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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: soGGi
Commit: 42e62106443c3f1fc2643899b0a83e47db5ce33c
Author: ThomasCarroll <tc.infomatics@gmail.com>
Date: 2025-10-13 13:55:45 -0400
Commit message:

 Fix ggplot2 v4
Package: Rsubread
Commit: 10b9c7627a7b982dc7c4c3c9dd761b5ea56b0392
Author: Yang Liao (Monash University) <yliao@m3-login2.massive.org.au>
Date: 2025-10-14 04:36:43 +1100
Commit message:

 fixed another bug in cellCounts
Package: visiumStitched
Commit: 8243db29f9fc5da714c5cb4b9d213f1b8b88bfbf
Author: Nick-Eagles <nick.eagles@libd.org>
Date: 2025-10-13 13:21:07 -0400
Commit message:

 Add dependency on GenomeInfoDb to try to resolve a BBS build error; bump version
Package: imcRtools
Commit: e0ffb09868279e6914149ec572068f6352abc27c
Author: SchulzDan <shooltz@gmx.de>
Date: 2025-10-13 19:07:06 +0200
Commit message:

 Merge pull request #144 from BodenmillerGroup/read_from_tiff

Read from tiff
Package: imcRtools
Commit: 5ff2ae6ac0cda66f283198eecc86d26fac5dc2a8
Author: Ubuntu <ubuntu@spo-server.cloud.science-it.uzh.ch>
Date: 2025-10-10 12:41:00 +0000
Commit message:

 cosmetic change
Package: imcRtools
Commit: e5adcb34775ffd09e970756e1f6c423e0a0277e9
Author: Ubuntu <ubuntu@spo-server.cloud.science-it.uzh.ch>
Date: 2025-10-10 10:03:51 +0000
Commit message:

 removed catalyst import
Package: imcRtools
Commit: 8f5e27ddc8816e913b6881896cee28f446a76a3b
Author: Ubuntu <ubuntu@spo-server.cloud.science-it.uzh.ch>
Date: 2025-10-10 09:53:45 +0000
Commit message:

 added refs and links
Package: imcRtools
Commit: 860f231bfee086d9123c0f9824f851e1e2685938
Author: Ubuntu <ubuntu@spo-server.cloud.science-it.uzh.ch>
Date: 2025-10-09 21:19:21 +0000
Commit message:

 CATALYST import and calls
Package: imcRtools
Commit: 3d60343adfd42ce30a2aefe6300a782ac27d4f18
Author: Ubuntu <ubuntu@spo-server.cloud.science-it.uzh.ch>
Date: 2025-10-09 14:56:36 +0000
Commit message:

 small test change
Package: imcRtools
Commit: 545116899bd8dc9a67068b5841f6b0692d285fd3
Author: Ubuntu <ubuntu@spo-server.cloud.science-it.uzh.ch>
Date: 2025-10-09 14:41:53 +0000
Commit message:

 added txt vs. tiff test case
Package: imcRtools
Commit: 60ea6f1a6508cf6ad6f9a0f92bb1bb46b7cec771
Author: Ubuntu <ubuntu@spo-server.cloud.science-it.uzh.ch>
Date: 2025-10-08 14:52:32 +0000
Commit message:

 fixed vignette
Package: imcRtools
Commit: 2ed62a9c738cff768dc3398cbcc3dcf8d08e0beb
Author: Ubuntu <ubuntu@spo-server.cloud.science-it.uzh.ch>
Date: 2025-10-08 14:36:56 +0000
Commit message:

 added new version
Package: imcRtools
Commit: da558df27505c6ebc3ad7d5d81362f4b15ded673
Author: Ubuntu <ubuntu@spo-server.cloud.science-it.uzh.ch>
Date: 2025-10-08 14:32:01 +0000
Commit message:

 Added XTi info to func description
Package: imcRtools
Commit: cf2b8a920c46ca0f29a6db0b5d44893a65cc9375
Author: Ubuntu <ubuntu@spo-server.cloud.science-it.uzh.ch>
Date: 2025-10-08 14:26:11 +0000
Commit message:

 added new author, changed vignette
Package: imcRtools
Commit: 2b42ea1e7df36d6812d2fad7425fff3feeac8db7
Author: Ubuntu <ubuntu@spo-server.cloud.science-it.uzh.ch>
Date: 2025-09-30 13:51:22 +0000
Commit message:

 finalized tests
Package: imcRtools
Commit: 7c737422ed2c5a844d771513994c83613fc9a34a
Author: Ubuntu <ubuntu@spo-server.cloud.science-it.uzh.ch>
Date: 2025-09-30 13:30:28 +0000
Commit message:

 Merge remote-tracking branch 'origin' into read_from_tiff
Package: imcRtools
Commit: 7095c148fe56fb5af8e36e5f6aa6cfc0cbfb5ba9
Author: Ubuntu <ubuntu@spo-server.cloud.science-it.uzh.ch>
Date: 2025-09-29 12:52:27 +0000
Commit message:

 corrected cell_meta creation
Package: imcRtools
Commit: 09c79ece8a883fa302d794f42eca6ba2ca4860cc
Author: Ubuntu <ubuntu@spo-server.cloud.science-it.uzh.ch>
Date: 2025-09-29 12:36:41 +0000
Commit message:

 changed cell_meta creation
Package: imcRtools
Commit: 2c1e09391192fe62074071aed4580b6b91e9ee0c
Author: Ubuntu <ubuntu@spo-server.cloud.science-it.uzh.ch>
Date: 2025-09-29 12:00:37 +0000
Commit message:

 fixed tests
Package: imcRtools
Commit: f588065b6b69f80870ff499c43b7d77a97d96be6
Author: Ubuntu <ubuntu@spo-server.cloud.science-it.uzh.ch>
Date: 2025-09-26 08:49:58 +0000
Commit message:

 added sample_metal and sample_mass
Package: imcRtools
Commit: 724c720241d68fecb267dca18b879260a5df7e12
Author: Ubuntu <ubuntu@spo-server.cloud.science-it.uzh.ch>
Date: 2025-09-26 08:00:26 +0000
Commit message:

 added valid func call
Package: imcRtools
Commit: bcf18af68194120d9cb92871da2ca8421cbe0fd1
Author: Ubuntu <ubuntu@spo-server.cloud.science-it.uzh.ch>
Date: 2025-09-26 07:55:46 +0000
Commit message:

 removed print statements
Package: imcRtools
Commit: 6d8538f1bc315ab44eb14b44e5e6b2a68485c095
Author: Ubuntu <ubuntu@spo-server.cloud.science-it.uzh.ch>
Date: 2025-09-25 17:54:52 +0000
Commit message:

 corrected func and channel order
Package: imcRtools
Commit: 4905e7e3f5f8f4df3026bc8ba5e572307c5e3923
Author: Ubuntu <ubuntu@spo-server.cloud.science-it.uzh.ch>
Date: 2025-09-25 16:59:19 +0000
Commit message:

 validation func for new spillover from tiff func
Package: imcRtools
Commit: 0b81586796ab1f5fbbb1b83ce5e9f3c31f740bb2
Author: Ubuntu <ubuntu@spo-server.cloud.science-it.uzh.ch>
Date: 2025-09-25 16:58:10 +0000
Commit message:

 new spillover tiff files to SCE function
Package: BayesSpace
Commit: 30eaa4f007ac79d252340efe227c47e09ae4a2e8
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2025-10-13 09:38:51 -0700
Commit message:

 BayesSpace 1.19.5

Update serialized SingleCellExperiment instance. Needed because of Seqinfo
move from GenomeInfoDb package to new Seqinfo package.
Package: CaDrA
Commit: 14385d2aef8003b4d20b91b92bba285a8aef3532
Author: RC-88 <lilychau999@gmail.com>
Date: 2025-10-13 11:42:09 -0400
Commit message:

 fix plot check due to ggplot update
Package: CaDrA
Commit: e39c55ff800417a24236eca64c20db4af8afd3fc
Author: RC-88 <lilychau999@gmail.com>
Date: 2025-10-13 11:18:36 -0400
Commit message:

 Merge remote-tracking branch 'upstream/devel' into devel
Package: CaDrA
Commit: be3fa7956df5ca27a5cab0ca56023ac71d0febac
Author: RC-88 <lilychau999@gmail.com>
Date: 2025-10-13 11:16:02 -0400
Commit message:

 fix plot due to ggplot update
Package: tximeta
Commit: 6f04435cc051c72bc4d43b7a682fb96c7e36fe16
Author: Mike Love <mikelove@users.noreply.github.com>
Date: 2025-10-13 11:25:54 -0400
Commit message:

 doc fix
Package: CEMiTool
Commit: 797a29e7b03b3e634f68ac7f7523b28ade61ea6a
Author: Pedro Russo <pedrostrusso@gmail.com>
Date: 2025-10-13 12:02:00 -0300
Commit message:

 Fixing gg error
Package: CEMiTool
Commit: d58df2cc95d58b8071b310b34d941c23129dd584
Author: Pedro Russo <pedrostrusso@gmail.com>
Date: 2025-09-29 10:25:32 -0300
Commit message:

 Updating docs
Package: CEMiTool
Commit: a7e6d01e13dd87246ea2b9fb0d155ea0845eb768
Author: Pedro Russo <pedrostrusso@gmail.com>
Date: 2025-09-29 10:23:42 -0300
Commit message:

 updating docs
Package: CEMiTool
Commit: d773230ffd61ba1da05bd8e92c6632d5b551f684
Author: Pedro Russo <pedrostrusso@gmail.com>
Date: 2025-09-29 10:11:42 -0300
Commit message:

 version bump
Package: CEMiTool
Commit: 588f17eb5cdffd99395c3ae8c0d6ae3590a7e5e9
Author: Pedro Russo <pedrostrusso@gmail.com>
Date: 2025-09-22 21:21:01 -0300
Commit message:

 Fixing version
Package: CEMiTool
Commit: 71c9ca04906ae8baa4e50b7cd00747f63f2417b3
Author: Pedro Russo <pedrostrusso@gmail.com>
Date: 2025-09-22 20:43:51 -0300
Commit message:

 Version bump
Package: CEMiTool
Commit: c96711abedbebaa46335e6f46d0adc071c542ffd
Author: Pedro Russo <pedrostrusso@gmail.com>
Date: 2025-09-22 20:34:55 -0300
Commit message:

 Version bump
Package: CEMiTool
Commit: e44088cd9e553ed226b586ad26ad3e4b960a4331
Author: Pedro Russo <pedrostrusso@gmail.com>
Date: 2025-09-22 20:34:00 -0300
Commit message:

 Fixing version number
Package: CEMiTool
Commit: 572f75ab9b23252bc53582ac5fa2dd72569fc66c
Author: Pedro Russo <pedrostrusso@gmail.com>
Date: 2025-09-22 20:25:35 -0300
Commit message:

 Fix release version
Package: CEMiTool
Commit: 263e0e56745f050b316177399d62c51f343ee184
Author: Pedro Russo <pedrostrusso@gmail.com>
Date: 2025-09-22 20:19:12 -0300
Commit message:

 version bump
Package: CEMiTool
Commit: a7db475c15396c86a33109f3a859ac7dbe807674
Author: Pedro Russo <pedrostrusso@gmail.com>
Date: 2025-09-22 20:17:58 -0300
Commit message:

 Fixing bug with S7 classes
Package: xcms
Commit: e2f76c8512bd0244f9524c075fe240138335f3e4
Author: Johannes Rainer <johannes.rainer@gmail.com>
Date: 2025-10-13 08:22:07 +0200
Commit message:

 fix: address Steffen's comments
Package: xcms
Commit: 92e277a81f99438f93a48921bda55d5db6b9ac2d
Author: Johannes Rainer <johannes.rainer@gmail.com>
Date: 2025-10-10 09:32:43 +0200
Commit message:

 feat: add parameter minMzWidthPpm

- `featureArea()` and `ChromPeakAreaParam()` gain additional parameter
  `minMzWidthPpm` that allows to define a minimal guaranteed m/z width of the
  reported feature areas respectively regions to integrate data for gap
  filling (issue #756).
Package: xcms
Commit: 559ed279e4d56dc23c0cacd614443fd72a2fe7e7
Author: Johannes Rainer <johannes.rainer@gmail.com>
Date: 2025-09-20 16:36:40 +0200
Commit message:

 fix: add missing import of spectraData method
Package: xcms
Commit: a3fa8b63c4c6658d4e031d1e6e9282d8904182e4
Author: Johannes Rainer <johannes.rainer@gmail.com>
Date: 2025-09-20 16:32:16 +0200
Commit message:

 tests: add unit tests for skipFilled for XcmsExperimentHdf5

- Add unit tests checking that parameter `skipFilled` works correctly for
  `featureSpectra()` for `XcmsExperimentHdf5` objects.
Package: xcms
Commit: a6b6808753087936a43d6b50c4c073bc41eae06e
Author: Johannes Rainer <johannes.rainer@gmail.com>
Date: 2025-09-20 12:31:25 +0200
Commit message:

 feat: featureSpectra gains full support for skipFilled

- Parameter `skipFilled` is now supported for `featureSpectra,XcmsExperiment`.
Package: xcms
Commit: b772eb16290ff40efc416f58588b5f191a4495a8
Author: Johannes Rainer <johannes.rainer@gmail.com>
Date: 2025-09-16 08:53:39 +0200
Commit message:

 feat: add support for parameter columns to XcmsExperimentHdf5

- Add support for parameter `columns` to the `chromPeakData()` method for
  `XcmsExperimentHdf5` objects.
Package: xcms
Commit: bcb853cd9adef8cb3220865b22d0c603836cebc8
Author: Johannes Rainer <johannes.rainer@gmail.com>
Date: 2025-09-16 08:37:20 +0200
Commit message:

 feat: add parameter columns to chromPeakData

- Add parameter `columns` to `chromPeakData()` for `XCMSnExp` and
  `XcmsExperiment` classes to allow extraction of selected columns.
Package: xcms
Commit: 859d80a3d88353ebd50c74f0363ddd586f841ed3
Author: Johannes Rainer <johannes.rainer@gmail.com>
Date: 2025-09-12 15:23:18 +0200
Commit message:

 fix wrong feature definitions in plotChromPeakDensity

- Fix issue #812 : parameters `minFraction` and `maxFeatures` were not correctly
  considered in `plotChromPeakDensity()`.
Package: xcms
Commit: 7aad79265469e890ff60dea7832244b23ee5f983
Author: Johannes Rainer <johannes.rainer@gmail.com>
Date: 2025-09-12 13:34:27 +0200
Commit message:

 documentation updates and new unit tests
Package: xcms
Commit: 9fdf93f0e7ac35454e14050f71be2c623797b11d
Author: Johannes Rainer <johannes.rainer@gmail.com>
Date: 2025-08-19 10:00:16 +0200
Commit message:

 fix: conversion from XcmsExperiment to XCMSnExp

- Fix issue #807
Package: Rsubread
Commit: b584b01f1afecc780df44c8fa76f2d5519e029a2
Author: Yang Liao (Monash University) <yliao@m3-login2.massive.org.au>
Date: 2025-10-14 00:40:41 +1100
Commit message:

 fixed a bug in cellCounts for junction detection
Package: imageTCGA
Commit: 016b155e542596e53e13b8cc8138f6a4b97ce91c
Author: billila <ilaria.billato@studenti.unipd.it>
Date: 2025-10-13 15:17:52 +0200
Commit message:

 bump version
Package: imageTCGA
Commit: 3f2303ae5d92fa85d1d16c40b138464faa60acd5
Author: billila <ilaria.billato@studenti.unipd.it>
Date: 2025-10-13 15:11:41 +0200
Commit message:

 minor fix
Package: wiggleplotr
Commit: c3f72f8bcfa4a53a2d13d14b8bf0273b405d6be6
Author: Kaur Alasoo <kauralasoo@gmail.com>
Date: 2025-10-13 14:46:09 +0300
Commit message:

 Fix old typo
Package: DoReMiTra
Commit: 8fe501bd2b94f25059bda6c6f0adfdd8f2cfe17d
Author: AhmedSAHassan <155752718+AhmedSAHassan@users.noreply.github.com>
Date: 2025-10-13 11:48:24 +0200
Commit message:

 version bump, 0.99.2
Package: DoReMiTra
Commit: 45aa7f6a728e372179dbe9a0862122f93a58a17f
Author: AhmedSAHassan <155752718+AhmedSAHassan@users.noreply.github.com>
Date: 2025-10-13 11:47:54 +0200
Commit message:

 updated news
Package: DoReMiTra
Commit: 5199a190e8afcb7a74c10670a7cd51e4c5e9690f
Author: AhmedSAHassan <155752718+AhmedSAHassan@users.noreply.github.com>
Date: 2025-10-13 11:45:46 +0200
Commit message:

 updated Rbuildignore and gitignore
Package: DoReMiTra
Commit: 31e9e09b1556af07c7f3724e5b5c83924eef5f83
Author: AhmedSAHassan <155752718+AhmedSAHassan@users.noreply.github.com>
Date: 2025-10-13 11:44:56 +0200
Commit message:

 updating roxygen version
Package: DoReMiTra
Commit: d0becc0517ff4722285d9d79260aef4810b8ad1e
Author: AhmedSAHassan <155752718+AhmedSAHassan@users.noreply.github.com>
Date: 2025-10-13 11:44:33 +0200
Commit message:

 adjust the text to match the function
Package: DoReMiTra
Commit: 57ee2445f9349f5f1dbddbe7a76539cde29b275e
Author: AhmedSAHassan <155752718+AhmedSAHassan@users.noreply.github.com>
Date: 2025-10-13 11:44:20 +0200
Commit message:

 specifying the name of the vignette to be displayed
Package: DoReMiTra
Commit: 9c6dccefd01b98a6b859700893ca7287b59f8250
Author: AhmedSAHassan <155752718+AhmedSAHassan@users.noreply.github.com>
Date: 2025-10-12 01:29:29 +0200
Commit message:

 choose another dataset to filter and load
Package: DoReMiTra
Commit: 58d1ec09d5366d807be1d091f9df13271dd033ac
Author: AhmedSAHassan <155752718+AhmedSAHassan@users.noreply.github.com>
Date: 2025-10-12 01:28:58 +0200
Commit message:

 choosing another dataset to filter and load
Package: DoReMiTra
Commit: 303823c924bbb2bfed806166271de6b62ec6d88b
Author: AhmedSAHassan <155752718+AhmedSAHassan@users.noreply.github.com>
Date: 2025-10-12 01:21:13 +0200
Commit message:

 correcting a typo
Package: DoReMiTra
Commit: e3cc86cc2c48cafaa7063e023bf707b9cc63b1a8
Author: AhmedSAHassan <155752718+AhmedSAHassan@users.noreply.github.com>
Date: 2025-10-12 01:21:00 +0200
Commit message:

 use the right test
Package: DoReMiTra
Commit: fe499cbad9e89594d29a2f0a460ce1b020a5f41b
Author: AhmedSAHassan <155752718+AhmedSAHassan@users.noreply.github.com>
Date: 2025-10-12 01:20:46 +0200
Commit message:

 use message instead of print
Package: DoReMiTra
Commit: 928e3f4f0ce62d62d39de5a1c5fcfd890d64c3ff
Author: AhmedSAHassan <155752718+AhmedSAHassan@users.noreply.github.com>
Date: 2025-10-12 01:16:55 +0200
Commit message:

 using vapply instead of sapply
Package: DoReMiTra
Commit: 4647e78ea303c983f8f72c73a7b3f57c912d6865
Author: AhmedSAHassan <155752718+AhmedSAHassan@users.noreply.github.com>
Date: 2025-10-12 01:15:09 +0200
Commit message:

 Renaming vignette to DoReMiTra
Package: ClustIRR
Commit: ab318618971262a0ac08df8465cd5c6925dbd145
Author: snaketron <simo.kitanovski@proton.me>
Date: 2025-10-13 11:25:40 +0200
Commit message:

 commit changes
Package: gDRutils
Commit: f4317a5ad6175c3bffb0486eb561bb5401742391
Author: Bartek <32614650+bczech@users.noreply.github.com>
Date: 2025-10-13 11:11:46 +0200
Commit message:

 Merge pull request #173 from gdrplatform/GDR-2524

Gdr 2524
Package: gDRutils
Commit: 214ec440fbb9ee976fca9600dac0d08d995eeb42
Author: Bartek Czech <bartosz.w.czech@gmail.com>
Date: 2025-10-07 10:34:07 +0200
Commit message:

 refactor: update as per review
Package: gDRutils
Commit: 861e0f834cd76911da0f1d2ad01d6419438397d7
Author: Bartek Czech <bartosz.w.czech@gmail.com>
Date: 2025-10-06 16:34:48 +0200
Commit message:

 test: update unit tests
Package: gDRutils
Commit: 6c6a2fb7ef2ebbcecaa2c63fa3c480881db3b402
Author: Bartek Czech <bartosz.w.czech@gmail.com>
Date: 2025-10-06 16:24:02 +0200
Commit message:

 refactor: fix logic
Package: gDRutils
Commit: ca782f22799b489861384549c63f96cfd9bcb15e
Author: Bartek Czech <bartosz.w.czech@gmail.com>
Date: 2025-10-02 20:24:29 +0200
Commit message:

 doc: reoxygenate
Package: gDRutils
Commit: 4002ff658ca6320c531153788b9a702ec1fd616b
Author: Bartek Czech <bartosz.w.czech@gmail.com>
Date: 2025-10-02 20:16:46 +0200
Commit message:

 test: add unit tests
Package: gDRutils
Commit: 8f35740cab6e93fa370f0a249cb2b266246cd288
Author: Bartek Czech <bartosz.w.czech@gmail.com>
Date: 2025-10-02 20:13:58 +0200
Commit message:

 refactor: update as per review (II)
Package: gDRutils
Commit: 5b8a0cc6303bfc32364757c87a7bde18aff5f250
Author: Bartek Czech <bartosz.w.czech@gmail.com>
Date: 2025-10-02 20:13:23 +0200
Commit message:

 refactor: update as per review
Package: gDRutils
Commit: 9bca97989d40a0356f21215234ea70829b9f5509
Author: Bartek Czech <bartosz.w.czech@gmail.com>
Date: 2025-10-02 20:12:45 +0200
Commit message:

 refactor: update doc as per review with example
Package: gDRutils
Commit: 06f5ab1ccc3d9e16c6f86b1e0ed4ba683e7b8de9
Author: Bartek Czech <bartosz.w.czech@gmail.com>
Date: 2025-10-01 12:59:47 +0200
Commit message:

 refactor: update packages.R
Package: gDRutils
Commit: 83ae43a67bdd936d2ef20fff3e27aef16878bc84
Author: Bartek Czech <bartosz.w.czech@gmail.com>
Date: 2025-10-01 10:56:42 +0200
Commit message:

 doc: update keywords
Package: gDRutils
Commit: e96282e3b47279fcfdbef1c03cdc00cf6663e067
Author: Bartek Czech <bartosz.w.czech@gmail.com>
Date: 2025-10-01 09:03:06 +0200
Commit message:

 doc: appease lintr
Package: gDRutils
Commit: 62b8b721f1d073b7f98d5738352980a71336093b
Author: Bartek Czech <bartosz.w.czech@gmail.com>
Date: 2025-09-30 20:29:33 +0200
Commit message:

 doc: reoxygenate
Package: gDRutils
Commit: a75398c2d3ca5e08fb810890f78a1ab83c4b8638
Author: Bartek Czech <bartosz.w.czech@gmail.com>
Date: 2025-09-30 20:27:44 +0200
Commit message:

 doc: reoxygenate
Package: gDRutils
Commit: 5b6a43abd1b1d3dba3c27944d5c9f02f4cb95fcf
Author: Bartek Czech <bartosz.w.czech@gmail.com>
Date: 2025-09-30 20:27:13 +0200
Commit message:

 test: add unit tests
Package: gDRutils
Commit: 3ea3b1d0722484d01e2547ddb7c4e8aac28840d6
Author: Bartek Czech <bartosz.w.czech@gmail.com>
Date: 2025-09-30 20:27:04 +0200
Commit message:

 feat: add  function
Package: gDRutils
Commit: c06ff5a2211459fc937981467e1249099bf06980
Author: Bartek Czech <bartosz.w.czech@gmail.com>
Date: 2025-09-30 20:26:51 +0200
Commit message:

 chore: bump version and update NEWS.md
Package: methodical
Commit: 5d9a451f617f2ea6ecf0cdd1054582ae320bf37e
Author: Richard Heery <richardheery@gmail.com>
Date: 2025-10-13 09:49:08 +0100
Commit message:

 Bumped version
Package: SpectriPy
Commit: c258967fce5153de7c7cb4fa5f69f457b3b1235e
Author: Johannes Rainer <5506112+jorainer@users.noreply.github.com>
Date: 2025-10-13 07:59:32 +0200
Commit message:

 Merge pull request #85 from rformassspectrometry/jomain

update: use matchms version 0.31
Package: SpectriPy
Commit: 1bc1ab34f28c2983f8ca6dafbf175ff06a435779
Author: jorainer <johannes.rainer@gmail.com>
Date: 2025-10-10 15:20:21 +0200
Commit message:

 update: use matchms version 0.31
Package: COTAN
Commit: f624c0538a7663150014f7214e2a8136f5491dff
Author: trinetra75 <marco.fantozzi@gmail.com>
Date: 2025-10-11 22:40:33 +0200
Commit message:

 Fixed tests tolerances for other architectures
Package: singscore
Commit: d18e545b5dc13c38e2a58ecfcf441d8671d203a1
Author: Malviakh <malvika.kharbanda@adelaide.edu.au>
Date: 2025-10-13 15:02:01 +1000
Commit message:

 Bump version for Bioconductor devel build
Package: singscore
Commit: 7a85aeb2cb8757d9219f5076cc564308aca1030b
Author: Malviakh <malvika.kharbanda@adelaide.edu.au>
Date: 2025-10-13 15:00:48 +1000
Commit message:

 chore: ignore local dev artefacts
Package: rhdf5client
Commit: 85445aa1b10886d0f881274289d2ddceec14ead5
Author: Vince Carey <stvjc@channing.harvard.edu>
Date: 2025-10-12 23:44:35 -0400
Commit message:

 Merge pull request #10 from assaron/main

switch to alserglab.wustl.edu/hsds/ for test files
Package: rhdf5client
Commit: 42dd1aca9eb3ea4e0e322adc68a7046aa738b1ef
Author: Alexey Sergushichev <alsergbox@gmail.com>
Date: 2025-10-12 21:57:07 -0500
Commit message:

 update version
Package: rhdf5client
Commit: 30ba5e19bd6f5fbd2418f27cc18719c6d842db23
Author: Alexey Sergushichev <alsergbox@gmail.com>
Date: 2025-10-12 21:52:05 -0500
Commit message:

 regenerate docs
Package: rhdf5client
Commit: e4de7d041eeceb03df49d174cf957536da48b68c
Author: Alexey Sergushichev <alsergbox@gmail.com>
Date: 2025-10-12 21:49:52 -0500
Commit message:

 fix listDomains implementation for HSDS?
Package: rhdf5client
Commit: cb901035ed6f208fae20f6ca54a048b3b1e1e189
Author: Alexey Sergushichev <alsergbox@gmail.com>
Date: 2025-10-12 21:49:17 -0500
Commit message:

 move the rest of test files to alserglab server
Package: rhdf5client
Commit: 60efd8478649b3a91a2664e8bd44e8df4cc76a55
Author: Alexey Sergushichev <alsergbox@gmail.com>
Date: 2025-10-11 12:27:01 -0500
Commit message:

 switch to alserglab.wustl.edu/hsds/ for some of the test files
Package: rhdf5client
Commit: 521f7619afd5e0955aa0fb6650cddcc52b87c3bf
Author: vjcitn <stvjc@channing.harvard.edu>
Date: 2025-10-08 12:16:31 -0400
Commit message:

 Merge branch 'devel' of git.bioconductor.org:packages/rhdf5client
Package: rhdf5client
Commit: cc956ce33d312b9852e038fee5080da921045acc
Author: Vince Carey <stvjc@channing.harvard.edu>
Date: 2025-08-18 12:46:19 -0400
Commit message:

 Merge pull request #9 from shwetagopaul92/feature/list-files-on-directory

Adding functions listDomains() and getHSDSFileList() in R/File.R
Package: rhdf5client
Commit: b281181dc4f335351e97af2275a2a78f35788af1
Author: sgopaulakr <sgopaulakr@illumina.com>
Date: 2025-07-06 16:11:31 -0700
Commit message:

 Adding functions listDomains() and getHSDSFileList() in R/File.R to retrieve files from directories on HSDS server; added test in tests/testthat/test.R; bumped package version to 1.27.2'
Package: tidySummarizedExperiment
Commit: 87445757d2d0332e7d335d22cd28f73568b7db66
Author: Stefano Mangiola <mangiolastefano@gmail.com>
Date: 2025-08-31 18:06:26 +0930
Commit message:

 Add references to the tidyomics ecosystem and relevant R packages in append_samples, select, and unnest documentation files for improved citation and attribution.
Package: tidySummarizedExperiment
Commit: 66e169a841d68b63ee69b71d262c98493c8d37ec
Author: Stefano Mangiola <mangiolastefano@gmail.com>
Date: 2025-08-31 18:05:41 +0930
Commit message:

 Fix the assays assignment error
Package: tidySummarizedExperiment
Commit: 5c311700cb23789cc1430cc5438dc048fb803683
Author: Stefano Mangiola <mangiolastefano@gmail.com>
Date: 2025-08-30 22:07:29 +1000
Commit message:

 Merge pull request #107 from tidyomics/copilot/fix-100

Add tidyomics reference to all exported functions
Package: tidySummarizedExperiment
Commit: 7e3db9afbc96f5cba7734d35b5ab7d58f2213659
Author: Stefano Mangiola <mangiolastefano@gmail.com>
Date: 2025-08-30 18:24:48 +0930
Commit message:

 Add references to the tidyomics ecosystem and relevant R packages in multiple documentation files for improved citation and attribution.
Package: tidySummarizedExperiment
Commit: 4dc864c55e25ea8b28389e50d5610bc8c434d3d3
Author: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Date: 2025-08-30 08:39:28 +0000
Commit message:

 Clean up artifacts and complete tidyomics reference addition

Co-authored-by: stemangiola <7232890+stemangiola@users.noreply.github.com>
Package: tidySummarizedExperiment
Commit: 5c183cfecffe870339541ef13f3d89a2a858c792
Author: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Date: 2025-08-30 08:38:24 +0000
Commit message:

 Add tidyomics references to 4 missing exported functions

Co-authored-by: stemangiola <7232890+stemangiola@users.noreply.github.com>
Package: tidySummarizedExperiment
Commit: 334a25fe50911e3f60a4403bebdd65c54a407cc8
Author: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Date: 2025-08-30 08:30:48 +0000
Commit message:

 Initial plan
Package: tidySummarizedExperiment
Commit: b0c95b875fa00bedce756cc693a4008736f9a45a
Author: Stefano Mangiola <mangiolastefano@gmail.com>
Date: 2025-07-11 16:09:54 +0930
Commit message:

 Merge pull request #105 from stemangiola/append_samples

Append samples
Package: tidySummarizedExperiment
Commit: 8e5382a7885f0a4a44d41a9eb70452a3a072e2d6
Author: Stefano Mangiola <mangiolastefano@gmail.com>
Date: 2025-07-11 13:46:38 +0930
Commit message:

 add prettydoc
Package: tidySummarizedExperiment
Commit: e43a1490e9054270e4ffa693984b70ee5413b184
Author: Stefano Mangiola <mangiolastefano@gmail.com>
Date: 2025-07-11 13:32:47 +0930
Commit message:

 Update vignette output settings in introduction.Rmd to enable table of contents, section numbering, and figure captions for improved navigation and readability.
Package: tidySummarizedExperiment
Commit: b47a6e26abf8c0fa8270e341bc52282b9f37169a
Author: Stefano Mangiola <mangiolastefano@gmail.com>
Date: 2025-07-11 13:18:47 +0930
Commit message:

 Update vignette output format to use prettydoc with enhanced features including table of contents, section numbering, and figure captions for improved readability.
Package: tidySummarizedExperiment
Commit: 4c0828e9f79726bbc77a18ab43236e7e6a06b0f8
Author: Stefano Mangiola <mangiolastefano@gmail.com>
Date: 2025-07-10 22:10:28 +0930
Commit message:

 dummy
Package: tidySummarizedExperiment
Commit: 2f158a38e5bf1c39ec0f8b76036aad008ed89ce0
Author: Stefano Mangiola <mangiolastefano@gmail.com>
Date: 2025-07-10 20:43:05 +0930
Commit message:

 Remove deprecated documentation for bind_rows and bind_cols methods in dplyr_methods.R, and delete the corresponding Rd file. Update examples to be hidden from documentation.
Package: tidySummarizedExperiment
Commit: 2d38911b7f2e9c95b66e0ce4fc2b84b5f39dfd54
Author: Stefano Mangiola <mangiolastefano@gmail.com>
Date: 2025-07-10 20:26:27 +0930
Commit message:

 add append_samples method for SummarizedExperiment, and soft deprecate bind_rows in favor of append_samples. Update documentation and tests accordingly.
Package: tidySummarizedExperiment
Commit: 6cc0a715628aa2dc9156d51107d62f05994e0626
Author: Stefano Mangiola <mangiolastefano@gmail.com>
Date: 2025-07-10 18:39:32 +0930
Commit message:

 Merge pull request #103 from stemangiola/add-references

Update DESCRIPTION file and add references to methods. Added citation…
Package: tidySummarizedExperiment
Commit: f4a03cd063b742997c2628e7254b877c3b4cc369
Author: Stefano Mangiola <mangiolastefano@gmail.com>
Date: 2025-07-10 11:36:55 +0930
Commit message:

 Update DESCRIPTION file and add references to methods. Added citation information for the tidyomics ecosystem in multiple R files, enhancing documentation and ensuring proper attribution in publications.
Package: tidySummarizedExperiment
Commit: 275b3f35a594e61155f377606851b4e24d858648
Author: Stefano Mangiola <mangiolastefano@gmail.com>
Date: 2025-07-10 18:17:33 +0930
Commit message:

 Merge pull request #102 from stemangiola/drop-printing

remove deprecated print method, and adjust NAMESPACE. Add startup mes…
Package: tidySummarizedExperiment
Commit: a9ecb7d04cfa42e888a952b17e2a1ff77fbdd649
Author: Stefano Mangiola <mangiolastefano@gmail.com>
Date: 2025-07-10 16:35:56 +0930
Commit message:

 Update NEWS for version 1.19.2 to reflect changes including improved documentation on S3 method structure, enhanced ggplot2 compatibility, and user guidance towards tidyprint for visualization.
Package: tidySummarizedExperiment
Commit: e69bc5c6509189d59c5c42618fafe5b7fcbc543b
Author: Stefano Mangiola <mangiolastefano@gmail.com>
Date: 2025-07-10 12:04:48 +0930
Commit message:

 remove deprecated print method, and adjust NAMESPACE. Add startup message for external printing handling.
Package: tidySummarizedExperiment
Commit: 589a02d21f1e2cdb45f7be16d9179db06570882a
Author: Stefano Mangiola <mangiolastefano@gmail.com>
Date: 2025-07-10 16:06:58 +0930
Commit message:

 Merge pull request #104 from stemangiola/adapt-ggplot-S7

No major adaptations are needed for ggplot2 s7
Package: tidySummarizedExperiment
Commit: 70381383afdfde9d12addff79d4f936c0963ef21
Author: Stefano Mangiola <mangiolastefano@gmail.com>
Date: 2025-07-10 15:37:28 +0930
Commit message:

 Refactor ggplot2 method to simplify compatibility with ggplot2 4.0.0 by removing S7 method registration. Update DESCRIPTION to remove S7 as a suggested dependency and enhance NEWS documentation for clarity.
Package: tidySummarizedExperiment
Commit: 00714789b0c385591d69c6ed04daae98d64744af
Author: Stefano Mangiola <mangiolastefano@gmail.com>
Date: 2025-07-10 15:29:39 +0930
Commit message:

 Refactor ggplot method registration to use S7::method directly for improved clarity and compatibility with ggplot2.
Package: tidySummarizedExperiment
Commit: 67b9bd9f997fba2c50d780e01d460d69716882ab
Author: Stefano Mangiola <mangiolastefano@gmail.com>
Date: 2025-07-10 15:26:39 +0930
Commit message:

 Update DESCRIPTION for Roxygen version, adjust NEWS for Bioconductor 3.22 release, enhance documentation for as_tibble and ggplot methods, and add new import for cli package.
Package: tidySummarizedExperiment
Commit: e15d0a0c5b3ee4e53d12479ff92548358672336e
Author: Stefano Mangiola <mangiolastefano@gmail.com>
Date: 2025-07-10 14:45:41 +0930
Commit message:

 Merge branch 'devel' of git.bioconductor.org:packages/tidySummarizedExperiment into adapt-ggplot-S7
Package: tidySummarizedExperiment
Commit: e2dce00091576159d8f1c3d9a3053eddb102f3a9
Author: Stefano Mangiola <mangiolastefano@gmail.com>
Date: 2025-07-10 14:44:48 +0930
Commit message:

 Update version to 1.15.2, add S7 as a suggested dependency, and improve README formatting for better readability. Enhance ggplot method for compatibility with ggplot2 4.0.0 using S7 methods.
Package: tidySummarizedExperiment
Commit: 987165f4cf6c78914bf6666f865969dc5292ae37
Author: Stefano Mangiola <mangiolastefano@gmail.com>
Date: 2025-07-10 13:57:52 +0930
Commit message:

 Merge branch 'master' of https://github.com/stemangiola/tidySummarizedExperiment
Package: tidySummarizedExperiment
Commit: 97817f3fc754a16cbd4de97d0d4b7fd9eb10f177
Author: Stefano Mangiola <mangiolastefano@gmail.com>
Date: 2025-07-10 13:57:33 +0930
Commit message:

 Update DESCRIPTION to include rbibutils as a suggested package
Package: tidySummarizedExperiment
Commit: 29b1ae5205f73064fc66d3bb95484106a8a90bfa
Author: Stefano Mangiola <mangiolastefano@gmail.com>
Date: 2025-07-10 13:40:47 +0930
Commit message:

 dummy change
Package: TrIdent
Commit: d3f46ddba990b28fae7f6c19f34e2f7d31c16c6a
Author: jlmaier <jlmaier@ncsu.edu>
Date: 2025-10-12 20:30:09 -0400
Commit message:

 bug fix
Package: TrIdent
Commit: 263e0783a8ee9c5166c306173120179f71b6b96e
Author: jlmaier <jlmaier@ncsu.edu>
Date: 2025-10-11 21:17:50 -0400
Commit message:

 update vignette
Package: TrIdent
Commit: e76e67ac8c00ecce590faec53cbfc7bb856699f7
Author: jlmaier <jlmaier@ncsu.edu>
Date: 2025-08-07 20:50:22 -0400
Commit message:

 version update
Package: TrIdent
Commit: 44997642149de8562a1cd4c642e92c5697ebc5b4
Author: jlmaier <jlmaier@ncsu.edu>
Date: 2025-08-07 20:49:10 -0400
Commit message:

 Bug fixes
Package: Rsubread
Commit: 8cdaf3cd2a7e3cb055552edffc13de9cbcb0324c
Author: Yang Liao (Monash University) <yliao@m3v108.massive.org.au>
Date: 2025-10-13 11:06:27 +1100
Commit message:

 enabled junction detection in BCL/CBCL input reads.
Package: GeneTonic
Commit: f393aa8d4f1ecfa1bb71370b39d1bab953c82232
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2025-10-06 21:44:51 +0200
Commit message:

 Merge remote-tracking branch 'origin' into devel
Package: GeneTonic
Commit: f2ddb9204765f7cd59d4a832b15f3de1c0f550c7
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2025-10-06 21:44:21 +0200
Commit message:

 Merge pull request #70 from federicomarini/newbackbone

Newbackbone
Package: GeneTonic
Commit: 2eed4f3d95623b844407c12e2a019a05f75baba1
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2025-10-06 21:00:16 +0200
Commit message:

 updated roxygen version
Package: GeneTonic
Commit: 6154e8dae8c93b3b685271aed0127f0ed2843993
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2025-09-26 17:31:30 +0200
Commit message:

 cleanup of the commented code
Package: GeneTonic
Commit: c0a042da3f0dee085faf1cc0d41fdf9093d489a6
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2025-09-23 17:23:37 +0200
Commit message:

 version bump, 3.3.3
Package: GeneTonic
Commit: fdee641beddad0b26de70aecb5735ad3782ce55b
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2025-09-23 17:23:29 +0200
Commit message:

 updated news
Package: GeneTonic
Commit: 530b8ee75d48ce6654d52968217a996804f3bea9
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2025-09-23 17:21:22 +0200
Commit message:

 updating unit tests to skip the bb_fullinfo portions
Package: GeneTonic
Commit: cad13433fc31b16815b748513b95cede4de2116d
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2025-09-23 17:21:04 +0200
Commit message:

 re-rendering manpages
Package: GeneTonic
Commit: 58e2be0d306f22cbf12115611b9f745de69ad5dc
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2025-09-23 17:20:51 +0200
Commit message:

 removing the bb_fullinfo parameter and its associated functionality
Package: GeneTonic
Commit: ce7056b287521c39405de37f84d8aba65f7102f3
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2025-09-23 17:20:24 +0200
Commit message:

 updating dispatch and processing
Package: GeneTonic
Commit: 5a35b5a3b1b8542d5b1e5995aafbfef7133e62be
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2025-09-23 17:18:58 +0200
Commit message:

 handling the namespace imports
Package: bedbaser
Commit: 2535e67dd7368d400bd1189f3aa28e1d448809c9
Author: Wokaty <awokaty@users.noreply.github.com>
Date: 2025-10-12 15:51:16 -0400
Commit message:

 Bump version to 1.1.3
Package: bedbaser
Commit: fd7ffe6eeb41526da70954cb4cc506a54570c64a
Author: Wokaty <awokaty@users.noreply.github.com>
Date: 2025-10-12 12:44:44 -0400
Commit message:

 Fix bb_bed_text_search
Package: bedbaser
Commit: 54e87308eeb9e20b2d63cce7dc060862b0315b8d
Author: jwokaty <jwokaty@users.noreply.github.com>
Date: 2025-07-22 10:24:42 -0400
Commit message:

 Update action, use release for pkgdown site (#19)
Package: omicsViewer
Commit: b7d1b387eae3dc8f6c96e73d57bc87ec2daef455
Author: mengchen18 <mengchen18@gmail.com>
Date: 2025-10-12 21:12:23 +0200
Commit message:

 update dynamic heatmap

Dynamic heatmap will react to the selection of features and samples from table.
Package: omicsViewer
Commit: cc8766f4747d80827b009a29f1a854d721cea914
Author: mengchen18 <mengchen18@gmail.com>
Date: 2025-10-12 20:00:01 +0200
Commit message:

 update ORA

when only one feature is selected, the ORA panel won't update.
Package: UPDhmm
Commit: 40b77b9774dd3dd945dd98dd1dc24e35b129cc4f
Author: martasevill <martasevillaporras@gmail.com>
Date: 2025-10-12 20:15:43 +0200
Commit message:

 Updating vignette
Package: UPDhmm
Commit: 60538cc67a92d4de50bb12db6a4975167cc76915
Author: martasevilla <94392624+martasevilla@users.noreply.github.com>
Date: 2025-10-12 20:12:40 +0200
Commit message:

 Update DESCRIPTION
Package: UPDhmm
Commit: 053f66ad2ecb6f9da9ac3db2b92ab1a5402e30de
Author: martasevilla <94392624+martasevilla@users.noreply.github.com>
Date: 2025-10-12 20:02:29 +0200
Commit message:

 Update UPDhmm.Rmd
Package: UPDhmm
Commit: 1c3db0674be8824530870fc1156bfad44531c35c
Author: martasevilla <94392624+martasevilla@users.noreply.github.com>
Date: 2025-10-12 19:59:07 +0200
Commit message:

 Update NEWS.md
Package: maaslin3
Commit: e7106d56fdc7a37323108ac44c1cb38c9fcf9289
Author: Will Nickols <willnickols@college.harvard.edu>
Date: 2025-10-12 08:00:51 -0700
Commit message:

 Update DESCRIPTION
Package: maaslin3
Commit: 5381385af00ebd050a7a21603eb2b0fda505d9b2
Author: Will Nickols <willnickols@college.harvard.edu>
Date: 2025-10-12 08:00:06 -0700
Commit message:

 Update DESCRIPTION
Package: maaslin3
Commit: 789d87bd8b19a08bf2bf4b6ec5ffa0aad7c2722e
Author: Will Nickols <willnickols@college.harvard.edu>
Date: 2025-10-12 07:58:53 -0700
Commit message:

 Update DESCRIPTION
Package: scGraphVerse
Commit: 7e59b3e702969767984febb249d501f7816b7049
Author: francescoc <francesco.cecerengs@gmail.com>
Date: 2025-10-12 15:41:07 +0200
Commit message:

 fix README
Package: scGraphVerse
Commit: 57bf048f8cca50e49c8a48ff3037f903438d9431
Author: francescoc <francesco.cecerengs@gmail.com>
Date: 2025-10-12 15:21:53 +0200
Commit message:

 review Bioconductor
Package: RbowtieCuda
Commit: a50a88c3becb693a0ddb97ee6f45b7311dbd690f
Author: FranckRICHARD01 <franckrichard033@gmail.com>
Date: 2025-10-12 10:54:57 +0200
Commit message:

 Installation Changes
Package: STADyUM
Commit: b71dd9ebf6ff96ef9336096a797dbb84cbc974f8
Author: Rebecca Hassett <hassett@cshl.edu>
Date: 2025-10-12 00:15:56 -0400
Commit message:

 fix dependency issue
Package: maaslin3
Commit: 112f76b2905f4f4168d4f94fb1fb8df3aa063d2a
Author: Will Nickols <willnickols@college.harvard.edu>
Date: 2025-10-11 20:21:26 -0700
Commit message:

 Merge remote-tracking branch 'upstream/devel' into devel
Package: maaslin3
Commit: d86d19cb95cdb43ed5c07a6f42b1b710c11d21d6
Author: Will Nickols <willnickols@college.harvard.edu>
Date: 2025-09-25 14:28:27 -0700
Commit message:

 Change prevalence max to 1.01
Package: maaslin3
Commit: dddc03d5907817e5884e03aa6f55f5337387855f
Author: Will Nickols <willnickols@college.harvard.edu>
Date: 2025-09-25 13:11:46 -0700
Commit message:

 Update test_maaslin_log_arguments.R
Package: maaslin3
Commit: 8c2999cce487459c72d62537ef46bed9e0877d5f
Author: Will Nickols <willnickols@college.harvard.edu>
Date: 2025-09-25 12:51:30 -0700
Commit message:

 Update viz.R
Package: maaslin3
Commit: 6751345cd8b53eb84617edf62add53388fbb832d
Author: Will Nickols <willnickols@college.harvard.edu>
Date: 2025-09-25 09:56:48 -0700
Commit message:

 Add max_prevalence option
Package: maaslin3
Commit: e278c1cbd6c86025175e93f905a91c81e744ee82
Author: Will Nickols <willnickols@college.harvard.edu>
Date: 2025-07-04 11:04:15 -0700
Commit message:

 Update DESCRIPTION
Package: maaslin3
Commit: c0c0bc6632d16c903bc417e367fe66afb042f6c9
Author: Will Nickols <willnickols@college.harvard.edu>
Date: 2025-07-04 11:03:01 -0700
Commit message:

 Update utility_scripts.R
Package: maaslin3
Commit: 6f0905533e6b904f73c744a77ddd25a24c31fe89
Author: Will Nickols <willnickols@college.harvard.edu>
Date: 2025-06-18 14:45:29 -0700
Commit message:

 Version bump
Package: maaslin3
Commit: 6c3a93077d0828a25678f517cd46ad3526318bf7
Author: Will Nickols <willnickols@college.harvard.edu>
Date: 2025-06-18 14:42:05 -0700
Commit message:

 Fixed evaluate_only = 'prevalence'
Package: gVenn
Commit: bb07b670615e899a0f1e9ca3463d6267916d18a5
Author: Christophe Tav <christophe.tav@gmail.com>
Date: 2025-10-11 22:28:54 -0400
Commit message:

 update vignette
Package: gVenn
Commit: 572922117e86d2e55898651f29be785a845e09db
Author: Christophe Tav <christophe.tav@gmail.com>
Date: 2025-10-11 22:08:07 -0400
Commit message:

 test white background in dark mode
Package: gVenn
Commit: b58ee9bd228f170ba303d42c3f75da13cbe975ac
Author: Christophe Tav <christophe.tav@gmail.com>
Date: 2025-10-11 22:04:38 -0400
Commit message:

 bump to version 0.9.2 + add NEWS
Package: gVenn
Commit: 38be14f0a657eb0370af36533ec74d41a96bbbc8
Author: Christophe Tav <christophe.tav@gmail.com>
Date: 2025-10-11 21:57:47 -0400
Commit message:

 review vignette
Package: gVenn
Commit: 959cf4bf7483ab0a4584339cc603a4efddc679e1
Author: Christophe Tav <christophe.tav@gmail.com>
Date: 2025-10-11 21:40:39 -0400
Commit message:

 fix type in README
Package: gVenn
Commit: 660fcad7079a512b44ab7eaaeb1715a0010b31f3
Author: Christophe Tav <christophe.tav@gmail.com>
Date: 2025-10-11 21:33:22 -0400
Commit message:

 remove extension in example
Package: gVenn
Commit: 28dc16f100fad778557b25d6d2025082c8906657
Author: Christophe Tav <36061268+ckntav@users.noreply.github.com>
Date: 2025-10-11 18:12:49 -0400
Commit message:

 Merge pull request #1 from ckntav/enhance-plotVenn-customisation

Enhance plot venn customisation
Package: gVenn
Commit: 8b945fa0ed50888cf03b7f6dc37b958fe0a3d9f3
Author: Christophe Tav <christophe.tav@gmail.com>
Date: 2025-10-11 14:43:18 -0400
Commit message:

 add customization options in vignettes + installation instructions
Package: gVenn
Commit: e8a951a84d67c8e06b4156828e4ccc237169b960
Author: Christophe Tav <christophe.tav@gmail.com>
Date: 2025-10-11 14:02:13 -0400
Commit message:

 add more customisation options to plotVenn
Package: gVenn
Commit: 8a3cc7fffee8b432a8476d7198be251bb99e975a
Author: Christophe Tav <christophe.tav@gmail.com>
Date: 2025-10-09 23:26:46 -0400
Commit message:

 update README
Package: gVenn
Commit: 49c02865023c65be8eea7a0e4e127d044793b1da
Author: Christophe Tav <christophe.tav@gmail.com>
Date: 2025-10-09 23:23:11 -0400
Commit message:

 update README
Package: gVenn
Commit: dd1e366cdff5b903763039eb05204ae13c17d6dc
Author: Christophe Tav <christophe.tav@gmail.com>
Date: 2025-10-09 23:21:22 -0400
Commit message:

 update README
Package: gVenn
Commit: c85a5354f683bd2e205433ec93483ae4781fc615
Author: Christophe Tav <christophe.tav@gmail.com>
Date: 2025-10-09 23:06:28 -0400
Commit message:

 adapt link color dark mode
Package: gVenn
Commit: ad05bcb6e3762182052113931d5d66298a04fd7d
Author: Christophe Tav <christophe.tav@gmail.com>
Date: 2025-10-07 16:17:17 -0400
Commit message:

 change link color
Package: gVenn
Commit: 4bb89191fe604a8a2dfcedcf631931bf31e174a5
Author: Christophe Tav <christophe.tav@gmail.com>
Date: 2025-10-07 15:48:24 -0400
Commit message:

 modify header in yaml pkgdown
Package: gVenn
Commit: b1755577d515480e6c236bec4187c4a4d0d0d550
Author: Christophe Tav <christophe.tav@gmail.com>
Date: 2025-09-26 00:26:39 -0400
Commit message:

 add logo
Package: gVenn
Commit: 073f292137840c6b3e4c0e440423edf5a0460f7f
Author: Christophe Tav <christophe.tav@gmail.com>
Date: 2025-09-26 00:26:32 -0400
Commit message:

 update display website
Package: gVenn
Commit: 7c2dd8dee089824fec0c6bef1042d1eefa5fb495
Author: Christophe Tav <christophe.tav@gmail.com>
Date: 2025-09-26 00:04:31 -0400
Commit message:

 update pkgdown website
Package: gVenn
Commit: 4cf74c2859ff0c4fc320038010f7aef6c146b7fd
Author: Christophe Tav <christophe.tav@gmail.com>
Date: 2025-09-25 23:18:17 -0400
Commit message:

 update README
Package: gVenn
Commit: 99e19e7837b1392e6b22c9652e8cc02f6bc8e4d1
Author: Christophe Tav <christophe.tav@gmail.com>
Date: 2025-09-25 23:16:51 -0400
Commit message:

 update README
Package: gVenn
Commit: 73d7d1250e11f2b9e17bec472f60b43edae88c1a
Author: Christophe Tav <christophe.tav@gmail.com>
Date: 2025-09-25 15:10:00 -0400
Commit message:

 build website
Package: gVenn
Commit: 6b74989050a9e7a72cdbd2d0c57d27dd4b11dbfb
Author: Christophe Tav <christophe.tav@gmail.com>
Date: 2025-09-25 15:02:31 -0400
Commit message:

 update
Package: gVenn
Commit: e359a44e8ded16f5f22542a9db0f26fab4a67950
Author: Christophe Tav <christophe.tav@gmail.com>
Date: 2025-09-11 09:46:15 -0400
Commit message:

 update
Package: gVenn
Commit: a23d52fa3dee792aaa95dff2741f6f8e65dbf6fb
Author: Christophe Tav <christophe.tav@gmail.com>
Date: 2025-09-11 09:45:20 -0400
Commit message:

 update
Package: gVenn
Commit: 4b77e26876378aab913ad1c67fb594d1c46fd260
Author: Christophe Tav <christophe.tav@gmail.com>
Date: 2025-09-11 09:44:00 -0400
Commit message:

 update
Package: gVenn
Commit: adc28866d5582693eda7fd8d0efb7e4c88ea08ac
Author: Christophe Tav <christophe.tav@gmail.com>
Date: 2025-09-11 09:41:06 -0400
Commit message:

 update
Package: gVenn
Commit: 04a77400d2915cf0c529cb58e4b4e19af28859a2
Author: Christophe Tav <christophe.tav@gmail.com>
Date: 2025-09-11 09:40:25 -0400
Commit message:

 update
Package: gVenn
Commit: ce38b8310ce898f075b40d141e8aeb067fd47f19
Author: Christophe Tav <christophe.tav@gmail.com>
Date: 2025-09-11 09:39:36 -0400
Commit message:

 update
Package: gVenn
Commit: 1160a49ef15841a31cd99f48230cca154e8deb0a
Author: Christophe Tav <christophe.tav@gmail.com>
Date: 2025-09-11 09:38:29 -0400
Commit message:

 modify badge position
Package: gVenn
Commit: 255e7e277cc90c0f8da562c65cb0ea7cc8af4abe
Author: Christophe Tav <christophe.tav@gmail.com>
Date: 2025-09-08 23:15:42 -0400
Commit message:

 add badges in readme
Package: AlphaMissenseR
Commit: c25f39996487cc854ef695b1da4242765822dc3e
Author: Martin Morgan <mtmorgan.xyz@gmail.com>
Date: 2025-10-11 18:16:24 -0400
Commit message:

 version bump and NEWS entry
Package: AlphaMissenseR
Commit: 822e44e1491d02126e4a2c652f4357f21a9bc527
Author: Martin Morgan <mtmorgan.xyz@gmail.com>
Date: 2025-10-11 18:08:27 -0400
Commit message:

 ensure AlphaFold prediction returns exact match to query

- apparently asking for uniprot xxx also returns xxx-1, etc
Package: AlphaMissenseR
Commit: ce84b4af93e299f0885765e363e413d86b82ed82
Author: Martin Morgan <mtmorgan.xyz@gmail.com>
Date: 2025-10-11 18:07:31 -0400
Commit message:

 remove gghalves from benchmark vignette

- incompatibility with updated ggplot2
Package: Rarr
Commit: 9dbf021f89cfdf629805df7f223095b07a1ccb44
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-10-11 23:09:00 +0200
Commit message:

 Fix GitHub links in DESCRIPTION
Package: Rarr
Commit: dfb455133420586e5b869e96bd206bc0a9ac10b1
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-10-09 17:23:52 +0200
Commit message:

 Do not run benchmarks on draft PRs
Package: Rarr
Commit: 868fc744646eb11ed8f6e0d7b9942ceb03462842
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-10-08 17:13:55 +0200
Commit message:

 Remove unused get_chunk_size() function
Package: Rarr
Commit: 22c6642c8cac8615a236daa73d906bfa182ed5e0
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-10-08 13:57:52 +0200
Commit message:

 Add test for mixed v2/v3 files
Package: STADyUM
Commit: cfca0687f860642790d4808c36509538a62db99c
Author: Rebecca Hassett <hassett@cshl.edu>
Date: 2025-10-11 15:35:12 -0400
Commit message:

 fix vignette typos
Package: STADyUM
Commit: 6a370a7b73e27a47cb2559bab12a8b527a8ca400
Author: Rebecca Hassett <hassett@cshl.edu>
Date: 2025-10-11 15:24:17 -0400
Commit message:

 fix typo in vignette
Package: STADyUM
Commit: 302eaeb5003f71b72061e09207760a8e391e86c6
Author: Rebecca Hassett <hassett@cshl.edu>
Date: 2025-10-11 15:15:08 -0400
Commit message:

 update documentation
Package: STADyUM
Commit: 61a6b37ad290d08e57f585a3a384c003a35441ee
Author: Rebecca Hassett <hassett@cshl.edu>
Date: 2025-10-11 15:12:06 -0400
Commit message:

 fix typos
Package: STADyUM
Commit: 1b1f45104fe9cdfb3db97450664309c2884505c8
Author: Rebecca Hassett <hassett@cshl.edu>
Date: 2025-10-11 15:00:01 -0400
Commit message:

 Fix bug in documentation
Package: STADyUM
Commit: 5e64de8164e95efcc5231450626e1b9da4dfade0
Author: Rebecca Hassett <hassett@cshl.edu>
Date: 2025-10-11 14:43:06 -0400
Commit message:

 update version
Package: STADyUM
Commit: c294d1a34a9f7bbd64986ea9281774df36c89861
Author: Rebecca Hassett <hassett@cshl.edu>
Date: 2025-10-11 13:10:47 -0400
Commit message:

 Update tstats calc
Package: STADyUM
Commit: 705d2ba20f516910509ab2943562af5f71048569
Author: Rebecca Hassett <hassett@cshl.edu>
Date: 2025-10-10 22:19:16 -0400
Commit message:

 update documentation and tests
Package: STADyUM
Commit: ca8fab2d50f4810856f29584820560dc68d84357
Author: Rebecca Hassett <hassett@cshl.edu>
Date: 2025-10-08 12:49:28 -0400
Commit message:

 update citations with bib file
Package: STADyUM
Commit: 5b2e4893b61eb65aa2358280bf427f9d74f30018
Author: Rebecca Hassett <hassett@cshl.edu>
Date: 2025-10-07 00:18:37 -0400
Commit message:

 reknit readme
Package: STADyUM
Commit: 0c0c6e5c630f5e6867a6bab5fb4dfed9864f6ef2
Author: Rebecca Hassett <hassett@cshl.edu>
Date: 2025-10-06 19:33:18 -0400
Commit message:

 replace remaining ggpubr function with ggplot
Package: STADyUM
Commit: 0e102c4d6358cfe479105943edda9df3664aeebb
Author: Rebecca Hassett <hassett@cshl.edu>
Date: 2025-10-06 18:07:27 -0400
Commit message:

 replace ggpubr ggdensity with geom_density from ggplot2
Package: STADyUM
Commit: 705c1fe1f16b6fad6fb19a37813fe1828986e96c
Author: Rebecca Hassett <hassett@cshl.edu>
Date: 2025-10-06 18:02:22 -0400
Commit message:

 import rlang
Package: STADyUM
Commit: 4b68bc9b39746bc4d485a3a6fda9417ef6e2e8ef
Author: Rebecca Hassett <hassett@cshl.edu>
Date: 2025-10-06 17:58:52 -0400
Commit message:

 replace deprecated ggplot functions
Package: STADyUM
Commit: c9049dbed0e20e313071f7536b94663ac9f791af
Author: Rebecca Hassett <hassett@cshl.edu>
Date: 2025-10-06 16:33:51 -0400
Commit message:

 replace ggpubr dependencies with ggplot2
Package: STADyUM
Commit: 76b4829aa1cde169f168829daa36e4c71347c54f
Author: Rebecca Hassett <hassett@cshl.edu>
Date: 2025-10-06 15:51:56 -0400
Commit message:

 update description version for R
Package: STADyUM
Commit: 06d775ca96a3d6484cebb4758b4ad0048cc02056
Author: Rebecca Hassett <hassett@cshl.edu>
Date: 2025-10-06 14:38:40 -0400
Commit message:

 remove extra license and readme html file
Package: CTexploreR
Commit: 64e2ed7515b7b3bc09c42dbef5f6d083bbde843b
Author: Julie Devis <julie.devis@uclouvain.be>
Date: 2025-10-11 19:24:42 +0200
Commit message:

 Bumped version and updated NEWS
Package: CTexploreR
Commit: 86d62cc50b758e0ff785d746bafcbe62877ed9ab
Author: Julie Devis <julie.devis@uclouvain.be>
Date: 2025-10-11 19:24:19 +0200
Commit message:

 Removed documentation for internal functions
Package: CTexploreR
Commit: 71cf4d47dc5b054b675e347249013b307189a569
Author: Laurent Gatto <lgatto@protonmail.ch>
Date: 2025-10-11 10:20:40 +0200
Commit message:

 fix bioc version
Package: CTexploreR
Commit: 9a2d05e4361018035451f2c191857e82a949f80a
Author: Laurent Gatto <lgatto@protonmail.ch>
Date: 2025-10-11 10:17:40 +0200
Commit message:

 update actions/cache to v4
Package: DEGreport
Commit: a55a6e648db9dc51c8fd735867dfcfe4e1807112
Author: Lorena Pantano <lorena.pantano@gmail.com>
Date: 2025-10-11 13:32:22 -0400
Commit message:

 fix error in ggplot2
Package: BreastSubtypeR
Commit: 8e84bae88d2e4e119e7cf72f92123f5703f58ac5
Author: Qiao Yang <yq.kiuo@gmail.com>
Date: 2025-10-11 19:09:33 +0200
Commit message:

 v1.1.8 feat(auto): enforce v2-only for ER/HER2-defined cohorts; add TN cutoff (18); sync docs
Package: methodical
Commit: 9c2a85ec60b5f9b5cbeb2543631c4f367d395d89
Author: Richard Heery <richardheery@gmail.com>
Date: 2025-10-11 14:02:32 +0100
Commit message:

 Merge branch 'devel' of git.bioconductor.org:packages/methodical into devel
Package: methodical
Commit: d956856fbbc27e57f95fa2a34fed8af9776999e1
Author: Richard Heery <richardheery@gmail.com>
Date: 2025-10-11 13:45:41 +0100
Commit message:

 Merge branch 'update' into RELEASE_3_21
Package: methodical
Commit: fe40c47c7d29734221150a5ab8cadd8f21b3a1f1
Author: Richard Heery <richardheery@gmail.com>
Date: 2025-10-11 13:36:08 +0100
Commit message:

 Updated version to 1.4.0
Package: methodical
Commit: b8edbde788a506137db72dcbcb999d34b7c6b404
Author: Richard Heery <richardheery@gmail.com>
Date: 2025-10-11 13:08:32 +0100
Commit message:

 update
Package: methodical
Commit: 45ad43471b5b5de10c459401674e04f3d7321972
Author: Richard Heery <richardheery@gmail.com>
Date: 2025-10-11 12:43:35 +0100
Commit message:

 Renamed .split_input_files_into_chunks to .split_bedgraphs_into_chunks
Package: methodical
Commit: 05d9ba7c180f70fda416f9f2f291178ff8d3aeb2
Author: Richard Heery <richardheery@gmail.com>
Date: 2025-10-11 11:46:37 +0100
Commit message:

 update
Package: methodical
Commit: e03659e4074c93af09ff58c42f4a199f03f34cde
Author: Richard Heery <richardheery@gmail.com>
Date: 2025-10-10 14:17:22 +0100
Commit message:

 Updated documentation
Package: methodical
Commit: 872f7f3f71cfafe6131964158043c1b162773d87
Author: Richard Heery <richardheery@gmail.com>
Date: 2025-10-09 21:39:31 +0100
Commit message:

 Merge branch 'update' of github.com:richardheery/methodical into update
Package: methodical
Commit: 161dd6349c03f518abdbd974e6c161ffc85b1b1b
Author: Richard Heery <richardheery@gmail.com>
Date: 2025-10-01 09:04:53 +0100
Commit message:

 Removed .expand_transcript_regions since it wasn't used bu any other functions
Package: methodical
Commit: dc9d7943e1a8259392fe80e25d0642d8dcdfff44
Author: Richard Heery <richardheery@gmail.com>
Date: 2025-09-30 16:59:54 +0100
Commit message:

 Updated tubb6_correlation_plot to for R 4.5
Package: methodical
Commit: f5905dc3d4cd091eaeca7ed7a1ea44f9be64e055
Author: Richard Heery <richardheery@gmail.com>
Date: 2025-09-28 15:47:16 +0100
Commit message:

 Moved rangesRelativeToTSS to plotting_functions.R
Package: methodical
Commit: 0b85268bc82048276f2633d52ea506199e1a2065
Author: Richard Heery <richardheery@gmail.com>
Date: 2025-09-28 14:44:47 +0100
Commit message:

 Adde minimum nubmer of samples to rapid_cor_test
Package: methodical
Commit: 7e7746b8ea003d3fb4b9644bbbbd569cce816507
Author: Richard Heery <richardheery@gmail.com>
Date: 2025-09-26 16:35:30 +0100
Commit message:

 updated manuals
Package: methodical
Commit: 54db0e175ddf17aa1e56da78cab818c39410d19c
Author: Richard Heery <richardheery@gmail.com>
Date: 2025-09-26 10:33:31 +0100
Commit message:

 Updated default BPPARAM to SerialParam
Package: methodical
Commit: 646d7e24ed203d1e3e594472b3dbf127014ba84d
Author: Richard Heery <richardheery@gmail.com>
Date: 2025-09-26 08:36:27 +0100
Commit message:

 Changted geom_line to geom_smooth inside plotRegionValues
Package: methodical
Commit: d10448b78bf396ef31981391e38806890179cb13
Author: Richard Heery <richardheery@gmail.com>
Date: 2025-09-25 17:08:11 +0100
Commit message:

 Renamed plotMethylationValues plotRegionValues and updated it to allow easier control of geom_point() and geom_line() parameters
Package: methodical
Commit: a177c31b469d3b0f246ec3e93ee77cb2e55d3cc3
Author: Richard Heery <richardheery@gmail.com>
Date: 2025-09-24 17:03:26 +0100
Commit message:

 Modified summarizeRegionMethylation and calculateRegionMethylationTranscriptCors to use GRanges strings as names if none provided for regions
Package: methodical
Commit: 5806c3f59d4a8f646b46932171a1c75260383898
Author: Richard Heery <richardheery@gmail.com>
Date: 2025-09-24 14:07:04 +0100
Commit message:

 Fixed error with liftoverMethRSE when target assembly contains chromosomes not present in the source assembly
Package: methodical
Commit: 69a585392c0125dd82c50f365533671f356ebe1f
Author: Richard Heery <richardheery@gmail.com>
Date: 2025-09-04 08:30:06 +0100
Commit message:

 Fixed bug specifying sequences in createRandomRegions
Package: methodical
Commit: 65e74fb343634673c7e7adda8d3a0a266f081f4f
Author: Richard Heery <richardheery@gmail.com>
Date: 2025-07-04 16:53:15 +0100
Commit message:

 Updated expand_granges so that it restores strand of regions
Package: methodical
Commit: a83525e15ef091cd5f6e5b2415900a141b97b37a
Author: Richard Heery <richardheery@gmail.com>
Date: 2025-05-12 09:59:07 +0100
Commit message:

 Assigned min_number_complete_pairs in .tss_correlations
Package: methodical
Commit: d33dcad467ddb0609a5cc769bff837f838f8f522
Author: Richard Heery <richardheery@gmail.com>
Date: 2025-05-11 16:18:20 +0100
Commit message:

 Updated documentation
Package: methodical
Commit: f1bf4f8f3499e331d682802d8070a61043b021ae
Author: Richard Heery <richardheery@gmail.com>
Date: 2025-05-11 12:54:35 +0100
Commit message:

 Added min_number_complete_pairs parameter to calculateMethSiteTranscriptCors
Package: methodical
Commit: 1e8ceac2a9e6249b9a5958650162dbef8346d4bf
Author: Richard Heery <richardheery@gmail.com>
Date: 2025-05-11 12:34:15 +0100
Commit message:

 Added manuals
Package: methodical
Commit: 8f732a9018be8fa8c13abde6029720312a3fb743
Author: Richard Heery <richardheery@gmail.com>
Date: 2025-05-11 12:30:24 +0100
Commit message:

 Added min_number_complete_pairs paramter to rapidCorTest
Package: methodical
Commit: bd85b9df4acc5e81417874e71cc61f2f0460faf4
Author: Richard Heery <richardheery@gmail.com>
Date: 2025-04-19 16:23:55 +0100
Commit message:

 Added first draft of calculate_meth_fraction_and_total_reads
Package: methodical
Commit: 7f759dcdc518f534f673c74b6429b1dac1db87aa
Author: Richard Heery <richardheery@gmail.com>
Date: 2025-04-16 13:41:25 +0100
Commit message:

 Fixed small errors in make_met_rse.R and meth_rse_functions.R
Package: methodical
Commit: 32a122d2db01a68ffcfc1586e5df78cf5aca0888
Author: Richard Heery <richardheery@gmail.com>
Date: 2025-04-16 13:22:46 +0100
Commit message:

 Updated sampleMethSites to allow filter for seqnames
Package: methodical
Commit: 7d1635eaf2b8b5d4c7e94626042aba8c36e8392d
Author: Richard Heery <richardheery@gmail.com>
Date: 2025-03-18 14:25:12 +0000
Commit message:

 Fixed annotatePlot so that it works when meth_site_plot was created with reverse_x_axis = T set
Package: methodical
Commit: 364e2ce1571d614665c99cc71981ba42905668a5
Author: Richard Heery <richardheery@gmail.com>
Date: 2025-03-17 17:19:45 +0000
Commit message:

 Fixed error in annotatePlot which was drawing dashed lines for regions
Package: methodical
Commit: 302d9e2f248895b11a79a9dda119234c48922c55
Author: Richard Heery <richardheery@gmail.com>
Date: 2025-01-30 09:59:50 +0000
Commit message:

 Added .BBSoptions to indicate that Windows is unsupported
Package: methodical
Commit: 815decdc5fb2860022cf85fdca09baf6c8234605
Author: Richard Heery <richardheery@gmail.com>
Date: 2024-12-26 17:29:59 +0000
Commit message:

 Fixed calculating_methylation_transcription_correlations vignette
Package: methodical
Commit: 0ac111c4fce8f2d1f26794de05253bd41737265e
Author: Richard Heery <richardheery@gmail.com>
Date: 2024-12-26 13:49:29 +0000
Commit message:

 Fixed examples and vignettes
Package: CTexploreR
Commit: d1e6efaad0099462aea00c14d07a41d72dc061e4
Author: Laurent Gatto <lgatto@protonmail.ch>
Date: 2025-10-11 10:15:32 +0200
Commit message:

 fix conflict
Package: CTexploreR
Commit: 88abdd62ce51501c9134099523157b9bfbd3f7d5
Author: Laurent Gatto <lgatto@protonmail.ch>
Date: 2025-10-11 10:14:34 +0200
Commit message:

 bump version and update news
Package: CTexploreR
Commit: dd7ffd8ec7862f2edd271518396ae750753c9a15
Author: aloriot <axelle.loriot@uclouvain.be>
Date: 2025-10-10 13:50:26 +0200
Commit message:

 created longtests folder
Package: CTexploreR
Commit: 50c566acda089e1a0458dccd7a05ca93d0452fda
Author: aloriot <axelle.loriot@uclouvain.be>
Date: 2025-10-10 13:49:37 +0200
Commit message:

 nothing
Package: CTexploreR
Commit: 4b10eb96cc5e3f87c01bdd44e2b583f0f1cf4be4
Author: aloriot <axelle.loriot@uclouvain.be>
Date: 2025-10-10 13:38:00 +0200
Commit message:

 transfered long testis units to longtests folder
Package: strandCheckR
Commit: 94914468617c478a3b16f10a6c282036921d59fd
Author: Stevie Ped <stephen.pederson.au@gmail.com>
Date: 2025-10-11 12:52:54 +1030
Commit message:

 Version bump after bugfix
Package: strandCheckR
Commit: 4e32127803361e011ccfa204618385bb8e885dfd
Author: Stevie Ped <stephen.pederson.au@gmail.com>
Date: 2025-10-11 12:40:47 +1030
Commit message:

 Corrected missing links from manpages
Package: gINTomics
Commit: 7d7f668fbdfa58aa14011b5efb99d92cebbf8c6a
Author: angeve96 <angeve89@gmail.com>
Date: 2025-10-10 22:28:01 +0200
Commit message:

 version bump
Package: gINTomics
Commit: 02ae750818bcee47e34ddd4f5a9f5b72e5b66389
Author: angeve96 <angeve89@gmail.com>
Date: 2025-10-10 22:27:36 +0200
Commit message:

 omnipathr fix
Package: gINTomics
Commit: 102964aecffcf676dfceb78918aa3748051170da
Author: angeve96 <angeve89@gmail.com>
Date: 2025-10-10 21:52:55 +0200
Commit message:

 first commit
Package: MetNet
Commit: 862d9ecbd384c1741ae8b4bc179c790403ebab15
Author: Thomas Naake <thomasnaake@gmx.de>
Date: 2025-10-10 21:37:01 +0200
Commit message:

 version bump to 1.27.2 in devel
Package: MetNet
Commit: 807aff249102bbb285c810406c8e729ac384c22f
Author: Thomas Naake <thomasnaake@gmx.de>
Date: 2025-10-10 21:32:50 +0200
Commit message:

 bug fix: extend unit test
Package: MetNet
Commit: f2f25a5df11bfdbfd0dac3c5c8881cd0551a276d
Author: Thomas Naake <thomasnaake@gmx.de>
Date: 2025-10-08 19:01:29 +0200
Commit message:

 update yml to current RELEASE_3_21
Package: MetNet
Commit: 9b49a4ba0cd096a84ce5d93bff8feacbffa7ecc0
Author: Thomas Naake <thomasnaake@gmx.de>
Date: 2025-10-08 18:55:21 +0200
Commit message:

 update yml to current RELEASE_3_21
Package: MetNet
Commit: 93b097f7afaf66a36d26bcddaa7853b42c5f8d50
Author: Thomas Naake <thomasnaake@gmx.de>
Date: 2025-10-08 18:52:01 +0200
Commit message:

 update yml to current RELEASE_3_21
Package: iModMix
Commit: 3e95f82a555f4863b0c3143b2a4dfae82e5e6665
Author: IsisNarvaez <isis.narvaez@upr.edu>
Date: 2025-10-10 15:52:43 -0400
Commit message:

 Bioconductor comments
Package: SpiecEasi
Commit: 57d54bf7eb4d3b15481d347cbc632526a17c2b5b
Author: Zachary Kurtz <zdkurtz@gmail.com>
Date: 2025-10-10 15:00:09 -0400
Commit message:

 address build warnings
Package: SpiecEasi
Commit: 085b970a4b023300d31e0f4f578d18a91f7304c0
Author: Zachary Kurtz <zdkurtz@gmail.com>
Date: 2025-10-10 14:42:49 -0400
Commit message:

 catch NA condition
Package: scRNAseq
Commit: c47ea394f4bbfe35f58909a91cffa617c072b552
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2025-10-10 11:11:42 -0700
Commit message:

 Added an unpublished Perturb-seq dataset from GEO.
Package: SpiecEasi
Commit: c32dd5f08867b602c1676f1f0157a09dc810b1bd
Author: Zachary Kurtz <zdkurtz@gmail.com>
Date: 2025-10-10 14:02:07 -0400
Commit message:

 use seq_along
Package: SpiecEasi
Commit: c0f1ab7e012f9446038a3e0525e5879080964d41
Author: Zachary Kurtz <zdkurtz@gmail.com>
Date: 2025-10-10 13:58:36 -0400
Commit message:

 fix object trimming for vignettes
Package: anansi
Commit: 369b937b0f5bcaad948689bf5d2ad603e37bd630
Author: Thomaz <thomazbastiaanssen@gmail.com>
Date: 2025-10-10 19:49:55 +0200
Commit message:

 Merge pull request #61 from thomazbastiaanssen/thomazbastiaanssen-patch-1

Bump version
Package: anansi
Commit: eed57b57f2075617383bf974e9e0a45d194a23c3
Author: Thomaz <thomazbastiaanssen@gmail.com>
Date: 2025-10-10 19:49:34 +0200
Commit message:

 Bump version
Package: anansi
Commit: 4aa26f48bd7240496b7a2af57084df27fe41e2e3
Author: thomaz <thomazbastiaanssen@gmail.com>
Date: 2025-10-10 19:47:33 +0200
Commit message:

 add chunk names
Package: scLANE
Commit: 6c6f57e57d38a0d42b1cd88f48349424aab0c32a
Author: Jack Leary <jrleary@live.unc.edu>
Date: 2025-10-10 13:56:02 -0400
Commit message:

 fixed LICENSE issue i hope
Package: anansi
Commit: a340778f6d1d2b128948e897882b6836c72cbe3d
Author: thomaz <thomazbastiaanssen@gmail.com>
Date: 2025-10-10 19:20:04 +0200
Commit message:

 Address final notes
Some long figure names & URLs remain.
Package: anansi
Commit: bf0b39955744cbe0d909e32a79b33351735be993
Author: Thomaz <thomazbastiaanssen@gmail.com>
Date: 2025-10-10 18:18:26 +0200
Commit message:

 Merge pull request #60 from thomazbastiaanssen/giulio

Shorten vignette output
Package: anansi
Commit: a29ab9ee9c1f57c1a600fb22016d3800d68c8e28
Author: thomaz <thomazbastiaanssen@gmail.com>
Date: 2025-10-10 18:15:30 +0200
Commit message:

 Address bioc review
Package: anansi
Commit: 9af96bdd170b8e0d9138537e7691d1ff93af43ff
Author: Giulio <giuliobene2000@gmail.com>
Date: 2025-10-05 22:57:04 +0900
Commit message:

 Shorten vignette output
Package: PhyloProfile
Commit: f3488bdea2c244e969d457378a7a2507bb22b67c
Author: AnnamTran <trvinh@gmail.com>
Date: 2025-10-10 19:16:29 +0200
Commit message:

 auto update db source for demo data
Package: MultiRNAflow
Commit: 790c01570e60e89b9e2eb64d68d8146af293c003
Author: Rodolphe Loubaton <loubaton.rodolphe@gmail.com>
Date: 2025-10-10 19:03:14 +0200
Commit message:

 New version: 20251010
Package: MultiRNAflow
Commit: 544c773dcf5086cb69eaf118662927a2bf056c6b
Author: Rodolphe Loubaton <loubaton.rodolphe@gmail.com>
Date: 2025-10-10 18:50:41 +0200
Commit message:

 New version: 20251010
Package: scLANE
Commit: 616e9d0c6ae674c3dc4a949521c251a945fdc846
Author: Jack Leary <jrleary@live.unc.edu>
Date: 2025-10-10 12:08:26 -0400
Commit message:

 fixing version number
Package: scLANE
Commit: 6b21a2b68a6674a515f915c28989340bac868159
Author: Jack Leary <jrleary@live.unc.edu>
Date: 2025-10-10 12:05:54 -0400
Commit message:

 final tweak for bioconductor submission
Package: bsseq
Commit: 8be0d5139f3796f27cc7d612dd102288d7fff2b6
Author: Kasper Daniel Hansen <kasperdanielhansen@gmail.com>
Date: 2025-10-10 11:22:10 -0400
Commit message:

 deprecating read.modklit and read.modbam2bed
Package: bsseq
Commit: 84bf7e6f40ea1e60b609fde32109cb0d1a197b1a
Author: Kasper Daniel Hansen <kasperdanielhansen@gmail.com>
Date: 2025-10-04 11:07:28 -0400
Commit message:

 Fixing an issue where collapseBSseq() would emit an error on some objects.
Package: bsseq
Commit: 825e2e549ee4817cb0c3d6fde55b1ec2e3a44266
Author: Kasper Daniel Hansen <kasperdanielhansen@gmail.com>
Date: 2025-10-04 09:31:42 -0400
Commit message:

 updating GA using biocthis
Package: bsseq
Commit: f38889bf96b7c509b49ff16a4d884468610090a7
Author: Kasper Daniel Hansen <kasperdanielhansen@gmail.com>
Date: 2025-09-05 10:30:57 -0400
Commit message:

 Merge pull request #150 from hansenlab/fix_149

Fix #149
Package: bsseq
Commit: 4cce30f9ffe78a2aaaf22dcb018774b30352ce2e
Author: Peter Hickey <peter.hickey@gmail.com>
Date: 2025-07-10 16:17:27 +1000
Commit message:

 Fix #149
Package: BatChef
Commit: 67e19b6de395c64c02f5e53795561d9ee8a90073
Author: zuinelena3 <elena.zuin3@gmail.com>
Date: 2025-10-10 16:40:58 +0200
Commit message:

 Bump version: 0.99.3
Package: BatChef
Commit: 5df5c14ff82737bfa845739b270fe949a4287b68
Author: zuinelena3 <elena.zuin3@gmail.com>
Date: 2025-10-09 16:06:25 +0200
Commit message:

 Basilisk py_env: change OpenSSL version from 3.2.0 to 3.1.1
Package: spacexr
Commit: 4bce0a43cd084cb86a94d64e2704b1ca9d711604
Author: Gabriel Grajeda <gabriel.grajeda@gmail.com>
Date: 2025-10-10 10:43:44 -0400
Commit message:

 Add Rafael Irizarry to list of authors
Package: spacexr
Commit: 3122f4be118edcfe0293c9ad2bd252693f019570
Author: Gabriel Grajeda <gabriel.grajeda@gmail.com>
Date: 2025-10-10 10:25:00 -0400
Commit message:

 Revert to original RELEASE_3_21

This reverts commit 6cb3e2606efdf3b5e3a4b004767dc5b1c18a0558.
Package: spacexr
Commit: 0e5418b1ca9a834befbd6d48e734d320583ee0a8
Author: Gabriel Grajeda <gabriel.grajeda@gmail.com>
Date: 2025-10-10 10:21:56 -0400
Commit message:

 Normalize weights matrix
Package: spacexr
Commit: 2ded15fff4a63ee1c74a8f2bfaa631e81dfa31fe
Author: Gabriel Grajeda <gabriel.grajeda@gmail.com>
Date: 2025-07-08 10:40:02 -0400
Commit message:

 Return doublet_mat in RCTD colData
Package: spacexr
Commit: 0d040f644acb805c239a08d40b64804563feaa39
Author: Gabriel Grajeda <gabriel.grajeda@gmail.com>
Date: 2025-07-08 10:36:41 -0400
Commit message:

 Set up initial RICE algorithm
Package: spacexr
Commit: 27b65e239beb1a4b44353b770ec1fec2273af704
Author: Gabriel Grajeda <gabriel.grajeda@gmail.com>
Date: 2025-06-30 15:12:34 -0400
Commit message:

 Rename RCTDmode in config to doublet_mode
Package: spacexr
Commit: 04f2e5476df81e8ec26aa83dd8614fbb1c2caf9b
Author: Gabriel Grajeda <gabriel.grajeda@gmail.com>
Date: 2025-06-17 15:15:37 -0400
Commit message:

 Refactor some RICE initialization functions

Note: This will need some pretty heavy refactoring later. Ideally, we should be able to use the createRctd function to set up the RICE algorithm.
Package: spacexr
Commit: 592587e013a2500d92181e90d13fb826d629644e
Author: Gabriel Grajeda <gabriel.grajeda@gmail.com>
Date: 2025-06-16 16:45:05 -0400
Commit message:

 Add initial RICE implementation
Package: spacexr
Commit: b0e3f953e3f587be90df153552caaebfa69eda95
Author: Gabriel Grajeda <gabriel.grajeda@gmail.com>
Date: 2025-06-16 15:19:20 -0400
Commit message:

 Move CSIDE attributes to RctdConfig
Package: spacexr
Commit: f1e180900bd735bfc25179c3991cc8a58e4c7e38
Author: Gabriel Grajeda <gabriel.grajeda@gmail.com>
Date: 2025-05-30 13:51:00 -0400
Commit message:

 Refactor CSIDE function documentation

Shared parameters are now documented in one function: run.CSIDE.general
Package: spacexr
Commit: 6730eb3dbc05e13f3114f66ca2e8b48125cf22fd
Author: Gabriel Grajeda <gabriel.grajeda@gmail.com>
Date: 2025-05-28 16:39:13 -0400
Commit message:

 Fix unbound variables in CSIDE functions

The variables x, y in get_spline_matrix still need to be fixed
Package: spacexr
Commit: c2c5c5d95dff5316904ec6c76537a781f8ddda35
Author: Gabriel Grajeda <gabriel.grajeda@gmail.com>
Date: 2025-05-22 11:15:07 -0400
Commit message:

 Add Sequencing to biocViews to appease BiocCheck
Package: spacexr
Commit: 57ec7d12f93726520914ddc6558d49baf4c71603
Author: Gabriel Grajeda <gabriel.grajeda@gmail.com>
Date: 2025-05-22 11:06:23 -0400
Commit message:

 Fix parentheses in find_sig_genes_categorical significance test
Package: spacexr
Commit: 4d15e7f1ed84d5e0ccf1a3f2b1610a97c2be9b40
Author: Gabriel Grajeda <gabriel.grajeda@gmail.com>
Date: 2025-05-22 10:58:27 -0400
Commit message:

 Reformat CSIDE functions to have line length <= 80 chars
Package: spacexr
Commit: e3c40ee8a40876a4c0c97f5608775decf81fcd0d
Author: Gabriel Grajeda <gabriel.grajeda@gmail.com>
Date: 2025-05-21 14:16:42 -0400
Commit message:

 Reformat message/warning/stop condition signals
Package: spacexr
Commit: 7fd241d1808ec7eef4500651d9e00566d47c2b47
Author: Gabriel Grajeda <gabriel.grajeda@gmail.com>
Date: 2025-05-21 13:29:29 -0400
Commit message:

 Run styler::style_dir to fix indentation
Package: spacexr
Commit: 147642ebb9293c6eed1a674a2d9eabc1c6ca9f74
Author: Gabriel Grajeda <gabriel.grajeda@gmail.com>
Date: 2025-05-21 13:06:01 -0400
Commit message:

 Use <- for assignment in CSIDE functions
Package: spacexr
Commit: 475e1bac5700a28c3588dc8887321add66cd4c8f
Author: Gabriel Grajeda <gabriel.grajeda@gmail.com>
Date: 2025-05-21 11:57:04 -0400
Commit message:

 Replace 1:... with seq_len or seq_along in CSIDE functions
Package: spacexr
Commit: d76bbba32d372113be715092af3f6ee867039685
Author: Gabriel Grajeda <gabriel.grajeda@gmail.com>
Date: 2025-05-21 11:32:50 -0400
Commit message:

 Use TRUE/FALSE instead of T/F in CSIDE functions
Package: spacexr
Commit: e613482deaa0a4240f1316719232e96de0b4c067
Author: Gabriel Grajeda <gabriel.grajeda@gmail.com>
Date: 2025-05-14 11:21:11 -0400
Commit message:

 Format roxygen comments for CSIDE functions
Package: spacexr
Commit: 7a31a3e45362c7d56f06a139b509dbe69c0643c3
Author: Gabriel Grajeda <gabriel.grajeda@gmail.com>
Date: 2025-04-28 17:14:58 -0400
Commit message:

 Add initial CSIDE implementation

This commit implements an updated version of CSIDE adapted to work with Bioconductor objects.

Very few modifications have been made to the original source code; there are still a number of warnings and errors from R CMD CHECK and BiocCheck.

These issues will be fixed in upcoming commits. Tests will also be added to ensure code consistency.

DO NOT COMMIT TO BIOCONDUCTOR
Package: spacexr
Commit: 6cb3e2606efdf3b5e3a4b004767dc5b1c18a0558
Author: Gabriel Grajeda <gabriel.grajeda@gmail.com>
Date: 2025-04-28 17:14:58 -0400
Commit message:

 Update RCTD functions in preparation for CSIDE implementation
Package: metaseqR2
Commit: 1e96df6aea24a69793dee32c61fbf560ac0a7fd1
Author: Panagiotis Moulos <pmoulos@gmail.com>
Date: 2025-10-10 14:26:16 +0000
Commit message:

 Fixed latest BioC error - attempt 1
Package: Moonlight2R
Commit: 8a3d59a143e6aa96068a03baf6f6dd878660105e
Author: AlessiaCampo <59013682+AlessiaCampo@users.noreply.github.com>
Date: 2025-10-10 15:26:27 +0200
Commit message:

 Fix151 timing errors in examples (#152)

* updates in the GLS and GMA examples to reduce the running time

* Updated the version in DESCRIPTION and NEWS.md

---------

Co-authored-by: Alessia Campo <acampo@kb-bioinfo01.cancer.dk>
Package: Spectra
Commit: 353488c251dc211f5f35701d471c27fb0f4b6afe
Author: Johannes Rainer <5506112+jorainer@users.noreply.github.com>
Date: 2025-10-10 15:08:32 +0200
Commit message:

 Merge pull request #370 from rformassspectrometry/jomain

feat: add spectraVariableMapping methods for Spectra
Package: Spectra
Commit: 781df97befee0979447fd3f74ca40d545a49745b
Author: Johannes Rainer <johannes.rainer@gmail.com>
Date: 2025-10-10 14:45:35 +0200
Commit message:

 feat: add spectraVariableMapping methods for Spectra

- Add implementations of `spectraVariableMapping()` and
  `spectraVariableMapping<-` methods for `Spectra` and `MsBackend`.
Package: KEGGREST
Commit: 071e86880282a9a890f7e6adaf3c7d6428c86e68
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-10-10 08:56:20 -0400
Commit message:

 version bump 1.49.2
Package: KEGGREST
Commit: d209c29055787a56424bcf87543f356bb1a35695
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-10-10 08:56:14 -0400
Commit message:

 update source argument docs in keggLink
Package: DESeq2
Commit: 6fdaf4bb71de424e6e87e99b8db9ef258ded9306
Author: Mike Love <mikelove@users.noreply.github.com>
Date: 2025-10-10 08:11:54 -0400
Commit message:

 fixing arma deprecation max(arma::uword&) for .index_max()
Package: spatialFDA
Commit: 93358c07530ce2ce237a3b96be0365ff2d85a4b9
Author: mjemons <martin.emons@gmail.com>
Date: 2025-10-10 13:08:16 +0200
Commit message:

 updated NEWS file
Package: spatialFDA
Commit: bf478899c9cb4b7929c5cb1d0d0e57e8069a5ad8
Author: mjemons <martin.emons@gmail.com>
Date: 2025-10-10 13:07:24 +0200
Commit message:

 changes to messages and correction passing
Package: Aerith
Commit: da2d914793ef6f1983881df2739439e24e62b793
Author: xyz1396 <1074082710@qq.com>
Date: 2025-10-10 03:34:58 -0500
Commit message:

 bump version
Package: Aerith
Commit: 57e3c515e4f8d7839537ed54cd40871b5952b9cf
Author: xyz1396 <1074082710@qq.com>
Date: 2025-10-10 00:10:27 -0500
Commit message:

 add demos to some rcpp function, optimize vignettes
Package: nmrdata
Commit: b1f6209beaf0a5391ad76a365114533f0193e815
Author: tk <tkimhofer@gmail.com>
Date: 2025-10-10 10:19:43 +0200
Commit message:

 Added pck-level doc & version bump
Package: iModMix
Commit: 7c88e326798263aeaa35a7cf034de55773351e2f
Author: Isis Narvaez-Bandera <isis.narvaez@upr.edu>
Date: 2025-10-10 02:36:43 -0400
Commit message:

 Bioconductor suggestions
Package: edgeR
Commit: 1f747a2eacbbb8a60310e527db4b3e4d37dd194a
Author: Yunshun Chen <yuchen@wehi.edu.au>
Date: 2025-10-10 16:13:11 +1100
Commit message:

 Update the users guide pdf and test files
Package: OSCA.workflows
Commit: 318c3ab439ea525d813ef7cd20dd0ad319477d5e
Author: Peter Hickey <peter.hickey@gmail.com>
Date: 2025-10-10 15:49:55 +1100
Commit message:

 Update hca-bone-marrow.Rmd (#7)

* Update hca-bone-marrow.Rmd

- Note that MNN-corected values may vary across systems due to the randomized SVD
- Make `cluster.choice` robust to these differences
- This was verified on Ubuntu (x86_64) and macOS (aarch64)

* Version bump
Package: edgeR
Commit: f8df538e6f2a0b375448c0877d7b78c82570d9c0
Author: Yunshun Chen <yuchen@wehi.edu.au>
Date: 2025-10-10 15:23:11 +1100
Commit message:

 Update documentations
Package: edgeR
Commit: 52d8e55e6a888759b5c271d73b89cc527c935cb1
Author: Yunshun Chen <yuchen@wehi.edu.au>
Date: 2025-10-10 15:16:44 +1100
Commit message:

 Update rpkm()
Package: edgeR
Commit: 9ca2462fc2f7bad0a8ca073df533b67f9c4ab63a
Author: Yunshun Chen <yuchen@wehi.edu.au>
Date: 2025-10-10 15:03:27 +1100
Commit message:

 Add cpm(), rpkm() and tpm() functionality for MArrayLM objects.
Package: gdsfmt
Commit: caccdd9274625cef60e205b0227b1f33b65eb610
Author: Xiuwen Zheng <zhengxwen@gmail.com>
Date: 2025-10-09 20:39:06 -0500
Commit message:

 fix a strange bug on MacOS
Package: edgeR
Commit: 8802f877057a0fff38b4380a468cd9eb94f0b3c4
Author: Yunshun Chen <yuchen@wehi.edu.au>
Date: 2025-10-10 11:34:39 +1100
Commit message:

 Update NAMESPACE and bump up version number
Package: masstools
Commit: 56c71ee7231e447e0f2cac3f4a20b1471dd20da8
Author: chain-buds <bspchemy@gmail.com>
Date: 2025-10-10 08:24:01 +0800
Commit message:

 modify from suggestions of https://github.com/Bioconductor/Contributions/issues/3885#issuecomment-3319842354
Package: edgeR
Commit: 9c93f47ac6ca346f930b70e1f1016c720bf2d3eb
Author: Yunshun Chen <yuchen@wehi.edu.au>
Date: 2025-10-10 11:28:23 +1100
Commit message:

 Add tpm() and tpmProp()
Package: edgeR
Commit: 3792bafd08516295a658f7a749ec98902dc8766d
Author: Yunshun Chen <yuchen@wehi.edu.au>
Date: 2025-10-10 11:17:56 +1100
Commit message:

 Update the CITATION
Package: VisiumIO
Commit: 5a26b32c28bdb5a8a500a7f77449d9bc7226534c
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-10-09 18:21:08 -0400
Commit message:

 version bump 1.5.10
Package: VisiumIO
Commit: 25c6b792ff6658ca16f614da161448de83d0cfc1
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-10-07 13:56:12 -0400
Commit message:

 add st_invert_y utility function
Package: gemma.R
Commit: b74648368778f641569e6ce1cec6031559712c44
Author: OganM <ogan.mancarcii@gmail.com>
Date: 2025-10-09 14:44:18 -0700
Commit message:

 version bump
Package: gemma.R
Commit: bdc3fe2d2fab860768d9f53e2b095d63bcfe222c
Author: OganM <ogan.mancarcii@gmail.com>
Date: 2025-10-09 14:44:01 -0700
Commit message:

 remove test until gemma release
Package: gemma.R
Commit: 767df49cdb78239ed0bcd705f757bbae3c759cb3
Author: OganM <ogan.mancarcii@gmail.com>
Date: 2025-10-09 14:42:25 -0700
Commit message:

 re-trigger tests
Package: UPDhmm
Commit: fc8c29bde3837a0e710efdc91cd9e1df8a797cbb
Author: martasevill <martasevillaporras@gmail.com>
Date: 2025-10-09 23:20:02 +0200
Commit message:

 Merge remote-tracking branch 'upstream/devel' into devel
Package: UPDhmm
Commit: 90b6c554605d70ab3d9434d7f01c788fe4ccd80c
Author: martasevilla <94392624+martasevilla@users.noreply.github.com>
Date: 2025-10-09 20:34:44 +0200
Commit message:

 Update DESCRIPTION
Package: UPDhmm
Commit: 0c82da47ec2a4174535cba4346dcc0bc34878117
Author: martasevilla <94392624+martasevilla@users.noreply.github.com>
Date: 2025-10-09 20:30:19 +0200
Commit message:

 Update DESCRIPTION
Package: UPDhmm
Commit: 3e6219c01287501a5124b917c97d25e5b4361edd
Author: martasevill <martasevillaporras@gmail.com>
Date: 2025-10-09 18:42:08 +0200
Commit message:

 New version of the package with new functions and vignettes
Package: wompwomp
Commit: 1aa91c468cf49167b6d99bef9090d9d0e28db10f
Author: josephrich98 <josephrich98@gmail.com>
Date: 2025-10-09 14:12:38 -0700
Commit message:

 updated vignette bug
Package: wompwomp
Commit: aaf1a66812104532e5e23326748bc6c122039d20
Author: josephrich98 <josephrich98@gmail.com>
Date: 2025-10-09 14:03:02 -0700
Commit message:

 updated unit test images
Package: wompwomp
Commit: cdd7a312a09c1cdcaffb8fdda81d07df6c5a0dc6
Author: josephrich98 <josephrich98@gmail.com>
Date: 2025-10-09 14:01:07 -0700
Commit message:

 fixed vignette small bug
Package: wompwomp
Commit: e4e734e439bb8fc755d41674330f53f874e86410
Author: Conrad Oakes <oakesconrad@gmail.com>
Date: 2025-10-09 13:48:34 -0700
Commit message:

 Default behavior of axis labels changed to include x axis labels
Package: wompwomp
Commit: b6f2bc03fd465d362e93fd0bb80e5445ceb6ead8
Author: josephrich98 <josephrich98@gmail.com>
Date: 2025-10-09 13:22:59 -0700
Commit message:

 addressed bioc feedback and version bump
Package: wompwomp
Commit: 4aadcc9e547d20579a99590ee616688021573c97
Author: Conrad Oakes <oakesconrad@gmail.com>
Date: 2025-10-06 13:01:47 -0700
Commit message:

 Updated python axis text sizes
Package: wompwomp
Commit: 75323e3f460e325953bd2474975f188bfa47fd04
Author: Conrad Oakes <oakesconrad@gmail.com>
Date: 2025-10-03 14:20:03 -0700
Commit message:

 Updated autofit text and color assignment

Autofit text now includes the option to remove labels that become too small

color_dict can now only partially cover the available stratum/alluvium options, and wompywompy will automatically generate colors for the remainder. Can toggle off by setting fill_missing_colors equal to the color for unmapped values
Package: wompwomp
Commit: 307c444f8f45687ae5122835610d82769726f918
Author: Conrad Oakes <oakesconrad@gmail.com>
Date: 2025-10-03 13:34:58 -0700
Commit message:

 Added options to reduce alluvial border thickness and turn of autofitting text
Package: wompwomp
Commit: 9da4ef7a1047283524577a3302709c945fcc5414
Author: Conrad Oakes <oakesconrad@gmail.com>
Date: 2025-10-03 13:33:52 -0700
Commit message:

 Bug fixing in greedy_wolf algorithm
Package: wompwomp
Commit: 0fdbbf81c44dfbb483c4744ce8f73ac80a3ca56e
Author: Conrad Oakes <oakesconrad@gmail.com>
Date: 2025-10-02 16:17:48 -0700
Commit message:

 Added pure python implementation
Package: mobileRNA
Commit: b06a94067ed83790dc6ec665921e44fd6894adf0
Author: KJeynesCupper <kejc@illinois.edu>
Date: 2025-10-09 13:48:27 -0500
Commit message:

 updated version

1.0.16 to 1.5.0
Package: DMRcaller
Commit: d5231aaf0c06dccff7a55acf8a49cfad3f6a41a3
Author: nrzabet <r.zabet@qmul.ac.uk>
Date: 2025-10-09 19:48:29 +0100
Commit message:

 added support for ONT methylation data
Package: DMRcaller
Commit: df5e78b0f935e1ffd4143fa99b89cea844af8c01
Author: nrzabet <r.zabet@qmul.ac.uk>
Date: 2025-10-09 19:48:19 +0100
Commit message:

 added support for ONT methylation data
Package: Rsubread
Commit: 4be6b68fb842318b70887313a54f0bafc2143868
Author: Yang Liao (Monash University) <yliao@m3-login2.massive.org.au>
Date: 2025-10-10 05:39:45 +1100
Commit message:

 Removed last warning.
Package: Rsubread
Commit: 530ab38459cbec91c0120b27d177263d8b70938a
Author: Yang Liao (Monash University) <yliao@m3v106.massive.org.au>
Date: 2025-10-09 05:54:18 +1100
Commit message:

 enabled maximum search times in cellCounts
Package: beachmat.hdf5
Commit: fedbe05577ae40294f19c8b21809c66d85bdc965
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2025-10-09 11:34:48 -0700
Commit message:

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

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

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

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

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

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

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

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

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

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

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

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

 Merge pull request #93 from thelovelab/doc-edits

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

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

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

 Bugfix: prob zero underflow error (#126)

* Solved underflow error in `funProbZero()`

Solved in related `torch` implementation too

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

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

* Updated test.dataset and associated saved test data.

* Updated test.dataset to more realistic example

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

 mobile detection options

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

 BiocGenerics 0.55.3: Better fix for updateObject() infinite recursion

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

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

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

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

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

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

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

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

 Merge pull request #129 from jessmcc22/devel

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

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

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

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

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

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

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

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

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

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

 Merge pull request #23 from kauralasoo/coverage_refactor

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

 Merge pull request #22 from kerimoff/coverage_refactor

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

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

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

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

 Merge pull request #13 from matmu/patch-1

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

 Update wiggleplotr.R

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

 BiocGenerics 0.55.2: Fix updateObject() on old ggplot instances

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

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

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

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

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

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

 Deprecated

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

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

 deprecate

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

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

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

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

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

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

 Deprecated

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

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

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

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

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

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

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

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

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

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

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

 Merge pull request #118 from saezlab/main

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

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

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

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

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

 Merge pull request #117 from saezlab/devel

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

 Deprecated

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

 Deprecate

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

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

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

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

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

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

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

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

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

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

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

 removed warning from cellCounts.