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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: VisiumIO
Commit: b0a2476b94cca19d8e4d286df4dcb5ee1e935f2c
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-10-09 12:50:25 -0400
Commit message:

 version bump 1.5.9
Package: VisiumIO
Commit: abf929a912d0c92d54dfadd393132ffa57da412a
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-10-09 12:46:15 -0400
Commit message:

 update spacerangeOut argument in docs (/outs optional)
Package: VisiumIO
Commit: 11c84de31da6a75e32a0eedf83a2b553df316134
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-10-09 12:45:29 -0400
Commit message:

 update function examples with /outs directories
Package: VisiumIO
Commit: 5acd1e5ab8253b4a298190f2b6a15e60aa2ac782
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-10-09 12:44:41 -0400
Commit message:

 update unit tests with /outs inputs
Package: VisiumIO
Commit: 247e58104757d2d45865a6dddf1cb4387f861ae3
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-10-09 12:44:16 -0400
Commit message:

 integrate .find_convert_resources and .find_convert_spatial with TENxVisium and TENxVisiumList
Package: VisiumIO
Commit: 2190a30775cc635ffbd8da8972d47eca409458c2
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-10-09 11:20:58 -0400
Commit message:

 remove elipses from .find_convert_resources
Package: VisiumIO
Commit: c543909830477301510a56c1ddfe7e86a2df4d67
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-10-09 11:15:53 -0400
Commit message:

 move segmented_outputs example
Package: VisiumIO
Commit: b442033d5f608d8a7d34548683d31c15621d6a93
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-10-09 10:56:40 -0400
Commit message:

 refactor .find_convert_resources and .find_convert_spatial
Package: tximeta
Commit: b9ca20590f496d1c93318f0a0b5617a823834973
Author: Mike Love <mikelove@users.noreply.github.com>
Date: 2025-10-09 12:24:11 -0400
Commit message:

 version bump
Package: tximeta
Commit: fd059a64e6c162db947850151a664ab07cf32dc4
Author: Mike Love <mikelove@users.noreply.github.com>
Date: 2025-10-09 12:20:11 -0400
Commit message:

 Merge branch 'devel' of github.com:thelovelab/tximeta into devel
Package: tximeta
Commit: 788c7ab44146d474e0c01d9da830d4cedf3c9cfb
Author: Mike Love <mikelove@users.noreply.github.com>
Date: 2025-10-09 12:17:29 -0400
Commit message:

 work on docs
Package: tximeta
Commit: 44a66cb040e960da8ec3ba8f0331078a20a389bc
Author: Michael Love <mikelove@users.noreply.github.com>
Date: 2025-10-09 12:11:36 -0400
Commit message:

 Merge pull request #93 from thelovelab/doc-edits

Fix some typos
Package: tximeta
Commit: 137f4ba9ab46b422de67df31b8598542c0317d66
Author: Charlotte Soneson <charlottesoneson@gmail.com>
Date: 2025-10-09 17:23:40 +0200
Commit message:

 Fix some typos
Package: COTAN
Commit: 6b2782c13ca6c32e85fc85c03901ef83c0f984e4
Author: trinetra75 <marco.fantozzi@gmail.com>
Date: 2025-10-09 17:51:25 +0200
Commit message:

 Updated NEWS.md and bumped-up version
Package: COTAN
Commit: 4b3385600755c5e6a90acfbeb93e6bab6f77038c
Author: Marco Fantozzi <57561972+trinetra75@users.noreply.github.com>
Date: 2025-10-09 13:17:13 +0200
Commit message:

 Bugfix: prob zero underflow error (#126)

* Solved underflow error in `funProbZero()`

Solved in related `torch` implementation too

Using `mc.preschedule = TRUE` for improved system stability

Solved issue with `COTAN.LogLevel` options:
it did have non trivial attribuites

* Updated test.dataset and associated saved test data.

* Updated test.dataset to more realistic example

* Aligned examples and fixed broken tests
Package: signeR
Commit: c48176749006baa5c45929ca8dfb48bd25101a80
Author: Renan Valieris <renan.valieris@accamargo.org.br>
Date: 2025-10-09 11:51:00 -0300
Commit message:

 Move VariantAnnotation from Depends to Imports
Package: spatialFDA
Commit: 5dd5cc2b2e0ca3dd59f5b8ea91a3b93057431961
Author: mjemons <martin.emons@gmail.com>
Date: 2025-10-09 16:22:54 +0200
Commit message:

 only returning transformed curves plus empty assays for better memory reqs
Package: benchdamic
Commit: 7c5727b9782c442daa52e579f993a1cfcfc522e3
Author: Matteo Calgaro <mcalgaro93@gmail.com>
Date: 2025-10-09 15:40:05 +0200
Commit message:

 Version bump in devel
Package: benchdamic
Commit: 3a4458a864ff801779ba7b33dacc897103dc52d3
Author: Matteo Calgaro <mcalgaro93@gmail.com>
Date: 2025-10-09 15:35:44 +0200
Commit message:

 Bug-fix: old p-value threshold was not working as expected. Changes in limma?
Package: benchdamic
Commit: ee6a4a1eeda92262d3716e97a51946be25645fc3
Author: Matteo Calgaro <mcalgaro93@gmail.com>
Date: 2025-10-09 15:34:37 +0200
Commit message:

 Roxygen changes
Package: GSVA
Commit: c0f8f6895bb8173a7ecf17f5389993b3fbac5c2d
Author: Robert Castelo <robert.castelo@upf.edu>
Date: 2025-10-09 15:17:55 +0200
Commit message:

 Fix gene mapping when input gene sets are in a GeneSetCollection object with NullIdentifier metadata. Added unit test to catch this type of errors
Package: CalibraCurve
Commit: e7a4c4338ac970d5fda3b4f5d961690766760549
Author: KarinSchork <karin.schork@rub.de>
Date: 2025-10-09 14:49:59 +0200
Commit message:

 version bump
Package: CalibraCurve
Commit: 9c8d1646bbb84ae89f54a94a79ffd8c726ab6e74
Author: KarinSchork <karin.schork@rub.de>
Date: 2025-10-09 13:32:00 +0200
Commit message:

 fix bug in saving result as rds file
Package: rhdf5
Commit: 919a739fe5cc4e1b8e862c15d75a5b636975f3fc
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-10-09 11:30:36 +0200
Commit message:

 Bump patch version
Package: rhdf5
Commit: 242793eefa4ecbc6205f24d10b55e391d83679b3
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-10-09 11:30:22 +0200
Commit message:

 Mention cset removal in NEWS
Package: rhdf5
Commit: b212227b7aaf4ec5267203bff33502fac209390e
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-10-09 11:26:03 +0200
Commit message:

 Remove deprecated cset argument
Package: DOtools
Commit: 95e75eedf408d3955bcf21d1cf635fe5404b8709
Author: MarianoRuzJurado <mariani95@gmx.de>
Date: 2025-10-09 11:46:33 +0200
Commit message:

 Merge remote-tracking branch 'upstream/devel' into devel
Package: DOtools
Commit: 953c06f94a914e38b72246eda3ab7b67fc36e967
Author: MarianoRuzJurado <mariani95@gmx.de>
Date: 2025-10-06 16:02:42 +0200
Commit message:

 -Fixed a bug in VlnPlot
Package: mobileRNA
Commit: 6098b4efb9d03cfbfb88372a36741139b6508f1e
Author: KJeynesCupper <kejc@illinois.edu>
Date: 2025-10-08 23:41:11 -0500
Commit message:

 updated version
Package: mobileRNA
Commit: 90a2da70fbc590d1259b9840496ae14da1bad087
Author: KJeynesCupper <kejc@illinois.edu>
Date: 2025-10-08 22:25:25 -0500
Commit message:

 mobile detection options

removed baymobil draft changes
Package: BiocGenerics
Commit: 9b179a49370a4fd575b50ab93d76b5e69567ee25
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2025-10-08 17:56:44 -0700
Commit message:

 BiocGenerics 0.55.3: Better fix for updateObject() infinite recursion

Replace workaround implemented in commit fbeb3e6 with a fix that actually
addresses the real problem (which is that updateObject() was broken on
an environment that contains itself).
Package: hpAnnot
Commit: 09db666516ae994a1e025a87bea248cc6cca0e0b
Author: Marta Hidalgo <marta.hidalgo@outlook.es>
Date: 2025-10-09 01:01:00 +0200
Commit message:

 adding AnnotationHub to dependencies of the package, and bumping to 1.1.1
Package: DominoEffect
Commit: 4c767bddece157eae7e863d72d67ca42088c9c0e
Author: Peter Blattmann <peter_blattmann@bluewin.ch>
Date: 2025-10-09 00:00:06 +0200
Commit message:

 Merge branch 'devel' of git.bioconductor.org:packages/DominoEffect into devel
Package: DominoEffect
Commit: 94fdafffab63282cd8b6a4f0f0269b08e9cbccd3
Author: Peter Blattmann <peter_blattmann@bluewin.ch>
Date: 2025-10-08 23:59:37 +0200
Commit message:

 v1.29.4: Put Maintainer on same line
Package: SWATH2stats
Commit: ab821f654b1bf94ca44eaf89ab038017633da1d5
Author: Peter Blattmann <peter_blattmann@bluewin.ch>
Date: 2025-10-08 23:49:10 +0200
Commit message:

 Merge branch 'devel' of git.bioconductor.org:packages/SWATH2stats into devel
Package: SWATH2stats
Commit: 3554e9701e164361b497c4b95c788c079b8620a6
Author: Peter Blattmann <peter_blattmann@bluewin.ch>
Date: 2025-10-08 23:46:21 +0200
Commit message:

 v1.33.2: updated some tests with all.equal that failed
Package: BatchQC
Commit: d9e3b44e4fbf3e6b87236d607972bd641cbe8653
Author: jessmcc22Mac <jessmcc@bu.edu>
Date: 2025-10-08 17:16:40 -0400
Commit message:

 Updated line character count
Package: BatchQC
Commit: 01361f976943932bbdd4b60633f14449be6811e4
Author: jessmcc22Mac <jessmcc@bu.edu>
Date: 2025-10-08 16:27:42 -0400
Commit message:

 Update version and News description
Package: BatchQC
Commit: 17e1f093666c8eefc1731e618d92d6728be38995
Author: Jessica <102758461+jessmcc22@users.noreply.github.com>
Date: 2025-10-08 16:18:15 -0400
Commit message:

 Merge pull request #129 from jessmcc22/devel

Updated Vignette, UMAP example, and kBET tab location
Package: BatchQC
Commit: 890fae7af7ed51643f1732745a5ecf3e8ae5b4a4
Author: Jessica <102758461+jessmcc22@users.noreply.github.com>
Date: 2025-10-08 16:17:29 -0400
Commit message:

 Merge branch 'wejlab:devel' into devel
Package: BatchQC
Commit: f0446345438771ec66de2eee783edf9c96133c38
Author: jessmcc22Mac <jessmcc@bu.edu>
Date: 2025-10-08 16:16:36 -0400
Commit message:

 Updated vignette to reflect new BatchQC tools (distribution checks, kBET, UMAP) and to use TB example data
Package: BatchQC
Commit: 3f7624d62da28077776926e401a04911e06027e4
Author: jessmcc22Mac <jessmcc@bu.edu>
Date: 2025-10-08 16:15:33 -0400
Commit message:

 Updated placement of the kBET tab in shiny app
Package: BatchQC
Commit: 4818f611bcfeab023b7c7251fa6665e6ca5e04f1
Author: jessmcc22Mac <jessmcc@bu.edu>
Date: 2025-10-08 16:15:10 -0400
Commit message:

 Added covar variable to example in UMAP function
Package: BatchQC
Commit: 658a5d7b82fd20083e44d676afc17d20b28cd2bf
Author: jessmcc22Mac <jessmcc@bu.edu>
Date: 2025-10-08 16:14:38 -0400
Commit message:

 Corrected negative binomial sampled logic
Package: BiocGenerics
Commit: 18f498b2fc9898960b9ee79a91f8c66266f0389a
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2025-10-08 13:12:36 -0700
Commit message:

 oops
Package: wiggleplotr
Commit: 1de21b24fed0499d7b3691bb3735765428ff1e71
Author: Kaur Alasoo <kauralasoo@gmail.com>
Date: 2025-10-08 23:02:14 +0300
Commit message:

 Update DESCRIPTION
Package: wiggleplotr
Commit: c8306c4d4c993e58044f67b2db5e4b67c8af6a09
Author: Kaur Alasoo <kauralasoo@gmail.com>
Date: 2025-10-08 22:57:27 +0300
Commit message:

 Update vignette.
Package: wiggleplotr
Commit: e32334e92fbe52b40f3619fc20fdc6f4a1e926b9
Author: Kaur Alasoo <kauralasoo@gmail.com>
Date: 2025-10-08 22:30:03 +0300
Commit message:

 Merge remote-tracking branch 'upstream/devel'
Package: wiggleplotr
Commit: bcb4decc5d05b0296c74cb85c880d4122fffff65
Author: Kaur Alasoo <kauralasoo@gmail.com>
Date: 2022-06-27 22:54:46 +0300
Commit message:

 Merge pull request #23 from kauralasoo/coverage_refactor

Coverage refactor
Package: wiggleplotr
Commit: b397b07dd853f573cac6390a079814466c8de90c
Author: Kaur Alasoo <kauralasoo@gmail.com>
Date: 2022-06-27 22:52:51 +0300
Commit message:

 Merge pull request #22 from kerimoff/coverage_refactor

added show_legend options
Package: wiggleplotr
Commit: e109f07f5d805894cc82875bd076df808f5e420c
Author: Kaur Alasoo <kauralasoo@gmail.com>
Date: 2022-06-27 22:49:30 +0300
Commit message:

 Update documentation for show legend
Package: wiggleplotr
Commit: 443f2f7a38257f7c679baa93fe8e8587e0ab18fa
Author: Nurlan Kerimov <34273025+kerimoff@users.noreply.github.com>
Date: 2022-06-26 13:45:59 +0300
Commit message:

 added show_legend options
Package: wiggleplotr
Commit: d3a0ca8975cafabd81a0150e6e699d4742155557
Author: Kaur Alasoo <kauralasoo@gmail.com>
Date: 2022-06-21 15:22:31 +0300
Commit message:

 Refactor plotCoverage to separate data preparation code from the plotting code.
Package: wiggleplotr
Commit: 30d66f6fac374b2070cc9d54ac93ce689608a817
Author: Kaur Alasoo <kaur.alasoo@gmail.com>
Date: 2021-07-16 15:30:20 +0300
Commit message:

 Merge pull request #13 from matmu/patch-1

Update wiggleplotr.R
Package: wiggleplotr
Commit: 00a4819feb7d22dee2a1c62147db1f9da991aa4b
Author: Matthias Munz <matthias.munz@gmx.de>
Date: 2021-07-15 16:36:25 +0200
Commit message:

 Update wiggleplotr.R

If empty list of GRanges objects is passed for cdss, an error is returned.
Package: BiocGenerics
Commit: fbeb3e695c5d0584ca47952c1e813f9c2fc7f488
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2025-10-08 12:10:48 -0700
Commit message:

 BiocGenerics 0.55.2: Fix updateObject() on old ggplot instances

This implements a workaround to avoid the infinite recursion that
we get when calling updateObject() on an old ggplot instance.
Package: SpiecEasi
Commit: 4275055ceb6f9bfe4c2b4aa13bb8e1b1932cb488
Author: Zachary Kurtz <zdkurtz@gmail.com>
Date: 2025-10-08 13:25:13 -0400
Commit message:

 update docs
Package: SpiecEasi
Commit: 25484230b21d084dc91fbfaff7b138bfcc15393e
Author: Zachary Kurtz <zdkurtz@gmail.com>
Date: 2025-10-08 13:07:55 -0400
Commit message:

 better vignette caches
Package: MetaProViz
Commit: 4e6a9a47b90a995fa9feac1b78449dcbb1805d52
Author: Christina Schmidt <christina.schmidt1@outlook.de>
Date: 2025-10-08 19:20:37 +0200
Commit message:

 Bump version: 3.99.3 → 3.99.4
Package: MetaProViz
Commit: 255e5e31ca03b2eb2a2aac62c60ddc243deed4cb
Author: Christina Schmidt <christina.schmidt1@outlook.de>
Date: 2025-10-08 19:20:19 +0200
Commit message:

 Fixed error in @example syntax error in equivalent_id
Package: TBSignatureProfiler
Commit: 5cd5fd2459ac59026da7109a6d8e2399c7527ad2
Author: lshep <lori.shepherd@roswellpark.org>
Date: 2025-10-08 11:39:01 -0400
Commit message:

 Fix broken description
Package: seqArchR
Commit: 444c04b1913666aff75639cf25ffb07cef29b070
Author: lshep <lori.shepherd@roswellpark.org>
Date: 2025-10-08 11:35:06 -0400
Commit message:

 Deprecated

 - unresponsive
Package: BatChef
Commit: 674535ce50bb0df79f80e06f3e582d56c82e9a9c
Author: zuinelena3 <elena.zuin3@gmail.com>
Date: 2025-10-08 17:31:41 +0200
Commit message:

 Bump version: 0.99.2
Package: seqArchRplus
Commit: 6959746ffeba2cbc3e5828e76941ac28bff9ef0e
Author: lshep <lori.shepherd@roswellpark.org>
Date: 2025-10-08 11:28:20 -0400
Commit message:

 deprecate

 - unresponsive
Package: MetaProViz
Commit: fe6b26af2510924c91e4a60e69f4c087d423c854
Author: deeenes <turei.denes@gmail.com>
Date: 2025-10-08 16:25:36 +0200
Commit message:

 Bump version: 3.99.2 → 3.99.3
Package: MetaProViz
Commit: d23622a0e46203c4b274595f0b494596de64f790
Author: deeenes <turei.denes@gmail.com>
Date: 2025-10-08 16:25:25 +0200
Commit message:

 Merge branch 'devel' of github.com:saezlab/MetaProViz into devel
Package: MetaProViz
Commit: 66a8882190d3c4dab65f23de3b0c0d662d9eddf6
Author: deeenes <turei.denes@gmail.com>
Date: 2025-10-08 16:25:19 +0200
Commit message:

 docs rebuild
Package: MetaProViz
Commit: 9ed3f8684717c7622464dda710e393c4cbe4adde
Author: deeenes <turei.denes@gmail.com>
Date: 2025-10-08 16:23:54 +0200
Commit message:

 `compare_pk`: disabled docstring examples due to complexUpset issue on build servers
Package: SPICEY
Commit: 9164b4b1e62233f582db88c68fbf531d57e39121
Author: georginafp <georgina.fuentes@upf.edu>
Date: 2025-10-08 17:14:07 +0200
Commit message:

 Update README file with new heatmap plot
Package: bgx
Commit: ada6b7d2ecdf866ed24fbac6ea69670a7dc80ca7
Author: lshep <lori.shepherd@roswellpark.org>
Date: 2025-10-08 11:12:18 -0400
Commit message:

 Deprecated

 - unresponsive
Package: SPICEY
Commit: b2b9104cdd0c5f3c9a2e3fe2f7b8075601a6436e
Author: georginafp <georgina.fuentes@upf.edu>
Date: 2025-10-08 16:54:37 +0200
Commit message:

 Change to normal SPICEY scores in heatmap, update vignette, news and description file
Package: VisiumIO
Commit: c17c6639fc6274d4e159dd5b3adbb925f0a6c85a
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-10-07 16:47:18 -0400
Commit message:

 version bump 1.5.8
Package: VisiumIO
Commit: 445f5f5b3e396e64a99c7d4d04562d9a4aef7531
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-10-07 16:47:13 -0400
Commit message:

 minor: add spaces
Package: VisiumIO
Commit: 45ee2b0fcd136df77d8b470affd4fa55d17817b3
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-10-07 16:46:59 -0400
Commit message:

 update supported formats
Package: VisiumIO
Commit: 3daef412f32cfac76fefef573e7abaee041e4e0b
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-10-07 16:33:35 -0400
Commit message:

 reset cache and use version
Package: ProteinGymR
Commit: 7a3382040dae6f8f507ed07ee38219a9a48b699a
Author: tram-nguyen-n <tram_nguyen@hms.harvard.edu>
Date: 2025-10-06 14:34:00 +0000
Commit message:

 bump devel
Package: ProteinGymR
Commit: f723aac091750b811b3c863612862fbd95fab23a
Author: tram-nguyen-n <tram_nguyen@hms.harvard.edu>
Date: 2025-10-06 14:31:22 +0000
Commit message:

 center the annotations
Package: ProteinGymR
Commit: 2dcf2efcd0a7c75eaae4ffcf33559a9c9e729f73
Author: tram-nguyen-n <tram_nguyen@hms.harvard.edu>
Date: 2025-10-06 14:29:34 +0000
Commit message:

 removed `gghalves` and instead use point jitter
Package: ProteinGymR
Commit: 46b6c8c6c5cc78c865c2e7cb00ff9eceece39786
Author: tram-nguyen-n <tram_nguyen@hms.harvard.edu>
Date: 2025-09-26 16:09:21 +0000
Commit message:

 bump devel
Package: ProteinGymR
Commit: 2b1337eb07e9d4e18036426cfe05f1c42694e504
Author: tram-nguyen-n <tram_nguyen@hms.harvard.edu>
Date: 2025-09-26 16:09:04 +0000
Commit message:

 correct package for `colorRamp2` function
Package: MetaProViz
Commit: 35b8935bbee6bf77a265b89d1d7446bb7b1fc068
Author: Christina Schmidt <christina.schmidt1@outlook.de>
Date: 2025-10-08 15:18:23 +0200
Commit message:

 Merge pull request #118 from saezlab/main

Merge pull request #117 from saezlab/devel
Package: MetaProViz
Commit: 08a370d8fc0eb77d35d200f9841857c723208c30
Author: Christina Schmidt <christina.schmidt1@outlook.de>
Date: 2025-10-08 15:14:58 +0200
Commit message:

 moved citation into inst
Package: MetaProViz
Commit: 6907d0142a01b2810fb31cb11c835413635b37de
Author: Christina Schmidt <christina.schmidt1@outlook.de>
Date: 2025-10-08 15:04:55 +0200
Commit message:

 Bump version: 3.99.1 → 3.99.2
Package: MetaProViz
Commit: fc52fb836e61de4f7b82c0a8931cf1ad2497d148
Author: Christina Schmidt <christina.schmidt1@outlook.de>
Date: 2025-10-08 15:02:37 +0200
Commit message:

 Create CITATION
Package: MetaProViz
Commit: 2e60e74eb290663d758a9983dfd76ea712a55b22
Author: deeenes <turei.denes@gmail.com>
Date: 2025-10-08 14:53:40 +0200
Commit message:

 removed `MetaProViz.Rproj` from git tracking
Package: MetaProViz
Commit: 9ecbd3367de570e10a69aa4a8c414184eea6bff8
Author: Christina Schmidt <christina.schmidt1@outlook.de>
Date: 2025-10-08 14:01:36 +0200
Commit message:

 Merge pull request #117 from saezlab/devel

Merge devel into main
Package: MetaProViz
Commit: d4eaca70c358311ac2d09303c4addf3e630519dc
Author: deeenes <turei.denes@gmail.com>
Date: 2025-10-07 23:49:47 +0200
Commit message:

 Bump version: 3.99.0 → 3.99.1
Package: MetaProViz
Commit: 6ec3153f795a4088ebb044952ee126731ea907c9
Author: deeenes <turei.denes@gmail.com>
Date: 2025-10-07 23:42:51 +0200
Commit message:

 moved pkgdown only vignettes to `vignettes/pkgdown`
Package: MetaProViz
Commit: 1d58cb2a0ddfba729f3af5b9694c53dca0a0e811
Author: deeenes <turei.denes@gmail.com>
Date: 2025-10-07 23:40:32 +0200
Commit message:

 updated `pkgdown` site articles section layout
Package: MetaProViz
Commit: d03d98abc1e5958802b3649ae93b226eb74ea104
Author: deeenes <turei.denes@gmail.com>
Date: 2025-10-07 17:30:08 +0200
Commit message:

 updated title of main vignette
Package: MetaProViz
Commit: a71874f2a8b6ef1e095cf3ed0b863758b1971fae
Author: Christina Schmidt <christina.schmidt1@outlook.de>
Date: 2025-10-07 14:44:45 +0200
Commit message:

 Create quick-overview.Rmd
Package: MetaProViz
Commit: 6ef6306fe8bef5fe7aeb8d2dbb81a392ae84a8b0
Author: Christina Schmidt <christina.schmidt1@outlook.de>
Date: 2025-10-07 10:34:10 +0200
Commit message:

 Merge branch 'devel' of github.com:saezlab/MetaProViz into devel
Package: MetaProViz
Commit: c748e033c24bce60fc5de2783dc97a79f364e395
Author: jannikfranken <jannik8513@gmail.com>
Date: 2025-10-06 23:23:56 +0100
Commit message:

 fixed missing space issue of strings which originated due to line breaks
Package: MetaProViz
Commit: b4631c63dd9d5bb0fd6210f35a0ea4a2a965c7bd
Author: jannikfranken <jannik8513@gmail.com>
Date: 2025-10-06 10:49:12 +0100
Commit message:

 test push
Package: MetaProViz
Commit: 38a2b67dbf424213b86fb88885ad29f673076cb3
Author: jannikfranken <jannik8513@gmail.com>
Date: 2025-10-03 11:47:41 +0100
Commit message:

 test push
Package: MetaProViz
Commit: 810e3a58cf460bb6e65bb2d3456cdf83868b31cd
Author: jannikfranken <jannik8513@gmail.com>
Date: 2025-10-02 17:41:08 +0100
Commit message:

 typo
Package: MetaProViz
Commit: c5488cd03ceafdbd826094cd5da7c50734c261e7
Author: jannikfranken <jannik8513@gmail.com>
Date: 2025-10-02 16:46:57 +0100
Commit message:

 code formatting of compare_pk function
Package: MetaProViz
Commit: 469aa5bbd31c68c26787c3e072417fe14c535f4c
Author: jannikfranken <jannik8513@gmail.com>
Date: 2025-10-02 16:27:33 +0100
Commit message:

 code formatting of add_info function
Package: MetaProViz
Commit: e1b724ecfb9439c6c85b2aaaeb4c3d24fc97a56c
Author: jannikfranken <jannik8513@gmail.com>
Date: 2025-10-02 16:24:17 +0100
Commit message:

 fixed small error due to missing comma
Package: MetaProViz
Commit: 8fd6e961577191a351fcd1f12d889b74edab45ca
Author: jannikfranken <jannik8513@gmail.com>
Date: 2025-10-02 16:02:21 +0100
Commit message:

 fixed small error due to missing comma in string concatenation
Package: MetaProViz
Commit: 88f233227cdc7325a30466bd191eee28fd676373
Author: jannikfranken <jannik8513@gmail.com>
Date: 2025-10-02 16:00:52 +0100
Commit message:

 code formatting of cluster_pk function
Package: MetaProViz
Commit: e2007325e3700966cc8ce4470df77473a25f2af5
Author: jannikfranken <jannik8513@gmail.com>
Date: 2025-10-02 15:31:45 +0100
Commit message:

 code formatting of checkmatch_pk_to_data function
Package: MetaProViz
Commit: 2725d1b4fc0b83133a51300992270bf3315a4b8a
Author: jannikfranken <jannik8513@gmail.com>
Date: 2025-10-02 12:33:49 +0100
Commit message:

 code formatting of mapping_ambiguity function
Package: MetaProViz
Commit: 7635f7f16933cb3e57867264ab971dd822da0726
Author: jannikfranken <jannik8513@gmail.com>
Date: 2025-10-02 11:48:32 +0100
Commit message:

 code formatting of equivalent_id function
Package: MetaProViz
Commit: b3a001d6b994bccab45babbb51e0e4e1e3a17984
Author: jannikfranken <jannik8513@gmail.com>
Date: 2025-10-02 11:27:43 +0100
Commit message:

 code formatting of translate_id function
Package: MetaProViz
Commit: dabebeb49a92ad9cb0aa20fab94e5623c6349eac
Author: jannikfranken <jannik8513@gmail.com>
Date: 2025-10-01 16:42:54 +0100
Commit message:

 changed indentation after error
Package: MetaProViz
Commit: e0f2e6799beab751299afcf33db7211e63431d97
Author: jannikfranken <jannik8513@gmail.com>
Date: 2025-10-01 16:29:26 +0100
Commit message:

 code formatting on vst function
Package: MetaProViz
Commit: b37cce93b22482502a20487f68268adae4da0ccf
Author: jannikfranken <jannik8513@gmail.com>
Date: 2025-10-01 16:24:35 +0100
Commit message:

 code formatting for barlett function
Package: MetaProViz
Commit: 87c46351f91ecfc47611687ac50dea045174544f
Author: jannikfranken <jannik8513@gmail.com>
Date: 2025-10-01 16:18:54 +0100
Commit message:

 code formatting on shapiro function
Package: MetaProViz
Commit: 49f7c4bea23838a901405948f335bfa3475e51ec
Author: jannikfranken <jannik8513@gmail.com>
Date: 2025-10-01 15:45:58 +0100
Commit message:

 code formatting of dma_stat_limma function
Package: MetaProViz
Commit: 8501d13d1d7564a7258190dd5173f1f79d044e0d
Author: jannikfranken <jannik8513@gmail.com>
Date: 2025-10-01 15:27:56 +0100
Commit message:

 code formatting welch function
Package: MetaProViz
Commit: f6cd2a5517a8018675ca2e5ca56d4d7fb9d82fc8
Author: jannikfranken <jannik8513@gmail.com>
Date: 2025-10-01 14:51:12 +0100
Commit message:

 code formatting of kruskal function
Package: MetaProViz
Commit: f91045abae919c43e801b112b95526de409d7663
Author: jannikfranken <jannik8513@gmail.com>
Date: 2025-10-01 14:32:00 +0100
Commit message:

 code formatting on aov function
Package: MetaProViz
Commit: 7aa25affa4e0cfd07d91445c427578ca9a64c330
Author: jannikfranken <jannik8513@gmail.com>
Date: 2025-10-01 14:05:11 +0100
Commit message:

 code formatting of dma_stat_single function
Package: MetaProViz
Commit: d42ec60e1ee3b613c0cb1be25b981ee57ed9cf28
Author: Christina Schmidt <christina.schmidt1@outlook.de>
Date: 2025-09-26 12:03:15 +0200
Commit message:

 Bump version: 3.1.3 → 3.2.0
Package: rRDPData
Commit: 89850140184ad1b375f489ec265d5d23d3a8f395
Author: lshep <lori.shepherd@roswellpark.org>
Date: 2025-10-08 08:10:50 -0400
Commit message:

 Deprecated

 - requested on bioc-devel
Package: rRDP
Commit: 03187f384e6717afe226b33776755722abab8335
Author: lshep <lori.shepherd@roswellpark.org>
Date: 2025-10-08 08:06:46 -0400
Commit message:

 Deprecate

 - requested on bioc-devel
Package: TFEA.ChIP
Commit: 64f087ff3875a8c33e40fdff39cf54394a5c0d79
Author: yosra <yosraberrouayel@gmail.com>
Date: 2025-10-08 10:18:03 +0200
Commit message:

 cite biorxiv
Package: plaid
Commit: b45a5b01abb9465d8501dd0979c66b06ce8a57d1
Author: ESCRI11 <xavier.escriba.montagut@gmail.com>
Date: 2025-10-08 09:54:40 +0200
Commit message:

 antonino registered to support
Package: igblastr
Commit: 48ab9429b2271c83fdf748531def482b6c4ebe44
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2025-10-08 00:00:07 -0700
Commit message:

 igblastr 0.99.22: Add examples of TCR analysis with igblastn()

The man page for igblastn() and package vignette now contain examples
of TCR analysis with igblastn().

Also add and document rm_germline_db() to remove a germline db from
igblastr's persistent cache. See '?rm_germline_db'.
Package: ceRNAnetsim
Commit: 8f8fbe111841725c8d9cb318da45eac37e746575
Author: selcenari <selcenarii@gmail.com>
Date: 2025-10-08 09:28:14 +0300
Commit message:

 version bump in devel
Package: ceRNAnetsim
Commit: 5cd8ed47a6172fa44211b250fb92e7da335a8f5c
Author: selcenari <selcenarii@gmail.com>
Date: 2025-10-08 09:27:40 +0300
Commit message:

 fixing test of ggplot2
Package: ceRNAnetsim
Commit: b022f58716dab171acb382c6610c6ac8c25cd282
Author: selcenari <selcenarii@gmail.com>
Date: 2025-10-08 08:39:33 +0300
Commit message:

 Merge branch 'devel' of git.bioconductor.org:packages/ceRNAnetsim into devel
Package: ceRNAnetsim
Commit: 7452858c7482430cf5c5dce338f6f2aa3883c6f5
Author: selcenari <selcenarii@gmail.com>
Date: 2023-12-18 12:05:04 +0300
Commit message:

 dev clone issue
Package: BreastSubtypeR
Commit: 2b6f00c078e6c5922e095c1d55849b3e2524b56e
Author: Qiao Yang <yq.kiuo@gmail.com>
Date: 2025-10-08 07:14:05 +0200
Commit message:

 v1.1.6 Add: Citation
Package: Rsubread
Commit: cadf5b34fb42f3d8b3ac3dbf4ea2ebe82da4dc1e
Author: Yang Liao (Monash University) <yliao@m3-login2.massive.org.au>
Date: 2025-10-08 15:10:13 +1100
Commit message:

 removed warning from cellCounts.
Package: Rsubread
Commit: fe8f1e6b81dc8645480a946f11653fdd39a93e52
Author: Yang Liao (Monash University) <yliao@m3-login2.massive.org.au>
Date: 2025-10-08 15:00:16 +1100
Commit message:

 removed all warnings from R check
Package: ClassifyR
Commit: ecbb2eb069225a3264e43af0f7aefff14572ef95
Author: Dario Strbenac <dario@maths.usyd.edu.au>
Date: 2025-10-08 10:00:06 +1100
Commit message:

 Precision pathways gains an all-combinations-of-all-subsets mode.
Package: ClassifyR
Commit: a1abc9c477097593bea870f62e505d049cd5083b
Author: Dario Strbenac <dario@maths.usyd.edu.au>
Date: 2025-08-28 10:50:05 +1000
Commit message:

 - User-specified lambda parameter no longer ignored by penalised regression functions.
- k-NN preset option for 1 to 5 nearest restored.
Package: ClassifyR
Commit: e3b87965be0342832cb9c833255975a339621da1
Author: Dario Strbenac <dario@maths.usyd.edu.au>
Date: 2025-08-26 22:30:26 +1000
Commit message:

 If tuning parameters are specified but tuneMode left at default of "none", gracefully handled.
Package: vidger
Commit: 213dc463ff43c1af21f571ba528263b435c4a110
Author: Brandon Monier <brandon.monier@gmail.com>
Date: 2025-10-07 16:50:17 -0500
Commit message:

 Version bump
Package: vidger
Commit: 6fc52fdb923f35f97d95f9e5ac1d857db84eb63d
Author: Brandon Monier <brandon.monier@gmail.com>
Date: 2025-10-07 16:40:42 -0500
Commit message:

 Merge remote-tracking branch 'upstream/devel'
Package: vidger
Commit: 51e683a0f6c031be83c8689b4033c5163479d8da
Author: Brandon Monier <brandon.monier@gmail.com>
Date: 2025-10-07 16:40:38 -0500
Commit message:

 Version bump
Package: vidger
Commit: 589383e2f6860381a70c1f4fd0e6f3f429102f1d
Author: Brandon Monier <brandon.monier@gmail.com>
Date: 2025-10-07 16:05:43 -0500
Commit message:

 Fix S7 and data return issues
Package: vidger
Commit: 2d12a26409428d9e73e27217957d57f5f1cf8975
Author: Brandon Monier <brandon.monier@gmail.com>
Date: 2025-10-07 14:42:41 -0500
Commit message:

 Merge remote-tracking branch 'origin/RELEASE_3_9'
Package: vidger
Commit: fb90c0af75f42a7421ca0110e3bd1f7e9da2a0a2
Author: Brandon Monier <brandon.monier@gmail.com>
Date: 2019-07-15 15:36:09 -0400
Commit message:

 Version bump
Package: vidger
Commit: a60929f3a7544b95cabe6cc32b2ca79bad75dfc4
Author: Brandon Monier <brandon.monier@gmail.com>
Date: 2019-07-15 15:35:40 -0400
Commit message:

 bug fix: stat annotation error on matrix functions
Package: vidger
Commit: b8dd28a313dcdee29a44078c54f84e4b139a5ba5
Author: Brandon Monier <brandon.monier@gmail.com>
Date: 2019-07-15 15:35:12 -0400
Commit message:

 Add new badges; modify installation procedure
Package: vidger
Commit: 5f565cab6d9845730230b0cae3a3771e34639748
Author: Brandon Monier <brandon.monier@gmail.com>
Date: 2019-07-15 15:34:17 -0400
Commit message:

 Add Rproj extensions
Package: vidger
Commit: 51fbf8682aeb30dccf10577bcb6f0247eff0e9b0
Author: Brandon Monier <brandon.monier@gmail.com>
Date: 2019-07-15 15:33:51 -0400
Commit message:

 Remove appveyor check
Package: vidger
Commit: 60b2da444d1880d30d6ed83e03f89dfa01b66565
Author: Brandon Monier <brandon.monier@gmail.com>
Date: 2019-07-15 15:32:30 -0400
Commit message:

 Initial commit
Package: vidger
Commit: 5bf4e20d453fd4855b0679627064e4f611c1e295
Author: Brandon Monier <brandon.monier@gmail.com>
Date: 2019-07-15 15:06:09 -0400
Commit message:

 update RELEASE version 3.9
Package: vidger
Commit: 64b01f739ed98e352e1843f6127d6afe53617da1
Author: Brandon Monier <brandon.monier@gmail.com>
Date: 2019-07-15 14:58:59 -0400
Commit message:

 update RELEASE 3.9
Package: vidger
Commit: c75ca974f1816a97e4c575d91831f63cacf7ff5f
Author: Brandon Monier <brandon.monier@gmail.com>
Date: 2019-07-07 15:10:46 -0400
Commit message:

 bug fix: stat annotation error on matrix functions
Package: vidger
Commit: 1e535a62422a5510833d44cf490b43389a7a0940
Author: Brandon Monier <brandon.monier@gmail.com>
Date: 2019-07-07 15:05:25 -0400
Commit message:

 bug fix: stat annotation error on matrix functions
Package: RAIDS
Commit: 3a182ebc4dabdf0cc70362e74bc1efe9d7754151
Author: belleau <belleau@gyges.cshl.edu>
Date: 2025-10-07 16:32:58 -0400
Commit message:

 Version bump in devel
Package: RAIDS
Commit: fce9d5affe136a144c043b2682ab47044b63d6e3
Author: belleau <belleau@gyges.cshl.edu>
Date: 2025-10-07 16:28:43 -0400
Commit message:

 Merge remote-tracking branch 'origin/main'
Package: RAIDS
Commit: 259ecb9c392187b167a2a1ecc56f3a4ae97184ec
Author: Astrid Deschênes <adeschen@users.noreply.github.com>
Date: 2025-09-16 17:51:43 -0400
Commit message:

 Merge pull request #615 from adeschen/main

Update of the github action check-bioc
Package: RAIDS
Commit: e52e06a1457fa1939566e9b0aea20f6dbd3a67b4
Author: Astrid Deschênes <adeschen@users.noreply.github.com>
Date: 2025-09-16 16:34:58 -0400
Commit message:

 Merge branch 'KrasnitzLab:main' into main
Package: RAIDS
Commit: 9d1655cb6001ae0b29bc2024ba268d905ee46f56
Author: Astrid Deschênes <adeschen@users.noreply.github.com>
Date: 2025-09-16 14:54:59 -0400
Commit message:

 Merge pull request #11 from adeschen/adeschen-patch-2

Update check-bioc.yaml
Package: RAIDS
Commit: 5a07c2af590ea86144954d13e31ee2998e3ba45c
Author: Astrid Deschênes <adeschen@users.noreply.github.com>
Date: 2025-09-16 14:54:25 -0400
Commit message:

 Update check-bioc.yaml
Package: RAIDS
Commit: 24f9cad7f6e3f54b07886c5a638817b2fcefd345
Author: Astrid Deschênes <adeschen@users.noreply.github.com>
Date: 2025-09-16 14:50:12 -0400
Commit message:

 Update check-bioc.yaml
Package: RAIDS
Commit: 6c6b9fe2bdebf7f67625bd4822be28c52262f4a0
Author: Astrid Deschênes <adeschen@users.noreply.github.com>
Date: 2025-09-16 14:47:30 -0400
Commit message:

 Merge pull request #10 from adeschen/adeschen-patch-1

Adeschen patch 1
Package: RAIDS
Commit: 9784d60ab4654210eec9c3c4d5a05d2c57ae5cdb
Author: Astrid Deschênes <adeschen@users.noreply.github.com>
Date: 2025-09-16 14:45:53 -0400
Commit message:

 Update check-bioc.yaml
Package: RAIDS
Commit: 0c0ccf41245ad3f0669bdd0b168fd642d6a957d0
Author: Astrid Deschênes <adeschen@users.noreply.github.com>
Date: 2025-09-16 14:43:06 -0400
Commit message:

 Update check-bioc.yaml
Package: RAIDS
Commit: 10df291231a418cf9a9404d8fb5d8427f819b4ab
Author: Astrid Deschênes <adeschen@users.noreply.github.com>
Date: 2025-09-16 00:00:18 -0400
Commit message:

 Update check-bioc.yaml
Package: RAIDS
Commit: 3731d5a45e612f275717b80718ec79a8ca6adfa7
Author: Astrid Deschênes <adeschen@users.noreply.github.com>
Date: 2025-09-15 23:57:13 -0400
Commit message:

 Update check-bioc.yaml
Package: RAIDS
Commit: 08c7adf7527840e0102f6109c5b8921381695450
Author: Astrid Deschênes <adeschen@users.noreply.github.com>
Date: 2025-09-15 21:06:52 -0400
Commit message:

 Update check-bioc.yaml
Package: RAIDS
Commit: dc4987d5c0244ab8d43847bd108d7644fc339948
Author: adeschen <adeschen@hotmail.com>
Date: 2025-09-11 12:50:15 -0400
Commit message:

 Update check-bioc actions
Package: RAIDS
Commit: ea520d437f0f8afe3e386c7f166b8812ef91a9a9
Author: Astrid Deschênes <adeschen@users.noreply.github.com>
Date: 2025-09-11 12:47:54 -0400
Commit message:

 Merge pull request #613 from adeschen/main

Update default parameter in snpgdsIBDKING() function and adjust unit test
Package: RAIDS
Commit: 60ce1ba43c8b5a127ac176cb9ac468ed0c2a44c6
Author: adeschen <adeschen@hotmail.com>
Date: 2025-09-10 18:29:39 -0400
Commit message:

 Update R version for github action
Package: RAIDS
Commit: 6b31ab3f7ad692ca728765a2c06d4173f16af442
Author: adeschen <adeschen@hotmail.com>
Date: 2025-09-10 18:24:19 -0400
Commit message:

 Update default version for github action
Package: RAIDS
Commit: 283fcdb51beef18f1f9e545a637948bc4dc1e442
Author: adeschen <adeschen@hotmail.com>
Date: 2025-09-10 18:17:28 -0400
Commit message:

 Update default parameter in snpgdsIBDKING() function and adjust unit tests
Package: RAIDS
Commit: ca81f2b34a04cca921f1f26ca8f9bb3fb07329d2
Author: Astrid Deschênes <adeschen@users.noreply.github.com>
Date: 2025-05-12 20:41:13 -0400
Commit message:

 Merge pull request #612 from adeschen/main

Update unit test annotation
Package: RAIDS
Commit: d12b60b44c361a26bfc596a06a362dc1538d59b9
Author: adeschen <adeschen@hotmail.com>
Date: 2025-05-12 20:13:23 -0400
Commit message:

 Update unit test annotation
Package: RAIDS
Commit: 4f0e34abb37e75a9c05379849025974ad01c487a
Author: Astrid Deschênes <adeschen@users.noreply.github.com>
Date: 2025-05-12 20:00:18 -0400
Commit message:

 Merge pull request #611 from adeschen/main

Add unit test for pruning1KGbyChr() function
Package: RAIDS
Commit: e3f69f9665278edeb94cca989e94b5076cd41797
Author: adeschen <adeschen@hotmail.com>
Date: 2025-05-12 17:55:47 -0400
Commit message:

 Add unit test for pruning1KGbyChr() function
Package: RAIDS
Commit: 5aaebca29cda6de7c773697fd00c6c16e81bee18
Author: Astrid Deschênes <adeschen@users.noreply.github.com>
Date: 2025-05-09 20:04:59 -0400
Commit message:

 Merge pull request #610 from adeschen/main

Adding unit test for calcAFMLRNA() function
Package: RAIDS
Commit: 626fae1eb15de72cd9fd2992dccf3d18d0dbd33b
Author: adeschen <adeschen@hotmail.com>
Date: 2025-05-09 19:32:44 -0400
Commit message:

 Adding unit test for calcAFMLRNA() function
Package: RAIDS
Commit: dbd17586370bdb01a16ef9acc9f282a3ba214103
Author: Astrid Deschênes <adeschen@users.noreply.github.com>
Date: 2025-05-09 19:26:18 -0400
Commit message:

 Merge pull request #609 from adeschen/main

Adding unit test from computeAllelicFractionRNA() function
Package: RAIDS
Commit: 4ac7fac56b5b02a6df61700b9a1932580da1afca
Author: adeschen <adeschen@hotmail.com>
Date: 2025-05-09 18:58:01 -0400
Commit message:

 Adding unit test from computeAllelicFractionRNA() function
Package: RAIDS
Commit: 85e8b5ce5b019d3d0d4b6a9bd82c79afbfda4435
Author: Astrid Deschênes <adeschen@users.noreply.github.com>
Date: 2025-05-09 15:25:22 -0400
Commit message:

 Merge pull request #608 from adeschen/main

Add unit tests for processBlockChr() function
Package: RAIDS
Commit: a47ddbfd3d55bed6b14a4edbeeadf5630035591f
Author: adeschen <adeschen@hotmail.com>
Date: 2025-05-09 14:50:51 -0400
Commit message:

 Add unit tests for processBlockChr() function
Package: RAIDS
Commit: c79ab96c4fa2a6d43b453f4416600bbdccf99c5d
Author: Astrid Deschênes <adeschen@users.noreply.github.com>
Date: 2025-05-09 14:50:15 -0400
Commit message:

 Merge pull request #607 from adeschen/main

Correct length of lines in tools_internal.R
Package: RAIDS
Commit: cb2bba51af5a1580a591595393dc733d13696aec
Author: adeschen <adeschen@hotmail.com>
Date: 2025-05-09 13:49:46 -0400
Commit message:

 Correct length of lines in tools_internal.R
Package: RAIDS
Commit: 2bed9f2dc91005cda20dad20fe7cbd0778823abf
Author: Astrid Deschênes <adeschen@users.noreply.github.com>
Date: 2025-05-08 22:48:41 -0400
Commit message:

 Merge pull request #606 from adeschen/main

Indents functions correctly
Package: RAIDS
Commit: 6991f937cd1cd19ca12a22ec45d7cbb9fdaec47a
Author: adeschen <adeschen@hotmail.com>
Date: 2025-05-08 20:17:34 -0400
Commit message:

 Update indents in allelicFraction_internal.R file
Package: RAIDS
Commit: 5b319beb96ce491eda6bf041fdcf3272eb26a3b8
Author: adeschen <adeschen@hotmail.com>
Date: 2025-05-08 19:53:58 -0400
Commit message:

 Re-indent function in gdsWrapper_internal.R file
Package: RAIDS
Commit: 6a5cca80e7ccd2466c25058c8d5f055937de8e6f
Author: Astrid Deschênes <adeschen@users.noreply.github.com>
Date: 2025-05-08 19:35:49 -0400
Commit message:

 Merge pull request #605 from adeschen/main

Add unit test for readSNVBAM() function
Package: RAIDS
Commit: c7ac3970380be28853b93e255130dece194f7cee
Author: Astrid Deschênes <adeschen@users.noreply.github.com>
Date: 2025-05-08 17:54:31 -0400
Commit message:

 Merge pull request #604 from adeschen/main

Add example to readSNVBAM() function
Package: RAIDS
Commit: 8ce729c8f84958072db1c0f836110724f5b291fa
Author: adeschen <adeschen@hotmail.com>
Date: 2025-05-08 17:54:21 -0400
Commit message:

 Add unit test for readSNVBAM() function
Package: RAIDS
Commit: 87f971c5090dcd10f7eba3ddce9c69d4aa748242
Author: adeschen <adeschen@hotmail.com>
Date: 2025-05-08 17:03:11 -0400
Commit message:

 Add example to readSNVBAM() function
Package: RAIDS
Commit: b368f4ba9eba70867664f8f543dd1a466b617166
Author: Astrid Deschênes <adeschen@users.noreply.github.com>
Date: 2025-05-08 17:00:35 -0400
Commit message:

 Merge pull request #603 from adeschen/main

Update doc for readSNVVCF() and unit test
Package: RAIDS
Commit: 908d0669d4529d4baa1dc7a4fb6c8d5f787d9d18
Author: Astrid Deschênes <adeschen@users.noreply.github.com>
Date: 2025-05-08 15:25:15 -0400
Commit message:

 Merge pull request #602 from adeschen/main

Adding unit test for readSNVVCF() function
Package: RAIDS
Commit: 7e5c0b4386607888608ec716fbd5e3273a4153af
Author: adeschen <adeschen@hotmail.com>
Date: 2025-05-08 14:22:19 -0400
Commit message:

 Update doc for readSNVVCF() and unit test
Package: RAIDS
Commit: 5ffb02cee0aa18fa6ca61ac5fc1c4c97ab2b9778
Author: adeschen <adeschen@hotmail.com>
Date: 2025-05-08 12:26:11 -0400
Commit message:

 Adding unit test for readSNVVCF() function
Package: RAIDS
Commit: e8afa57cb3cc8b4ef28c19fed9ed607e40aec4ef
Author: Astrid Deschênes <adeschen@users.noreply.github.com>
Date: 2025-05-07 18:17:54 -0400
Commit message:

 Merge pull request #601 from adeschen/main

Add unit test for readSNVFileGeneric() function
Package: RAIDS
Commit: 09b7924f622c1b12e6f1541584c2e775caa1a524
Author: adeschen <adeschen@hotmail.com>
Date: 2025-05-07 17:10:47 -0400
Commit message:

 Add unit tess for readSNVFileGeneric() function
Package: RAIDS
Commit: 0cf6904390d14e5e4a36f24a0bb7728b56a46b54
Author: Astrid Deschênes <adeschen@users.noreply.github.com>
Date: 2025-05-07 16:45:40 -0400
Commit message:

 Merge pull request #600 from adeschen/main

Simplifying graph functions and adding unit tests
Package: RAIDS
Commit: 6a6f5da4aa317b1c0722e02151fea5d4e1abfe5a
Author: adeschen <adeschen@hotmail.com>
Date: 2025-05-07 12:41:21 -0400
Commit message:

 Simplifying graph functions and adding unit tests
Package: RAIDS
Commit: f9120e0a4ff5f867ee2de40cc617f0d5b4e4139b
Author: Astrid Deschênes <adeschen@users.noreply.github.com>
Date: 2025-05-07 12:17:45 -0400
Commit message:

 Merge pull request #599 from adeschen/main

Update createAccuracGraph() code and add unit tests
Package: RAIDS
Commit: 2a9ecf876ed6b65da4ff942be3e3d77fe4fcc7bf
Author: adeschen <adeschen@hotmail.com>
Date: 2025-05-07 11:44:50 -0400
Commit message:

 Update createAccuracGraph() code and add unit tests
Package: RAIDS
Commit: 6c4531b6886e05fd0937474bf0a3b5df38fdfd0d
Author: Astrid Deschênes <adeschen@users.noreply.github.com>
Date: 2025-05-06 22:33:26 -0400
Commit message:

 Merge pull request #598 from adeschen/main

Adding internal function to validate createAUROCgraph() parameters an…
Package: RAIDS
Commit: c42b590bc5897125a306405aa01b42bf06dea427
Author: adeschen <adeschen@hotmail.com>
Date: 2025-05-06 17:33:46 -0400
Commit message:

 Adding internal function to validate createAUROCgraph() parameters and correcting unit tests
Package: RAIDS
Commit: 19131a093067a3d2b29ecc3cc507b75279f60371
Author: Astrid Deschênes <adeschen@users.noreply.github.com>
Date: 2025-05-06 17:25:30 -0400
Commit message:

 Merge pull request #597 from adeschen/main

Update createAUROCGraph() function to follow changes in ggplot2 and a…
Package: RAIDS
Commit: eacc7368f99440e3a74a219eed310b0255980297
Author: adeschen <adeschen@hotmail.com>
Date: 2025-05-06 16:50:49 -0400
Commit message:

 Update createAUROCGraph() function to follow changes in ggplot2 and add unit test
Package: RAIDS
Commit: b94b86fe9892f6f524cd1cce1be3e85d5c25ded9
Author: Astrid Deschênes <adeschen@users.noreply.github.com>
Date: 2025-05-06 16:49:36 -0400
Commit message:

 Merge pull request #596 from adeschen/main

Adding unit test for createAccuracyGraph() function
Package: RAIDS
Commit: bd6fd5aa72ef072ec61e6e94d8bd3d11c1166c49
Author: adeschen <adeschen@hotmail.com>
Date: 2025-05-06 15:52:02 -0400
Commit message:

 Adding unit test for createAccuracyGraph() function
Package: RAIDS
Commit: da57936e398b7a39d845372363f428dfcd5cb8fa
Author: Astrid Deschênes <adeschen@users.noreply.github.com>
Date: 2025-05-06 15:49:51 -0400
Commit message:

 Merge pull request #595 from adeschen/main

Update createAccuracyGraph() to follow changes in ggplot2 library and…
Package: RAIDS
Commit: e542059ec8fd2033bfc83b5bf94769acaa4446e8
Author: adeschen <adeschen@hotmail.com>
Date: 2025-05-06 15:04:10 -0400
Commit message:

 Update createAccuracyGraph() to follow changes in ggplot2 library and add unit tests
Package: RAIDS
Commit: 19f3a978b5fe449e7d932130f5ea66714771690a
Author: Astrid Deschênes <adeschen@users.noreply.github.com>
Date: 2025-05-02 17:53:00 -0400
Commit message:

 Merge pull request #594 from adeschen/main

Update codecov badge
Package: RAIDS
Commit: eac329f61027f175ea2532b539eadd635bb7361f
Author: Astrid Deschênes <adeschen@users.noreply.github.com>
Date: 2025-05-02 17:06:44 -0400
Commit message:

 Merge pull request #9 from adeschen/adeschen-patch-1

Update README.md
Package: RAIDS
Commit: 64dfaffd31712655716dd747b631238568b8e0d4
Author: Astrid Deschênes <adeschen@users.noreply.github.com>
Date: 2025-05-02 16:22:39 -0400
Commit message:

 Update README.md

Update badge codecov
Package: RAIDS
Commit: 56140307e0c74cb5b863817a2e932733b80ae2c4
Author: Astrid Deschênes <adeschen@users.noreply.github.com>
Date: 2025-05-01 17:04:47 -0400
Commit message:

 Merge pull request #593 from adeschen/main

Update test-coverage yaml file
Package: RAIDS
Commit: c6d83ba4b2fc4330051af7cd0e97ae8e210c21e4
Author: Astrid Deschênes <adeschen@users.noreply.github.com>
Date: 2025-05-01 15:56:31 -0400
Commit message:

 Merge pull request #8 from adeschen/adeschen-patch-5

Update test-coverage.yaml
Package: RAIDS
Commit: a1c206beff044531961a18accb387a46952a0586
Author: Astrid Deschênes <adeschen@users.noreply.github.com>
Date: 2025-05-01 14:19:43 -0400
Commit message:

 Update test-coverage.yaml
Package: RAIDS
Commit: ae2ec823e7cf9c8c1a5212e04f3cddc9cc120c46
Author: Astrid Deschênes <adeschen@users.noreply.github.com>
Date: 2025-04-16 10:37:59 -0400
Commit message:

 Merge pull request #590 from belleau/main

Merge with Bioconductor devel
Package: VisiumIO
Commit: 4cab9f721ca51aa2c6da90aa161d129370dba95c
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-10-07 16:23:41 -0400
Commit message:

 version bump 1.5.7
Package: VisiumIO
Commit: e4a08a8b70152fdce412b333efe57dd12a013478
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-10-07 15:29:26 -0400
Commit message:

 add unit tests for segmented_outputs
Package: VisiumIO
Commit: fd90f2236515ca303efc1e998943de7f4554a481
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-10-07 15:16:59 -0400
Commit message:

 add example for TENxVisiumHD with segmented_outputs

- includes example data
Package: VisiumIO
Commit: e7922e5ad41d3242033296f336cb4647587ac0a6
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-10-07 14:24:24 -0400
Commit message:

 update NEWS.md
Package: VisiumIO
Commit: ec86ea353fd36530faf54d9c2b5ecd6343ed52b0
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-10-07 13:58:42 -0400
Commit message:

 add sf to Suggests field
Package: VisiumIO
Commit: f3992e47947a74a03a31b3884e77e565341d4af8
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-10-07 13:45:16 -0400
Commit message:

 add cell_id to coords rownames
Package: VisiumIO
Commit: 57454b232605f42e995e855393fd795de4ae969a
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-10-07 13:39:46 -0400
Commit message:

 keep original cell_ids
Package: VisiumIO
Commit: f793ceca2471ac78521c02d16e482cb282c8c4fb
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-10-07 13:21:29 -0400
Commit message:

 use spatialCoords argument
Package: VisiumIO
Commit: e75b7afa066a8f5794dff60c03db0808dc99284d
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-10-07 12:19:50 -0400
Commit message:

 add geo_data to metadata
Package: VisiumIO
Commit: 005a189072cc0fd849ad1443675ebbd8a89e9feb
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-10-07 11:51:46 -0400
Commit message:

 bug fix: include type in .find_file_or_dir helper
Package: VisiumIO
Commit: 3b5bb6c0817a566e2fdd7ee8075538217ae0243f
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-10-03 15:29:42 -0400
Commit message:

 add small example file for TENxGeoJSON
Package: VisiumIO
Commit: 3e9899582626db89e17f288fe91a64f263e812a6
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-10-03 15:22:32 -0400
Commit message:

 document TENxGeoJSON class
Package: VisiumIO
Commit: a2a5f37a60921dd589d51e27a9fe33064b85878d
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-10-03 15:15:58 -0400
Commit message:

 document segmented_outputs arg
Package: VisiumIO
Commit: 72d840765109adaa55a4f3746ca790f849ecf4b3
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-10-03 15:13:02 -0400
Commit message:

 add rownames to ffcolData
Package: VisiumIO
Commit: 7f3ffd17386ae105f9c4d91e63f0b67195f32d2d
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-10-07 13:55:23 -0400
Commit message:

 update import method for segmented_outputs
Package: VisiumIO
Commit: 37afe1432a4aeaef63707efad4de71c4b969b705
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-10-07 13:55:08 -0400
Commit message:

 optional tissuePos and binSize for segmented_outputs
Package: VisiumIO
Commit: 14550b475126f941cdba15c8f878e60a2b3df85f
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-10-07 13:53:14 -0400
Commit message:

 support barcode and cell types for x_feature_y_matrix
Package: VisiumIO
Commit: 96a7427eea6ed5c98d39a9a4276dcf4332cb580c
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-10-07 13:50:36 -0400
Commit message:

 add support for TENxGeoJSON
Package: VisiumIO
Commit: 6c32a08504d6ea4f9b65fe83ea3d2e1184e658fd
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-09-10 11:26:44 -0400
Commit message:

 use VisiumIO example files
Package: igblastr
Commit: 7f98b8f313d2c354cd59595e59fe73d8f0c305a3
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2025-10-07 12:45:25 -0700
Commit message:

 igblastr 0.99.21: More cleanup of temp files after igblastn(), again
Package: TCGAbiolinks
Commit: 3eab81fdd420b6c0f40a70cb340b9d1fa63c3dc5
Author: Tiago Chedraoui Silva <tiagochst@gmail.com>
Date: 2025-10-07 12:16:56 -0700
Commit message:

 Removing old test
Package: Pirat
Commit: 34ac75e0b40e2181f9373deacba371184e3f3c37
Author: Lucas Etourneau <lucas.etourneau@berkeley.edu>
Date: 2025-10-07 11:50:44 -0700
Commit message:

 Downgrade pytorch python
Package: tximeta
Commit: 361994810177788dbb19368c905c04e0b730091a
Author: Mike Love <mikelove@users.noreply.github.com>
Date: 2025-10-07 14:29:18 -0400
Commit message:

 final code to get update working...
Package: tximeta
Commit: 56d4a6f1aa720e543878b5d4e994cc1bad50b24e
Author: Mike Love <mikelove@users.noreply.github.com>
Date: 2025-10-07 10:48:40 -0400
Commit message:

 not fully fixed, just saving work
Package: tximeta
Commit: 47b38c4ffd8d9075638196ada8228ccb51378fb9
Author: Mike Love <mikelove@users.noreply.github.com>
Date: 2025-10-06 14:36:07 -0400
Commit message:

 linkedTxpData working up to inspection
Package: tximeta
Commit: dc966131dc5a786707808bda82f42c071377406c
Author: Mike Love <mikelove@users.noreply.github.com>
Date: 2025-10-06 08:13:37 -0400
Commit message:

 fix again
Package: tximeta
Commit: 1a66648828f71dfab8c6604b57b19362d033a124
Author: Mike Love <mikelove@users.noreply.github.com>
Date: 2025-10-06 07:04:23 -0400
Commit message:

 fix bfc missing bug
Package: tximeta
Commit: 9b384c62dce98b911ec3c3b4981389fcf534685f
Author: Mike Love <mikelove@users.noreply.github.com>
Date: 2025-10-05 16:41:04 -0400
Commit message:

 roll back 'prefer' column
Package: tximeta
Commit: 57dd3935f55ccf4ce3ca3dfbe43418b6dea33235
Author: Mike Love <mikelove@users.noreply.github.com>
Date: 2025-10-03 22:16:16 -0400
Commit message:

 work on updater and streamlining the stashing of linked things
Package: tximeta
Commit: 40098b6172e87b40e562ad6ebb55172468ea92e0
Author: Mike Love <mikelove@users.noreply.github.com>
Date: 2025-10-03 16:18:46 -0400
Commit message:

 file reorg
Package: tuberculosis
Commit: a6d57f6c7480e0bdb91bf44d578b84d800ed3a3f
Author: schifferl <schifferl@users.noreply.github.com>
Date: 2025-10-07 13:11:37 -0400
Commit message:

 remove hrbrthemes dependency
Package: scLANE
Commit: 5d86bdaf2f5cab7d6958049d2f16226e3a37aeff
Author: Jack Leary <jrleary@live.unc.edu>
Date: 2025-10-07 13:08:00 -0400
Commit message:

 minor fixed for BioConductor and version bump to v0.99.9
Package: scLANE
Commit: c046dd5db2706763ba345bce7aa14f97c41e8a72
Author: Jack Leary <j.leary@ufl.edu>
Date: 2025-10-04 15:26:33 -0400
Commit message:

 v0.99.9 for BioConductor submission with many small tweaks
Package: DMRcaller
Commit: 2059daa6928f80b8085f8e885a40edb25c2a3870
Author: nrzabet <r.zabet@qmul.ac.uk>
Date: 2025-10-07 18:05:07 +0100
Commit message:

 added support for ONT methylation data
Package: DMRcaller
Commit: 3605caae9002568f6df0ce17ac39574c5fcfe3e4
Author: nrzabet <r.zabet@qmul.ac.uk>
Date: 2025-10-07 18:04:36 +0100
Commit message:

 added support for ONT methylation data
Package: igblastr
Commit: 7dd7a60fe3f79a1caa9ce9d58e18c3ce63a99975
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2025-10-07 09:37:53 -0700
Commit message:

 igblastr 0.99.20: More cleanup of temp files after igblastn()
Package: ExploreModelMatrix
Commit: 2c34b726c015187015c90132c4e978ff752e999a
Author: Charlotte Soneson <charlottesoneson@gmail.com>
Date: 2025-10-07 17:46:16 +0200
Commit message:

 Bug fix in VisualizeDesign (horizontal/vertical lines - adapt to ggplot2 4.0.0)
Package: transmogR
Commit: 368f48344f43433f7fadaf61e6753d520c8363c8
Author: Stevie Ped <stephen.pederson.au@gmail.com>
Date: 2025-10-08 01:21:59 +1030
Commit message:

 Merge conflict
Package: transmogR
Commit: f06a81e1568ae67c91dfbd9374e6dc1283a2bf56
Author: Stevie Ped <stephen.pederson.au@gmail.com>
Date: 2025-10-08 01:17:40 +1030
Commit message:

 Fixed dead link
Package: transmogR
Commit: 13a8beb8319f408cf3461559ed1f7ac6d7cc81f6
Author: Stevie Ped <stephen.pederson.au@gmail.com>
Date: 2025-10-08 00:33:46 +1030
Commit message:

 Fixed tests for upset plots
Package: transmogR
Commit: c84bd9d6472925eb4a3f8bc8134809bead984b90
Author: Stevie Ped <stephen.pederson.au@gmail.com>
Date: 2025-10-04 00:16:27 +0930
Commit message:

 Version bump
Package: transmogR
Commit: 08880eaba4c6a6a11a524a4164870b3a0eb89454
Author: Stevie Ped <stephen.pederson.au@gmail.com>
Date: 2025-10-04 00:16:07 +0930
Commit message:

 Migrated to SimpleUpset
Package: transmogR
Commit: 246532c89988367bbf1c5540d9708fbcfb142808
Author: Stevie Ped <stephen.pederson.au@gmail.com>
Date: 2025-09-18 00:07:17 +0930
Commit message:

 Fixed except for upsetVarByCol
Package: transmogR
Commit: 25a14473742a272a3c6818130ea57132f06828e5
Author: Stevie Ped <stephen.pederson.au@gmail.com>
Date: 2025-04-25 00:05:15 +0930
Commit message:

 Version bump after bugfix
Package: transmogR
Commit: 3cfdef8d77cfa1e26777ad309e75a9ce040841ad
Author: Stevie Ped <stephen.pederson.au@gmail.com>
Date: 2025-04-25 00:04:42 +0930
Commit message:

 Bugfix in digestSalmon
Package: plaid
Commit: 105a4b56db283d13c217ddcb61e9436025fab58c
Author: ESCRI11 <xavier.escriba.montagut@gmail.com>
Date: 2025-10-07 16:44:11 +0200
Commit message:

 trigger build
Package: MungeSumstats
Commit: c37839b398a83a01ebf62dcffd9e6edc7ab1cf6b
Author: Al-Murphy <alanmurph94@hotmail.com>
Date: 2025-10-07 10:12:01 -0400
Commit message:

 Bug Fix: infer effect allele
Package: Rarr
Commit: 867576637136aa465a5026ad00204665efdc5b27
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-10-07 15:07:18 +0200
Commit message:

 Restore ZarrArray-class test
Package: Rarr
Commit: 2f0d4b5baca3f471a4dd2763cecb14016445da36
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-10-07 15:07:01 +0200
Commit message:

 Add bogus s3 argument to test uncovered code sections
Package: Rarr
Commit: 9f7d380d36631301cb93862fe0eabd12274e9dfe
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-10-07 11:13:12 +0200
Commit message:

 Silence some linters in tests/
Package: Rarr
Commit: beccdb68c1d7adaead7a33622ae7faeefc2704fc
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-10-07 11:04:05 +0200
Commit message:

 Fix test url parsing
Package: Rarr
Commit: 6ecdd4c48961bdc2b4176575a533743d0447e063
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-10-07 10:56:10 +0200
Commit message:

 Bump version
Package: Rarr
Commit: a0717c7e9d47f2a7eaae6a2291b966dac88727c2
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-10-07 10:56:04 +0200
Commit message:

 Mention switch to testthat in NEWS
Package: Rarr
Commit: d93459d8d54c62bc2e902fdcb13c14238e1193c5
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-10-07 10:54:28 +0200
Commit message:

 Remove tinytest
Package: Rarr
Commit: 02390a25cc438b58423b0cb4d087c142418cca5c
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-10-07 10:24:00 +0200
Commit message:

 Fix some lints in tests/
Package: Rarr
Commit: 2e3eb24c07ac2cab1bd82289d87c5dd8d02e5f48
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-10-06 22:26:45 +0200
Commit message:

 Restore mocked test for missing metadata on S3
Package: Rarr
Commit: 3a4d8555815b186e1fcee4b95b1c8a50b0ed53c7
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-10-06 19:24:29 +0200
Commit message:

 Simplify snapshot tests
Package: Rarr
Commit: 5527e2d11ccc32646eb80086c190f1458e5b80dc
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-10-06 19:18:37 +0200
Commit message:

 Use expect_identical() where possible
Package: Rarr
Commit: 7a4022c9077be354ac921d1271d39bcd9da4e03d
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-10-06 19:09:25 +0200
Commit message:

 Fix multiple updates test
Package: Rarr
Commit: 435e9eae1fed9ad145e5a743cd6901f0538fe673
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-10-06 19:03:16 +0200
Commit message:

 Use withr
Package: Rarr
Commit: 6949fc60ff30c74e55b6b03abe8ecdcbcf6dc38b
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-10-06 19:03:09 +0200
Commit message:

 Run tests in parallel
Package: Rarr
Commit: 588efc85dd056be8dde615a316a09cc61de844b3
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-10-06 18:44:42 +0200
Commit message:

 Fix path definition for url_parsing test
Package: Rarr
Commit: 3a51aa1ab53547696e18537d1355e3406ac31e65
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-10-06 18:40:15 +0200
Commit message:

 Avoid hitting online S3 server
Package: Rarr
Commit: 8156d2b2817cef435ca584711b8c66ee8bde2130
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-10-06 18:17:24 +0200
Commit message:

 Fix arg name in expect_error()
Package: Rarr
Commit: c6ff634d4efe4be3c34abf4603fdb9578c679079
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-10-06 18:15:57 +0200
Commit message:

 Fix array expectation
Package: Rarr
Commit: d44819d3c2bab4da8430affd770753224f1a9ffc
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-10-06 18:12:34 +0200
Commit message:

 Remove Rarr::: prefix
Package: Rarr
Commit: 786efb24ca7c37154a403c1a64c9a22ff9300dd3
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-10-06 17:46:13 +0200
Commit message:

 Automatic creation of testthat files from tinytest files
Package: Rarr
Commit: 6f17c032e87aa98edf27d422406501f60cef7be1
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-10-07 10:30:39 +0200
Commit message:

 Fix test-coverage workflow triggers
Package: Rarr
Commit: a834941ccb77fb4bbd4e24455c43eba88b8c3e9d
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-10-07 10:24:39 +0200
Commit message:

 Fix badge table
Package: extraChIPs
Commit: 333a0ada5d18029d4a22ec3b1aecbb3f825b37fd
Author: Stevie Ped <stephen.pederson.au@gmail.com>
Date: 2025-10-07 23:59:58 +1030
Commit message:

 BiocCheck-based edit
Package: extraChIPs
Commit: 420b1c5f87726d92bba74c779711b5850eb85076
Author: Stevie Ped <stephen.pederson.au@gmail.com>
Date: 2025-10-07 23:47:07 +1030
Commit message:

 Udated NEWS.md
Package: TFEA.ChIP
Commit: d164c37807dfaf4334f26e1eafbd832192509e53
Author: yosra <yosraberrouayel@gmail.com>
Date: 2025-10-07 15:21:50 +0200
Commit message:

 changed vignette
Package: smoppix
Commit: 178579b8f5caffb170513197f2ecc821468abba7
Author: stijn <stijn.hawinkel@psb.ugent.be>
Date: 2025-10-07 14:27:59 +0200
Commit message:

 Latest changes in the nes file
Package: smoppix
Commit: 14ed9f5d2bb73ff5dfe15001ef2153e41d079939
Author: stijn <stijn.hawinkel@psb.ugent.be>
Date: 2025-10-07 14:13:26 +0200
Commit message:

 Showcase vignette
Package: smoppix
Commit: 6cd28973cabbfe969cb31b12f19921f4e8998d8c
Author: stijn <stijn.hawinkel@psb.ugent.be>
Date: 2025-10-07 13:40:34 +0200
Commit message:

 Buildvigneetes in readme
Package: extraChIPs
Commit: 3700c68b3800501660efe9b5a18d8c906e43694c
Author: Stevie Ped <stephen.pederson.au@gmail.com>
Date: 2025-10-03 22:33:39 +0930
Commit message:

 Version bump after update
Package: extraChIPs
Commit: 2e416cd31b1154356dd639127531c46958170c3b
Author: Stevie Ped <stephen.pederson.au@gmail.com>
Date: 2025-10-03 22:33:18 +0930
Commit message:

 Migrated to SimpleUpset
Package: extraChIPs
Commit: 9fc2a2726633746baa30e4789943583fe2aac08f
Author: Stevie Ped <stephen.pederson.au@gmail.com>
Date: 2025-09-14 17:52:40 +0930
Commit message:

 Fixed all functions & tests up until `plotOverlaps()`
Package: SpaceTrooper
Commit: 4b26f4d5170407f63447d86f58a7da78a4f8c5a6
Author: Dario <dario.righelli@gmail.com>
Date: 2025-10-07 11:22:09 +0100
Commit message:

 bumping version 99.43
Package: SpaceTrooper
Commit: a929d738cf011caafcfa7a6a0e201f2cbf499934
Author: Dario <dario.righelli@gmail.com>
Date: 2025-10-07 11:21:49 +0100
Commit message:

 readXenium was failing when not computing missing metrics.
Package: SpaceTrooper
Commit: c8af14cf23484650edcabaed175087f5a3599ac4
Author: Dario <dario.righelli@gmail.com>
Date: 2025-10-06 15:30:54 +0100
Commit message:

 updating README
Package: pengls
Commit: 02aa3f0a711eecd36bea61fd4e23f0ef101c8f9d
Author: stijn <stijn.hawinkel@psb.ugent.be>
Date: 2025-10-07 10:41:53 +0200
Commit message:

 Compiled news file
Package: pengls
Commit: 19da355e4c595899483e823c765b222db15a5ba3
Author: stijn <stijn.hawinkel@psb.ugent.be>
Date: 2025-10-07 10:41:36 +0200
Commit message:

 With correct citation file
Package: pengls
Commit: 831af1a34deb3109b94b1d95b12d1b02d8d798cb
Author: stijn <stijn.hawinkel@psb.ugent.be>
Date: 2025-10-06 17:32:07 +0200
Commit message:

 With modern citation
Package: plaid
Commit: 1815c96e820899b3c10f36716c3218139b0161ad
Author: ESCRI11 <xavier.escriba.montagut@gmail.com>
Date: 2025-10-07 10:36:20 +0200
Commit message:

 make antonino the maintainer

he is the one subscribed to devel email list
Package: smoppix
Commit: e4155590529d370ec93e85eb123816dd5e1a6001
Author: stijn <stijn.hawinkel@psb.ugent.be>
Date: 2025-10-07 10:32:47 +0200
Commit message:

 example for named.contr.sum
Package: smoppix
Commit: 268f055c3839181249db85eec0e1506565bd0050
Author: stijn <stijn.hawinkel@psb.ugent.be>
Date: 2025-10-07 10:10:07 +0200
Commit message:

 Added citation file and version bump
Package: multistateQTL
Commit: 1519f123131fbca928a7393d57f17514c91a42dc
Author: dunstone-a <amelia.dunstone@gmail.com>
Date: 2025-10-07 17:45:07 +1100
Commit message:

 Update callSignificance
- Bug where if there is only one state then there is an error in this function.
Package: Spectra
Commit: 3540c00a0e5000701fa4ea76308a911a9761c9d3
Author: Johannes Rainer <5506112+jorainer@users.noreply.github.com>
Date: 2025-10-06 07:38:50 +0200
Commit message:

 Merge pull request #368 from rformassspectrometry/jomain

tests: add additional unit tests
Package: Spectra
Commit: c76332504080c11efb1d3857d1da85c4299a243d
Author: Johannes Rainer <johannes.rainer@gmail.com>
Date: 2025-10-03 08:52:58 +0200
Commit message:

 fix test
Package: Spectra
Commit: b66811df9bb708ffb9d239c82978264f1dd82985
Author: Johannes Rainer <johannes.rainer@gmail.com>
Date: 2025-10-03 08:12:06 +0200
Commit message:

 tests: add additional unit tests
Package: Spectra
Commit: 33c7afdf58b55534b1a77f0764c0ff40505b577f
Author: Johannes Rainer <5506112+jorainer@users.noreply.github.com>
Date: 2025-09-24 09:46:01 +0200
Commit message:

 Merge pull request #367 from stanstrup/patch-2

Specrta typo
Package: Spectra
Commit: a6bc524306e95e5b9a34ef69311f289e86631bf5
Author: Jan Stanstrup <stanstrup@gmail.com>
Date: 2025-09-22 14:17:41 +0200
Commit message:

 Specrta typo
Package: MsBackendSql
Commit: c03a805252904c0d704d1f844972db9605ea321b
Author: Johannes Rainer <5506112+jorainer@users.noreply.github.com>
Date: 2025-10-07 07:48:20 +0200
Commit message:

 Merge pull request #29 from rformassspectrometry/jomain

feat: add longForm method for MsBackendSql
Package: MsBackendSql
Commit: c08a3f2a0e01c7c06b17d71ab341dd2f0931d335
Author: Johannes Rainer <johannes.rainer@gmail.com>
Date: 2025-10-06 16:05:43 +0200
Commit message:

 ci: update Bioc versions
Package: MsBackendSql
Commit: 5afbed1fbd1e7cf29add97a43a4f3ca84f613bef
Author: Johannes Rainer <johannes.rainer@gmail.com>
Date: 2025-10-06 15:35:56 +0200
Commit message:

 feat: add longForm method for MsBackendSql
Package: OSCA.advanced
Commit: 4a83341bf08556d6ecae34074cb27459313cfc61
Author: PeteHaitch <peter.hickey@gmail.com>
Date: 2025-10-07 15:03:23 +1100
Commit message:

 Version bump
Package: OSCA.advanced
Commit: 79e1387761db5ce3aced5e7de3ddafee8b4403fd
Author: PeteHaitch <peter.hickey@gmail.com>
Date: 2025-10-07 15:03:08 +1100
Commit message:

 Update more-clustering.Rmd

- Tweak sanity check and corresponding text
Package: OSCA.advanced
Commit: deb4431313071e85b616e7ce9ee652bd77955533
Author: Peter Hickey <peter.hickey@gmail.com>
Date: 2025-10-07 14:59:57 +1100
Commit message:

 Version bump
Package: OSCA.advanced
Commit: b7a4ffcc5715df0999605ce22c6c4b7abd4fe7f1
Author: Peter Hickey <peter.hickey@gmail.com>
Date: 2025-10-07 14:59:35 +1100
Commit message:

 Update droplet-processing.Rmd

- Address #21.
- Reducing `lower` from its default value of 100 to 90 does enable it to run. It gives qualitatively similar barcode rank plots, although the knee/inflection points (not used here) will likely be different to the old results due the other changes in knee/inflection point identification (e.g., https://github.com/MarioniLab/DropletUtils/pull/124 and https://github.com/MarioniLab/DropletUtils/pull/125)
Package: iscream
Commit: 43c6d25ef87b5638061ef719bd7400410e969528
Author: James Eapen <james.eapen@vai.org>
Date: 2025-10-06 20:37:19 -0400
Commit message:

 chore(DESCRIPTION): bump version after first review
Package: iscream
Commit: 590bb9f5873b117c1d83e7494079364a9312c082
Author: James Eapen <james.eapen@vai.org>
Date: 2025-10-06 20:35:58 -0400
Commit message:

 chore: remove unused lintr
Package: iscream
Commit: 53754ad9cd7d358b8f1ad44831fe9ff39f18c23d
Author: James Eapen <james.eapen@vai.org>
Date: 2025-10-03 16:26:06 -0400
Commit message:

 ci(check-bioc): add windows
Package: iscream
Commit: c08bdd10f8409b547dcbb3f7ac89700e3029f502
Author: James Eapen <james.eapen@vai.org>
Date: 2025-10-03 16:05:57 -0400
Commit message:

 chore: remove windows as UnsupportedPlatforms
Package: iscream
Commit: d1a409df7e0e23e42c230f46baadf6650746c831
Author: James Eapen <james.eapen@vai.org>
Date: 2025-10-03 15:17:48 -0400
Commit message:

 fix(Makevars): add Makevars.win with Rhtslib; add configure stub
Package: iscream
Commit: ae35a3c3049eec8da1ba294d485c923fdab36d95
Author: James Eapen <james.eapen@vai.org>
Date: 2025-10-03 15:24:49 -0400
Commit message:

 chore(DESCRIPTION): update RoxygenNote
Package: iscream
Commit: 9f6122bd2b4d65d0725a13744bb3ab744f06deda
Author: James Eapen <james.eapen@vai.org>
Date: 2025-10-03 15:17:24 -0400
Commit message:

 chore(DESCRIPTION): add GNU make as system req for Rhtslib makevars population
Package: iscream
Commit: 74bfe800cbbb5c48dc52e4e8eff5a8423dd7c671
Author: James Eapen <james.eapen@vai.org>
Date: 2025-10-03 10:16:49 -0400
Commit message:

 fix(summarize_regions): convert path to string explicitly for win
Package: iscream
Commit: d3ac609d78856177f2bbb24334ba07ef4ceef103
Author: James Eapen <james.eapen@vai.org>
Date: 2025-10-03 10:12:20 -0400
Commit message:

 docs(vignettes): add bsseq require call in example
Package: iscream
Commit: 42efd48bf7b113274085d39f214bb53581f74388
Author: James Eapen <james.eapen@vai.org>
Date: 2025-10-03 09:41:41 -0400
Commit message:

 docs(threads): donttest setting threads
Package: iscream
Commit: 1bd81e49efd46e194a850229683ad9ed22ece74c
Author: James Eapen <james.eapen@vai.org>
Date: 2025-10-02 16:57:19 -0400
Commit message:

 docs(meth): clarify CpG/H
Package: iscream
Commit: 7f1306b0a29246aece834779c8c990cec1a4158a
Author: James Eapen <james.eapen@vai.org>
Date: 2025-10-02 16:55:22 -0400
Commit message:

 docs(vignette): add other vignette references
Package: iscream
Commit: ab3853de42cda3ed96a6edc4b773f2c3024f3aef
Author: James Eapen <james.eapen@vai.org>
Date: 2025-10-02 16:55:05 -0400
Commit message:

 docs: replace CpG references with more general methylation
Package: iscream
Commit: efbb950c067f81b8d89c2eaaca72e658ef996df8
Author: James Eapen <james.eapen@vai.org>
Date: 2025-10-02 16:43:35 -0400
Commit message:

 chore(DESCRIPTION): update Description with methylation support
Package: iscream
Commit: 0dba6c35d10921ea698b0d1da2db2a6d6a20332f
Author: James Eapen <james.eapen@vai.org>
Date: 2025-10-02 16:22:38 -0400
Commit message:

 chore(flake): add missing Suggests

BiocFileCache
microbenchmark
Rsamtools
Package: iscream
Commit: a395d9bde6233539e684b5d556e6dec03d867f0b
Author: James Eapen <james.eapen@vai.org>
Date: 2025-10-02 16:18:34 -0400
Commit message:

 chore(DESCRIPTION): add bsseq as Suggests for example and vignettes
Package: iscream
Commit: c8f6f1182b8e8473d5ec64ea66c3a4302e86ac91
Author: James Eapen <james.eapen@vai.org>
Date: 2025-10-02 16:21:14 -0400
Commit message:

 docs(make_mat_bsseq): run bsseq creation example
Package: iscream
Commit: 17a5fd2733072cc2f07ab2d777f6cf92014a5c46
Author: James Eapen <james.eapen@vai.org>
Date: 2025-10-02 16:17:44 -0400
Commit message:

 docs(make_mat_bsseq): switch dontrun bsseq building to donttest
Package: iscream
Commit: 4a6fdeb019706ad51f2d0b50641adb096b6589a5
Author: James Eapen <james.eapen@vai.org>
Date: 2025-10-02 16:08:40 -0400
Commit message:

 docs(vignettes): remove redundant color scheme in TSS summary plot
Package: iscream
Commit: a9c92c39bf28624f97ed2b3e4f294632b29587e5
Author: James Eapen <james.eapen@vai.org>
Date: 2025-10-02 16:07:00 -0400
Commit message:

 chore(DESCRIPTION): add BiocFileCache as Suggests
Package: iscream
Commit: 175a9a84c96738e434d2272560b1e7534483c7c2
Author: James Eapen <james.eapen@vai.org>
Date: 2025-10-02 16:06:19 -0400
Commit message:

 docs(make_mat_bsseq): expand on Bitpacking limits
Package: iscream
Commit: 1ef43af5d5748119690bfaa575feea24402e57ce
Author: James Eapen <james.eapen@vai.org>
Date: 2025-10-02 15:30:12 -0400
Commit message:

 docs(threads): fix documentation formatting, typo
Package: iscream
Commit: 20be2d7cbfa8e4cad8fd2daeb215a8c5bfb260f7
Author: James Eapen <james.eapen@vai.org>
Date: 2025-10-02 13:37:47 -0400
Commit message:

 docs(vignettes): fix extra column name in reading genes file
Package: iscream
Commit: d3d319c706c3c0dcbb28282a5fd01a7ecef4f333
Author: James Eapen <james.eapen@vai.org>
Date: 2025-10-02 11:33:01 -0400
Commit message:

 docs(vignettes): use BiocFileCache for downloading data
Package: iscream
Commit: 0a67454a81dc337276eec0e94b972a9bdabe0306
Author: James Eapen <james.eapen@vai.org>
Date: 2025-10-02 10:48:47 -0400
Commit message:

 fix: use file.path instead of paste for all paths
Package: iscream
Commit: bea0fbd6fa09ab7b18ce3b68bb392d781be5c243
Author: James Eapen <james.eapen@vai.org>
Date: 2025-10-02 10:40:47 -0400
Commit message:

 fix(src): remove unused variables
Package: iscream
Commit: 5062d4ad25bc531ca26c08531d906fbd66c15963
Author: James Eapen <james.eapen@vai.org>
Date: 2025-10-01 16:18:07 -0400
Commit message:

 docs(vignettes): rerun tabix vignettes knit
Package: iscream
Commit: 0844a9cfc8b93bfa6708af24a78615179d0fa253
Author: James Eapen <james.eapen@vai.org>
Date: 2025-10-01 16:20:51 -0400
Commit message:

 fix(configure): use = instead of invalid == for Darwin check
Package: iscream
Commit: d1dd791cae7530fe94a0bffbfe3fda29448e4a87
Author: James Eapen <james.eapen@vai.org>
Date: 2025-10-01 11:42:40 -0400
Commit message:

 docs(vignettes): fix missing mats input to bsseq
Package: iscream
Commit: 8324f7d4b01a29e3659225b158455e291492e147
Author: James Eapen <james.eapen@vai.org>
Date: 2025-09-30 17:48:22 -0400
Commit message:

 fix(configure): MacOS and clang compatibility fixes

- check if mac
- don't check version if clang
- use otool to check for libdeflate
Package: iscream
Commit: 53cd970b138cd5d5a7215b7f3831bad80b002a9e
Author: James Eapen <james.eapen@vai.org>
Date: 2025-09-30 16:19:46 -0400
Commit message:

 !fix(make_mat_bsseq): consistent mat_mat_* naming to make_mat_bsseq
Package: iscream
Commit: cd57980055217e9e083cf935a3dc98d9d4ed039a
Author: James Eapen <james.eapen@vai.org>
Date: 2025-09-30 15:59:41 -0400
Commit message:

 chore(vignettes): set htslib to BiocStyle
Package: iscream
Commit: cea9dc090e1a27415e4bd03972a04c29f3c57e8b
Author: James Eapen <james.eapen@vai.org>
Date: 2025-08-28 12:53:45 -0400
Commit message:

 refactor(tabix): properly return from tabix.single
Package: iscream
Commit: fdf048f2198b4657a0e58a330a983d4bb3c34736
Author: James Eapen <james.eapen@vai.org>
Date: 2025-10-06 20:23:30 -0400
Commit message:

 feat(tabix): add progress bar to tabix
Package: iscream
Commit: 4f6fbaf9609bf1141251d8e1a61a9338135b2c97
Author: James Eapen <james.eapen@vai.org>
Date: 2025-10-03 20:28:24 -0400
Commit message:

 docs(vignettes): rerun tabix benchmark to correct timings
Package: iscream
Commit: 9ca2f46edb10993b6c9a2b1a0b105a572b314b59
Author: James Eapen <james.eapen@vai.org>
Date: 2025-09-30 16:20:58 -0400
Commit message:

 chore(flake): move shellHook into devShell scope
Package: iscream
Commit: 1b342b19ba1fd34efd590be0e6ec3788f75a82bb
Author: James Eapen <james.eapen@vai.org>
Date: 2025-09-30 10:29:59 -0400
Commit message:

 chore(flake): flake update
Package: iscream
Commit: 7aa591c3865d0e73fb9637894318ea3827078e97
Author: James Eapen <james.eapen@vai.org>
Date: 2025-09-30 10:29:46 -0400
Commit message:

 chore(flake): add gcc for macos compilations
Package: iscream
Commit: 3aa3cee4bf3f646096fdcf54b005b0d6d723a194
Author: James Eapen <james.eapen@vai.org>
Date: 2025-09-30 10:25:23 -0400
Commit message:

 chore(DESCRIPTION): update title and more informative Description
Package: iscream
Commit: f6303ef810489587b2c710aabfe870cff2747659
Author: James Eapen <james.eapen@vai.org>
Date: 2025-09-02 10:33:32 -0400
Commit message:

 test(tabix): reset tabix method to htslib after switching to shell
Package: epiSeeker
Commit: fdab7186cd4603bada1fe22f5d78f652cff103c6
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2025-10-07 08:04:04 +0800
Commit message:

 bump version
Package: epiSeeker
Commit: 19069f1ee8d90a78d521b39eb1e4790e486fe020
Author: liming <limiang929@gmail.com>
Date: 2025-10-06 23:58:56 +0800
Commit message:

 reduce size of vignettes
Package: epiSeeker
Commit: beaf568e2216db06e690ae3bebcdc3c1d1956ec4
Author: liming <limiang929@gmail.com>
Date: 2025-10-06 21:15:01 +0800
Commit message:

 fixed note from BioCheck
Package: epiSeeker
Commit: 189faca4ab6b9708bb4ea25840e2c290a3d97a48
Author: liming <limiang929@gmail.com>
Date: 2025-10-06 20:28:24 +0800
Commit message:

 replace sapply and assignment operator(=)
Package: epiSeeker
Commit: e39d500da03412b0ec05763d5401758857b4e7a9
Author: liming <limiang929@gmail.com>
Date: 2025-10-06 19:29:29 +0800
Commit message:

 reduce example time
Package: epiSeeker
Commit: e494cbbcdbccc0c91cf50171c2c19057360b7e38
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2025-10-06 13:48:29 +0800
Commit message:

 update
Package: epiSeeker
Commit: 42e1e108c0131d77ffe53684e0f41f44477fb707
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2025-10-06 13:27:13 +0800
Commit message:

 update
Package: ggspavis
Commit: d2d8e66c536704ee9e81de5bae79b3910f66b680
Author: Lukas Weber <lmweb012@gmail.com>
Date: 2025-10-06 19:41:14 -0400
Commit message:

 Merge pull request #20 from estellad/estellad

Add Visium HD, Imaging-based, and Dimension Reduction on text annotation in vignette
Package: ggspavis
Commit: a8314a421c66698c2f78a264daecea2b2df7daaf
Author: Lukas Weber <lmweb012@gmail.com>
Date: 2025-10-06 19:39:06 -0400
Commit message:

 version
Package: ggspavis
Commit: d3207bb9fa04be0ac0fdd930e56ce4afbc5e55de
Author: Lukas Weber <lmweb012@gmail.com>
Date: 2025-10-06 19:38:49 -0400
Commit message:

 minor edits - Slide-seq, wrap long lines, wording, etc
Package: ggspavis
Commit: 90b643f7664a4a5e3ff4d1a2cc066a3ea154226e
Author: Lukas Weber <lmweb012@gmail.com>
Date: 2025-10-06 19:22:03 -0400
Commit message:

 move arrow to Suggests
Package: ggspavis
Commit: 475eaf0574a191c3ad62973d5cf0cafe8d5fbb35
Author: estellad <estelladong729@gmail.com>
Date: 2025-10-05 17:55:58 +0200
Commit message:

 add sticker
Package: ggspavis
Commit: 27506a94f7f432998d7ea5b90f711328ac2a2de1
Author: estellad <estelladong729@gmail.com>
Date: 2025-10-04 23:02:44 +0200
Commit message:

 add vhd and img visualization in vignette
Package: ggspavis
Commit: 1e6dec7a486113858b54923226428a91c72db32a
Author: estellad <estelladong729@gmail.com>
Date: 2025-06-24 09:15:56 +0200
Commit message:

 change vignette
Package: igblastr
Commit: 6658916098d87c403bd890dd99274c9afdff7c14
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2025-10-06 15:38:28 -0700
Commit message:

 igblastr 0.99.19: Make sure igblastn() cleans after itself

No more littering of tempdir() with empty igblastn_stderr_*.txt files.
This can cause issues when calling igblastn() in a giant loop on systems
with little space in /tmp, like on some HPC systems.
Package: musicatk
Commit: fd4134737428512457457316c2680ad9d8c2c1ff
Author: Josh Campbell <joshua-d-campbell@gmail.com>
Date: 2025-10-06 17:40:49 -0400
Commit message:

 version bump
Package: musicatk
Commit: f1aaa3837001942bb4b9da9066536ee5c9c3805d
Author: Josh Campbell <joshua-d-campbell@gmail.com>
Date: 2025-10-06 17:37:17 -0400
Commit message:

 Merge remote-tracking branch 'campbio/devel' into devel
Package: musicatk
Commit: 34bf5b9df04ee658df8881c744d90f82eca81b94
Author: Joshua D. Campbell <joshua.d.campbell@gmail.com>
Date: 2025-08-22 07:26:29 -0400
Commit message:

 Merge pull request #88 from nqgurevich/refactor

Correction of IND plotting x-axis labels
Package: musicatk
Commit: a4a9c7e139e2f74bb81fe293dad17f575f2dce53
Author: Natasha Gurevich <ngurevich@dot1x-nat-10-222-36-127.bumc.bu.edu>
Date: 2025-08-19 13:14:57 -0400
Commit message:

 Correction of IND plotting x-axis labels
Package: scruff
Commit: ef8838f23f8516ff289a4e96f18cfb45197cf360
Author: Josh Campbell <joshua-d-campbell@gmail.com>
Date: 2025-10-06 15:16:04 -0400
Commit message:

 Merge remote-tracking branch 'campbio/devel' into devel
Package: scruff
Commit: 6cf1cf6b0490f0f1235658ce020dfee7c14b61e5
Author: Joshua D. Campbell <joshua.d.campbell@gmail.com>
Date: 2025-09-29 21:14:37 -0400
Commit message:

 Merge pull request #190 from zhewa/devel

fix invalid class "GGbio" object: invalid object for slot "ggplot"
Package: scruff
Commit: 9486e9f9e77cd62389f4f18c14da711495929cc0
Author: Zhe Wang <zhe@bu.edu>
Date: 2025-09-29 17:15:59 -0400
Commit message:

 update check-r-package@v2
Package: scruff
Commit: 7c124a29315013e182170b3b9df95cd54da3c47b
Author: Zhe Wang <zhe@bu.edu>
Date: 2025-09-29 17:04:00 -0400
Commit message:

 update github actions
Package: scruff
Commit: 33ab6284605e4ab0fd183b1cc60a8f559d1eb888
Author: zhewa <zhe@bu.edu>
Date: 2025-09-26 11:24:57 -0400
Commit message:

 Merge branch 'RELEASE_3_21' of github-zhewa:zhewa/scruff into devel
Package: scruff
Commit: 148d3a315f78ffba136b57f76125520c44d05807
Author: zhewa <zhe@bu.edu>
Date: 2025-09-26 11:24:26 -0400
Commit message:

 version bump
Package: scruff
Commit: f6d4ca6597170fbb948c2c40b4f9355edb0e6ea2
Author: zhewa <zhe@bu.edu>
Date: 2025-09-26 11:24:02 -0400
Commit message:

 Merge branch 'devel' of https://git.bioconductor.org/packages/scruff into devel
Package: scruff
Commit: 3bdf082f5025e8101ac43118ed6e45d26d895f59
Author: zhewa <zhe@bu.edu>
Date: 2025-09-26 11:18:50 -0400
Commit message:

 use patchwork to combine plots in vignette
Package: scruff
Commit: bdab7a5a0951945f205527058ecf3711ccafd56d
Author: zhewa <zhe@bu.edu>
Date: 2025-09-26 10:31:38 -0400
Commit message:

 fix invalid class "GGbio" object: invalid object for slot "ggplot"
Package: scruff
Commit: 984c00e9d7e36c58efa08829e6b64dd6b3b6632e
Author: zhewa <zhe@bu.edu>
Date: 2025-09-26 10:03:54 -0400
Commit message:

 Merge branch 'RELEASE_3_21' of https://git.bioconductor.org/packages/scruff into RELEASE_3_21
Package: scruff
Commit: 20870ffe047e01d5858dc772f66dfe83d2954600
Author: Zhe Wang <zhe@bu.edu>
Date: 2024-03-27 21:40:44 -0400
Commit message:

 Merge pull request #187 from zhewa/devel

Devel
Package: decemedip
Commit: 0615c991ec1f93d8ce0cebdc7b4834fb57e0a761
Author: nshen7 <shenning1997@gmail.com>
Date: 2025-10-06 18:15:49 +0000
Commit message:

 bump version
Package: decemedip
Commit: b8825042149b6c4dbf8a3053153cddef93941e8c
Author: nshen7 <shenning1997@gmail.com>
Date: 2025-10-06 18:14:09 +0000
Commit message:

 r version
Package: decemedip
Commit: 305ed9514ea4cb019d91e4bcc09c6c1724d019c8
Author: nshen7 <shenning1997@gmail.com>
Date: 2025-10-06 18:11:47 +0000
Commit message:

 lightweight examples
Package: decemedip
Commit: b71d2a80799456729e7d81be891b444fe26b4814
Author: nshen7 <shenning1997@gmail.com>
Date: 2025-08-24 14:07:18 -0700
Commit message:

 minor fixes
Package: decemedip
Commit: fb1901854539841dff371173e54b2f1d92142113
Author: nshen7 <shenning1997@gmail.com>
Date: 2025-08-24 11:37:03 -0700
Commit message:

 address R CMD check notes caused by dplyr
Package: decemedip
Commit: 579a98ff5242cd27b46532ffa002da34d2541ada
Author: nshen7 <shenning1997@gmail.com>
Date: 2025-08-20 18:06:52 -0700
Commit message:

 change R version
Package: decemedip
Commit: 75d4b3c0c72ceaf78f58ae1452890a827a1d2fdf
Author: nshen7 <shenning1997@gmail.com>
Date: 2025-08-20 21:27:36 +0000
Commit message:

 Address R CMD check notes
Package: decemedip
Commit: 284ac4546bcf49a1e2b3b16d534af489ff83c791
Author: nshen7 <shenning1997@gmail.com>
Date: 2025-08-20 18:15:01 +0000
Commit message:

 Increment version number to 0.99.6
Package: decemedip
Commit: f7946fb15e8a58a50a9ad6077a9d01876543eee2
Author: nshen7 <shenning1997@gmail.com>
Date: 2025-08-20 18:13:45 +0000
Commit message:

 resolve R CMD check notes
Package: decemedip
Commit: fadad67381f057924cefcec5a15238e9a7b9b1c1
Author: nshen7 <shenning1997@gmail.com>
Date: 2025-08-18 20:40:29 +0000
Commit message:

 address bioc comments try 2
Package: decemedip
Commit: 081da126ab85470cddb6e58f4e52d9ce6684bfd4
Author: Ning Shen <38674209+nshen7@users.noreply.github.com>
Date: 2025-08-18 13:16:48 -0700
Commit message:

 Update README.md
Package: BreastSubtypeR
Commit: 306f124484dde596692d08b180d9bd8288074d76
Author: Qiao Yang <yq.kiuo@gmail.com>
Date: 2025-10-06 19:55:11 +0200
Commit message:

 v1.1.5 Fix: LaTeX errors
Package: Pirat
Commit: 0a1c52235bdf00bece46eb540afeb7926f8dd38f
Author: Lucas Etourneau <lucas.etourneau@berkeley.edu>
Date: 2025-10-06 10:14:46 -0700
Commit message:

 Upgrade pytorch
Package: BatchSVG
Commit: 90398e8cb7acd4e526e9dfd5330306ceca6a7bab
Author: Kinnary Shah <kinnaryshahh@gmail.com>
Date: 2025-10-06 13:04:34 -0400
Commit message:

 update maintainer
Package: smoppix
Commit: 7258619df48363720c3ec90d8903d84719d033de
Author: stijn <stijn.hawinkel@psb.ugent.be>
Date: 2025-10-06 18:00:48 +0200
Commit message:

 With proper citation
Package: smoppix
Commit: 1c59b788bb1fd6872b000850244495cb2914a653
Author: stijn <stijn.hawinkel@psb.ugent.be>
Date: 2025-10-06 17:44:46 +0200
Commit message:

 Adding a citation file
Package: smoppix
Commit: 9e3b88a185a0bcd52c02c402e1c70451f09ee010
Author: stijn <stijn.hawinkel@psb.ugent.be>
Date: 2025-09-30 17:44:46 +0200
Commit message:

 Insert citations to hawinkel2025
Package: smoppix
Commit: f6d7e5eba710e73a33b594c56bdbaec4ece5546d
Author: stijn <stijn.hawinkel@psb.ugent.be>
Date: 2025-09-30 14:19:45 +0200
Commit message:

 Typo in biocmanager
Package: dittoSeq
Commit: 7727ea80a10d9c20e0ed43d2cadd189d14f5cccd
Author: dtm2451 <daniel.bunis@ucsf.edu>
Date: 2025-10-06 11:22:10 -0400
Commit message:

 missed ggplot-v4 compatibility update, ComplexHeatmap drop_levels update
Package: lcmsPlot
Commit: f36313180320452b54f6eb08de793be592030e2a
Author: Ossama Edbali <ossedb@gmail.com>
Date: 2025-10-06 16:17:39 +0100
Commit message:

 chore: Bump dev version
Package: lcmsPlot
Commit: 9a602173842527e179d0a79bbb99b18e42610ca4
Author: Ossama Edbali <ossedb@gmail.com>
Date: 2025-10-06 16:16:15 +0100
Commit message:

 chore: Add return in docs and standardise
Package: lcmsPlot
Commit: e9f96a6762051ebda19dc2cb8a57efd4fbec503a
Author: Ossama Edbali <ossedb@gmail.com>
Date: 2025-10-06 15:40:55 +0100
Commit message:

 fix: Add xcms namespace to test helper
Package: Rarr
Commit: 96bc9c6a0ed1b7d55538d6f31eb9cc7049facb7e
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-10-06 15:57:06 +0200
Commit message:

 Update test-coverage workflow
Package: Rarr
Commit: c8f17f51683d1de99772256540c72782b5641827
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-10-06 15:55:04 +0200
Commit message:

 Run devtools::document()
Package: Rarr
Commit: 9f241c8047cc4d8582d0bd139236db49fda84882
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-10-06 15:42:55 +0200
Commit message:

 Disable mocking test for now
As it seems to be leaking to other tests
Package: Rarr
Commit: 9d4a4adaefdad5709e0b46fa7c308219cc0ca624
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-10-06 14:43:34 +0200
Commit message:

 Ensure "Denied Access" is properly reported to users
Package: Rarr
Commit: 453f2ac1f9baf8ebecf2838823abbc7702f646cb
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-10-06 14:41:29 +0200
Commit message:

 Adjust mocked test to take into account new existence test
Package: Rarr
Commit: e901dbabe7c5e7bb57dad992dec0bd29918bfaf7
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-10-06 13:52:59 +0200
Commit message:

 Skip failing vignette chunk for now

This should be reactivated once valid credentials are available
Package: Rarr
Commit: 94ee81ef294cacb25b2ef1cd229d11b6f54d6ac6
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-10-03 18:27:57 +0200
Commit message:

 Avoid indiscriminately catching all errors in .s3_object_exists

This leads us to hide "Access Denied" errors
Package: lcmsPlot
Commit: 75777f6e4061a665dbcd236235fd5e7c9cd851b4
Author: Ossama Edbali <ossedb@gmail.com>
Date: 2025-10-06 15:29:18 +0100
Commit message:

 fix: Use AnnotatedDataFrame instead of NAnnotatedDataFrame
Package: DOtools
Commit: 3dea7b8e77e52daa74aae8394ada9e73d76aba04
Author: MarianoRuzJurado <mariani95@gmx.de>
Date: 2025-10-06 16:02:42 +0200
Commit message:

 -Solving R CMD Notes
Package: SpaceTrooper
Commit: c930e13e660bb383812c24c144e00bae9be85e72
Author: Dario <dario.righelli@gmail.com>
Date: 2025-10-06 14:28:09 +0100
Commit message:

 version bump
Package: SpaceTrooper
Commit: ceb76b3d7e1a68dd1f552f9ab1bef92e036108b3
Author: Dario <dario.righelli@gmail.com>
Date: 2025-10-06 14:22:10 +0100
Commit message:

 missing comma in DESCRIPTION file
Package: SpaceTrooper
Commit: ec88f4dcfbf929a4398c8514d3f6624f77e29b01
Author: Dario <dario.righelli@gmail.com>
Date: 2025-10-06 14:14:31 +0100
Commit message:

 adding default GHA from biocthis
Package: SpaceTrooper
Commit: b27c8ad9e60ea38252656226d24411ad1ee2f911
Author: Dario <dario.righelli@gmail.com>
Date: 2025-10-06 11:02:43 +0100
Commit message:

 authors role
Package: DuplexDiscovereR
Commit: 7e5c418380e16f3920fed74e84bcd93e5b74edcb
Author: Egors01 <yegor.smb@gmail.com>
Date: 2025-10-06 15:18:34 +0200
Commit message:

 fixed R CMD check error caused by vctrs
Package: plaid
Commit: e665f2e298dede3adaf4a051d5fc11d6cd687b28
Author: ESCRI11 <xavier.escriba.montagut@gmail.com>
Date: 2025-10-06 15:08:56 +0200
Commit message:

 bump version to trigger build
Package: plaid
Commit: cc951dfc50281b58a9354e48045975e9d359d627
Author: ESCRI11 <xavier.escriba.montagut@gmail.com>
Date: 2025-10-06 15:04:29 +0200
Commit message:

 fix: bioC warnings
Package: geomeTriD
Commit: ae68b917d246039c40261e69c5eab7c665b592cc
Author: Jianhong Ou <jianhong.ou@gmail.com>
Date: 2025-10-06 08:19:24 -0400
Commit message:

 update authoer list.
Package: Repitools
Commit: 07ba2e25ee2f99158eb30847a6fcb20e307a66e8
Author: lshep <lori.shepherd@roswellpark.org>
Date: 2025-10-06 08:19:18 -0400
Commit message:

 Deprecate

 - maintainer requested at bioconductorcoreteam
Package: DominoEffect
Commit: a6955cc885fbf4a39794a7911fcdc04cad3b558c
Author: lshep <lori.shepherd@roswellpark.org>
Date: 2025-10-06 08:16:14 -0400
Commit message:

 Un-deprecate
Fixed package
Package: QTLExperiment
Commit: 4bc5633c00de96714ec652667de5dfbf9c411f1c
Author: dunstone-a <amelia.dunstone@gmail.com>
Date: 2025-09-30 18:13:13 +1000
Commit message:

 Update NEWS and version bump
Package: QTLExperiment
Commit: b5fc7155410dddbad7dd0e0e461722b381cdc1ad
Author: dunstone-a <amelia.dunstone@gmail.com>
Date: 2025-09-30 18:07:41 +1000
Commit message:

 Add support for QTLExperiment objects with one state
- There was a bug? where sumstats2qtle() and QTLExperiment() wouldn't work if only one state was provided.
Package: pathMED
Commit: 5a1b067ea404ef6af1405dc80d5404dbf34679ed
Author: jordimartorell <jmartorellm@gmail.com>
Date: 2025-10-06 13:44:30 +0200
Commit message:

 Fix trainModel
Package: lcmsPlot
Commit: 54e19cca44d75dd7749ec450367ca902da6229b3
Author: Ossama Edbali <ossedb@gmail.com>
Date: 2025-10-06 12:28:58 +0100
Commit message:

 fix: Namespacing (xcms and patchwork)
Package: lcmsPlot
Commit: 0d695c4f09d80750bada0ad63352a59f0015c50f
Author: Ossama Edbali <ossedb@gmail.com>
Date: 2025-10-06 12:20:32 +0100
Commit message:

 fix: Vignette MulticoreParam call
Package: lcmsPlot
Commit: d101649b00f8712d11710108de1f5dbb17b94171
Author: Ossama Edbali <ossedb@gmail.com>
Date: 2025-10-06 12:13:06 +0100
Commit message:

 chore: Bump dev version
Package: lcmsPlot
Commit: 0bd3409b0b160b4641d190f42c01cd03be9a8f79
Author: Ossama Edbali <ossedb@gmail.com>
Date: 2025-10-06 11:07:44 +0100
Commit message:

 fix: Namespace register (BiocParallel) in vignette
Package: SpaceTrooper
Commit: 0fa6f0b016948a0ddbd1b9df5946949b10d3c5ab
Author: Dario <dario.righelli@gmail.com>
Date: 2025-10-06 10:39:08 +0100
Commit message:

 version bump
Package: SpaceTrooper
Commit: 02ecb729690970efc9049d97a5432fe2a4536add
Author: Dario <dario.righelli@gmail.com>
Date: 2025-10-05 20:58:20 +0100
Commit message:

 document deprecation
Package: SpaceTrooper
Commit: a5941155ab10fdcbe46ca7a076cacec16965335f
Author: Dario <dario.righelli@gmail.com>
Date: 2025-10-05 20:54:11 +0100
Commit message:

 adding deprecation
Package: spatialFDA
Commit: db4b9090610b4170e15b6ddb94cc3e17885bdafe
Author: mjemons <martin.emons@gmail.com>
Date: 2025-10-06 11:16:16 +0200
Commit message:

 fix ylim in plotFbPlot
Package: spatialFDA
Commit: 4a3bfb8c97da8af581c5008601bd8548984c7142
Author: mjemons <martin.emons@gmail.com>
Date: 2025-10-06 10:42:43 +0200
Commit message:

 changes to subsetby variable
Package: miaViz
Commit: b5f6c1cced76e1155515d491b4afca6b610e6d8e
Author: Muluh <127390183+Daenarys8@users.noreply.github.com>
Date: 2025-09-10 09:24:15 +0300
Commit message:

 plotLoadings: Flexible number of features for n<10 (#199)

Signed-off-by: Daena Rys <rysdaena8@gmail.com>
Co-authored-by: Tuomas Borman <tvborm@utu.fi>
Package: scider
Commit: 102940a03611e5bce016916d6ceb7fa734cb14f9
Author: Yunshun Chen <yuchen@wehi.edu.au>
Date: 2025-10-06 17:04:02 +1100
Commit message:

 scider v1.7.2
- Fixed a bug in C compilation under Mac
- Update the default arguments in findNbrsSNN
Package: STexampleData
Commit: 3ff80b03a095a5102b4f289ab2810505d56f89d6
Author: Lukas Weber <lmweb012@gmail.com>
Date: 2025-10-06 00:39:36 -0400
Commit message:

 wording
Package: STexampleData
Commit: 02f5b012c38d7b73b97e82af9ec51f078063fe8f
Author: Lukas Weber <lmweb012@gmail.com>
Date: 2025-10-06 00:34:37 -0400
Commit message:

 update readme text
Package: epiSeeker
Commit: 039333445bbb908725c1af8f943821d315303112
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2025-10-06 12:24:11 +0800
Commit message:

 bump version
Package: epiSeeker
Commit: 7d4d5075e0fef3db486ba06e868c50809cd41ba6
Author: liming <limiang929@gmail.com>
Date: 2025-10-06 11:51:49 +0800
Commit message:

 add news
Package: epiSeeker
Commit: f401cb1fae97561cb221545d0b9894981ffa6cab
Author: liming <limiang929@gmail.com>
Date: 2025-10-06 11:34:57 +0800
Commit message:

 add news
Package: epiSeeker
Commit: f2596f590153e322b1f6f17027870d9839e5820a
Author: liming <limiang929@gmail.com>
Date: 2025-10-06 00:47:58 +0800
Commit message:

 fixed R check
Package: epiSeeker
Commit: 5d77f5418401ec0ff27949e2bedc0f8e58afee48
Author: liming <limiang929@gmail.com>
Date: 2025-10-06 00:45:05 +0800
Commit message:

 fixed R check
Package: epiSeeker
Commit: bc3ef2d32a90e298ce4d2c9e496de265e843c1d1
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2025-10-05 18:37:32 +0800
Commit message:

 typo
Package: scrapper
Commit: e62b9f31bd90f9dc68b832812acd79f72321f15f
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2025-10-05 21:22:24 -0700
Commit message:

 Updates to runTsne binding for new qdtsne.
Package: assorthead
Commit: 8dffb341aa2d13b6de255f8f8c5619f2e9bf4bd6
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2025-10-05 21:10:55 -0700
Commit message:

 Updated versions of various libaries.
Package: STexampleData
Commit: a458c75f692598d49986949d978e66511731b478
Author: Lukas Weber <lmweb012@gmail.com>
Date: 2025-10-05 22:48:17 -0400
Commit message:

 update GHA
Package: STexampleData
Commit: 53664196a0ad57a714fc1091eb1448571a55c687
Author: Lukas Weber <lmweb012@gmail.com>
Date: 2025-10-05 22:29:13 -0400
Commit message:

 Merge pull request #8 from 'estellad-devel' into devel

update Visium breast cancer make-data script and add sticker
Package: STexampleData
Commit: 2d161ac3596866e624c4a635886874852431a921
Author: Lukas Weber <lmweb012@gmail.com>
Date: 2025-10-05 22:26:43 -0400
Commit message:

 update date
Package: STexampleData
Commit: 23174544db2e51d2c43a6306c6e0a6811fad96b1
Author: Lukas Weber <lmweb012@gmail.com>
Date: 2025-10-05 22:23:03 -0400
Commit message:

 update version number for Bioc 3.22
Package: STexampleData
Commit: 7088577c7adddf0b67c9911d50657d396fa5bcf7
Author: estellad <estelladong729@gmail.com>
Date: 2025-10-05 17:56:22 +0200
Commit message:

 add sticker
Package: STexampleData
Commit: ce62ce8ef4cc36192f0003740d505c0a05a3cee8
Author: Estella Yixing Dong <estelladong729@gmail.com>
Date: 2025-10-05 17:29:13 +0200
Commit message:

 Merge branch 'lmweber:devel' into devel
Package: STexampleData
Commit: a8bc94b088c600274678597f4a41aac24af5393d
Author: estellad <estelladong729@gmail.com>
Date: 2024-09-25 15:25:20 +0200
Commit message:

 update data generation
Package: GenomicSuperSignature
Commit: cec203906cda0ef090b3fae1c0e189e3729a2cad
Author: Sehyun Oh <shbrief@gmail.com>
Date: 2025-10-05 22:12:57 -0400
Commit message:

 version bump
Package: MPAC
Commit: 8834db5c7aa9a54e46c4f727bffdb242845de138
Author: pliu55 <pliu55@wisc.edu>
Date: 2025-10-05 16:03:24 -0500
Commit message:

 update citation to Bioinformatics
Package: OSTA
Commit: a4bf4b93ee26f83d9dcd840eaaebdb8c53cba2b3
Author: Lukas Weber <lmweb012@gmail.com>
Date: 2025-10-05 16:20:23 -0400
Commit message:

 version
Package: GSVA
Commit: c433005a7727de7ac2cbc73c76b55d9956c75e34
Author: Robert Castelo <robert.castelo@upf.edu>
Date: 2025-10-05 20:32:04 +0200
Commit message:

 Update to adapt gsvaEnrichment(plot="ggplot") to ggplot2 4.0
Package: Sconify
Commit: 89835080bcc8d2a2e74dbd47fc44860dc1c45e20
Author: Tyler Burns <burns.tyler@gmail.com>
Date: 2025-10-05 19:59:52 +0200
Commit message:

 Updated version number.
Package: Sconify
Commit: dcd973fb181295bb50c890e5dd1b3cb27ffbcd99
Author: Tyler Burns <burns.tyler@gmail.com>
Date: 2025-10-05 19:54:56 +0200
Commit message:

 Changed return in plot functions for new ggplot2
Package: consICA
Commit: 8e4d70866dea381073c019825deaa46e1bba45cd
Author: Maryna Chepeleva <maryna.chepeleva@gmail.com>
Date: 2025-10-05 19:57:27 +0200
Commit message:

 [R][example] set ncores=1 (for CMD CHECK timeout) + bunp 2.7.2
Package: OSTA
Commit: 496c98eeaa04dd63ee9aca54153f8d87d7e29cad
Author: Lukas Weber <lmweb012@gmail.com>
Date: 2025-10-05 13:48:48 -0400
Commit message:

 version and date
Package: OSTA
Commit: 60f3b078b914943a17d254b06f5b10a18f6186f7
Author: Lukas Weber <lmweb012@gmail.com>
Date: 2025-10-05 13:07:19 -0400
Commit message:

 Merge pull request #221 from lmweber/bioc-review

Bioc submission review comments
Package: OSTA
Commit: 56d1aae758a4ed9fe3fdd8fec5822e07faad0a0b
Author: Lukas Weber <lmweb012@gmail.com>
Date: 2025-10-05 13:03:56 -0400
Commit message:

 Merge pull request #225 from lmweber/bioc-review_hlc

bioc-review revision
Package: OSTA
Commit: 90a6478b9f49186ef4212eb7a5e8e13a704dcc73
Author: HelenaLC <helena@crowell.eu>
Date: 2025-10-05 18:09:38 +0200
Commit message:

 omit 'this is', reformat date, reorder & rephrase
Package: OSTA
Commit: d67f662f64e9871a076b1a8fae3765f9a32f4c2a
Author: HelenaLC <helena@crowell.eu>
Date: 2025-10-05 18:06:44 +0200
Commit message:

 hide comment from readers
Package: OSTA
Commit: 9a1f3197629ed59500916973dd1d081e09d98d6d
Author: HelenaLC <helena@crowell.eu>
Date: 2025-10-05 15:16:04 +0200
Commit message:

 revise deps to what is truly needed
Package: OSTA
Commit: 0b782203883b9525df3c42b1395d1b8571e5e8ba
Author: HelenaLC <helena@crowell.eu>
Date: 2025-10-05 15:13:38 +0200
Commit message:

 bug fix: do not load SpaNorm
Package: OSTA
Commit: 66945176ab439037bed5d72cda6aa694fc935c35
Author: Helena L. Crowell <helena@crowell.eu>
Date: 2025-10-05 12:45:58 +0200
Commit message:

 +ind-normalization
Package: OSTA
Commit: 3099da67c90c4247371fdf181686d80773bd3d10
Author: HelenaLC <helena@crowell.eu>
Date: 2025-10-05 12:44:33 +0200
Commit message:

 aesthetic revision
Package: OSTA
Commit: 0d3c2700136278a6f26d9b77dc610a5f1b388eff
Author: HelenaLC <helena@crowell.eu>
Date: 2025-10-05 10:59:40 +0200
Commit message:

 add refs for zellkonverter, reticulate, basilisk
Package: OSTA
Commit: 6520be7a10f203dd84e2fd6b90a9c11b57c5abc9
Author: HelenaLC <helena@crowell.eu>
Date: 2025-10-05 10:36:54 +0200
Commit message:

 simplify landing page version info display
Package: OSTA
Commit: 812f9189f1aa2961132f8cb0cd70230d4e0cd1c8
Author: Lukas Weber <lmweb012@gmail.com>
Date: 2025-10-03 15:38:33 -0400
Commit message:

 update version info text on index page
Package: OSTA
Commit: f7696008d28639da39b943d2f7f920cb83dbbe6f
Author: Davide Risso <risso.davide@gmail.com>
Date: 2025-10-03 15:26:01 +0200
Commit message:

 Small change
Package: OSTA
Commit: 4db67497abdea7ff9dc1054061c1fde5fed40ca7
Author: Davide Risso <risso.davide@gmail.com>
Date: 2025-10-03 15:24:53 +0200
Commit message:

 Finish norm chapter
Package: OSTA
Commit: 5580880b10de180d9cc73bf11449167496731e4a
Author: Lukas Weber <lmweb012@gmail.com>
Date: 2025-10-02 16:50:39 -0400
Commit message:

 clarify date
Package: OSTA
Commit: 90fefd7f20b9c22c9513856bb532120fd27ad300
Author: Lukas Weber <lmweb012@gmail.com>
Date: 2025-10-02 16:00:40 -0400
Commit message:

 update BugReports to link directly to GitHub issues
Package: OSTA
Commit: 8be23ec658b2385934b63f977f956c2034bf174e
Author: Lukas Weber <lmweb012@gmail.com>
Date: 2025-10-02 15:59:17 -0400
Commit message:

 remove code for colnames from barcodes - no longer needed
Package: OSTA
Commit: 50cbd204ff0774c953017b337552e4f47056724f
Author: Lukas Weber <lmweb012@gmail.com>
Date: 2025-10-02 15:55:28 -0400
Commit message:

 add summary of links to key packages and tools
Package: OSTA
Commit: 8676e526141854252ad45ae5f72507d4e3c88df9
Author: Lukas Weber <lmweb012@gmail.com>
Date: 2025-10-02 15:25:11 -0400
Commit message:

 show versions on index page for reproducibility
Package: OSTA
Commit: 92b397d31029d2a7dcec8c8c180d4aba29676064
Author: Davide Risso <risso.davide@gmail.com>
Date: 2025-10-02 14:44:04 +0200
Commit message:

 Adding normalization chapter
Package: OSTA
Commit: dc07db17407086a4d999b9204680a006a5f4d69b
Author: Davide Risso <risso.davide@gmail.com>
Date: 2025-09-22 09:16:14 +0200
Commit message:

 Revert "Adding normalization content"

This reverts commit dac187a923592d614a26509999d4b07c1b616292.
Package: OSTA
Commit: dac187a923592d614a26509999d4b07c1b616292
Author: Davide Risso <risso.davide@gmail.com>
Date: 2025-09-18 12:49:01 +0200
Commit message:

 Adding normalization content
Package: PhyloProfile
Commit: 70712c9d5a49166920255e253079f5c1e5ab270d
Author: AnnamTran <trvinh@gmail.com>
Date: 2025-10-05 14:05:12 +0200
Commit message:

 removed shinybs
Package: epiSeeker
Commit: 2175e71e2faff98adfc96c5e6fdf6990ffdd94c1
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2025-10-05 18:09:11 +0800
Commit message:

 update version
Package: epiSeeker
Commit: bf090f8861d316d2ddb3a0f7ce4519c7f5578ce8
Author: ming li <mingli@mings-MacBook-Air.local>
Date: 2025-10-04 21:14:21 +0800
Commit message:

 fixed R check
Package: XAItest
Commit: 419fe30beb51170e56d7f64c7608f4fb6aa30518
Author: gui <ghislain.fievet@gmail.com>
Date: 2025-10-05 09:47:18 +0200
Commit message:

 vers bump
Package: SpaceTrooper
Commit: 6a8635bbdd0a3f69217018a0efc953597eab12b9
Author: Dario <dario.righelli@gmail.com>
Date: 2025-10-04 22:38:58 +0100
Commit message:

 fixing .make_outlier_plot issue, show legend must be logical, switching from "polygon" to TRUE
Package: gINTomics
Commit: 5fc6154f706beecbaa663ee88b08ef3e2a01440c
Author: angeve96 <angeve89@gmail.com>
Date: 2025-10-04 15:11:00 +0200
Commit message:

 version bump
Package: epiSeeker
Commit: b886c9d6cc92b720d997d45f5366a4555f25dd63
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2025-10-04 15:47:54 +0800
Commit message:

 fixed R check
Package: EnrichDO
Commit: 0da128f71abc2627c51fa9e96c29a75847075d23
Author: CHENGliang!@#123 <liangcheng@hrbmu.edu.cn>
Date: 2025-10-04 13:57:08 +0800
Commit message:

 v1.3.1
Package: EnrichDO
Commit: f89094669d324291f48bf2d5313ac9c94f784631
Author: CHENGliang!@#123 <liangcheng@hrbmu.edu.cn>
Date: 2025-10-04 13:56:23 +0800
Commit message:

 v1.4.0
Package: EnrichDO
Commit: dbaea16c6fa331bc72c147eee2d25adba2bca19d
Author: CHENGliang!@#123 <liangcheng@hrbmu.edu.cn>
Date: 2025-10-04 13:53:33 +0800
Commit message:

 v1.4.0
Package: EnrichDO
Commit: abebae157cedb725dd6f9696740114cd39c5050c
Author: CHENGliang!@#123 <liangcheng@hrbmu.edu.cn>
Date: 2025-10-04 13:53:06 +0800
Commit message:

 v1.4.0
Package: EnrichDO
Commit: 3e1f8a777199a7d1edd1e6206cb6efaaf11c611e
Author: CHENGliang!@#123 <liangcheng@hrbmu.edu.cn>
Date: 2025-10-04 13:52:43 +0800
Commit message:

 v1.4.0
Package: EnrichDO
Commit: e8ab71733be6ea3a213bbda44b03ad3c4a3f3aeb
Author: CHENGliang!@#123 <liangcheng@hrbmu.edu.cn>
Date: 2025-10-04 13:52:22 +0800
Commit message:

 v1.4.0
Package: EnrichDO
Commit: 14a6e54e8458b076c418ed029665bcf3b3c76884
Author: CHENGliang!@#123 <liangcheng@hrbmu.edu.cn>
Date: 2025-10-04 13:51:59 +0800
Commit message:

 v1.4.0
Package: EnrichDO
Commit: 4829c3e7ee711f9cd19da59554a1708bdffabe92
Author: CHENGliang!@#123 <liangcheng@hrbmu.edu.cn>
Date: 2025-10-04 13:51:25 +0800
Commit message:

 v1.4.0
Package: EnrichDO
Commit: 5606a3c59185c41d9785102666b6f4112989926a
Author: CHENGliang!@#123 <liangcheng@hrbmu.edu.cn>
Date: 2025-10-04 13:45:16 +0800
Commit message:

 v1.4.0
Package: EnrichDO
Commit: 87cbeb1801b98022620f5ea425042dc3e0a05416
Author: CHENGliang!@#123 <liangcheng@hrbmu.edu.cn>
Date: 2025-10-04 13:44:55 +0800
Commit message:

 v1.4.0
Package: EnrichDO
Commit: 8865b1119aef87320300b174d1840e1d52f245b3
Author: CHENGliang!@#123 <liangcheng@hrbmu.edu.cn>
Date: 2025-10-04 13:44:08 +0800
Commit message:

 v1.4.0
Package: EnrichDO
Commit: c56a2a8d16959698621c3cb4c98230ba3a817bd9
Author: CHENGliang!@#123 <liangcheng@hrbmu.edu.cn>
Date: 2025-10-04 10:01:35 +0800
Commit message:

 v1.4.0
Package: EnrichDO
Commit: 7e36461a4eb3a3db6100c76238f2f96e05fd0f44
Author: CHENGliang!@#123 <liangcheng@hrbmu.edu.cn>
Date: 2025-10-04 09:34:48 +0800
Commit message:

 v1.3.1
Package: Pirat
Commit: 4fc9022f6cd68a783c81367b18e54d9548eee9c1
Author: Lucas Etourneau <lucas.etourneau@berkeley.edu>
Date: 2025-10-03 15:26:45 -0700
Commit message:

 Change version pytorch
Package: gINTomics
Commit: 9dbaa6dd600b62ce34041cc11958c87880de2373
Author: angeve96 <angeve89@gmail.com>
Date: 2025-10-03 22:05:37 +0200
Commit message:

 ggplot fix
Package: RESOLVE
Commit: 8ccfb79d7cf43c54d22a322f7098074cd614c29a
Author: Luca De Sano <luca.desano@gmail.com>
Date: 2025-10-03 19:04:20 +0200
Commit message:

 update to 1.11.2
Package: SparseSignatures
Commit: fe885035221110e9f4e173d525e2ccdde6fa960b
Author: Luca De Sano <luca.desano@gmail.com>
Date: 2025-10-03 19:00:02 +0200
Commit message:

 update to 2.19.2
Package: Rarr
Commit: 55cab049f515779602048e71c9d5521d3a945821
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-10-03 09:57:30 +0200
Commit message:

 Bump version
Package: Rarr
Commit: 75eca25a71fafe9ca075a8af0288265e41031477
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-10-01 14:28:26 +0200
Commit message:

 As deNBI as funder
Package: Rarr
Commit: b44d3fc9e5a449cb226980af3c1f1fbd844d9eba
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-10-01 14:27:45 +0200
Commit message:

 Add Artür and Sharla as ctb
Package: Rarr
Commit: 9c2c46813cb2187274716f1b02ed560a2bdce89e
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-10-01 14:25:57 +0200
Commit message:

 Set Hugo as new maintainer
Package: Rarr
Commit: 2e10f8d8388b5ab04f9e6bb0ac296769567e73bf
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-10-01 14:24:18 +0200
Commit message:

 Run desc::desc_normalize()