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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: GSVA
Commit: 56c76c8afac663f46e25c1c1ed37f42b858bd924
Author: Robert Castelo <robert.castelo@upf.edu>
Date: 2025-11-26 20:42:46 +0100
Commit message:

 Bump version
Package: GSVA
Commit: 8c8344b23fe5fe535d4b511d668384995066de6f
Author: Robert Castelo <robert.castelo@upf.edu>
Date: 2025-11-26 20:42:33 +0100
Commit message:

 Fix in fetching rows from SVT_SparseArray matrices
Package: igblastr
Commit: 52f6a5fe59bf29ef6e4200bd708af2eecb632a13
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2025-11-26 11:36:59 -0800
Commit message:

 Add information in README.md on how to cite the package
Package: StatescopeR
Commit: 30a76749f80c14306e5dfc95d4285a834fbdfe05
Author: MSteketee <m.f.b.steketee@amsterdamumc.nl>
Date: 2025-11-26 20:36:33 +0100
Commit message:

 Removed minimizing geneset again as it didnt add much. Aligned samples in examples and test
Package: AlphaMissenseR
Commit: b6b791dc959257852bee49ad0af988bc86c4e4a6
Author: Martin Morgan <mtmorgan.xyz@gmail.com>
Date: 2025-11-26 14:35:47 -0500
Commit message:

 version bump
Package: AlphaMissenseR
Commit: 05f721b91557d84313e8271c14a97c08ef61c0bd
Author: Martin Morgan <mtmorgan.xyz@gmail.com>
Date: 2025-11-26 14:33:44 -0500
Commit message:

 update af_prediction() unit test

- expected table columns match those returned
Package: StatescopeR
Commit: b6f172b304610ee5ba1aea49aa5198bb9a0c3768
Author: MSteketee <m.f.b.steketee@amsterdamumc.nl>
Date: 2025-11-26 19:52:36 +0100
Commit message:

 Reduced number of samples in examples, vignette and test
Package: StatescopeR
Commit: 03758fd29cf5adc42473c6bc8ef5be3b42271aac
Author: MSteketee <m.f.b.steketee@amsterdamumc.nl>
Date: 2025-11-26 18:59:31 +0100
Commit message:

 Version bump
Package: methylCC
Commit: f22993392425ca12fc16392b1d5420f4516e1877
Author: Stephanie Hicks <stephaniechicks@gmail.com>
Date: 2025-11-26 11:03:42 -0500
Commit message:

 bumping to 1.25.2 to trigger new build
Package: methylCC
Commit: 9a3a86a1ab5ffc4db79a8a6778f61bf41d547096
Author: Stephanie Hicks <stephaniechicks@gmail.com>
Date: 2025-11-24 13:09:44 -0500
Commit message:

 and removed plyranges from namespace
Package: smoppix
Commit: 24524f06faa48296b62b409ec270eeab83dd04e2
Author: stijn <stijn.hawinkel@psb.ugent.be>
Date: 2025-11-26 16:14:50 +0100
Commit message:

 Hard coded the tolerance for now
Package: smoppix
Commit: ac19a96120b0dc014f0d07f45f4bdab483149c06
Author: stijn <stijn.hawinkel@psb.ugent.be>
Date: 2025-11-26 16:03:05 +0100
Commit message:

 Correction due to updates lme4
Package: smoppix
Commit: 30e0f2dbfc809317a63e863826c9c08fbdc55f1e
Author: stijn <stijn.hawinkel@psb.ugent.be>
Date: 2025-11-13 10:19:24 +0100
Commit message:

 with latest tikz
Package: GeDi
Commit: 896db8613ac6e84dc95131e80820ae8ab11d84e1
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2025-11-26 16:21:02 +0100
Commit message:

 version bump, 1.7.1
Package: GeDi
Commit: 83c78a287e88d1ec0764beadbc3885c256449da8
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2025-11-26 16:13:38 +0100
Commit message:

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

# Conflicts:
#	DESCRIPTION
Package: GeDi
Commit: dc35da44fd0905a3c92becb490d93e85e6d07809
Author: AnnekathrinSilvia <33468358+AnnekathrinSilvia@users.noreply.github.com>
Date: 2025-11-12 11:53:24 +0100
Commit message:

 Merge pull request #28 from AnnekathrinSilvia/revision_improvements

Revision improvements
Package: GeDi
Commit: df86aed5f47c0343540c1e4a64e026a7f3f6f44f
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2025-11-12 11:51:38 +0100
Commit message:

 version bump, 1.5.1
Package: GeDi
Commit: 97dbf940ed3a21f5b1000fcd8b5218298cfe666a
Author: Annekathrin Silvia Ludt <annekathrin@Annekathrins-MacBook-Pro.local>
Date: 2025-11-12 11:36:18 +0100
Commit message:

 Fixed typo
Package: GeDi
Commit: 2acdba4f9f0150eb060a939919b16b6deedbff5d
Author: Annekathrin Silvia Ludt <annekathrin@Annekathrins-MacBook-Pro.local>
Date: 2025-11-12 11:35:47 +0100
Commit message:

 Added description of the new network metrics to the vignette
Package: GeDi
Commit: bb85008de0a127ed1e9035e21cf3305cc7d2277f
Author: Annekathrin Silvia Ludt <annekathrin@Annekathrins-MacBook-Pro.fritz.box>
Date: 2025-11-07 09:36:32 +0100
Commit message:

 Added the new path_to_GeDi funciton to the vignette
Package: GeDi
Commit: 18f8b55a55e0ba4e8fa31a9067787f62aac1e1dd
Author: Annekathrin Silvia Ludt <annekathrin@Annekathrins-MacBook-Pro.fritz.box>
Date: 2025-11-07 09:16:34 +0100
Commit message:

 Finalised the new distance heatmap implementation
Package: GeDi
Commit: 929e08149eba94e5476d65e8cb2db2e790b06d23
Author: Annekathrin Silvia Ludt <annekathrin@Annekathrins-MacBook-Pro.fritz.box>
Date: 2025-11-07 09:15:10 +0100
Commit message:

 Changed the path_to_GeDi function to expect a data.frame for all enrichment packages
Package: GeDi
Commit: cf8b784b52931e9b1a7f06f75595b0e74443b3d5
Author: Annekathrin Silvia Ludt <annekathrin@Annekathrins-MacBook-Pro.local>
Date: 2025-11-06 16:37:45 +0100
Commit message:

 Added documentation on the new path_to_GeDi function
Package: GeDi
Commit: 8d2aef85c5072aff3e70ecd81490bd5340c15c8f
Author: Annekathrin Silvia Ludt <annekathrin@Annekathrins-MacBook-Pro.local>
Date: 2025-11-06 16:36:57 +0100
Commit message:

 Added the info on the new path_to_GeDi function to the NEWS file
Package: GeDi
Commit: ad786994292143c68ca41ba967bbab20efaded10
Author: Annekathrin Silvia Ludt <annekathrin@Annekathrins-MacBook-Pro.local>
Date: 2025-11-06 16:32:44 +0100
Commit message:

 Fixed errors in the stopifnot conditions in the new path_to_GeDi function
Package: GeDi
Commit: 49a4e05b6ff46290a888cfe089cadd09969d88d6
Author: Annekathrin Silvia Ludt <annekathrin@Annekathrins-MacBook-Pro.local>
Date: 2025-11-06 15:34:40 +0100
Commit message:

 Finished documentation for the new function
Package: GeDi
Commit: 24380d2011592c8c8b8583ea5c461c8deb12d9af
Author: Annekathrin Silvia Ludt <annekathrin@Annekathrins-MacBook-Pro.local>
Date: 2025-11-06 15:15:54 +0100
Commit message:

 Added a new funciton called path_to_GeDi() to prepare the output of various enrichment analysis packages for the use in GeDi
Package: GeDi
Commit: 2e4beee6722639c5a0977238952928f1245bcd19
Author: Annekathrin Silvia Ludt <annekathrin@Annekathrins-MacBook-Pro.local>
Date: 2025-11-06 11:12:16 +0100
Commit message:

 Restructured the table below the clustering graph to now also reflect graph metrics such as betweenness, centrality and other graph measurements
Package: GeDi
Commit: 239d65074722bd634c96701b3112558e9dba63c6
Author: Annekathrin Silvia Ludt <annekathrin@Annekathrins-MacBook-Pro.local>
Date: 2025-11-05 19:42:50 +0100
Commit message:

 Fixed all distance score implementations to now use the correct speed up versions
Package: GeDi
Commit: 1599120aab42c9ee393b88345f4342a2c84c1428
Author: Annekathrin Silvia Ludt <annekathrin@MacBookPro.fritz.box>
Date: 2025-11-04 17:19:49 +0100
Commit message:

 Removed old kappa implementation and renamed the new, more efficient one to make sure that the app still runs correctly
Package: GeDi
Commit: 9295f73b0a53756c6116df3afa4fcd35498332f7
Author: Annekathrin Silvia Ludt <annekathrin@MacBookPro.fritz.box>
Date: 2025-11-04 17:13:12 +0100
Commit message:

 Removed the old Jaccard implementation and renamed the new implementation to ensure that the code still works
Package: GeDi
Commit: a7d1972e275897f902cbc5bb9c535389a013825a
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2025-11-04 16:43:09 +0100
Commit message:

 imports fixed in the code of the specific functions
Package: GeDi
Commit: afb365b5944e2e72ad13f89fd7fe08ef28207a3f
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2025-11-04 16:42:44 +0100
Commit message:

 imports fixed
Package: GeDi
Commit: 8d52bf1858f72b2b39a202de01a21be0c45cef4a
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2025-11-04 16:34:41 +0100
Commit message:

 Merge branch 'revision_dh' of github.com:AnnekathrinSilvia/GeDi into revision_dh
Package: GeDi
Commit: 59cd9232bf3258f5ce30579dc42433c164313ea0
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2025-11-04 16:34:31 +0100
Commit message:

 Merge branch 'revision_improvements' into revision_dh
Package: GeDi
Commit: eca4943b1e7be30b7c77d3b31152072bdd2e37c9
Author: Annekathrin Silvia Ludt <annekathrin@MacBookPro.fritz.box>
Date: 2025-11-04 16:33:22 +0100
Commit message:

 Resolved merged conflicts in clustering_wordcloud.R

Merge branch 'revision_dh' of https://github.com/AnnekathrinSilvia/GeDi into revision_dh

# Conflicts:
#	R/clustering_wordcloud.R
Package: GeDi
Commit: 69db4f006d54c715dc6b30125f4b13f65e2e29f6
Author: Annekathrin Silvia Ludt <annekathrin@MacBookPro.fritz.box>
Date: 2025-11-04 16:29:48 +0100
Commit message:

 Changed enrichmentWordcloud to now have two additional parameters
Package: GeDi
Commit: e7b3c22aaf2bafd4aa5a0be2a518b133b9c3766e
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2025-11-04 16:09:11 +0100
Commit message:

 updated the news in the upcoming devel version
Package: GeDi
Commit: 2a84e05bc17e18a0c32abc00bdee29cf045dd3cb
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2025-11-04 15:47:43 +0100
Commit message:

 tiny bit of linting with spacing
Package: GeDi
Commit: a0b7e0e3981ebff626684b2950365506480f6e8f
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2025-11-04 15:16:10 +0100
Commit message:

 Merge branch 'revision_dh' of github.com:AnnekathrinSilvia/GeDi into revision_dh
Package: GeDi
Commit: 0908bf0bb01d14994aa3a84b8f0aa4a4cd4cd85f
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2025-11-04 15:15:55 +0100
Commit message:

 a bit of linting on the go similarity
Package: GeDi
Commit: 78c69820c9c99793cf90df7fc75b783a241ce090
Author: Annekathrin Silvia Ludt <annekathrin@MacBookPro.fritz.box>
Date: 2025-11-04 15:10:33 +0100
Commit message:

 Decoupled the option to filter generic terms and individual terms in the wordcloud implementation. Also made the generic terms a global variable.
Package: GeDi
Commit: 830f56eaf5eddca5d6c4e6bcd5f86e0ddede0daa
Author: Annekathrin Silvia Ludt <annekathrin@MacBookPro.fritz.box>
Date: 2025-11-04 14:55:02 +0100
Commit message:

 Now completely removed the old implementation of the goDistance function. Also updated the documentaiton to reflect the new implementation
Package: GeDi
Commit: 91ef80a9fa976c3dddda87cc7915f8b4f10b24d6
Author: Annekathrin Silvia Ludt <annekathrin@AnnekathrinsMBP.fritz.box>
Date: 2025-11-03 17:22:15 +0100
Commit message:

 Implemented a revised goDistance funciton using the simona package
Package: GeDi
Commit: 773405078bca2211c0d5ef2cf13f9b62e032f0a3
Author: Annekathrin Silvia Ludt <annekathrin@AnnekathrinsMBP.fritz.box>
Date: 2025-11-03 17:19:33 +0100
Commit message:

 Fixed the color scale in the revised distance heatmap version to a one hue version.
Package: GeDi
Commit: 963880cba04809f410d43b797facbe9746b4a036
Author: Annekathrin Silvia Ludt <annekathrin@AnnekathrinsMBP.fritz.box>
Date: 2025-11-03 17:19:00 +0100
Commit message:

 Added the option to filter generic terms from the wordcloud.
Package: GeDi
Commit: 0ce8a5d34e6fc745963e706486ee143b90a0eb0b
Author: Annekathrin Silvia Ludt <annekathrin@AnnekathrinsMBP.fritz.box>
Date: 2025-11-03 15:54:41 +0100
Commit message:

 Added a revised implementation of the GO distance scoring using the simona package
Package: GeDi
Commit: 99c06c7b6fb85e039f70efba8fce2d4f84c764b4
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2025-10-31 17:42:28 +0100
Commit message:

 finished round on the meet min matrix calculations
Package: GeDi
Commit: 81d8fb396ae502fd977511b249bcd8731c8ff412
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2025-10-31 17:36:39 +0100
Commit message:

 sorensen dice, reimplemented and with. benchmarks in
Package: GeDi
Commit: 2ed6863ea7d5ce20584569d502f78d602555e9bf
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2025-10-31 17:36:14 +0100
Commit message:

 full go at the kappa distance implementations
Package: GeDi
Commit: 46cc19e32ba3b0df08d1aecce242f16cbbeec1ba
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2025-10-31 17:15:06 +0100
Commit message:

 assignment operator preferred
Package: GeDi
Commit: 1b0ad743b30b977351660e73e285d410145aced1
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2025-10-31 17:14:25 +0100
Commit message:

 adding all different flavors on the jaccard distance functions
Package: GeDi
Commit: e84e21f533eb7a74039a2afbc8627bfb8c763bee
Author: Annekathrin Silvia Ludt <annekathrin@AnnekathrinsMBP.fritz.box>
Date: 2025-10-31 16:42:27 +0100
Commit message:

 Added the possibility to change the distance_heatmap to a similarity heatmap. Also added scaling of colors to be based on 10th and 90th percentile of values
Package: GeDi
Commit: 97571401ee50b28e89eb2434b6815b2f2817f063
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2025-10-30 23:27:37 +0100
Commit message:

 fixing the example
Package: GeDi
Commit: e6db89d55cc0f45856dc9f9502b7ba0249043ac2
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2025-10-13 00:13:03 +0200
Commit message:

 leaving GeneTonic in as suggested dependency, as it is supported with its objects in the main GeDi functionality of the app
Package: GeDi
Commit: 3a48894846dcbc5788899dffbfe8caf471656b36
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2025-10-13 00:10:45 +0200
Commit message:

 added manpages for the now internal functions
Package: GeDi
Commit: 70bb2a428a925419b30eb27407d1c5e4fee36793
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2025-10-13 00:10:33 +0200
Commit message:

 fixing imports and adjusting namespace
Package: GeDi
Commit: 1dbe68075536cc90c6889df965075afe1f164963
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2025-10-13 00:10:11 +0200
Commit message:

 adding documentation for the internal .map_to_color
Package: GeDi
Commit: 9e8898d8d81b1cba9bb495dda31aad1d69155019
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2025-10-13 00:09:51 +0200
Commit message:

 bringing in cluster_markov as .cluster_markov to chop away a pretty heavy dependency on GeneTonic (still worth suggesting..)
Package: GeDi
Commit: ae3b65bf4267c55b7af925b44ab073c48c4919cf
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2025-10-13 00:08:58 +0200
Commit message:

 removing unrequired mention in the vignette
Package: GeDi
Commit: 0bd7887fce56c8101cde79aa4a88425077e405c7
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2025-10-13 00:04:36 +0200
Commit message:

 fixing some tests while at it
Package: GeDi
Commit: 7d49d9431f7e326dd1dbd89e1fa4735989b7c9ca
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2025-10-13 00:04:24 +0200
Commit message:

 map2color to internal .map_to_color
Package: GeDi
Commit: b761b40485fe0b62eb46376d713cdf167d195988
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2025-10-12 23:20:22 +0200
Commit message:

 removing heavy dependency of pcaExplorer, preferring to use the lighter mosdef
Package: GeDi
Commit: 747026feda0f97f93f4eb0b79012bf0027669e41
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2025-10-12 23:19:46 +0200
Commit message:

 updated required roxygen version to the latest
Package: GeDi
Commit: f8c5c5b4e8eb87fd9bd591224d5482aaaa396c2c
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2025-07-16 14:49:31 +0200
Commit message:

 removing obsolete GHAs
Package: GeDi
Commit: b3f543c06d08c4e30c55926c15587babe72834b3
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2025-07-16 14:13:11 +0200
Commit message:

 [packages] replaced by `packages` to avoid the note
Package: GeDi
Commit: 46d9c76cd10d3ca0919f8ebfdcae1e69f698f7fb
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2025-05-02 10:02:06 +0200
Commit message:

 Merge remote-tracking branch 'upstream/devel' into devel
Package: GeDi
Commit: 6b1ff54024d20e3e7c056b8eb609f400abaf0625
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2025-03-07 14:35:33 +0100
Commit message:

 updating GHA to a more recent cache version
Package: gDRimport
Commit: 4fd39bd91785927616f0da105c8881c1d3123e84
Author: Bartek <32614650+bczech@users.noreply.github.com>
Date: 2025-11-26 15:39:58 +0100
Commit message:

 Merge pull request #110 from gdrplatform/CBM-11976

Cbm 11976
Package: gDRimport
Commit: ca9e69a017951ae81ee25ffb823f88bd43ddd902
Author: Bartek Czech <bartosz.w.czech@gmail.com>
Date: 2025-11-25 10:45:59 +0100
Commit message:

 refactor: appease lintr
Package: gDRimport
Commit: 2b0f856565d4caa8bca9149c42ac1bf41ae39619
Author: Bartek Czech <bartosz.w.czech@gmail.com>
Date: 2025-11-24 17:32:01 +0100
Commit message:

 refactor: update namespace
Package: gDRimport
Commit: 56434eb2880389073ff2118001de19bfbe1e511b
Author: Bartek Czech <bartosz.w.czech@gmail.com>
Date: 2025-11-24 14:33:00 +0100
Commit message:

 ci: trigger build
Package: gDRimport
Commit: d45de10527b47e418bf4afce853ac58d1ad69bcf
Author: Bartek Czech <bartosz.w.czech@gmail.com>
Date: 2025-11-24 11:41:51 +0100
Commit message:

 refactor: update package
Package: gDRimport
Commit: d552ffb7f8d46bc2b1a343445ac567eacd46f614
Author: Bartek Czech <bartosz.w.czech@gmail.com>
Date: 2025-11-19 12:38:11 +0100
Commit message:

 test: update unit tests
Package: gDRimport
Commit: 6462c6c19f87d101ffe5aca3d0746fa8b0766e7f
Author: Bartek Czech <bartosz.w.czech@gmail.com>
Date: 2025-11-18 11:18:14 +0100
Commit message:

 refactor: update testthat
Package: gDRimport
Commit: d1e8155c78c3008222948e7dda8b4a7c8b65c3b2
Author: Bartek Czech <bartosz.w.czech@gmail.com>
Date: 2025-11-18 11:00:17 +0100
Commit message:

 refactor: update as per review
Package: gDRimport
Commit: c578e5ae65ae400cdff5c4e2e0fbc5990d394ec2
Author: Bartek Czech <bartosz.w.czech@gmail.com>
Date: 2025-11-17 10:57:40 +0100
Commit message:

 doc: reoxygenate
Package: gDRimport
Commit: d42062549a968bfe4896335aa40b5ae41ad883c6
Author: Bartek Czech <bartosz.w.czech@gmail.com>
Date: 2025-11-17 10:50:19 +0100
Commit message:

 doc: update documentation
Package: gDRimport
Commit: 5de83afad73ae68adccc9033898e9cb41eda9efc
Author: Bartek Czech <bartosz.w.czech@gmail.com>
Date: 2025-11-17 10:49:16 +0100
Commit message:

 doc: bump version
Package: gDRimport
Commit: bae2a6deac447884285ff8a43d77ba5f124abc77
Author: Bartek Czech <bartosz.w.czech@gmail.com>
Date: 2025-11-17 10:48:11 +0100
Commit message:

 doc: bump version
Package: gDRimport
Commit: 11e12bc56c0bba6f7cfd316334bae6b693e393ea
Author: Bartek Czech <bartosz.w.czech@gmail.com>
Date: 2025-11-17 10:47:23 +0100
Commit message:

 refactor: add support for new envision format
Package: StatescopeR
Commit: d4424b307b083f76c71ba2b76cca01b4f6965da8
Author: MSteketee <m.f.b.steketee@amsterdamumc.nl>
Date: 2025-11-26 12:49:08 +0100
Commit message:

 R dependency >= 4.6.0 reflecting new Bioconductor release and minimized
geneset of scRNAseq for quicker vignette/examples
Package: MIRit
Commit: c2813dc9ffc060ae7912753a6ce26a31565dc30b
Author: jacopo-ronchi <jacopo.ronchi@unimib.it>
Date: 2025-11-26 09:54:37 +0000
Commit message:

 build: version bump in devel.
Package: MIRit
Commit: 46d96cbcb76eddbcbd0dfb2432c4ed47d8d2ee87
Author: jacopo-ronchi <jacopo.ronchi@unimib.it>
Date: 2025-11-26 09:54:04 +0000
Commit message:

 docs: the README file has been updated.
Package: SparseArray
Commit: deda046b0537374414a88386fa2977acf1e1f2f8
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2025-11-25 22:55:36 -0800
Commit message:

 small tweak
Package: damidBind
Commit: 4534ab2da115f8a1bfe1e7efd9163290da1d87c6
Author: Owen Marshall <owen.marshall@utas.edu.au>
Date: 2025-11-26 06:28:06 +0000
Commit message:

 Updated to v0.99.6
Package: damidBind
Commit: aaab42553819295a84a95cc6c657aaae28f10852
Author: Owen Marshall <owen.marshall@utas.edu.au>
Date: 2025-11-26 06:26:31 +0000
Commit message:

 Updated man pages
Package: damidBind
Commit: 9f62ee0b8d24a9414a5303fc8b37ada7d38be22a
Author: Owen Marshall <owen.marshall@utas.edu.au>
Date: 2025-11-26 06:25:43 +0000
Commit message:

 Updated tests
Package: damidBind
Commit: 2bc2f2e45507f171f3777b283bbd87f4e2f38826
Author: Owen Marshall <owen.marshall@utas.edu.au>
Date: 2025-11-26 06:25:16 +0000
Commit message:

 Adapted to new `cond` logic handling
Package: damidBind
Commit: e86d2769099c0335c48eddc481ad06c0e9dff922
Author: Owen Marshall <owen.marshall@utas.edu.au>
Date: 2025-11-26 06:24:47 +0000
Commit message:

 Added new `cond` logic and negative occupancy loci filtering.
Package: damidBind
Commit: 8f1a1ab40b3b5622c95d5ea1819130f2f8e27f17
Author: Owen Marshall <owen.marshall@utas.edu.au>
Date: 2025-11-26 06:24:21 +0000
Commit message:

 Added in point sampling routines, adapted to new `cond` logic.
Package: damidBind
Commit: 89efaf8328387d5bad535452c155d5aced808cc2
Author: Owen Marshall <owen.marshall@utas.edu.au>
Date: 2025-11-26 06:23:43 +0000
Commit message:

 Fixed example for new `cond` logic.
Package: damidBind
Commit: 9af0a112acdd2737a72b218a9c1071f9650e25a6
Author: Owen Marshall <owen.marshall@utas.edu.au>
Date: 2025-11-26 06:23:32 +0000
Commit message:

 Fixed example for new `cond` logic.
Package: damidBind
Commit: 3c000369078762eea2106dfc6938d956d35f26ab
Author: Owen Marshall <owen.marshall@utas.edu.au>
Date: 2025-11-26 06:23:16 +0000
Commit message:

 Fixed example for new `cond` logic.
Package: damidBind
Commit: 0992475db751bb9073978506fd8c00ff1707b7f9
Author: Owen Marshall <owen.marshall@utas.edu.au>
Date: 2025-11-26 06:22:37 +0000
Commit message:

 Fixed example for new `cond` logic.
Package: damidBind
Commit: ac7b6de53f8698e7db96752aac0ed555a70432df
Author: Owen Marshall <owen.marshall@utas.edu.au>
Date: 2025-11-26 06:22:16 +0000
Commit message:

 Removed FDR universe filtering (replaced by more appropriate low-signal filtering earlier in the pipeline)
Package: damidBind
Commit: d422f599d4aae580a79404c7f1e934992724a90a
Author: Owen Marshall <owen.marshall@utas.edu.au>
Date: 2025-11-26 06:20:56 +0000
Commit message:

 Install instructions changed to direct Bioconductor path
Package: damidBind
Commit: 24533d70d2679b94952cc3ec64e897f3927d3541
Author: Owen Marshall <owen.marshall@utas.edu.au>
Date: 2025-11-26 06:19:50 +0000
Commit message:

 Updated to v0.99.6
Package: OSTA
Commit: 325d00ecf23cf7d527c793837e1c96539ba6e07b
Author: Lukas Weber <lmweb012@gmail.com>
Date: 2025-11-26 00:09:16 -0500
Commit message:

 version and date
Package: OSTA
Commit: cf9154f07ecbbd349db7b40b1e1d1e52ce0dfb35
Author: Helena L. Crowell <helena@crowell.eu>
Date: 2025-11-25 20:47:19 +0100
Commit message:

 Merge pull request #266 from lmweber/estella

Estella
Package: OSTA
Commit: 5caf1dad01ca1d9ae7682677236c8857df0b090f
Author: HelenaLC <helena@crowell.eu>
Date: 2025-11-25 20:46:29 +0100
Commit message:

 code formatting
Package: OSTA
Commit: eb261b23f4d8882460715166b139bc0c66b4d720
Author: HelenaLC <helena@crowell.eu>
Date: 2025-11-25 20:46:17 +0100
Commit message:

 change link to landing site
Package: OSTA
Commit: e956b9a271e4a0f40d3280885c8d95b46f880787
Author: Estella Yixing Dong <estelladong729@gmail.com>
Date: 2025-11-25 20:07:35 +0100
Commit message:

 Merge branch 'lmweber:sandbox' into sandbox
Package: OSTA
Commit: c86e1cc3f2aa7efdd0b8c80fb1bfc0b14c639b37
Author: Estella Yixing Dong <estelladong729@gmail.com>
Date: 2025-11-25 20:07:17 +0100
Commit message:

 Merge pull request #15 from estellad/vhdcellsegread

Vhdcellsegread
Package: OSTA
Commit: 23aa25bc6f79916a8dff23b23fa8fd476e10cb53
Author: estellad <estelladong729@gmail.com>
Date: 2025-11-25 20:05:43 +0100
Commit message:

 simplify ggspavis
Package: OSTA
Commit: 6f592486789ee36c164e8bf31fb4a945485087b6
Author: Lukas Weber <lmweb012@gmail.com>
Date: 2025-11-25 13:44:15 -0500
Commit message:

 Merge pull request #263 from lmweber/everev

evening revision
Package: OSTA
Commit: fe77d5e389eb75ff3e8527b7756b3ae7c0245ad8
Author: Lukas Weber <lmweb012@gmail.com>
Date: 2025-11-25 13:43:20 -0500
Commit message:

 fix visium-hd-seg
Package: OSTA
Commit: f5ecbea1b0f1f04661653509f3e871aab3776da4
Author: HelenaLC <helena@crowell.eu>
Date: 2025-11-25 19:39:01 +0100
Commit message:

 rmv local env
Package: OSTA
Commit: 92b1dc443b14fd4543a4a373598cfe09039c4ee5
Author: Lukas Weber <lmweb012@gmail.com>
Date: 2025-11-25 13:31:12 -0500
Commit message:

 missing comma
Package: OSTA
Commit: f55094c88ce4955faf841433c992cee36c4813b1
Author: estellad <estelladong729@gmail.com>
Date: 2025-11-25 19:29:24 +0100
Commit message:

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

get updates
Package: OSTA
Commit: 006078e679feabc7d21b94e5b6bb4b854cde3c9c
Author: Lukas Weber <lmweb012@gmail.com>
Date: 2025-11-25 13:20:27 -0500
Commit message:

 add link to citation chapter
Package: OSTA
Commit: ad14379223a0929713345a78765c7752f9019982
Author: HelenaLC <helena@crowell.eu>
Date: 2025-11-25 19:01:26 +0100
Commit message:

 revise acknowledgments
Package: OSTA
Commit: ea8843d9a9aa85b3d6104167a949e5f49e542a58
Author: HelenaLC <helena@crowell.eu>
Date: 2025-11-25 19:01:11 +0100
Commit message:

 add bioRxiv
Package: OSTA
Commit: 1c15cac81628f602c14ec8d7420b955015e16b1a
Author: HelenaLC <helena@crowell.eu>
Date: 2025-11-25 18:12:08 +0100
Commit message:

 suppress ggplot-related messages/warnings
Package: OSTA
Commit: 1f127ac29478767cb8c5bd29f94206d843ee5510
Author: HelenaLC <helena@crowell.eu>
Date: 2025-11-25 18:11:45 +0100
Commit message:

 consistent code style revision
Package: OSTA
Commit: ab8b512c7b660477fd10b4ebe151fb831875562a
Author: HelenaLC <helena@crowell.eu>
Date: 2025-11-25 17:45:28 +0100
Commit message:

 fix VisHD cross-refs
Package: OSTA
Commit: b9076ad28de55f05903cc70b97bea88a380a510b
Author: Helena L. Crowell <helena@crowell.eu>
Date: 2025-11-25 16:04:42 +0100
Commit message:

 Merge pull request #262 from lmweber/downtime

fix typo -.-
Package: OSTA
Commit: efeb43e874c52b61ff58c089227944e19ac23b1f
Author: HelenaLC <helena@crowell.eu>
Date: 2025-11-25 16:04:13 +0100
Commit message:

 fix typo -.-
Package: OSTA
Commit: 3d935fe27f35c1487220d3bb5706a5f23786d8d3
Author: Helena L. Crowell <helena@crowell.eu>
Date: 2025-11-25 13:23:12 +0100
Commit message:

 mol=addTx=FALSE everywhere
Package: OSTA
Commit: 1773d19f9e64b407ef4a389f53f695b95119dd42
Author: HelenaLC <helena@crowell.eu>
Date: 2025-11-25 13:22:16 +0100
Commit message:

 fix #260
Package: OSTA
Commit: b91cc4ff5a3aa47d7f7c8ab52388cb5bad73166b
Author: HelenaLC <helena@crowell.eu>
Date: 2025-11-25 13:22:04 +0100
Commit message:

 mol=addTx=FALSE everywhere
Package: OSTA
Commit: eb918c6d58f40220b56537f06194d7e32f258a7e
Author: Helena L. Crowell <helena@crowell.eu>
Date: 2025-11-25 11:41:38 +0100
Commit message:

 Merge pull request #259 from lmweber/downtime

add tryCatch to SpatialLIBDB part
Package: OSTA
Commit: 0e3a3b8b03e57f2207b850d1bce316c9b13c6b0e
Author: HelenaLC <helena@crowell.eu>
Date: 2025-11-25 11:40:45 +0100
Commit message:

 add tryCatch to SpatialLIBDB part
Package: OSTA
Commit: 6f609577b24826b0c0bf3ca12427dc41a2e09a7a
Author: Helena L. Crowell <helena@crowell.eu>
Date: 2025-11-25 10:42:07 +0100
Commit message:

 Merge pull request #258 from lmweber/downtime

skip tx.parquet retrieval
Package: OSTA
Commit: e922c96460d1c0fb2fe05dee8aecc64d28b5f5b8
Author: HelenaLC <helena@crowell.eu>
Date: 2025-11-25 10:41:30 +0100
Commit message:

 skip tx.parquet retrieval
Package: OSTA
Commit: b6a4722feaf10c6f1134adefc4fbd072d9980fe8
Author: Helena L. Crowell <helena@crowell.eu>
Date: 2025-11-25 07:32:13 +0100
Commit message:

 Merge pull request #256 from lmweber/merge_sandbox

Merge sandbox
Package: OSTA
Commit: 8eac04ce7b4e57080ace553acfd15e37845a6f2d
Author: HelenaLC <helena@crowell.eu>
Date: 2025-11-25 07:31:01 +0100
Commit message:

 Merge branch 'sandbox' into merge_sandbox
Package: OSTA
Commit: 6a27dbb6166378b75769e808f9aa61884c8e5e2b
Author: HelenaLC <helena@crowell.eu>
Date: 2025-11-24 20:24:08 +0100
Commit message:

 rmv superfluous subheader
Package: OSTA
Commit: 04a5a6d8fcd36e0ded59de58ba6e10ba07c79763
Author: Helena L. Crowell <helena@crowell.eu>
Date: 2025-11-24 20:15:36 +0100
Commit message:

 DPLFC revision

revision to vertically unclutter by
- placing selected content in collapsed boxes
- reduce some prints, e.g., using `head()`
- code style adhering to remainder of the book
Package: OSTA
Commit: 14c347d53c36d2f2b3241556108e0129647d4250
Author: HelenaLC <helena@crowell.eu>
Date: 2025-11-24 20:14:01 +0100
Commit message:

 dplfc revision
Package: OSTA
Commit: 053a57174917ea59cf02a90670ce0ffef486a6ea
Author: Helena L. Crowell <helena@crowell.eu>
Date: 2025-11-24 19:24:16 +0100
Commit message:

 seq-quality-control revision

major code revision to...

- adhere with code style of the remainder of the book
- suppress messages/warnings in some figures
- make code/spacing more compact vertically
- fold selected code chunks

...but no content-related alterations.
Package: OSTA
Commit: dd3058d23a9b668e9a84e43e6e37330d2052d369
Author: HelenaLC <helena@crowell.eu>
Date: 2025-11-24 19:21:54 +0100
Commit message:

 seq-qc revision
Package: OSTA
Commit: a58a17b5f4abc7276c29c721c745824b1d29a20c
Author: Helena L. Crowell <helena@crowell.eu>
Date: 2025-11-24 18:23:57 +0100
Commit message:

 Merge pull request #252 from lmweber/coloc

diff-co-localization revision
Package: OSTA
Commit: d6e52b6601723f3daa68cbe14dac41b8aad8eac8
Author: HelenaLC <helena@crowell.eu>
Date: 2025-11-24 18:23:00 +0100
Commit message:

 fix messages/warnings/verbosity
Package: OSTA
Commit: 5b5202b21deb5ff6d28116b5a6847ec06882062a
Author: Helena L. Crowell <helena@crowell.eu>
Date: 2025-11-24 17:35:06 +0100
Commit message:

 crs-imputation revision

- add theory box on single-cell integration
- add theory box on quantifying batch effect/removal
- do exemplary PCR on cluster/batch before/after integration
- add references in imputation chapter & appendix
Package: OSTA
Commit: d2e687899f00abcd7bd3757d21d37d21f473430b
Author: HelenaLC <helena@crowell.eu>
Date: 2025-11-24 17:30:02 +0100
Commit message:

 add box on theory & PCR; add references
Package: OSTA
Commit: 1d5ab86517dfb5f7095e6d46a242e224ca10e47c
Author: HelenaLC <helena@crowell.eu>
Date: 2025-11-24 17:20:30 +0100
Commit message:

 eval decon
Package: OSTA
Commit: 465b7701540a798baa598b638ee01d679756d458
Author: HelenaLC <helena@crowell.eu>
Date: 2025-11-24 17:20:16 +0100
Commit message:

 fix typo
Package: OSTA
Commit: 3d15b98b769522938a9b4afcab61466ab732562e
Author: HelenaLC <helena@crowell.eu>
Date: 2025-11-24 16:01:58 +0100
Commit message:

 eval decon
Package: OSTA
Commit: 5dbcaa994d29bba4ee6faec63a4049d82160312f
Author: Helena L. Crowell <helena@crowell.eu>
Date: 2025-11-24 14:50:09 +0100
Commit message:

 Merge pull request #246 from lmweber/vhd

Workflow: Visium HD (segmented)
Package: OSTA
Commit: b4eeff083a732e1b99ce2c263206acb611dcf1f2
Author: HelenaLC <helena@crowell.eu>
Date: 2025-11-24 14:49:52 +0100
Commit message:

 +Imports: sf
Package: OSTA
Commit: 3844ee9b2fe71752e247591aaf7860e23461d8f7
Author: HelenaLC <helena@crowell.eu>
Date: 2025-11-24 14:46:06 +0100
Commit message:

 alter fig sizing
Package: OSTA
Commit: ef3265239cb9208c827e8606717435b63f211f4a
Author: HelenaLC <helena@crowell.eu>
Date: 2025-11-24 14:29:37 +0100
Commit message:

 update spacexr hyperlink
Package: OSTA
Commit: c6bb782df572a0b19d8e4ad2652577dde7f8104b
Author: HelenaLC <helena@crowell.eu>
Date: 2025-11-24 14:21:46 +0100
Commit message:

 fix typo
Package: OSTA
Commit: e52ab51e187159819c680651fed1eacc9ceb1333
Author: HelenaLC <helena@crowell.eu>
Date: 2025-11-24 14:20:29 +0100
Commit message:

 fix msigdbr-related warning
Package: OSTA
Commit: 36aab61d23a39cffbab2cbd9447339e96ff5988e
Author: HelenaLC <helena@crowell.eu>
Date: 2025-11-24 14:19:18 +0100
Commit message:

 fix msigdbr-related warning
Package: OSTA
Commit: bd8662875bbd926e81e5ae4da5085ca9dec9e777
Author: HelenaLC <helena@crowell.eu>
Date: 2025-11-24 14:14:28 +0100
Commit message:

 rmv unneeded dep; add RCDT ref
Package: OSTA
Commit: 7e8537e2b12755b7857258864984ba5b1ed98b5c
Author: HelenaLC <helena@crowell.eu>
Date: 2025-11-24 14:04:39 +0100
Commit message:

 revise wording; remove caching
Package: OSTA
Commit: 4bfa0a8b0ec5c44c6af68841e382e942fb94538c
Author: HelenaLC <helena@crowell.eu>
Date: 2025-11-24 13:57:11 +0100
Commit message:

 Merge branch 'sandbox' into vhd
Package: OSTA
Commit: 2c71cb23a68d26869801f5914e347bc64ab72d35
Author: Lukas Weber <lmweb012@gmail.com>
Date: 2025-11-23 22:16:16 -0500
Commit message:

 Merge pull request #245 from lmweber/refs

`apx-citation` draft
Package: OSTA
Commit: 4c447b1b380bf68360332c1a9e4212ff15eccdff
Author: estellad <estelladong729@gmail.com>
Date: 2025-11-23 16:34:43 +0100
Commit message:

 fix conflict
Package: OSTA
Commit: e7bde723ed65bddf08a851725db26af2f370f6b6
Author: estellad <estelladong729@gmail.com>
Date: 2025-11-23 16:31:41 +0100
Commit message:

 add bin/cell overlay nuc cell polygons
Package: OSTA
Commit: 64f19bd99d30d75d55d36bdef2f96f4553837aa1
Author: HelenaLC <helena@crowell.eu>
Date: 2025-11-23 16:00:20 +0100
Commit message:

 eval spicyR part with reduced runtime
Package: OSTA
Commit: 4bdbddf6a5b69927d0840ab40c57bdf2b510797a
Author: Estella Yixing Dong <estelladong729@gmail.com>
Date: 2025-11-23 15:39:49 +0100
Commit message:

 Merge branch 'lmweber:sandbox' into sandbox
Package: OSTA
Commit: 88500e2b44454e12437ab4453b4dcbee2bd1e539
Author: HelenaLC <helena@crowell.eu>
Date: 2025-11-23 15:03:43 +0100
Commit message:

 fix runtime recording
Package: OSTA
Commit: ffb3215e70437c02b81fe7faf573e99b29106ca5
Author: HelenaLC <helena@crowell.eu>
Date: 2025-11-23 14:12:39 +0100
Commit message:

 Merge branch 'sandbox' into vhd
Package: OSTA
Commit: d680d85f0214f622b3ff05f6a7cd78e0208311e3
Author: HelenaLC <helena@crowell.eu>
Date: 2025-11-23 14:11:25 +0100
Commit message:

 change symbols
Package: OSTA
Commit: 49bea8c786b86143fdff57cea1c2b206cdc3d248
Author: HelenaLC <helena@crowell.eu>
Date: 2025-11-23 14:10:02 +0100
Commit message:

 change symbols
Package: OSTA
Commit: 96f7bfd270847864ca5bae38b88083715f5a9a1a
Author: HelenaLC <helena@crowell.eu>
Date: 2025-11-23 14:09:43 +0100
Commit message:

 change symbols
Package: OSTA
Commit: 92bbbbae1c9cf4fe93de0ee755e6b7ef1ef627e3
Author: HelenaLC <helena@crowell.eu>
Date: 2025-11-23 11:59:01 +0100
Commit message:

 retrigger
Package: OSTA
Commit: 8964e58786cedd7ad6d09a64bfad5568a40af26d
Author: HelenaLC <helena@crowell.eu>
Date: 2025-11-23 11:53:03 +0100
Commit message:

 revise code invalidation note
Package: OSTA
Commit: 1ca53e0c4eb3f022666dd53e5c5758fdd6db3238
Author: HelenaLC <helena@crowell.eu>
Date: 2025-11-23 11:36:42 +0100
Commit message:

 couple more words on QC
Package: OSTA
Commit: 55b6e6b32611ff33f4908d6bc0f79d9c012afe5b
Author: HelenaLC <helena@crowell.eu>
Date: 2025-11-23 11:31:09 +0100
Commit message:

 merge sandbox
Package: OSTA
Commit: 1c30b9b7f178c7c6a69becebf2eea2ecf598b414
Author: HelenaLC <helena@crowell.eu>
Date: 2025-11-23 11:14:45 +0100
Commit message:

 w/o superscripting
Package: OSTA
Commit: 1ef1013dcb27ca556fcbacc278b105a9bb6ca799
Author: HelenaLC <helena@crowell.eu>
Date: 2025-11-23 11:12:01 +0100
Commit message:

 fix now?
Package: OSTA
Commit: badb1a17fdbb93c941302a15ecde5f92c065d05b
Author: HelenaLC <helena@crowell.eu>
Date: 2025-11-23 11:10:22 +0100
Commit message:

 fix symbols
Package: OSTA
Commit: 00674c2a5886ca47662bf1c952dcdafb1cff3222
Author: HelenaLC <helena@crowell.eu>
Date: 2025-11-23 11:07:00 +0100
Commit message:

 simplified readme including citation
Package: OSTA
Commit: 1f8f549855a5ea9a7980faeb8c373ad407c2b6af
Author: HelenaLC <helena@crowell.eu>
Date: 2025-11-23 10:41:33 +0100
Commit message:

 trigger deploy from sandbox
Package: OSTA
Commit: 34e25c218c9a6b59c6ab5cdaae9771a614586607
Author: HelenaLC <helena@crowell.eu>
Date: 2025-11-23 10:15:41 +0100
Commit message:

 add decon refs
Package: OSTA
Commit: cd31bf967bd7726d8b88230ef737b85172a8ce9d
Author: HelenaLC <helena@crowell.eu>
Date: 2025-11-23 09:34:00 +0100
Commit message:

 Merge branch 'sandbox' into refs
Package: OSTA
Commit: 1c5dfd92c450689abadd6041752c06f64750a3d9
Author: Helena L. Crowell <helena@crowell.eu>
Date: 2025-11-23 09:22:04 +0100
Commit message:

 Merge pull request #249 from lmweber/bfc

- bkg-datasets: add note on cache invalidation
- fix 'incomplete final lines' warnings
Package: OSTA
Commit: f64749d9f8cc04c289aa176b47ca23de4dbead84
Author: HelenaLC <helena@crowell.eu>
Date: 2025-11-23 09:21:16 +0100
Commit message:

 fix 'incomplete final line' warnings
Package: OSTA
Commit: b5884fc310560d02a87c097bfd36b3d403657679
Author: HelenaLC <helena@crowell.eu>
Date: 2025-11-23 09:14:54 +0100
Commit message:

 Merge branch 'sandbox' into bfc
Package: OSTA
Commit: 90cb4a1469a7c1db5f66a0c54c9af527029e5284
Author: HelenaLC <helena@crowell.eu>
Date: 2025-11-23 09:14:34 +0100
Commit message:

 add note on cache invalidation
Package: OSTA
Commit: af5a1955c27266e0014e99972e43dd3f49f0d4ac
Author: Helena L. Crowell <helena@crowell.eu>
Date: 2025-11-22 22:55:33 +0100
Commit message:

 Merge pull request #248 from Artur-man/giotto_ref
Package: OSTA
Commit: c142e186269cf7d261bb460ba3b39069cc2ce6b2
Author: Artur-man <artur-man@hotmail.com>
Date: 2025-11-22 22:46:35 +0100
Commit message:

 fix giotto ref
Package: OSTA
Commit: 63b7e56a3b4b071f023761bf1905133cbbbfd62a
Author: Artür Manukyan <artur-man@hotmail.com>
Date: 2025-11-22 22:44:47 +0100
Commit message:

 Merge pull request #2 from lmweber/sandbox

Sandbox
Package: OSTA
Commit: 195b4433f571732f95775f7b1a6b2163ffc7a802
Author: HelenaLC <helena@crowell.eu>
Date: 2025-11-22 12:44:06 +0100
Commit message:

 revise wording
Package: OSTA
Commit: 035b5233e10ba4f8faf911f7e53beeb4db41a296
Author: HelenaLC <helena@crowell.eu>
Date: 2025-11-22 12:41:10 +0100
Commit message:

 add part on bin/cell mixing
Package: OSTA
Commit: 0ba578f640eaf349b80ceb286309cacb6d9814bc
Author: HelenaLC <helena@crowell.eu>
Date: 2025-11-22 12:28:25 +0100
Commit message:

 +vhd-seg draft
Package: OSTA
Commit: a988e2ab4ced16b26414cc94152c66e64e3f1e79
Author: HelenaLC <helena@crowell.eu>
Date: 2025-11-22 08:48:35 +0100
Commit message:

 Merge branch 'refs' into vhd
Package: OSTA
Commit: 87d8888d2fcfb404e27cba757908893d4012dc30
Author: HelenaLC <helena@crowell.eu>
Date: 2025-11-22 08:48:32 +0100
Commit message:

 split vhd bin/seg
Package: OSTA
Commit: 0b38948b33228d448ac5120184ac20ab1b1e7542
Author: estellad <estelladong729@gmail.com>
Date: 2025-11-20 21:21:12 +0100
Commit message:

 attempt vhdcell read; to collapse chunks
Package: OSTA
Commit: 2c2ad523287e6b4f4f5337a143626a3b5d29f5ce
Author: Estella Yixing Dong <estelladong729@gmail.com>
Date: 2025-11-20 21:19:54 +0100
Commit message:

 Merge branch 'lmweber:sandbox' into sandbox
Package: OSTA
Commit: 51c9f8b5ed795d584a1cc5820fcdaf037991d161
Author: HelenaLC <helena@crowell.eu>
Date: 2025-11-19 20:34:32 +0100
Commit message:

 update refs
Package: OSTA
Commit: 4c5b37180a9bdc6b87416d6f36bf2ce6b95469d0
Author: HelenaLC <helena@crowell.eu>
Date: 2025-11-08 09:06:28 +0100
Commit message:

 added infrastructure refs
Package: OSTA
Commit: 0a7f8b34af2008228f33934d9fd2151ae7525d2a
Author: HelenaLC <helena@crowell.eu>
Date: 2025-11-08 08:50:07 +0100
Commit message:

 +spatialGE
Package: OSTA
Commit: f1a58153d89c1a2cbc804d14c7ac0a247cea20d5
Author: HelenaLC <helena@crowell.eu>
Date: 2025-11-08 08:37:58 +0100
Commit message:

 add missing final lines
Package: OSTA
Commit: faef85949ad023f46ab4cb7842c016d834dbed18
Author: HelenaLC <helena@crowell.eu>
Date: 2025-11-07 15:54:36 +0100
Commit message:

 fix typo
Package: OSTA
Commit: f040b153266617998ec748394c5cd3daa976bbaa
Author: HelenaLC <helena@crowell.eu>
Date: 2025-11-07 15:53:54 +0100
Commit message:

 fill missing entry
Package: OSTA
Commit: d54747f6dfb333b902a656657b83ca895f1024ab
Author: HelenaLC <helena@crowell.eu>
Date: 2025-11-07 15:52:34 +0100
Commit message:

 avoid dup header
Package: OSTA
Commit: 263a749bee412069b8ad5376fca33e8c7725ad4f
Author: HelenaLC <helena@crowell.eu>
Date: 2025-11-07 15:45:30 +0100
Commit message:

 add citation draft
Package: OSTA
Commit: bc62056d3c78168420d39c677894d64552f1dfdc
Author: Estella Yixing Dong <estelladong729@gmail.com>
Date: 2025-10-08 14:23:56 +0200
Commit message:

 Merge branch 'lmweber:sandbox' into sandbox
Package: OSTA
Commit: cd249bf4c9ec81c9a9f6f95cae7ebe5a8690139c
Author: Estella Yixing Dong <estelladong729@gmail.com>
Date: 2025-10-08 14:23:15 +0200
Commit message:

 Merge pull request #13 from estellad/vhdcell

remove tidyverse from DES
Package: OSTA
Commit: eaf6abb40009cce871371a8aba891bd4847e4a4e
Author: estellad <estelladong729@gmail.com>
Date: 2025-10-08 14:22:29 +0200
Commit message:

 remove tidyverse from DES
Package: OSTA
Commit: 268ef2ae5b45a77133e490d9cc55054065523d30
Author: estellad <estelladong729@gmail.com>
Date: 2025-10-08 08:54:17 +0200
Commit message:

 testing Marcel reader
Package: txdbmaker
Commit: 7ccea65e4737a6c93dcebd1d9d5361fb04c11e87
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2025-11-25 17:29:40 -0800
Commit message:

 Minor edits and version bump (to 1.7.2)
Package: txdbmaker
Commit: 570b63034fe267159fa635fe91138c09c4dee2ca
Author: I-Hsuan Lin <9032946+ycl6@users.noreply.github.com>
Date: 2025-11-26 00:56:23 +0000
Commit message:

 Add Taxonomy ID to TxDb object returned by makeTxDbFromEnsembl() (#13)

Like for other makeTxDbFrom* functions, the new 'taxonomyId' argument of makeTxDbFromEnsembl() is set to NA by default. So if the user doesn't supply a Taxonomy ID via the argument, GenomeInfoDb:::lookup_tax_id_by_organism() is used to retrieve the taxonomy ID for the supplied 'organism'. Otherwise GenomeInfoDb:::check_tax_id() is used to check the user-supplied taxonomic ID.
Package: GenomeInfoDb
Commit: 2af6568290811ea712bbd31f0a7e683a4fad5e27
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2025-11-25 15:03:04 -0800
Commit message:

 GenomeInfoDb 1.47.1: Register several assemblies for naked mole-rat

Register the following NCBI genome assemblies for Heterocephalus
glaber (naked mole-rat):

- HetGla_1.0:
    https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_000230445.1/

- HetGla_female_1.0:
    https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_000247695.1/

- Naked mole-rat maternal:
    https://www.ncbi.nlm.nih.gov/datasets/genome/GCA_944319715.1/

- Naked mole-rat paternal:
    https://www.ncbi.nlm.nih.gov/datasets/genome/GCA_944319725.1/

as well as the following UCSC genomes assemblies:

- hetGla1 (based on HetGla_1.0):
    https://genome.ucsc.edu/cgi-bin/hgGateway?db=hetGla1

- hetGla2 (based on HetGla_female_1.0):
    https://genome.ucsc.edu/cgi-bin/hgGateway?db=hetGla2
Package: BSgenomeForge
Commit: 01d527db51912e9915292b5affd2c2030af32ea3
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2025-11-25 14:46:05 -0800
Commit message:

 BSgenomeForge 1.11.1: Fix issue in internal helper drop_rows_with_NA_accns()
Package: BatchSVG
Commit: 0b8ee3f90e29c275cceb2edcc9d5bb4650eaa341
Author: Kinnary Shah <kinnaryshahh@gmail.com>
Date: 2025-11-25 17:45:45 -0500
Commit message:

 update vignette
Package: STADyUM
Commit: 64f0021eefb1d703bf2cb17c891814e709d1accc
Author: Rebecca Hassett <hassett@cshl.edu>
Date: 2025-11-25 17:08:17 -0500
Commit message:

 update package version
Package: STADyUM
Commit: e4aa124dabc9b180b3b105a6f6dae915bdb15bee
Author: Rebecca Hassett <hassett@cshl.edu>
Date: 2025-11-25 17:07:00 -0500
Commit message:

 Merge remote-tracking branch 'upstream/devel'
Package: STADyUM
Commit: b2ef2f3b27ccf192c383f7b9fa3d7be8672eb45c
Author: Rebecca Hassett <hassett@cshl.edu>
Date: 2025-11-25 17:06:05 -0500
Commit message:

 Remove plyranges dependencies
Package: SparseArray
Commit: 44735905a04d8e68e7a472dfeb552aafc960fba9
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2025-11-25 11:31:20 -0800
Commit message:

 SparseArray 1.11.6: Multithreaded extract_array()

The extract_array() methods for SVT_SparseArray and NaArray objects
are now multithreaded when the number of rows to extract is "small".
Package: variancePartition
Commit: 441f6d46bf8205abe4056ce9d4b602669e452c59
Author: Gabriel Hoffman <gabriel.hoffman@gmail.com>
Date: 2025-11-25 12:45:45 -0500
Commit message:

 1.41.1
Package: variancePartition
Commit: 298b0281b44c2e5fc06b54505b20965e5a8487ee
Author: Gabriel Hoffman <gabriel.hoffman@gmail.com>
Date: 2025-11-25 12:32:30 -0500
Commit message:

 1.41.1
Package: variancePartition
Commit: 6bf63b0ef21beac1a0b8a75f24e011bd9b5340f1
Author: Gabriel Hoffman <gabriel.hoffman@gmail.com>
Date: 2025-11-25 12:32:30 -0500
Commit message:

 stash
Package: drugfindR
Commit: 97a400a6e4a0d96f9d67caa4beead801f8823ded
Author: Ali Sajid Imami <395482+AliSajid@users.noreply.github.com>
Date: 2025-11-25 08:27:26 -0500
Commit message:

 style: fix object_usage_linter issues
Package: drugfindR
Commit: b59ba2266180690b3bab73c88752535a480be08a
Author: Ali Sajid Imami <395482+AliSajid@users.noreply.github.com>
Date: 2025-11-25 00:42:01 -0500
Commit message:

 style: fixed minor style issues
Package: drugfindR
Commit: f2e69a9913a2ce3b1a6dc82b807699e9e9abcb3f
Author: Ali Sajid Imami <395482+AliSajid@users.noreply.github.com>
Date: 2025-11-25 00:18:02 -0500
Commit message:

 style: use more streamlined options for tests
Package: drugfindR
Commit: 8773948bd867e6ce48d841b550c107a278e6ab1a
Author: Ali Sajid Imami <395482+AliSajid@users.noreply.github.com>
Date: 2025-11-25 00:04:22 -0500
Commit message:

 style: convert all pipes to |>
Package: drugfindR
Commit: a96f2d175101c2c262d259a7be488d7aa13e7e4d
Author: Ali Sajid Imami <395482+AliSajid@users.noreply.github.com>
Date: 2025-11-24 23:54:14 -0500
Commit message:

 style: fix style issues with the project
Package: drugfindR
Commit: 724785519cdc24cd5996ea26d92d68e1cf8428aa
Author: Ali Sajid Imami <395482+AliSajid@users.noreply.github.com>
Date: 2025-11-24 21:24:53 -0500
Commit message:

 test: remove the unnecessary failing test
Package: drugfindR
Commit: c34acec9511a021f966bad0edbff7aee46bfb551
Author: Ali Sajid Imami <395482+AliSajid@users.noreply.github.com>
Date: 2025-11-24 20:13:23 -0500
Commit message:

 tests: update the tests for universal test coverage
Package: drugfindR
Commit: d2885b45f77f44dce440b49019585e6171656585
Author: Ali Sajid Imami <395482+AliSajid@users.noreply.github.com>
Date: 2025-11-13 12:43:12 -0500
Commit message:

 test: remove the httptest2 style test files
Package: drugfindR
Commit: 4302f809630a7844186a2508fae575257d36ef9b
Author: Ali Sajid Imami <395482+AliSajid@users.noreply.github.com>
Date: 2025-11-13 12:39:59 -0500
Commit message:

 docs: remove non-ascii symbols from docs
Package: drugfindR
Commit: 45f05b1c0bf2543991e36b24f4d42e71ebd4e153
Author: Ali Sajid Imami <395482+AliSajid@users.noreply.github.com>
Date: 2025-11-13 12:10:13 -0500
Commit message:

 feat: remove the is_L1000 column
Package: drugfindR
Commit: a64063f08fbf795e5db1cb6d80a121fce0eabf83
Author: Ali Sajid Imami <395482+AliSajid@users.noreply.github.com>
Date: 2025-11-13 12:08:20 -0500
Commit message:

 feat: rename calculateSingleThreshold with a leading dot
Package: drugfindR
Commit: 94a8a3a6c9a111b1c4a8ee4adcc7f6ef5bf48f82
Author: Ali Sajid Imami <395482+AliSajid@users.noreply.github.com>
Date: 2025-11-13 12:01:57 -0500
Commit message:

 fix: don't import dplyr::desc to avoid collision warning
Package: drugfindR
Commit: d46b3797212a8ca190ec3794a9d10dc3cbab15bd
Author: Ali Sajid Imami <395482+AliSajid@users.noreply.github.com>
Date: 2025-11-12 16:08:40 -0500
Commit message:

 test: fix the failing tests by aligning expectations
Package: drugfindR
Commit: a9770b04396a0230bb3af2f322e66127255a53b4
Author: Ali Sajid Imami <395482+AliSajid@users.noreply.github.com>
Date: 2025-11-12 15:02:01 -0500
Commit message:

 feat: align consensusConcordants and its tests with the rest of the package
Package: drugfindR
Commit: f8f7c289b00f6d084ea8a0c8d77935c20bcc1213
Author: Ali Sajid Imami <395482+AliSajid@users.noreply.github.com>
Date: 2025-11-12 11:26:49 -0500
Commit message:

 style: fix formatting
Package: drugfindR
Commit: afab4da0ba795977e79ebf0bbf9b14f3664a9f3c
Author: Ali Sajid Imami <395482+AliSajid@users.noreply.github.com>
Date: 2025-11-12 11:25:42 -0500
Commit message:

 feat: update the system data for l1000
Package: drugfindR
Commit: a02830ee772a1d0a424cb1e5eb0d2427587c4502
Author: Ali Sajid Imami <395482+AliSajid@users.noreply.github.com>
Date: 2025-11-11 23:01:39 -0500
Commit message:

 fix: streamlined getConcordants for working
Package: drugfindR
Commit: fdce1350fddb6119cb88ea2024b85c05d7273b81
Author: Ali Sajid Imami <395482+AliSajid@users.noreply.github.com>
Date: 2025-11-11 18:09:38 -0500
Commit message:

 fix: add different cases to generate dummy data
Package: drugfindR
Commit: c28524a84ebd1bd8e99ff3c82d9916bbaad3f4c3
Author: Ali Sajid Imami <395482+AliSajid@users.noreply.github.com>
Date: 2025-11-11 13:51:42 -0500
Commit message:

 fix: update the function call for preparesignature
Package: drugfindR
Commit: a39275e07fb5f279404dca99a8e045fc2bc57401
Author: Ali Sajid Imami <395482+AliSajid@users.noreply.github.com>
Date: 2025-11-11 12:31:27 -0500
Commit message:

 test: simplify the test helpers
Package: drugfindR
Commit: 57edd6151114b5df49527f934b7f743c3ff0ffad
Author: Ali Sajid Imami <395482+AliSajid@users.noreply.github.com>
Date: 2025-11-10 21:57:20 -0500
Commit message:

 feat: update internal logic and add consensusConcordants tests
Package: drugfindR
Commit: 4ea80d360579425ea909d1f0d6c13fb417200673
Author: Ali Sajid Imami <395482+AliSajid@users.noreply.github.com>
Date: 2025-10-03 14:17:02 -0400
Commit message:

 docs: add missing docs for helper functions

Signed-off-by: Ali Sajid Imami <395482+AliSajid@users.noreply.github.com>
Package: drugfindR
Commit: 76a2cbc3b22a13e60c24c84bfd2de0b6247f12ce
Author: Ali Sajid Imami <395482+AliSajid@users.noreply.github.com>
Date: 2025-10-03 13:07:14 -0400
Commit message:

 feat: add updated prepareSignature.R function
Package: drugfindR
Commit: 6b7e98fef13bdaa1162d067401f3dda5b794d49c
Author: Ali Sajid Imami <395482+AliSajid@users.noreply.github.com>
Date: 2025-08-29 12:40:44 -0400
Commit message:

 tests: add httptest2 tests for getConcordants
Package: drugfindR
Commit: ca4a8ce7d35c15b4982660a7b8eaf6c27b55a98d
Author: Ali Sajid Imami <395482+AliSajid@users.noreply.github.com>
Date: 2025-08-27 20:29:27 -0400
Commit message:

 tests: add mocked httptest2-backed tests for getSignature

Signed-off-by: Ali Sajid Imami <395482+AliSajid@users.noreply.github.com>
Package: drugfindR
Commit: baa5c63121c0ac3ecc9ba5708804040d7f700fea
Author: Ali Sajid Imami <395482+AliSajid@users.noreply.github.com>
Date: 2025-08-27 20:26:41 -0400
Commit message:

 tests: add httptest2 for better mocking
Package: drugfindR
Commit: cd09af99746b3df627d66473fb5b25aa5e23b263
Author: Ali Sajid Imami <395482+AliSajid@users.noreply.github.com>
Date: 2025-08-25 21:23:17 -0400
Commit message:

 docs: update the documentation for new helper functions

Signed-off-by: Ali Sajid Imami <395482+AliSajid@users.noreply.github.com>
Package: drugfindR
Commit: e6cf30a8ce13f5868cfd0ed8a6f7a50d73671260
Author: Ali Sajid Imami <395482+AliSajid@users.noreply.github.com>
Date: 2025-08-02 11:51:32 -0400
Commit message:

 feat: improve and modularize getConcordants
Package: drugfindR
Commit: 3be377d3dbd7391e6dd8ba5b89d238a103d4c150
Author: Ali Sajid Imami <395482+AliSajid@users.noreply.github.com>
Date: 2025-07-27 02:15:19 -0400
Commit message:

 feat: improve and modularize filterSignature
Package: drugfindR
Commit: de0fccb2c02f62d2a5c41bc3cc1734ddf81b94d4
Author: Ali Sajid Imami <395482+AliSajid@users.noreply.github.com>
Date: 2025-07-25 15:16:19 -0400
Commit message:

 build: update renv dependencies
Package: drugfindR
Commit: 1f889265764f84b752a8e95d36aa82bec6b74037
Author: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com>
Date: 2025-11-21 01:31:09 +0000
Commit message:

 chore(deps): update actions/checkout action to v6
Package: drugfindR
Commit: 4e554759604882bedc7a13a1ebc7c1d509782b83
Author: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com>
Date: 2025-11-19 02:47:26 +0000
Commit message:

 chore(deps): update actions/checkout action to v5.0.1
Package: drugfindR
Commit: cd6ec2913ccbd4424c0b8ff60750a5a9050ebc8d
Author: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com>
Date: 2025-11-19 02:46:46 +0000
Commit message:

 chore(deps): update actions/checkout digest to 93cb6ef
Package: drugfindR
Commit: 5fa51565cb91396d3e45ec7df80040a26607e345
Author: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com>
Date: 2025-10-27 02:37:02 +0000
Commit message:

 chore(deps): update actions/upload-artifact action to v5
Package: drugfindR
Commit: b9385eb4edc15c6e253061801bc726ba5d34ef23
Author: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com>
Date: 2025-10-13 00:47:12 +0000
Commit message:

 chore(deps): update pre-commit hook compilerla/conventional-pre-commit to v4.3.0
Package: drugfindR
Commit: 661facf1b87c412383cbbf1f1707691f27907332
Author: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com>
Date: 2025-10-09 01:38:30 +0000
Commit message:

 chore(deps): update r-lib/actions action to v2.11.4
Package: drugfindR
Commit: 0450e295bd0c9b7da312b16417638741fad8ce81
Author: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com>
Date: 2025-10-09 01:37:28 +0000
Commit message:

 chore(deps): update r-lib/actions digest to 6f6e5bc
Package: drugfindR
Commit: 65a396c50e0ecd12b5f878b59961d764c807f1b2
Author: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com>
Date: 2025-08-14 01:11:38 +0000
Commit message:

 chore(deps): update actions/checkout action to v5
Package: drugfindR
Commit: ef6a1e417a8874daa3f2c5cafe1d125564b55327
Author: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com>
Date: 2025-08-13 02:04:33 +0000
Commit message:

 chore(deps): update actions/checkout action to v4.3.0
Package: drugfindR
Commit: 13ce7845efb33154636e50fcb7dea1fde2b2983d
Author: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com>
Date: 2025-08-13 02:03:56 +0000
Commit message:

 chore(deps): update actions/checkout digest to 08eba0b
Package: drugfindR
Commit: d61010fd2d5d5e2e420975eb3ea42548a51b7813
Author: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com>
Date: 2025-08-11 00:48:56 +0000
Commit message:

 chore(deps): update pre-commit hook pre-commit/pre-commit-hooks to v6
Package: drugfindR
Commit: 8a735390971970886abcb584e39972ca24ed9eb1
Author: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com>
Date: 2025-07-21 22:47:35 +0000
Commit message:

 chore(config): migrate config renovate.json
Package: drugfindR
Commit: bf93cbec7f10048aa8f0a0b8ce140e665988a49b
Author: Ali Sajid Imami <395482+AliSajid@users.noreply.github.com>
Date: 2025-05-28 11:31:07 -0400
Commit message:

 build: refresh for a new build

Signed-off-by: Ali Sajid Imami <395482+AliSajid@users.noreply.github.com>
Package: drugfindR
Commit: e5d4fa8aea2fd169b35606e41901681b8c941e75
Author: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com>
Date: 2025-05-06 01:45:51 +0000
Commit message:

 chore(deps): update pre-commit hook compilerla/conventional-pre-commit to v4.2.0
Package: drugfindR
Commit: a1dfbeb03b0c30d4f8c14624c6595e0db260c7c3
Author: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com>
Date: 2025-04-30 03:25:48 +0000
Commit message:

 chore(deps): update pre-commit hook compilerla/conventional-pre-commit to v4.1.0
Package: drugfindR
Commit: e8952a5a881d0adef3a6879765921963b6138236
Author: Ali Sajid Imami <395482+AliSajid@users.noreply.github.com>
Date: 2025-04-15 20:51:46 -0400
Commit message:

 docs: update the path to the pdf file for the joss paper
Package: drugfindR
Commit: 5567aa1a83cce42d7741a35d999207d5d4580166
Author: Ali Sajid Imami <395482+AliSajid@users.noreply.github.com>
Date: 2025-04-15 20:44:02 -0400
Commit message:

 ci: correct the concurrency of the release function
Package: drugfindR
Commit: 496ecfa291746d5f22dc66814ba62847ef052097
Author: Ali Sajid Imami <395482+AliSajid@users.noreply.github.com>
Date: 2025-04-15 20:42:20 -0400
Commit message:

 ci: remove the graphite check-ci action
Package: drugfindR
Commit: 9e495fbf0fbee2fad050ccfa1625051efa652a56
Author: Ali Sajid Imami <395482+AliSajid@users.noreply.github.com>
Date: 2025-04-15 20:40:51 -0400
Commit message:

 build: cleanup and comment the utility scripts
Package: drugfindR
Commit: 1d28fb8689c154c1b565d53fa478a32a871f3758
Author: Ali Sajid Imami <395482+AliSajid@users.noreply.github.com>
Date: 2025-04-15 20:39:05 -0400
Commit message:

 build: update the pre-commit config
Package: drugfindR
Commit: 1263fc517b8e27596ae18b07d71b57fd4b285d15
Author: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com>
Date: 2025-04-16 00:45:11 +0000
Commit message:

 chore(deps): pin dependencies
Package: drugfindR
Commit: 83bb7dca245b6373a08ed55fa1d234780cdfc7bf
Author: Ali Sajid Imami <395482+AliSajid@users.noreply.github.com>
Date: 2025-04-15 19:07:20 -0400
Commit message:

 fix: fix syntax error in DESCRIPTION file
Package: drugfindR
Commit: 1f2eeddd5d240e8389690e944dbb024d1bb70dc4
Author: Ali Sajid Imami <395482+AliSajid@users.noreply.github.com>
Date: 2025-04-15 16:01:24 -0400
Commit message:

 build: update renv dependencies x2
Package: drugfindR
Commit: bcc84ca173c65b69a3c8d9c766a7cc6d7a234f4d
Author: Ali Sajid Imami <395482+AliSajid@users.noreply.github.com>
Date: 2025-04-15 15:47:30 -0400
Commit message:

 build: update renv dependencies
Package: drugfindR
Commit: 2ba0424a8d06a7cd6d69212e8ea3ccd16f39abe4
Author: Ali Sajid Imami <395482+AliSajid@users.noreply.github.com>
Date: 2025-04-15 15:46:48 -0400
Commit message:

 feat: add one more author
Package: drugfindR
Commit: 041896e84d38154a9f99dd6bb1a79b17a6219e40
Author: Ali Sajid Imami <395482+AliSajid@users.noreply.github.com>
Date: 2025-04-15 15:26:30 -0400
Commit message:

 feat: add the structure of the joss paper
Package: drugfindR
Commit: 13949cc2c0b542770d210dc7fafa88e7fc46719e
Author: Ali Sajid Imami <395482+AliSajid@users.noreply.github.com>
Date: 2025-04-15 15:22:15 -0400
Commit message:

 build: add pdf files t the gitignore
Package: drugfindR
Commit: f56508fb35a68dffc7fa1ca642412d7926eb37c9
Author: Ali Sajid Imami <395482+AliSajid@users.noreply.github.com>
Date: 2025-04-15 10:42:05 -0400
Commit message:

 build: update the gitignore file and renv
Package: drugfindR
Commit: 7c98cb09d8d9c18f3f2f2981ea193eb4ad96bd48
Author: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com>
Date: 2025-03-25 03:08:01 +0000
Commit message:

 chore(deps): update r-lib/actions action to v2.11.3
Package: drugfindR
Commit: 94e6a8d0e57b0fe75676320a49c3a9f7eecb4a88
Author: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com>
Date: 2025-03-25 03:07:22 +0000
Commit message:

 chore(deps): update r-lib/actions digest to bd49c52
Package: drugfindR
Commit: 4b32129c0a4b1d5b56d93af928b4c52eea072c89
Author: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com>
Date: 2025-03-20 02:03:00 +0000
Commit message:

 chore(deps): update actions/upload-artifact digest to ea165f8
Package: drugfindR
Commit: 51d1c6b65057cfd6699ab65ff1d5f519f6363be5
Author: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com>
Date: 2025-02-24 02:59:05 +0000
Commit message:

 chore(deps): update actions/upload-artifact digest to 4cec3d8
Package: drugfindR
Commit: 8166bac3b23799dbc2e40e16582304978e1d9f87
Author: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com>
Date: 2025-02-20 03:11:27 +0000
Commit message:

 chore(deps): update r-lib/actions action to v2.11.2
Package: drugfindR
Commit: 7e449613823ea8e23bdefc5d5201c2c4a1219151
Author: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com>
Date: 2025-02-20 03:10:29 +0000
Commit message:

 chore(deps): update r-lib/actions digest to 14a7e74
Package: CytoMDS
Commit: 4342b9c22f8633b7008ed153785c0ba5e5f6774b
Author: phauchamps <philippehauchamps@hotmail.com>
Date: 2025-11-24 19:57:02 +0100
Commit message:

 bumped version to 1.7.1
Package: CytoMDS
Commit: e66a2d9d1f833afd3c1157dca176fa3d8518d207
Author: phauchamps <philippehauchamps@hotmail.com>
Date: 2025-11-24 19:56:06 +0100
Commit message:

 fixed unit tests with new version of ggplot2
Package: CytoMDS
Commit: 3f3cf827b155925705ef9bbce112cf7f74ece45f
Author: phauchamps <philippehauchamps@hotmail.com>
Date: 2025-11-24 15:58:36 +0100
Commit message:

 - moved yml file to Bioc 3.23/R 4.6
- updated NEWS.md to be more explicit regarding versions with no devel (incremented only due to Bioc releases)
Package: CytoMDS
Commit: 65d0530f8a40cc4fd13cb2c9fac4a06f60663825
Author: phauchamps <philippehauchamps@hotmail.com>
Date: 2025-11-24 15:49:20 +0100
Commit message:

 updated version in NEWS.md to 1.7
Package: CytoMDS
Commit: 4d111438e0b800ca1862b4b4f3716ee3e79acdcd
Author: phauchamps <philippehauchamps@hotmail.com>
Date: 2025-11-24 15:47:45 +0100
Commit message:

 Merge branch 'devel'
Package: CytoMDS
Commit: 05e395e016405008c17cc521859d9e9bd1f46fb6
Author: phauchamps <philippehauchamps@hotmail.com>
Date: 2025-08-19 12:06:59 +0200
Commit message:

 updated licence file and statements in R files to 2025
Package: CytoMDS
Commit: 870151f8aec900e2e49f11b9099ef6c9383f65df
Author: phauchamps <philippehauchamps@hotmail.com>
Date: 2025-05-15 12:00:03 +0200
Commit message:

 GHA migrated to Bioc 3.22
Package: CytoMDS
Commit: efaeb1447162efe1ec1e59481280e18a089b8f03
Author: phauchamps <philippehauchamps@hotmail.com>
Date: 2025-05-15 09:19:23 +0200
Commit message:

 bumped version to 1.5.0 (Bioc 3.22)
Package: MetaProViz
Commit: 762de61c1bf1b34006fa9989cbb952e55a388520
Author: deeenes <turei.denes@gmail.com>
Date: 2025-11-24 16:28:05 +0100
Commit message:

 Bump version: 3.99.27 → 3.99.28
Package: MetaProViz
Commit: a4fe11ecab1400d04c19333a47e4845052288155
Author: deeenes <turei.denes@gmail.com>
Date: 2025-11-24 16:26:39 +0100
Commit message:

 log message with `OmnipathR` version from `metaproviz_init` and `equivalent_id`
Package: MsCoreUtils
Commit: d2a2f9ec28470aab452568fff8949169d3b7bbc1
Author: Laurent Gatto <lgatto@protonmail.ch>
Date: 2025-11-25 08:53:29 +0100
Commit message:

 fix version and news
Package: MsCoreUtils
Commit: 217f3f73688081f29986dc7c2a9491d81312fcc6
Author: Laurent Gatto <lgatto@protonmail.ch>
Date: 2025-11-25 08:48:27 +0100
Commit message:

 update r/bioc versions
Package: MsCoreUtils
Commit: da0befdf85e3d171c20c13293f4a94eb2ec5516a
Author: Laurent Gatto <lgatto@protonmail.ch>
Date: 2025-11-25 08:45:16 +0100
Commit message:

 Fix and close issue #135
Package: SparseArray
Commit: 7a76318209113850b829e6a5ad05297e577aeea4
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2025-11-24 20:32:02 -0800
Commit message:

 SparseArray 1.11.5: Various improvements

o Rename internal helper subset_SVT_by_Nindex() -> .subset_SVT_as_SVT()

o Revisit and optimize implementation of extract_array() method for
  SVT_SparseArray arrays. Old implementation was doing:

      as.array(.subset_SVT_as_SVT(x, index))

  New implementation is based on new internal helper .subset_SVT_as_Rarray()
  which avoids the intermediate SVT_SparseArray representation. With these
  improvements, extract_array() is now 3 to 4 times faster than in BioC
  3.22.

o Extracting a single row from an SVT_SparseMatrix object 'x' with

      x[i, ]

  is now 15% to 20% faster.

o Add unit tests for .subset_SVT_as_SVT() and .subset_SVT_as_Rarray().

o Speed up nzvals() on SVT_SparseMatrix objects and nnavals() on NaArray
  objects by overriding the default methods with specific methods
  implemented in C. This yields a 15x to 20x speedup.
Package: S4Arrays
Commit: b7ddb8c08db4f065c4e3f0674940b248b0936459
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2025-11-24 20:30:23 -0800
Commit message:

 S4Arrays 1.11.1: Add 'drop' argument to subset_Array_by_Nindex()
Package: HPiP
Commit: e6c77abc7dbd64bb6cbb294a062845b9e5e095da
Author: Matineh Rahmatbakhsh <matinerb.94@gmail.com>
Date: 2025-11-23 14:13:33 -0600
Commit message:

 Fix ggplot unit() usage in pred_ensembel; harden calculateBE; bump version
Package: GEOquery
Commit: ccaa9cd422598e468b17ea417c681484fc404f3f
Author: Sean Davis <seandavi@gmail.com>
Date: 2025-11-24 17:27:25 -0500
Commit message:

 Merge branch 'devel' of git.bioconductor.org:packages/GEOquery into devel
Package: GEOquery
Commit: 135eafbd53a0534f5b6144bc9f01fb4ae450c61b
Author: Sean Davis <seandavi@gmail.com>
Date: 2025-11-24 17:23:40 -0500
Commit message:

 Merge pull request #162 from seandavi/copilot/fix-getgeo-error

Fix parseGSEMatrix crash on files with irregular metadata lines
Package: GEOquery
Commit: 52fe93db5103c3c3b0d1a7e4bffdaa486742537f
Author: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Date: 2025-11-24 22:17:56 +0000
Commit message:

 Fix sample line parsing by extracting !Sample_ lines directly from loaded data

Co-authored-by: seandavi <92435+seandavi@users.noreply.github.com>
Package: GEOquery
Commit: 97499c6bc04ef8b0a00bad3f72736226adfa79da
Author: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Date: 2025-11-24 18:51:56 +0000
Commit message:

 Add NEWS entry for GSE425 parsing fix

Co-authored-by: seandavi <92435+seandavi@users.noreply.github.com>
Package: GEOquery
Commit: 40cb81c15be7c1f1f377126f5bb419592c3a8426
Author: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Date: 2025-11-24 18:49:04 +0000
Commit message:

 Fix GSE matrix parsing with malformed sample lines by adding fill=TRUE to fread calls

Co-authored-by: seandavi <92435+seandavi@users.noreply.github.com>
Package: GEOquery
Commit: 49b79cdaee194d9d8f8fc397102dcd6d54013654
Author: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Date: 2025-11-24 18:44:23 +0000
Commit message:

 Initial plan
Package: GEOquery
Commit: 213155b5935fa4a635374efc6c560dc51a29f707
Author: Sean Davis <seandavi@gmail.com>
Date: 2025-09-03 16:35:38 -0400
Commit message:

 Small changes to theming and vignette formatting
Package: GEOquery
Commit: 7a1fb5648915ab662f077c1b263d3a5b96f94992
Author: Sean Davis <seandavi@gmail.com>
Date: 2025-09-03 16:01:09 -0400
Commit message:

 Turn off single-cell eval to check GH actions
Package: GEOquery
Commit: 8d51468d0c8e988be31da085f237850d01779d57
Author: Sean Davis <seandavi@gmail.com>
Date: 2025-09-03 14:57:47 -0400
Commit message:

 Simplify workflow triggers and change runner to macOS
Package: GEOquery
Commit: d99a32cf7994f0992cb5c6fcf480066a28f64ebc
Author: Sean Davis <seandavi@gmail.com>
Date: 2025-09-03 14:49:42 -0400
Commit message:

 Merge branch 'devel' of https://github.com/seandavi/GEOquery into devel
Package: GEOquery
Commit: cd034e31a0c9c98ff0710fb21110db7de539569f
Author: Sean Davis <seandavi@gmail.com>
Date: 2025-09-03 14:48:54 -0400
Commit message:

 Change vignetteengine to quarto::html

see https://cran.r-project.org/web/packages/quarto/vignettes/hello.html
Package: GEOquery
Commit: e2e93aa88fd721ae7ad97382dbc63ae60f92ac91
Author: Sean Davis <seandavi@gmail.com>
Date: 2025-09-03 14:43:19 -0400
Commit message:

 Add Quarto setup action to pkgdown workflow
Package: GEOquery
Commit: 035e1c276c9bf34338070633c4e7e5f20531dce0
Author: Sean Davis <seandavi@gmail.com>
Date: 2025-09-03 11:14:11 -0400
Commit message:

 Update branches for R-CMD-check workflow
Package: GEOquery
Commit: 8bd7c48c4a94aaa1a9a5a767d8b4c131a6207371
Author: Sean Davis <seandavi@gmail.com>
Date: 2025-09-03 11:13:52 -0400
Commit message:

 Update branches for pkgdown workflow
Package: methylCC
Commit: 18261487e652c6a28c656af4805c65b0fd6148f2
Author: Stephanie Hicks <stephaniechicks@gmail.com>
Date: 2025-11-24 12:49:07 -0500
Commit message:

 removing dep on plyrange
Package: geomeTriD
Commit: f2c416014c074a29eb2f2e705b094caea7675a43
Author: Jianhong Ou <jianhong.ou@gmail.com>
Date: 2025-11-24 12:29:31 -0500
Commit message:

 add citation.
Package: rhinotypeR
Commit: cf7ced949c974eda70e34b146d3afcd8a76761c1
Author: marthaluka <mawia.martha@gmail.com>
Date: 2025-11-24 10:43:42 +0000
Commit message:

 update CITATION
Package: mCSEA
Commit: 3a08149e5e7ef27c6c47b6233b43ed8707a1f308
Author: jordimartorell <jmartorellm@gmail.com>
Date: 2025-11-24 10:57:43 +0100
Commit message:

 Fix unit test
Package: BreastSubtypeR
Commit: ffbf5d880c7bfc058778ef7c51b4b05c9d54fa0e
Author: Qiao Yang <yq.kiuo@gmail.com>
Date: 2025-11-23 10:16:11 +0100
Commit message:

 v1.3.1: Fix ssBC, 1-sample mode; sync docs
Package: BreastSubtypeR
Commit: 463c8db33b7dd5d475955b388df38e4bdbfab4ca
Author: Qiao Yang <yq.kiuo@gmail.com>
Date: 2025-11-23 10:09:22 +0100
Commit message:

 v1.3.1: Fix ssBC, 1-sample mode; sync docs
Package: sesameData
Commit: 9bffe1f1bfa10334879503c4b040bfcc45ebdeed
Author: Wanding Zhou <zhouwanding@gmail.com>
Date: 2025-11-22 22:54:40 -0500
Commit message:

 bump to 1.29.7, added KYCG MSA files
Package: sesameData
Commit: ec65149fbe6b56a1e6378e9cfa92aee92a1d2591
Author: Wanding Zhou <zhouwanding@gmail.com>
Date: 2025-11-19 12:32:45 -0500
Commit message:

 bump to 1.29.6
Package: crisprDesign
Commit: 3eae211260897438ee4cd44353bd05d875d833aa
Author: Jean-Philippe Fortin <fortin946@gmail.com>
Date: 2025-11-22 20:33:03 -0500
Commit message:

 Fixed editedAlleles accessorr
Package: crisprShiny
Commit: bc6a7248e4dba236f7256a16ff2b079956305d27
Author: Jean-Philippe Fortin <fortin946@gmail.com>
Date: 2025-11-22 17:13:32 -0800
Commit message:

 Bumped version up
Package: crisprShiny
Commit: 6df67d800a831b5f5e7f72dd6c8dd174896150fd
Author: Jean-Philippe Fortin <fortin946@gmail.com>
Date: 2025-11-22 17:12:52 -0800
Commit message:

 Merged with bioc
Package: crisprShiny
Commit: 8fe145900fa2af5e150add27c8a9853f4a0cf774
Author: Jean-Philippe Fortin <fortin946@gmail.com>
Date: 2025-11-22 17:11:49 -0800
Commit message:

 Added pwalign package
Package: GSVA
Commit: ad0d25f72ef18169394c5f8d70194597ae25241f
Author: Robert Castelo <robert.castelo@upf.edu>
Date: 2025-11-22 20:18:29 +0100
Commit message:

 Bump version
Package: GSVA
Commit: d3c0e8b7bdfe998c4830d7440da64a659848c683
Author: Robert Castelo <robert.castelo@upf.edu>
Date: 2025-11-22 20:18:05 +0100
Commit message:

 Fixes in memory management and documentation
Package: SparseArray
Commit: c9c55f713a783e0aa5f6ac06b69f0f599b2d10a8
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2025-11-22 09:37:53 -0800
Commit message:

 Refactor SparseArray:::subset_SVT_by_Nindex()

SparseArray:::subset_SVT_by_Nindex() is the workhorse behind endomorphic
N-dimensional subsetting of an SVT_SparseArray object.

This new implementation is 2 to 5 times faster than the previous one.
Package: PolySTest
Commit: fb86072bb603c36ff24bd502d8c35c79c79ca3cf
Author: veitveit <veits@bmb.sdu.dk>
Date: 2025-11-22 16:45:00 +0100
Commit message:

 reduced upset plot for large data sts
Package: PolySTest
Commit: e4b89f767c1a2ab45b4200c2eb145fad37d66404
Author: veitveit <veits@bmb.sdu.dk>
Date: 2025-11-22 16:44:36 +0100
Commit message:

 reduced upset plot for large data sts
Package: PolySTest
Commit: 0dd1f0acf1d1984b5ee41f431487d21f252d9ee3
Author: veitveit <veits@bmb.sdu.dk>
Date: 2025-11-22 16:41:41 +0100
Commit message:

 reduced upset plot for large data sts
Package: PolySTest
Commit: de8721a2f999d2a97b71f42fc961ee8f336b51c9
Author: veitveit <veits@bmb.sdu.dk>
Date: 2025-11-22 16:40:11 +0100
Commit message:

 reduced upset plot for large data sts
Package: PolySTest
Commit: db3d7cb5414ea00a44511f2ca1c9439031881fce
Author: veitveit <veits@bmb.sdu.dk>
Date: 2025-08-22 16:29:51 +0200
Commit message:

 version update
Package: PolySTest
Commit: 52d261651ea17ebde9628f1d0b6b01cae93335ca
Author: veitveit <veits@bmb.sdu.dk>
Date: 2025-06-23 18:36:32 +0200
Commit message:

 fixes errors in plots of 2 proteins
Package: LimROTS
Commit: 661e25cfd44ce4b85ea118b3e7a7e916ef2b4caa
Author: Ali Youssef <aliali.mostafa99@gmail.com>
Date: 2025-11-22 12:45:41 +0200
Commit message:

 Add GPL-2.0-or-later license
Package: Rarr
Commit: 2d4e829c34bac3c977ea55917d400e061733f408
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-11-21 23:59:37 +0100
Commit message:

 Bump version
Package: Rarr
Commit: 1f2ef678432e41da30e75d7bf159da53a47b14ef
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-11-21 23:59:31 +0100
Commit message:

 Document snappy update
Package: Rarr
Commit: 8defc9549de0eb3edf0cfbed708d85f96ee05f67
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-11-21 23:58:50 +0100
Commit message:

 Save new snappy patch file
Package: Rarr
Commit: 6986f5a2a3d6355ec86f5376fda4dc0e1f6e7fd4
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-11-21 23:39:49 +0100
Commit message:

 Silence assert calls for R
Package: Rarr
Commit: 467f435578dd16a999089655e67fa35e64f77ead
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-11-21 21:44:11 +0100
Commit message:

 Convert snappy-stubs-publish.h.in to snappy-stubs-publish.h
Package: Rarr
Commit: a731d0882cc80e48b5b5021e7bfe8cd6d6d10b51
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-11-21 22:42:55 +0100
Commit message:

 Update snappy lib version number in external build files
Package: Rarr
Commit: 4e5490164bcc0325b785e5bf71c69b5fe9c7a9b8
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-11-21 21:30:30 +0100
Commit message:

 Upload upstream snappy 1.2.2 code
Package: Rarr
Commit: ef713bb621e055fc3cc8c02d931c1d264dc62268
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-11-21 11:47:57 +0100
Commit message:

 Bump version
Package: Rarr
Commit: ba0381d313340bd595497f649924d6717598c5df
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-11-21 11:47:31 +0100
Commit message:

 Edit benchmark to reflect potential changes in blosc
Package: Rarr
Commit: 8ce1887aaa0d9bdfc643aec5d48c196c78f49e87
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-11-21 11:45:04 +0100
Commit message:

 Mention blosc update in NEWS
Package: Rarr
Commit: 69972a8cf7a891e678614e98bc7efecd00e34ef7
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-11-21 11:43:25 +0100
Commit message:

 Upload new patch file
Package: Rarr
Commit: 876218a36572fd2903578b5146c1812588a202a5
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-11-20 16:54:46 +0100
Commit message:

 Edit version number in other files
Package: Rarr
Commit: 6bb6e43d471147c844e41ded3c8e2d8eb130bba5
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-11-20 16:44:40 +0100
Commit message:

 Patch blosc library for use in Rarr
Package: Rarr
Commit: 3c781d94dbf7b9383bdc17a83e413723279782e3
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-11-20 17:20:40 +0100
Commit message:

 Upload untouched upstream library
Package: Rarr
Commit: 2585a1f603bf101bc2e93aff4bf4593b214a467c
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-11-18 17:45:46 +0100
Commit message:

 Add s3 test in actual test suite
Package: Rarr
Commit: 104af522635faac95f39ff0e26a53e1dedcbe64d
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-11-18 17:40:02 +0100
Commit message:

 Use update credentials to demo S3 access in vignette
Package: Rarr
Commit: 43e33276c86e12b7160f149cb18353fa7730b58a
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-11-12 12:21:31 +0100
Commit message:

 Bump version
Package: Rarr
Commit: a2c420d613990560884935353127fef7a819fff3
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-11-12 12:21:11 +0100
Commit message:

 Document uncompressed array metadata fix
Package: Rarr
Commit: 4c0af4366111ad10aa1c79bb27af650071687b9d
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-11-17 16:25:55 +0100
Commit message:

 Harmonize output for uncompressed data
Package: Rarr
Commit: 5c13a67908d0d85773473be98ff99336bab1af5a
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-11-17 16:19:37 +0100
Commit message:

 Improve comment & error message
Package: Rarr
Commit: 23c8e96a729d9e22de6c57649fd338bf2b823e7c
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-11-12 12:34:17 +0100
Commit message:

 Tweak metadata snapshot to make path portable
Package: Rarr
Commit: e92cf5596f3b7766202f5dd7a1a6c9a365c05551
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-11-12 11:04:30 +0100
Commit message:

 Add test for complex consolidated metadata
Package: Rarr
Commit: 4a7335022fa3f7817bd94737c33ebdf576e16ebc
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-11-12 10:30:49 +0100
Commit message:

 Name codecs in v3 metadata
Package: Rarr
Commit: 4862617c34b0ab6ab1f5a09dd25b32e049d73853
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-11-12 09:30:43 +0100
Commit message:

 Name codecs and account for more missing values in v3 metadata conversion
Package: metapod
Commit: d6e7e64f858b345cdbea0345998c00130c470ec2
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2025-11-22 17:16:32 +1100
Commit message:

 Missed a fix, also added Encoding to shut up roxygen.
Package: metapod
Commit: 6bf89ae433a0f0cf847baf99383cf6272ace8d7f
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2025-11-22 17:08:08 +1100
Commit message:

 Minor docfix.
Package: biocmake
Commit: db9e0919f727bb14eb4aff1cc8ff997bf6749d8c
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2025-11-22 11:41:01 +1100
Commit message:

 More informative error when the CMake version can't be found.
Package: SparseArray
Commit: b46311b5d610c831d7005755daf4ea9300d64f93
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2025-11-21 14:40:59 -0800
Commit message:

 minor tweak to C-level helper _subassign_leaf_with_Rvector_block()
Package: crisprVerse
Commit: 4ea8be4ec25a00957d3cac8985dfcad1fa32a337
Author: Jean-Philippe Fortin <fortin946@gmail.com>
Date: 2025-11-21 17:39:11 -0500
Commit message:

 Removed getAzimuth dependency
Package: crisprVerse
Commit: 29db25c12fc2ee21dfbfaa6a7c25f935486ed46a
Author: Jean-Philippe Fortin <fortin946@gmail.com>
Date: 2025-11-21 17:38:46 -0500
Commit message:

 Merge remote-tracking branch 'upstream/devel'
Package: crisprVerse
Commit: f6eb422df4a98df71e7aeea19bfdb43d77917d3f
Author: Jean-Philippe Fortin <fortin946@gmail.com>
Date: 2025-11-21 17:38:39 -0500
Commit message:

 Changed namespace
Package: crisprDesign
Commit: 5ab9b5e5c37b6e78660be98a01818a13a124a267
Author: Jean-Philippe Fortin <fortin946@gmail.com>
Date: 2025-11-21 17:33:22 -0500
Commit message:

 Shorten on-target tests
Package: rigvf
Commit: 8b6e9d08155bcd759a9ab4f3083ab43819dadb5c
Author: Mike Love <mikelove@users.noreply.github.com>
Date: 2025-11-21 14:54:00 -0500
Commit message:

 try new workflow
Package: h5mread
Commit: 6ead8d5cee6fe373aca041d0e1b6b18f6a196641
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2025-11-21 06:30:37 -0800
Commit message:

 h5mread 1.3.1: Add example of how to use an H5File with the rhdf5 package
Package: MetaProViz
Commit: b8ff4f3c048f8bd7678ae66fdf9e844b609da94d
Author: deeenes <turei.denes@gmail.com>
Date: 2025-11-21 13:04:04 +0100
Commit message:

 Merge branch 'devel' of git.bioconductor.org:packages/MetaProViz into devel
Package: MetaProViz
Commit: a09a5e805c7e0f9291695b7505f562a13360cc3f
Author: deeenes <turei.denes@gmail.com>
Date: 2025-11-21 12:53:59 +0100
Commit message:

 Bump version: 3.99.26 → 3.99.27
Package: MetaProViz
Commit: 9f40e2ed40107cd92409b8308c248aaec9710fef
Author: deeenes <turei.denes@gmail.com>
Date: 2025-11-21 12:53:30 +0100
Commit message:

 Revert "Merge branch 'bioc-submission' into devel"

This reverts commit c2bbb6f3395209c0832a684b617c8b693393de57, reversing
changes made to 314373acda1efeae23cdc66dd33e9c28028a5e08.
Package: MetaProViz
Commit: c2bbb6f3395209c0832a684b617c8b693393de57
Author: deeenes <turei.denes@gmail.com>
Date: 2025-11-21 12:53:16 +0100
Commit message:

 Merge branch 'bioc-submission' into devel
Package: MetaProViz
Commit: 314373acda1efeae23cdc66dd33e9c28028a5e08
Author: deeenes <turei.denes@gmail.com>
Date: 2025-11-21 12:10:45 +0100
Commit message:

 license update in `DESCRIPTION`: GPLv3 → BSD 3-clause
Package: MetaProViz
Commit: fa7e1b729f9b2ff444aa8fc14b512a6db8e9e27f
Author: deeenes <turei.denes@gmail.com>
Date: 2025-11-20 15:24:15 +0100
Commit message:

 Bump version: 3.99.25 → 3.99.26
Package: MetaProViz
Commit: ca98fa8e405ffde44cd993e5502d245b528b81de
Author: deeenes <turei.denes@gmail.com>
Date: 2025-11-20 15:24:03 +0100
Commit message:

 license update: GPLv3 → BSD 3-clause
Package: MetaProViz
Commit: aea083231c0cc15255b211bfc5d5b2d5dcc4d478
Author: jannikfranken <jannik8513@gmail.com>
Date: 2025-11-20 14:41:39 +0000
Commit message:

 handling BioC NOTE: not using paste in conditional statements
Package: MetaProViz
Commit: 57bcb6933fbed3fc30a6d42304581a2f8f4d6c90
Author: deeenes <turei.denes@gmail.com>
Date: 2025-11-20 14:25:53 +0100
Commit message:

 Bump version: 3.99.24 → 3.99.25
Package: MetaProViz
Commit: f30899cfaa71272da069c567de3228354f4488e8
Author: jannikfranken <jannik8513@gmail.com>
Date: 2025-11-20 13:46:57 +0000
Commit message:

 NA handling for metabolites without assigned pathways
Package: MetaProViz
Commit: c51796fc82d9a38a2e361775349d375a70006dfb
Author: jannikfranken <jannik8513@gmail.com>
Date: 2025-11-20 13:30:31 +0000
Commit message:

 added and fixed VizVolcano plotting in case of nrow(Inputvolcano) = 0
Package: MetaProViz
Commit: b17e8a14ebdfd1012402ea5ea7d5fe0bbefbdf60
Author: jannikfranken <jannik8513@gmail.com>
Date: 2025-11-20 11:33:49 +0000
Commit message:

 changed block eval to TRUE
Package: MetaProViz
Commit: 45c856914833fa1ec982ae65fdaa94c55d2fb705
Author: jannikfranken <jannik8513@gmail.com>
Date: 2025-11-20 11:01:30 +0000
Commit message:

 disabled upset_plot plotting
Package: MetaProViz
Commit: 0ca71e3e401470ff60edd58ac4004ea3bcb1cf36
Author: jannikfranken <jannik8513@gmail.com>
Date: 2025-11-20 10:38:56 +0000
Commit message:

 wrapped second viz_upset in tryCatch block
Package: MetaProViz
Commit: 826e55e8bf2b6aa98fba489f90d2a1a71fa8907d
Author: jannikfranken <jannik8513@gmail.com>
Date: 2025-11-20 10:12:58 +0000
Commit message:

 enabled block eval and fixed data load
Package: MetaProViz
Commit: fdb661ae4f6197a9352c3c62b04ca6b725c31a13
Author: jannikfranken <jannik8513@gmail.com>
Date: 2025-11-20 10:12:09 +0000
Commit message:

 wrapped viz_upset in tryCatch
Package: MetaProViz
Commit: 66571d97c9c4198a7d583cf99cd9a605bc822db1
Author: jannikfranken <jannik8513@gmail.com>
Date: 2025-11-19 17:23:13 +0000
Commit message:

 added variable declaration in VizVolcano and reordered denominator-numerator naming
Package: MetaProViz
Commit: 33c3f170d7ce5bff1562010e21e27a2c1341af76
Author: deeenes <turei.denes@gmail.com>
Date: 2025-11-18 19:34:35 +0100
Commit message:

 well, the bioc container's tag is `latest`
Package: MetaProViz
Commit: d8981cb060eb33b099eded4ff3d7d8e5221c17b7
Author: deeenes <turei.denes@gmail.com>
Date: 2025-11-18 19:27:03 +0100
Commit message:

 pkgdown action: run on `bionconductor:release` container + added some custom pkg installation steps, not sure all necessary
Package: MetaProViz
Commit: 20872ced418e739b94b2d2964dfcdfc38d2e1d47
Author: deeenes <turei.denes@gmail.com>
Date: 2025-11-18 18:37:49 +0100
Commit message:

 Merge branch 'devel'
Package: MetaProViz
Commit: 8fdde5a79b1d1e2b0074c98d32add69a4347327f
Author: deeenes <turei.denes@gmail.com>
Date: 2025-11-18 18:37:41 +0100
Commit message:

 Bump version: 3.99.23 → 3.99.24
Package: MetaProViz
Commit: bcb268f17c8d5576d89762c63ad9868bae0686a1
Author: deeenes <turei.denes@gmail.com>
Date: 2025-11-18 18:06:57 +0100
Commit message:

 docs rebuild
Package: MetaProViz
Commit: 288559a266402cbb427f91599f5ab1638c28d68b
Author: deeenes <turei.denes@gmail.com>
Date: 2025-11-18 18:06:46 +0100
Commit message:

 Merge branch 'devel' of github.com:saezlab/MetaProViz into devel
Package: MetaProViz
Commit: 352057fc69e53430665d953b42800af92333d63f
Author: deeenes <turei.denes@gmail.com>
Date: 2025-11-18 18:06:38 +0100
Commit message:

 docs rebuild
Package: MetaProViz
Commit: d5306d9fd0024870695ff8f632e1190d561b6e17
Author: jannikfranken <jannik8513@gmail.com>
Date: 2025-11-18 16:52:37 +0000
Commit message:

 Merge branch 'devel' of https://github.com/saezlab/MetaProViz into devel
Package: MetaProViz
Commit: aa92f1da7d8fee5e74fd433989877849dbcffb8d
Author: jannikfranken <jannik8513@gmail.com>
Date: 2025-11-18 16:51:22 +0000
Commit message:

 mca_core example issue
Package: MetaProViz
Commit: b41b5779c8c6038483a3fdac97c461a5c2ca0a08
Author: jannikfranken <jannik8513@gmail.com>
Date: 2025-11-18 15:19:12 +0000
Commit message:

 make_gene_metab_set folder and subfolder handling logic for different input combinations
Package: MetaProViz
Commit: 72c9bda388b0821234d084cbf951ec8d52364b67
Author: deeenes <turei.denes@gmail.com>
Date: 2025-11-18 15:44:22 +0100
Commit message:

 added claude notes & instructions
Package: MetaProViz
Commit: db17bad8d3984a8d895f28a792f33c1e66c5eff8
Author: jannikfranken <jannik8513@gmail.com>
Date: 2025-11-18 14:25:42 +0000
Commit message:

 typo
Package: MetaProViz
Commit: 3560f1b63f59815e0ee5a2f65b4ca419af2f99ef
Author: deeenes <turei.denes@gmail.com>
Date: 2025-11-18 15:21:48 +0100
Commit message:

 Bump version: 3.99.22 → 3.99.23
Package: MetaProViz
Commit: 11430b0e67f7220ec1c9cfd90a36eb6e973cd690
Author: deeenes <turei.denes@gmail.com>
Date: 2025-11-18 15:21:37 +0100
Commit message:

 Merge branch 'devel' of github.com:saezlab/MetaProViz into devel
Package: MetaProViz
Commit: f2595c9d4324fcf0c0a95bb780ddf626e1b4371d
Author: jannikfranken <jannik8513@gmail.com>
Date: 2025-11-18 14:18:42 +0000
Commit message:

 fixed ALL other missing magrittr function in roxygen strings and added double colon magrittr:: calls
Package: MetaProViz
Commit: 584c02a0da778aefae293c4fc668bcfd034ce491
Author: jannikfranken <jannik8513@gmail.com>
Date: 2025-11-18 14:04:11 +0000
Commit message:

 fixed missing magrittr function in roxygen strind and added double colon magrittr:: call
Package: MetaProViz
Commit: 444f241d66b63fd2a246b992145b5144035ae89d
Author: jannikfranken <jannik8513@gmail.com>
Date: 2025-11-18 13:49:26 +0000
Commit message:

 fix viz_volcano() metadata_info bool check logic
Package: MetaProViz
Commit: 3da8ae5b6aa67bbd22693b04615f32168ea0ac1c
Author: jannikfranken <jannik8513@gmail.com>
Date: 2025-11-18 13:38:21 +0000
Commit message:

 fixing logical values stored as stirings in ORA
Package: MetaProViz
Commit: 57f0156cc3a995f1394958bae787da39cd466077
Author: jannikfranken <jannik8513@gmail.com>
Date: 2025-11-18 13:31:05 +0000
Commit message:

 simplify ORA top/bottom logical check
Package: MetaProViz
Commit: 8a1e8793ff7ce591f6a5a936da46d63266bb99e2
Author: jannikfranken <jannik8513@gmail.com>
Date: 2025-11-18 13:21:54 +0000
Commit message:

 Fix ORA top/bottom logical check
Package: MetaProViz
Commit: 5bab062598b2326ce76b4276537005e15d60bfff
Author: jannikfranken <jannik8513@gmail.com>
Date: 2025-11-18 13:12:54 +0000
Commit message:

 Fix ORA case_when
Package: MetaProViz
Commit: 73fcf3ac3da99980effd554e3c8212ea91533f9e
Author: jannikfranken <jannik8513@gmail.com>
Date: 2025-11-18 13:06:13 +0000
Commit message:

 Fix processing() outlier merge pipe
Package: MetaProViz
Commit: 92153d5a2e4391e6f19b83a9bafd27ebf702bdfd
Author: jannikfranken <jannik8513@gmail.com>
Date: 2025-11-18 12:59:38 +0000
Commit message:

 fixed missing pipe assignment
Package: MetaProViz
Commit: 97345461653d8bbeaa36b3ef778a874908d2553d
Author: jannikfranken <jannik8513@gmail.com>
Date: 2025-11-18 11:18:33 +0000
Commit message:

 fixed processing() error, non-connected pipe
Package: MetaProViz
Commit: c61dffc6e0118f2795e0f3bb8221452895719d75
Author: jannikfranken <jannik8513@gmail.com>
Date: 2025-11-18 10:53:26 +0000
Commit message:

 fixed featurefilt check of processing() call
Package: MetaProViz
Commit: e83fcb4ee4abe011c9192dfc665106803b0bb067
Author: deeenes <turei.denes@gmail.com>
Date: 2025-11-07 12:56:07 +0100
Commit message:

 Bump version: 3.99.21 → 3.99.22
Package: MetaProViz
Commit: 11f0f9be9ce84e3122dd54f760727ed30be5877a
Author: deeenes <turei.denes@gmail.com>
Date: 2025-11-07 12:56:02 +0100
Commit message:

 docs rebuild
Package: MetaProViz
Commit: 305cc6e9be53e6fa4748fc64021a83f5f039c6cf
Author: deeenes <turei.denes@gmail.com>
Date: 2025-11-07 12:55:47 +0100
Commit message:

 long lines in docstring examples
Package: MetaProViz
Commit: f14719f28b7b15d37048e071386f6c0bac667707
Author: deeenes <turei.denes@gmail.com>
Date: 2025-11-06 18:13:55 +0100
Commit message:

 docs rebuild
Package: MetaProViz
Commit: c958f8487a4178e91478f6aae35d03d22d93edc2
Author: deeenes <turei.denes@gmail.com>
Date: 2025-11-06 13:02:33 +0100
Commit message:

 Bump version: 3.99.20 → 3.99.21
Package: MetaProViz
Commit: 75a6c40cf08f4069a175e8bf53faf2db538be254
Author: deeenes <turei.denes@gmail.com>
Date: 2025-11-04 12:57:45 +0100
Commit message:

 Bump version: 3.99.19 → 3.99.20
Package: MetaProViz
Commit: 75fbbe72c6259099344422d282c28bc41b077857
Author: deeenes <turei.denes@gmail.com>
Date: 2025-11-06 13:02:20 +0100
Commit message:

 enabled doctests of small infrastructure functions
Package: MetaProViz
Commit: edf96d6e0431f4ce4116bc3a7ccdb16cbacd4bd5
Author: deeenes <turei.denes@gmail.com>
Date: 2025-11-03 01:45:48 +0100
Commit message:

 Bump version: 3.99.18 → 3.99.19
Package: MetaProViz
Commit: d677f0505b4af3372fa00af173e7c9c34a5ccc63
Author: deeenes <turei.denes@gmail.com>
Date: 2025-11-03 01:41:43 +0100
Commit message:

 `RefactPK`: various formatting
Package: MetaProViz
Commit: d9f851523fe6045e13883fea3ab9f4b84211a19d
Author: deeenes <turei.denes@gmail.com>
Date: 2025-11-03 01:33:10 +0100
Commit message:

 docs rebuild
Package: MetaProViz
Commit: 63520e216a359d11d24f643de6a58b5a29f6895d
Author: deeenes <turei.denes@gmail.com>
Date: 2025-11-03 01:30:39 +0100
Commit message:

 `MetabClustAn`: indentations & line breaks
Package: MetaProViz
Commit: 1f3350abfcf6b2549647f5a4c7028bd6608ab00c
Author: deeenes <turei.denes@gmail.com>
Date: 2025-11-03 01:20:29 +0100
Commit message:

 long messages: breaking them by `paste0` + also send them to the log
Package: MetaProViz
Commit: 768becae3c1fcd5d7431fd3c24f91aad92f9938b
Author: deeenes <turei.denes@gmail.com>
Date: 2025-11-03 01:09:29 +0100
Commit message:

 spacing around `else if`
Package: MetaProViz
Commit: de817bcb351c47318a2f0a39ad7bc5553a261c3e
Author: deeenes <turei.denes@gmail.com>
Date: 2025-11-03 01:04:51 +0100
Commit message:

 use `%<>%` pipe
Package: MetaProViz
Commit: 4bbf0398284b3494b0546683b677ca10774590bd
Author: deeenes <turei.denes@gmail.com>
Date: 2025-11-03 00:49:56 +0100
Commit message:

 indentation
Package: MetaProViz
Commit: 650a748651135506dbf3e0fa1392316013308347
Author: deeenes <turei.denes@gmail.com>
Date: 2025-11-03 00:48:24 +0100
Commit message:

 break lines of `mutate(case_when(...))` expressions
Package: MetaProViz
Commit: eae4c158a0db1d4d720e1cbc7460af9b5129c8b1
Author: deeenes <turei.denes@gmail.com>
Date: 2025-11-03 00:25:05 +0100
Commit message:

 spaces around `<-` operators
Package: MetaProViz
Commit: 13d1dbd56c903306334ba2b259060ad7e2530c67
Author: deeenes <turei.denes@gmail.com>
Date: 2025-11-03 00:22:32 +0100
Commit message:

 break long lines at boolean operators
Package: MetaProViz
Commit: 24880f68a6f973f599387fceaa406e45e3e396db
Author: deeenes <turei.denes@gmail.com>
Date: 2025-11-02 23:44:59 +0100
Commit message:

 indentation
Package: MetaProViz
Commit: 114c204a9c5eca676ce1557c13e6eba8f3424d48
Author: deeenes <turei.denes@gmail.com>
Date: 2025-11-02 23:28:20 +0100
Commit message:

 formatting of comments
Package: MetaProViz
Commit: 9d63ff5c820e26a2edb5d11d4a9cdeffe46c31d7
Author: deeenes <turei.denes@gmail.com>
Date: 2025-11-02 23:08:42 +0100
Commit message:

 inconsistent spacing around `==`
Package: MetaProViz
Commit: c803ba2feebce234d24726e6a9b956e3b7fa7223
Author: deeenes <turei.denes@gmail.com>
Date: 2025-11-02 23:05:01 +0100
Commit message:

 inconsistent spacing around pipes
Package: MetaProViz
Commit: 828917147163fb141b4f2cab49c6c68b38c7d340
Author: deeenes <turei.denes@gmail.com>
Date: 2025-11-02 22:57:17 +0100
Commit message:

 inconsistent spacing around commas
Package: MetaProViz
Commit: 5a5925775b25416c35372098e3ee99e83ccbe6b8
Author: deeenes <turei.denes@gmail.com>
Date: 2025-11-02 21:59:29 +0100
Commit message:

 inconsistent spacing around `=`
Package: MetaProViz
Commit: 66c08ed31770a53fc66a88347928ddb4b316546c
Author: deeenes <turei.denes@gmail.com>
Date: 2025-11-02 21:51:13 +0100
Commit message:

 break long conditionals at boolean operators
Package: MetaProViz
Commit: a5c261f1779b20a5318c714f5111459288e32bf6
Author: deeenes <turei.denes@gmail.com>
Date: 2025-11-02 21:41:22 +0100
Commit message:

 fixed indentation and `else if` → `if` issues introduced by claude + further manual cleanup of messy code
Package: MetaProViz
Commit: 84a218bc3ae25c7eb1ec6d06c226a18e310e2e3a
Author: deeenes <turei.denes@gmail.com>
Date: 2025-11-02 19:24:18 +0100
Commit message:

 manually fixed some ugly checks for parameter presence in list arguments
Package: MetaProViz
Commit: 53b01674015e89f129ed91fb13b49ba56df8eedd
Author: deeenes <turei.denes@gmail.com>
Date: 2025-11-02 18:51:31 +0100
Commit message:

 cleaned up redundant ` == TRUE` and ` == FALSE` expressions in boolean conditions
Package: MetaProViz
Commit: af8f221934a8bb0e05d9467739917be2dea33df3
Author: deeenes <turei.denes@gmail.com>
Date: 2025-10-31 16:20:33 +0100
Commit message:

 formatting: fixed indentation of verbs within pipes
Package: MetaProViz
Commit: 02b00288804d53cd1400cb14550cec9286aa8451
Author: deeenes <turei.denes@gmail.com>
Date: 2025-10-31 15:45:42 +0100
Commit message:

 Merge branch 'devel' of github.com:saezlab/MetaProViz into devel
Package: MetaProViz
Commit: 2c74212028d2505f49d3686f6f1e6bcc06992701
Author: deeenes <turei.denes@gmail.com>
Date: 2025-10-31 15:22:56 +0100
Commit message:

 code formatting: break long argument lists
Package: ORFik
Commit: 7b43c67a171ffa1f2d83347d21d256e54e5eed9e
Author: Roleren <hauken_heyken@hotmail.com>
Date: 2025-11-21 12:05:35 +0100
Commit message:

 Merge branch 'master' into devel
Package: ORFik
Commit: 4d4f7205f30fc97b24a975b5cc2a72f287bf619c
Author: Roleren <hauken_heyken@hotmail.com>
Date: 2025-11-21 12:05:22 +0100
Commit message:

 added more docs and fixed examples
Package: ORFik
Commit: 07d7500a9337930825c9efc4806f366bb0cfa1ec
Author: Roleren <hauken_heyken@hotmail.com>
Date: 2025-11-21 10:47:23 +0100
Commit message:

 bump version
Package: ORFik
Commit: 41de42bb1973575ccfb4ce07141fb36ae84096ce
Author: Roleren <hauken_heyken@hotmail.com>
Date: 2025-11-21 10:46:45 +0100
Commit message:

 Merge branch 'devel' of git.bioconductor.org:packages/ORFik into devel
Package: ORFik
Commit: de0c0812e3666fb5b7a04bc293bf7b94bc0cc372
Author: Roleren <hauken_heyken@hotmail.com>
Date: 2025-11-21 10:46:22 +0100
Commit message:

 Merge branch 'master' into devel
Package: ORFik
Commit: 6a9536af0dae1d366fbf97522ad81a5458893e35
Author: Roleren <hauken_heyken@hotmail.com>
Date: 2025-11-14 15:25:28 +0100
Commit message:

 Improved widthPerGroup + more tests
Package: ORFik
Commit: dd30b0f51120b61f4526b189c7fde9c6c96a49a8
Author: Roleren <hauken_heyken@hotmail.com>
Date: 2025-11-14 14:22:13 +0100
Commit message:

 New speedups for grl getter / setters
Package: ORFik
Commit: 42552d875dd044da79999c65cb65157fa38c0d76
Author: Roleren <hauken_heyken@hotmail.com>
Date: 2025-11-14 12:34:53 +0100
Commit message:

 Massive speedups for grl getters
Package: ORFik
Commit: 9e5a2dd6b873226833605057015f7a34dfd4e41f
Author: Roleren <hauken_heyken@hotmail.com>
Date: 2025-11-13 15:32:12 +0100
Commit message:

 Added makeGRangesFromDataFrameFast
Package: ORFik
Commit: 79daa480d581c1bdb49588fe4411d50087b45e90
Author: Roleren <hauken_heyken@hotmail.com>
Date: 2025-11-11 13:04:18 +0100
Commit message:

 Improved go plotting
Package: ORFik
Commit: 1b734addd2f4ebf436b52152fb23544df158ecb8
Author: Roleren <hauken_heyken@hotmail.com>
Date: 2025-11-11 12:40:46 +0100
Commit message:

 Added GOrilla plot similar to clusterProfiler
Package: ORFik
Commit: 2698a4478a748d791ed263b1781142a04bb07b73
Author: Roleren <hauken_heyken@hotmail.com>
Date: 2025-11-05 22:27:50 +0100
Commit message:

 Small fix DEG plot
Package: ORFik
Commit: b1342cdc1dc3a6111b4a45d9247d730f49add6ff
Author: Roleren <hauken_heyken@hotmail.com>
Date: 2025-11-05 22:00:04 +0100
Commit message:

 Now save optimized ranges in qs, not sure why this was not here yet for some reason, also improved DEG plotting
Package: ORFik
Commit: ba005cda1930270218f90d99cdd442207fc369a2
Author: Roleren <hauken_heyken@hotmail.com>
Date: 2025-10-29 16:06:41 +0100
Commit message:

 Added working example to collapse function
Package: ORFik
Commit: ef3a4ec306e7046c6fb63bb0168068bb5ca75cca
Author: Roleren <hauken_heyken@hotmail.com>
Date: 2025-10-29 13:40:53 +0100
Commit message:

 Improved collapsing
Package: ORFik
Commit: d7589e56cf30f9a28b60dd71c7d9d84810ea76b3
Author: Roleren <hauken_heyken@hotmail.com>
Date: 2025-10-21 15:08:21 +0200
Commit message:

 Added some checks for gorilla copy function
Package: ORFik
Commit: f70a41dfde60a1cd4cb04930598ced5786298f85
Author: Roleren <hauken_heyken@hotmail.com>
Date: 2025-10-21 14:26:39 +0200
Commit message:

 Added gorilla copy local function
Package: ORFik
Commit: 2df5a890e08f53c7293c126d846387b409242df6
Author: Roleren <hauken_heyken@hotmail.com>
Date: 2025-10-13 23:49:16 +0200
Commit message:

 Improved bed12
Package: ORFik
Commit: 1ceed998c59d3dbccdf3e158c0965969bb77322a
Author: Roleren <hauken_heyken@hotmail.com>
Date: 2025-10-08 14:21:57 +0200
Commit message:

 Fixed bug categorize_and_filter_ORFs
Package: ORFik
Commit: 5f83a8831720e84de21d6213718cd58601a9105a
Author: Roleren <hauken_heyken@hotmail.com>
Date: 2025-09-26 12:59:34 +0200
Commit message:

 Improved coveragePerTiling
Package: ORFik
Commit: 15bcdfa3e517dad811b1d8cfe2db1eb35f791012
Author: Roleren <hauken_heyken@hotmail.com>
Date: 2025-09-25 15:34:14 +0200
Commit message:

 Massive speed up for countOverlaps on covRle
Package: ORFik
Commit: e538aa99fa7d0751df264a2701d088f1244beaf7
Author: Roleren <hauken_heyken@hotmail.com>
Date: 2025-09-24 13:47:04 +0200
Commit message:

 STAR added more checks on trim inputs
Package: ORFik
Commit: 66739dcf0dcb7e52974fd00d7a132367b9940c86
Author: Roleren <hauken_heyken@hotmail.com>
Date: 2025-09-19 14:40:13 +0200
Commit message:

 Improved docs
Package: BioNAR
Commit: 5e908e7e135a2f2829f2525dc1a6473debcffb02
Author: Anatoly Sorokin <lptolik@gmail.com>
Date: 2025-11-21 10:40:16 +0000
Commit message:

 convert Entrez to characters for annotation
Package: LimROTS
Commit: 4c0a6dc1ccbd980bd5cfbc5aa5f6e470588536cf
Author: Ali Youssef <aliali.mostafa99@gmail.com>
Date: 2025-11-21 10:53:49 +0200
Commit message:

 Core functions reimplemented and refactored
Package: crisprDesign
Commit: a739727c863c807fdbf8a43430b1db9979b7870d
Author: Jean-Philippe Fortin <fortin946@gmail.com>
Date: 2025-11-20 23:38:16 -0500
Commit message:

 Adapted to new crisprScore paradigm
Package: crisprScore
Commit: c805e178225327be206352ef0612db4aaa555762
Author: Jean-Philippe Fortin <fortin946@gmail.com>
Date: 2025-11-20 17:04:11 -0500
Commit message:

 Added note re. RS3 tracer
Package: crisprScore
Commit: b5d8888e3b2a2e4c3331b9af131d974e5de852a9
Author: Jean-Philippe Fortin <fortin946@gmail.com>
Date: 2025-11-20 17:02:50 -0500
Commit message:

 Ready to push
Package: crisprScore
Commit: 22dd03ce20b4af2aa6def2123cf02450376bcb03
Author: Jean-Philippe Fortin <fortin946@gmail.com>
Date: 2025-11-20 16:11:19 -0500
Commit message:

 Ready to write vignette
Package: crisprScore
Commit: 0e3c216773bff006df2a0a82434cad3c808f301e
Author: Jean-Philippe Fortin <fortin946@gmail.com>
Date: 2025-11-20 15:49:36 -0500
Commit message:

 Conda env arguments added
Package: crisprScore
Commit: 2643bc2f9d9176a7d08654e0d1cb05745eb9de68
Author: Jean-Philippe Fortin <fortin946@gmail.com>
Date: 2025-11-19 23:43:42 -0500
Commit message:

 Updated basilisk
Package: crisprScore
Commit: b358c1b0760b2ffbe9b77093305fa8753782a4b8
Author: Jean-Philippe Fortin <fortin946@gmail.com>
Date: 2025-11-19 23:43:11 -0500
Commit message:

 Fixed enpamgb score
Package: crisprScore
Commit: ba76282360b8f89a31814c6255faa9fb02802ad3
Author: Jean-Philippe Fortin <fortin946@gmail.com>
Date: 2025-11-19 21:00:27 -0500
Commit message:

 Removed azimuth
Package: crisprScore
Commit: 02b4c566f9b640ce8e522279c3ba2b0331b723b6
Author: Jean-Philippe Fortin <fortin946@gmail.com>
Date: 2025-11-19 20:59:07 -0500
Commit message:

 Fixed DeepHF and RuleSet3 scores
Package: crisprScore
Commit: 2b69581ac85d2e66366e287a2b187c570ef913f3
Author: Jean-Philippe Fortin <fortin946@gmail.com>
Date: 2025-11-19 16:59:09 -0500
Commit message:

 Removed python2-based scores
Package: InPAS
Commit: f16f6421b703190599d63d52962399215c221772
Author: Jianhong Ou <jianhong.ou@gmail.com>
Date: 2025-11-20 21:24:51 -0500
Commit message:

 remove plyranges::filter.

Merge branch 'RELEASE_3_22' into devel

# Conflicts:
#	DESCRIPTION
Package: InPAS
Commit: 5e70ec51c0ad3f244d6a29856c4f1447c722a9de
Author: Jianhong Ou <jianhong.ou@gmail.com>
Date: 2025-11-20 21:19:47 -0500
Commit message:

 remove plyranges::filter
Package: SparseArray
Commit: 612972d0bbabaa7e08bec016be514a5aa126573a
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2025-11-20 16:00:03 -0800
Commit message:

 SparseArray 1.11.4: Refactor subassignment with a "short" right vector

Refactor SparseArray:::.subassign_SVT_with_short_Rvector().
This is the workhorse behind subassignment of an SVT_SparseArray object
with a "short" vector on the right e.g.
    svt[i, j, k] <- 0
or
    svt[i, j, k] <- c(4, 0, -1, 1)
where each of i, j, k is either missing or a vector of subscripts.

The new implementation is simpler, cleaner, faster.
Package: BiocCheck
Commit: 318b33b6e2fbd88e72a45d7932bef59c4ea885c6
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-11-20 17:55:37 -0500
Commit message:

 version bump 1.47.5
Package: BiocCheck
Commit: 4de856b280f8e1f0d94854f2ebf508b162c87a46
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-11-20 17:55:33 -0500
Commit message:

 update docs to explain use NULL and FALSE for dot-options
Package: BiocCheck
Commit: 41b0bb7b11a642f20c3086b2c31ab8163326ad32
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-11-20 17:35:01 -0500
Commit message:

 version bump 1.47.4
Package: BiocCheck
Commit: 9cc228ae50c149c18c8bf214e3a578fad13e07cf
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-11-20 17:34:46 -0500
Commit message:

 installation should be done when install is NULL or TRUE
Package: BiocCheck
Commit: 40e1f9eb400a8de7cf620c058e9e492a24dbdce7
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-11-20 17:25:32 -0500
Commit message:

 explicitly check for TRUE for !is.null options
Package: BiocCheck
Commit: 5c5e27ebaa0390d22f5052e2b5df1746c76b9e8e
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-11-20 17:25:08 -0500
Commit message:

 check for NULL or FALSE in negative options e.g. no-check-deprecated
Package: BiocCheck
Commit: b3d9eb6e017174ade5ac3a42c972e5d5fd413969
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-11-20 15:27:31 -0500
Commit message:

 version bump 1.47.3
Package: BiocCheck
Commit: 89101051d2eaddf76888f5d2827489d8a699610b
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-11-20 15:26:09 -0500
Commit message:

 use .BiocCheck consistently
 </pre>
    </div>
  
    

      Package: BiocCheck

      Commit: 0972766e50eb4a863f65366766d6f8765c8dc186

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2025-11-20 15:25:50 -0500

      Commit message:


	  
		
 remove example from param dots and move to dot-options section
 

    

  
    

      Package: BiocCheck

      Commit: 06719a429eb8baf598bd1d9b68249bfeecd0cb09

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2025-11-20 15:24:58 -0500

      Commit message:


	  
		
 use md for R CMD build cmd
 

    

  
    

      Package: BiocCheck

      Commit: 94b6f7350abaafb1e41b99e2a66b7ef335fbe18b

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2025-11-20 15:24:26 -0500

      Commit message:


	  
		
 add skip installation section in docs
 

    

  
    

      Package: BiocCheck

      Commit: 1445420e8c735eee8556d47cfe62b14669c86a0c

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2025-11-20 15:23:32 -0500

      Commit message:


	  
		
 document dot-options value options, TRUE, NULL, other
 

    

  
    

      Package: CATALYST

      Commit: a1cad2251f4c1d34617daf11f03c32e9f2405b74

      Author:  HelenaLC <helena@crowell.eu> 

      Date: 2025-11-20 20:04:37 +0100

      Commit message:


	  
		
 fix #204 on devel
 

    

  
    

      Package: CATALYST

      Commit: 4f0aaa011d1818561f66d4acd7f7b26dd65988dd

      Author:  HelenaLC <helena@crowell.eu> 

      Date: 2025-11-20 19:42:54 +0100

      Commit message:


	  
		
 fix typo; plz work now :(
 

    

  
    

      Package: CATALYST

      Commit: 7fafa8537fbbd2449283e6c4a705dde1a4f879ad

      Author:  HelenaLC <helena@crowell.eu> 

      Date: 2025-11-20 19:07:24 +0100

      Commit message:


	  
		
 add final line?
 

    

  
    

      Package: CATALYST

      Commit: 39eb277d6ffd48b194b858762e889eb10573c4fc

      Author:  HelenaLC <helena@crowell.eu> 

      Date: 2025-11-20 19:05:13 +0100

      Commit message:


	  
		
 fix R CMD warning
 

    

  
    

      Package: CATALYST

      Commit: 3c44e1cdb32f546105226a95285d8915d28dec0d

      Author:  HelenaLC <helena@crowell.eu> 

      Date: 2025-11-20 18:26:20 +0100

      Commit message:


	  
		
 add code comms
 

    

  
    

      Package: CATALYST

      Commit: 0db8f7f01c6bb9a38aa455d73bd39c07a886e0ec

      Author:  HelenaLC <helena@crowell.eu> 

      Date: 2025-11-20 18:21:40 +0100

      Commit message:


	  
		
 fix CITATION
 

    

  
    

      Package: CATALYST

      Commit: 5acbc7109eea062ac983391201a64a4eb6555728

      Author:  HelenaLC <helena@crowell.eu> 

      Date: 2025-11-20 17:05:13 +0100

      Commit message:


	  
		
 add CITATION
 

    

  
    

      Package: CATALYST

      Commit: 6890b94f038940a0c34fdd0c5f9b0a5204c7262d

      Author:  HelenaLC <helena@crowell.eu> 

      Date: 2025-11-20 17:00:26 +0100

      Commit message:


	  
		
 plotSpillmat fix (#204)
 

    

  
    

      Package: CATALYST

      Commit: f9e5c3e60f6cd09bbf3e39d54f2e17322ea0f0ca

      Author:  HelenaLC <helena@crowell.eu> 

      Date: 2025-11-02 08:10:23 +0100

      Commit message:


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

    

  
    

      Package: CATALYST

      Commit: 57f08a51c4e5cd57023cc7b8b67dbc79b47537bb

      Author:  HelenaLC <helena@crowell.eu> 

      Date: 2025-10-05 22:30:55 +0200

      Commit message:


	  
		
 update GHA
 

    

  
    

      Package: CATALYST

      Commit: eb014a23bb4d76532b403ff6c99ff86388872705

      Author:  HelenaLC <helena@crowell.eu> 

      Date: 2025-10-05 22:30:13 +0200

      Commit message:


	  
		
 fix #424 on devel
 

    

  
    

      Package: CATALYST

      Commit: 6a1220abf5e154419fbb8d4a5d2ffcb40eef3839

      Author:  HelenaLC <helena@crowell.eu> 

      Date: 2025-09-21 11:54:11 +0200

      Commit message:


	  
		
 update roxygen & GHA
 

    

  
    

      Package: BiocCheck

      Commit: be1d6943badb02b0bb7283a10815c15e07349542

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2025-11-20 14:36:28 -0500

      Commit message:


	  
		
 version bump 1.47.2
 

    

  
    

      Package: BiocCheck

      Commit: dcc254b30b2dd24b55367cf4cbe467ac7dc4f423

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2025-11-20 14:35:45 -0500

      Commit message:


	  
		
 replace installAndLoad with .tryInstallwLoad
 

    

  
    

      Package: BiocCheck

      Commit: 6751e2804290e5c2bf297456e7a0e08386f128a4

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2025-11-20 14:19:58 -0500

      Commit message:


	  
		
 version bump RoxyenNote
 

    

  
    

      Package: BiocCheck

      Commit: 4bdfa8ae6282d9351dc6facecee54aea7b41d998

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2025-11-20 14:19:45 -0500

      Commit message:


	  
		
 add installation section to vignette
 

    

  
    

      Package: BiocCheck

      Commit: 234e47cbcaddb3e15d08c51b275891fd22008f6b

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2025-11-19 18:46:16 -0500

      Commit message:


	  
		
 add install dot option and document
 

    

  
    

      Package: BiocCheck

      Commit: 202c10d46eac9cbd3f38c810b923967b13d0a9f6

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2025-11-04 13:37:35 -0500

      Commit message:


	  
		
 version bump 1.47.1
 

    

  
    

      Package: BiocCheck

      Commit: 5236447bf2226b63529884b3dacf9fb7a3e5c06f

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2025-11-04 13:35:36 -0500

      Commit message:


	  
		
 minor update spacing
 

    

  
    

      Package: BiocCheck

      Commit: 8b552fd0ccee61ea43bed743afa73bb642345f1a

      Author:  LiNk-NY <marcel.ramos@sph.cuny.edu> 

      Date: 2025-11-04 13:35:27 -0500

      Commit message:


	  
		
 use default package size in checkPackageSize call
 

    

  
  


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