd9b3ef
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2025-12-03 12:12:34 -0800
Commit message:

 igblastr 1.1.3: Add 'loci' argument to install_IMGT_germline_db()

The user can now use the new 'loci' argument to select what
loci to include in the germline db to install from IMGT.
See '?install_IMGT_germline_db' for the details.
Package: GSVA
Commit: fc07560c8b1f123b59f99fe378964b14f4b13644
Author: Robert Castelo <robert.castelo@upf.edu>
Date: 2025-12-03 20:05:01 +0100
Commit message:

 Bump version
Package: GSVA
Commit: 15a15201e09defbf569d0b03179615c0cc2dbea2
Author: Robert Castelo <robert.castelo@upf.edu>
Date: 2025-12-03 20:04:46 +0100
Commit message:

 Fix on the propagation of NA values with the GSVA methods and performance improvement in the calculation of GSVA scores from ranks
Package: crisprDesign
Commit: 3365b08a7aef57a2430c79d22b0d4f2b88d2263f
Author: Jean-Philippe Fortin <fortin946@gmail.com>
Date: 2025-12-03 10:55:28 -0800
Commit message:

 Bumped version
Package: crisprDesign
Commit: 19d8036b2596aa003da074fb24dd2ec5466f3ef1
Author: Jean-Philippe Fortin <fortin946@gmail.com>
Date: 2025-12-03 09:15:21 -0800
Commit message:

 Fixed splicing junctions aa annotation
Package: EventPointer
Commit: b184430e2d6c24e90048d3aa87fd7615090317c2
Author: JFerrer-B <jafhernandez@tecnun.es>
Date: 2025-12-03 18:07:53 +0100
Commit message:

 remove GenomicFeatures dependency and add corresponding txdbmaker dependency
Package: LimROTS
Commit: 0f6ef1b890408909943005e7470c122cfd68eda5
Author: Ali Youssef <aliali.mostafa99@gmail.com>
Date: 2025-12-03 18:21:15 +0200
Commit message:

 Change license to GPL-2.0-or-later in DESCRIPTION
Package: LimROTS
Commit: 722add47e550890feae635459d498553baa12cbf
Author: Ali Youssef <aliali.mostafa99@gmail.com>
Date: 2025-12-03 18:02:32 +0200
Commit message:

 Update NEWS.md
Package: LimROTS
Commit: 9f793e6f1668cdf1d345b1827142a5b1b5288a4b
Author: Ali Youssef <aliali.mostafa99@gmail.com>
Date: 2025-12-03 18:01:38 +0200
Commit message:

 Bumped version to 1.3.10
Package: LimROTS
Commit: 14b344e9f075a312a516f6a717bc1054946dade0
Author: Ali Youssef <aliali.mostafa99@gmail.com>
Date: 2025-12-03 18:01:03 +0200
Commit message:

 Change the license from Artistic-2.0 to GPL-2.0-or-later
Package: LimROTS
Commit: 9a69b4dac546be06ee38c21f58ffe6417c976f16
Author: Ali Youssef <aliali.mostafa99@gmail.com>
Date: 2025-12-03 17:48:48 +0200
Commit message:

 Reverting to version 1.3.2
Package: LimROTS
Commit: 751682281bbaff0c323eda81b5ffb1d38a21f5a5
Author: Ali Youssef <aliali.mostafa99@gmail.com>
Date: 2025-12-03 17:41:33 +0200
Commit message:

 revert to version 1.3.0
Package: ClustIRR
Commit: 92396c2d6ca0102f16e4063efe853b6dd9f9f0ed
Author: snaketron <simo.kitanovski@uni-due.de>
Date: 2025-12-03 16:30:38 +0100
Commit message:

 cosine similarity matrxi
Package: CrcBiomeScreen
Commit: e37201fd7dff4e3ed80584801b96a510694b40d2
Author: Chronostasis <ngzh5554@leeds.ac.uk>
Date: 2025-12-03 15:14:27 +0000
Commit message:

 Fix examples, tests, and documentation
Package: EventPointer
Commit: e5e2cff2763b243d48745a3624debc150513a59b
Author: JFerrer-B <jafhernandez@tecnun.es>
Date: 2025-12-03 15:49:44 +0100
Commit message:

 update of description
Package: CrcBiomeScreen
Commit: 2d491955a68ed065f6a385f80914ffe596ee70b1
Author: Chronostasis <ngzh5554@leeds.ac.uk>
Date: 2025-12-03 14:44:43 +0000
Commit message:

 Update for Bioconductor "Build report"- version.
Package: CrcBiomeScreen
Commit: c2f6cde6ca8533e33dac6f5f66b01a2903651603
Author: Chronostasis <ngzh5554@leeds.ac.uk>
Date: 2025-12-03 14:43:00 +0000
Commit message:

 Update for Bioconductor "Build report" +1.
Package: CrcBiomeScreen
Commit: 99a94d6743ed0973cdaad238323132ed814845f6
Author: Chronostasis <ngzh5554@leeds.ac.uk>
Date: 2025-12-03 14:42:49 +0000
Commit message:

 Update for Bioconductor "Build report".
Package: StatescopeR
Commit: 9e8c71915846f853b312ac38f5836928acd27e0d
Author: MSteketee <m.f.b.steketee@amsterdamumc.nl>
Date: 2025-12-03 15:23:55 +0100
Commit message:

 Adjusted installation in readme to be code formatted
Package: Rarr
Commit: 9061bcc82a3aaca4de6ae5ea1fb3da27b548ce79
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-12-02 20:04:33 +0100
Commit message:

 Add short-circuit to transpose codec
Package: Rarr
Commit: 03110b3b34ceb063d9629eb636062f2fcd26c611
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-12-02 18:06:52 +0100
Commit message:

 Avoid repeatedly looping over codec list
Package: Rarr
Commit: 10b56fb0db5d3c0973a680bc8bad605ad46f4c4d
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-12-02 15:56:21 +0100
Commit message:

 Bump version
Package: Rarr
Commit: 0bc4ac739b47fc3f9aa8e9252c373d5808a67b5b
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-12-02 15:06:13 +0100
Commit message:

 Mention reading v3 support
Package: Rarr
Commit: df3fc1256c138cbbcb9c54429037a0c4767382a6
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-12-02 14:47:02 +0100
Commit message:

 Fix lint
Package: Rarr
Commit: 47a1ce64d167a0ed61ce9fca9ce44cbcf6375624
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-12-02 14:45:20 +0100
Commit message:

 Remove expect_no_condition on expected out of bound warnings
Package: Rarr
Commit: 719f62243c7a47d00e3eb4fe424fa10ab525df34
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-11-20 10:19:08 +0100
Commit message:

 Mark that complex data types are not supported now
Package: Rarr
Commit: db3342263708890cba505a073cfeb80db2731258
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-11-20 09:40:48 +0100
Commit message:

 Add equivalence tests for v2 and v3
Package: Rarr
Commit: be27bfbc2a35473dde2bc675a67a1c565692f591
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-11-19 21:40:58 +0100
Commit message:

 Fix transpose codec for v3
Package: Rarr
Commit: 848eaf04b8a8b9d0b7d5566451037f3fd8f798fe
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-11-19 21:39:15 +0100
Commit message:

 Support 1 byte data types
Package: Rarr
Commit: 0d5a7344a83ad2d57553285ef09ef0d9a0c5dec3
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-11-19 21:38:58 +0100
Commit message:

 Add c/ prefix to v3 chunks
Package: Rarr
Commit: 8211d65b8bfea8db725e642dc6ead2d456048a5e
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-11-19 16:11:59 +0100
Commit message:

 Parse data type for v3 as well
Package: Rarr
Commit: 607d9433a7a029e71a740f17aae31faf14cc422e
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-11-19 09:45:38 +0100
Commit message:

 Add script to create v3 test data
Package: Rarr
Commit: 32477225d9d122930c88164544b52983b9687df4
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-11-18 18:02:25 +0100
Commit message:

 Hit the switch on reading v3 arrays
Package: Rarr
Commit: 4c1ce16c195a8aacce110da593792e67b5419645
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-11-13 18:40:15 +0100
Commit message:

 Use both metadata v2 and v3 in .update_chunk() for now
Package: Rarr
Commit: 718417c1da800cb672674d2dd6b7d9295d1e190e
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-11-13 18:29:14 +0100
Commit message:

 Add support for VLEN-UTF8
Package: Rarr
Commit: d5a309d3935d183f78e5a2422ab49a6afd4750d0
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-11-13 18:12:40 +0100
Commit message:

 Restore .parse_datatype() for consolidated metadata
Package: Rarr
Commit: 549cfeed26f1bc382be2be70d0d4e4bda328b6ca
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-11-12 08:35:35 +0100
Commit message:

 Restore v3 error msg for now
Package: Rarr
Commit: 27b42c4705a5808c33a6a363ba29239bf4614319
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-11-11 21:22:04 +0100
Commit message:

 Read v2 as v3
Package: qpgraph
Commit: 3ecb67ee7cc5bfa88b38d1e31d630235e5420c15
Author: Robert Castelo <robert.castelo@upf.edu>
Date: 2025-12-03 13:43:10 +0100
Commit message:

 Amended codecov badge in README and added rhub check workflow
Package: StatescopeR
Commit: d437e0b0a920873713568b9cf2a9952ad023d659
Author: MSteketee <m.f.b.steketee@amsterdamumc.nl>
Date: 2025-12-03 13:01:55 +0100
Commit message:

 Merge branch 'origin' into devel
Package: StatescopeR
Commit: 9268543192bfac57b74f7fd52ccc42803403177d
Author: MSteketee <m.f.b.steketee@amsterdamumc.nl>
Date: 2025-12-03 12:56:22 +0100
Commit message:

 test
Package: StatescopeR
Commit: 0c0bb35b346bccc43784cb181c2a3be04d97cc2a
Author: MSteketee <70577986+MSteketee@users.noreply.github.com>
Date: 2025-10-15 14:32:59 +0200
Commit message:

 Update README.md
Package: StatescopeR
Commit: 150924560c3c96d0a9f6c6aae8b7672329357e4c
Author: MSteketee <70577986+MSteketee@users.noreply.github.com>
Date: 2025-10-15 14:31:31 +0200
Commit message:

 Create README.md
Package: StatescopeR
Commit: dcdf291444e9545fc44367d6f933a974852c3c51
Author: MSteketee <m.f.b.steketee@amsterdamumc.nl>
Date: 2025-07-16 12:22:47 +0200
Commit message:

 title updated
Package: StatescopeR
Commit: 79f4751f7909a0ee8dcb80173fa6a1e915f7c16d
Author: MSteketee <m.f.b.steketee@amsterdamumc.nl>
Date: 2025-07-16 11:21:37 +0200
Commit message:

 Version bump
Package: CrcBiomeScreen
Commit: c15363a493140c1f61fa72581baf16d946709af9
Author: Chronostasis <ngzh5554@leeds.ac.uk>
Date: 2025-12-03 10:59:02 +0000
Commit message:

 Merge remote-tracking branch 'upstream/devel' into devel
Package: CrcBiomeScreen
Commit: e435fbe81846027349b2afc7fecbfe4a770188ae
Author: Chronostasis <ngzh5554@leeds.ac.uk>
Date: 2025-12-03 10:54:52 +0000
Commit message:

 Bump version to trigger new Bioconductor build
Package: CrcBiomeScreen
Commit: 669182be5bc581c6edf02f43a87517b1ef4267fb
Author: Chronostasis <ngzh5554@leeds.ac.uk>
Date: 2025-11-23 18:53:56 +0000
Commit message:

 Delete the unnecessary files.
Package: CrcBiomeScreen
Commit: 0c6344a3f3ffade16a905953ee4a372a789a80df
Author: Chronostasis <ngzh5554@leeds.ac.uk>
Date: 2025-11-23 18:52:06 +0000
Commit message:

 Remove temporary swap file and update .gitignore
Package: gDRutils
Commit: 83b0077e66deb354096274385ca9fe74fed9165e
Author: Bartek <32614650+bczech@users.noreply.github.com>
Date: 2025-12-03 09:26:54 +0100
Commit message:

 Merge pull request #177 from gdrplatform/GDR-3186

Gdr 3186
Package: gDRutils
Commit: 8159603fb0b5e22a2f7256adb9d080b8d505fdab
Author: Bartek Czech <bartosz.w.czech@gmail.com>
Date: 2025-12-02 13:36:49 +0100
Commit message:

 doc: reoxygenate
Package: gDRutils
Commit: bad8ddccf673d1a66e234acb360d610201f68d80
Author: Bartek <32614650+bczech@users.noreply.github.com>
Date: 2025-12-02 13:28:14 +0100
Commit message:

 Apply suggestions from code review

Co-authored-by: j-smola <31825957+j-smola@users.noreply.github.com>
Package: gDRutils
Commit: 226decaf5cc227da52c91cfaef148822692e1040
Author: Bartek Czech <bartosz.w.czech@gmail.com>
Date: 2025-12-02 13:26:06 +0100
Commit message:

 refactor: resolve conflict
Package: gDRutils
Commit: 5027e6bd84ef93b000ac08e7a0481a74497ecf07
Author: Czech <czechb3@sc1nc001is01.eth.rsiec.sc1.science.roche.com>
Date: 2025-11-19 10:55:15 +0000
Commit message:

 refactor: remove reduntant spaces
Package: gDRutils
Commit: 14f48ee171d046eafc76b95ef6fd87dc7ef3d3ec
Author: Czech <czechb3@sc1nc001is01.eth.rsiec.sc1.science.roche.com>
Date: 2025-11-19 10:53:05 +0000
Commit message:

 refactor: update logic
Package: gDRutils
Commit: f60caaba4b6b2a56a90d23cffe5b900eb0d75fe4
Author: Czech <czechb3@sc1nc001is01.eth.rsiec.sc1.science.roche.com>
Date: 2025-11-19 10:51:59 +0000
Commit message:

 refactor: update comments
Package: gDRutils
Commit: 4483af1c1c08b2c957dc9baa5e7534163bfc88b0
Author: Czech <czechb3@sc1nc001is01.eth.rsiec.sc1.science.roche.com>
Date: 2025-11-19 10:51:09 +0000
Commit message:

 doc: update comments
Package: gDRutils
Commit: 38cc562cd63acc97e33452b89707a634a3d1eb45
Author: Czech <czechb3@sc1nc001is01.eth.rsiec.sc1.science.roche.com>
Date: 2025-11-19 10:44:42 +0000
Commit message:

 chore: bump version and update changelog
Package: gDRutils
Commit: 1eee69b45e01f0cbb6ee3cbb0e28f820a3d78f42
Author: Czech <czechb3@sc1nc001is01.eth.rsiec.sc1.science.roche.com>
Date: 2025-11-19 10:44:33 +0000
Commit message:

 test: update unit tests
Package: gDRutils
Commit: ede913897a1a4c94d01bd995e2bc34383ba90b48
Author: Czech <czechb3@sc1nc001is01.eth.rsiec.sc1.science.roche.com>
Date: 2025-11-19 10:44:23 +0000
Commit message:

 doc: reoxygenate
Package: gDRutils
Commit: fc320352a3ca832aa4ed6124fde08941ed0255a2
Author: Czech <czechb3@sc1nc001is01.eth.rsiec.sc1.science.roche.com>
Date: 2025-11-19 10:44:04 +0000
Commit message:

 feat: add support for merging additional vars in the convert_se_assay_to_dt fun
Package: BenchHub
Commit: 2de419c995a5b3f39034f02f2f2cf822061bafb1
Author: Nicholas Robertson <nickrrrr@gmail.com>
Date: 2025-12-03 08:36:47 +0100
Commit message:

 bump version
Package: BenchHub
Commit: 4683e480c65cd9e9ff216ad54f6672462d2f083a
Author: Nicholas Robertson <nickrrrr@gmail.com>
Date: 2025-12-03 08:35:52 +0100
Commit message:

 add value to man
Package: MetaProViz
Commit: 25d6042ace41bafd6417d2a549cb7f0c2a7be8f5
Author: deeenes <turei.denes@gmail.com>
Date: 2025-12-02 18:15:41 +0100
Commit message:

 Bump version: 3.99.28 → 3.99.29
Package: MetaProViz
Commit: da71d9406da3fd709c0ac6ba373cac830f2f6906
Author: deeenes <turei.denes@gmail.com>
Date: 2025-12-02 18:15:35 +0100
Commit message:

 docs rebuils
Package: MetaProViz
Commit: a376ed292dbb35a35d1491f2021834e2f7d50e46
Author: deeenes <turei.denes@gmail.com>
Date: 2025-12-02 18:15:24 +0100
Commit message:

 debugging code for `OmnipathR::taxon_names_table` issue (specific to BioC single package builder)
Package: EnhancedVolcano
Commit: b1f351b13cf5e6dd203e41fdd1871428b58a9a26
Author: Jared Andrews <jared.andrews07@gmail.com>
Date: 2025-12-03 00:13:45 -0600
Commit message:

 version bump
Package: EnhancedVolcano
Commit: e8ef354d4911e647837709402f990541fd066fe0
Author: Jared Andrews <jared.andrews07@gmail.com>
Date: 2025-12-03 00:05:25 -0600
Commit message:

 Merge pull request #145 from kevinblighe/ggalt_fix

Remove ggalt suggestions, various fixes
Package: EnhancedVolcano
Commit: ab449e48f8e1593faea512bed5819ae43c14aba0
Author: Jared Andrews <jared.andrews07@gmail.com>
Date: 2025-12-03 00:02:23 -0600
Commit message:

 Remove ggalt suggestions, various fixes
Package: RCy3
Commit: 120ba273d257dc35d71ab7cbf965c29b528d01f1
Author: jingjingbic <jingjingbic@gmail.com>
Date: 2025-12-02 16:08:39 -0800
Commit message:

 version bump
Package: RCy3
Commit: 1b44d414289c62ec01c3b8cbb90dccffbc0e4138
Author: Alexander Pico <apico@gladstone.ucsf.edu>
Date: 2025-11-13 09:55:46 -0800
Commit message:

 new maintainer
Package: knowYourCG
Commit: cacf7f6078dbd8ba08aeca86d758fcbcc5b27d62
Author: Wanding Zhou <zhouwanding@gmail.com>
Date: 2025-12-02 16:35:10 -0500
Commit message:

 fix testProbeProximity output inconsistency issue
Package: immApex
Commit: c5c1d2a6de7f84ac4c04ddc91cf368f5cffbd2be
Author: theHumanBorch <ncborch@gmail.com>
Date: 2025-12-02 14:54:00 -0600
Commit message:

 Merge branch 'main' into devel
Package: immApex
Commit: 01a032309354406bda40a15024a02bf54cab314e
Author: theHumanBorch <ncborch@gmail.com>
Date: 2025-12-02 14:52:39 -0600
Commit message:

 remove .o file
Package: immApex
Commit: 6a0ea4462c4cd3994b928f95befccb08a43e56df
Author: theHumanBorch <ncborch@gmail.com>
Date: 2025-11-24 12:47:10 -0600
Commit message:

 Update README.md
Package: immApex
Commit: 53bc6519566c9cc74a910a72ae08cd77c502f69b
Author: theHumanBorch <ncborch@gmail.com>
Date: 2025-11-24 12:44:09 -0600
Commit message:

 Merge pull request #17 from BorchLab/buildNetwork-Expansion

update github action
Package: immApex
Commit: cc2948b63c305064e8fcd05d8e95295572825682
Author: theHumanBorch <ncborch@gmail.com>
Date: 2025-11-24 12:32:05 -0600
Commit message:

 reduce computational footprint of vignette
Package: immApex
Commit: 79c3db83180904b07e652a320d3309fd75bb6805
Author: theHumanBorch <ncborch@gmail.com>
Date: 2025-11-24 12:16:22 -0600
Commit message:

 Update immApex.Rmd

removing imgt-dependent vignette
Package: immApex
Commit: 3880a391ba6d881534bd4aaf535a35ead32bb521
Author: theHumanBorch <ncborch@gmail.com>
Date: 2025-11-24 10:10:51 -0600
Commit message:

 Update immApex.Rmd
Package: immApex
Commit: 045cc5a2c83ca864667a96c39d1662eecf741b8a
Author: theHumanBorch <ncborch@gmail.com>
Date: 2025-11-24 09:46:18 -0600
Commit message:

 updating vignette for eval
Package: immApex
Commit: 15b192600641d8e238c413f261d4aa0f7f4c9319
Author: theHumanBorch <ncborch@gmail.com>
Date: 2025-11-24 08:46:50 -0600
Commit message:

 Update immApex.Rmd
Package: immApex
Commit: e723113f569057b370775e9d51df1173988a7f80
Author: theHumanBorch <ncborch@gmail.com>
Date: 2025-11-24 08:46:40 -0600
Commit message:

 no eval of getIMGT
Package: immApex
Commit: a4cafc397c6f4e32a1f1d80b5d46e5dbbcaf62ae
Author: theHumanBorch <ncborch@gmail.com>
Date: 2025-11-24 08:36:15 -0600
Commit message:

 removing basilisk
Package: immApex
Commit: 80d19abd2fdb5322fca65666582a68304c88c393
Author: theHumanBorch <ncborch@gmail.com>
Date: 2025-11-24 08:22:25 -0600
Commit message:

 Update README.md
Package: immApex
Commit: 67871a19654230208acfced9c3eba067071c3cbc
Author: theHumanBorch <ncborch@gmail.com>
Date: 2025-11-24 08:09:30 -0600
Commit message:

 update github action
Package: immApex
Commit: f3395eb561de31366a8da09c4a373c5989d88e52
Author: theHumanBorch <ncborch@gmail.com>
Date: 2025-11-24 07:21:39 -0600
Commit message:

 Merge pull request #16 from BorchLab/buildNetwork-Expansion

fixing new buildNetwork
Package: immApex
Commit: 9605d5e3e8e3ea2a530fb69f22eb2db9576540d7
Author: theHumanBorch <ncborch@gmail.com>
Date: 2025-11-21 15:29:27 -0600
Commit message:

 Update test-buildNetwork.R
Package: immApex
Commit: 22cb221fe309dcd7a8d57c7471f18dd32f0f1f7e
Author: theHumanBorch <ncborch@gmail.com>
Date: 2025-11-21 15:12:14 -0600
Commit message:

 fixing new buildNetwork
Package: immApex
Commit: c8f073f6b48aa74ba84097b887cc2ee155ffe774
Author: theHumanBorch <ncborch@gmail.com>
Date: 2025-10-31 08:02:17 -0500
Commit message:

 Merge pull request #15 from BorchLab/expand-buildNetwork

Expand build network functionality
Package: immApex
Commit: 263241defe9ba7c00d8ed4edb6c96aed11038ef8
Author: theHumanBorch <ncborch@gmail.com>
Date: 2025-10-28 13:08:25 -0500
Commit message:

 expanding buildNetwork

per issue #13
Package: immApex
Commit: aff479f68e8bee49dd2d847e5874b3f51f4179f9
Author: theHumanBorch <ncborch@gmail.com>
Date: 2025-10-24 10:40:56 -0500
Commit message:

 Merge pull request #14 from BorchLab/devel

Devel
Package: EnhancedVolcano
Commit: 10f8b41bbf39d5c98017446f02c27dcb48b15a88
Author: Jared Andrews <jared.andrews07@gmail.com>
Date: 2025-12-02 14:34:51 -0600
Commit message:

 Delete EnhancedVolcano.Rproj
Package: EnhancedVolcano
Commit: 1b84ee6a77829d2c3fa8079c69b68f0c88738770
Author: Jared Andrews <jared.andrews07@gmail.com>
Date: 2025-12-01 11:50:18 -0600
Commit message:

 update maintainer
Package: EnhancedVolcano
Commit: 1007e717767e9d24b32d331e51ec9e2e66814fcd
Author: Jared Andrews <jared.andrews07@gmail.com>
Date: 2025-12-01 11:06:07 -0600
Commit message:

 Merge remote-tracking branch 'upstream/devel' into devel
Package: EnhancedVolcano
Commit: ab0428ef29e2a3bf35aec63d4eeb8f9302963645
Author: Ubuntu <ubuntu@ip-172-31-31-212.eu-west-1.compute.internal>
Date: 2023-09-24 10:58:03 +0000
Commit message:

 library.bib
Package: EnhancedVolcano
Commit: 6e23180c49806a70ddc0ac5f2bb5d3c710aecdbb
Author: Kevin Blighe <kevin.blighe@ranchobiosciences.com>
Date: 2023-09-24 12:56:04 +0200
Commit message:

 Update library.bib
Package: EnhancedVolcano
Commit: 860054b163cf948836279ba6f4d9419c69f5e238
Author: Kevin Blighe <kevin.blighe@ranchobiosciences.com>
Date: 2023-09-24 12:55:15 +0200
Commit message:

 Update library.bib
Package: pathlinkR
Commit: d83c30eb60bd327d4323d6b726b2324b625310a8
Author: Travis Blimkie <travis.m.blimkie@gmail.com>
Date: 2025-12-02 12:07:55 -0800
Commit message:

 Bumped roxygen version. Minimum requirement for ggforce to prevent error.
Package: SparseArray
Commit: 513682b89b1da513cf6dfda510bbfb99facc1d31
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2025-12-02 12:05:22 -0800
Commit message:

 SparseArray 1.11.8: Fix flawed no-op detection logic in subsetting
Package: gatom
Commit: fa3c8c8e8b6d9e19fe36851f7eee8c4498f63131
Author: Alexey Sergushichev <alsergbox@gmail.com>
Date: 2025-12-02 12:54:01 -0600
Commit message:

 version bump
Package: gatom
Commit: dd2be9c8106e3ea66a339b142a0f96780076cac3
Author: Alexey Sergushichev <alsergbox@gmail.com>
Date: 2025-12-02 10:50:48 -0600
Commit message:

 updated igraph objects
Package: gatom
Commit: 9fd7fb5a141aa508dfca6b4ceb19218b6d2e2ba4
Author: Alexey Sergushichev <alsergbox@gmail.com>
Date: 2025-12-02 10:30:34 -0600
Commit message:

 remove pryr dependency
Package: drugfindR
Commit: 527e71d28a5bb7816e59af8b47ac16f6194d3cd9
Author: Ali Sajid Imami <395482+AliSajid@users.noreply.github.com>
Date: 2025-12-02 12:48:10 -0500
Commit message:

 fix: ensure internal functions example as correct
Package: drugfindR
Commit: 6cfae88fc2603b35f0eb0319827862bd396d7b68
Author: Ali Sajid Imami <395482+AliSajid@users.noreply.github.com>
Date: 2025-12-02 11:39:21 -0500
Commit message:

 docs: update README.R/md
Package: drugfindR
Commit: e3426df15644ad10aacbabec17ee9e6ebe8ead38
Author: Ali Sajid Imami <395482+AliSajid@users.noreply.github.com>
Date: 2025-12-02 10:49:21 -0500
Commit message:

 docs: add pkgdown for building the website
Package: drugfindR
Commit: 66d92991a5c4ad61523ad1306e13d635cb390aab
Author: Ali Sajid Imami <395482+AliSajid@users.noreply.github.com>
Date: 2025-12-02 09:54:27 -0500
Commit message:

 docs: cleanup rd tags from markdown docs
Package: drugfindR
Commit: 7ae60c9553e9006144c23d5a449aff39b003e515
Author: Ali Sajid Imami <395482+AliSajid@users.noreply.github.com>
Date: 2025-12-01 19:00:41 -0500
Commit message:

 feat: ensure DataFrame compatibility
Package: drugfindR
Commit: 2eb1e124f1763f76e3ea67f39b9822e0e21fa4f2
Author: Ali Sajid Imami <395482+AliSajid@users.noreply.github.com>
Date: 2025-11-30 13:29:36 -0500
Commit message:

 feat: update the documentation for the included data file
Package: BatchSVG
Commit: c246dded33955f7e079aac3a504a13c8f0092087
Author: Kinnary Shah <kinnaryshahh@gmail.com>
Date: 2025-12-02 12:48:12 -0500
Commit message:

 update description
Package: graph
Commit: 54934609950884e84cf71b78feeace6f321099ad
Author: Vince Carey <stvjc@channing.harvard.edu>
Date: 2025-12-02 12:07:34 -0500
Commit message:

 Merge pull request #26 from Bisaloo/stack-imbalance

Fix PROTECT/UNPROTECT imbalance
Package: graph
Commit: 9f0f27f7bc76eb62a10ae42326d4046b125de713
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-12-02 14:23:51 +0100
Commit message:

 Bump version
Package: graph
Commit: c316f4b0db77ee5d72812ae3be0e16372ea3e399
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-12-02 14:03:47 +0100
Commit message:

 Fix PROTECT/UNPROTECT imbalance
Package: BenchHub
Commit: aa780b152845bb81ed7e0df11e454dbe025199cf
Author: Nicholas Robertson <nickrrrr@gmail.com>
Date: 2025-12-02 17:55:15 +0100
Commit message:

 bump version
Package: BenchHub
Commit: 2375e888be3ff7affa2d9e3d75f818aaa786e215
Author: Nicholas Robertson <nickrrrr@gmail.com>
Date: 2025-12-02 17:54:43 +0100
Commit message:

 fix biocCheck issues
Package: BenchHub
Commit: eb17553989c77d811ff14cb925ed57a089c25aa8
Author: Nicholas Robertson <nickrrrr@gmail.com>
Date: 2025-12-02 16:59:55 +0100
Commit message:

 Remove yaml frontmatter delimiters
Package: CSOA
Commit: c85d2c7c91077763f1ab3fbf43e09a6c8e43fb45
Author: andrei-stoica26 <andreistoica@foxmail.com>
Date: 2025-12-02 23:54:42 +0800
Commit message:

 Bumped version
Package: CSOA
Commit: 43d385cd12373d1dc4048f4b3698aebff6161e4e
Author: andrei-stoica26 <andreistoica@foxmail.com>
Date: 2025-12-02 23:52:48 +0800
Commit message:

 Resolved merge conflict
Package: CSOA
Commit: 395e5779c58526c2d9ae2f9ee899527ce7800f1f
Author: andrei-stoica26 <andreistoica@foxmail.com>
Date: 2025-12-02 23:25:34 +0800
Commit message:

 Local changes before pulling upstream devel
Package: BenchHub
Commit: 0ca99353008487b3960e94e8c98903177db938e4
Author: Nicholas Robertson <nickrrrr@gmail.com>
Date: 2025-12-02 16:48:29 +0100
Commit message:

 bump version
Package: BenchHub
Commit: e98bcf662d61340e44b65fed7abcb0656484e496
Author: Nicholas Robertson <nickrrrr@gmail.com>
Date: 2025-12-02 16:34:34 +0100
Commit message:

 fix documentation
Package: BenchHub
Commit: 2602ec2f5fa7fa01351c094beb4d9e484be3776c
Author: Nicholas Robertson <nickrrrr@gmail.com>
Date: 2025-12-02 15:33:14 +0100
Commit message:

 remove recsys
Package: BenchHub
Commit: 527d664f23397ec4f6a5a88bc3d8e6d47b6beb7e
Author: Nicholas Robertson <nickrrrr@gmail.com>
Date: 2025-11-21 11:48:49 +0100
Commit message:

 don't eval GEO in vignette
Package: BenchHub
Commit: 516e0d51238d56b50dd39c8f00ec26cfa661d614
Author: Nicholas Robertson <nickrrrr@gmail.com>
Date: 2025-11-21 08:47:01 +0100
Commit message:

 rename vignette
Package: BenchHub
Commit: a4f5ffd60ef5f0086bc2ec995c35c6c4ed9c3e43
Author: Nicholas Robertson <nickrrrr@gmail.com>
Date: 2025-11-21 08:46:09 +0100
Commit message:

 fix vignette
Package: BenchHub
Commit: 3f9ae0ad9874fbc10074b2a20d5ddbbd9c53c124
Author: Yue Cao <yue.cao.au@gmail.com>
Date: 2025-11-20 23:06:43 +1100
Commit message:

 add benchmarkstudy vignette
Package: BenchHub
Commit: a0aa00f6aa3f51ae58d3449b665188de78ad9b69
Author: Nicholas Robertson <nickrrrr@gmail.com>
Date: 2025-11-17 17:12:33 +0100
Commit message:

 Fixes Unnecessary File Matching Question
Fixes #86
Package: BenchHub
Commit: 7f5de0c5b491dba82da7741ecc5a8fe5aa2254a6
Author: Nicholas Robertson <nickrrrr@gmail.com>
Date: 2025-10-27 18:38:44 +0100
Commit message:

 update docs
Package: BenchHub
Commit: cebdda0c476d3752b1bd4ebbbcc9d8ac6cf85879
Author: Nicholas Robertson <nickrrrr@gmail.com>
Date: 2025-10-27 18:38:28 +0100
Commit message:

 fix vignette error
Package: BenchHub
Commit: b66451b11899d7ec17bc632abe3e6dc064b5ef00
Author: Nicholas Robertson <nickrrrr@gmail.com>
Date: 2025-10-27 18:26:26 +0100
Commit message:

 Enhance dataset matching logic with multiple strategies for improved accuracy
Package: BenchHub
Commit: 05edb6f0e66c28d3f9c6570f6f94bf0be60f43fd
Author: Nicholas Robertson <nickrrrr@gmail.com>
Date: 2025-10-27 17:21:49 +0100
Commit message:

 Fix test error
Package: BenchHub
Commit: 9f0375d22dd134a1a0569b1a2229aa40d43a37ac
Author: Nicholas Robertson <nickrrrr@gmail.com>
Date: 2025-10-27 17:16:57 +0100
Commit message:

 use name for dataset matching
Package: BenchHub
Commit: 3dd1f35b57f289a7a9f4df4d0a782c8d3b7ed457
Author: Nicholas Robertson <nickrrrr@gmail.com>
Date: 2025-10-27 17:01:59 +0100
Commit message:

 mapping function not downloaded correctly
Fixes #102
Package: BenchHub
Commit: b87a68545a2fc1bdf2ee65b30dd5c4fe4b4f6285
Author: Nicholas Robertson <nickrrrr@gmail.com>
Date: 2025-10-06 17:44:07 +0200
Commit message:

 Revert "evidence not being downloaded"

This reverts commit c0e4f15ed752248fb08b636ff406645c5cab79a7.
Package: BenchHub
Commit: c0e4f15ed752248fb08b636ff406645c5cab79a7
Author: Nicholas Robertson <nickrrrr@gmail.com>
Date: 2025-10-01 16:44:26 +0200
Commit message:

 evidence not being downloaded
Fixes #101
Package: BenchHub
Commit: 4a5e1d107dda0799145f62f467d9464da0afdd90
Author: Nicholas Robertson <nickrrrr@gmail.com>
Date: 2025-09-26 17:04:31 +0200
Commit message:

 run formatter
Package: BenchHub
Commit: 19dabc4cd75161a42968a84189d6af85cc9e1de4
Author: Dario Strbenac <dario@maths.usyd.edu.au>
Date: 2025-09-16 11:25:16 +1000
Commit message:

 Vignette 2 runs smoothly again. If evidence is a function, also apply it to the predictions.
Package: BenchHub
Commit: 8396c1248c7b98389f05803d58bf06bac5e989d1
Author: Dario Strbenac <dario@maths.usyd.edu.au>
Date: 2025-09-16 10:35:07 +1000
Commit message:

 Restore hidden Google account authorisation prompt. Fixes #100.
Package: BenchHub
Commit: b1fd10c6f96a2516299f1f644a01a48aa989968a
Author: Nicholas Robertson <nickrrrr@gmail.com>
Date: 2025-09-09 14:55:48 +0200
Commit message:

 fix tests
Package: BenchHub
Commit: a91bbd2c1360aec5c78d311356060b5b17819ff8
Author: Nicholas Robertson <nickrrrr@gmail.com>
Date: 2025-09-09 14:04:31 +0200
Commit message:

 Cannot retrieve Trio by name in Benchhubstudy evaluate function
Fixes #90
Package: BenchHub
Commit: 1c8a6e0587c6b86547297ec8885c00c4c25f7567
Author: Nicholas Robertson <nickrrrr@gmail.com>
Date: 2025-09-05 17:02:17 +0200
Commit message:

 fix test
Package: BenchHub
Commit: 36d17cd47b0368936f9d9aa474a860b9bfa7fafa
Author: Nicholas Robertson <nickrrrr@gmail.com>
Date: 2025-09-05 16:08:52 +0200
Commit message:

 add connectivity checks to gist functions
Package: BenchHub
Commit: 73b780d72c1b13fdfad2d53f9e2b6b3e4a4452bf
Author: Nicholas Robertson <nickrrrr@gmail.com>
Date: 2025-09-05 15:45:57 +0200
Commit message:

 delete mistaken commits
Package: BenchHub
Commit: 4cdc36ab985b574536266150b4006bb6703255f9
Author: Nicholas Robertson <nickrrrr@gmail.com>
Date: 2025-09-05 15:30:19 +0200
Commit message:

 change benchhubstudy to benchmarkstudy
Fixes #94
Package: BenchHub
Commit: 32ea85a183b530603562f75ff74fa720aca3c104
Author: Nicholas Robertson <nickrrrr@gmail.com>
Date: 2025-09-03 15:38:15 +0200
Commit message:

 add native gist functionality
Package: BenchHub
Commit: 6502e7b4cfedd63f044b89cd1ca1d85c67130043
Author: Nicholas Robertson <nickrrrr@gmail.com>
Date: 2025-08-28 14:46:27 +0200
Commit message:

 Fixes #89
Package: BenchHub
Commit: 3d98de37034d6d774e76ddfcaa9bd648f4d411c2
Author: Nicholas Robertson <nickrrrr@gmail.com>
Date: 2025-08-28 14:09:05 +0200
Commit message:

 google sheet link does not work
Fixes #88
Package: BenchHub
Commit: 45c57cc841ce7bd679fb6653ad3508749db6806d
Author: Nicholas Robertson <nickrrrr@gmail.com>
Date: 2025-08-28 14:01:48 +0200
Commit message:

 Spaces in Metric List Name are Unhandled
Fixes #83
Package: BenchHub
Commit: 48d9fc775d7766b375797cf230500bbbe530727c
Author: Nicholas Robertson <nickrrrr@gmail.com>
Date: 2025-08-28 13:45:51 +0200
Commit message:

 Inconsistent Ordering of Predicted and Known Vectors
Fixes #85
Package: BenchHub
Commit: 310fc8a0bd9510d86d6fddf1eba38ff011b25d92
Author: Nicholas Robertson <nickrrrr@gmail.com>
Date: 2025-08-28 13:40:44 +0200
Commit message:

 Number of Repeats Recorded in Spreadsheet is Incorrect
Fixes #87
Package: BenchHub
Commit: dda510c249f52753ab866b5e56661443533badf0
Author: Nicholas Robertson <nickrrrr@gmail.com>
Date: 2025-08-28 08:45:47 +0200
Commit message:

 Two E-mail Input Bugs Break writeCTD
Fixes #84
Package: BenchHub
Commit: 57f0577212074c4d4beb36dc3e3a2a68c0eb0bd9
Author: Nicholas Robertson <nickrrrr@gmail.com>
Date: 2025-08-27 14:29:12 +0200
Commit message:

 Save Author in writeCTD
Fixes #77
Package: BenchHub
Commit: a2fe33e264fd2e1b3a826834134ec8f42bd3b886
Author: Nicholas Robertson <nickrrrr@gmail.com>
Date: 2025-08-27 14:11:28 +0200
Commit message:

 Save splitIndex in the sheet
Fixes #74
Package: BenchHub
Commit: f96615a5bb9eb0c9bea87fbc011eb6b0b152b109
Author: Nicholas Robertson <nickrrrr@gmail.com>
Date: 2025-08-27 13:58:53 +0200
Commit message:

 closes #80
Package: BenchHub
Commit: 9adaf87a2fe64178c3f651325f9047a778c93296
Author: Nicholas Robertson <nickrrrr@gmail.com>
Date: 2025-08-27 13:08:25 +0200
Commit message:

 remove browser statement
Package: BenchHub
Commit: da5e91048bb899843a830ab3b3498daf0a4ce66b
Author: Dario Strbenac <dario@maths.usyd.edu.au>
Date: 2025-08-27 15:30:04 +1000
Commit message:

 Evidence downloaded into Trio if sourceID differs to data.
Package: BenchHub
Commit: 9f53dbcf24c13f66f56eb21be73bd66d7fc6e6c8
Author: Dario Strbenac <dario@maths.usyd.edu.au>
Date: 2025-08-27 12:00:16 +1000
Commit message:

 Removed unnecessary ID emptiness check that was preventing writing of data to disk.
Package: BenchHub
Commit: cf066ee73f1ee6e6c04a6141e77000bcdab8d9b8
Author: Dario Strbenac <dario@maths.usyd.edu.au>
Date: 2025-08-26 17:30:06 +1000
Commit message:

 - Vignette 2 updated with new constructors.
- splitIndex banished from evaluate.
- Unless created by a function, evidence must have sample names to avoid matching by position. If not present and not function-generated, names are added to evidence from data by order, with a warning.
- isTabular checker function.
Package: BenchHub
Commit: 585a51bc0baeeff98a94796e4dc8c426c702ad4b
Author: Dario Strbenac <dario@maths.usyd.edu.au>
Date: 2025-08-25 12:00:07 +1000
Commit message:

 - Added the capability to extract evidence even if using data source and data set IDs, rather than curated data.
- Construction of Trios removes supporting evidence from data if is within it, to avoid accidentally training with the outcome variables as covariates.
- Vignette 1 updated to demonstrate new functionality.
Package: BenchHub
Commit: 06f8b72388211ec355913da20fdfbde3450680a7
Author: Nicholas Robertson <nickrrrr@gmail.com>
Date: 2025-08-22 16:02:30 +0200
Commit message:

 fix bugs
Package: BenchHub
Commit: cad46e9da7674c7c5f89d7cd40509971eb0cc113
Author: Nicholas Robertson <nickrrrr@gmail.com>
Date: 2025-08-14 16:34:01 +0200
Commit message:

 fix docs
Package: BenchHub
Commit: 6fd437fd7a5d5a8f1a23ae14814bae7ca821b310
Author: Nicholas Robertson <nickrrrr@gmail.com>
Date: 2025-08-13 17:02:08 +0200
Commit message:

 Merge branch 'devel' of github.com:SydneyBioX/BenchHub into devel
Package: BenchHub
Commit: 33a56e16a63084c86056dc3de3ad805a2f51001a
Author: Nicholas Robertson <nickrrrr@gmail.com>
Date: 2025-08-13 17:01:11 +0200
Commit message:

 add list studies
Package: BenchHub
Commit: 219ea1bc6cd1de3d0348d156d91f918289e2c066
Author: Nicholas Robertson <nickrrrr@gmail.com>
Date: 2025-08-13 16:28:31 +0200
Commit message:

 remove source filter
Package: BenchHub
Commit: 49043f3aa82635add0c8243ee8d6a1a535389ca4
Author: MarniTorkel <mtorkel@gmail.com>
Date: 2025-08-11 15:56:32 +1000
Commit message:

 Rename benchhubStudy
Package: BenchHub
Commit: d486641d21a56e47f726da58138a9c794ae377f9
Author: MarniTorkel <mtorkel@gmail.com>
Date: 2025-08-11 15:53:30 +1000
Commit message:

 Rename benchmarkInsights
Package: BenchHub
Commit: ae1a0f493e7aa2704879340b03fbd9336065a1a5
Author: littlecabiria <71769896+littlecabiria@users.noreply.github.com>
Date: 2025-08-08 23:14:49 +1000
Commit message:

 changed all benchmarkInsight to BenchmarkInsights
Package: BenchHub
Commit: 928a4de8bd90ce9b370af596a877af8d36c80ec4
Author: Nicholas Robertson <nickrrrr@gmail.com>
Date: 2025-07-30 12:24:25 +0200
Commit message:

 implement various todos
Package: BenchHub
Commit: aa2bb77625bc8601ff71b93e542f5614b76484d4
Author: Nicholas Robertson <nickrrrr@gmail.com>
Date: 2025-07-30 11:48:46 +0200
Commit message:

 Tell the user how to list the available datasets.
Package: BenchHub
Commit: b9e7e1798b74fdf31f69cecf9f274982d28d11ec
Author: Nicholas Robertson <nickrrrr@gmail.com>
Date: 2025-07-30 11:47:00 +0200
Commit message:

 Ask the user if the dataset is available in one of the databases
Package: BenchHub
Commit: 26834de8f5940b69e43c3e1759ffb4f44933f88e
Author: Nicholas Robertson <nickrrrr@gmail.com>
Date: 2025-07-30 11:45:04 +0200
Commit message:

 validate metrics
Package: BenchHub
Commit: 4a1f1c6a3d7262237781f64b32738eca1fc209a1
Author: Nicholas Robertson <nickrrrr@gmail.com>
Date: 2025-07-29 12:27:01 +0200
Commit message:

 Add version field
Package: BenchHub
Commit: 37d9304e4b7f78b3c8ae0bdf14d7e90a99f95658
Author: Nicholas Robertson <nickrrrr@gmail.com>
Date: 2025-07-29 12:05:39 +0200
Commit message:

 add parameters to writeCTD function
Package: BenchHub
Commit: b2d3e471be2ccfdb91eeffc9545a1f2588187b0b
Author: Nicholas Robertson <nickrrrr@gmail.com>
Date: 2025-07-29 11:38:59 +0200
Commit message:

 allow writeCTD to run on parameters rather than requiring user input
Package: BenchHub
Commit: ee089f32bcefaf368dd161883cd1c3feb6aa3976
Author: Nicholas Robertson <nickrrrr@gmail.com>
Date: 2025-07-29 11:38:08 +0200
Commit message:

 fix initialize bug and ensure camelCase
Package: BenchHub
Commit: 3a049b834a2a905258e8caedddfc753a885a2312
Author: Nicholas Robertson <nickrrrr@gmail.com>
Date: 2025-07-28 17:01:43 +0200
Commit message:

 docs
Package: BenchHub
Commit: 31d22ab20f1ac2bb2309b979359806e7d7c77fe6
Author: Nicholas Robertson <nickrrrr@gmail.com>
Date: 2025-07-28 17:01:24 +0200
Commit message:

 snake case to camel
Package: BenchHub
Commit: 0379bac657d2c3dc087dc03d230684af7646f01c
Author: Nicholas Robertson <nickrrrr@gmail.com>
Date: 2025-07-28 16:49:03 +0200
Commit message:

 update docs
Package: BenchHub
Commit: 5807c85bf9ac447da0097b8aa6cbb28f2c45682b
Author: Nicholas Robertson <nickrrrr@gmail.com>
Date: 2025-07-28 16:43:32 +0200
Commit message:

 BenchHubStudy can now be vreated from CTD
Package: BenchHub
Commit: cb274f7198435558c9fd579b8249e92a21dfa2b9
Author: Nicholas Robertson <nickrrrr@gmail.com>
Date: 2025-07-28 16:43:00 +0200
Commit message:

 add print method to BenchHubStudy
Package: BenchHub
Commit: a8a60119d8e4566a8de1a04e8300205fe7e66a0e
Author: Nicholas Robertson <nickrrrr@gmail.com>
Date: 2025-07-28 11:21:58 +0200
Commit message:

 linting changes
Package: BenchHub
Commit: 10bc0ea6736da3d882acfa0753b1c8bb7462a9b5
Author: Nicholas Robertson <nickrrrr@gmail.com>
Date: 2025-07-28 11:15:54 +0200
Commit message:

 change warning message
Package: BenchHub
Commit: 49d8bd472fd67c7ab5987c9f151b532b16f4acfa
Author: Nicholas Robertson <nickrrrr@gmail.com>
Date: 2025-07-28 11:03:38 +0200
Commit message:

 remove browser
Package: BenchHub
Commit: 77957fd5eabfbde2def6eb3d36d5bdf262fb7aed
Author: Nicholas Robertson <nickrrrr@gmail.com>
Date: 2025-07-28 11:02:57 +0200
Commit message:

 improve loadData archive handling. Fixes #71
Package: BenchHub
Commit: 0211ed9df00ccc88c9139c0682b7bae866f127ec
Author: Nicholas Robertson <nickrrrr@gmail.com>
Date: 2025-07-28 10:52:26 +0200
Commit message:

 add support to populateTrio to methods and evidence uploaded using writeCTD
Package: BenchHub
Commit: 531abf486fdf6a205a0f1bf2063d71255fef4c4c
Author: Nicholas Robertson <nickrrrr@gmail.com>
Date: 2025-07-25 14:52:25 +0200
Commit message:

 refactor from hell
Package: BenchHub
Commit: 8527d7c72c16179daaa9834809eda1d7a706d1dd
Author: Nicholas Robertson <nickrrrr@gmail.com>
Date: 2025-07-24 16:11:06 +0200
Commit message:

 qol improvements
Package: BenchHub
Commit: 5d4bad59bcf31666157c4358fbbc25767f48a0c0
Author: Nicholas Robertson <nickrrrr@gmail.com>
Date: 2025-07-24 15:44:23 +0200
Commit message:

 allow the user to choose the file name from the figshare and override md5 check
Package: BenchHub
Commit: 3839486a00e4d48bb38fa3f4bea9bc4b880021c1
Author: Nicholas Robertson <nickrrrr@gmail.com>
Date: 2025-07-24 15:36:13 +0200
Commit message:

 fix bug for figshare's with many files
Package: BenchHub
Commit: ff385aeca5b22038d359b661b66f1bfe00396fc3
Author: Nicholas Robertson <nickrrrr@gmail.com>
Date: 2025-07-24 15:20:40 +0200
Commit message:

 make state consistent in writeCTD
Package: BenchHub
Commit: 72f6a6b8f101453f1630143efdf1aab87b619759
Author: Nicholas Robertson <nickrrrr@gmail.com>
Date: 2025-07-24 15:03:20 +0200
Commit message:

 refactor writeCTD
Package: BenchHub
Commit: 9ba910f7dcdc172d8188388de145867e9a9b2650
Author: Nicholas Robertson <nickrrrr@gmail.com>
Date: 2025-07-24 08:50:40 +0200
Commit message:

 fix bug
Package: BenchHub
Commit: 341f683d01c9b12714e718ac4ca3481119f5b96b
Author: Nicholas Robertson <nickrrrr@gmail.com>
Date: 2025-07-23 16:29:31 +0200
Commit message:

 writeCTD uploads a list of auxData instead of each individual file
Package: BenchHub
Commit: 0440a5cba8bf4012df7a1b713d0403c9a124a51a
Author: Nicholas Robertson <nickrrrr@gmail.com>
Date: 2025-07-18 15:32:03 +0200
Commit message:

 Update Trio creation
Package: BenchHub
Commit: 5700e1f5a8dfea9ea1d49876419c4c92c0e60908
Author: Nicholas Robertson <nickrrrr@gmail.com>
Date: 2025-07-09 16:22:07 +0200
Commit message:

 update docs
Package: BenchHub
Commit: ff75c364c2fe2a186d79e0206b7b9db39fb735c3
Author: Nicholas Robertson <nickrrrr@gmail.com>
Date: 2025-07-09 16:17:13 +0200
Commit message:

 final touches
Package: BenchHub
Commit: 4eda939fc625d14ed7fa3299beefc7da116c3047
Author: Nicholas Robertson <nickrrrr@gmail.com>
Date: 2025-07-09 15:30:12 +0200
Commit message:

 lintr settings
Package: BenchHub
Commit: 5f41524fc184ad386aa5232598c7416d29b2b65a
Author: Nicholas Robertson <nickrrrr@gmail.com>
Date: 2025-07-09 15:12:29 +0200
Commit message:

 ignore case
Package: BenchHub
Commit: d15069589b1cc9418c11de23dd8fb2b00b318143
Author: Nicholas Robertson <nickrrrr@gmail.com>
Date: 2025-07-07 16:39:07 +0200
Commit message:

 improve writeCTD logic
Package: BenchHub
Commit: f36789b3e4c8a8c857d02d6484110c0e53ec857d
Author: Nicholas Robertson <nickrrrr@gmail.com>
Date: 2025-07-07 16:38:42 +0200
Commit message:

 harmonise funcitons
Package: BenchHub
Commit: 48c347089eccab40a0694a795a6b26d741ad64d8
Author: Nicholas Robertson <nickrrrr@gmail.com>
Date: 2025-07-02 17:12:29 +0200
Commit message:

 move vignette
Package: BenchHub
Commit: f54c9e3c510a18cf8c42d08a1e5d215ef9c52b59
Author: Nicholas Robertson <nickrrrr@gmail.com>
Date: 2025-07-02 17:07:53 +0200
Commit message:

 bug
Package: BenchHub
Commit: 92342fa453f879c53854279c1307eed999b2a46f
Author: Nicholas Robertson <nickrrrr@gmail.com>
Date: 2025-07-02 17:01:00 +0200
Commit message:

 update docs
Package: BenchHub
Commit: 936e5ecc2b2862a72288cf158d37e8b22897e7d7
Author: Nicholas Robertson <nickrrrr@gmail.com>
Date: 2025-07-02 16:59:00 +0200
Commit message:

 enhance data upload flow: improve prompts and validation for dataset and auxData uploads to Figshare
Package: BenchHub
Commit: f4c786eda2f12dcbc4329a1f671608559bd4e317
Author: Nicholas Robertson <nickrrrr@gmail.com>
Date: 2025-07-02 16:58:08 +0200
Commit message:

 check if dataset/auxData are already available in the folder
Package: BenchHub
Commit: 5bdd8c5605557b5395e330228d4eca3577e066e3
Author: Nicholas Robertson <nickrrrr@gmail.com>
Date: 2025-07-02 16:56:47 +0200
Commit message:

 add auxDataSource and auxDataSourceID fields to Trio class
Package: BenchHub
Commit: 5f9a77599f2a7f685df6307dc6730cfb7822d832
Author: Nicholas Robertson <nickrrrr@gmail.com>
Date: 2025-07-02 16:55:48 +0200
Commit message:

 refactor figshareDl function and add figshareListFiles for improved API handling
Package: BenchHub
Commit: 5c6fe7d8dddbeb05b816bbc04db6902ef26e8f18
Author: Nicholas Robertson <nickrrrr@gmail.com>
Date: 2025-07-02 15:01:34 +0200
Commit message:

 ignore .vscode
Package: BenchHub
Commit: 2d33569039dd359989efbc2ffeefb9318c900d83
Author: Nicholas Robertson <nickrrrr@gmail.com>
Date: 2025-07-02 15:00:49 +0200
Commit message:

 separate auxData and dataset saving
Package: BenchHub
Commit: 7b5d7a241d711ec9026742a6fd204f0f2de4be0b
Author: Nicholas Robertson <nickrrrr@gmail.com>
Date: 2025-07-02 09:48:51 +0200
Commit message:

 fix geoDl bug
Package: BenchHub
Commit: 343243f57b991ba33f56773bd5814c4ebbbb6525
Author: Nicholas Robertson <nickrrrr@gmail.com>
Date: 2025-06-30 14:53:34 +0200
Commit message:

 bump
Package: BenchHub
Commit: c0a1863d0a4b281422b9f5c6475f61161a1cf2a0
Author: Nicholas Robertson <nickrrrr@gmail.com>
Date: 2025-06-30 14:12:55 +0200
Commit message:

 add DT dependency
Package: BenchHub
Commit: 5fbf8db68455786cab0a72e972757f1b0c3409f8
Author: Nicholas Robertson <nickrrrr@gmail.com>
Date: 2025-06-30 14:12:01 +0200
Commit message:

 update docs
Package: BenchHub
Commit: 42d0515d57fc212d1903df42d5b2cc8f34e7b795
Author: Nicholas Robertson <nickrrrr@gmail.com>
Date: 2025-06-30 14:11:52 +0200
Commit message:

 fix bug
Package: BenchHub
Commit: 16738b345132b5422e714ac765aa1a4c2cdf25b0
Author: Nicholas Robertson <nickrrrr@gmail.com>
Date: 2025-06-30 14:06:37 +0200
Commit message:

 fix loadFile function to use data.table for reading CSV files
Package: BenchHub
Commit: 3b2689b483d3579ce0c477ea14bd05dfa638b328
Author: Nicholas Robertson <nickrrrr@gmail.com>
Date: 2025-06-30 13:58:17 +0200
Commit message:

 add writeBenchHubStudy function
Package: BenchHub
Commit: 895b11dad82abc210c512f0a8bc0dfeb6f7af137
Author: Nicholas Robertson <nickrrrr@gmail.com>
Date: 2025-06-30 13:57:57 +0200
Commit message:

 remove janky fix
Package: BenchHub
Commit: 9935d399e11e24688c61723c1cada1bba10ef111
Author: Nicholas Robertson <nickrrrr@gmail.com>
Date: 2025-06-17 15:03:10 +0200
Commit message:

 Merge branch 'devel' of github.com:SydneyBioX/BenchHub into devel
Package: BenchHub
Commit: 03c47eb8b316cee2e4ad1560e3b6491c57bbcad3
Author: Nicholas Robertson <nickrrrr@gmail.com>
Date: 2025-06-17 15:02:42 +0200
Commit message:

 fix export issue
Package: BenchHub
Commit: a4c5e81e78d1d4791763cbf39eb76ab604cac7ac
Author: Yue Cao <yue.cao.au@gmail.com>
Date: 2025-06-16 17:47:58 +1000
Commit message:

 add name to benchhubStudy object
Package: BenchHub
Commit: b7f187d084597c440166efb8884087c0637be315
Author: Dario Strbenac <dario@maths.usyd.edu.au>
Date: 2025-06-13 23:02:08 +1000
Commit message:

 Merge branch 'devel' of https://github.com/SydneyBioX/BenchHub into devel
Package: BenchHub
Commit: f25fe143de06247565cfb8a8b73a589d54844af3
Author: Dario Strbenac <dario@maths.usyd.edu.au>
Date: 2025-06-13 23:00:03 +1000
Commit message:

 zenodoDl function created to download file(s) from Zenodo based on D.O.I.
Package: BenchHub
Commit: 1b30b3667c0ae67cee0d0d43bac16fe3a2aa9482
Author: Nicholas Robertson <nickrrrr@gmail.com>
Date: 2025-06-05 09:40:05 +0200
Commit message:

 fix bug with datasetID parsing
Package: BenchHub
Commit: 0088ea64094ec4b9e176a76345d13ffc4529e98c
Author: Nicholas Robertson <nickrrrr@gmail.com>
Date: 2025-06-05 09:14:44 +0200
Commit message:

 fix benchhubstudy val func
Package: BenchHub
Commit: 3563fb2d7751734dc911a4ef29bc7dad40e21d7a
Author: Nicholas Robertson <nickrrrr@gmail.com>
Date: 2025-06-04 15:37:58 +0200
Commit message:

 fix site
Package: BenchHub
Commit: bfa31d90b715f8fa129d961b0596cd819f3a33ad
Author: Nicholas Robertson <nickrrrr@gmail.com>
Date: 2025-06-04 15:37:47 +0200
Commit message:

 closes Passthrough parameters to `splitTools::create_folds` for improved flexibility #60
Package: BenchHub
Commit: 263337122915151caba3f7f04b5937ac1b4c91c7
Author: Nicholas Robertson <nickrrrr@gmail.com>
Date: 2025-06-04 15:29:05 +0200
Commit message:

 closes #66
Package: BenchHub
Commit: 68ad7aafcd913bb45fb2f41bb54824469dd2a626
Author: Nicholas Robertson <nickrrrr@gmail.com>
Date: 2025-06-04 15:20:08 +0200
Commit message:

 fixes #70
Package: BenchHub
Commit: 4bec0508a43d9b63b1150fd935761ec3f0bec1e4
Author: Nicholas Robertson <nickrrrr@gmail.com>
Date: 2025-05-29 14:40:14 +0200
Commit message:

 add documentation and basic functionality for to BenchHubStudy
Package: BenchHub
Commit: 68f16105fd1a5064de247cfda8c12520176dd969
Author: Nicholas Robertson <nickrrrr@gmail.com>
Date: 2025-05-28 15:24:41 +0200
Commit message:

  auxData-metric relationships are writtent to sheet
Package: BenchHub
Commit: d33ba9b28cce7756d0ddee0fd1d21890929589c8
Author: Nicholas Robertson <nickrrrr@gmail.com>
Date: 2025-05-27 15:01:32 +0200
Commit message:

 revert breaking change change
Package: BenchHub
Commit: cb4f8a4cbd270ede78f73b0f70593258f468d033
Author: Nicholas Robertson <nickrrrr@gmail.com>
Date: 2025-05-23 11:27:07 +0200
Commit message:

 add separatemetods false in base case
Package: BenchHub
Commit: fdf746b5de07a41039c6910a7acb15d0111503f7
Author: Nicholas Robertson <nickrrrr@gmail.com>
Date: 2025-05-15 09:02:54 +0200
Commit message:

 fix bug
Package: BenchHub
Commit: 537c19bb8f7c498cf25508bc6caa7d0c5e5f985e
Author: Nicholas Robertson <nickrrrr@gmail.com>
Date: 2025-05-14 13:38:31 +0200
Commit message:

 fix bug
Package: BenchHub
Commit: 4f1ffbd8ada8c4d9e11fbaf3c537851063915771
Author: Nicholas Robertson <nickrrrr@gmail.com>
Date: 2025-05-14 12:45:16 +0200
Commit message:

 improve vingnette
Package: BenchHub
Commit: d7dc42dad017daeb494b75ba69c7653453a80d41
Author: Nicholas Robertson <nickrrrr@gmail.com>
Date: 2025-05-14 12:42:42 +0200
Commit message:

 fix saveAuxData bug
Package: BenchHub
Commit: 09268555689ef934167b5846e7ce50f21f0711f4
Author: Nicholas Robertson <nickrrrr@gmail.com>
Date: 2025-05-14 12:03:01 +0200
Commit message:

 fix md5 issue
Package: BenchHub
Commit: 729ccd8c22f984b847311196d220c1675828cf23
Author: Nicholas Robertson <nickrrrr@gmail.com>
Date: 2025-05-14 09:29:33 +0200
Commit message:

 use deauth mode when non interactive mode
Package: BenchHub
Commit: 586d904d42aee03545dd63725dc0ea209d3f33e6
Author: Nicholas Robertson <nickrrrr@gmail.com>
Date: 2025-05-13 16:02:11 +0200
Commit message:

 Fix a few bugs
Package: BenchHub
Commit: 9f985de140630c8cd0be02c51e957ced56232519
Author: Nicholas Robertson <nickrrrr@gmail.com>
Date: 2025-05-13 15:24:23 +0200
Commit message:

 fix bugs
Package: BenchHub
Commit: bcd3ac98ec2371475644ddf996a215c276d45c7c
Author: Nicholas Robertson <nickrrrr@gmail.com>
Date: 2025-05-13 14:49:26 +0200
Commit message:

 first iteration of Trio uploading
Package: Rarr
Commit: 9798d458543994a0c19885de2e09dece522298de
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-12-02 13:01:58 +0100
Commit message:

 Add benchmarks for blosc lz4
Package: Rarr
Commit: 6f1a4146b6ac9258146342f637caa73ecd141250
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-12-02 13:00:31 +0100
Commit message:

 Bump version
Package: Rarr
Commit: b03135208f6b4ce360ae24d81ed308f858f71def
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-12-02 13:00:16 +0100
Commit message:

 Mention lz4 update in NEWS
Package: Rarr
Commit: 9f531a8d25b4a214e673860ce5c129acd90e430d
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-12-02 13:00:05 +0100
Commit message:

 Remove lz4-1.9.2
Package: Rarr
Commit: 62ba844a6256f33aac6cb399632b53c0e978fc73
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-11-27 16:31:14 +0100
Commit message:

 Update version number in external files
Package: Rarr
Commit: a618fb4470026cce2433548d8dde065adf29cf4f
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-11-27 16:14:27 +0100
Commit message:

 Upload lz4-1.10.0 files
Package: GSABenchmark
Commit: 324cddc10ded258ca732a246b8abe961dd696ea2
Author: andrei-stoica26 <andreistoica@foxmail.com>
Date: 2025-12-02 22:45:00 +0800
Commit message:

 Refactoring
Package: EpiCompare
Commit: 7ecd95bf398a2b32b8218775951825bde7de41d2
Author: HDash <16350928+HDash@users.noreply.github.com>
Date: 2025-12-01 11:52:22 +0000
Commit message:

 Round heatmap cell values
Package: hammers
Commit: 7bd97bff731c103934e1b286a963dbbc394b532e
Author: andrei-stoica26 <andreistoica@foxmail.com>
Date: 2025-12-02 21:13:37 +0800
Commit message:

 Minor fixes and updates
Package: scifer
Commit: 110a7017d6cdd0ae35eb8de1f5d7265d67e4915d
Author: Rodrigo Arcoverde <rodrigo.arcoverdi@gmail.com>
Date: 2025-12-02 13:15:03 +0100
Commit message:

 Merge remote-tracking branch 'origin/devel' into devel
Package: scifer
Commit: 0119d4c7ba79e5343e918068d6d134f365707f86
Author: Rodrigo Arcoverde <rodrigo.arcoverdi@gmail.com>
Date: 2025-12-02 13:12:51 +0100
Commit message:

 version bump to build
Package: scifer
Commit: eba8e1b6eda8362d0b8e24e3ce32b122cc7b8ecf
Author: Rodrigo Arcoverde <rodrigo.arcoverdi@gmail.com>
Date: 2025-12-02 13:11:33 +0100
Commit message:

 version bump devel
Package: scifer
Commit: d3a88945bf47767863b116b894e008c4a4c931eb
Author: Rodrigo Arcoverde <rodrigo.arcoverdi@gmail.com>
Date: 2025-12-02 13:09:38 +0100
Commit message:

 version bump
Package: scifer
Commit: fd1215a66c33b327a2f9a72ae2b6c53e31bca494
Author: Rodrigo Arcoverde <rodrigo.arcoverdi@gmail.com>
Date: 2025-12-02 13:08:25 +0100
Commit message:

 Revert "version bump"

This reverts commit cc0180cca3be2fa7622e23001af3c9f15640c92c.
Package: scifer
Commit: 600f0678857f16ac8bf7b7b73e3777fc7dae0fb2
Author: Rodrigo Arcoverde <rodrigo.arcoverdi@gmail.com>
Date: 2025-12-02 13:06:30 +0100
Commit message:

 version bump
Package: scifer
Commit: e66ce38f1223b935b56f585e7f9e77a78c2ceb08
Author: Rodrigo Arcoverde <rodrigo.arcoverdi@gmail.com>
Date: 2025-12-02 12:00:08 +0100
Commit message:

 Handles potential null return values in `mclapply`

Ensures that the `summarise_quality` function gracefully handles cases where `summarise_abi_file` returns null.  This prevents errors and ensures the function continues to operate correctly even if some files cannot be processed. It achieves this by adding a check for null return values when creating the `summaries` data frame. If a null value is detected, a placeholder data frame of NAs is returned, maintaining data integrity and preventing unexpected downstream errors. Also disables `mc.preschedule` in `mclapply` calls.
Package: scifer
Commit: 1a979b2eb01a19b5bac7f5dd6824d968c8f89121
Author: Rodrigo Arcoverde <rodrigo.arcoverdi@gmail.com>
Date: 2025-12-02 11:59:50 +0100
Commit message:

 Handles edge cases when trimming sequence

Adds a check to ensure that `trim.start` is actually less than
`trim.finish` before subsetting the sequence. This prevents
errors when these values are incorrectly set.

Falls back to an empty sequence if trimming fails.
Package: scifer
Commit: ad46edf97332a14cbfa74104c0e15a88a892db33
Author: Rodrigo Arcoverde <rodrigo.arcoverdi@gmail.com>
Date: 2025-12-02 13:12:51 +0100
Commit message:

 version bump to build
Package: scifer
Commit: fd14cf33616dc645cee1bf5ca5cd3f00e916001e
Author: Rodrigo Arcoverde <rodrigo.arcoverdi@gmail.com>
Date: 2025-12-02 13:12:05 +0100
Commit message:

 Merge remote-tracking branch 'upstream/devel' into devel
Package: scifer
Commit: 5bf08d45f0526e0f0a1c7e5e55bdd73b692137d8
Author: Rodrigo Arcoverde <rodrigo.arcoverdi@gmail.com>
Date: 2025-12-02 13:11:33 +0100
Commit message:

 version bump devel
Package: scifer
Commit: b8e41fd64e631a15a1a80e100f99435d9b4b3caa
Author: Rodrigo Arcoverde <rodrigo.arcoverdi@gmail.com>
Date: 2025-12-02 13:10:12 +0100
Commit message:

 Merge branch 'master' into devel
Package: scifer
Commit: dda24a65147b57c56d2745908bba10787ae0f708
Author: Rodrigo Arcoverde <rodrigo.arcoverdi@gmail.com>
Date: 2025-12-02 13:09:38 +0100
Commit message:

 version bump
Package: scifer
Commit: 12ae52f5a289ff57a009e65930753267b622b418
Author: Rodrigo Arcoverde <rodrigo.arcoverdi@gmail.com>
Date: 2025-12-02 13:08:25 +0100
Commit message:

 Revert "version bump"

This reverts commit cc0180cca3be2fa7622e23001af3c9f15640c92c.
Package: scifer
Commit: cc0180cca3be2fa7622e23001af3c9f15640c92c
Author: Rodrigo Arcoverde <rodrigo.arcoverdi@gmail.com>
Date: 2025-12-02 13:06:30 +0100
Commit message:

 version bump
Package: scifer
Commit: 9af8d13904545869fe693c18dfe50377f6916511
Author: Rodrigo Arcoverde <rodrigo.arcoverdi@gmail.com>
Date: 2025-12-02 13:02:17 +0100
Commit message:

 Merge branch 'devel'
Package: scifer
Commit: 0f5ac5bf6589f0c67b1d7745d4bcf84f6e50f3f3
Author: Rodrigo Arcoverde <rodrigo.arcoverdi@gmail.com>
Date: 2025-12-02 12:00:08 +0100
Commit message:

 Handles potential null return values in `mclapply`

Ensures that the `summarise_quality` function gracefully handles cases where `summarise_abi_file` returns null.  This prevents errors and ensures the function continues to operate correctly even if some files cannot be processed. It achieves this by adding a check for null return values when creating the `summaries` data frame. If a null value is detected, a placeholder data frame of NAs is returned, maintaining data integrity and preventing unexpected downstream errors. Also disables `mc.preschedule` in `mclapply` calls.
Package: scifer
Commit: 9c7f888bf8e70d87d04adab0ec8eaa1d9db5120a
Author: Rodrigo Arcoverde <rodrigo.arcoverdi@gmail.com>
Date: 2025-12-02 11:59:50 +0100
Commit message:

 Handles edge cases when trimming sequence

Adds a check to ensure that `trim.start` is actually less than
`trim.finish` before subsetting the sequence. This prevents
errors when these values are incorrectly set.

Falls back to an empty sequence if trimming fails.
Package: SparseArray
Commit: 4045476d69c29ae0a29b7b5742c56f802239f5e4
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2025-12-01 19:22:52 -0800
Commit message:

 SparseArray 1.11.7: Fix regression in subassignment of NaArray objects

- Fix regression introduced recently in the C code behind subassignment
  of NaArray objects. See issue #23.

- NaArray objects now support subassignment by an N-index, not just by an
  L-index or M-index. Like SVT_SparseArray objects, the replacement value
  (a.k.a. right value) can be a "short" vector, an ordinary array, or
  another NaArray object.

- Add extensive unit tests for subassignment of NaArray objects.

- Fix mishandling of NaN elements in is_nonna(), nnacount(), nnawhich(),
  and nnavals() default methods. Clarify the meaning of non-NA element
  in the man page for these functions.
Package: hypeR
Commit: fd8fff7f60757e6d769fcfda12ae3ddf80b1cbda
Author: lshep <lori.shepherd@roswellpark.org>
Date: 2025-12-01 14:17:48 -0500
Commit message:

 Undeprecate
Package: mosdef
Commit: 06b8376200b6148b37b87b8f550473c293722326
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2025-12-01 17:51:38 +0100
Commit message:

 Merge remote-tracking branch 'upstream/devel' into devel
Package: mosdef
Commit: dc01a3e805f6875f92cb8352137b5c203a80e1df
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2025-12-01 17:51:32 +0100
Commit message:

 updated roxygen note
Package: mosdef
Commit: 8ffe203b35816cb8dea5928c08ab9366d8cd13e0
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2025-05-15 10:39:07 +0200
Commit message:

 better handling the case of "all objects provided" to enrichment functions - shows the user what the behavior will be + better check on when NOT to run this if specifying up/down only (assumes the presence of a res_de)
Package: quantiseqr
Commit: 800b9ffd5db36ce7bf0295cb2207d9aa1c539ccc
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2025-12-01 17:45:50 +0100
Commit message:

 Merge remote-tracking branch 'upstream/devel' into devel
Package: quantiseqr
Commit: 5ac0fa8a5742bdf47a140ed984a2ed313b48c6ca
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2025-05-02 10:00:59 +0200
Commit message:

 Merge remote-tracking branch 'upstream/devel' into devel
Package: quantiseqr
Commit: 33f70fdf42a334f7d3bb647bb20468d45636624d
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2025-03-07 15:55:58 +0100
Commit message:

 updated GHAs for the cache action
Package: quantiseqr
Commit: 43b7a8815549ea335fd0b66c186333a0bd4d4c28
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2024-12-19 21:40:03 +0100
Commit message:

 new alt spec for pkg documentation
Package: quantiseqr
Commit: 6d178bedfa0c8db2307557c822143d9fbf14fb07
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2024-12-19 21:39:46 +0100
Commit message:

 updated roxygen version
Package: HCAData
Commit: 2a738d3342f0059e8f8ef2c7bab5cd60314a2454
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2025-12-01 17:44:35 +0100
Commit message:

 Merge remote-tracking branch 'upstream/devel' into devel
Package: HCAData
Commit: 2375448f10f48c90301002a9b674d471a91900fa
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2025-05-02 10:00:07 +0200
Commit message:

 Merge remote-tracking branch 'upstream/devel' into devel
Package: HCAData
Commit: 61cf28bc1f48ef89715354acd76447ec87718858
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2025-03-07 14:46:36 +0100
Commit message:

 updating GHA to a more recent cache version
Package: GeneTonic
Commit: 32dba0b3e92c10dd2f4fe90e13a7a2821d54e246
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2025-12-01 17:40:48 +0100
Commit message:

 Merge remote-tracking branch 'upstream/devel' into devel
Package: GeneTonic
Commit: 1651fa95bfa0097ed956eacd2d4a8c3b40897294
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2025-12-01 17:40:12 +0100
Commit message:

 adding ORCID for Edo
Package: flowcatchR
Commit: 03614bd89cdc38b8d659c1c3038ccb24922d1943
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2025-12-01 17:39:10 +0100
Commit message:

 Merge remote-tracking branch 'upstream/devel' into devel
Package: flowcatchR
Commit: 3eef2e0f3c00b56e0e4ab8cc807b31e646485236
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2025-05-02 08:59:13 +0200
Commit message:

 Merge remote-tracking branch 'upstream/devel' into devel
Package: flowcatchR
Commit: d6e5e3f47d694eae5aa92c112199604bacebbcd0
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2025-03-07 14:42:03 +0100
Commit message:

 updating GHA to a more recent cache version
Package: ideal
Commit: 496947b407668b40a5aab8af0acaf7316f1bb0c6
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2025-12-01 17:37:41 +0100
Commit message:

 Merge remote-tracking branch 'upstream/devel' into devel
Package: ideal
Commit: efa43e2de43c97fbbf019e9218e41a5fa9cbe3bb
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2025-05-02 09:00:27 +0200
Commit message:

 Merge remote-tracking branch 'upstream/devel' into devel
Package: ideal
Commit: 8cc841451931ea1d6606dd5808f4dcb160bca9a5
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2025-03-07 14:32:39 +0100
Commit message:

 updating GHA to a more recent cache version
Package: pcaExplorer
Commit: c9ab3ab38e3d19305996b7749b22f5ba52a50180
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2025-12-01 17:35:37 +0100
Commit message:

 version bump, 3.5.1
Package: pcaExplorer
Commit: 59cc8647ab62e44b007e838b9481a5cf8641deb9
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2025-12-01 17:35:24 +0100
Commit message:

 news updated
Package: pcaExplorer
Commit: 9d9d32491f4ac77331bd62b6b579caf925f647be
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2025-12-01 17:33:53 +0100
Commit message:

 defaulting segment color in pcaplot to a shade of grey
Package: pcaExplorer
Commit: f1d9fb2ec19ae6d8b27fa56af52cca703f57e91e
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2025-12-01 17:31:24 +0100
Commit message:

 Merge remote-tracking branch 'upstream/devel' into devel
Package: pcaExplorer
Commit: a78352d5f51fda5d39ef5e990ed7a37be8d1c0a5
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2025-05-02 08:59:54 +0200
Commit message:

 Merge remote-tracking branch 'upstream/devel' into devel
Package: pcaExplorer
Commit: 14eaa4fe67f0d3e82faf8418310e7f6e9d196bbf
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2025-03-07 14:44:32 +0100
Commit message:

 updating GHA to a more recent cache version
Package: BatchSVG
Commit: 409e10b47a77daa046b7ac08c66749b4edc5f637
Author: Kinnary Shah <kinnaryshahh@gmail.com>
Date: 2025-12-01 11:19:07 -0500
Commit message:

 grammar
Package: BatchSVG
Commit: 9590efa94d89699a966f47d827d7449728f0f6bc
Author: Kinnary Shah <kinnaryshahh@gmail.com>
Date: 2025-12-01 11:17:02 -0500
Commit message:

 fix spacing errors in DESCRIPTION file
Package: SparseArray
Commit: 33930ea31b59e7ba2ea3382012a5d9136abb9fcf
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2025-12-01 08:15:39 -0800
Commit message:

 small edit in comment
Package: DESeq2
Commit: 3a8522f0ae619158eb115df9917b7d10504d9376
Author: Mike Love <mikelove@users.noreply.github.com>
Date: 2025-12-01 08:43:25 -0500
Commit message:

 version bump
Package: DESeq2
Commit: 62293c648ab5a63d8e91ded7c0b1690308958cd0
Author: Mike Love <mikelove@users.noreply.github.com>
Date: 2025-12-01 08:27:48 -0500
Commit message:

 cleanup docs
Package: tximeta
Commit: 1b6daa295061a468ff64b43fb22bf0080e1a8e3c
Author: Mike Love <mikelove@users.noreply.github.com>
Date: 2025-12-01 08:25:54 -0500
Commit message:

 work later on edgeR pieces
Package: tximeta
Commit: dab0a38f9cfc8cd0ef4a9f02d6dae6a64c2b9445
Author: Mike Love <mikelove@users.noreply.github.com>
Date: 2025-11-21 14:56:37 -0500
Commit message:

 fix edgeR code until its ready
Package: tximeta
Commit: 3ebc8c4768cea79ffc1f8121a3743fa7f9f045a4
Author: Mike Love <mikelove@users.noreply.github.com>
Date: 2025-11-21 12:34:56 -0500
Commit message:

 fix
Package: tximeta
Commit: 61967df6d0b583e5afb85051cd59a77599d2aa6a
Author: Mike Love <mikelove@users.noreply.github.com>
Date: 2025-11-21 12:30:59 -0500
Commit message:

 work on edgeR RTA disp
Package: tximeta
Commit: f9d9bcf725b17186bb933bd555f5975e38d95612
Author: Mike Love <mikelove@users.noreply.github.com>
Date: 2025-11-14 13:54:11 -0500
Commit message:

 version bump
Package: tximeta
Commit: ec044dd4a04bbf244af479356231987736e89612
Author: Mike Love <mikelove@users.noreply.github.com>
Date: 2025-11-14 13:53:08 -0500
Commit message:

 tweak
Package: tximeta
Commit: 078183fe90960d6f443b054f67fd8851949da909
Author: Mike Love <mikelove@users.noreply.github.com>
Date: 2025-11-14 13:26:14 -0500
Commit message:

 moving deseq2 to uneval
Package: tximeta
Commit: 85931b3891a9c03a39b233d076047308463f6923
Author: Mike Love <mikelove@users.noreply.github.com>
Date: 2025-11-14 12:41:13 -0500
Commit message:

 add more docs around mixed refs
Package: tximeta
Commit: 26ab246511e535454eed71489d5104aaf6f605d7
Author: Mike Love <mikelove@users.noreply.github.com>
Date: 2025-10-13 15:32:05 -0400
Commit message:

 adding prompt for digest in precomputed, fixed #91
Package: IsoformSwitchAnalyzeR
Commit: aa1418e54a0fc6040a82ae2553c9c1434878cc8e
Author: Kristoffer Vitting-Seerup <kvittingseerup@users.noreply.github.com>
Date: 2025-12-01 11:36:14 +0100
Commit message:

 Merge master into Bioc devel and resolve DESCRIPTION/NAMESPACE conflicts
Package: IsoformSwitchAnalyzeR
Commit: fbc1e230fb790cb0539bc304e8aeaa3e8ae2bb9b
Author: Kristoffer Vitting-Seerup <kvittingseerup@users.noreply.github.com>
Date: 2025-12-01 11:28:56 +0100
Commit message:

 Clean ignore files and remove DS_Store artefacts
Package: IsoformSwitchAnalyzeR
Commit: 58b97cc55dc3729d2291b7b924b20a19970166b0
Author: Kristoffer Vitting-Seerup <kvittingseerup@users.noreply.github.com>
Date: 2025-12-01 11:24:41 +0100
Commit message:

 Fine-tuning for BioC push - see NEWS
Package: IsoformSwitchAnalyzeR
Commit: dcac393453182daec2dd4d55f2ac7c44c35d4ade
Author: Kristoffer Vitting-Seerup <23721187+kvittingseerup@users.noreply.github.com>
Date: 2025-12-01 09:03:50 +0100
Commit message:

 Merge pull request #294 from elena-iri/my-feature-branch

Updated deprecated functions and minor modifications
Package: IsoformSwitchAnalyzeR
Commit: eea276e36a5b84815e89191b130592be55ac015b
Author: elena-iri <eleni.iriondo2@gmail.com>
Date: 2025-11-21 09:26:44 +0100
Commit message:

 Updated deprecated functions in isoform_plots.R and analyze_switch_consequences.R, updated ISAR version number and fixed a few typos.
Package: IsoformSwitchAnalyzeR
Commit: 283e09069572f78796660506fe46cd60b3a684d8
Author: elena-iri <154343900+elena-iri@users.noreply.github.com>
Date: 2025-10-07 16:32:14 +0200
Commit message:

 Merge pull request #290 from prireto/bugfix-preFilter

Bugfix: Fix typo the preFilter() function
Package: IsoformSwitchAnalyzeR
Commit: 16bf2fe0422c9842ad29977b148db417b389b0b6
Author: 74370325+prireto@users.noreply.github.com <74370325+prireto@users.noreply.github.com>
Date: 2025-09-12 15:00:24 +0200
Commit message:

 Bugfix: In the preFilter() function, setting acceptedBiotype caused an error, because it attempted to use the function setdff() insteat of setdiff(). Fixed the typo.
Package: IsoformSwitchAnalyzeR
Commit: 9f0d50c9f740c1cb7fe4920cdc6869b9fbcdfbac
Author: Kristoffer Vitting-Seerup <k.vitting.seerup@gmail.com>
Date: 2025-02-01 13:15:09 +0100
Commit message:

 Merge pull request #266 from chunxubioinfor/master

See NEWS
Package: IsoformSwitchAnalyzeR
Commit: 9ac446ef6dc8d07f1f06e2aef3f00f2199d20188
Author: chunxubioinfor <chunxuhan007@gmail.com>
Date: 2025-01-31 17:55:25 +0800
Commit message:

 see NEWS
Package: IsoformSwitchAnalyzeR
Commit: 8308d2a4198f7a5afe897096f6dd0f58ef0cea65
Author: chunxubioinfor <chunxuhan007@gmail.com>
Date: 2025-01-19 15:59:49 +0100
Commit message:

 see NEWS
Package: IsoformSwitchAnalyzeR
Commit: f63d47d78efe013909ff6c66d733b647b56d8cd4
Author: Kristoffer Vitting-Seerup <k.vitting.seerup@gmail.com>
Date: 2024-12-30 10:38:20 +0100
Commit message:

 Merge pull request #262 from chunxubioinfor/master

see NEWS
Package: IsoformSwitchAnalyzeR
Commit: acd4eb7b5112c9da78fa800df35e49af3beb9342
Author: Chunxu Han <62064246+chunxubioinfor@users.noreply.github.com>
Date: 2024-12-29 16:32:57 +0100
Commit message:

 Merge branch 'kvittingseerup:master' into master
Package: IsoformSwitchAnalyzeR
Commit: 8cc23946af66bf551512acdbf1562fe3cb7b36e4
Author: chunxubioinfor <chunxuhan007@gmail.com>
Date: 2024-12-29 15:51:55 +0100
Commit message:

 importPairedGSEA update
Package: IsoformSwitchAnalyzeR
Commit: 67023a1ae8869cae6844cda14e47e3318c6481f8
Author: chunxubioinfor <chunxuhan007@gmail.com>
Date: 2024-12-02 18:01:20 +0100
Commit message:

 see NEWS
Package: IsoformSwitchAnalyzeR
Commit: f6cd48a4c311db3a4ab6bfb95e6210d5177f69e5
Author: Kristoffer Vitting-Seerup <k.vitting.seerup@gmail.com>
Date: 2024-06-28 12:36:02 +0200
Commit message:

 Merge pull request #250 from chunxubioinfor/master

see NEWS
Package: IsoformSwitchAnalyzeR
Commit: cb8a72889d5e43aa7b80e9c36d54a5acd99c25fb
Author: chunxubioinfor <chunxuhan007@gmail.com>
Date: 2024-06-27 11:38:24 +0200
Commit message:

 see NEWS
Package: IsoformSwitchAnalyzeR
Commit: d70e5d54ddaf2d5c7f1355edeaeded5b019300ff
Author: Kristoffer Vitting-Seerup <k.vitting.seerup@gmail.com>
Date: 2024-01-09 14:06:40 +0100
Commit message:

 Merge pull request #223 from chunxubioinfor/master

bug fix
Package: IsoformSwitchAnalyzeR
Commit: 186052954794c179f9edb5d35a4e1dff6982eeb2
Author: Chunxu Han <62064246+chunxubioinfor@users.noreply.github.com>
Date: 2024-01-06 15:52:08 +0100
Commit message:

 Merge branch 'kvittingseerup:master' into master
Package: IsoformSwitchAnalyzeR
Commit: 98939b88139e3ece8dd53d5a4d0d640e6d10816a
Author: chunxubioinfor <chunxuhan007@gmail.com>
Date: 2024-01-06 15:45:22 +0100
Commit message:

 see NEWS
Package: IsoformSwitchAnalyzeR
Commit: 0591411edccbc90a7121308c838a6799a4f0677e
Author: Kristoffer Vitting-Seerup <k.vitting.seerup@gmail.com>
Date: 2023-12-12 14:39:02 +0100
Commit message:

 Merge pull request #220 from chunxubioinfor/master

see NEWS
Package: IsoformSwitchAnalyzeR
Commit: 46b24ed0ab7b2f99b9f8647ca00625abe024fba8
Author: chunxubioinfor <chunxuhan007@gmail.com>
Date: 2023-12-03 13:38:35 +0100
Commit message:

 see NEWS
Package: IsoformSwitchAnalyzeR
Commit: 3951bfb4931bf5ac6a2ed1019acc1572df8bccfb
Author: Kristoffer Vitting-Seerup <k.vitting.seerup@gmail.com>
Date: 2023-11-21 15:50:13 +0100
Commit message:

 Merge pull request #216 from chunxubioinfor/master

NetSurfP3 support
Package: IsoformSwitchAnalyzeR
Commit: abb6704b7bc117bd9f4bde6f31fa59bda7c67693
Author: chunxubioinfor <chunxuhan007@gmail.com>
Date: 2023-11-21 14:56:14 +0100
Commit message:

 NetSurfP3 support
Package: IsoformSwitchAnalyzeR
Commit: ea1235b05a11babac029b1f37c953553251a44fb
Author: Kristoffer Vitting-Seerup <krivi@dtiu-c02drj2cml7h.clients.net.dtu.dk>
Date: 2023-11-10 11:50:00 +0100
Commit message:

 Fixed author roles
Package: IsoformSwitchAnalyzeR
Commit: 8e19cfd3383d3d042728a23673f4fd22e3e9fd16
Author: Kristoffer Vitting-Seerup <krivi@dtiu-c02drj2cml7h.clients.net.dtu.dk>
Date: 2023-10-27 11:02:32 +0200
Commit message:

 Fixed devel/master conflict

Merge branch 'master' into devel

# Conflicts:
#	DESCRIPTION
Package: IsoformSwitchAnalyzeR
Commit: c160543952492ecb4f2a3a9876cbba38c1aaee99
Author: Kristoffer Vitting-Seerup <krivi@dtiu-c02drj2cml7h.clients.net.dtu.dk>
Date: 2023-10-27 10:59:05 +0200
Commit message:

 Added maintainer
Package: IsoformSwitchAnalyzeR
Commit: 5f471360da38101777d37d9eb91a99c3ac81eda4
Author: Kristoffer Vitting-Seerup <krivi@dtiu-c02drj2cml7h.clients.net.dtu.dk>
Date: 2023-06-30 13:04:50 +0200
Commit message:

 R version update
Package: IsoformSwitchAnalyzeR
Commit: f1899189a64af97495c9dd66bf3d611cd2231cae
Author: Kristoffer Vitting-Seerup <krivi@dtiu-c02drj2cml7h.clients.net.dtu.dk>
Date: 2023-06-30 12:46:41 +0200
Commit message:

 R dependency decrease
Package: IsoformSwitchAnalyzeR
Commit: 83aa34e3230da9cf411b1da5f2902d035cf939ee
Author: Kristoffer Vitting-Seerup <krivi@dtiu-c02drj2cml7h.clients.net.dtu.dk>
Date: 2023-06-27 15:50:13 +0200
Commit message:

 Better description
Package: BSgenomeForge
Commit: b2d250d2151ba307f8e108c48ec0d7ad8a4501b8
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2025-11-30 22:28:18 -0800
Commit message:

 BSgenomeForge 1.11.2: Remove outdated links from inst/pkgtemplates/BSgenome_datapkg/man/package.Rd and inst/pkgtemplates/MaskedBSgenome_datapkg/man/package.Rd
Package: tidySpatialExperiment
Commit: 002a6a575bdbf21baa7ed1b3087ea95d06b4c61d
Author: William Hutchison <william.8191@fastmail.com>
Date: 2025-12-01 11:37:47 +1100
Commit message:

 Version up
Package: tidySpatialExperiment
Commit: 39210f0c464efcf2efb49d5d7889ef0fb168bc2d
Author: William Hutchison <william.8191@fastmail.com>
Date: 2025-12-01 11:34:11 +1100
Commit message:

 Fix inverted y axis in gate path record
Package: GSVA
Commit: 90ed711934e27a4b82b543c3cd3ca37e9ad9a8f2
Author: Robert Castelo <robert.castelo@upf.edu>
Date: 2025-11-30 19:32:02 +0100
Commit message:

 Bump version
Package: GSVA
Commit: b831c81335a093eed2acef5a66d9a24991306944
Author: Robert Castelo <robert.castelo@upf.edu>
Date: 2025-11-30 19:31:48 +0100
Commit message:

 Fix on the handing of missing data with the GSVA method. Bug reported in issue #257.
Package: drugfindR
Commit: 0d0de664680b7045c70a752f66ac31fc27cabaf9
Author: Ali Sajid Imami <395482+AliSajid@users.noreply.github.com>
Date: 2025-11-30 09:34:03 -0500
Commit message:

 chore: Merge pull request #169 from CogDisResLab/fix/dfplyr-name-collision-rename
Package: drugfindR
Commit: e85e06f955f599996c1c37013f408d820c4c0e7c
Author: Ali Sajid Imami <395482+AliSajid@users.noreply.github.com>
Date: 2025-11-30 00:49:55 -0500
Commit message:

 fix: remove the conflicting import for dplyr::rename
Package: enrichplot
Commit: 114dc01f380d01b116829e72d25e2aa138256311
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2025-11-30 17:17:05 +0800
Commit message:

 fixed R check
Package: enrichplot
Commit: 906a3ca79d629bb639ba12e6dbef700486c1e392
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2025-11-30 16:07:23 +0800
Commit message:

 bump version
Package: enrichplot
Commit: cef3e21277b68b0c3cf7089e0ca52a25157869e5
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2025-11-30 16:02:00 +0800
Commit message:

 Merge branch 'devel' of github.com:YuLab-SMU/enrichplot into devel
Package: enrichplot
Commit: b2796c9dce52c289c1aeb0a574395a93b2ec3b3e
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2025-11-30 16:01:49 +0800
Commit message:

 cleanup code
Package: enrichplot
Commit: dfabb1a9362b817285108d615e8789b461a10ef2
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2025-11-30 15:30:17 +0800
Commit message:

 Merge pull request #338 from ivokwee/devel

Add fc_threshold parameter to cnetplot
Package: enrichplot
Commit: 2b93e5b79bff065351b5e2189c9981232942cba3
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2025-11-30 14:38:10 +0800
Commit message:

 bug fixed #339
Package: enrichplot
Commit: 3385c7ed7b1a8a8f03fab7069f9886d3b74be927
Author: Ivo Kwee <ivo.kwee@gmail.com>
Date: 2025-11-22 20:34:43 +0100
Commit message:

 Merge pull request #3 from ivokwee/cnetplot-addthreshold

Add fc_threshold parameter to cnetplot
Package: enrichplot
Commit: 5647eb4b7f8bbd330f8155266c747a825def1ae5
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2025-11-23 00:20:35 +0800
Commit message:

 changes according to #335
Package: enrichplot
Commit: e00d9aa6686af6ec55685c3e81718ff5ce04b797
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2025-11-23 00:08:50 +0800
Commit message:

 Merge pull request #335 from ivokwee/devel

Improvements heatplot and treeplot
Package: enrichplot
Commit: 17ae657fdfc35865bc080102e4b4e8d44e66b739
Author: Ivo Kwee <ivo.kwee@gmail.com>
Date: 2025-11-21 18:13:31 +0100
Commit message:

 Add fc_threshold parameter to cnetplot for filtering genes by fold change

Add new fc_threshold parameter that filters genes to only include those
with absolute fold change greater than the threshold. This allows users
to plot only genes with |foldChange| > fc_threshold (e.g., fc_threshold = 1).

🤖 Generated with [Claude Code](https://claude.com/claude-code)

Co-Authored-By: Claude <noreply@anthropic.com>
Package: enrichplot
Commit: ad1497b23ea641ab9cd5b6ffc86468d8847f62a5
Author: Ivo Kwee <ivo.kwee@gmail.com>
Date: 2025-11-21 14:00:03 +0100
Commit message:

 Merge pull request #2 from ivokwee/heatplot-revcolors

Fix reversed colors in heatmap plot: add REVERSE=FALSE
Package: enrichplot
Commit: 9f0eb5e8fdffe05b2d71ba5499bccdbe495c1787
Author: Ivo Kwee <ivo.kwee@gmail.com>
Date: 2025-11-21 13:59:21 +0100
Commit message:

 Merge pull request #1 from ivokwee/fix-treeplot-sizecolor

add size_var; fix color
Package: enrichplot
Commit: fd11e6915703246b7255d2cd00e8122b1436afd8
Author: Ivo Kwee <ivo.kwee@gmail.com>
Date: 2025-11-21 12:32:43 +0100
Commit message:

 add size_var; fix color
Package: enrichplot
Commit: e73995eebaae6902ff2b4121bc7a2b185f22d1cb
Author: Ivo Kwee <ivo.kwee@gmail.com>
Date: 2025-11-21 10:58:51 +0100
Commit message:

 Fix reversed colors in heatmap plot: add REVERSE=FALSE
Package: enrichplot
Commit: 001416a2efd9efe6eee304b7048f459c250ed273
Author: Ivo Kwee <ivo.kwee@gmail.com>
Date: 2025-11-20 16:26:15 +0100
Commit message:

 change sorting
Package: enrichplot
Commit: b2a49c1c6c4eaeff1be809cda1757657c0c89965
Author: Ivo Kwee <ivo.kwee@gmail.com>
Date: 2025-11-20 16:24:51 +0100
Commit message:

 change sorting
Package: enrichplot
Commit: 943b081b9053c2996d7c99f99d9b17d888318f6f
Author: Ivo Kwee <ivo.kwee@gmail.com>
Date: 2025-11-20 16:07:21 +0100
Commit message:

 add showTop parameter to limit number of genes in plot
Package: epiSeeker
Commit: d473b967f9c87a5ef2be37979623043ecb243ac1
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2025-11-30 16:55:30 +0800
Commit message:

 bump version
Package: epiSeeker
Commit: 3e91ef4aee63df20a26f367154f594bb256d59b7
Author: liming <limiang929@gmail.com>
Date: 2025-11-30 13:08:27 +0800
Commit message:

 add test for most of export functions
Package: epiSeeker
Commit: 21c56548fb9d2f5e952507c7e6517d268b739167
Author: liming <limiang929@gmail.com>
Date: 2025-11-27 12:16:47 +0800
Commit message:

 add runnable examples, add demo bisseq file, fix note for lazy data
Package: epiSeeker
Commit: 9fa95191cdbaf7f86ce4e8cc5f8b738ae788dc60
Author: liming <limiang929@gmail.com>
Date: 2025-11-26 13:06:25 +0800
Commit message:

 add provenance and data structure information
Package: epiSeeker
Commit: 9a12062029bd5c9a3f8cf4c3f46b07a09e0350b2
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2025-11-26 08:53:38 +0800
Commit message:

 add fnd role
Package: epiSeeker
Commit: 498686c660eb1e1f45ee2a280c73ed29ffb6c68f
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2025-11-26 08:51:23 +0800
Commit message:

 update DESCRIPTION
Package: epiSeeker
Commit: f9e91f17d20bb5492a8db20e582ed3268362b796
Author: liming <limiang929@gmail.com>
Date: 2025-11-25 20:56:17 +0800
Commit message:

 update R to 4.5.0
Package: epiSeeker
Commit: 46b20e2af67ebb86fc37a1585640ff20b406641f
Author: liming <limiang929@gmail.com>
Date: 2025-11-25 19:00:30 +0800
Commit message:

 remove lazy data
Package: DOTSeq
Commit: c8988856a8819c8f93521c4bd9db2b3233f2bc70
Author: lcscs12345 <lcscs12345@gmail.com>
Date: 2025-11-30 20:07:49 +1300
Commit message:

 add seqlevels_style and bam_output_dir
Package: mariner
Commit: 84a2021d924f07035c05abbd7985d35c1ae5e84d
Author: Eric Davis <31807001+EricSDavis@users.noreply.github.com>
Date: 2025-11-29 23:37:34 -0500
Commit message:

 Fix version in DESCRIPTION.
Package: mariner
Commit: 7c77ca10137fdd49cb980bd971ddef38dec4cf93
Author: Eric Davis <31807001+EricSDavis@users.noreply.github.com>
Date: 2025-11-29 23:33:29 -0500
Commit message:

 Merge branch 'dev' into devel
Package: mariner
Commit: 2d0f84fe978643c38af32f553b2aad970f66f990
Author: Eric Scott Davis <ericscottdavis@outlook.com>
Date: 2025-11-30 04:17:59 +0000
Commit message:

 Version bump
Package: mariner
Commit: 858b0ff8cf2eaae00a5fcf57afbc992345192003
Author: Eric Scott Davis <ericscottdavis@outlook.com>
Date: 2025-11-30 03:45:34 +0000
Commit message:

 Update code in response to changed exports from plyranges.
Package: drugfindR
Commit: 30ed47452e7655688e628ad7f43f0ac6b5ef05ef
Author: Ali Sajid Imami <395482+AliSajid@users.noreply.github.com>
Date: 2025-11-29 23:30:13 -0500
Commit message:

 docs: clarify package documentation
Package: drugfindR
Commit: 77abe58b281a18ef083b795539f629001c883b7c
Author: Ali Sajid Imami <395482+AliSajid@users.noreply.github.com>
Date: 2025-11-29 23:05:59 -0500
Commit message:

 chore: Merge pull request #168 from CogDisResLab/fix/dfplyr-name-collision
Package: drugfindR
Commit: 252a661fe44bc2dd037ab318695d0eb47cbee160
Author: Ali Sajid Imami <395482+AliSajid@users.noreply.github.com>
Date: 2025-11-25 23:14:00 -0500
Commit message:

 fix: remove the conflicting import
Package: drugfindR
Commit: e9b55e24781d887e63570e3eba05d8a36f432bff
Author: Ali Sajid Imami <395482+AliSajid@users.noreply.github.com>
Date: 2025-11-25 22:30:04 -0500
Commit message:

 style: ensure that other lints are addressed
Package: drugfindR
Commit: e1bb280641cdb44118a306b1e9ee87a80e2065f4
Author: Ali Sajid Imami <395482+AliSajid@users.noreply.github.com>
Date: 2025-11-25 20:33:42 -0500
Commit message:

 style: ensure consistent indentation across the project
Package: drugfindR
Commit: 1beaf081d22e73fca871ee5e64f3cb588824e111
Author: Ali Sajid Imami <395482+AliSajid@users.noreply.github.com>
Date: 2025-11-25 09:06:50 -0500
Commit message:

 test: update the argument order in fliter signature
Package: DOTSeq
Commit: d5e8832c3731a877cd15e2e6a444db241aad1448
Author: lcscs12345 <lcscs12345@gmail.com>
Date: 2025-11-30 16:57:21 +1300
Commit message:

 add tests
Package: DOTSeq
Commit: 19eb7e89b5e020a2be1ae7775df2c989477c0232
Author: Chun Shen Lim <chunshen.lim@otago.ac.nz>
Date: 2025-11-21 19:47:33 +1300
Commit message:

 rename directory
Package: DOTSeq
Commit: 8956ce6e8d8382b08c2c09d1eefaaa4f3efd6685
Author: Chun Shen Lim <chunshen.lim@otago.ac.nz>
Date: 2025-11-21 19:36:41 +1300
Commit message:

 add generate_extdata.sh
Package: DOTSeq
Commit: 12be971e58b7c0494782e7508e8c4e58bb913981
Author: lcscs12345 <lcscs12345@gmail.com>
Date: 2025-11-09 12:39:44 +1300
Commit message:

 add info on annotation
Package: DOTSeq
Commit: 4f73758cb97236db0be8ec5fc464aca474fa6b19
Author: lcscs12345 <lcscs12345@gmail.com>
Date: 2025-11-08 13:17:19 +1300
Commit message:

 rename function
Package: DOTSeq
Commit: de7a3fad67a2408534237c18f1a97cd372e691bd
Author: lcscs12345 <lcscs12345@gmail.com>
Date: 2025-11-08 13:16:01 +1300
Commit message:

 rename function
Package: DOTSeq
Commit: fefc656833d6933cb1747e9c06b9f396ad50136d
Author: Chun Shen Lim <chunshen.lim@otago.ac.nz>
Date: 2025-11-07 14:40:35 +1300
Commit message:

 add getExonicReads
Package: DOTSeq
Commit: 3e2fc15aaa8ce7c705063b013c4de9be554dde0d
Author: Chun Shen Lim <chunshen.lim@otago.ac.nz>
Date: 2025-11-07 13:44:01 +1300
Commit message:

 add getExonicReads
Package: DOTSeq
Commit: c69ab677a1e94f8f0081398809f3aed359093a3f
Author: Chun Shen Lim <chunshen.lim@otago.ac.nz>
Date: 2025-11-07 13:34:32 +1300
Commit message:

 save TxDb
Package: DOTSeq
Commit: 1b664f8b494e3642a5fbf5637ad469144663a5be
Author: Chun Shen Lim <chunshen.lim@otago.ac.nz>
Date: 2025-11-07 13:33:48 +1300
Commit message:

 save TxDb
Package: DOTSeq
Commit: 353201aa14f14725db2c5b21bc5f5f6c066eca79
Author: Chun Shen Lim <chunshen.lim@otago.ac.nz>
Date: 2025-11-07 12:59:31 +1300
Commit message:

 save TxDb
Package: DOTSeq
Commit: 5f8a8e6f6021d5d32109f37ed6c5c4671a2e5f7b
Author: Chun Shen Lim <chunshen.lim@otago.ac.nz>
Date: 2025-11-07 10:35:11 +1300
Commit message:

 add getExonicReads
Package: DOTSeq
Commit: 1d3393f15f0846988833d689b7c6ff0c01021918
Author: Chun Shen Lim <chunshen.lim@otago.ac.nz>
Date: 2025-11-07 10:20:30 +1300
Commit message:

 add getExonicReads