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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: OAtools
Commit: eb540d95f34d593b47a8b686c430753acd7a7d71
Author: Aidan Shea <aidantshea@gmail.com>
Date: 2026-04-16 15:49:35 -0700
Commit message:

 build: remove .BBSoptions

Removes the .BBSoptions file in favor of specifying the operating
systems to be exluded under the DESCRIPTION. This change is made in
preparation for Bioconductor's switch to R Universe for builds per
Andres Wokaty.
Package: OAtools
Commit: 28d9e1b7f4f4c17c6f4d1f1b59361d12c93d987c
Author: Aidan Shea <aidantshea@gmail.com>
Date: 2026-03-09 17:35:02 -0700
Commit message:

 chore: rename plot title
Package: S4Vectors
Commit: 5727ec00578543fd8e277e3bd71dacde8e3ab9af
Author: Michael Lawrence <lawremi@gmail.com>
Date: 2026-04-16 15:44:16 -0700
Commit message:

 version bump
Package: MSstatsBig
Commit: 15a1b7f4cf250ad0f5af565dbbcff82900fdf2a1
Author: tonywu1999 <wu.anthon@northeastern.edu>
Date: 2026-04-16 18:14:07 -0400
Commit message:

 Bump version from 1.9.2 to 1.9.3
Package: MSstatsBig
Commit: 556490f62b3c5c7cd691420167f818d559cec60c
Author: Devon Kohler <35807256+devonjkohler@users.noreply.github.com>
Date: 2026-03-02 18:25:12 -0500
Commit message:

 Comment out MSstatsMakeAnnotation call

Temporary fix to DIA-NN big converter. Removing annotation file.
Package: MSstatsBig
Commit: 24d3d1b22019e68178f85dc284fd916d23fb5e64
Author: Devon Kohler <35807256+devonjkohler@users.noreply.github.com>
Date: 2026-03-02 11:22:10 -0500
Commit message:

 added anomaly model to MSstatsClean call (#14)
Package: MSstatsPTM
Commit: c753b855c13dd8937d26017345d35018acea7ecb
Author: tonywu1999 <wu.anthon@northeastern.edu>
Date: 2026-04-16 18:09:57 -0400
Commit message:

 Bump version from 2.13.1 to 2.13.2
Package: MSstatsPTM
Commit: e27ceea366d7090ae2b51bcb3ace8e204835e2ac
Author: tonywu1999 <wu.anthon@northeastern.edu>
Date: 2026-04-09 11:12:53 -0400
Commit message:

 fix(pkgdown): Fix url to the MSstatsPTM github page (#128)
Package: ADaCGH2
Commit: de3993917ac6bda26c9c3054219a24749157f122
Author: Ramon @ Triturus
Date: 2026-04-16 22:36:44 +0200
Commit message:

 2.51.3
</div>
Package: ZarrArray
Commit: d3bb9168087b372a3d200def31fa1910ee38794c
Author: Artür Manukyan <artur-man@hotmail.com>
Date: 2026-04-16 22:01:13 +0200
Commit message:

 Update TODO list for ZarrArray integration (#5)

Both ImageArray and SpatialData now depend on ZarrArray.
Package: ZarrArray
Commit: f711a225e93bf956c1cc8c2992c5ccba54ab4271
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2026-04-07 22:30:02 -0700
Commit message:

 ZarrArray 0.99.4: Add 'fill_value' argument to ZarrRealizationSink()

Also greatly improve unit tests for ZarrRealizationSink methods.
Package: OncoSimulR
Commit: a14195950ca1cbab3581ffd901fb4378fe4dfe21
Author: Ramon @ Triturus
Date: 2026-04-16 21:54:57 +0200
Commit message:

  4.13.4: miscell minor notes and warnings from r-universe
</div>
Package: staRgate
Commit: 04bfb326929784177a3e3bfea28bf96dda1b8f9e
Author: LeeJ22 <lee.jasme@gmail.com>
Date: 2026-04-16 15:22:03 -0400
Commit message:

 ver bump for hexsticker
Package: staRgate
Commit: 282c1839d1422b84196c26ca58fdb590b6001e72
Author: LeeJ22 <lee.jasme@gmail.com>
Date: 2026-04-16 15:06:40 -0400
Commit message:

 resize hexsticker
Package: staRgate
Commit: f9a3ca92698fbd46a6ec8bb5871ba21e5f543121
Author: LeeJ22 <lee.jasme@gmail.com>
Date: 2026-04-16 13:38:52 -0400
Commit message:

 trying a diff theme and make logo bigger
Package: staRgate
Commit: e023999965d03a2bce361caf7a4d5f1f254ca436
Author: LeeJ22 <lee.jasme@gmail.com>
Date: 2026-04-16 11:01:13 -0400
Commit message:

 added hex sticker. test if it shows up on webpage
Package: staRgate
Commit: d99ffebb9219bb1e474c9ec08bac1e01a6e3dc47
Author: LeeJ22 <lee.jasme@gmail.com>
Date: 2026-04-09 15:36:51 -0400
Commit message:

 downgraded the required R ver
Package: MSstatsBioNet
Commit: a480faa0985ac0a749cb53fada537393f180ed38
Author: tonywu1999 <wu.anthon@northeastern.edu>
Date: 2026-04-16 14:02:53 -0400
Commit message:

 Bump version from 1.3.5 to 1.3.6
Package: ShortRead
Commit: 43f8fc82a6c35a5dc471fad550e11730c2dd4b1a
Author: vjcitn <stvjc@channing.harvard.edu>
Date: 2026-04-16 17:25:27 +0000
Commit message:

 try to scotch more warnings
Package: ShortRead
Commit: 13c27b7645aaaad7a0ae5267dcdece60bddfb3b6
Author: vjcitn <stvjc@channing.harvard.edu>
Date: 2026-04-16 17:12:08 +0000
Commit message:

 scotch two warnings from io.c
Package: ShortRead
Commit: 2e3368a35e3955a0a92b7f3e2c8dface6709d135
Author: vjcitn <stvjc@channing.harvard.edu>
Date: 2026-04-16 16:54:15 +0000
Commit message:

 fixapi
Package: ShortRead
Commit: 8b550a875de350ab4ac461af053440f51967479d
Author: vjcitn <stvjc@channing.harvard.edu>
Date: 2026-04-16 16:53:48 +0000
Commit message:

 bump version
Package: MSstatsBioNet
Commit: 732fba014fdb98a1a747f3e106ad948e8e91d14a
Author: tonywu1999 <wu.anthon@northeastern.edu>
Date: 2026-04-16 13:52:33 -0400
Commit message:

 feat(deletion): Add code to delete an edge programmatically
Package: flowPloidy
Commit: 2d140b4f44c6bb4f7df81bad0f1cccc8898b489c
Author: smithty <smithty@ONOTTRA825833PL.agr.gc.ca>
Date: 2026-04-16 13:51:57 -0400
Commit message:

 updated docs, version bump
Package: flowPloidy
Commit: 6ba265209b27203cf61196f2744b7abfaebd60eb
Author: smithty <smithty@ONOTTRA825833PL.agr.gc.ca>
Date: 2026-04-16 13:41:04 -0400
Commit message:

 Merge branch 'master' into devel

Also bumped version number.
Package: flowPloidy
Commit: 02b35c80cf3499112f8f1b617fea3fdc74f1d694
Author: smithty <smithty@ONOTTRA825833PL.agr.gc.ca>
Date: 2026-03-30 16:29:38 -0400
Commit message:

 chasing down bugs related to fhName

Previously I used fhName and fhField mostly, but not completely,
interchangeably. It may take some poking before we find all the little
breakages.
Package: flowPloidy
Commit: 7e8089ab6f7166dccfc21ad989f2cfa739f227b3
Author: smithty <smithty@ONOTTRA825833PL.agr.gc.ca>
Date: 2026-03-27 16:23:45 -0400
Commit message:

 Version bump, a handful of formatting updates
Package: flowPloidy
Commit: 6e25baf529144eb2172cb4e2f457a108926291bd
Author: smithty <smithty@ONOTTRA825833PL.agr.gc.ca>
Date: 2026-03-27 16:22:10 -0400
Commit message:

 Added nameField: pick metadata descriptor for sample name

Same default behaviour (GUID), but now you can pick a different field if
that's no good.
Package: flowPloidy
Commit: 606a0e68b1d8a9a49a436b5b28b3fb3ace10dfc5
Author: smithty <smithty@ONOTTRA825833PL.agr.gc.ca>
Date: 2026-03-27 16:18:37 -0400
Commit message:

 added fhMetadata

Provides an improved version of viewFlowChannels, with additional details
about the data, and a selection of metadata parametes.
Package: flowPloidy
Commit: 2a661281f854e446edde57f9580c75f9a80dbcb0
Author: smithty <smithty@ONOTTRA825833PL.agr.gc.ca>
Date: 2026-03-27 16:16:28 -0400
Commit message:

 Improved/clarified documentation of trimRaw
Package: flowPloidy
Commit: 32c26b3b80cb2e802267c079ef455a38f186b608
Author: smithty <smithty@ONOTTRA825833PL.agr.gc.ca>
Date: 2026-03-27 13:02:03 -0400
Commit message:

 Change fhFile, Readme

Not sure how relevant these are in 2026. Will need to review as part of the
general refresh.
Package: flowPloidy
Commit: 9a37af453b41099916840f52b5a534b09e100082
Author: smithty <smithty@ONOTTRA825833PL.agr.gc.ca>
Date: 2026-03-27 13:01:20 -0400
Commit message:

 formatting changes to DESCRIPTION
Package: flowPloidy
Commit: e9f5a800f01de31853978f8566c4a63a271dfefc
Author: smithty <smithty@ONOTTRA802465XL.agr.gc.ca>
Date: 2023-03-17 10:50:06 -0400
Commit message:

 updated readme

removed out of date notes about endopolyploidy.
Package: flowPloidy
Commit: 4831ed810a2c157c3d08957755d3104117bcd225
Author: smithty <smithty@ONOTTRA802465XL.agr.gc.ca>
Date: 2023-03-17 10:43:04 -0400
Commit message:

 Changed fhFile to use $FILENAME instead of $GUID

Should be more consistent across different flow cytometers this way. Note
that I use basename, as some cytometers report the full name with paths,
others just the basename.
Package: GSVA
Commit: 96182d6ff196951601abd01c565574d40a3b167d
Author: Robert Castelo <robert.castelo@upf.edu>
Date: 2026-04-16 19:09:36 +0200
Commit message:

 Code refactoring. Added unit test for spatial data input
Package: SingleCellSignalR
Commit: 2f421d2ac2f042996d743404a1bf621e2f6c943e
Author: jcolinge <65902924+jcolinge@users.noreply.github.com>
Date: 2026-04-16 18:29:39 +0200
Commit message:

 update resampling and added cellNetHeatmap
Package: SingleCellSignalR
Commit: f50bfdd48b5650d635ceb4d2316bcf483c67df06
Author: jcolinge <65902924+jcolinge@users.noreply.github.com>
Date: 2026-03-30 15:34:47 +0200
Commit message:

 sync with github
Package: SingleCellSignalR
Commit: 7f8b887f539c9e4eadfeb3a2103c955e09e3234e
Author: jcolinge <65902924+jcolinge@users.noreply.github.com>
Date: 2026-03-30 15:24:08 +0200
Commit message:

 sync with github
Package: msdata
Commit: 04043a9e735c68d55a308833b1a8b7107e2f923e
Author: Laurent Gatto <lgatto@protonmail.ch>
Date: 2026-04-16 17:59:49 +0200
Commit message:

 fix
Package: GSVA
Commit: a71ecf62e5cfffcde612f9b8b157df13cbf0bf7c
Author: Robert Castelo <robert.castelo@upf.edu>
Date: 2026-04-16 17:26:56 +0200
Commit message:

 Added support for PLAGE to work with large datasets stored using a DelayedArray backend, such as HDF5.
Package: MetaboCoreUtils
Commit: 1daa859a3d23e108531f28b46d44e6094bbf3b02
Author: Johannes Rainer <johannes.rainer@gmail.com>
Date: 2026-04-16 16:47:56 +0200
Commit message:

 docs: add Gabriele as author and add mapping info
Package: MetaboCoreUtils
Commit: 2c5bc40bddc3134bcf1b47bcc3a8f8f4d45759d9
Author: Johannes Rainer <5506112+jorainer@users.noreply.github.com>
Date: 2026-04-16 16:20:32 +0200
Commit message:

 Merge pull request #88 from rformassspectrometry/gabri

feat: new mapping/translation utilities for translating columns name
Package: MetaboCoreUtils
Commit: af81754d00e0319f3c1c97984022695661d59a94
Author: Gabriele Tomè <39188419+gabrieletome@users.noreply.github.com>
Date: 2026-04-16 15:32:18 +0200
Commit message:

 refactor: default `map` to `softwareMappingSchema()`
Package: MetaboCoreUtils
Commit: b0233637afa00bae8accb52ab611a83bf5868b91
Author: Gabriele Tomè <39188419+gabrieletome@users.noreply.github.com>
Date: 2026-04-16 14:38:48 +0200
Commit message:

 refactor: address Johannes comments.
Package: MetaboCoreUtils
Commit: cfc5d0bfae0860da352f911c231d296b03709ea6
Author: Gabriele Tomè <39188419+gabrieletome@users.noreply.github.com>
Date: 2026-04-13 16:47:24 +0200
Commit message:

 feat: new mapping/translation utilities for translating columns names across different software.
Package: MSstatsBioNet
Commit: 8991901fbddff64892d0aa3872f1562a2388e6aa
Author: tonywu1999 <wu.anthon@northeastern.edu>
Date: 2026-04-16 10:57:04 -0400
Commit message:

 fix(visualization): Remove bidirectional edges (#97)
Package: MSstatsBioNet
Commit: 3a8dadd4e341e32777b688fc4881e752054f09b4
Author: tonywu1999 <wu.anthon@northeastern.edu>
Date: 2026-04-16 10:32:19 -0400
Commit message:

 feat(cytoscapeNetworks): Add functionality to delete an edge (#96)
Package: MungeSumstats
Commit: 5dfb8a62cabc8de8596f4952e341f9bcbe10065e
Author: Al-Murphy <alanmurph94@hotmail.com>
Date: 2026-04-16 10:12:47 -0400
Commit message:

 Bug Fix: saving VCFs as gzip files
Package: tximeta
Commit: 84442de89872056810c7f2cd2fe2b5f3af187d66
Author: Mike Love <mikelove@users.noreply.github.com>
Date: 2026-04-16 10:07:26 -0400
Commit message:

 version bump
Package: tximeta
Commit: ef4fe7b38b01a61f1112af6fdc2b664dbbbdab4d
Author: Michael Love <mikelove@users.noreply.github.com>
Date: 2026-04-16 10:07:01 -0400
Commit message:

 Merge pull request #100 from plbaldoni/devel

Adding egdeR/limma reference for DTU analysis pipeline
Package: tximeta
Commit: 370b9d2ee6b8563b8d8801df9537970bc55a4264
Author: Pedro Baldoni <pedrobaldoni@gmail.com>
Date: 2026-04-16 13:56:40 +1000
Commit message:

 Adding egdeR/limma reference for DTU analysis pipeline
Package: MSstats
Commit: 1c9655510a77e6fe2ad3f89c8e248b7c8240b2ca
Author: Mateusz Staniak <mtst@mstaniak.pl>
Date: 2026-04-16 15:13:51 +0200
Commit message:

 version bump
Package: MSstats
Commit: 0dc6686446e16a388a8dec992dd93ba1eea065cb
Author: Tony Wu <wu.anthon@northeastern.edu>
Date: 2026-04-14 17:21:19 -0400
Commit message:

 Revert "fix(profile-plot): Only add error bars to profile plots if bounds exist (#197)"

This reverts commit 9b4cf2396fa8e718422c11e57094db833033e999.
Package: MSstats
Commit: 9b4cf2396fa8e718422c11e57094db833033e999
Author: tonywu1999 <wu.anthon@northeastern.edu>
Date: 2026-04-14 17:15:27 -0400
Commit message:

 fix(profile-plot): Only add error bars to profile plots if bounds exist (#197)
Package: MSstats
Commit: 293e522638c13d5307ee4a4dddca906fe5e0f229
Author: tonywu1999 <wu.anthon@northeastern.edu>
Date: 2026-04-14 17:08:57 -0400
Commit message:

 fix(profile-plot): Fix summaries for profile plots for protein turnover (#196)
Package: MSstats
Commit: 8ebaa573f46b33f75396294f56a7d4c5ff4b80fc
Author: tonywu1999 <wu.anthon@northeastern.edu>
Date: 2026-04-14 16:52:07 -0400
Commit message:

 fix(profile-plots): Add summary abundance value to summary profile plot (#195)
Package: MSstats
Commit: f07eeeb0801aa41dde90b2dbc8607822b9c3a3a9
Author: tonywu1999 <wu.anthon@northeastern.edu>
Date: 2026-04-14 16:36:33 -0400
Commit message:

 feat(plotting): Refactor QC plot headings to be compatible for protein turnover (#194)
Package: MSstats
Commit: 941aa84002aed08c82fbca3fa827cf9a5035a3bb
Author: tonywu1999 <wu.anthon@northeastern.edu>
Date: 2026-04-14 15:24:34 -0400
Commit message:

 feat(protein turnover): per-label statistics and multi-label summarization (#193)
Package: MSstats
Commit: 5b5042ca8feb72f4061d990f4e5da44e6bb041c9
Author: tonywu1999 <wu.anthon@northeastern.edu>
Date: 2026-04-13 13:14:39 -0400
Commit message:

 feat(normalization): Introduce normalization with unlabeled peptides for protein turnover (#192)
Package: MSstats
Commit: e0ee7f954c117f86e7dcf4cf96bf4c5d2e7167e2
Author: tonywu1999 <wu.anthon@northeastern.edu>
Date: 2026-04-13 09:13:03 -0400
Commit message:

 fix(summarization): Fix Rename ref regression covariate to ref_covariate for SRM experiments (#191)
Package: MSstats
Commit: df6f00579e3aeeff333efb6b0cdd916cd8375af1
Author: tonywu1999 <wu.anthon@northeastern.edu>
Date: 2026-04-12 18:03:27 -0400
Commit message:

 refactor(summarization): Rename ref regression covariate to ref_covariate for SRM experiments (#190)
Package: MSstats
Commit: d9418ed4956489de61ea31985fe86161db1341e6
Author: tonywu1999 <wu.anthon@northeastern.edu>
Date: 2026-04-12 17:21:27 -0400
Commit message:

 fix(checks): support 'heavy'/'light' IsotopeLabelType explicitly (#189)
Package: MSstats
Commit: 0cd7d27352dc119515c2d1e8954a983ed7fb510d
Author: tonywu1999 <wu.anthon@northeastern.edu>
Date: 2026-04-07 15:38:38 -0400
Commit message:

 tests(normalization): Add unit tests for normalization (#188)
Package: MSstats
Commit: daf666db9514f344f55af76d25ee39b9d58c57eb
Author: tonywu1999 <wu.anthon@northeastern.edu>
Date: 2026-04-07 10:11:58 -0400
Commit message:

 tests(anomaly-scores): Fix unit tests for anomaly score based summarization (#187)
Package: MSstats
Commit: eb64e4f38a62af2e4c293195154d820892ea1eaa
Author: Devon Kohler <35807256+devonjkohler@users.noreply.github.com>
Date: 2026-03-13 13:27:56 -0400
Commit message:

 Fix weight calculation to avoid division by zero
Package: MSstats
Commit: 27d176b73c7932a1a15141ca07b735331dda5546
Author: Devon Kohler <35807256+devonjkohler@users.noreply.github.com>
Date: 2026-03-13 13:07:46 -0400
Commit message:

 Add variance floor to address degenerate variance estimates
Package: MSstats
Commit: 58084b96ae84cdae9f887d7410195476e5ead18e
Author: Devon Kohler <35807256+devonjkohler@users.noreply.github.com>
Date: 2026-03-11 09:41:11 -0400
Commit message:

 Fix single feature bug in linear summarization
Package: MSstats
Commit: 2448662fb84abf1bb9b58045454f119401f6edc9
Author: Devon Kohler <35807256+devonjkohler@users.noreply.github.com>
Date: 2026-03-09 13:27:56 -0400
Commit message:

 Fix parallel export of variables in data processing
Package: MSstats
Commit: 217fc3b71e1ebbaf95851a2eaa4c645f742d6aec
Author: tonywu1999 <wu.anthon@northeastern.edu>
Date: 2026-02-25 17:14:49 -0500
Commit message:

 fix(linear-summarization): Remove interaction term check to enable features with colons (#183)
Package: MSstats
Commit: dc8bc9a915954409fe7bea399e69abd85252c9bc
Author: devonjkohler <devonjkohler@gmail.com>
Date: 2026-02-21 08:09:21 -0500
Commit message:

 updated anomaly weighting
Package: MSstats
Commit: de817e134819d8f3ea389c47c4c66740e02284be
Author: tonywu1999 <wu.anthon@northeastern.edu>
Date: 2026-01-29 15:58:32 -0500
Commit message:

 fix(global-standards): Enable multiple precursors for the same reference peptide (#180)
Package: wavClusteR
Commit: 201d8d890f22558cc06c2e45f538c8cbd089c9e6
Author: FedericoComoglio <federico.comoglio@gmail.com>
Date: 2026-04-16 14:55:49 +0200
Commit message:

 Fix import of makeTxDbFromUCSC
Package: SMAD
Commit: f6c002551ff7e2698cf9893c548977ed1a4259d4
Author: Qingzhou Zhang <5545472+zqzneptune@users.noreply.github.com>
Date: 2026-04-16 09:42:57 -0300
Commit message:

 docs: update PE definition and copyright year in README
Package: SMAD
Commit: 257bbc1dde95f172f5fca62b6694ecad994aa98c
Author: Qingzhou Zhang <5545472+zqzneptune@users.noreply.github.com>
Date: 2026-04-16 09:40:13 -0300
Commit message:

 docs: update documentation to include BioID support and correct PE algorithm references
Package: SMAD
Commit: 35ba48ca729deadb01d69a845ac425186b97c882
Author: Qingzhou Zhang <5545472+zqzneptune@users.noreply.github.com>
Date: 2026-04-16 09:34:51 -0300
Commit message:

 fix: update PE and SAINTexpress algorithm citations and documentation links
Package: SMAD
Commit: b5f1b5c0c53927f65ccca4998fd7743931e3cc00
Author: Qingzhou Zhang <5545472+zqzneptune@users.noreply.github.com>
Date: 2026-04-16 09:12:09 -0300
Commit message:

 docs: update README to include BioID support, expanded algorithm descriptions, and usage examples
Package: SMAD
Commit: e885d568cd84d8af024c2105ee1fce39cb1e7bd2
Author: Qingzhou Zhang <5545472+zqzneptune@users.noreply.github.com>
Date: 2026-04-16 09:07:14 -0300
Commit message:

 chore: update documentation to reflect package version 1.27.4
Package: SMAD
Commit: 0d3005841c95e7a6406913d791ae2db169c3c523
Author: Qingzhou Zhang <5545472+zqzneptune@users.noreply.github.com>
Date: 2026-04-16 09:01:51 -0300
Commit message:

 fix: correct logical operators in GetDICE.cpp, simplify Fastmat constructor declarations, and increment package version to 1.27.4
Package: gDRutils
Commit: cc6fa624c9c1934522b57130bd80e9e0ed344ac7
Author: Bartek <32614650+bczech@users.noreply.github.com>
Date: 2026-04-16 12:55:43 +0200
Commit message:

 Merge pull request #183 from gdrplatform/GDR-3306

Gdr 3306
Package: gDRutils
Commit: 96d8ba1116215c892280be4fdb7c04152792ac87
Author: Bartosz Czech <czechb3@sc1nc004is02.eth.rsiec.sc1.science.roche.com>
Date: 2026-04-14 07:05:16 +0000
Commit message:

 test: update unit tests
Package: gDRutils
Commit: e38c8e7f8722f466c86ca701dbc2f6cee25e1bbd
Author: Bartosz Czech <czechb3@sc1nc004is02.eth.rsiec.sc1.science.roche.com>
Date: 2026-04-14 07:03:07 +0000
Commit message:

 chore: bump version and update NEWS.md
Package: gDRutils
Commit: 2a3f3398b3ee9a2ad54e5be9ecc361fa05922548
Author: Bartosz Czech <czechb3@sc1nc004is02.eth.rsiec.sc1.science.roche.com>
Date: 2026-04-14 07:03:01 +0000
Commit message:

 test: add unit tests
Package: gDRutils
Commit: 093446db985d4856d0c5a8a77296ac7e5630e0cb
Author: Bartosz Czech <czechb3@sc1nc004is02.eth.rsiec.sc1.science.roche.com>
Date: 2026-04-14 07:02:48 +0000
Commit message:

 doc: reoxygenate
Package: gDRutils
Commit: 1a2285c56de95b953f4d4141c8417c398b4d85cb
Author: Bartosz Czech <czechb3@sc1nc004is02.eth.rsiec.sc1.science.roche.com>
Date: 2026-04-14 07:02:38 +0000
Commit message:

 refactor: add support for metadata
Package: DOtools
Commit: 16d61849e7de4c03061260df1eabce549432a742
Author: MarianoRuzJurado <mariani95@gmx.de>
Date: 2026-04-16 11:43:41 +0200
Commit message:

 Fix missing import in Description
Package: GSVA
Commit: fbc462a62e1edcf9f67fbdc3480a3aa7eb31a3ba
Author: Robert Castelo <robert.castelo@upf.edu>
Date: 2026-04-16 11:02:10 +0200
Commit message:

 Code refactoring
Package: MetMashR
Commit: d3308d4812d841ab2b289f44536800dcf00bcee8
Author: Gavin Rhys Lloyd <grlloyd@users.noreply.github.com>
Date: 2026-04-16 10:00:12 +0100
Commit message:

 import gglpot2 and rebuild

bump version
update news
documentation
add ggplot2 to namespace import
Package: MetMashR
Commit: 133ad42c8fcc3ed8de9804963a717657ba0e7f57
Author: Gavin Rhys Lloyd <grlloyd@users.noreply.github.com>
Date: 2026-04-16 09:29:07 +0100
Commit message:

 Merge remote-tracking branch 'upstream/devel' into devel
Package: MetMashR
Commit: 2df19c288fb47bf236d336027739263aedd6a56b
Author: Gavin Rhys Lloyd <grlloyd@users.noreply.github.com>
Date: 2025-10-03 08:25:08 +0100
Commit message:

 bump github actions cache
Package: SpectriPy
Commit: 17b98dec60a602119e21ad7ffbd6a4fcd8716d35
Author: Johannes Rainer <5506112+jorainer@users.noreply.github.com>
Date: 2026-04-16 09:53:16 +0200
Commit message:

 Merge pull request #92 from rformassspectrometry/jomain

Performance and stability improvements
Package: SpectriPy
Commit: 909af13426b06e975985a7be3f421c5ab2ebb21d
Author: jorainer <johannes.rainer@gmail.com>
Date: 2026-04-16 09:11:35 +0200
Commit message:

 feat: force realization of subset on data replacement

- All data replacement functions force the Python data to have the same subset
  than the backend (issue #90).
Package: SpectriPy
Commit: f3a6fbf713371d3351974e11c538811c2b1cfd5a
Author: jorainer <johannes.rainer@gmail.com>
Date: 2026-04-16 07:00:16 +0200
Commit message:

 refactor: improve assignment operations

- Improve `$<-` etc replacement operations avoiding to replace the full data.
- Update documentation.
- Add `py_realize_subset()` to subset the data structure in Python based on the
  lazy/delayed subset operation in R (issue #90).
Package: SpectriPy
Commit: 291cdc408275b6390048a20114111efb70c26fe9
Author: jorainer <johannes.rainer@gmail.com>
Date: 2026-04-10 14:55:59 +0200
Commit message:

 feat: add spectraNames<- method for MsBackendPy
Package: structToolbox
Commit: b88a25e4258e765282b8ea4b2af51b47bdace64a
Author: Gavin Rhys Lloyd <grlloyd@users.noreply.github.com>
Date: 2026-04-16 08:49:31 +0100
Commit message:

 version bump and update news
Package: structToolbox
Commit: a2d0c9d0d0f29f837f35796b742de3470eff35ca
Author: Gavin Rhys Lloyd <grlloyd@users.noreply.github.com>
Date: 2026-04-15 18:53:28 +0100
Commit message:

 remove stato

(deprecated; see https://github.com/computational-metabolomics/struct/pull/40)
Package: structToolbox
Commit: 23b3f77aad7018846040f822dd0cf877a6934a56
Author: Gavin Rhys Lloyd <grlloyd@users.noreply.github.com>
Date: 2026-02-21 17:33:59 +0000
Commit message:

 Update .Rbuildignore
Package: structToolbox
Commit: 9ec75b1c1b99e7161567ac078e1eea05688f0dd1
Author: Gavin Rhys Lloyd <grlloyd@users.noreply.github.com>
Date: 2026-02-21 12:45:44 +0000
Commit message:

 pkgdown update

- split vignette for website
Package: structToolbox
Commit: 26684e1b0b844c541c092be3fc7a0ac0f76c9bf9
Author: Gavin Rhys Lloyd <grlloyd@users.noreply.github.com>
Date: 2026-02-20 15:40:00 +0000
Commit message:

 Update check-bioc.yml
Package: zellkonverter
Commit: 3ef5a2bfde3ed67e0478ca5972c7a5c9dab6d0d7
Author: Luke Zappia <luke@data-intuitive.com>
Date: 2026-04-16 09:25:37 +0200
Commit message:

 Prepare NEWS for Bioc 3.23 release
Package: spatialFDA
Commit: 72ba4df95507f3134e011f2be06f3db2d3cab392
Author: mjemons <martin.emons@gmail.com>
Date: 2026-04-16 09:25:53 +0200
Commit message:

 add bioRxiv preprint
Package: splatter
Commit: 007df795eb844a45840e137947ec01ec0d340c44
Author: Luke Zappia <luke@data-intuitive.com>
Date: 2026-04-16 09:12:19 +0200
Commit message:

 Fix mfa deprecation tests
Package: igblastr
Commit: 0456d02c14e87160f0d71d9f883e1cfd2064d1f6
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2026-04-15 23:25:38 -0700
Commit message:

 igblastr 1.1.28

o Rename makeogrannote() --> extract_intdata_from_ogrdb_json()
o Add extract_auxdata_from_ogrdb_json()
o Add auxdata to all the OGRDB built-in germline dbs for mouse.
Package: HIBAG
Commit: dd2c9ff3fde89ecb38192abf394a0091258d408a
Author: Xiuwen Zheng <zhengxwen@gmail.com>
Date: 2026-04-16 00:07:39 -0500
Commit message:

 AArch64 NEON code
Package: SAIGEgds
Commit: dadbd385d93d16a9537b31737d5c2a3ac8b5696a
Author: Xiuwen Zheng <zhengxwen@gmail.com>
Date: 2026-04-15 22:52:06 -0500
Commit message:

 use R_useDynamicSymbols
Package: SMAD
Commit: 1487bd81e0e6fb1cc1390ea2fdf68ff5398982a8
Author: Qingzhou Zhang <5545472+zqzneptune@users.noreply.github.com>
Date: 2026-04-16 00:14:23 -0300
Commit message:

 version bump
Package: dnaEPICO
Commit: 69c98c524fe0c2545c00ef21771f283fe47604cd
Author: Paul Ruiz <ruizpint@qut.edu.au>
Date: 2026-04-16 12:29:55 +1000
Commit message:

 Bioconductor Review changes 0.99.13
Package: twoddpcr
Commit: 1db19f1057b323c7a5820b4409ef5c3d175e28e2
Author: ctta <ctta@Totos-MacBook-Air.local>
Date: 2026-04-15 23:13:33 +0100
Commit message:

 Fixes stochastic k-NN test failure by setting seed
Package: GSVA
Commit: 6bca9090e0fcf35fff1fba5fecb46bfe926e5f66
Author: Robert Castelo <robert.castelo@upf.edu>
Date: 2026-04-15 21:11:46 +0200
Commit message:

 Some code reorganization and unit test fixing
Package: SeqArray
Commit: 44f15cc059c8df08c03b7df3d67543e31c26ad1f
Author: Xiuwen Zheng <zhengxwen@gmail.com>
Date: 2026-04-15 13:54:02 -0500
Commit message:

 use R_useDynamicSymbols
Package: GSVA
Commit: f0b36cb0a86d64482131f24ad72b5f30a1f0b8b2
Author: Robert Castelo <robert.castelo@upf.edu>
Date: 2026-04-15 20:37:39 +0200
Commit message:

 Fixing unit tests for KCDF estimation
Package: DeconvoBuddies
Commit: 2ec3f7ea5053abdd943e28b9f47a910870795e55
Author: lahuuki <lahuuki@gmail.com>
Date: 2026-04-15 13:59:30 -0400
Commit message:

 Add update message for 1.3.3
Package: DeconvoBuddies
Commit: 11e249735ead9d3310ebf45a4ca1ee1994f25fae
Author: lahuuki <lahuuki@gmail.com>
Date: 2026-04-15 13:53:54 -0400
Commit message:

 Updaet Description version + date
Package: DeconvoBuddies
Commit: a20ca2a72ca4772c80ed5884d114a9c062e09d2a
Author: lahuuki <lahuuki@gmail.com>
Date: 2026-04-15 13:53:23 -0400
Commit message:

 Import ggrepel
Package: DeconvoBuddies
Commit: a5c297b10f14d2d6bf78cb76d67390fc442fb5ad
Author: lahuuki <lahuuki@gmail.com>
Date: 2026-04-15 13:52:53 -0400
Commit message:

 Update docs
Package: DeconvoBuddies
Commit: 7bae8ae5531369a769fa7b8f1f4ef0bae0ecd2b6
Author: lahuuki <lahuuki@gmail.com>
Date: 2026-04-15 13:52:23 -0400
Commit message:

 Add lable_points example + improve param description
Package: DeconvoBuddies
Commit: 4174d7633f4fc6f7b913d3bf0eed99a01b497879
Author: lahuuki <lahuuki@gmail.com>
Date: 2026-04-15 13:51:54 -0400
Commit message:

 Update RoxygenNote
Package: DeconvoBuddies
Commit: 085104c60be20d8e795cf6c081bd8e0293e56e87
Author: lahuuki <lahuuki@gmail.com>
Date: 2026-04-15 13:21:00 -0400
Commit message:

 use !!sym(catagorey) to preserve x-axis label
Package: PlinkMatrix
Commit: b2afa0bdca1f4337eb62ee3a790854251233a7a3
Author: vjcitn <stvjc@channing.harvard.edu>
Date: 2026-04-15 13:16:53 -0400
Commit message:

 finally scotch last warning by putting a return tag on the -pkg doxygen
Package: wavClusteR
Commit: 9a88711102c9115968708d9f684214d3be384e11
Author: FedericoComoglio <federico.comoglio@gmail.com>
Date: 2026-04-15 18:05:38 +0200
Commit message:

 Bump version
Package: GSVA
Commit: f9f541d9570904b23bc69db2bb653374a09eef0a
Author: Robert Castelo <robert.castelo@upf.edu>
Date: 2026-04-15 18:08:17 +0200
Commit message:

 Fixing NAMESPACE imports
Package: GSVA
Commit: c5c09ed8fc5525e4592a380c8d21ed56e122221d
Author: Robert Castelo <robert.castelo@upf.edu>
Date: 2026-04-15 17:24:56 +0200
Commit message:

 Added support for Z-score to work with large datasets stored using a DelayedArray backend, such as HDF5. Some R code reorganization. Added some unit tests.
Package: velociraptor
Commit: df72d5d0e9acc8a0025c2b587954b383fec1b145
Author: Kevin Rue-Albrecht <kevinrue67@gmail.com>
Date: 2026-04-15 16:19:32 +0100
Commit message:

 fix PyPI dependencies for MacOSXArm (#106)

* fix pypi dependencies for MacOSXArm

* caching issue on mac?

* caching issue

* try disabling caching with /nocache
Package: BatChef
Commit: 363bea5fd7b67e4477dafab963674737f6b4f320
Author: zuinelena3 <elena.zuin3@gmail.com>
Date: 2026-04-15 17:06:50 +0200
Commit message:

 Bump version: 0.99.12
Package: BatChef
Commit: 4b75f32c53bed5ee5cfb9aafee7c4d8fbc497020
Author: zuinelena3 <elena.zuin3@gmail.com>
Date: 2026-04-15 17:06:13 +0200
Commit message:

 Solve errors in tests
Package: destiny
Commit: a20a8122d19db1c9ad5e1aa045ca3bb64e77923e
Author: Philipp A. <flying-sheep@web.de>
Date: 2026-04-15 17:03:43 +0200
Commit message:

 fix: scores in plot_gene_relevance (#71)
Package: ChromSCape
Commit: 07f11b08088f1ab5319d545deb158175a3b128fe
Author: Pacome Prompsy <pacome.pr@gmail.com>
Date: 2026-04-15 16:31:40 +0200
Commit message:

 Fixed DESCRIPTION file
Package: Rarr
Commit: dbe43af5aa360a37bd1db45b5e947e35a6f95505
Author: Hugo Gruson <git@hugogruson.fr>
Date: 2026-04-15 16:19:50 +0200
Commit message:

 Re-render README
Package: Rarr
Commit: a650e6df90bd4d97daaaa76e1e5159df9c64901c
Author: Hugo Gruson <git@hugogruson.fr>
Date: 2026-04-15 16:05:10 +0200
Commit message:

 Use simpler check workflow
Package: Rarr
Commit: 200027b39e5d95b4827e933c40bc4520e82ba423
Author: Hugo Gruson <git@hugogruson.fr>
Date: 2026-04-15 15:42:29 +0200
Commit message:

 Set permission on main workflow
Package: DeeDeeExperiment
Commit: 714b2f84dc32fe441bb6b93614e83c3ed71c2291
Author: Najla Abassi <abassi.nejla96@gmail.com>
Date: 2026-04-15 15:13:49 +0200
Commit message:

 updating news and version
Package: DeeDeeExperiment
Commit: b3b8567716bdcd3865e2504aa6e8b0c00f19d5cb
Author: Najla Abassi <abassi.nejla96@gmail.com>
Date: 2026-04-15 15:13:23 +0200
Commit message:

 harmonizing the column names in the shaken formats of FEA tables
Package: DeeDeeExperiment
Commit: 94dd550476afc23335f6a3f3aa7c5258113ee26a
Author: Najla Abassi <abassi.nejla96@gmail.com>
Date: 2026-04-15 15:10:46 +0200
Commit message:

 adding citation to the DDE paper
Package: PlinkMatrix
Commit: 67f20199abadcf435cb663a3f322b34591c6bfb5
Author: vjcitn <stvjc@channing.harvard.edu>
Date: 2026-04-15 09:00:03 -0400
Commit message:

 removing docs to scotch warning, bumping version
Package: AnnotationHubData
Commit: e77fbe8fdb32d67b1773d4b2c4c99f6880738826
Author: lshep <lori.shepherd@roswellpark.org>
Date: 2026-04-15 08:18:20 -0400
Commit message:

 Add Parquet as valid source type
Package: destiny
Commit: 2463b0ef1569b812b8e2a38b2eb5f88b54ffa3e8
Author: Philipp A. <flying-sheep@web.de>
Date: 2026-04-15 13:31:53 +0200
Commit message:

 fix: vendor smth.gaussian (#73)
Package: scTypeEval
Commit: 8d66e4d6780eda1e8bf67dc1142002119032417b
Author: JGarnica22 <j.garnica22@gmail.com>
Date: 2026-04-15 13:15:00 +0200
Commit message:

 upgrade version
Package: scTypeEval
Commit: 10104dd68d8f248a003dd1638f7656ca3dc90365
Author: JGarnica22 <j.garnica22@gmail.com>
Date: 2026-04-15 13:11:53 +0200
Commit message:

 fix: do not test verbose FALSE as scran is giving warning deprecated messages
Package: scTypeEval
Commit: 5cf5c5dbd228f7eb1c6133fb3f5d6b3635326c88
Author: JGarnica22 <j.garnica22@gmail.com>
Date: 2026-04-14 14:27:43 +0200
Commit message:

 add: correct 4.3 release
Package: igblastr
Commit: b2b6b346452611726667754b20df8dbb6fd6be45
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2026-04-15 03:55:06 -0700
Commit message:

 igblastr 1.1.27

o Add helper function parse_imgt_fasta_headers().

o Add arguments 'codon_starts' and 'no.warning' to compute_auxdata().

o Add arguments 'with.auxdata' and 'imgt.fasta' to
  install_custom_germline_db(). Not documented yet.

o Improve auxiliary data computed by install_IMGT_germline_db() by
  using the 8th field (codon start) of the IMGT FASTA headers to
  eliminate NAs in the coding_frame_start and extra_bps columns
  of the auxdata data.frame. Thanks to this, these two columns
  are now NA-free for most organisms supported by IMGT.
  This improvement allows us to include the auxiliary data in
  the resulting germline db of most IMGT organisms.
Package: velociraptor
Commit: 3a5440c948f8a3ec16a16a02d9fafcb04b128b5b
Author: Kevin Rue-Albrecht <kevinrue67@gmail.com>
Date: 2026-04-15 11:45:00 +0100
Commit message:

 Attempt to fix macOS environment (#105)

* toy with the macOSArm environment

* fix version and news
Package: SMAD
Commit: 13c39c65eaee0d91bc3becd81c65bc031248edcf
Author: Qingzhou Zhang <5545472+zqzneptune@users.noreply.github.com>
Date: 2026-04-13 15:18:35 -0300
Commit message:

 refactor: modernize C++ code and remove legacy Boost dependencies to address compiler warnings
Package: SMAD
Commit: 455f64763120c2562c920a3a3eaa4efcc6634544
Author: Qingzhou Zhang <5545472+zqzneptune@users.noreply.github.com>
Date: 2026-04-13 15:09:43 -0300
Commit message:

 chore: fix macOS build by removing cached binaries and adding BH dependency
Package: SMAD
Commit: c4418acb343dd47eb2b01d9f4657be9a72f40bbd
Author: Qingzhou Zhang <5545472+zqzneptune@users.noreply.github.com>
Date: 2026-04-13 15:09:33 -0300
Commit message:

 chore: fix macOS build by removing cached binaries and adding BH dependency
Package: GSVA
Commit: bc3fa775657808b5f02251421b9d2b1646d80798
Author: Robert Castelo <robert.castelo@upf.edu>
Date: 2026-04-15 11:38:08 +0200
Commit message:

 Adding the ondisk and nzcount slots and methods to the zscoreParam class. Some unit tests have been amended
Package: Chromatograms
Commit: 01b62cfda77a71325871b3827a01fb21f82d1dd4
Author: Philippine Louail <philippine.louail@outlook.com>
Date: 2026-04-15 10:16:12 +0200
Commit message:

 Merge pull request #53 from rformassspectrometry/phili

fix FUN and MAPFUN parameter  passing.
Package: Chromatograms
Commit: 9609d876506bbe6039c0e91bb6dc7284af1995c7
Author: Philippine Louail <127301965+philouail@users.noreply.github.com>
Date: 2026-04-15 09:54:35 +0200
Commit message:

 fix param passing
Package: Chromatograms
Commit: cb8ae8ae704ce65f830f32fdc752b4ab964999f1
Author: Philippine Louail <127301965+philouail@users.noreply.github.com>
Date: 2026-04-08 18:09:03 +0200
Commit message:

 Update helpers.R
Package: Chromatograms
Commit: 700718db6c878ff408ec105c53a78420e9fcace7
Author: Philippine Louail <127301965+philouail@users.noreply.github.com>
Date: 2026-04-08 16:57:17 +0200
Commit message:

 optimizes matchRtimes and fix parameter passing to FUN and MAPFUN
Package: FLAMES
Commit: 445c76fe4ead5b96892785508db0d64e1ec018f8
Author: Changqing Wang <wang.ch@wehi.edu.au>
Date: 2026-04-14 23:33:40 +1000
Commit message:

 fix: scuttle deprecation warning
Package: FLAMES
Commit: 21ec6f5edf42c02048bdd7da444f3b24586ae5a0
Author: Changqing Wang <wang.ch@wehi.edu.au>
Date: 2026-04-14 17:32:57 +1000
Commit message:

 fix: reduce quantify_gene RAM usage
Package: FLAMES
Commit: dcb57f69256a26c9345c02f5ce17d489baa5ccc3
Author: Changqing Wang <wang.ch@wehi.edu.au>
Date: 2026-04-14 16:50:04 +1000
Commit message:

 misc: typos
Package: FLAMES
Commit: 10a0a0ae675bb6b99b64f07c777f415f096630a3
Author: Changqing Wang <wang.ch@wehi.edu.au>
Date: 2026-04-14 16:26:20 +1000
Commit message:

 misc: add more tests
Package: wavFeatExt
Commit: 8d72788513f49048c1f6c1ce683810afa51d2f13
Author: Maharani Ahsani Ummi <maharaniahsani@itb.ac.id>
Date: 2026-04-15 11:24:51 +0700
Commit message:

 Address reviewer comments: documentation, vignette, naming, examples
Package: wavFeatExt
Commit: a5e397171c1c1fdac3b32ea20da74c9dacf8e8b8
Author: Maharani Ahsani Ummi <maharaniahsani@itb.ac.id>
Date: 2026-04-15 10:56:18 +0700
Commit message:

 Address reviewer comments: documentation, vignette, naming, examples
Package: wavFeatExt
Commit: ff0952d2c1686e705a1c2eddbad101928606d430
Author: Maharani Ahsani Ummi <maharaniahsani@itb.ac.id>
Date: 2026-04-15 10:33:15 +0700
Commit message:

 Address reviewer comments: documentation, vignette, naming, examples
Package: wavFeatExt
Commit: 94bb92ce778954d84b628c68dd10146b8d2ee18b
Author: Maharani Ahsani Ummi <maharaniahsani@itb.ac.id>
Date: 2026-04-15 10:20:09 +0700
Commit message:

 Address reviewer comments: documentation, vignette, naming, examples
Package: imageTCGAutils
Commit: b8249cb9e944cc14a7603ed924ebdb848eb86d7a
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2026-04-14 19:38:37 -0400
Commit message:

 version bump 0.99.24
Package: SNPRelate
Commit: ca5d9bcd09a1cda85d3568176ef504fcef2cab23
Author: Xiuwen Zheng <zhengxwen@gmail.com>
Date: 2026-04-14 17:40:34 -0500
Commit message:

 gnrDistPerm to .Call
Package: dnaEPICO
Commit: d3d24bbd3e2358ab1365c7a0c48cc139dbd6eb21
Author: Paul Ruiz <ruizpint@qut.edu.au>
Date: 2026-04-15 08:16:44 +1000
Commit message:

 Bioconductor Review changes 0.99.12
Package: dnaEPICO
Commit: 591e545779ac6e3848beef044a00c6656375389d
Author: Paul Ruiz <ruizpint@qut.edu.au>
Date: 2026-04-15 08:13:19 +1000
Commit message:

 Bioconductor Review changes 0.99.12
Package: sigvar
Commit: a99da2a200c44749b8aea3d074f3a289ac3c9dfa
Author: Maike mac mini <maike.morrison@gmail.com>
Date: 2026-04-14 16:09:51 -0600
Commit message:

 Remove sigvar.rproj from github
Package: sigvar
Commit: 5302b0fc9f2f7a0cbf545fe52c2a3bad5a290c64
Author: Maike Morrison <52480745+MaikeMorrison@users.noreply.github.com>
Date: 2026-04-14 16:08:04 -0600
Commit message:

 Delete sigvar.Rproj
Package: OncoSimulR
Commit: da7bcce36a71b0fd5cc5cee1c6c478d96b8463e1
Author: Ramon @ Triturus
Date: 2026-04-14 23:50:39 +0200
Commit message:

 4.13.3: new exprtk;  all.equal correctly using check.attributes = FALSE
</div>
Package: rhdf5
Commit: 34ead9799748f9e420522f8e989e0935e09841ed
Author: Hugo Gruson <git@hugogruson.fr>
Date: 2026-03-14 12:37:29 +0100
Commit message:

 Add CRAN machines workflow
Package: rhdf5
Commit: a70feca88b155c41f3319a76962601f9948590e4
Author: Hugo Gruson <git@hugogruson.fr>
Date: 2026-03-12 15:38:02 +0100
Commit message:

 Document ... arg in deprecated H5Pget_version()
Package: sigvar
Commit: 84a4ea143f20869f675c4565c39b9ba0a153359b
Author: Maike mac mini <maike.morrison@gmail.com>
Date: 2026-04-14 15:41:44 -0600
Commit message:

 Descrive version 0.99.6
Package: sigvar
Commit: 7881a4353fcfd87cd5c7607f596a5094f6c530ee
Author: Maike mac mini <maike.morrison@gmail.com>
Date: 2026-04-14 15:40:28 -0600
Commit message:

 Increment version number to 0.99.6
Package: sigvar
Commit: bbdc2b0a5f4ecff8ac3bf7036d96a9f4bd7300f5
Author: Maike mac mini <maike.morrison@gmail.com>
Date: 2026-04-14 15:40:19 -0600
Commit message:

 Update documentation -- switching Maike and Nicolas as maintainer
Package: HistoImagePlot
Commit: 8f585f5d7e88f7891f422fd9f5de0a561fb276c2
Author: billila <ilaria.billato@studenti.unipd.it>
Date: 2026-04-14 22:49:51 +0200
Commit message:

 version bump 0.99.10
Package: HistoImagePlot
Commit: 1e51a1957ebf691db2098ec124c3f63ae3fbdb2d
Author: billila <ilaria.billato@studenti.unipd.it>
Date: 2026-04-14 22:48:57 +0200
Commit message:

 add Software in biocViews
Package: imageTCGAutils
Commit: dd1a784711f25ff88c09b62e9dce4b8c88722d85
Author: billila <ilaria.billato@studenti.unipd.it>
Date: 2026-04-14 22:20:22 +0200
Commit message:

 version bump 0.99.23
Package: imageTCGAutils
Commit: 41001d501af8b6bcf202313016f0166c3eafd212
Author: billila <ilaria.billato@studenti.unipd.it>
Date: 2026-04-14 21:26:33 +0200
Commit message:

 add Software in biocViews
Package: OncoSimulR
Commit: aec09e3f9c0656545cbe529598c2e403b483ea2d
Author: Ramon @ Triturus
Date: 2026-04-14 22:30:26 +0200
Commit message:

 4.13.2; fixed vignette engine and miscell tests and minor functions
</div>
Package: ADaCGH2
Commit: 0f5b7c2f1af987d63ff7360040627dbdc826299f
Author: Ramon @ Triturus
Date: 2026-04-14 21:47:49 +0200
Commit message:

 2.51.2: mainly fixed Authors@R
</div>
Package: imageFeatureTCGA
Commit: 6fb8e9f54327728d3ea0707c3a041cd64d44a4b9
Author: billila <ilaria.billato@studenti.unipd.it>
Date: 2026-04-14 22:08:37 +0200
Commit message:

 version bump 0.99.69
Package: imageFeatureTCGA
Commit: 67afce4aec7e731e9533e064039082ece3bd6753
Author: billila <ilaria.billato@studenti.unipd.it>
Date: 2026-04-14 22:08:03 +0200
Commit message:

 add AnnotationDbi
Package: rnaseqGene
Commit: 0d7e27dde3ca9875cf94770ed9de35e346dd3676
Author: Mike Love <mikelove@users.noreply.github.com>
Date: 2026-04-14 15:28:39 -0400
Commit message:

 typo
Package: imageFeatureTCGA
Commit: 311b63bf1c90e29207173eb7639490f4de87545f
Author: billila <ilaria.billato@studenti.unipd.it>
Date: 2026-04-14 21:17:12 +0200
Commit message:

 version bump 0.99.68
Package: imageFeatureTCGA
Commit: 257bf5b8218f8caeccaa8b11b58adaf63fb6a39d
Author: billila <ilaria.billato@studenti.unipd.it>
Date: 2026-04-14 21:16:51 +0200
Commit message:

 typo (ops)
Package: rnaseqGene
Commit: 4c092a2676654a23e4a23d924a52819af3a07b8c
Author: Mike Love <mikelove@users.noreply.github.com>
Date: 2026-04-14 14:46:25 -0400
Commit message:

 some edits to organization
Package: rnaseqGene
Commit: 454839dd003006564153d43f3a7015c2b3f46767
Author: Michael Love <mikelove@users.noreply.github.com>
Date: 2026-04-14 11:27:12 -0400
Commit message:

 Merge pull request #7 from vjcitn/vjc

This fixes one dead link and provides more operational details in an appendix
Package: rnaseqGene
Commit: e3e5660b0555301d8681bbf4a53c0ee3f160ea67
Author: vjcitn <stvjc@channing.harvard.edu>
Date: 2026-04-13 10:00:41 -0400
Commit message:

 bump version
Package: rnaseqGene
Commit: 0bb1b5c863eac85d2f32c3d97963e04d419435ef
Author: vjcitn <stvjc@channing.harvard.edu>
Date: 2026-04-13 10:00:19 -0400
Commit message:

 finish new text, test
Package: rnaseqGene
Commit: b97aca409a5729b7e89efa32f0c8d211f7823bcd
Author: vjcitn <stvjc@channing.harvard.edu>
Date: 2026-04-13 06:53:55 -0400
Commit message:

 fix dead link on 'executing snakemake' and add some explanation of snakemake parameters,
one of which may be obsolete.
Package: imageFeatureTCGA
Commit: a12cfca129e79382c8cfa192993bc726875f213d
Author: billila <ilaria.billato@studenti.unipd.it>
Date: 2026-04-14 20:57:26 +0200
Commit message:

 version bump 0.99.67
Package: imageFeatureTCGA
Commit: 94deedc36ca202b5c2c0a3183e5278a79377f568
Author: billila <ilaria.billato@studenti.unipd.it>
Date: 2026-04-14 20:55:19 +0200
Commit message:

 add yml in Suggests and Software in biocViews
Package: imageTCGAutils
Commit: 7e38019428cb4dcc7a6e16ec1fd9b5932425095a
Author: billila <ilaria.billato@studenti.unipd.it>
Date: 2026-04-14 20:41:30 +0200
Commit message:

 version bump 0.99.22
Package: imageTCGAutils
Commit: 17616bbee15e340613e99c2520ce8e00c3444e95
Author: billila <ilaria.billato@studenti.unipd.it>
Date: 2026-04-14 16:28:15 +0200
Commit message:

 add importCONCH function
Package: imageTCGAutils
Commit: ba8c2c0c07891411d629b7ae94bbaf54d9ce00dd
Author: billila <ilaria.billato@studenti.unipd.it>
Date: 2026-04-14 16:22:57 +0200
Commit message:

 rename CONCH in importCONCH
Package: imageTCGAutils
Commit: a38cd3e8385036917838d21e71efe2a26c365cfe
Author: billila <ilaria.billato@studenti.unipd.it>
Date: 2026-04-14 16:22:34 +0200
Commit message:

 rename CONCH in importCONCH
Package: imageTCGAutils
Commit: 3bb0eb722a172042a49528ae80a7de199e5f08be
Author: billila <ilaria.billato@studenti.unipd.it>
Date: 2026-04-14 16:17:11 +0200
Commit message:

 release version
Package: imageTCGAutils
Commit: 3e48c82b1558eafde2d316018f7c20c79eb86bd2
Author: billila <ilaria.billato@studenti.unipd.it>
Date: 2026-04-14 16:16:25 +0200
Commit message:

 keep old version
Package: imageTCGAutils
Commit: 6e1269d36374f522ed23075e48e1b62ae8473b39
Author: billila <ilaria.billato@studenti.unipd.it>
Date: 2026-04-14 16:15:17 +0200
Commit message:

 release version
Package: imageTCGAutils
Commit: 87f76560a63abda10ebce577b292c0ce3fd94ad1
Author: billila <ilaria.billato@studenti.unipd.it>
Date: 2026-04-14 12:49:08 +0200
Commit message:

 typo
Package: imageTCGAutils
Commit: 336722e9f4a38311fe9d6634ed84faab49e41b9a
Author: billila <ilaria.billato@studenti.unipd.it>
Date: 2026-04-14 12:48:31 +0200
Commit message:

 add installation in vignette
Package: imageTCGAutils
Commit: 2d16c7507e9eee1dbfc0422d511b2b7a10ab3b80
Author: billila <ilaria.billato@studenti.unipd.it>
Date: 2026-04-14 12:46:24 +0200
Commit message:

 remove Software in biocViews
Package: imageTCGAutils
Commit: e7cb52214929d5c076ad571d25b738297dc31d55
Author: Marcel Ramos Pérez <LiNk-NY@users.noreply.github.com>
Date: 2026-03-26 12:31:46 -0400
Commit message:

 Migrate pr_check.yml to ci.yml (#6)

* Add ci.yml reusable-workflow wrapper

* Remove pr_check.yml (replaced by ci.yml)
Package: imageFeatureTCGA
Commit: 749664ac924029d47cf1be5b9d8bda16f3297501
Author: billila <ilaria.billato@studenti.unipd.it>
Date: 2026-04-14 20:34:09 +0200
Commit message:

 version bump 0.99.66
Package: imageFeatureTCGA
Commit: a95843b4872f9ce63d5a6202a281824742175c77
Author: billila <ilaria.billato@studenti.unipd.it>
Date: 2026-04-14 12:42:58 +0200
Commit message:

 remove Software in biocViews
Package: imageFeatureTCGA
Commit: 2d756a5d75d8c7844ac8bc32fa10f8c266e88ed7
Author: Marcel Ramos Pérez <LiNk-NY@users.noreply.github.com>
Date: 2026-03-26 12:09:56 -0400
Commit message:

 Migrate pr_check.yml to ci.yml (#47)

* Add ci.yml reusable-workflow wrapper

* Remove pr_check.yml (replaced by ci.yml)
Package: sigvar
Commit: e5d5ae138a1aa3c08851a73118e3c8aaab9078be
Author: Maike mac mini <maike.morrison@gmail.com>
Date: 2026-04-14 11:56:05 -0600
Commit message:

 Make Nicolas maintainer again and add returns entry for time_weights
Package: sigvar
Commit: adf4c3c735ee1491dfd4b07184905b2ea8ee1c9f
Author: Maike mac mini <maike.morrison@gmail.com>
Date: 2026-04-14 11:50:55 -0600
Commit message:

 Add withr to DESCRIPTION for local seed setting
Package: sigvar
Commit: 12ed1403c427180e68a246cc145281623cd43d73
Author: Maike mac mini <maike.morrison@gmail.com>
Date: 2026-04-14 11:43:28 -0600
Commit message:

 Replace set.seed with withr::with_seed to satisfy bioconductor requirements
Package: sigvar
Commit: 0b275df924f91d2142e36c9b920e9319c6f3ed35
Author: Maike mac mini <maike.morrison@gmail.com>
Date: 2026-04-14 11:24:24 -0600
Commit message:

 Replace T/F with TRUE/FALSE or use different variable name for t or T
Package: parati
Commit: 9232fff2bd7e17ffc0ede189fc9f342f7dabc07b
Author: liangyong1991 <496187474@qq.com>
Date: 2026-04-15 01:21:56 +0800
Commit message:

 Fix haplotype inference bug and add helper module
Package: GSVA
Commit: eb92b8c56d1ab2d4ddcb64b9d64f7e6e0e79e058
Author: Robert Castelo <robert.castelo@upf.edu>
Date: 2026-04-14 18:49:43 +0200
Commit message:

 Added unit test for ggplotting with gsvaEnrichment()
Package: scRNAseqApp
Commit: 0f153a29107506bd619a1d54305e034c4152b0f2
Author: Jianhong Ou <jianhong.ou@gmail.com>
Date: 2026-04-14 12:25:27 -0400
Commit message:

 add datasets available date
Package: biocViews
Commit: 22333758f19906cbeb86732735da45c6989105db
Author: A Wokaty <awokaty@users.noreply.github.com>
Date: 2026-04-14 12:01:30 -0400
Commit message:

 Bump version to 1.79.6
Package: biocViews
Commit: 1992e98d0dbd90c6d8e57c0352f9693d1189ccd7
Author: A Wokaty <awokaty@users.noreply.github.com>
Date: 2026-04-14 12:00:38 -0400
Commit message:

 Add UnsupportedPlatforms
Package: HistoImagePlot
Commit: 2592ac1cce75236e31afba3c4f710d55043639c0
Author: billila <ilaria.billato@studenti.unipd.it>
Date: 2026-04-14 17:27:52 +0200
Commit message:

 version bump 0.99.9
Package: HistoImagePlot
Commit: 068add6652925d4a13ba15a453ab591951c6da19
Author: billila <ilaria.billato@studenti.unipd.it>
Date: 2026-04-14 16:32:57 +0200
Commit message:

 NEWS 1.0.0 release version
Package: HistoImagePlot
Commit: 66654cadbbe41e3b74e482039e4ace26220fadc3
Author: billila <ilaria.billato@studenti.unipd.it>
Date: 2026-04-14 12:44:27 +0200
Commit message:

 package:HistoImagePlot
Package: HistoImagePlot
Commit: e5eba3c32f68ebb7525806ed97f6d4726e4a1166
Author: billila <ilaria.billato@studenti.unipd.it>
Date: 2026-04-14 12:21:49 +0200
Commit message:

 add Installation in vignette
Package: HistoImagePlot
Commit: 9d63d0d3cafbceec7e1524d8ffcf7e8fa52eef8d
Author: billila <ilaria.billato@studenti.unipd.it>
Date: 2026-04-14 12:21:33 +0200
Commit message:

 add a sentence in DESCRIPTION file
Package: HistoImagePlot
Commit: 74722dcd4a43f494794fa240a7b2d1bf462d0ca4
Author: billila <ilaria.billato@studenti.unipd.it>
Date: 2026-04-14 10:31:36 +0200
Commit message:

 add HistoImagePlot name in vignette
Package: HistoImagePlot
Commit: 898cf69694639ab23a48cd74cdbc6de813120065
Author: billila <ilaria.billato@studenti.unipd.it>
Date: 2026-04-14 10:30:30 +0200
Commit message:

 rm software biocViews
Package: GSVA
Commit: 3e3c9d1fc289dbcd04d1e792544c21f2165cba79
Author: Robert Castelo <robert.castelo@upf.edu>
Date: 2026-04-14 17:33:55 +0200
Commit message:

 Some R code cleanup, fixed some unit tests
Package: CrcBiomeScreen
Commit: 6dc7ff67c363d2b090a50352e5f576a912192918
Author: Chronostasis <ngzh5554@leeds.ac.uk>
Date: 2026-04-14 15:00:39 +0100
Commit message:

 Address reviewer comments: update vignette, functions and test-example.
Package: GSVA
Commit: 42ef069d24dd745eb3fbc48f54dcfcccef42e556
Author: Robert Castelo <robert.castelo@upf.edu>
Date: 2026-04-14 15:58:03 +0200
Commit message:

 Fixed several potential bugs
Package: MsCoreUtils
Commit: 27729469bf57aba85021931795f6827bad62ee22
Author: Johannes Rainer <5506112+jorainer@users.noreply.github.com>
Date: 2026-04-14 15:47:35 +0200
Commit message:

 Merge pull request #147 from gabrieletome/gabri

fix: handle all type of errors
Package: MsCoreUtils
Commit: c686c6b2a0e1eb28feb01189de14b52dc17ff28f
Author: Gabriele Tomè <39188419+gabrieletome@users.noreply.github.com>
Date: 2026-04-14 13:39:16 +0200
Commit message:

 refactor: add tests for non simpleError in retry()
Package: MsCoreUtils
Commit: ce0fb97e4ac2061f34790c40fccd7f6184215540
Author: Gabriele Tomè <39188419+gabrieletome@users.noreply.github.com>
Date: 2026-04-13 16:03:31 +0200
Commit message:

 fix: handle all type of errors
Package: MsCoreUtils
Commit: 9b66007de781f2012fe64a65082993e50b99584f
Author: Johannes Rainer <5506112+jorainer@users.noreply.github.com>
Date: 2026-04-09 11:17:07 +0200
Commit message:

 Merge pull request #146 from rformassspectrometry/jomain

refactor: add parameters warningsAsErrors and verbose to retry()
Package: MsCoreUtils
Commit: 2a02c66bf94f76769c9ca0d0027f5f4afba7442c
Author: Johannes Rainer <johannes.rainer@gmail.com>
Date: 2026-04-09 11:08:23 +0200
Commit message:

 fix: unit test error messages
Package: MsCoreUtils
Commit: 0376375f17eb323144fbd70faa07db330c085bb1
Author: Johannes Rainer <johannes.rainer@gmail.com>
Date: 2026-04-09 09:06:26 +0200
Commit message:

 refactor: add parameters warningsAsErrors and verbose to retry()
Package: kissDE
Commit: e433b63b8d8b58889957e55daaf94ca700620152
Author: Aurélie Siberchicot <aurelie.siberchicot@univ-lyon1.fr>
Date: 2026-04-14 12:44:25 +0200
Commit message:

 Add a codemeta.json file
Package: kissDE
Commit: fa407f6add080e88eceb455044688de4d815c6c3
Author: Aurélie Siberchicot <aurelie.siberchicot@univ-lyon1.fr>
Date: 2026-04-14 12:41:38 +0200
Commit message:

 Correct some misprints
Package: kissDE
Commit: f67bddef0b40337128289c084b3a5e351b912bc2
Author: Aurélie Siberchicot <aurelie.siberchicot@univ-lyon1.fr>
Date: 2026-04-07 13:23:34 +0200
Commit message:

 Merge pull request #16 from lbbe-software/devel

Merge pull request #15 from lbbe-software/master
Package: kissDE
Commit: bfa1875cd26584097eb5f5dc3674d7af6c0383a4
Author: Aurélie Siberchicot <aurelie.siberchicot@univ-lyon1.fr>
Date: 2026-04-07 13:23:01 +0200
Commit message:

 Merge pull request #15 from lbbe-software/master

Merge
Package: kissDE
Commit: d8f89e199729d373599fa3a7a3be74ba7cdee0d0
Author: Aurélie Siberchicot <aurelie.siberchicot@univ-lyon1.fr>
Date: 2026-04-07 11:30:35 +0200
Commit message:

 Merge pull request #14 from lbbe-software/devel

Update the R-CMD-check workflow
Package: kissDE
Commit: db3c69ae557287be7da8939822d259e5f0ec1db3
Author: Aurélie Siberchicot <aurelie.siberchicot@univ-lyon1.fr>
Date: 2026-03-30 14:46:47 +0200
Commit message:

 Merge pull request #13 from lbbe-software/devel

Devel
Package: kissDE
Commit: 3216c677a3f0e5e476f0f2f6e666d4b75055d01c
Author: Aurélie Siberchicot <aurelie.siberchicot@univ-lyon1.fr>
Date: 2026-03-26 18:12:36 +0100
Commit message:

 Merge pull request #12 from lbbe-software/devel

Update R-CMD-check workflow
Package: kissDE
Commit: 3fe3bda5dec3e724499bae97ddc25f109b1af4b0
Author: Aurélie Siberchicot <aurelie.siberchicot@univ-lyon1.fr>
Date: 2026-03-26 18:06:21 +0100
Commit message:

 Merge pull request #11 from lbbe-software/devel

Update the R-CMD-check workflow
Package: kissDE
Commit: d948e8c07b1db9cb6c30623dc6bf475606920061
Author: Aurélie Siberchicot <aurelie.siberchicot@univ-lyon1.fr>
Date: 2026-03-26 16:28:05 +0100
Commit message:

 Merge pull request #10 from lbbe-software/devel

Devel
Package: kissDE
Commit: 83612c05132bde97efff874b85eb5478a3219ff1
Author: Aurélie Siberchicot <aurelie.siberchicot@univ-lyon1.fr>
Date: 2026-03-26 15:56:35 +0100
Commit message:

 Merge pull request #9 from lbbe-software/devel

Update the R-CMD-check workflow
Package: kissDE
Commit: 8fde7354d4f011dbdbe42f2e41af091843cacc05
Author: Aurélie Siberchicot <aurelie.siberchicot@univ-lyon1.fr>
Date: 2026-03-26 15:35:41 +0100
Commit message:

 Merge pull request #8 from lbbe-software/devel

Update the R-CMD-check workflow to test the check with the quarto vig…
Package: kissDE
Commit: b2175cb218d256d52109181043564fdd8747f35c
Author: Aurélie Siberchicot <aurelie.siberchicot@univ-lyon1.fr>
Date: 2026-03-25 17:38:40 +0100
Commit message:

 Merge pull request #7 from lbbe-software/devel

Devel
Package: kissDE
Commit: 31e179a62fb9bd2f33e89de70e6d5e028fa3d70d
Author: Aurélie Siberchicot <aurelie.siberchicot@univ-lyon1.fr>
Date: 2026-03-23 17:58:56 +0100
Commit message:

 Merge pull request #6 from lbbe-software/devel

Devel
Package: kissDE
Commit: 4a60676b029ff9701c17850bca5184baedb98d06
Author: Aurélie Siberchicot <aurelie.siberchicot@univ-lyon1.fr>
Date: 2026-03-23 16:55:48 +0100
Commit message:

 Merge pull request #5 from lbbe-software/devel

Devel
Package: msqrob2
Commit: 56df1a31bc76e0d4104901022d236934b5579de7
Author: Lieven <lieven@MacBook-Pro-van-Lieven-2.local>
Date: 2026-04-14 09:35:32 +0200
Commit message:

 label all chunks vignettes
Package: msqrob2
Commit: 5ac47583190f2b5257264d9b8cc625623d502fa9
Author: Lieven <lieven@vpnk097.ugent.be>
Date: 2026-04-13 23:50:56 +0200
Commit message:

 include sessionInfo in DIA-NN vignette
Package: msqrob2
Commit: a152d0e0077a0ed8c818239b7bc2e01c8c04cda7
Author: Lieven <lieven@vpnk097.ugent.be>
Date: 2026-04-13 23:48:44 +0200
Commit message:

 include sessionInfo in spectronaut vignette
Package: msqrob2
Commit: c60a389936c817367aedbaf2a3445686db93cdc0
Author: Lieven <lieven@MacBook-Pro-van-Lieven-2.local>
Date: 2026-04-13 22:18:10 +0200
Commit message:

 update NEWS
Package: msqrob2
Commit: efda2d3c10f9720d86785667bc76812d958f8bf9
Author: Lieven <lieven@MacBook-Pro-van-Lieven-2.local>
Date: 2026-04-13 22:09:51 +0200
Commit message:

 update version bump to odd
Package: msqrob2
Commit: 994990ba6b9c438bc2fbfb533167ca78f1f8b5c5
Author: Lieven <lieven@MacBook-Pro-van-Lieven-2.local>
Date: 2026-04-13 21:52:02 +0200
Commit message:

 update vignettes
Package: msqrob2
Commit: 82aa75c15c9e4dd6860e8ee2fa54358860e05010
Author: Lieven <lieven@MacBook-Pro-van-Lieven-2.local>
Date: 2026-04-13 19:32:45 +0200
Commit message:

 add packages for vignettes to suggest
Package: msqrob2
Commit: 034d81b0dfbcfdf9f091392095d98934aef5e8da
Author: Lieven <lieven@MacBook-Pro-van-Lieven-2.local>
Date: 2026-04-13 19:26:35 +0200
Commit message:

 add packages for vignettes to suggest
Package: msqrob2
Commit: f8d446ea861f4dfc2597b941966800696f222bba
Author: Lieven <lieven@MacBook-Pro-van-Lieven-2.local>
Date: 2026-04-13 19:20:51 +0200
Commit message:

 update vignettes
Package: msqrob2
Commit: c71525a288e8b45f48c4cf609f6507bd70893265
Author: Lieven <lieven@vpnz080.ugent.be>
Date: 2026-04-11 00:58:38 +0200
Commit message:

 improve style collect-plot-results.R and calculateNormFactors.R
Package: msqrob2
Commit: d85762d4025405b96817f6cff4e893d063eff69c
Author: Lieven <lieven@MacBook-Pro-van-Lieven-2.local>
Date: 2026-04-10 23:19:57 +0200
Commit message:

 add example to msqrobCollect in collect-plot-results.R
Package: msqrob2
Commit: b990e47369b1ac589b5c832deb8e857dd1f03cb7
Author: Lieven <lieven@MacBook-Pro-van-Lieven-2.local>
Date: 2026-04-10 22:42:35 +0200
Commit message:

 nobars is moved to reformulas, however it is still included in lme4 for legacy. This gives one warning per session. However, when formally importing nobars from reformulas we get a warning in the build process and do not pas R CMD check.
Package: msqrob2
Commit: 9ec0b2694997f87b5cd622d33ef068933688a20f
Author: Lieven <lieven@MacBook-Pro-van-Lieven-2.local>
Date: 2026-04-10 22:02:23 +0200
Commit message:

 resolve warnings and notes bioc-Check
Package: msqrob2
Commit: 3989d87618d214ad91232d62e1e99a4750a9cfae
Author: Lieven <lieven@MacBook-Pro-van-Lieven-2.local>
Date: 2026-04-10 21:02:48 +0200
Commit message:

 fix note w.r.t. no visible binding for global variables in pipes (plotVolcano) and no visible binding for  global functions
Package: msqrob2
Commit: 0ec042e4d3f351f96152282f10f7eefcdd5b872a
Author: Lieven <lieven@MacBook-Pro-van-Lieven-2.local>
Date: 2026-04-10 20:37:40 +0200
Commit message:

 fix error in example plotVolcano add library(ggplot)
Package: msqrob2
Commit: 983dbd1b13603e179c3292c0554925c149c2175e
Author: Lieven <lieven@MacBook-Pro-van-Lieven-2.local>
Date: 2026-04-10 20:28:27 +0200
Commit message:

 add createPairwiseContrasts function to msqrob-utils.R
Package: msqrob2
Commit: 0e3068e8575dfb5731b4f7f85e00c8e8a11ebb4b
Author: Lieven <lieven@MacBook-Pro-van-Lieven-2.local>
Date: 2026-04-10 19:02:46 +0200
Commit message:

 add collect_plot_results.R wiht  msqrobCollect volcanoPlot functions
Package: msqrob2
Commit: 7b05f4ea5fb6dfc5dc154b63b18546a9d13ca22f
Author: Lieven <lieven@MacBook-Pro-van-Lieven-2.local>
Date: 2026-04-10 13:07:44 +0200
Commit message:

 fix calcNormFactors documentation
Package: msqrob2
Commit: a151f2f2cfbd26d8dc603e8b2dfba41e3e4f95a5
Author: Lieven <lieven@vpnz193.ugent.be>
Date: 2026-04-10 01:44:42 +0200
Commit message:

 fix aliases calculateNormFactors and corresponding documentation
Package: msqrob2
Commit: 3f5dccba7a837caaaaaa6f34c6a24fea38fc297a
Author: Lieven <lieven@vpnz193.ugent.be>
Date: 2026-04-10 01:30:35 +0200
Commit message:

 update msqrob.R remove argument w from .create_model, remove ::: call for .vcovUnscaled, properly use constructed vcovUnscaled in case of missing parameters
Package: msqrob2
Commit: 32fae13ad69af3281ff1025755bc5265be65811a
Author: Lieven <lieven@vpnz193.ugent.be>
Date: 2026-04-10 00:31:28 +0200
Commit message:

 add aliases calculateNormFactors + fix example
Package: msqrob2
Commit: 16374d94dd503f739db6b440c2c6698502c8d942
Author: Lieven <lieven@vpnz193.ugent.be>
Date: 2026-04-09 23:58:19 +0200
Commit message:

 add importFrom stats median to calculateNormFactors + roxygenize
Package: msqrob2
Commit: a7d07bbd3fdb5117b6aafcc1877b0b9e57e63840
Author: Lieven <lieven@vpnz193.ugent.be>
Date: 2026-04-09 23:19:56 +0200
Commit message:

 change R version from 4.6 to devel in check-bioc.yml + add matrixStats to import field in description file
Package: msqrob2
Commit: b14db0019e44ad9f53d23b0d46153304172ac694
Author: Lieven <lieven@vpnz193.ugent.be>
Date: 2026-04-09 22:31:52 +0200
Commit message:

 calculateNormFactors: add to collate field + add roxygen documentation / update R version for devel
Package: msqrob2
Commit: 3e3532a81f79b0705e2dc3639bc9c1bb2861d180
Author: Lieven <lieven@MacBook-Pro-van-Lieven-2.local>
Date: 2026-04-09 19:57:08 +0200
Commit message:

 add calculation of norm factors
Package: Moonlight2R
Commit: 8b179eaf5e3b2d3f0e16fdf43bed6a865df3c9af
Author: AlessiaCampo <59013682+AlessiaCampo@users.noreply.github.com>
Date: 2026-04-14 11:51:27 +0200
Commit message:

 Fix160 fgsea implementation (#161)

* Added new DAPsmatrix dataset and implemented fgsea in the FEA() method

* Updated NEWS.md

* Update FEA data input parameter name, added new FEA dataset for fgsea results, added new test for fgsea

* Fix on versioning, added DAPsmatrix in datalist, fixes in spacing and descriptions

---------

Co-authored-by: Alessia Campo <acampo@kb-bioinfo01.cancer.dk>
Package: dnaEPICO
Commit: 0e1b0ede73ffd49fc81536b6ccec4e8795f8127b
Author: Paul Ruiz <ruizpint@qut.edu.au>
Date: 2026-04-14 19:16:20 +1000
Commit message:

 Bioconductor Review changes 0.99.11
Package: dnaEPICO
Commit: 76d15ec64d93af87bc0f2e66621ebd258e193fc3
Author: Paul Ruiz <ruizpint@qut.edu.au>
Date: 2026-04-14 19:09:12 +1000
Commit message:

 Bioconductor Review changes 0.99.11
Package: dnaEPICO
Commit: 99f76ecf80315c5c6ead38dbb9c8bb259a1b59ff
Author: Paul Ruiz <ruizpint@qut.edu.au>
Date: 2026-04-14 17:52:40 +1000
Commit message:

 Bioconductor Review changes 0.99.11
Package: dnaEPICO
Commit: 194cbedea998b2d4c928d5716b6ca7e04d853f9c
Author: Paul Ruiz <ruizpint@qut.edu.au>
Date: 2026-04-14 17:38:36 +1000
Commit message:

 Bioconductor Review changes 0.99.11
Package: dnaEPICO
Commit: 87b84d9e4ae7e0b8fcbd8c16797c4d98e70c1a98
Author: Paul Ruiz <ruizpint@qut.edu.au>
Date: 2026-04-14 17:23:53 +1000
Commit message:

 Bioconductor Review changes 0.99.11
Package: dnaEPICO
Commit: 728de2707cfb27ac08100c32d85b1b4218c6d2c3
Author: Paul Ruiz <ruizpint@qut.edu.au>
Date: 2026-04-14 17:09:04 +1000
Commit message:

 Bioconductor Review changes 0.99.11
Package: dnaEPICO
Commit: b536a30dec3cb280220dc6ba57db5f82ee87c921
Author: Paul Ruiz <ruizpint@qut.edu.au>
Date: 2026-04-14 16:10:24 +1000
Commit message:

 Bioconductor Review changes 0.99.11
Package: dnaEPICO
Commit: 980e28333c70ba18386bafe721a6584ae64402c1
Author: Paul Ruiz <ruizpint@qut.edu.au>
Date: 2026-04-14 14:27:53 +1000
Commit message:

 Bioconductor Review changes 0.99.11
Package: dnaEPICO
Commit: 3cdc927a5768edaad3231c3c5238d9ff51678713
Author: Paul Ruiz <ruizpint@qut.edu.au>
Date: 2026-04-14 11:46:56 +1000
Commit message:

 Recover dnaEPICO refactor files
Package: dnaEPICO
Commit: 7d270313505159ab17362b3fc4a38dd74271b733
Author: Paul Ruiz <ruizpint@qut.edu.au>
Date: 2026-04-08 10:25:51 +1000
Commit message:

 estimateLC.R salivaEPIC
Package: BASiCS
Commit: 743d2620fd4b2cfe006c103022ad1ccc86c41cc8
Author: Catalina Vallejos <catalina.vallejos@ed.ac.uk>
Date: 2026-04-14 10:05:29 +0100
Commit message:

 version bump
Package: BASiCS
Commit: 401e7678d1628cd4fa8331a194b8717b751ca750
Author: Catalina Vallejos <catalina.vallejos@ed.ac.uk>
Date: 2026-04-14 10:04:53 +0100
Commit message:

 change & to &&
Package: BASiCS
Commit: fd0fa71bb75d3bf36feaecf9c2d2c77f44d6db0e
Author: Catalina Vallejos <catalina.vallejos@ed.ac.uk>
Date: 2026-04-14 09:19:48 +0100
Commit message:

 remove :::
Package: BASiCS
Commit: b5737b877ec0433b3f157af4aac88b988b92ceab
Author: Catalina Vallejos <catalina.vallejos@ed.ac.uk>
Date: 2026-04-14 09:19:10 +0100
Commit message:

 Remove :::
Package: amplican
Commit: b9832827ed13ca4786004f54f561925638be5319
Author: JokingHero <kornel.labun@gmail.com>
Date: 2026-04-14 10:45:57 +0200
Commit message:

 somehow data.frame instead of data.table
Package: amplican
Commit: 5719175b095e0c3c7c9f2664913c054832d073c6
Author: JokingHero <kornel.labun@gmail.com>
Date: 2026-04-01 19:38:03 +0200
Commit message:

 remove heterogeneity plot as it completely fails on large data and is a source of failures when knitting
Package: amplican
Commit: 3081b8c854323314b580710a0d33e2a5dde320b8
Author: JokingHero <kornel.labun@gmail.com>
Date: 2026-04-01 15:05:58 +0200
Commit message:

 improve memory efficiency in the reports / templates
Package: amplican
Commit: 13cf4f43ced534275153f40bf3abbda8384aab68
Author: JokingHero <kornel.labun@gmail.com>
Date: 2026-03-31 16:50:50 +0200
Commit message:

 further memory efficiency improvements
Package: Rarr
Commit: bea1d4b51eaf506308c5dd4f1e1bfe00895cc015
Author: Hugo Gruson <git@hugogruson.fr>
Date: 2026-04-14 10:18:07 +0200
Commit message:

 Add missing newline in error msg
Package: Rarr
Commit: af84c6ea441c2709a0a91d0223ae989966135da7
Author: Hugo Gruson <git@hugogruson.fr>
Date: 2026-04-13 12:43:35 +0200
Commit message:

 Bump version
Package: Rarr
Commit: 6f218273d84dc47efb5858eae3eb8558e082e103
Author: Hugo Gruson <git@hugogruson.fr>
Date: 2026-04-13 11:59:11 +0200
Commit message:

 Run touchstone on r-devel again
Package: Rarr
Commit: 88e8a141011281afdbe2c47a4f07874322b6687f
Author: Hugo Gruson <git@hugogruson.fr>
Date: 2026-04-13 11:49:36 +0200
Commit message:

 Skip transpose codec for arrays of dimension 1
Package: Rarr
Commit: 2572b44c3bbaf101680fc0c52bdd2eac5cca7b68
Author: Hugo Gruson <git@hugogruson.fr>
Date: 2026-04-13 11:22:11 +0200
Commit message:

 Fix codecs ordering

Fix #146
Package: struct
Commit: 72c97d41e0608f4455899c5731c69508d6884f1c
Author: Gavin Rhys Lloyd <grlloyd@users.noreply.github.com>
Date: 2026-04-13 17:24:06 +0100
Commit message:

 Chore/39/replace rols dependency (#40)

* remove deprecated stato classes

these were deprecated several releases ago and are no longer used

* remove rols

replace with internal implementation

* fix for when ontology is zero length

* add .onload

sets ontology online option to true/false and detects correct state when loading the package

* add ontology method for model_seq

returns ontology for all models as well as the model sequence itself as a nested list

* fix typo in documentation

* rename ontology_set_online()

shortened to ontology_online()

* update vignette...

...to reflect changes to ontology interface

* Update README.rst

* import jsonlite

* fix .onload

defer the message to .onattach as per guidance

* import URLencode

* add documentation...

...for ontology(M) where M is a model sequence

* fix terms documentation for ontology_list

* remove stato generics

* fix tests for ontology_online

* import httr2

* fix BiocCheck warnings

- Use of "Error" in error message
- Use of class(m)[1]== in iterators
- Use of paste0 in stop()
- Escape curly brackets in roxygen blocks

* update news and version bump
Package: mutscan
Commit: 971f0ecb33196d86e7adbf16af5709ad9f85961f
Author: Charlotte Soneson <charlottesoneson@gmail.com>
Date: 2026-04-14 09:18:01 +0200
Commit message:

 Redocument

Co-authored-by: Michael Stadler <stadler.michael@gmail.com>
Co-authored-by: Charlotte Soneson <charlottesoneson@gmail.com>
Package: mutscan
Commit: 06b96c239219bf2018de4f1eaf83db53da6785c3
Author: Charlotte Soneson <charlottesoneson@gmail.com>
Date: 2026-04-14 09:17:50 +0200
Commit message:

 Update C++ standard to C++17

Co-authored-by: Michael Stadler <stadler.michael@gmail.com>
Co-authored-by: Charlotte Soneson <charlottesoneson@gmail.com>
Package: mutscan
Commit: acc2cd8aa3e7cc2c4afba8d581e5a141d17ad694
Author: Charlotte Soneson <charlottesoneson@gmail.com>
Date: 2026-04-14 09:17:26 +0200
Commit message:

 Adapt to changes in limma 3.67.1

Co-authored-by: Michael Stadler <stadler.michael@gmail.com>
Co-authored-by: Charlotte Soneson <charlottesoneson@gmail.com>
Package: mutscan
Commit: d5b6fd6f8dd076f420ca46ba8462d3b6fc4b19f7
Author: Charlotte Soneson <charlottesoneson@gmail.com>
Date: 2026-04-14 09:16:35 +0200
Commit message:

 Replace calcNormFactors with normLibSizes

Co-authored-by: Michael Stadler <stadler.michael@gmail.com>
Co-authored-by: Charlotte Soneson <charlottesoneson@gmail.com>
Package: mutscan
Commit: 600b89df71e0cad23f4daa9e651db6231a587a4d
Author: Charlotte Soneson <charlottesoneson@gmail.com>
Date: 2026-04-14 09:15:23 +0200
Commit message:

 Bump version

Co-authored-by: Michael Stadler <stadler.michael@gmail.com>
Co-authored-by: Charlotte Soneson <charlottesoneson@gmail.com>
Package: mutscan
Commit: 81fe91ee4854576979fb15d18fa50168e87a421a
Author: Charlotte Soneson <charlottesoneson@gmail.com>
Date: 2025-10-29 20:17:50 +0100
Commit message:

 Merge remote-tracking branch 'upstream/devel' into devel
Package: mutscan
Commit: 005b1c34c21955508dbb8080c434948bcd7a7530
Author: Charlotte Soneson <charlottesoneson@gmail.com>
Date: 2025-09-12 08:55:54 +0200
Commit message:

 Fix branch names, clean up GHA
Package: atacInferCnv
Commit: e9986d81ef0a666732225ef1c6de0f39c4aea5c6
Author: Konstantin Okonechnikov <k.okonechnikov@gmail.com>
Date: 2026-04-14 09:12:17 +0200
Commit message:

 Re-wrte plotting via ggplot2
Package: atacInferCnv
Commit: aff50f72dfc341c295e7a91cfed03f80ef152b4c
Author: Konstantin Okonechnikov <k.okonechnikov@gmail.com>
Date: 2026-04-13 15:46:10 +0200
Commit message:

 Add support of SingleCellExperiment object as input
Package: atacInferCnv
Commit: bcdbdbc97bdb0c9933e63bb3518c281a70319870
Author: Konstantin Okonechnikov <k.okonechnikov@gmail.com>
Date: 2026-04-12 15:43:54 +0200
Commit message:

 Fix issues with paste0
Package: GSVA
Commit: 10d9d605129c8b637059294c722cda9aab81b8fd
Author: Robert Castelo <robert.castelo@upf.edu>
Date: 2026-04-14 08:13:52 +0200
Commit message:

 Fixed bug
Package: scECODA
Commit: f1182a2527f8a099534417ed7440ad2151f90676
Author: halterc <chalterbio@gmail.com>
Date: 2026-04-14 08:29:36 +0200
Commit message:

 Version bump
Package: FLAMES
Commit: 8a8797549e4fdcfc91e53de6f3d5a3462b102f33
Author: Changqing Wang <wang.ch@wehi.edu.au>
Date: 2026-04-14 15:08:20 +1000
Commit message:

 fix: remove ggbio dependency
due to incompatiblity with new ggplot2 releases
Package: FLAMES
Commit: 703f6eda4fd87ec0eb4139f4f3c2c03d7564dea3
Author: Changqing Wang <wang.ch@wehi.edu.au>
Date: 2026-04-09 12:10:41 +1000
Commit message:

 feat: resume for BulkPipeline
Package: SCArray
Commit: b480c17ce93ffdd7093d8f38e7ac8f3ab76ce2ee
Author: Xiuwen Zheng <zhengxwen@gmail.com>
Date: 2026-04-13 23:56:47 -0500
Commit message:

 fix the package anchors for all Rd
Package: HIBAG
Commit: 380b68329b9cb6ec7a30ddae02f8e2895f996f67
Author: Xiuwen Zheng <zhengxwen@gmail.com>
Date: 2026-04-13 23:24:58 -0500
Commit message:

 tweak
Package: SNPRelate
Commit: 5a8a64ef4c665e3c595696814c6767d9adac5172
Author: Xiuwen Zheng <zhengxwen@gmail.com>
Date: 2026-04-13 22:59:49 -0500
Commit message:

 fix the package anchors for all Rd
Package: edgeR
Commit: 2567da3171202fa927b107f825bcaa2c0430234c
Author: Gordon Smyth <smyth@wehi.edu.au>
Date: 2026-04-14 08:22:34 +1000
Commit message:

 edgeR 4.9.7
- voomLmFit() now supports offset.prior
Package: LRDE
Commit: 9465d47effe2e0f1607aa0c68fb7762030e17473
Author: Ziyang Liu <jacobleo773@gmail.com>
Date: 2026-04-13 14:06:17 -0700
Commit message:

 Update Description
Package: ontoProc2
Commit: 8fd6e13cad6e32bcb539147593d5f789c0213396
Author: vjcitn <stvjc@channing.harvard.edu>
Date: 2026-04-13 16:45:23 -0400
Commit message:

 bumping version
Package: ontoProc2
Commit: 515a441dace49f39a8cce9acff61422a7af1d238
Author: vjcitn <stvjc@channing.harvard.edu>
Date: 2026-04-13 16:45:00 -0400
Commit message:

 removing 'empty' folders
Package: clusterExperiment
Commit: 63e007e3e2cdaa1035eef2cef8af2e7a9409f5d3
Author: Elizabeth Purdom <epurdom@stat.berkeley.edu>
Date: 2026-04-13 13:13:52 -0700
Commit message:

 fix tests based on recent error
Package: dreamlet
Commit: 14c7ab2a4847f6d4adfdc68a6ddddac42cecdea1
Author: Gabriel Hoffman <gabriel.hoffman@gmail.com>
Date: 2026-04-13 15:08:06 -0400
Commit message:

 1.9.2
Package: dreamlet
Commit: 405a151a16af6640b47c56d35f15c009c84f7857
Author: Gabriel Hoffman <gabriel.hoffman@gmail.com>
Date: 2026-02-02 16:32:36 -0500
Commit message:

 update docs
Package: dreamlet
Commit: aec9d232bd2f9862bc5bee55c0d097daa78b1702
Author: Gabriel Hoffman <gabriel.hoffman@gmail.com>
Date: 2026-01-25 20:45:43 -0500
Commit message:

 1.9.1
Package: dreamlet
Commit: c36648ebd1c1a909caad28d565d6523a694e5c34
Author: Gabriel Hoffman <gabriel.hoffman@gmail.com>
Date: 2025-09-22 09:56:08 -0400
Commit message:

 update docs
Package: dreamlet
Commit: 445c5bf18bc7f6cfb291ea5be4807555fbe9526d
Author: Gabriel Hoffman <gabriel.hoffman@gmail.com>
Date: 2025-04-24 15:42:16 -0400
Commit message:

 update docs
Package: scECODA
Commit: 971f671ba764f3219208b9d6f83e8330aca731a2
Author: halterc <chalterbio@gmail.com>
Date: 2026-04-13 21:03:04 +0200
Commit message:

 Version bump. Added funding agency and author ORCID
Package: scECODA
Commit: bb380ba2daf6ea8b044159195d1d9c6ae47e1f25
Author: halterc <chalterbio@gmail.com>
Date: 2026-04-13 21:02:33 +0200
Commit message:

 calc_modularity: dontrun example
Package: scECODA
Commit: 3404463619b00c60fcb56745f280037b0a84dfae
Author: halterc <chalterbio@gmail.com>
Date: 2026-04-13 21:02:11 +0200
Commit message:

 Added parameter input checks
Package: scECODA
Commit: ceaec89e60c79a148fa24605a5ca3ffc9f729da7
Author: Massimo Andreatta <massimo.andreatta@unige.ch>
Date: 2026-04-13 17:27:07 +0200
Commit message:

 Add installation instructions
Package: carnation
Commit: 2ee1987b5a57298b5f7591151b93b720f45929c2
Author: Apratim Mitra <16709900+mitraak@users.noreply.github.com>
Date: 2026-04-13 14:47:00 -0400
Commit message:

 Merge pull request #27 from NICHD-BSPC/v0.99.10

V0.99.10

- add edgeR/limma support
- allow addition of degPatterns/pattern analysis results via UI
- improve object validation
- add helper functions to edit carnation default settings
- misc bug fixes
Package: carnation
Commit: 5668ea97f4e16c03754d3b1d8f08a1e52ccb9a53
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2026-04-13 13:06:46 -0400
Commit message:

 version bump
Package: carnation
Commit: b3f018d414640dbb40e1b04f2dc1768f05797eae
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2026-04-13 13:06:32 -0400
Commit message:

 repin R to 4.6
Package: carnation
Commit: f74198051fb6b815e44ac7e2464c114b7e571f30
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2026-04-13 12:03:04 -0400
Commit message:

 get supported col names frm def config
Package: carnation
Commit: 07ddaa7b132423a456ffe8eab71e32ac3975012a
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2026-04-13 11:22:21 -0400
Commit message:

 rm non ascii character
Package: carnation
Commit: a014b74a7e6c7a83813d08123e43c5d3061dd55a
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2026-04-13 11:21:37 -0400
Commit message:

 fix 'name' bug
Package: carnation
Commit: 7f39d9fe347f21f89bb9ab09724ba0758311dfa6
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2026-04-13 11:20:49 -0400
Commit message:

 updt Rd
Package: carnation
Commit: 4381b424ca490d94998316d6e2d6148ef67f2236
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2026-04-13 11:20:40 -0400
Commit message:

 add examples
Package: carnation
Commit: 64bfccd51bffdf3ddf2fd2747581f28d43472465
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2026-04-13 11:17:59 -0400
Commit message:

 switch to examplesIf
Package: carnation
Commit: 679114e18b792839be1b2663d026b4f296cd2a92
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2026-04-13 11:17:30 -0400
Commit message:

 rm head call
Package: carnation
Commit: c4691b18c1ad8f844e20f1563e307795bf310e1a
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2026-04-13 11:16:08 -0400
Commit message:

 add comment
Package: carnation
Commit: cf76f499534a6303b8e542fd038c55e66fbf157a
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2026-04-13 11:15:57 -0400
Commit message:

 add examples
Package: carnation
Commit: ca85db554ccd816c1f59d2c276654d59fe96edc0
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2026-04-13 11:15:29 -0400
Commit message:

 repl sapply w apply
Package: carnation
Commit: 0b988a9e6f5cd926e687554d4d6195ceaf180397
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2026-04-13 11:13:55 -0400
Commit message:

 updt imports
Package: carnation
Commit: 9302ab6aee262af3a503b0c7e4a725effda7fce5
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2026-04-13 11:13:32 -0400
Commit message:

 rm redundant 'warning' string in message
Package: carnation
Commit: bd0e20a9b80fba8fc411703080ac0272ce2031b2
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2026-04-13 11:12:55 -0400
Commit message:

 updt NAMESPACE
Package: carnation
Commit: 59619eb1a3ca78a6365e6494b33f15aad43cc929
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2026-04-13 11:11:49 -0400
Commit message:

 updt DESCRIPTION
Package: carnation
Commit: bc0615007609165a3d583912d54d30cc42f408c6
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2026-04-13 09:20:02 -0400
Commit message:

 temporarily pin R to check tests
Package: carnation
Commit: 62a3fbe2fdd19be4a89a9b0e1a52f96ebb623ab7
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2026-04-13 09:19:54 -0400
Commit message:

 updt NEWS
Package: carnation
Commit: 4eb7009d7ab8d7cd3f08501991eefdd858489805
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2026-04-08 16:27:10 -0400
Commit message:

 updt NAMESPACE
Package: carnation
Commit: bf59ffe4b65471698500da44445b5ee368fbc4f6
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2026-04-08 16:26:57 -0400
Commit message:

 updt aut email
Package: carnation
Commit: 5e5983368da7fea1d335f122cd82f41731154e42
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2026-04-08 16:26:10 -0400
Commit message:

 add new Rds
Package: carnation
Commit: 4b4e86cb5d45dfb6c12d407790728020f99f9cb1
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2026-04-08 16:25:54 -0400
Commit message:

 add tests fr config funcs
Package: carnation
Commit: 4b10afcea1f756ad494d9f2b9798daa3c4eeb60f
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2026-04-08 16:24:35 -0400
Commit message:

 updt Rd
Package: carnation
Commit: 0de72ecef9e51808b92f1a445e26e676cbb93073
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2026-04-08 16:24:15 -0400
Commit message:

 add funcs to init, set, merge local config
Package: carnation
Commit: 4931dc536ec736885cf881e9b6510dfe6679f841
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2026-04-08 16:23:18 -0400
Commit message:

 add config param to run_carnation
Package: carnation
Commit: 9615e018aa9d896b19f60ac30bfd46254f6bfb7a
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2026-04-08 16:22:39 -0400
Commit message:

 add func to get local config yaml
Package: carnation
Commit: 29f9d175d31fbcd558507c58c6b76bbe26a8eee4
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2026-04-08 16:07:15 -0400
Commit message:

 add tests fr validate funcs
Package: carnation
Commit: e22e6f4997dff20c4f171265b99c6017f163cdea
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2026-04-08 15:50:53 -0400
Commit message:

 materialize a new obj
Package: carnation
Commit: b09f5b00af02ded9709d0e3f19bdca5d159f3c68
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2026-04-08 15:49:29 -0400
Commit message:

 fixes for make_final_object
Package: carnation
Commit: 6d2d59e1d851aac3f005c319a7cb52e7ad071568
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2026-04-08 15:48:46 -0400
Commit message:

 factor out sanitize code to validation funcs
Package: carnation
Commit: f29cb3c3dc2a02b89b7a8c8f9caa31f9f86c5e24
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2026-04-08 15:46:14 -0400
Commit message:

 add validation functions for carnation obj
Package: carnation
Commit: 4336d2422d460b17cbda2b416bb99a4d6cf73efe
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2026-03-26 14:07:42 -0400
Commit message:

 correctly impute gene names into NA symbols
Package: carnation
Commit: 84749f4fe1f78639dfab0afd8316d59234af1881
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2026-03-26 14:06:59 -0400
Commit message:

 handle native obj incoming
Package: carnation
Commit: 527409ea7105e09c30a092fd32522fedad4e8a24
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2026-03-26 14:06:37 -0400
Commit message:

 only convert rownames that need conv
Package: carnation
Commit: 75ae23cd004a91eec89f983e1bc1ece8c0a09dd0
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2026-03-26 14:06:24 -0400
Commit message:

 mv idmap code to func
Package: carnation
Commit: deba25c5fdc77012bd166f6b21e1dedd3282bcc4
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2026-03-26 14:02:29 -0400
Commit message:

 check for supported cols fr new res upload
Package: carnation
Commit: be49d85939fc86f5ef166baaabc026b4d7a0c728
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2026-03-26 14:01:57 -0400
Commit message:

 check res cols, handle both obj forms for edit obj
Package: carnation
Commit: 3a91de589636d8eb84debb69f419338130521f0a
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2026-03-26 13:59:57 -0400
Commit message:

 check supported cols using internal func
Package: carnation
Commit: ce39859bf65e1413a3a56165d4e30ffe05339c35
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2026-03-25 11:34:36 -0400
Commit message:

 updt vignette to reflect supported tools
Package: carnation
Commit: 007d2c49fcec7c25a3b60ad8e619b7eddf96926a
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2026-03-25 11:34:18 -0400
Commit message:

 updt README formatting
Package: carnation
Commit: 50bd7455f122f2c954bf7f4ee0e24d7ba7499532
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2026-03-25 11:33:21 -0400
Commit message:

 show pagination ctrls fr proj desc
Package: carnation
Commit: 8e6ff4357c1bca392c36620084b96b6e6eecd06b
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2026-03-25 11:32:56 -0400
Commit message:

 updt text to reflect supported tools
Package: carnation
Commit: 0c0b2490540ea614e9876a8d0f84c17fc6891e19
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2026-03-25 11:32:16 -0400
Commit message:

 add col validation on input
Package: carnation
Commit: b6461fecd1172ffc8293699996ff1f066edf6dc5
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2026-03-25 11:31:51 -0400
Commit message:

 if no obj added, show notif
Package: carnation
Commit: 7513fdf445d0cdfd65d5de28bc7975afbc8b4c14
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2026-03-25 11:31:32 -0400
Commit message:

 skip don't stop during res validation
Package: carnation
Commit: 1f03a850b2fae22522c71decd2c85be991c24256
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2026-03-25 11:29:36 -0400
Commit message:

 updt incoming obj sanitization
Package: carnation
Commit: d0dc4352310467edde0444b17f6a37c93c98e591
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2026-03-25 09:26:12 -0400
Commit message:

 updt Singularity
Package: carnation
Commit: d1bf23e6b41b86e29a6f48a211cdec782717db4f
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2026-03-25 09:20:41 -0400
Commit message:

 cleanup README
Package: carnation
Commit: 2bd65b267c5411151afd2f054838c482cdb5ef6a
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2026-03-25 09:14:23 -0400
Commit message:

 use unpinned reqs, reinstall complexupset, use r4.3 branch
Package: carnation
Commit: 9e09d57b9476dcd24b7ea296ee446ef136ebab8c
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2026-03-21 09:38:57 -0400
Commit message:

 fix scatterplot showlegend bug
Package: GSVA
Commit: 6ae9c4a54fac072e9774f442fca95f5be3ab202b
Author: Robert Castelo <robert.castelo@upf.edu>
Date: 2026-04-13 20:14:19 +0200
Commit message:

 Debugging a unit test
Package: tximeta
Commit: a43e1f6afb93ca3ced6d82ebab6901b344eb699b
Author: Mike Love <mikelove@users.noreply.github.com>
Date: 2026-04-13 13:19:22 -0400
Commit message:

 more vignette updates
Package: tximeta
Commit: f793b31ef7a16ec86fcb0f12a1fe915616b43c8a
Author: Mike Love <mikelove@users.noreply.github.com>
Date: 2026-04-13 13:03:26 -0400
Commit message:

 adding edgeR funcs to vignette, resolves #98
Package: STRINGdb
Commit: 071ea9e46f0ea331f469c6863b7db69e2af933d9
Author: Damian Szklarczyk <damian@Damians-MacBook-Air.fritz.box>
Date: 2026-04-13 19:08:24 +0200
Commit message:

 Fix vignette Sweave LaTeX markup
Package: gDNAx
Commit: 01155c59571281c4fab2931415797ed65faa54bd
Author: Robert Castelo <robert.castelo@upf.edu>
Date: 2026-04-13 18:53:16 +0200
Commit message:

 Changed default useRMSK=TRUE to useRMSK=FALSE in gDNAdx()
Package: GSVA
Commit: 70dcc1a8617ce3c894fae57a6cff13f6c3519b2e
Author: Robert Castelo <robert.castelo@upf.edu>
Date: 2026-04-13 18:45:20 +0200
Commit message:

 Fixed some unit tests, clean up some C code
Package: tximport
Commit: 85b6972ddbe947554ec781258e66fd5a28fe9bd9
Author: Mike Love <mikelove@users.noreply.github.com>
Date: 2026-04-13 12:42:23 -0400
Commit message:

 version bump
Package: tximport
Commit: 1c84dc34a449a6b47d15137a02f18dd7f3330728
Author: Mike Love <mikelove@users.noreply.github.com>
Date: 2026-04-13 12:41:40 -0400
Commit message:

 get version correctly aligned with bioc
Package: tximport
Commit: 5eacb8e85edb25b4f998a9317c319005bd114db5
Author: Mike Love <mikelove@users.noreply.github.com>
Date: 2026-04-13 12:40:07 -0400
Commit message:

 update news
Package: tximport
Commit: bed7e5352250e406ae14ebe374389fe28a60df2c
Author: Mike Love <mikelove@users.noreply.github.com>
Date: 2026-04-13 12:35:50 -0400
Commit message:

 adding package refs and version info
Package: tximport
Commit: 7e384c95095cd18878db1633aad73dd4d270363b
Author: Mike Love <mikelove@users.noreply.github.com>
Date: 2026-04-13 12:18:09 -0400
Commit message:

 updates from edgeR team, resolves #62
Package: tximport
Commit: 03304834f68547ce39369c5f4a80a3fca42a7f34
Author: Mike Love <mikelove@users.noreply.github.com>
Date: 2025-09-30 10:16:19 -0400
Commit message:

 removing stray browser call
Package: tximport
Commit: 3b758c752355d7eab8307d74c1d79074a989b946
Author: Mike Love <mikelove@users.noreply.github.com>
Date: 2025-08-22 14:52:54 -0400
Commit message:

 tweak
Package: GSVA
Commit: 3367a1c8c97ff38e726a00725f977b7fd1b66cf5
Author: Robert Castelo <robert.castelo@upf.edu>
Date: 2026-04-13 18:20:09 +0200
Commit message:

 Added unit tests on KCDF estimation
Package: SMAD
Commit: 64855403c3c0eff6412cac5bd52b16bc85ebf388
Author: Qingzhou Zhang <5545472+zqzneptune@users.noreply.github.com>
Date: 2026-04-13 12:15:55 -0300
Commit message:

 feat: add utils::unstack dependency, include global variable definitions, and update test data loading
Package: MetaboAnnotatoR
Commit: b4a4f0df8d37680455b594d3471592bfc5855f07
Author: Gomes Da Graca <ggomesda@ic.ac.uk>
Date: 2026-04-13 16:10:10 +0100
Commit message:

 bug fix: deprecated package msdata replaced by MsDataHub in example
Package: MetaboAnnotatoR
Commit: 0464ea8036b7eda82326c2a3580db0c8a15c2f7d
Author: Gomes Da Graca <ggomesda@ic.ac.uk>
Date: 2026-04-13 16:08:30 +0100
Commit message:

 bump added and suggested MsDataHub added
Package: scECODA
Commit: f2325820fb4ddd57640d89ef13fc2ecf9525a094
Author: halterc <chalterbio@gmail.com>
Date: 2026-04-13 16:50:10 +0200
Commit message:

 refactor to SummarizedExperiment
Package: scECODA
Commit: 64d49624f6dfa69c0ca24e616b47fda538daba72
Author: halterc <chalterbio@gmail.com>
Date: 2026-04-13 16:48:41 +0200
Commit message:

 merge
Package: scECODA
Commit: 559aff374efb018037d5099e7a5ab00f4099803d
Author: halterc <chalterbio@gmail.com>
Date: 2026-04-13 16:37:54 +0200
Commit message:

 Added ORCID
Package: scECODA
Commit: faada0fd1c36d10b0965f873e717306ec9269bd7
Author: halterc <chalterbio@gmail.com>
Date: 2026-04-13 16:37:42 +0200
Commit message:

 Formatting
Package: scECODA
Commit: 7261a53d575e30af9369ee8d45aed7440dceaca2
Author: halterc <chalterbio@gmail.com>
Date: 2026-04-13 16:36:08 +0200
Commit message:

 Replaced @ accessor
Package: scECODA
Commit: 09d456e764a7da75502d3bae22775f451ca85331
Author: halterc <chalterbio@gmail.com>
Date: 2026-04-13 15:21:27 +0200
Commit message:

 Merge branch 'devel' of https://github.com/carmonalab/scECODA into devel
Package: scECODA
Commit: 3767a8e1b94aeebff3fd28ddfe17a48bac3816d9
Author: halterc <chalterbio@gmail.com>
Date: 2026-04-13 15:21:15 +0200
Commit message:

 Typo
Package: scECODA
Commit: 0578f7f2239f2d9457df5f8bcc25b6e2ab51ffca
Author: halterc <chalterbio@gmail.com>
Date: 2026-04-13 15:21:00 +0200
Commit message:

 Typos and missing documentation
Package: scECODA
Commit: 9b9da529c36e2b8556f0be59923d1d012d292dff
Author: halterc <chalterbio@gmail.com>
Date: 2026-04-13 14:59:39 +0200
Commit message:

 Removed (switched to SummarizedExperiment)
Package: scECODA
Commit: 51f0e65f39918bdbafb0f2a64a4c153727663ea3
Author: Massimo Andreatta <massimo.andreatta@unige.ch>
Date: 2026-04-13 15:18:49 +0200
Commit message:

 Add preprint link to Readme
Package: scECODA
Commit: 50309af84d364b8f3829d6617670a7f732e7e746
Author: halterc <chalterbio@gmail.com>
Date: 2026-04-13 14:59:39 +0200
Commit message:

 Added explanation on igraph for Seurat
Package: scECODA
Commit: 41bdb9fcf0412aa623fa0cce5722da1468eb3655
Author: halterc <chalterbio@gmail.com>
Date: 2026-04-13 14:56:30 +0200
Commit message:

 - Switched ECODA class to SummarizedExperimetn class to store data.
- Changed data format to SummarizedExperiment (from rows=samples and columns=features -> rows=features and columns=samples)
Package: scECODA
Commit: 017194f6a83f840f7009e6d130c72fc0e3a36621
Author: halterc <chalterbio@gmail.com>
Date: 2026-04-13 14:54:14 +0200
Commit message:

 Made igraph as suggest, not working on R 4.6 yet
Package: scECODA
Commit: 0044cd8b80012636c38861fd50306ec1c101190e
Author: halterc <chalterbio@gmail.com>
Date: 2026-04-13 14:52:22 +0200
Commit message:

 Fix documentation
Package: scECODA
Commit: def0c48bcf3dceb1e0875563c1d505fea6edde20
Author: halterc <chalterbio@gmail.com>
Date: 2026-04-10 16:23:37 +0200
Commit message:

 Adopted SummarizedExperiment class
Package: scECODA
Commit: 879ad3421a52547ed8397a2c16cfa8273632d299
Author: halterc <chalterbio@gmail.com>
Date: 2026-04-10 16:22:19 +0200
Commit message:

 Version bump
Package: scECODA
Commit: 5739694c51db75ba15c1d3591f8ea47ea2786bfa
Author: halterc <chalterbio@gmail.com>
Date: 2026-03-30 14:47:09 +0200
Commit message:

 Updated reference
Package: scECODA
Commit: 6942990a58b2c30afb27984670cd23648fe01fd4
Author: halterc <chalterbio@gmail.com>
Date: 2026-03-30 14:46:35 +0200
Commit message:

 Update NEWS file
Package: scECODA
Commit: 92f17b43c35130ae20d28ccb65570b897bf9a195
Author: halterc <chalterbio@gmail.com>
Date: 2026-03-30 14:46:24 +0200
Commit message:

 Version bump to 0.99.6
Package: scECODA
Commit: 40e1d0f32301e08a13dcd6aebb6b38b354ae91bc
Author: halterc <chalterbio@gmail.com>
Date: 2026-03-30 14:45:56 +0200
Commit message:

 Fixed typos
Package: scECODA
Commit: 295482eff7f5a1d00a7c66584c55aee17a0e411e
Author: halterc <chalterbio@gmail.com>
Date: 2026-03-30 14:42:06 +0200
Commit message:

 Update vignette:
- Added Installation section (including instructions for BiocManager)
- Added section "Motivation for Bioconductor Integration"
Package: scECODA
Commit: 08b6016843a98695101123150e8a607667baeda1
Author: halterc <chalterbio@gmail.com>
Date: 2026-03-30 14:22:10 +0200
Commit message:

 - Replaced for loops with *apply
- Fixed bug in comput_snn_graph (SNN were only calculated for samples that themselves were neighbours)
- Replaced for loops with apply
Package: scECODA
Commit: 4c8127fa451bbb9648210c6823acf214ca42f0a4
Author: halterc <chalterbio@gmail.com>
Date: 2026-03-30 14:20:41 +0200
Commit message:

 Added missing dependencies
Package: scECODA
Commit: a3fda0d2a38b6b847e650a657d3833f875103799
Author: halterc <chalterbio@gmail.com>
Date: 2026-03-30 14:20:11 +0200
Commit message:

 Added package man page
Package: scECODA
Commit: 1657353e2cd7ce4677f9d22469c8c23543b185ba
Author: halterc <chalterbio@gmail.com>
Date: 2026-03-30 12:19:38 +0200
Commit message:

 Replace :: with explicit imports with @importFrom
Package: scECODA
Commit: 822a33051e81b9bb32771eaa8e2a29347099ad7f
Author: halterc <chalterbio@gmail.com>
Date: 2026-03-30 11:39:41 +0200
Commit message:

 Update R to 4.6
Package: scECODA
Commit: e89c7b1714a764b2199db745516c231edf0a2537
Author: halterc <chalterbio@gmail.com>
Date: 2026-03-30 11:39:14 +0200
Commit message:

 Add chunk names
Package: scECODA
Commit: 854362ac235da50c5be526f3fc274eb228061fdf
Author: halterc <chalterbio@gmail.com>
Date: 2026-03-30 10:40:39 +0200
Commit message:

 Merge branch 'main' of https://github.com/carmonalab/scECODA
Package: scECODA
Commit: 5ac3eb3655038c23a752c3d1d09ca50aa18d0650
Author: halterc <chalterbio@gmail.com>
Date: 2026-03-30 10:40:25 +0200
Commit message:

 Last version compatible with R 4.4
Package: scECODA
Commit: 110b73d3309e31e6feb1c46474ad5f0f59020b5b
Author: Santiago Carmona <sjcarmona@gmail.com>
Date: 2026-03-26 20:26:05 +0100
Commit message:

 Update README.md
Package: scECODA
Commit: b6884d8b9f56c394738dd1ec57c7d3c7a64a438b
Author: Massimo Andreatta <massimo.andreatta@unige.ch>
Date: 2026-03-26 19:02:12 +0100
Commit message:

 Update README.md
Package: scECODA
Commit: 89f67d1f3ccb0b0badd03d72fe8e20e26f505321
Author: Santiago Carmona <sjcarmona@gmail.com>
Date: 2026-03-26 16:59:14 +0100
Commit message:

 Update README.md
Package: scECODA
Commit: adc20d5c08f08439ca68b58e3af67d303be90fea
Author: Santiago Carmona <sjcarmona@gmail.com>
Date: 2026-03-26 16:58:03 +0100
Commit message:

 Update README.md
Package: velociraptor
Commit: 88ac6d0aed1c5b0bba97370e5008c2c32d1e0009
Author: Kevin Rue-Albrecht <kevinrue67@gmail.com>
Date: 2026-04-13 14:50:53 +0100
Commit message:

 Pin version of all dependencies. (#100)

* add script that prints installed versions

* print package versions

* fix code to print python package versions

* pin all packages for all OS'es

* update news and description

* rephrase

* Update Bioconductor version to 3.23 in workflow

* Update macOS version in CI workflow

* Update R version to 'devel' in CI workflow

* Bump velociraptor version to 1.21.1

Updated version number to 1.21.1 and pinned dependencies.
Package: GSVA
Commit: e202fa1ef3c8250e4564263f4d943ff751794a05
Author: Robert Castelo <robert.castelo@upf.edu>
Date: 2026-04-13 14:59:00 +0200
Commit message:

 R code cleanup
Package: GSVA
Commit: 480ba13b65cbc05e5aed9ab9e7ae0c1b67f649e9
Author: Robert Castelo <robert.castelo@upf.edu>
Date: 2026-04-13 12:51:55 +0200
Commit message:

 Added unit test for gsvaEnrichment()
Package: DOtools
Commit: c325bf1c2bab4e3fbff10fe457db7ca792394911
Author: MarianoRuzJurado <mariani95@gmx.de>
Date: 2026-04-13 13:49:52 +0200
Commit message:

 Merge remote-tracking branch 'origin/devel' into devel
Package: DOtools
Commit: 93c07c5776ced1908f13d005b27977d4b57d30b9
Author: Mariano Ruz Jurado <60434009+MarianoRuzJurado@users.noreply.github.com>
Date: 2026-04-13 11:23:29 +0200
Commit message:

 Update NEWS.md
Package: DOtools
Commit: f9b62ca193015d45fb36075406954e183d1d207e
Author: MarianoRuzJurado <mariani95@gmx.de>
Date: 2026-04-13 13:49:25 +0200
Commit message:

 Merge remote-tracking branch 'upstream/devel' into devel
Package: DOtools
Commit: 8172c34b3a16433711572bc862edf395015a37db
Author: MarianoRuzJurado <mariani95@gmx.de>
Date: 2026-04-13 11:09:41 +0200
Commit message:

 Add description and citation information
Package: edgeR
Commit: 2054923c6c7878baa9a57fa463b4c4ce98bb5f66
Author: Gordon Smyth <smyth@wehi.edu.au>
Date: 2026-04-13 21:31:10 +1000
Commit message:

 edgeR 4.9.6
- cpm() and rpkm() now support prior offsets.
Package: MetaboDynamics
Commit: afe75894352fe6f8a80074aa5d4059ae105a1340
Author: Katja Danielzik <katja.danielzik@uni-due.de>
Date: 2026-04-13 13:12:42 +0200
Commit message:

 bug fix in estimates_dynamcis
Package: MsBackendMetaboLights
Commit: 8d83a338340ee8a4f4665e6c77ac463c82c0781e
Author: Johannes Rainer <5506112+jorainer@users.noreply.github.com>
Date: 2026-04-13 13:07:16 +0200
Commit message:

 Merge pull request #15 from rformassspectrometry/jomain

refactor: import retry() from MsCoreUtils
Package: MsBackendMetaboLights
Commit: b8d7f05530d6dba8fee183b71d8ac24705c64282
Author: Johannes Rainer <johannes.rainer@gmail.com>
Date: 2026-04-13 12:03:45 +0200
Commit message:

 refactor: fail safe mechanism for download
Package: MsBackendMetaboLights
Commit: 9d6935e43b4794b541cc7ee3720361a499367cd9
Author: Johannes Rainer <johannes.rainer@gmail.com>
Date: 2026-04-08 10:13:10 +0200
Commit message:

 Update retry pattern
Package: MsBackendMetaboLights
Commit: 2cf65e5a240380a33fff9c506496fe9a0ad08774
Author: Johannes Rainer <johannes.rainer@gmail.com>
Date: 2026-04-08 09:27:12 +0200
Commit message:

 refactor: update pattern
Package: MsBackendMetaboLights
Commit: f4a22cc1b72974f38281a4542d710afac265d718
Author: Johannes Rainer <johannes.rainer@gmail.com>
Date: 2026-04-08 08:17:29 +0200
Commit message:

 refactor: import retry() from MsCoreUtils

- Remove `retry()` function and import it from *MsCoreUtils*.
- Use a stringent pattern to retry downloading; this might cause failures until
  we get a complete list of connection-specific errors.
Package: ImageArray
Commit: 17d724cc9dd382d13af280aa27fe9176803d78e8
Author: Artur-man <artur-man@hotmail.com>
Date: 2026-04-13 13:06:35 +0200
Commit message:

 bump version
Package: ImageArray
Commit: ae61cf0052ef382b278a88545f6fb7fe1fe5d1bb
Author: Artur-man <artur-man@hotmail.com>
Date: 2026-04-13 13:05:23 +0200
Commit message:

 fix commits
Package: ImageArray
Commit: dbdf8618881c1f905ed8b9022244bfa5e74f5e64
Author: Artur-man <artur-man@hotmail.com>
Date: 2026-04-13 13:04:14 +0200
Commit message:

 Merge branch 'sandbox' into bioc_review
Package: ImageArray
Commit: 5eacfc79ea73e6af2a3434350f3aa19ac86d37c7
Author: Artür Manukyan <artur-man@hotmail.com>
Date: 2026-03-27 21:50:52 +0100
Commit message:

 Reduce the need for loops and extra function calls (#33)
Package: ImageArray
Commit: 8da163e752b299e46d8926311d58659c488cd58b
Author: Artur-man <artur-man@hotmail.com>
Date: 2026-03-27 20:55:02 +0100
Commit message:

 fix some stop calls
Package: ImageArray
Commit: ffabd6b1b10730560fa2868ef9ac8ea00e484bf5
Author: Artur-man <artur-man@hotmail.com>
Date: 2026-03-27 20:49:06 +0100
Commit message:

 more seq_along and paste corrections
Package: ImageArray
Commit: 4abe9716f0489152e4d12627111c3906bb25975f
Author: Hugo Gruson <git@hugogruson.fr>
Date: 2026-03-26 15:37:30 +0100
Commit message:

 Avoid sprintf() call in vapply()
Package: ImageArray
Commit: 9174b6f1e695ae3c2093a50c946d946a3327ba25
Author: Hugo Gruson <git@hugogruson.fr>
Date: 2026-03-26 15:34:18 +0100
Commit message:

 Remove unnecessary paste0() and vapply()
Package: ImageArray
Commit: a16482789f3c5114a43f7259a23203d7d9ec5250
Author: Hugo Gruson <git@hugogruson.fr>
Date: 2026-03-26 15:34:14 +0100
Commit message:

 Use seq_along() instead of seq_len(length())
Package: ImageArray
Commit: 1dad07c1ee721a427825b4cc4972d6bdbad767fa
Author: Hugo Gruson <git@hugogruson.fr>
Date: 2026-03-26 15:21:24 +0100
Commit message:

 Avoid paste0() within file.path()
Package: ImageArray
Commit: 8237e6fe14cf4695e4df07e82ab6a95a59add017
Author: Hugo Gruson <git@hugogruson.fr>
Date: 2026-03-26 15:20:12 +0100
Commit message:

 Use the dedicated lengths() function where appropriate
Package: ImageArray
Commit: 1beb05f1f09c90630391a1a9b541b61ef538ec4b
Author: Artur-man <artur-man@hotmail.com>
Date: 2026-03-18 11:48:53 +0100
Commit message:

 update README and fix some tests
Package: ImageArray
Commit: 2c0ffc1fdfa0e6ba26b66ccea9ee240a926b801c
Author: Artur-man <artur-man@hotmail.com>
Date: 2026-03-17 22:33:02 +0100
Commit message:

 add ZarrArray to DESC
Package: ImageArray
Commit: 629a9af967368027baa7631e605b5ea5dba93fee
Author: Artur-man <artur-man@hotmail.com>
Date: 2026-03-17 22:32:37 +0100
Commit message:

 switch from Rarr to ZarrArray
Package: MetaboDynamics
Commit: 81c4f8eea3cfd01ce2f0456581d4161ca77f865d
Author: Katja Danielzik <katja.danielzik@uni-due.de>
Date: 2026-04-13 12:59:14 +0200
Commit message:

 bug fix in estimates_dynamcis
Package: ImageArray
Commit: cb67650dcbb29f339c98c8badf4af83157770e88
Author: Artur-man <artur-man@hotmail.com>
Date: 2026-04-13 12:57:01 +0200
Commit message:

 bump version
Package: ChromSCape
Commit: cf8c7aa2a41288361a614ffcf3c6503040bfc49f
Author: Pacome Prompsy <pacome.pr@gmail.com>
Date: 2026-04-13 11:39:23 +0200
Commit message:

 Added flexdashboard to list of requirements to overcome WARNING
Package: ChromSCape
Commit: e6cb6c3c01b42a5dc06b84e59c42e3dea4fd5b6a
Author: Pacome Prompsy <pacome.pr@gmail.com>
Date: 2026-04-13 11:38:30 +0200
Commit message:

 Added flexdashboard to list of requirements to overcome WARNING
Package: DOtools
Commit: 8aeebdf4b40dbba75bc8c08b18b172ad50eaa210
Author: MarianoRuzJurado <mariani95@gmx.de>
Date: 2026-04-13 11:09:41 +0200
Commit message:

 Add description and citation information
Package: DOtools
Commit: cab91178a7efd11cee88915ebf8a63927eb901d8
Author: MarianoRuzJurado <mariani95@gmx.de>
Date: 2026-04-13 10:59:51 +0200
Commit message:

 Add DensityPlot functionality to DO.UMAP
Package: miloR
Commit: 936edb8053c89605430355308d8432a6f7350252
Author: MikeDMorgan <michael.morgan@abdn.ac.uk>
Date: 2026-04-13 09:51:39 +0100
Commit message:

 adjust c++std11 flags
Package: betterChromVAR
Commit: cca45837f01bfff0d827e5d893694ca3a2615b48
Author: plger <pl.germain@gmail.com>
Date: 2026-04-13 09:48:02 +0200
Commit message:

 disabled pkg update on windows
Package: betterChromVAR
Commit: 150fd5aec37512b4dcd3c3f868ac16676a3bba8c
Author: plger <pl.germain@gmail.com>
Date: 2026-04-13 08:56:56 +0200
Commit message:

 fixed typo
Package: betterChromVAR
Commit: 3132613913e2fb488e5d4c8a2204345586a8aa85
Author: plger <pl.germain@gmail.com>
Date: 2026-04-13 08:56:13 +0200
Commit message:

 clean up badges
Package: betterChromVAR
Commit: 0128fe0c43ac0fb9e3b88f86e51078ab08f34a19
Author: plger <pl.germain@gmail.com>
Date: 2026-04-13 08:52:28 +0200
Commit message:

 updated doc
Package: QUBIC
Commit: 31cfc46000e999a764455cf7687a1dc2ec78b959
Author: zy26 <zy26@users.noreply.github.com>
Date: 2026-04-13 11:30:03 +0800
Commit message:

 Bump version
Package: QUBIC
Commit: 80fdd64bd23764d94508c130516be227b3483dfd
Author: zy26 <zy26@users.noreply.github.com>
Date: 2026-04-13 11:14:29 +0800
Commit message:

 Fix biclust decoupling docs and vignette consistency
Package: bugsigdbr
Commit: 1e45c74201154d8e7e7e53ec14735d912f56b769
Author: lgeistlinger <ludwig.geistlinger@gmail.com>
Date: 2026-04-12 18:30:11 -0400
Commit message:

 Merge remote-tracking branch 'origin/devel' into devel
sync pull request #77
Package: bugsigdbr
Commit: 4d319f7d731a0854ef0fe09b1ac6836cd6bbcc3b
Author: lgeistlinger <ludwig.geistlinger@gmail.com>
Date: 2026-04-12 18:25:39 -0400
Commit message:

 EFO term update: fix ontology tests
Package: bugsigdbr
Commit: 96ae17859d0e8cfb6d67129a3eab8da542855505
Author: Levi Waldron <lwaldron.research@gmail.com>
Date: 2026-03-26 16:37:36 -0400
Commit message:

 Merge pull request #77 from waldronlab/funding/add-fnd-authors-r-23616418917
Package: bugsigdbr
Commit: 177f3ee7d4d76b3ed9976f6e3fc49024140e5765
Author: Marcel Ramos Pérez <LiNk-NY@users.noreply.github.com>
Date: 2026-03-26 20:28:20 +0000
Commit message:

 Add missing fnd entries to Authors@R in DESCRIPTION
Package: igblastr
Commit: 9f626e65049024a625a0c96628953c348cb22e96
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2026-04-12 14:41:08 -0700
Commit message:

 igblastr 1.1.26

Add the following built-in germline dbs:

o _OGRDB.mouse.CAST_EiJ.IGH+IGK+IGL.202603

  Contains sequences from OGRDB germline sets:
    - `CAST/EiJ IGH` version 2
    - `CAST/EiJ IGKV` version 1
    - `CAST/EiJ IGLV` version 2
    - `IGKJ (all strains)` version 1
    - `IGLJ (all strains)` version 1

o _OGRDB.mouse.LEWES_EiJ.IGH+IGK+IGL.202603

  Contains sequences from OGRDB germline sets:
    - `LEWES/EiJ IGH` version 2
    - `LEWES/EiJ IGKV` version 1
    - `LEWES/EiJ IGLV` version 1
    - `IGKJ (all strains)` version 1
    - `IGLJ (all strains)` version 1

o _OGRDB.mouse.MSM_MsJ.IGH+IGK+IGL.202603

  Contains sequences from OGRDB germline sets:
    - `MSM/MsJ IGH` version 1
    - `MSM/MsJ IGKV` version 1
    - `MSM/MsJ IGLV` version 2
    - `IGKJ (all strains)` version 1
    - `IGLJ (all strains)` version 1

Also rename the following built-in germline dbs:

o _OGRDB.mouse.NOD_ShiLtJ.IGH+IGK+IGL.202501 (original name)
  --> _OGRDB.mouse.NOD_ShiLtJ.IGH+IGK+IGL.202205 (new name)

o _OGRDB.mouse.PWD_PhJ.IGH+IGK+IGL.202501 (original name)
  --> _OGRDB.mouse.PWD_PhJ.IGH+IGK+IGL.202410 (new name)

The new names better reflect the release date of the OGRDB germline sets
that they contain. The two original germline dbs were kept for backward
compatibility but the user gets a warning when they use them. The warning
suggests to use the new names instead and to remove the original dbs.
Package: GSVA
Commit: 3c2b5de6e2501624f7dd8294d1fb763d32cb3309
Author: Robert Castelo <robert.castelo@upf.edu>
Date: 2026-04-12 21:30:00 +0200
Commit message:

 Updated unit tests
Package: GSVA
Commit: 80f0e4fd7a1f3ad8e90f2231fe13f561f0246a45
Author: Robert Castelo <robert.castelo@upf.edu>
Date: 2026-04-12 21:14:06 +0200
Commit message:

 Updated some unit tests
Package: GSVA
Commit: 83a6dab9d3477f0dce984d457c6847ee6dd72a3a
Author: Robert Castelo <robert.castelo@upf.edu>
Date: 2026-04-12 20:16:39 +0200
Commit message:

 Fixing some unit tests
Package: TPP
Commit: f1351ec873bd95da4b9d7106c9f51764349d71a5
Author: Dorothee Childs <childs@embl.de>
Date: 2026-04-12 18:30:06 +0200
Commit message:

 bump version
Package: TPP
Commit: c5f106aa6b6878c9a6fb996ad0ece18f70c4fb85
Author: Dorothee Childs <childs@embl.de>
Date: 2026-04-12 18:59:25 +0200
Commit message:

 Replace deprecated ggplot2 ..density.. usage with after_stat(density)
Package: TPP
Commit: 27a214ec6984ecc3f9031d6a4f87d9e05e77b15c
Author: Dorothee Childs <childs@embl.de>
Date: 2026-04-12 18:57:27 +0200
Commit message:

 Update ggplot2 deprecated aes_string() usage.
Package: TPP
Commit: 78f99ad842ee22064f3369c1b4981c6d1e35cee3
Author: Dorothee Childs <childs@embl.de>
Date: 2026-04-12 18:47:28 +0200
Commit message:

 Replace deprecated ggplot2 size arguments with linewidth.
Package: TPP
Commit: 5ae455fe4864293eac8747e49144fb99047b957b
Author: Dorothee Childs <childs@embl.de>
Date: 2026-04-12 18:27:21 +0200
Commit message:

 Replace mefa:::rep.data.frame with base row replication in tpptrSplineAUCs()
Package: TPP
Commit: d843b30c63ff523359ee91aedac58c046e627bc2
Author: Dorothee Childs <childs@embl.de>
Date: 2026-04-12 18:26:46 +0200
Commit message:

 Replace doParallel::: .options access with exported stopImplicitCluster()
Package: TPP
Commit: 09005c1cdc98d674706938f5611b2104b2160338
Author: Dorothee Childs <childs@embl.de>
Date: 2026-04-12 18:18:03 +0200
Commit message:

 Remove unused broom dependency from DESCRIPTION
Package: TPP
Commit: 358bf16641fa281aef7f7098b9b69cc95797d03a
Author: Dorothee Childs <childs@embl.de>
Date: 2026-04-12 18:13:57 +0200
Commit message:

 Refactor helper function into dedicated file for better maintainability.
Package: TPP
Commit: 2a2013724277a5e70bac25b7e85f74c300d5bd12
Author: Dorothee Childs <childs@embl.de>
Date: 2026-04-12 18:12:29 +0200
Commit message:

 Update documentation after changes to function parameters
Package: TPP
Commit: 9a641c3c711178abca90f47db28b316e125ac1f7
Author: Dorothee Childs <childs@embl.de>
Date: 2026-04-12 18:09:47 +0200
Commit message:

 Import rlang for sym() usage

Add reference to rlang in DESCRIPTION and NAMESPACE so rlang::sym() calls are properly declared for R CMD check.
Package: STRINGdb
Commit: ec9d5c8bf74d528d31736c1b0d9ada79a9d989c0
Author: Damian Szklarczyk <damian@Mac.fritz.box>
Date: 2026-04-12 18:43:58 +0200
Commit message:

 Enrichment figure + updated vignette.
Package: GSVA
Commit: 63f1fefa3b7ac36908c8a702efec15e82d421dca
Author: Robert Castelo <robert.castelo@upf.edu>
Date: 2026-04-12 16:25:40 +0200
Commit message:

 Updated unit tests
Package: STRINGdb
Commit: bb3d8cb0d3a6be071f4e3319ad1cc8c8e2d20d43
Author: Damian Szklarczyk <damian@Mac.fritz.box>
Date: 2026-04-12 15:51:05 +0200
Commit message:

 Expand network image and link options
Package: DEXSeq
Commit: c7c794955720be76af41a7c50e105ad59048fc79
Author: Hugo Gruson <git@hugogruson.fr>
Date: 2026-04-12 14:56:04 +0200
Commit message:

 Bump version
Package: DEXSeq
Commit: b04dfcf380c32ec4d986e043f4d4824186db9254
Author: Hugo Gruson <git@hugogruson.fr>
Date: 2026-04-12 14:55:44 +0200
Commit message:

 Use modern bibentry and c.person in CITATION
Package: STRINGdb
Commit: 155291b28cc252d1b7c29f2f3bcafc78db3de35b
Author: Damian Szklarczyk <damian@Mac.fritz.box>
Date: 2026-04-12 14:33:44 +0200
Commit message:

 Add interaction partners method
Package: GSABenchmark
Commit: 1767752c3e9c19fd82d24314006c609c37bf62c1
Author: andrei-stoica26 <andreistoica@foxmail.com>
Date: 2026-04-12 17:31:43 +0800
Commit message:

 Bumped version
Package: GSABenchmark
Commit: 007c4b884bbc3a6614802c20f37dca49a2e1bc13
Author: andrei-stoica26 <andreistoica@foxmail.com>
Date: 2026-04-12 17:31:11 +0800
Commit message:

 Fixed macOS testing issue
Package: STRINGdb
Commit: 9bc92f54e711405dc32f517d66d4b9a707ba3227
Author: Damian Szklarczyk <damian@Mac.fritz.box>
Date: 2026-04-12 10:19:10 +0200
Commit message:

 Test version update and bugfix
Package: S4Vectors
Commit: e1f1854f3a1bd75df2e0f88e79902150ebcf6ea0
Author: Michael Lawrence <lawremi@gmail.com>
Date: 2026-04-11 20:39:28 -0700
Commit message:

 replace promise walking in C with a pure R solution for determining the enclosure for evaluating quoted arguments; fixes #134
Package: SeqArray
Commit: ee638b1f4213ef5cbe33ecff05b0e5f4aaf6be29
Author: Xiuwen Zheng <zhengxwen@gmail.com>
Date: 2026-04-11 21:28:50 -0500
Commit message:

 fix the package anchors for all Rd
Package: biomformat
Commit: 9f77c5ea12e48208734060d602e92ae7c764ffac
Author: Paul J. McMurdie <joey711@gmail.com>
Date: 2026-04-11 16:23:13 -0700
Commit message:

 1.39.17 bug fixes
Package: SMAD
Commit: f6adaa39588fa5566a4313525a8ab4402c5d08ee
Author: Qingzhou Zhang <5545472+zqzneptune@users.noreply.github.com>
Date: 2026-04-11 19:20:52 -0300
Commit message:

 feat: integrate NLopt optimization library and expand SAINTexpress functionality with new C++ backends and documentation.
Package: igblastr
Commit: 211868089eb446060af0c7b16d6294cb5f935231
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2026-04-11 15:09:00 -0700
Commit message:

 igblastr 1.1.25: Minor doc improvements

Also disable GHA on windows-latest for now.
Package: PloidyPeaks
Commit: 7deeb26e3f92d40e8ef6ad2a0f2d6429453ff0f7
Author: ckostna <caitlinkostna@shaw.ca>
Date: 2026-04-11 16:38:22 -0500
Commit message:

 Changes in file structure for warnings
Package: PloidyPeaks
Commit: 136b7c8b81d41adf1bb351cc0f174513e285a674
Author: ckostna <caitlinkostna@shaw.ca>
Date: 2026-04-11 15:30:39 -0500
Commit message:

 Changes to fix vignette error
Package: ontoProc2
Commit: c8b64906b178c06b52470d2dc6057f03b452f376
Author: vjcitn <stvjc@channing.harvard.edu>
Date: 2026-04-11 13:52:57 -0400
Commit message:

 seems very clean now
Package: GSVA
Commit: 7e6cd9822d20adee54fe10ccd62d231442313e20
Author: Robert Castelo <robert.castelo@upf.edu>
Date: 2026-04-11 19:47:36 +0200
Commit message:

 *Param() functions report more informative errors when the input expression data or gene sets do not correspond to one of the expected object classes
Package: ontoProc2
Commit: c5b561ce7c8e73f692d5718af45f4464d83461c7
Author: vjcitn <stvjc@channing.harvard.edu>
Date: 2026-04-11 12:26:41 -0400
Commit message:

 midway in repairing how S7 generics are coded, to eliminate doc warnings
Package: augere.screen
Commit: 5df23e608a3cecb4866c35a190a6980a5c34d014
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2026-04-12 00:21:19 +1000
Commit message:

 Explicit suppression of plots to speed up execution.

This is more understandable than only generating plots when a graphics device
is active, as this depends on the current state of the R session.
Package: augere.gsea
Commit: e2848a6269a7beee43b77f141813ae8191bce46c
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2026-04-11 23:59:47 +1000
Commit message:

 Explicit suppression of plots to speed up execution.

This is more understandable than only generating plots when a graphics device
is active, as this depends on the current state of the R session.

</div> </div>