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Package: biocViews
Commit: 225a7fc66eff6d537e86063b534e6c4feeef8e6a
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-09-04 12:03:30 -0500
Commit message:

 version bump 1.77.4
Package: biocViews
Commit: 28d31b1dcdb104cb1ca467b458b6a2e09068680d
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-09-04 11:43:55 -0500
Commit message:

 update build-dbs.Rd
Package: biocViews
Commit: b4c39a6349bd3166ac18c208856b736a9394f322
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-09-04 11:36:02 -0500
Commit message:

 fix tools:write_PACKAGES man page name reference
Package: biocViews
Commit: e22fd2f94573537abd2e8b8352f4c61a5170ee5d
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-09-04 11:34:28 -0500
Commit message:

 fix use of middle in DESCRIPTION
Package: biocViews
Commit: 4298b20c6b8e07a31f17863de662ccbade1fbc12
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-05-24 11:15:17 -0400
Commit message:

 fix NOTE re undefined symbol
Package: biocViews
Commit: a3d86af1a1d66fa5f0b880aea0ba9b7568935457
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-05-24 11:15:06 -0400
Commit message:

 fix note re: biocViewsVocab
Package: biocViews
Commit: dfdc1cc7dcb776ef917c4d5fcd0a8f1ea7428fc8
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-05-24 11:14:24 -0400
Commit message:

 update to Authors@R
Package: spatialFDA
Commit: d89d20e7b98e560af0f9ad97ee78808a5f7a35fe
Author: mjemons <martin.emons@gmail.com>
Date: 2025-09-04 16:46:09 +0200
Commit message:

 below threshold values are not coloured
Package: spatialFDA
Commit: ee670f750727213da5288161cfa09f2b570ab6ec
Author: mjemons <martin.emons@gmail.com>
Date: 2025-09-04 15:36:46 +0200
Commit message:

 new QC, shape in heatmap plot and faster examples with bam
Package: Bioc.gff
Commit: 30c2f247b04f228acab6cd237d9e1e955248ca86
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-09-04 10:08:49 -0500
Commit message:

 version bump 0.99.13
Package: Bioc.gff
Commit: 38cdf62a386a5e79c4e8dc1c303803b97c5b21c3
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-09-04 11:02:49 -0400
Commit message:

 remove donttest in examples
Package: Bioc.gff
Commit: ff9cb1f83238c5f243b30fc7fde38a40c09c2bae
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-09-04 10:44:50 -0400
Commit message:

 version bump 0.99.12
Package: ClustIRR
Commit: e7d3be7912430d43ba748168fcfaed13325459de
Author: snaketron <simo.kitanovski@uni-due.de>
Date: 2025-09-04 15:07:10 +0200
Commit message:

 last bugfix in dco
Package: biocViews
Commit: 0344561c345bbd27186315d5378912e261c1c16d
Author: lshep <lori.shepherd@roswellpark.org>
Date: 2025-09-04 08:54:01 -0400
Commit message:

 Closes #20
Package: Ularcirc
Commit: 990980aed022dfff809198d8c9b129fc8f8076be
Author: David Humphreys <dth569@gadi-login-04.gadi.nci.org.au>
Date: 2025-09-04 22:09:10 +1000
Commit message:

 Fixing documentation for build
Package: ClustIRR
Commit: c59d8257d48c7b688ff0259a0b4c46b3801ab1c3
Author: snaketron <simo.kitanovski@uni-due.de>
Date: 2025-09-04 14:03:52 +0200
Commit message:

 community split, bump
Package: ClustIRR
Commit: da4a2ba2bfc87a2263ed12643c42ffbaf9a197b2
Author: snaketron <simo.kitanovski@proton.me>
Date: 2025-09-04 14:01:38 +0200
Commit message:

 merge
Package: ClustIRR
Commit: 9347c81bd781065dcc59189edcae467daf401f15
Author: snaketron <simo.kitanovski@proton.me>
Date: 2025-09-04 13:55:17 +0200
Commit message:

 updated dco.R
Package: ClustIRR
Commit: c65064efb43e93789e627383903ddc8e3b5db21b
Author: snaketron <simo.kitanovski@proton.me>
Date: 2025-09-04 13:54:59 +0200
Commit message:

 updated models
Package: ClustIRR
Commit: 928bf77575d95b69c0f99c9de062189f193f849d
Author: snaketron <simo.kitanovski@proton.me>
Date: 2025-07-14 16:04:26 +0200
Commit message:

 Merge branch 'main' of github.com:snaketron/ClustIRR
Package: ClustIRR
Commit: eb433bba0b838418e4240237d3e2742c0b6763bf
Author: snaketron <simo.kitanovski@proton.me>
Date: 2025-07-14 16:04:17 +0200
Commit message:

 merge
Package: ClustIRR
Commit: 5db8b954b934e2ae1ce7289fdeffca872e9de922
Author: snaketron <simo.kitanovski@uni-due.de>
Date: 2025-09-04 13:47:39 +0200
Commit message:

 man fix
Package: ClustIRR
Commit: 12c78aeb3705a3009b13c9f07d4dd46b34823b72
Author: snaketron <simo.kitanovski@uni-due.de>
Date: 2025-09-04 13:47:22 +0200
Commit message:

 update for 04. Sep. 2025
Package: ClustIRR
Commit: 3650419a19d14bf23fbde57adab0d29f18ba0848
Author: snaketron <simo.kitanovski@uni-due.de>
Date: 2025-09-04 12:53:22 +0200
Commit message:

 bugfix
Package: ClustIRR
Commit: 9bde1dac769367613d83c3e1b23f340bbb46fb57
Author: snaketron <simo.kitanovski@uni-due.de>
Date: 2025-09-04 12:13:57 +0200
Commit message:

 updated NEWS
Package: ClustIRR
Commit: b33d3f1a9009773d67367e4cd8f84bc2626d0ff2
Author: snaketron <simo.kitanovski@uni-due.de>
Date: 2025-09-04 12:13:37 +0200
Commit message:

 fixed T->TRUE, F->FALSE
Package: ClustIRR
Commit: 6ea6a39eed7010377eeb1dffb6afb30b6223803a
Author: snaketron <simo.kitanovski@uni-due.de>
Date: 2025-09-04 11:51:21 +0200
Commit message:

 update decoding communities, calculating purity
Package: Rarr
Commit: d4e9538af428173549175634cc1666c1c0e05b7d
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-09-03 18:09:22 +0200
Commit message:

 Bump version number
Package: Rarr
Commit: 5f9f401cc05eb6c2c925904b5460fd69bb902a89
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-09-03 18:09:03 +0200
Commit message:

 Document renames
Package: Rarr
Commit: 6e4a03c20572a677918e537ec65ce9a2fb3e3d66
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-09-03 17:12:51 +0200
Commit message:

 Run devtools::document()
Package: Rarr
Commit: 28c28eed6105d48c1f9e0641c9ef4dcca6ec387a
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-09-03 17:12:37 +0200
Commit message:

 Rename path argument to zarr_path

For consistency with read_zmetadata
Package: Rarr
Commit: 001de5bee74943bd4fedfb81f5a459fffbb8d1a8
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-09-03 16:08:59 +0200
Commit message:

 Move missing metadata test file to metadata test folder
Package: Rarr
Commit: 3e20809f72da582da1e382381f07c8ef49ffcee0
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-09-03 16:07:01 +0200
Commit message:

 Use leading dot in name for internal functions
Package: Rarr
Commit: 862d7058d4163f103b1f01c9e82b83c886f66ac6
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-09-03 16:05:48 +0200
Commit message:

 Add venv to Rbuildignore
Package: Rarr
Commit: 5d38a040db5948445acced5385b3ff8711a0930c
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-09-03 14:54:53 +0200
Commit message:

 Add test for read_zmetadata
Package: Rarr
Commit: 8af73ba5d37a2a5aaccd065332a6db3778038d68
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-09-03 14:16:20 +0200
Commit message:

 Explain what .zmetadata is in roxygen block
Package: Rarr
Commit: aa8a846d6df820936257e899d7d24f79b77b67a6
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-09-01 14:15:16 +0200
Commit message:

 Restore sys-lib testing mechanism

To test both system and bundled version of Blosc & Rarr
Package: Rsubread
Commit: 5bf87c530c3b85a2599de98f5e81d647b076d7cb
Author: Yang Liao (Monash University) <yliao@m3v109.massive.org.au>
Date: 2025-09-04 12:29:06 +1000
Commit message:

 Added junction.counts in output of cellCounts
Package: ChIPanalyser
Commit: 27504b973bb0c939ea58f0b46b410305839b057d
Author: patrickCNMartin <pcnmartin@gmail.com>
Date: 2025-09-03 11:37:38 -0700
Commit message:

 readme update
Package: ChIPanalyser
Commit: 2802681ca65943b679dedd6548e46b160e221893
Author: patrickCNMartin <pcnmartin@gmail.com>
Date: 2025-09-03 11:26:43 -0700
Commit message:

 plot occupancy update
Package: spARI
Commit: da771726f9800143a2f828881006e0c98ff0aa74
Author: Your Name <you@example.com>
Date: 2025-09-04 02:15:31 +0800
Commit message:

 0.99.15
Package: spARI
Commit: cdc3976d105403040a1d26e3a99909d1d80dc14f
Author: Your Name <you@example.com>
Date: 2025-09-04 02:12:18 +0800
Commit message:

 0.99.14
Package: spARI
Commit: 2cef2f69575f607b3262f27e5644a63bb66c45dd
Author: Your Name <you@example.com>
Date: 2025-09-04 01:57:21 +0800
Commit message:

 0.99.13
Package: scToppR
Commit: c792a1db872fd78947c02f43bb4705174a0c16bf
Author: Bryan Granger <grangerb@musc.edu>
Date: 2025-09-03 12:35:59 -0400
Commit message:

 version bump
Package: scToppR
Commit: f845e26dc22aed09fd0322c2da59315bc312f2d4
Author: Bryan Granger <grangerb@musc.edu>
Date: 2025-09-03 12:23:01 -0400
Commit message:

 vignette package load
Package: scToppR
Commit: 5207bed0d4a95fd3bceaa085e4a7b0f80717449b
Author: Bryan Granger <grangerb@musc.edu>
Date: 2025-09-03 12:17:32 -0400
Commit message:

 version bump
Package: scToppR
Commit: 08a723da5ad5981ffb8dc1a1d11def17ea29a7bb
Author: Bryan Granger <grangerb@musc.edu>
Date: 2025-09-03 12:16:49 -0400
Commit message:

 update man files
Package: BgeeDB
Commit: 6b7e351d3c06e63b2086abbab6c72b92a88ccf66
Author: Julien Wollbrett <julien.wollbrett@unil.ch>
Date: 2025-09-03 17:46:46 +0200
Commit message:

 bump version
Package: BgeeDB
Commit: a73056a9cb5b3b5437612b145e897b5adeacd242
Author: Julien Wollbrett <julien.wollbrett@unil.ch>
Date: 2025-09-03 17:44:04 +0200
Commit message:

 correct descendant retrieval for cellTypes and updated overal code quality
Package: scToppR
Commit: f0c53cc3a2e938403af7696e15021214f7143726
Author: Bryan Granger <grangerb@musc.edu>
Date: 2025-09-03 11:40:56 -0400
Commit message:

 version bump
Package: scToppR
Commit: a69f439fbefb925d2e7be899fe7c31f99ab1f48d
Author: Bryan Granger <grangerb@musc.edu>
Date: 2025-09-03 11:29:09 -0400
Commit message:

 cluster_col bug
Package: scToppR
Commit: 1b32c8e0d8c618d7b2aacef0e5c6e368eb4ff679
Author: Bryan Granger <grangerb@musc.edu>
Date: 2025-08-27 12:30:55 -0400
Commit message:

 vignette fix
Package: scToppR
Commit: 6da9a1ac0d762f73fa0c64adccc55f953bbb16ac
Author: Bryan Granger <grangerb@musc.edu>
Date: 2025-08-27 11:30:31 -0400
Commit message:

 httr2 update
Package: scToppR
Commit: 435a5c4042029a3f101cac0a893fd7ebbd4e22e8
Author: Bryan Granger <grangerb@musc.edu>
Date: 2025-05-01 10:41:36 -0400
Commit message:

 plot tweak
Package: scToppR
Commit: f24a991fbc526fc7dbb0bed68c93bd0f90eb2147
Author: Bryan Granger <grangerb@musc.edu>
Date: 2025-05-01 10:33:41 -0400
Commit message:

 add httr2
Package: scToppR
Commit: ff2135bdcd0385eaeb8832a00a1156535e13099b
Author: Bryan Granger <grangerb@musc.edu>
Date: 2025-04-01 13:39:18 -0400
Commit message:

 toppplot has 3 p's
Package: scToppR
Commit: 1e2f8635d0f5749bd14d611af940fa26d9699444
Author: Bryan Granger <grangerb@musc.edu>
Date: 2025-04-01 13:38:10 -0400
Commit message:

 readme update
Package: scToppR
Commit: cdee66f5813a2c95dd9cdfb8b730129d85cbd478
Author: Bryan Granger <grangerb@musc.edu>
Date: 2025-04-01 13:37:38 -0400
Commit message:

 readme update
Package: scToppR
Commit: e77e9abf6534b4a24eed78b6ed0d7f70fcde9492
Author: Bryan Granger <grangerb@musc.edu>
Date: 2025-04-01 13:36:24 -0400
Commit message:

 example updates
Package: scToppR
Commit: 2d3b885ebdabe470184ed605150b5a0e0623c148
Author: Bryan Granger <grangerb@musc.edu>
Date: 2025-04-01 13:21:26 -0400
Commit message:

 new data and marker list inputs
Package: scToppR
Commit: f7451da58e9b1e1ffa99cbf80d0aab0411d972de
Author: Bryan Granger <grangerb@musc.edu>
Date: 2025-03-25 12:25:33 -0400
Commit message:

 marker update
Package: GEOquery
Commit: 414557bd7d999b5c54c5c74478a834910929ac00
Author: Sean Davis <seandavi@gmail.com>
Date: 2025-09-03 10:54:23 -0400
Commit message:

 Version bump
Package: GEOquery
Commit: 77e01add4f7ecc751258ed8bada9a6ba894ada38
Author: Sean Davis <seandavi@gmail.com>
Date: 2025-09-03 10:53:49 -0400
Commit message:

 Add skeleton single-cell vignette
Package: GOexpress
Commit: 1f9c4631c489a3594004b147715ff1796bf333b2
Author: Kevin Rue <kevinrue@users.noreply.github.com>
Date: 2025-09-03 14:40:13 +0100
Commit message:

 update version and contributors
Package: GOexpress
Commit: 3eb4d2c3d79dd067888b33596a228ed67cc185f2
Author: Kevin Rue <kevinrue@users.noreply.github.com>
Date: 2025-09-03 14:38:06 +0100
Commit message:

 remove all mentions of curl
Package: GOexpress
Commit: a87dbb995d8b28e9502e83748d99faa2630f6c8c
Author: Kevin Rue <kevinrue@users.noreply.github.com>
Date: 2025-09-03 14:36:58 +0100
Commit message:

 Merge branch 'master' of github.com:kevinrue/GOexpress
Package: GOexpress
Commit: b6de86f80d8fbd89717dbb4ee02cc6f019ca33b0
Author: Kevin Rue-Albrecht <kevinrue67@gmail.com>
Date: 2025-09-03 14:36:28 +0100
Commit message:

 Merge pull request #4 from Bisaloo/fix-biomaRt-warnings

Remove deprecated curl argument in biomaRt::getBM()
Package: GOexpress
Commit: 532783a3a569f088315008293367ab55788c62e4
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-09-01 08:37:34 +0200
Commit message:

 Remove deprecated curl argument in biomaRt::getBM()

Fix R CMD check WARNING
Package: peakCombiner
Commit: fd2507d12524248b9cb36c16fe72d0e531332013
Author: Markus Muckenhuber <141941160+MarkusMuck@users.noreply.github.com>
Date: 2025-09-03 15:34:08 +0200
Commit message:

 Update DESCRIPTION
Package: peakCombiner
Commit: 91c71442590a153dcea373f1583ff85dc9e6756d
Author: Markus Muckenhuber <141941160+MarkusMuck@users.noreply.github.com>
Date: 2025-09-03 15:18:05 +0200
Commit message:

 Delete tests/.DS_Store
Package: peakCombiner
Commit: ac521e8a077b0d5d0cb8baf2abd39755fbb5a9f7
Author: Markus Muckenhuber <141941160+MarkusMuck@users.noreply.github.com>
Date: 2025-09-03 15:16:35 +0200
Commit message:

 Update .gitignore
Package: peakCombiner
Commit: 66017b08fbcebd279e174f3f5deb2c34ee773d23
Author: Markus Muckenhuber <141941160+MarkusMuck@users.noreply.github.com>
Date: 2025-09-03 15:15:38 +0200
Commit message:

 Update .gitignore
Package: mzR
Commit: 15fde15ae6ef3e59130acd5779e2fcd04f537eea
Author: Adriano Rutz <44283913+Adafede@users.noreply.github.com>
Date: 2025-09-02 15:59:24 +0200
Commit message:

 Merge pull request #1 from jorainer/adafede

Make electronBeamEnergy an optional header column for export
Package: mzR
Commit: 57c02f0d62d4935df07753e097909fc3c892d65e
Author: Johannes Rainer <johannes.rainer@gmail.com>
Date: 2025-09-02 15:37:37 +0200
Commit message:

 fix unit test
Package: mzR
Commit: ff6dbf10b12786f35b22506ffeec31d998f42836
Author: Johannes Rainer <johannes.rainer@gmail.com>
Date: 2025-09-02 15:29:42 +0200
Commit message:

 refactor: make electronBeamEnergy an optional header column
Package: mzR
Commit: 3c9edb060cda9185564fcf3a14ef3ac45719b6b3
Author: Johannes Rainer <johannes.rainer@gmail.com>
Date: 2025-09-02 10:13:59 +0200
Commit message:

 Merge remote-tracking branch 'adafede/devel' into adafede
Package: mzR
Commit: b45041090cc617e41507359491ba5cb74c0d62e8
Author: Adriano Rutz <44283913+Adafede@users.noreply.github.com>
Date: 2025-08-20 14:34:21 +0200
Commit message:

 Update DESCRIPTION

https://github.com/sneumann/mzR/pull/311#issuecomment-3205487869
Package: peakCombiner
Commit: c19cd07c030c024fb7c9b05f1e2049e69e05fb44
Author: Markus Muckenhuber <141941160+MarkusMuck@users.noreply.github.com>
Date: 2025-09-03 13:59:57 +0200
Commit message:

 Update DESCRIPTION version
Package: peakCombiner
Commit: e9102c2d3e230132f620d71b229f725f08fb1aca
Author: Markus Muckenhuber <141941160+MarkusMuck@users.noreply.github.com>
Date: 2025-09-03 13:55:35 +0200
Commit message:

 Delete peakCombiner.Rproj
Package: islify
Commit: c295fbfac0e992f6abc7edc94adb027671e05b3a
Author: Jakob Theorell <jakob.theorell@ki.se>
Date: 2025-09-03 12:44:26 +0200
Commit message:

 The "problematicUnevenDistribution" flag is introduced.
Package: msa
Commit: 946360ddd9ad51ae44141723b19898750f8186be
Author: UBod <ulrich@bodenhofer.com>
Date: 2025-09-03 12:22:33 +0200
Commit message:

 pull request from Rong-Zh merged to fix memory leak in Muscle; version number bumped to 1.41.2
Package: msa
Commit: 8f150f08f5011d5b040f6eabe583d765e1fa1a79
Author: UBod <ulrich@bodenhofer.com>
Date: 2025-09-03 12:19:34 +0200
Commit message:

 Merge pull request #38 from Rong-Zh/devel

Fix memory leak
Package: msa
Commit: 464c95ba38420af174a778ba88c478cb0a4c4c50
Author: Rong-Zh <zerelove@icloud.com>
Date: 2025-05-12 11:06:58 +0800
Commit message:

 Fix memory leak
Package: DMRcaller
Commit: 840d78ca2e287e0b51ffbceb675633cb7dd4078e
Author: nrzabet <r.zabet@qmul.ac.uk>
Date: 2025-09-03 11:28:17 +0100
Commit message:

 added support for ONT methylation data
Package: DMRcaller
Commit: fa43084717c15ec0d3b5498dd9622d9f8b6930a7
Author: nrzabet <r.zabet@qmul.ac.uk>
Date: 2025-09-03 11:27:31 +0100
Commit message:

 added support for ONT methylation data
Package: SingleCellAlleleExperiment
Commit: 51fab37dd964d172d51e3d2223befd43097215a0
Author: jonas-schuck <jonas_schuck@hotmail.de>
Date: 2025-09-03 11:37:02 +0200
Commit message:

 Adressing devel error for failing test after DropletUtils package update; Minor documentation update; version bump v1.5.1
Package: SingleCellAlleleExperiment
Commit: 641fa2f8b5d3082a6d99a450203856fe784f365c
Author: jonas-schuck <jonas_schuck@hotmail.de>
Date: 2025-09-03 09:51:59 +0200
Commit message:

 Merge remote-tracking branch 'upstream/devel' into devel
Merging upstream/devel into origin/devel to work on 3.22/devel test-errors
Package: SingleCellAlleleExperiment
Commit: 98eb7bfe150daea5c8efd43b32897982d592fda7
Author: Jonas Schuck <106832949+Jonas-Schuck@users.noreply.github.com>
Date: 2025-08-27 13:19:54 +0200
Commit message:

 Merge pull request #10 from AGImkeller/fixing_GHA

updating GHA to a more recent cache version
Package: SingleCellAlleleExperiment
Commit: 016d0e1f3f976d2e69cd312b27a29633a2036749
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2025-03-18 17:00:19 +0100
Commit message:

 while at it: updating the version of roxygen being used
Package: SingleCellAlleleExperiment
Commit: 55530191c5c1870096e3b2f600e3c115d13e9ad3
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2025-03-07 14:39:14 +0100
Commit message:

 updating GHA to a more recent cache version
Package: biomaRt
Commit: 8b8b9731a557581cc3ffe9f969596be990f6bbb9
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-09-03 11:19:05 +0200
Commit message:

 Fix partial matching warnings
Package: ChIPDBData
Commit: 929bc6bcc5b6e2fe4512c80f4a793028a398485a
Author: yosra <yosraberrouayel@gmail.com>
Date: 2025-09-03 10:56:21 +0200
Commit message:

 review changes
Package: spatialFDA
Commit: 2b4a687a48309bc4a8d0697dcc8c5585060fc180
Author: mjemons <martin.emons@gmail.com>
Date: 2025-09-02 15:26:55 +0200
Commit message:

 new test and better code for RSE calc
Package: spatialFDA
Commit: 768c4ec4e41a41c475ad52fbf0778b9ad7bdd55d
Author: mjemons <martin.emons@gmail.com>
Date: 2025-09-01 18:45:03 +0200
Commit message:

 implemented RSE TODO: write some assertions and tests
Package: spatialFDA
Commit: bbc5e97a9c228786bca8dd6ddab16f048bfbe7be
Author: mjemons <martin.emons@gmail.com>
Date: 2025-09-01 11:09:27 +0200
Commit message:

 changed to residual sum of squares per condition
Package: Spectra
Commit: 9e851b5421a81d718c1a642f12e60f8c695d9275
Author: Johannes Rainer <5506112+jorainer@users.noreply.github.com>
Date: 2025-09-03 08:56:02 +0200
Commit message:

 Merge pull request #365 from rformassspectrometry/jomain

Add default implementation for replacement methods
Package: Spectra
Commit: 865f8574d0c65687ac155f09103616a7f315641e
Author: Johannes Rainer <johannes.rainer@gmail.com>
Date: 2025-09-03 08:24:37 +0200
Commit message:

 refactor: define additional defaults for replacement methods
Package: Spectra
Commit: ee963717aa4d86fa1b5740ac7ee7aacba35bfcaa
Author: Johannes Rainer <johannes.rainer@gmail.com>
Date: 2025-09-02 09:57:23 +0200
Commit message:

 format: reformat applyProcessing code
Package: Rsubread
Commit: d014fc48731e3b2859598aae1f7338817660c438
Author: Yang Liao (Monash University) <yliao@m3v109.massive.org.au>
Date: 2025-09-03 11:30:57 +1000
Commit message:

 Multiple-sample cellCounts junction detection.
Package: Rsamtools
Commit: 47580dee3954e206d8b8b348b8c26553ff014678
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2025-09-02 17:47:55 -0700
Commit message:

 Rsamtools 2.25.3: Fix compillation problem on FreeBSD

See https://github.com/Bioconductor/Rsamtools/issues/66

Also add VariantAnnotation to Suggests.
Package: GEOquery
Commit: 92adad8c3737494237a3aba091334c9b62335d28
Author: Sean Davis <seandavi@gmail.com>
Date: 2025-09-02 20:31:08 -0400
Commit message:

 Version bump
Package: GEOquery
Commit: 558d8c28553e020d5ad89a95073dc12c16d4e4e2
Author: Sean Davis <seandavi@gmail.com>
Date: 2025-09-02 20:30:33 -0400
Commit message:

 Add capability to read GSE file listing

The GEO series records often include .tar files.
This added functionality exposes the contents of
a hidden (not accessible from the website) file
listing the contents of the files and .tar archive.
Package: gemma.R
Commit: eededbe4847d332fdcf9e1cb77988175d880d3bc
Author: OganM <ogan.mancarcii@gmail.com>
Date: 2025-09-02 15:52:30 -0700
Commit message:

 version bump
Package: gemma.R
Commit: 206bf1f762b0aca37a87b496708b490950acccf4
Author: OganM <ogan.mancarcii@gmail.com>
Date: 2025-09-02 15:52:14 -0700
Commit message:

 fix vignette for changed annotations
Package: SeqArray
Commit: 24e176dac79eaa01e5d4bfe714562a72d6b0dad5
Author: Xiuwen Zheng <zhengxwen@gmail.com>
Date: 2025-09-02 17:50:41 -0500
Commit message:

 fix
Package: smoothclust
Commit: 28375eec19cc43dda89fa2ea3e2312fbbabb39b1
Author: Lukas Weber <lmweb012@gmail.com>
Date: 2025-09-02 17:33:54 -0400
Commit message:

 version bump for testing
Package: GEOquery
Commit: 461800696a967c11d8cb691b8e601d4f58a352b3
Author: Sean Davis <seandavi@gmail.com>
Date: 2025-09-02 17:11:49 -0400
Commit message:

 Version bump
Package: GEOquery
Commit: 134a0ce06f64ae0b1026c91e9a1019d2a8a5ed53
Author: Sean Davis <seandavi@gmail.com>
Date: 2025-09-02 17:11:10 -0400
Commit message:

 refactor supplemental file handling

* Split out some functionality to separate functions
* Partial conversion to use 
 </pre>
    </div>
  
    

      Package: MetaboDynamics

      Commit: 2280d3fae90b9482b88006d91a1dcd1edbd36cee

      Author:  Katja Danielzik <katja.danielzik@stud.uni-due.de> 

      Date: 2025-09-02 20:43:13 +0200

      Commit message:


	  
		
 internal: euclidean distance and cell count model, longitudinalMetabolimics with simulated cell counts
 

    

  
    

      Package: assorthead

      Commit: a4768f36a734f43db3eae4841ce4496e78fc22e8

      Author:  LTLA <infinite.monkeys.with.keyboards@gmail.com> 

      Date: 2025-09-02 11:08:21 -0700

      Commit message:


	  
		
 Updated the vendored aarand, sanisizer and kmeans libraries.
 

    

  
    

      Package: MethylSeekR

      Commit: 8c943ee3abbc306ab6feff5e97ff78c9f6c13c6e

      Author:  LukasBurger <lukas.burger@fmi.ch> 

      Date: 2025-09-02 16:00:32 +0200

      Commit message:


	  
		
 bumped up version number
 

    

  
    

      Package: MethylSeekR

      Commit: 954ace29f926fe3be4395f9a0b877619578384bf

      Author:  LukasBurger <lukas.burger@fmi.ch> 

      Date: 2025-09-02 15:57:57 +0200

      Commit message:


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

    

  
    

      Package: MethylSeekR

      Commit: cea09d1bd51345eff6b5e5937e22ea329f81da65

      Author:  Burger <burgerlu@xenon7.fmi.ch> 

      Date: 2025-08-26 15:27:17 +0200

      Commit message:


	  
		
 fixed dependency
 

    

  
    

      Package: MethylSeekR

      Commit: a90891d344b14eccd365e3d91ce7db445f5f30ed

      Author:  Burger <burgerlu@xenon7.fmi.ch> 

      Date: 2025-08-19 13:55:10 +0200

      Commit message:


	  
		
 -add imports
 

    

  
    

      Package: MethylSeekR

      Commit: ae16de2894a149340627abe09c1aa4e30218e853

      Author:  Burger <burgerlu@xenon7.fmi.ch> 

      Date: 2025-08-12 09:23:17 +0200

      Commit message:


	  
		
 bumped up the version number
 

    

  
    

      Package: MethylSeekR

      Commit: e3b0562d571973d1ccb7c59c9b7c541edf630ee1

      Author:  Burger <burgerlu@xenon7.fmi.ch> 

      Date: 2025-08-05 09:42:11 +0200

      Commit message:


	  
		
 added GenomeInfoDb to Suggests in DESCRIPTION file
 

    

  
    

      Package: MethylSeekR

      Commit: efb31e260fd2be0a2e1310c552e07d91a048c4a4

      Author:  Michael Stadler <stadler.michael@gmail.com> 

      Date: 2021-06-21 08:13:09 +0200

      Commit message:


	  
		
 try without discontinued gfortran cask on macOS 

    

  
    

      Package: MethylSeekR

      Commit: d53baab8ec5bc16348fe416874d5edc89bd2104a

      Author:  Michael Stadler <stadler.michael@gmail.com> 

      Date: 2021-06-07 12:25:32 +0200

      Commit message:


	  
		
 use release R (4.1) for BioC devel (3.14) 

    

  
    

      Package: HiCaptuRe

      Commit: f42ac200e4d5862bc8c5e2b111423bcb0147c80f

      Author:  Laureano Tomás-Daza <lauretomas@gmail.com> 

      Date: 2025-09-02 14:42:21 +0200

      Commit message:


	  
		
 update docs, minor note and version bump
 

    

  
    

      Package: scRNAseqApp

      Commit: a9306a164c4055ad63419fa81fe5d138ea6b144a

      Author:  Jianhong Ou <jianhong.ou@gmail.com> 

      Date: 2025-09-02 08:21:16 -0400

      Commit message:


	  
		
 add flex-wrap for newcomment-form.
 

    

  
    

      Package: MetaboDynamics

      Commit: 4931ccf3ac7590e287b04302de51e041317496b7

      Author:  Katja Danielzik <katja.danielzik@stud.uni-due.de> 

      Date: 2025-09-02 14:10:18 +0200

      Commit message:


	  
		
 delta_t now as list of ordered visualizations
 

    

  
    

      Package: HiCaptuRe

      Commit: eaa3eadeac195cb69b5dad2080f07787135615c0

      Author:  Laureano Tomás-Daza <lauretomas@gmail.com> 

      Date: 2025-09-02 14:02:04 +0200

      Commit message:


	  
		
 version bump
 

    

  
    

      Package: biomaRt

      Commit: 00d5f87f57d6da035b43920c63f753f6457ed48a

      Author:  Hugo Gruson <10783929+Bisaloo@users.noreply.github.com> 

      Date: 2025-09-01 11:29:36 +0200

      Commit message:


	  
		
 Add extra step to convert NEWS to md in pkgdown workflow
 

    

  
    

      Package: biomaRt

      Commit: 291e571e627177692ad31091edb4d6c1772ccfa5

      Author:  Hugo Gruson <10783929+Bisaloo@users.noreply.github.com> 

      Date: 2025-09-01 11:21:18 +0200

      Commit message:


	  
		
 Document creation  of pkgdown website
 

    

  
    

      Package: biomaRt

      Commit: d47915291a6be4011d03769e93bb8cf93db6815c

      Author:  Hugo Gruson <10783929+Bisaloo@users.noreply.github.com> 

      Date: 2025-09-01 11:10:12 +0200

      Commit message:


	  
		
 Add Hugo as ctb
 

    

  
    

      Package: biomaRt

      Commit: 2abc4be3a69a7091f8a53c3dee77f92ac38b004a

      Author:  Hugo Gruson <10783929+Bisaloo@users.noreply.github.com> 

      Date: 2025-09-01 11:09:28 +0200

      Commit message:


	  
		
 Add de.NBI as funder
 

    

  
    

      Package: biomaRt

      Commit: 19e207439f9d5be24eecf39401386c7bd270ea51

      Author:  Hugo Gruson <10783929+Bisaloo@users.noreply.github.com> 

      Date: 2025-08-29 21:46:02 +0200

      Commit message:


	  
		
 Add logo
 

    

  
    

      Package: biomaRt

      Commit: 399fc490a20a02dd42da849c188f5fd1d4131d5f

      Author:  Hugo Gruson <10783929+Bisaloo@users.noreply.github.com> 

      Date: 2025-08-29 17:05:33 +0200

      Commit message:


	  
		
 Create pkgdown reference index
 

    

  
    

      Package: biomaRt

      Commit: fc90cc2b3485c84fc63db82ac63948f1c7e44819

      Author:  Hugo Gruson <10783929+Bisaloo@users.noreply.github.com> 

      Date: 2025-08-29 16:36:52 +0200

      Commit message:


	  
		
 Customize pkgdown GitHub Action for bioC
 

    

  
    

      Package: biomaRt

      Commit: 7b306f7aa916268b52c8ffc692037bde8079eec4

      Author:  Hugo Gruson <10783929+Bisaloo@users.noreply.github.com> 

      Date: 2025-08-29 16:33:45 +0200

      Commit message:


	  
		
 Get pkgdown github action from r-lib
 

    

  
    

      Package: biomaRt

      Commit: 0c423bec9b00d7bc3e0fec5f8904659237bc9cb2

      Author:  Hugo Gruson <10783929+Bisaloo@users.noreply.github.com> 

      Date: 2025-08-28 11:01:12 +0200

      Commit message:


	  
		
 Set up pkgdown
 

    

  
    

      Package: HiCaptuRe

      Commit: 52ce5ba1650f891db8cb8a31059b9caae0ec7def

      Author:  Laureano Tomás-Daza <lauretomas@gmail.com> 

      Date: 2025-09-02 13:17:14 +0200

      Commit message:


	  
		
 change invert default to FALSE
 

    

  
    

      Package: igblastr

      Commit: f61b1d0d8f87292a26d3f23556877bee798a7266

      Author:  Hervé Pagès <hpages.on.github@gmail.com> 

      Date: 2025-09-02 00:16:11 -0700

      Commit message:


	  
		
 small tweak to README.md
 

    

  
    

      Package: igblastr

      Commit: a3015435d053cb9700a149da7da4eff0fc137a68

      Author:  Hervé Pagès <hpages.on.github@gmail.com> 

      Date: 2025-09-01 23:22:08 -0700

      Commit message:


	  
		
 igblastr 0.99.15

Update list of built-in C-region dbs from:

  db_name                         C
  _IMGT.human.IGH+IGK+IGL.202412 76
  _IMGT.mouse.IGH.202412         31
  _IMGT.rabbit.IGH.202412        28
  _IMGT.rat.IGH.202508           18

to:

  db_name                                 C
  _IMGT.human.IGH+IGK+IGL.202412         76
  _IMGT.mouse.IGH.202509                 56
  _IMGT.rabbit.IGH.202412                28
  _IMGT.rat.IGH.202508                   18
  _IMGT.rhesus_monkey.IGH+IGK+IGL.202509 40

Note the updated db for mouse and the new db for rhesus monkey.

This new list reflects what's listed in the bottom left table at
https://www.imgt.org/vquest/refseqh.html on Sep 1, 2025 (ignoring Alpaca).
 

    

  
    

      Package: variancePartition

      Commit: e421210f3406bd07fdaf4c31d6bb572886189664

      Author:  Gabriel Hoffman <gabriel.hoffman@gmail.com> 

      Date: 2025-09-01 21:20:59 -0400

      Commit message:


	  
		
 1.39.2
 

    

  
    

      Package: EpipwR

      Commit: 191281918ca6722fb49c70528cf931d583fb0ee1

      Author:  Jackson <jbarth216@gmail.com> 

      Date: 2025-09-01 11:49:04 -0500

      Commit message:


	  
		
 Merge to main
 

    

  
    

      Package: EpipwR

      Commit: 1eb710367a96f268b812f79eeecbee6675174e64

      Author:  Jackson <jbarth216@gmail.com> 

      Date: 2025-09-01 11:48:55 -0500

      Commit message:


	  
		
 Version bump
 

    

  
    

      Package: EpipwR

      Commit: 80e6fabeb89138e1baea7cf612eb8d543691432d

      Author:  Jackson <jbarth216@gmail.com> 

      Date: 2025-09-01 11:33:02 -0500

      Commit message:


	  
		
 Minor updates
 

    

  
    

      Package: EpipwR

      Commit: 8f9943816475b340231d24bc52bb5707edb18cfb

      Author:  Jackson <jbarth216@gmail.com> 

      Date: 2025-08-04 14:55:19 -0500

      Commit message:


	  
		
 Updated README
 

    

  
    

      Package: EpipwR

      Commit: c1bf9b72b37d63256702926c5a3d7c04b34a2e74

      Author:  Jackson <jbarth216@gmail.com> 

      Date: 2025-08-04 14:48:15 -0500

      Commit message:


	  
		
 New pwrE_to_EpipwR function
 

    

  
    

      Package: EpipwR

      Commit: cc492478e8c15ef79791eea2e1154880a4296dab

      Author:  Jackson <jbarth216@gmail.com> 

      Date: 2025-04-16 10:01:51 -0500

      Commit message:


	  
		
 Update for custom phenotype data
 

    

  
    

      Package: EpipwR

      Commit: bbb9a9d6fa5b84e89c254ea6f8221dcda1ee7a63

      Author:  Jackson <jbarth216@gmail.com> 

      Date: 2024-12-04 09:37:06 -0600

      Commit message:


	  
		
 Remove .Rhistory
 

    

  
    

      Package: EpipwR

      Commit: 78633367f47c11b0b4ddc766d67d12e9d49c89ea

      Author:  Jackson <jbarth216@gmail.com> 

      Date: 2024-12-04 09:32:05 -0600

      Commit message:


	  
		
 Added "Custom" option for Tissue parameter
 

    

  
    

      Package: smoppix

      Commit: b943a7e69eed644547e1a416bf1df3d817b224f2

      Author:  stijn <stijn.hawinkel@psb.ugent.be> 

      Date: 2025-09-01 15:16:31 +0200

      Commit message:


	  
		
 Installer from biconductor
 

    

  
    

      Package: smoppix

      Commit: 85959e42dc13a7714d901d47eb0bd2cc420977d9

      Author:  stijn <stijn.hawinkel@psb.ugent.be> 

      Date: 2025-09-01 10:32:10 +0200

      Commit message:


	  
		
 Simplify readme header
 

    

  
    

      Package: smoppix

      Commit: 35518358ab29c988cd8ce2e2ecabbf0f98461f65

      Author:  stijn <stijn.hawinkel@psb.ugent.be> 

      Date: 2025-08-29 16:08:18 +0200

      Commit message:


	  
		
 Remove superfluous test
 

    

  
    

      Package: smoppix

      Commit: f071e79c4517453e7cf5f99b4b4092fe5073bfee

      Author:  stijn <stijn.hawinkel@psb.ugent.be> 

      Date: 2025-08-27 17:17:38 +0200

      Commit message:


	  
		
 Without colons
 

    

  
    

      Package: smoppix

      Commit: 267ee1476db8cee2a9cdbe017d3d904b52bd9cad

      Author:  stijn <stijn.hawinkel@psb.ugent.be> 

      Date: 2025-08-27 17:08:52 +0200

      Commit message:


	  
		
 also document namespace bplapply change
 

    

  
    

      Package: smoppix

      Commit: 575847312d4d38d64a5d264186bde1853ae48da0

      Author:  stijn <stijn.hawinkel@psb.ugent.be> 

      Date: 2025-08-27 17:08:34 +0200

      Commit message:


	  
		
 Avoid namespace headaches
 

    

  
    

      Package: smoppix

      Commit: 68daccae6cf2f5d77f6084cc146bae70df989571

      Author:  stijn <stijn.hawinkel@psb.ugent.be> 

      Date: 2025-08-27 15:36:17 +0200

      Commit message:


	  
		
 keep namesin loadbalancelappy
 

    

  
    

      Package: smoppix

      Commit: c68711d8d2d833cba216c7be67e79e24d2c42760

      Author:  stijn <stijn.hawinkel@psb.ugent.be> 

      Date: 2025-08-27 15:21:29 +0200

      Commit message:


	  
		
 no longer store result for loadbalancebplapply
 

    

  
    

      Package: edgeR

      Commit: 1fe6a4d26b82466ae10194759b59ce372c3d332a

      Author:  Gordon Smyth <smyth@wehi.edu.au> 

      Date: 2025-09-01 20:47:38 +1000

      Commit message:


	  
		
 edgeR 4.7.4
- chooseLowessSpan() now used to choose span for voomLmFit(), estimateDisp() and WLEB().
- Revise help page for diffSplice.DGEGLM().
 

    

  
    

      Package: Rarr

      Commit: ad154ea58f37669bcb515d8961c77625d2c6e874

      Author:  Sharla Gelfand <sharla.gelfand@gmail.com> 

      Date: 2025-08-29 12:07:53 -0400

      Commit message:


	  
		
 Error when no metadata found (#37)


 

    

  
    

      Package: biomaRt

      Commit: 933c3bc84d833394b97da9a9cd94bcba382a3fba

      Author:  Hugo Gruson <10783929+Bisaloo@users.noreply.github.com> 

      Date: 2025-08-30 20:20:14 +0200

      Commit message:


	  
		
 Run devtools::document()
 

    

  
    

      Package: biomaRt

      Commit: 6a7d8977c2ccf9f092ad494387531141eacf95a2

      Author:  Hugo Gruson <10783929+Bisaloo@users.noreply.github.com> 

      Date: 2025-08-30 09:51:48 +0200

      Commit message:


	  
		
 Avoid creating new duplicated var
 

    

  
    

      Package: biomaRt

      Commit: e7e78c4b84f44f2731db95ededd9c62b217bff91

      Author:  Hugo Gruson <10783929+Bisaloo@users.noreply.github.com> 

      Date: 2025-08-30 09:44:37 +0200

      Commit message:


	  
		
 Specify default for pattern in function arguments
 

    

  
    

      Package: biomaRt

      Commit: 480255502a516a96143d8c401cfc612349fb818b

      Author:  Hugo Gruson <10783929+Bisaloo@users.noreply.github.com> 

      Date: 2025-08-30 09:41:06 +0200

      Commit message:


	  
		
 Remove superseded code chunk

Since a scheme is always added at the beginning of this function
 

    

  
    

      Package: biomaRt

      Commit: 49e9bac8f1fc048c77ba72dfcbe93c911737f477

      Author:  Hugo Gruson <10783929+Bisaloo@users.noreply.github.com> 

      Date: 2025-08-30 09:40:20 +0200

      Commit message:


	  
		
 Use nzchar()
 

    

  
    

      Package: biomaRt

      Commit: 796ffcb7d29a79f814bcc01f6fe18c5dd3176fc9

      Author:  Hugo Gruson <10783929+Bisaloo@users.noreply.github.com> 

      Date: 2025-08-30 09:40:09 +0200

      Commit message:


	  
		
 Simplify pastes
 

    

  
    

      Package: biomaRt

      Commit: 3fa9b171c967de42754cdca65f46196dc0bffaa1

      Author:  Hugo Gruson <10783929+Bisaloo@users.noreply.github.com> 

      Date: 2025-08-30 09:39:40 +0200

      Commit message:


	  
		
 Close connection on.exit()
 

    

  
    

      Package: biomaRt

      Commit: 3a0da35f2d8ecea8e82d8fa0c3ceed06581f3e92

      Author:  Hugo Gruson <10783929+Bisaloo@users.noreply.github.com> 

      Date: 2025-08-30 09:39:01 +0200

      Commit message:


	  
		
 Fix typos
 

    

  
    

      Package: Pirat

      Commit: ea23c431ea9f9df6244ffc3e63db0bbee1c5b953

      Author:  Lucas Etourneau <lucas.etourneau@berkeley.edu> 

      Date: 2025-09-01 00:10:04 -0700

      Commit message:


	  
		
 Add coma
 

    

  
    

      Package: Pirat

      Commit: 8029b7fb365bdb1d00dd677991802f8d3044692e

      Author:  Lucas Etourneau <lucas.etourneau@berkeley.edu> 

      Date: 2025-09-01 00:08:16 -0700

      Commit message:


	  
		
 Add coma
 

    

  
    

      Package: spARI

      Commit: de1f7eb76b545121bcf5cb1125ea6f0e0d27de97

      Author:  Your Name <you@example.com> 

      Date: 2025-09-01 12:07:55 +0800

      Commit message:


	  
		
 commit 0.99.12
 

    

  
    

      Package: DMRcate

      Commit: 607fe30e7b9e1b9d7e18dc173fc18f3eec9b1785

      Author:  timpet <t.peters@garvan.org.au> 

      Date: 2025-08-31 17:13:55 +1000

      Commit message:


	  
		
 DMRcate_3.5.2
 

    

  
    

      Package: ProteinGymR

      Commit: 047692d35ebd532bd547074be1f9a130de44ef84

      Author:  tram-nguyen-n <tram_nguyen@hms.harvard.edu> 

      Date: 2025-08-30 18:01:05 -0400

      Commit message:


	  
		
 bump DEVEL version
 

    

  
    

      Package: ProteinGymR

      Commit: 9808d005d0283030b80502f1882821c5486754fa

      Author:  Tram Nguyen <tram_nguyen@hms.harvard.edu> 

      Date: 2025-08-30 17:55:32 -0400

      Commit message:


	  
		
 Merge branch 'RELEASE_3_21' into devel 

    

  
    

      Package: ProteinGymR

      Commit: bbd7f05257ea9e58a7794c54554d19442431b33e

      Author:  tram-nguyen-n <tram_nguyen@hms.harvard.edu> 

      Date: 2025-07-17 13:57:35 +0000

      Commit message:


	  
		
 version bump
 

    

  
    

      Package: ProteinGymR

      Commit: aa42a376c9efe9b78dd168b15168812fc3a367c1

      Author:  tram-nguyen-n <tram_nguyen@hms.harvard.edu> 

      Date: 2025-07-17 13:56:31 +0000

      Commit message:


	  
		
 finished merging
 

    

  
    

      Package: ProteinGymR

      Commit: 73273a5e12c285cd22b886d226cd2537d2b63387

      Author:  Tram Nguyen <tram_nguyen@hms.harvard.edu> 

      Date: 2025-07-17 09:39:26 -0400

      Commit message:


	  
		
 Merge pull request #49 from ccb-hms/devel

merge additional edits from devel 

    

  
    

      Package: ProteinGymR

      Commit: 29b29d0c5702c6fcf3ff64bf7bb25c30bd5471b3

      Author:  tram-nguyen-n <tram_nguyen@hms.harvard.edu> 

      Date: 2025-08-30 21:42:40 +0000

      Commit message:


	  
		
 bump version
 

    

  
    

      Package: ProteinGymR

      Commit: 760b73857858c6cef78180808d7202ca4e95040d

      Author:  tram-nguyen-n <tram_nguyen@hms.harvard.edu> 

      Date: 2025-08-30 21:41:33 +0000

      Commit message:


	  
		
 move plotting dependencies to Suggests
 

    

  
    

      Package: ProteinGymR

      Commit: 13bd9181371fcbd4c7ae57be8cf86fecb8b238fb

      Author:  tram-nguyen-n <tram_nguyen@hms.harvard.edu> 

      Date: 2025-08-30 21:19:17 +0000

      Commit message:


	  
		
 bump version
 

    

  
    

      Package: ProteinGymR

      Commit: 5c2e807546973c6e1944d22a0f4cf7417a02f986

      Author:  tram-nguyen-n <tram_nguyen@hms.harvard.edu> 

      Date: 2025-08-30 21:18:55 +0000

      Commit message:


	  
		
 reduce `plot_dms_heatmap` dependencies
 

    

  
    

      Package: spARI

      Commit: 8d85e533e33d3e0ad6003560a0f8920af49184ef

      Author:  Your Name <you@example.com> 

      Date: 2025-08-30 23:33:20 +0800

      Commit message:


	  
		
 commit 0.99.11
 

    

  
    

      Package: spARI

      Commit: 345b5cc382e55fca417fd2d2ddc2fb9e37788228

      Author:  Your Name <you@example.com> 

      Date: 2025-08-30 23:19:37 +0800

      Commit message:


	  
		
 commit 0.99.10
 

    

  
    

      Package: spARI

      Commit: 0280f4d45a493a1866192f3471e9570fea57e23a

      Author:  Your Name <you@example.com> 

      Date: 2025-08-30 23:04:52 +0800

      Commit message:


	  
		
 commit 0.99.9
 

    

  
    

      Package: spARI

      Commit: 24d527e7ee838a36b50c1ba9baad7ce0cb75ad76

      Author:  Your Name <you@example.com> 

      Date: 2025-08-30 22:21:13 +0800

      Commit message:


	  
		
 commit 0.99.8
 

    

  
    

      Package: limma

      Commit: 7073db8b7b05e090ee46cebce688ba9b6036f07d

      Author:  Gordon Smyth <smyth@wehi.edu.au> 

      Date: 2025-08-30 19:54:02 +1000

      Commit message:


	  
		
 More edits to diffSplice.Rd
 

    

  
    

      Package: dupRadar

      Commit: 41f3c82e430f745a8351284c8a82e7a2bdcb4792

      Author:  Sergi Sayols <sergisayolspuig@gmail.com> 

      Date: 2025-08-30 11:02:47 +0200

      Commit message:


	  
		
 feat: add tmpDir parameter to analyzeDuprates
 

    

  
    

      Package: OSTA.data

      Commit: 4c52a2ae27b4aecfefbeb705f20c9b51d550939f

      Author:  estellad <estelladong729@gmail.com> 

      Date: 2025-08-29 18:12:42 +0200

      Commit message:


	  
		
 update version
 

    

  
    

      Package: OSTA.data

      Commit: f613c376516e2c7dafbe0cd5b2ce419f8086e9be

      Author:  estellad <estelladong729@gmail.com> 

      Date: 2025-08-29 18:04:57 +0200

      Commit message:


	  
		
 update version
 

    

  
    

      Package: OSTA.data

      Commit: 090321a87b51b04d81ab95cb372f67c5a7493b98

      Author:  estellad <estelladong729@gmail.com> 

      Date: 2025-08-29 10:06:26 +0200

      Commit message:


	  
		
 update news add sticker
 

    

  
    

      Package: spatialFDA

      Commit: 6b8167f4da7c26323e2a8c48deb740b3f035b4c9

      Author:  mjemons <martin.emons@gmail.com> 

      Date: 2025-08-29 17:40:13 +0200

      Commit message:


	  
		
 mean residuals per condition and min nndist for delta
 

    

  
    

      Package: iSEEtree

      Commit: b1b4d6ebd16d4e53d2a6735fc4991c2a009e6b2f

      Author:  Giulio Benedetti <giuliobene2000@gmail.com> 

      Date: 2025-08-29 18:35:14 +0300

      Commit message:


	  
		
 Merge pull request #49 from microbiome/testing

Add unit tests for new panels 

    

  
    

      Package: iSEEtree

      Commit: fa98b751b53e13cd9bb0fddf857f70a8a71ffea6

      Author:  Giulio <giuliobene2000@gmail.com> 

      Date: 2025-08-29 17:58:49 +0300

      Commit message:


	  
		
 Add unit tests for new panels
 

    

  
    

      Package: biomaRt

      Commit: 6872436a07010ca664ebafdbfe4813fc0909d5aa

      Author:  Hugo Gruson <10783929+Bisaloo@users.noreply.github.com> 

      Date: 2025-08-29 16:25:35 +0200

      Commit message:


	  
		
 Simplify setEnsemblSSL with modifyList()
 

    

  
    

      Package: miloR

      Commit: be20c8ba7784b564be3d6e3738194696018b1449

      Author:  MikeDMorgan <michael.morgan@abdn.ac.uk> 

      Date: 2025-08-29 14:57:51 +0100

      Commit message:


	  
		
 version bump
 

    

  
    

      Package: miloR

      Commit: cb3216a46bcf204f99a7391e5ca268843a344a96

      Author:  MikeDMorgan <michael.morgan@abdn.ac.uk> 

      Date: 2025-08-29 14:51:58 +0100

      Commit message:


	  
		
 fix sporadic error when only 1 sigma is detected because of NA estimates
 

    

  
    

      Package: miloR

      Commit: c1a01b9c1f97d55e54a6d1384532e23c15442cdc

      Author:  MikeDMorgan <michael.morgan@abdn.ac.uk> 

      Date: 2025-08-28 18:46:58 +0100

      Commit message:


	  
		
 fix bug in GLMM with multiple random effects including with a GRM
 

    

  
    

      Package: MsBackendSql

      Commit: dc774fe6f804ae42fcbe15829609e34046ef728e

      Author:  Johannes Rainer <5506112+jorainer@users.noreply.github.com> 

      Date: 2025-08-29 13:50:21 +0200

      Commit message:


	  
		
 Merge pull request #27 from rformassspectrometry/duckdb

feat: add support for duckdb blob2 storage mode 

    

  
    

      Package: MsBackendSql

      Commit: ffa3fc46ec50f61dfcde6403c78af422cc18bc06

      Author:  Johannes Rainer <johannes.rainer@gmail.com> 

      Date: 2025-08-29 13:03:48 +0200

      Commit message:


	  
		
 feat: add support for duckdb blob2 storage mode
 

    

  
    

      Package: biomaRt

      Commit: 772036e4b0fe9da1c657bb47f5ac54529344134d

      Author:  Hugo Gruson <10783929+Bisaloo@users.noreply.github.com> 

      Date: 2025-08-29 12:18:43 +0200

      Commit message:


	  
		
 Make dependency on R 4.5 explicit

Follow up from 7b4e1102fd100e2c5da681276f89750b4028db74
 

    

  
    

      Package: igblastr

      Commit: 07d59d756b634b252c39be1744b8471a079e5833

      Author:  Hervé Pagès <hpages.on.github@gmail.com> 

      Date: 2025-08-28 22:44:34 -0700

      Commit message:


	  
		
 small tweaks to README.md
 

    

  
    

      Package: igblastr

      Commit: a0d72e6860bfaa0d1197b8889a52a2b93e7b217e

      Author:  Hervé Pagès <hpages.on.github@gmail.com> 

      Date: 2025-08-28 22:34:15 -0700

      Commit message:


	  
		
 igblastr 0.99.14

- More bells and whistles to the README.md file.
- Small improvement to igblastn() examples in man/igblastn.Rd.
- Some internal reorganization of the R/IMGT-utils.R code.
- Update TODO file.
 

    

  
    

      Package: h5mread

      Commit: 519affb2bcfa1452d019bb816fe7aaecb7d12345

      Author:  Hervé Pagès <hpages.on.github@gmail.com> 

      Date: 2025-08-28 20:12:22 -0700

      Commit message:


	  
		
 Improve and tweak README.md for better compatibility with pkgdown
 

    

  
    

      Package: S4Arrays

      Commit: acd60e82117b0a8d669da8ddf810add0f0eba07e

      Author:  Hervé Pagès <hpages.on.github@gmail.com> 

      Date: 2025-08-28 20:08:25 -0700

      Commit message:


	  
		
 Improve and tweak README.md for better compatibility with pkgdown
 

    

  
    

      Package: HDF5Array

      Commit: d8785db0ba4363f0f8e5f3c2e546b3b3b7f75c0a

      Author:  Hervé Pagès <hpages.on.github@gmail.com> 

      Date: 2025-08-28 20:03:32 -0700

      Commit message:


	  
		
 Improve and tweak README.md for better compatibility with pkgdown
 

    

  
    

      Package: SparseArray

      Commit: 2dd1bf90ea032006c22fe05149e52b404bfac781

      Author:  Hervé Pagès <hpages.on.github@gmail.com> 

      Date: 2025-08-28 19:55:59 -0700

      Commit message:


	  
		
 try again
 

    

  
    

      Package: SparseArray

      Commit: 95b9508a4a5a339b1a598f76974c6510caa5f4d6

      Author:  Hervé Pagès <hpages.on.github@gmail.com> 

      Date: 2025-08-28 19:52:21 -0700

      Commit message:


	  
		
 try again
 

    

  
    

      Package: SparseArray

      Commit: 1aa154b36349add6f0e0bb0125d044e671cca6fc

      Author:  Hervé Pagès <hpages.on.github@gmail.com> 

      Date: 2025-08-28 19:49:31 -0700

      Commit message:


	  
		
 try again
 

    

  
    

      Package: SparseArray

      Commit: d38de47810a4b772579220abc0508b0722844057

      Author:  Hervé Pagès <hpages.on.github@gmail.com> 

      Date: 2025-08-28 19:48:37 -0700

      Commit message:


	  
		
 try again
 

    

  
    

      Package: SparseArray

      Commit: 47d56ad7a6a07a70f39389ff00763ed4167ca456

      Author:  Hervé Pagès <hpages.on.github@gmail.com> 

      Date: 2025-08-28 19:47:41 -0700

      Commit message:


	  
		
 Try to improve layout of images in README.md
 

    

  
    

      Package: SparseArray

      Commit: c7972f27d40c22375bf4d9ce0645c420e0fb1535

      Author:  Hervé Pagès <hpages.on.github@gmail.com> 

      Date: 2025-08-28 19:44:28 -0700

      Commit message:


	  
		
 Improve and tweak README.md for better compatibility with pkgdown
 

    

  
    

      Package: DelayedArray

      Commit: 21982e41933d0fc4f2464b2282a07080cc65049a

      Author:  Hervé Pagès <hpages.on.github@gmail.com> 

      Date: 2025-08-28 18:53:06 -0700

      Commit message:


	  
		
 minor improvements to README.md
 

    

  
    

      Package: DelayedArray

      Commit: 2a2cf695f3e3648942dabb1c3b3c2a65513a9856

      Author:  Hervé Pagès <hpages.on.github@gmail.com> 

      Date: 2025-08-28 17:55:44 -0700

      Commit message:


	  
		
 tweak layout a little
 

    

  
    

      Package: DelayedArray

      Commit: d65b462b975c28a85fc8de4eb30d30e9481f1f5c

      Author:  Hervé Pagès <hpages.on.github@gmail.com> 

      Date: 2025-08-28 17:54:21 -0700

      Commit message:


	  
		
 add "build" and "platforms" shields for devel in addition to release
 

    

  
    

      Package: DelayedArray

      Commit: 2825f0c54923d254494d467560a3a5bb10ed82a2

      Author:  Marcel Ramos Pérez <LiNk-NY@users.noreply.github.com> 

      Date: 2025-08-28 20:43:55 -0400

      Commit message:


	  
		
 Tweak README.md for better compatibility with pkgdown (#124)

 

    

  
    

      Package: limma

      Commit: d39d01194a21d91260b8468d98f138871fa332b1

      Author:  Gordon Smyth <smyth@wehi.edu.au> 

      Date: 2025-08-29 10:13:32 +1000

      Commit message:


	  
		
 limma 3.65.4

- The default for `adaptive.span` in voom() and
  voomWithQualityWeights() is now `TRUE`. All the voom functions now
  use chooseLowessSpan() by default to choose the `span`.

- New argument `xlab` for plotSplice() to allow labeling in terms of
  transcripts or other splicing events instead of exons.

- The help pages for diffSplice(), topSplice() and plotSplice() have
  been updated to emphasize differential transcript usage instead of
  differential exon usage or differential splicing.
 

    

  
    

      Package: iscream

      Commit: 2aac56205878ba39f14d6a39a2c9f45adce65a43

      Author:  James Eapen <james.eapen@vai.org> 

      Date: 2025-08-28 19:10:19 -0400

      Commit message:


	  
		
 test(tabix): skip if tabix is not installed
 

    

  
    

      Package: assorthead

      Commit: dd199372a12a5f851db6a8b0f7e64d67d1211a91

      Author:  LTLA <infinite.monkeys.with.keyboards@gmail.com> 

      Date: 2025-08-28 15:11:43 -0700

      Commit message:


	  
		
 Updated the vendored nenesub.
 

    

  
    

      Package: iModMixData

      Commit: 7623b9a35bcc5ba53667afa9d13fd2d5c850b776

      Author:  Isis Narvaez-Bandera <isis.narvaez@upr.edu> 

      Date: 2025-08-28 13:29:27 -0400

      Commit message:


	  
		
 biocViews: ExperimentData, ExpressionData, MassSpectrometryData, ExperimentHub
 

    

  
    

      Package: biomaRt

      Commit: 7b4e1102fd100e2c5da681276f89750b4028db74

      Author:  Hugo Gruson <10783929+Bisaloo@users.noreply.github.com> 

      Date: 2025-08-28 19:08:06 +0200

      Commit message:


	  
		
 Remove dependencies superseded by new functions in tools (#140)

 

    

  
    

      Package: biomaRt

      Commit: 17bff63203ee6efd7e50e886679ef96ef695e37e

      Author:  Hugo Gruson <10783929+Bisaloo@users.noreply.github.com> 

      Date: 2025-08-28 11:54:00 +0200

      Commit message:


	  
		
 Add revdep/ to .Rbuildignore
 

    

  
    

      Package: biomaRt

      Commit: 3e4945f36e8189c65a8f20d38af8bfb9777f9339

      Author:  Hugo Gruson <10783929+Bisaloo@users.noreply.github.com> 

      Date: 2025-08-28 11:53:27 +0200

      Commit message:


	  
		
 Add revdep working folders in gitignore
 

    

  
    

      Package: Pirat

      Commit: 61999326e7a0673fc477d18c4fe238fa16930123

      Author:  Lucas Etourneau <lucas.etourneau@berkeley.edu> 

      Date: 2025-08-28 10:02:55 -0700

      Commit message:


	  
		
 Add channels
 

    

  
    

      Package: punKEGGer

      Commit: d46c8479cb0106588d8ed2fff721b29814276ea1

      Author:  gdj <gdeanda@inmegen.edu.mx> 

      Date: 2025-08-28 11:01:52 -0600

      Commit message:


	  
		
 Fix DESCRIPTION DCF (no leading ')', clean Authors@R) - v0.99.6
 

    

  
    

      Package: Pirat

      Commit: 2bed5c798e1e08732f26c6bbbd519e04c66061b5

      Author:  Lucas Etourneau <lucas.etourneau@berkeley.edu> 

      Date: 2025-08-28 09:52:09 -0700

      Commit message:


	  
		
 Change channel & package
 

    

  
    

      Package: spatialFDA

      Commit: 60ac7c86e8b499acc970fa62cc76f7a516018431

      Author:  mjemons <martin.emons@gmail.com> 

      Date: 2025-08-28 17:09:09 +0200

      Commit message:


	  
		
 major change in min threshold to calculate curves on - set to >1 point - print Rsq.adjust
 

    

  
    

      Package: punKEGGer

      Commit: 23de149f42d2b706328b8d7337ada7a314b1418c

      Author:  gdj <gdeanda@inmegen.edu.mx> 

      Date: 2025-08-28 10:31:16 -0600

      Commit message:


	  
		
 Version bump to 0.99.6 (force SPB rebuild)
 

    

  
    

      Package: GSEABase

      Commit: f9e1f78d51fcdf8b87daf79e65492aeef07fd4ca

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

      Date: 2025-08-28 11:42:23 -0400

      Commit message:


	  
		
 version bump 1.71.1
 

    

  
    

      Package: GSEABase

      Commit: 451a4471f883490ca935e2a8198f9f4d92ec8fcd

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

      Date: 2025-08-28 11:43:47 -0400

      Commit message:


	  
		
 add ignore files
 

    

  
    

      Package: GSEABase

      Commit: 60aaab4d5fe13311348354db0cd92c59257399c4

      Author:  Copilot <198982749+Copilot@users.noreply.github.com> 

      Date: 2025-08-28 11:37:03 -0400

      Commit message:


	  
		
 Add support for MSigDB mouse collection categories in BroadCollection (#12)

* Add support for MSigDB mouse collection categories

Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
 

    

  
    

      Package: GSEABase

      Commit: 8843b908da13c9b6eb6c59334e6de1a0c50d9159

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

      Date: 2025-08-27 11:07:39 -0400

      Commit message:


	  
		
 add copilot instructions
 

    

  
    

      Package: BiocFileCache

      Commit: 1fc61764ec373e29bb6436fe47551c8a0b0dd974

      Author:  lshep <lori.shepherd@roswellpark.org> 

      Date: 2025-08-28 11:38:51 -0400

      Commit message:


	  
		
 Merge pull request #68 from Bioconductor/trycatch_download

use tryCatch for bfcdownload when resource is unreliable 

    

  
    

      Package: BiocFileCache

      Commit: d4b686589269ca2e02e84db532ed5b137b8d4311

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

      Date: 2025-08-27 12:46:25 -0400

      Commit message:


	  
		
 use tryCatch for bfcdownload when resource is unreliable
 

    

  
    

      Package: mzR

      Commit: 7a0319adc132af38fdcdc22e57d1e521dfa67abe

      Author:  Steffen Neumann <sneumann@ipb-halle.de> 

      Date: 2025-08-28 15:26:28 +0200

      Commit message:


	  
		
 Bump version
 

    

  
    

      Package: mzR

      Commit: f04857874fa81bccdbc9edd8171709e889ec1b19

      Author:  Adriano Rutz <adriano.rutz@hotmail.com> 

      Date: 2025-08-15 16:46:30 +0200

      Commit message:


	  
		
 ignore more NaNs
 

    

  
    

      Package: mzR

      Commit: bcb82e383a618a7bc3d66a20ecbdc32ade625b18

      Author:  Adriano Rutz <adriano.rutz@hotmail.com> 

      Date: 2025-08-15 08:44:08 +0200

      Commit message:


	  
		
 ignore more NaNs
 

    

  
    

      Package: mzR

      Commit: b97523ca6318bbe5bbd983a25283fd89030ff560

      Author:  Adriano Rutz <adriano.rutz@hotmail.com> 

      Date: 2025-08-14 17:11:32 +0200

      Commit message:


	  
		
 ignore nan energies
 

    

  
    

      Package: mzR

      Commit: c24f9afdef20987cba491e0cc8eee8a4bb5c8332

      Author:  Adriano Rutz <adriano.rutz@hotmail.com> 

      Date: 2025-08-14 12:58:41 +0200

      Commit message:


	  
		
 add `electronBeamEnergy`
 

    

  
    

      Package: mzR

      Commit: 27c8edb42604522358b18573bda0c10ac88f78f9

      Author:  Adriano Rutz <adriano.rutz@hotmail.com> 

      Date: 2025-08-14 07:51:51 +0200

      Commit message:


	  
		
 ran `updateCvParams.sh`
 

    

  
    

      Package: mzR

      Commit: 0e6f9e9d42c1112e2a6a78e1216d7c3d473d7f71

      Author:  Steffen Neumann <sneumann@ipb-halle.de> 

      Date: 2025-08-12 22:37:39 +0200

      Commit message:


	  
		
 Merge pull request #309 from sneumann/sneumann-patch-5

Bump BioC Versions in github action
Fixes GH actions failure on Linux 

    

  
    

      Package: mzR

      Commit: a9041f108127ccb2ed0908299bc8cc23883c7ec5

      Author:  Steffen Neumann <sneumann@ipb-halle.de> 

      Date: 2025-08-12 22:04:15 +0200

      Commit message:


	  
		
 Bump BioC Versions in github action 

    

  
    

      Package: tximportData

      Commit: 04d30a42107dcd5e68444e1143520f84764376f2

      Author:  Mike Love <mikelove@users.noreply.github.com> 

      Date: 2025-08-28 08:12:34 -0400

      Commit message:


	  
		
 update number of novel in oarfish
 

    

  
    

      Package: msa

      Commit: 72ebbc23c46e5938093565e72fa39662c1970041

      Author:  Ulrich Bodenhofer <ulrichbodenhofer@TAMMISAARI.local> 

      Date: 2025-08-28 13:38:53 +0200

      Commit message:


	  
		
 fixed compilations problems for arm64; version number bumped to 1.41.1
 

    

  
    

      Package: Rarr

      Commit: 3fb74aaeeffb45be70f601e7daab3ed108d02722

      Author:  Hugo Gruson <10783929+Bisaloo@users.noreply.github.com> 

      Date: 2025-08-28 11:44:55 +0200

      Commit message:


	  
		
 Fix rchk PROTECT issues (#40)

 

    

  
    

      Package: Rarr

      Commit: d944a2efd2c735577773db11563e89b79990a790

      Author:  Hugo Gruson <10783929+Bisaloo@users.noreply.github.com> 

      Date: 2025-08-28 11:42:34 +0200

      Commit message:


	  
		
 Add note in README about lack of v3 support (#41)

 

    

  
    

      Package: Rarr

      Commit: 219dcad29b3aca5d662d44c629832c1fed8705ec

      Author:  Hugo Gruson <10783929+Bisaloo@users.noreply.github.com> 

      Date: 2025-08-28 09:18:17 +0200

      Commit message:


	  
		
 Use readBin() on a connection (#36)

 

    

  
    

      Package: Rarr

      Commit: ed3c844ce39ebb96f47760d55bd1884ad05be323

      Author:  Hugo Gruson <10783929+Bisaloo@users.noreply.github.com> 

      Date: 2025-08-28 08:17:51 +0200

      Commit message:


	  
		
 Set up r-hub to test on more uncommon platforms (#38)

 

    

  
    

      Package: peakCombiner

      Commit: 1a8c64bb8a6a8272ca38ff97c7a9482a6ea452af

      Author:  Muckenhuber, Markus <markus.muckenhuber@novartis.com> 

      Date: 2025-08-27 11:02:04 -0400

      Commit message:


	  
		
 Updated version to 0.99.60 for second round of review
 

    

  
    

      Package: peakCombiner

      Commit: fe6b778c8c37463534129d85a846c5ab95bc7d8e

      Author:  Muckenhuber, Markus <markus.muckenhuber@novartis.com> 

      Date: 2025-08-25 05:52:31 -0400

      Commit message:


	  
		
 Add Vignette as HTML and update gitignore
 

    

  
    

      Package: peakCombiner

      Commit: 96040a6c0897bd83219766339eb83446a59702d9

      Author:  Muckenhuber, Markus <markus.muckenhuber@novartis.com> 

      Date: 2025-08-22 09:07:02 -0400

      Commit message:


	  
		
 Updated test with new parameter removeFlankOverlap
 

    

  
    

      Package: peakCombiner

      Commit: e95697f44e02959e6b5938defdfc6ca4bdb6c4d1

      Author:  Muckenhuber, Markus <markus.muckenhuber@novartis.com> 

      Date: 2025-08-22 09:06:49 -0400

      Commit message:


	  
		
 Updated man with new parameter removeFlankOverlap
 

    

  
    

      Package: peakCombiner

      Commit: 559eeb41b81fe8aaef04e178c8601b679498c215

      Author:  Muckenhuber, Markus <markus.muckenhuber@novartis.com> 

      Date: 2025-08-22 09:06:21 -0400

      Commit message:


	  
		
 Added new parameter removeFlankOverlaps
 

    

  
    

      Package: peakCombiner

      Commit: 02a9a43cca9e4dcab87ad81a4592bebbf22a4c50

      Author:  Muckenhuber, Markus <markus.muckenhuber@novartis.com> 

      Date: 2025-08-22 09:05:54 -0400

      Commit message:


	  
		
 Added hex sticker to ignore
 

    

  
    

      Package: peakCombiner

      Commit: 7f58cd410c36bd50004d5e5ac95496798992f4b5

      Author:  Muckenhuber, Markus <markus.muckenhuber@novartis.com> 

      Date: 2025-08-22 09:04:50 -0400

      Commit message:


	  
		
 New version
 

    

  
    

      Package: peakCombiner

      Commit: 7644c840b70c18d07af07aac61dd79167a1e8f0d

      Author:  Muckenhuber, Markus <markus.muckenhuber@novartis.com> 

      Date: 2025-08-18 09:08:09 -0400

      Commit message:


	  
		
 Readd GenomeInfoDb
 

    

  
    

      Package: peakCombiner

      Commit: 9ce6b61cff8a0dfcdfe83ac324d561b4c6181142

      Author:  Muckenhuber, Markus <markus.muckenhuber@novartis.com> 

      Date: 2025-08-18 08:55:43 -0400

      Commit message:


	  
		
 Correct typo in parameter startsAreBased
 

    

  
    

      Package: peakCombiner

      Commit: 17ff90e30d6961594c4c410d46d2e3a6e0615fcb

      Author:  Muckenhuber, Markus <markus.muckenhuber@novartis.com> 

      Date: 2025-08-14 05:07:41 -0400

      Commit message:


	  
		
 For now added
 

    

  
    

      Package: peakCombiner

      Commit: ee62ba828b188dfe03ba466f6780654effe38207

      Author:  Muckenhuber, Markus <markus.muckenhuber@novartis.com> 

      Date: 2025-08-14 04:27:23 -0400

      Commit message:


	  
		
 For now add gitproject
 

    

  
    

      Package: peakCombiner

      Commit: 68dffe7a375bc7d4e8ff1d5bdbfcecc9442b174b

      Author:  Muckenhuber, Markus <markus.muckenhuber@novartis.com> 

      Date: 2025-08-14 04:24:11 -0400

      Commit message:


	  
		
 Replace GenomeInfoDB with Seqinfo (in devel now will be released with new BC version)
 

    

  
    

      Package: peakCombiner

      Commit: 3bd71a54fea850275a6602a3a15c930b86b576a9

      Author:  Muckenhuber, Markus <markus.muckenhuber@novartis.com> 

      Date: 2025-08-14 04:23:36 -0400

      Commit message:


	  
		
 For the moment remove one test as it seems the new seqinfo package is failing
 

    

  
    

      Package: peakCombiner

      Commit: 90ba8e1ad65af4e367eee274395bf028c8e61861

      Author:  Muckenhuber, Markus <markus.muckenhuber@novartis.com> 

      Date: 2025-08-14 04:23:09 -0400

      Commit message:


	  
		
 Update man with new package
 

    

  
    

      Package: peakCombiner

      Commit: 34e53e9a49f64315f970729542c66fc8ec51fed0

      Author:  Muckenhuber, Markus <markus.muckenhuber@novartis.com> 

      Date: 2025-08-14 04:22:54 -0400

      Commit message:


	  
		
 Replaced seqinfos with new package Seqinfo
 

    

  
    

      Package: peakCombiner

      Commit: e4b9198a73c4e14bffbf5092ce7f28938846bc6d

      Author:  Markus Muckenhuber <141941160+MarkusMuck@users.noreply.github.com> 

      Date: 2025-08-13 14:46:27 +0200

      Commit message:


	  
		
 Delete peakCombiner-git.Rproj 

    

  
    

      Package: peakCombiner

      Commit: e8852ada59436e61eda000a26a9a45a427e0779f

      Author:  Muckenhuber, Markus <markus.muckenhuber@novartis.com> 

      Date: 2025-08-13 08:09:54 -0400

      Commit message:


	  
		
 Corrected expected values in tests
 

    

  
    

      Package: peakCombiner

      Commit: 708cb72992a7bea4676a33bf16987e9e7346a019

      Author:  Muckenhuber, Markus <markus.muckenhuber@novartis.com> 

      Date: 2025-08-13 08:09:38 -0400

      Commit message:


	  
		
 Removed wrong line from man
 

    

  
    

      Package: peakCombiner

      Commit: d7f199160e716741a88b53418381a72cad7dca75

      Author:  Muckenhuber, Markus <markus.muckenhuber@novartis.com> 

      Date: 2025-08-13 08:09:25 -0400

      Commit message:


	  
		
 Readded name column
 

    

  
    

      Package: peakCombiner

      Commit: d03b4cdbce292f0b189424ed14226c2bc941950f

      Author:  Muckenhuber, Markus <markus.muckenhuber@novartis.com> 

      Date: 2025-08-13 08:09:09 -0400

      Commit message:


	  
		
 Removed commend which created error in Check
 

    

  
    

      Package: peakCombiner

      Commit: 963cfa45f34b391e3c7b88aada8c52593d5ccf04

      Author:  Muckenhuber, Markus <markus.muckenhuber@novartis.com> 

      Date: 2025-08-13 05:24:10 -0400

      Commit message:


	  
		
 Include setting 0-based option if needed
 

    

  
    

      Package: peakCombiner

      Commit: e8167d700b6def6b24a9843f000a4388445012dd

      Author:  Muckenhuber, Markus <markus.muckenhuber@novartis.com> 

      Date: 2025-08-13 05:23:45 -0400

      Commit message:


	  
		
 Update tests to new functions and syndata
 

    

  
    

      Package: peakCombiner

      Commit: 88d1039f8ed3aef0f2065860bcdc2633e87aa365

      Author:  Muckenhuber, Markus <markus.muckenhuber@novartis.com> 

      Date: 2025-08-13 05:23:27 -0400

      Commit message:


	  
		
 Update syn data
 

    

  
    

      Package: peakCombiner

      Commit: c09ad565258cf5de3c7f689720157ab1b0efb42c

      Author:  Muckenhuber, Markus <markus.muckenhuber@novartis.com> 

      Date: 2025-08-13 05:23:10 -0400

      Commit message:


	  
		
 Move hidding error messages to front of function and to reset default at the end
 

    

  
    

      Package: peakCombiner

      Commit: 0e1bc6f34961c430e82c17da6d39b81f1e8cef55

      Author:  Muckenhuber, Markus <markus.muckenhuber@novartis.com> 

      Date: 2025-08-13 05:22:44 -0400

      Commit message:


	  
		
 Set default to showMessages True
 

    

  
    

      Package: peakCombiner

      Commit: 17e0d24cae1fd4140e2f6a0763df11543b128936

      Author:  Muckenhuber, Markus <markus.muckenhuber@novartis.com> 

      Date: 2025-08-13 05:22:27 -0400

      Commit message:


	  
		
 Changed used dats
 

    

  
    

      Package: peakCombiner

      Commit: d644e001cff8221eaeb69dff7d4fe5d1b3d50ca2

      Author:  Muckenhuber, Markus <markus.muckenhuber@novartis.com> 

      Date: 2025-08-13 05:22:16 -0400

      Commit message:


	  
		
 Removed reset of error messages
 

    

  
    

      Package: peakCombiner

      Commit: 9c0f165204858e6dd37ec2efe5a90879d75af612

      Author:  Muckenhuber, Markus <markus.muckenhuber@novartis.com> 

      Date: 2025-08-12 10:22:44 -0400

      Commit message:


	  
		
 Added usage of blacklist to vignette
 

    

  
    

      Package: peakCombiner

      Commit: 7483bbf0cbe40c1bc8798825e4994591f126c522

      Author:  Muckenhuber, Markus <markus.muckenhuber@novartis.com> 

      Date: 2025-08-12 10:22:18 -0400

      Commit message:


	  
		
 Downloaded blacklist added to gitignore
 

    

  
    

      Package: peakCombiner

      Commit: 00d7a75c83e8dc82132129492952049abeaa7f37

      Author:  Muckenhuber, Markus <markus.muckenhuber@novartis.com> 

      Date: 2025-08-12 10:21:26 -0400

      Commit message:


	  
		
 Added new ShowMessages parameter
 

    

  
    

      Package: peakCombiner

      Commit: 64c042f3e43bacfc69582b55a7f9c882d7dc7db5

      Author:  Muckenhuber, Markus <markus.muckenhuber@novartis.com> 

      Date: 2025-08-12 10:21:08 -0400

      Commit message:


	  
		
 Changed order to silence messages and removed resets to default by error. And added the showMessages option to the check
 

    

  
    

      Package: peakCombiner

      Commit: 3fe1b3d7066ba8782ddc4d8d65067e5d1836c20d

      Author:  Muckenhuber, Markus <markus.muckenhuber@novartis.com> 

      Date: 2025-08-12 10:20:52 -0400

      Commit message:


	  
		
 Changed order to silence messages and removed resets to default by error. And added the showMessages option to the check. Added showMessagesto helper function
 

    

  
    

      Package: peakCombiner

      Commit: 8ee66a1c10c651b35a6d33944ebe54704191a1ef

      Author:  Muckenhuber, Markus <markus.muckenhuber@novartis.com> 

      Date: 2025-08-12 10:20:22 -0400

      Commit message:


	  
		
 Changed order to silence messages and removed resets to default by error. And added the showMessages option to the check
 

    

  
    

      Package: peakCombiner

      Commit: 9adac3f48d13ed04687c5952dd4ed7ebe121e4d5

      Author:  Muckenhuber, Markus <markus.muckenhuber@novartis.com> 

      Date: 2025-08-12 10:20:09 -0400

      Commit message:


	  
		
 Changed order to silence messages and removed resets to default by error. And added the showMessages option to the check
 

    

  
    

      Package: peakCombiner

      Commit: f24ac292c13ed946d60f41cd164de1e989d5ae6b

      Author:  Muckenhuber, Markus <markus.muckenhuber@novartis.com> 

      Date: 2025-08-12 10:19:44 -0400

      Commit message:


	  
		
 Added silence messages and removed resets to default by error
 

    

  
    

      Package: peakCombiner

      Commit: ed7308ff4adce67a64c1f695beaeb8ece26b07e3

      Author:  Muckenhuber, Markus <markus.muckenhuber@novartis.com> 

      Date: 2025-08-12 10:19:26 -0400

      Commit message:


	  
		
 Changed order to silence messages and removed resets to default by error
 

    

  
    

      Package: peakCombiner

      Commit: e12b1765c19e2058d915a8900e6d9060d796c290

      Author:  Muckenhuber, Markus <markus.muckenhuber@novartis.com> 

      Date: 2025-08-12 09:34:25 -0400

      Commit message:


	  
		
 Changed some parameters to camelCase.
Update information how to use blacklists and where to get them
 

    

  
    

      Package: peakCombiner

      Commit: 21c5ba2d65bc1a51edceb1da8756827e4f3479a6

      Author:  Muckenhuber, Markus <markus.muckenhuber@novartis.com> 

      Date: 2025-08-12 09:33:42 -0400

      Commit message:


	  
		
 Mayor updates on test to fit new parameter and function names. Check for new parameter and updated expected results for tests
 

    

  
    

      Package: peakCombiner

      Commit: edd22c7575d29ee9fd95027d72b73c36d566cb42

      Author:  Muckenhuber, Markus <markus.muckenhuber@novartis.com> 

      Date: 2025-08-12 09:33:04 -0400

      Commit message:


	  
		
 Updated tests to allow checking for correctly provided genome
 

    

  
    

      Package: peakCombiner

      Commit: b774b33b630e02f8914eb2f5e3a57d7ec8771841

      Author:  Muckenhuber, Markus <markus.muckenhuber@novartis.com> 

      Date: 2025-08-12 09:32:32 -0400

      Commit message:


	  
		
 Updated man
 

    

  
    

      Package: peakCombiner

      Commit: f14a3a65efc3d38da6fe8d2056aa2736cf1a3fda

      Author:  Muckenhuber, Markus <markus.muckenhuber@novartis.com> 

      Date: 2025-08-12 09:32:05 -0400

      Commit message:


	  
		
 New manual for re-named functions and parameters to follow camelCase
 

    

  
    

      Package: peakCombiner

      Commit: 82dcf65cb579d30655caa7611ee7bf04b69aeebf

      Author:  Muckenhuber, Markus <markus.muckenhuber@novartis.com> 

      Date: 2025-08-12 09:31:29 -0400

      Commit message:


	  
		
 Update how trimming is handeled and how genome infos are maintained
 

    

  
    

      Package: peakCombiner

      Commit: c221a86f0a27e501fda3ad9b3eecefc400075ee0

      Author:  Muckenhuber, Markus <markus.muckenhuber@novartis.com> 

      Date: 2025-08-12 09:30:49 -0400

      Commit message:


	  
		
 Update the way syn data is made to follow bed tools standards
 

    

  
    

      Package: peakCombiner

      Commit: b966293b5c4213a61e98428897f3fa7ef8e3f3b2

      Author:  Muckenhuber, Markus <markus.muckenhuber@novartis.com> 

      Date: 2025-08-12 09:30:20 -0400

      Commit message:


	  
		
 Update syn data to follow BED tool standards
 

    

  
    

      Package: peakCombiner

      Commit: 9701e143a0787b9cf38153f0869cc957c8a285db

      Author:  Muckenhuber, Markus <markus.muckenhuber@novartis.com> 

      Date: 2025-08-12 09:29:57 -0400

      Commit message:


	  
		
 Add new options to provide Genome information which is also maintained. Add the option to inform if input is 1 or 0-based. Outpu is now always 1-based
 

    

  
    

      Package: peakCombiner

      Commit: c6c39ad76067c33a8be005cb4bedc6774da7a8c0

      Author:  Muckenhuber, Markus <markus.muckenhuber@novartis.com> 

      Date: 2025-08-12 09:28:28 -0400

      Commit message:


	  
		
 Update usage of Blacklist doc and code. Also extract seqinfo from GRanges input and add it to output
 

    

  
    

      Package: peakCombiner

      Commit: 336ea86206cb8879c091b9024b1c6b0f00a6df9b

      Author:  Muckenhuber, Markus <markus.muckenhuber@novartis.com> 

      Date: 2025-08-12 09:27:46 -0400

      Commit message:


	  
		
 Extract SeqInfo from GRanges input and add it to outpu
 

    

  
    

      Package: peakCombiner

      Commit: 8028ff99915d77396653525840fad5f9e093e732

      Author:  Muckenhuber, Markus <markus.muckenhuber@novartis.com> 

      Date: 2025-08-12 09:27:07 -0400

      Commit message:


	  
		
 Update input test files to 0-based to follow BED tool standards
 

    

  
    

      Package: peakCombiner

      Commit: db511643de58669204b07942b143181801c3eae2

      Author:  Muckenhuber, Markus <markus.muckenhuber@novartis.com> 

      Date: 2025-08-12 09:26:34 -0400

      Commit message:


	  
		
 Rename function and options to camleCase
 

    

  
    

      Package: peakCombiner

      Commit: 745d7f4da30f22325a2554c76e56961976dd88e4

      Author:  Muckenhuber, Markus <markus.muckenhuber@novartis.com> 

      Date: 2025-08-12 09:26:04 -0400

      Commit message:


	  
		
 Implement solution to have all in 1-based and a way to extract genome info from input
 

    

  
    

      Package: peakCombiner

      Commit: 2fe0f2d031786de7109b11c15ce2a4fbd2d93df7

      Author:  Muckenhuber, Markus <markus.muckenhuber@novartis.com> 

      Date: 2025-08-12 09:24:56 -0400

      Commit message:


	  
		
 Added Annotation Hub to package list
 

    

  
    

      Package: peakCombiner

      Commit: 99865415fc85cd1605fbceb33c55d43089040514

      Author:  Muckenhuber, Markus <markus.muckenhuber@novartis.com> 

      Date: 2025-08-05 10:48:54 -0400

      Commit message:


	  
		
 Update parameter names to camaleCase from snake_case
 

    

  
    

      Package: peakCombiner

      Commit: 37a66a61b0d87daaf33cae8167d85f9100559da2

      Author:  Muckenhuber, Markus <markus.muckenhuber@novartis.com> 

      Date: 2025-08-05 10:05:07 -0400

      Commit message:


	  
		
 Change back the test push
 

    

  
    

      Package: peakCombiner

      Commit: 17daaf0dda01f10e9a69da63541582516fb0a536

      Author:  Muckenhuber, Markus <markus.muckenhuber@novartis.com> 

      Date: 2025-08-05 08:10:35 -0400

      Commit message:


	  
		
 Test pushing US
 

    

  
    

      Package: peakCombiner

      Commit: ea91f07f7e6c0283811032b48f2db6a8092256f8

      Author:  Markus Muckenhuber <141941160+MarkusMuck@users.noreply.github.com> 

      Date: 2025-08-04 15:09:19 +0200

      Commit message:


	  
		
 Update centerExpandRegions.R

Adjusted man 

    

  
    

      Package: peakCombiner

      Commit: 3d9bc06c17fe5bbfefe4ef599eb4b2f5222a8d8f

      Author:  Markus Muckenhuber <141941160+MarkusMuck@users.noreply.github.com> 

      Date: 2025-08-04 14:50:19 +0200

      Commit message:


	  
		
 Update peakCombiner.Rmd

Not execute install.package 

    

  
    

      Package: peakCombiner

      Commit: 1481dc1fe5d1f373320ec56501c6d994eb66a8ba

      Author:  Markus Muckenhuber <141941160+MarkusMuck@users.noreply.github.com> 

      Date: 2025-08-04 14:43:53 +0200

      Commit message:


	  
		
 Update peakCombiner.Rmd

Update how to install and load PeakCombiner 

    

  
    

      Package: peakCombiner

      Commit: 48254b3ad303ed2d8eeb7003124616de307f5833

      Author:  Markus Muckenhuber <141941160+MarkusMuck@users.noreply.github.com> 

      Date: 2025-08-04 14:40:12 +0200

      Commit message:


	  
		
 Update peakCombiner.Rmd 

    

  
    

      Package: peakCombiner

      Commit: b4afbb7a5eca6063822a773d6ba447615d97acb5

      Author:  Markus Muckenhuber <141941160+MarkusMuck@users.noreply.github.com> 

      Date: 2025-08-04 14:35:16 +0200

      Commit message:


	  
		
 Update peakCombiner.Rmd

Removed one opts_chunl$set 

    

  
    

      Package: peakCombiner

      Commit: 9f1a0b17ed994ebd6eea10178302a9c90eece1db

      Author:  Markus Muckenhuber <141941160+MarkusMuck@users.noreply.github.com> 

      Date: 2025-08-04 14:27:36 +0200

      Commit message:


	  
		
 Update peakCombiner.Rmd

Correct error in calling makeGRangesFromDataFrame 

    

  
    

      Package: peakCombiner

      Commit: a13d8de38522345d3a1bf26c51c9093a11b5203a

      Author:  Markus Muckenhuber <141941160+MarkusMuck@users.noreply.github.com> 

      Date: 2025-08-04 14:22:48 +0200

      Commit message:


	  
		
 Update peakCombiner.Rmd 

    

  
    

      Package: peakCombiner

      Commit: 6af872a29b2437252674bf59266324d0a58a78b4

      Author:  Markus Muckenhuber <muckema1@vv7q2gf9jc.eu.novartis.net> 

      Date: 2025-07-31 16:13:27 +0200

      Commit message:


	  
		
 Triggering GitHub Action
 

    

  
    

      Package: peakCombiner

      Commit: ca9634f3f734c4efe9ddfcfcd9dde89db0c31ac2

      Author:  Muckenhuber, Markus <markus.muckenhuber@novartis.com> 

      Date: 2025-07-30 15:52:03 +0200

      Commit message:


	  
		
 Updated the vignette to align with changed parameters and functionalities of the package
 

    

  
    

      Package: peakCombiner

      Commit: d7a54eb2ffe29349a8624d08f8d077d11d35dde7

      Author:  Muckenhuber, Markus <markus.muckenhuber@novartis.com> 

      Date: 2025-07-29 16:20:33 +0200

      Commit message:


	  
		
 Added BiocManager to suggestions
 

    

  
    

      Package: peakCombiner

      Commit: ae5f58684e86050684068067a8bd07e9b6a78bc1

      Author:  Muckenhuber, Markus <markus.muckenhuber@novartis.com> 

      Date: 2025-07-29 16:17:50 +0200

      Commit message:


	  
		
 Update the way the package is loaded and how some data sets are loaded
 

    

  
    

      Package: peakCombiner

      Commit: 10357883110098736589064174cd8171635baf47

      Author:  Muckenhuber, Markus <markus.muckenhuber@novartis.com> 

      Date: 2025-07-29 16:17:31 +0200

      Commit message:


	  
		
 Updated the test results
 

    

  
    

      Package: peakCombiner

      Commit: 0d4d92708a4188d1bef81416b45ed0434eb01446

      Author:  Muckenhuber, Markus <markus.muckenhuber@novartis.com> 

      Date: 2025-07-29 16:16:57 +0200

      Commit message:


	  
		
 Correct some errors in the description of required imputs
 

    

  
    

      Package: peakCombiner

      Commit: a6dc40a2b54a2a4c1a3f5cc77d832d8aa57846a0

      Author:  Muckenhuber, Markus <markus.muckenhuber@novartis.com> 

      Date: 2025-07-29 16:16:31 +0200

      Commit message:


	  
		
 Change the default parameter for trim_start
 

    

  
    

      Package: peakCombiner

      Commit: 72b06438b63aabc609f082e65e3c086406aa67fe

      Author:  Muckenhuber, Markus <markus.muckenhuber@novartis.com> 

      Date: 2025-07-29 15:40:52 +0200

      Commit message:


	  
		
 Correct some mistakes in the test of vignette
 

    

  
    

      Package: peakCombiner

      Commit: 5eb33f102cb041d54da8f13c4f9443487d0d31f4

      Author:  Muckenhuber, Markus <markus.muckenhuber@novartis.com> 

      Date: 2025-07-29 15:40:22 +0200

      Commit message:


	  
		
 Add test to see non-unique entries in sample_sheet
 

    

  
    

      Package: peakCombiner

      Commit: 666b42cbac5e2985a429f7542ac742970692602c

      Author:  Muckenhuber, Markus <markus.muckenhuber@novartis.com> 

      Date: 2025-07-29 15:35:14 +0200

      Commit message:


	  
		
 Added an check if values in "score_columns" are unique
 

    

  
    

      Package: peakCombiner

      Commit: 4886f03d5ffe6f228e5e0f2c9dfc7d840af54f3d

      Author:  Muckenhuber, Markus <markus.muckenhuber@novartis.com> 

      Date: 2025-07-29 15:34:25 +0200

      Commit message:


	  
		
 Errors in documentation about col names for sample sheet, which should be "file_path" not "path_peaks"
 

    

  
    

      Package: peakCombiner

      Commit: 26f8b04d047bbd58787c77100f1f3f426fb3bd23

      Author:  Muckenhuber, Markus <markus.muckenhuber@novartis.com> 

      Date: 2025-07-29 15:33:30 +0200

      Commit message:


	  
		
 Changed the default for trim_start to be true
 

    

  
    

      Package: peakCombiner

      Commit: b0be3e5465b3c99a7f649f0835242660f3be214a

      Author:  Muckenhuber, Markus <markus.muckenhuber@novartis.com> 

      Date: 2025-07-25 11:47:04 +0200

      Commit message:


	  
		
 Adjusted vignette with new options in functions
 

    

  
    

      Package: peakCombiner

      Commit: 574263441a98678a34e5f0909ddf9ea187596efb

      Author:  Muckenhuber, Markus <markus.muckenhuber@novartis.com> 

      Date: 2025-07-25 11:46:45 +0200

      Commit message:


	  
		
 Adjusted test for new options and test them
 

    

  
    

      Package: peakCombiner

      Commit: 46b9b898ca3bc334f73cc3d98d88ead897a04a94

      Author:  Muckenhuber, Markus <markus.muckenhuber@novartis.com> 

      Date: 2025-07-25 11:46:26 +0200

      Commit message:


	  
		
 Adjusted man with new options and their explanations
 

    

  
    

      Package: peakCombiner

      Commit: d1e609863631f4b413b059b247dd8e87e7ae032e

      Author:  Muckenhuber, Markus <markus.muckenhuber@novartis.com> 

      Date: 2025-07-25 11:46:07 +0200

      Commit message:


	  
		
 Added the GenomicRanges way to test if expanded regions are beyong chrom boarders. Then trim them
 

    

  
    

      Package: peakCombiner

      Commit: a1a49d7b02e6df2bae210cd05792512acb3cfd1b

      Author:  Muckenhuber, Markus <markus.muckenhuber@novartis.com> 

      Date: 2025-07-25 11:45:01 +0200

      Commit message:


	  
		
 Added GenomeInfoDB package for genome reference
 

    

  
    

      Package: peakCombiner

      Commit: 772e7666274f3967e23c661d50cc7f3c11676fc8

      Author:  Muckenhuber, Markus <markus.muckenhuber@novartis.com> 

      Date: 2025-07-23 16:44:30 +0200

      Commit message:


	  
		
 Rename main functions to camelCase
 

    

  
    

      Package: peakCombiner

      Commit: 2f9197d9fb29a543c7b2d839789b3bfeca266b18

      Author:  Muckenhuber, Markus <markus.muckenhuber@novartis.com> 

      Date: 2025-07-23 16:44:04 +0200

      Commit message:


	  
		
 Rename main functions to camelCase
 

    

  
    

      Package: peakCombiner

      Commit: 94704c7dd3710ea2fe17c036b5e58aefdb64e692

      Author:  Muckenhuber, Markus <markus.muckenhuber@novartis.com> 

      Date: 2025-07-23 15:33:21 +0200

      Commit message:


	  
		
 Improved code to solve error in test
 

    

  
    

      Package: peakCombiner

      Commit: 26521be3165e3fed06a57e17849b86c24c87b9ce

      Author:  Muckenhuber, Markus <markus.muckenhuber@novartis.com> 

      Date: 2025-07-23 15:32:58 +0200

      Commit message:


	  
		
 Fix error in transforming GenomicRanges to tibble
 

    

  
    

      Package: peakCombiner

      Commit: e6172f325d68b7667b141a7ae86cbe20c4b57698

      Author:  Muckenhuber, Markus <markus.muckenhuber@novartis.com> 

      Date: 2025-07-22 17:43:28 +0200

      Commit message:


	  
		
 Allow Granges Object as input
 

    

  
    

      Package: peakCombiner

      Commit: 6231fcb5fe7d13575a86c13ef71ef00dfb3f3025

      Author:  Muckenhuber, Markus <markus.muckenhuber@novartis.com> 

      Date: 2025-07-22 17:17:58 +0200

      Commit message:


	  
		
 Added the output_format to all function
 

    

  
    

      Package: peakCombiner

      Commit: af080a67d672bc0459f010f35501be20993a90f0

      Author:  Muckenhuber, Markus <markus.muckenhuber@novartis.com> 

      Date: 2025-07-22 16:58:34 +0200

      Commit message:


	  
		
 Missed one function to add the output_data
 

    

  
    

      Package: peakCombiner

      Commit: aba6e8154260884a6537c77d9e7225ccc4514927

      Author:  Muckenhuber, Markus <markus.muckenhuber@novartis.com> 

      Date: 2025-07-22 16:55:37 +0200

      Commit message:


	  
		
 Error in file name after adding the output_structur option
 

    

  
    

      Package: peakCombiner

      Commit: d1ab2e0879ef4640f4c2d890475dc1077ff04676

      Author:  Muckenhuber, Markus <markus.muckenhuber@novartis.com> 

      Date: 2025-07-22 16:53:38 +0200

      Commit message:


	  
		
 Add the output_format as option to the code
 

    

  
    

      Package: peakCombiner

      Commit: 20d1320b1514279332b11ad73167645cccbdd9d7

      Author:  Muckenhuber, Markus <markus.muckenhuber@novartis.com> 

      Date: 2025-07-22 16:53:22 +0200

      Commit message:


	  
		
 Add the output_format option to all required functions
 

    

  
    

      Package: peakCombiner

      Commit: 617c1969bf234b6dc6bf9e00c21bfee6b423e5a9

      Author:  Muckenhuber, Markus <markus.muckenhuber@novartis.com> 

      Date: 2025-07-22 16:53:03 +0200

      Commit message:


	  
		
 Add the output_format as option and the required code to check input and output
 

    

  
    

      Package: peakCombiner

      Commit: 955602417587aef9f8a92eb3bac0b6d410c16157

      Author:  Muckenhuber, Markus <markus.muckenhuber@novartis.com> 

      Date: 2025-07-22 16:52:56 +0200

      Commit message:


	  
		
 Add the output_format as option and the required code to check input and output
 

    

  
    

      Package: peakCombiner

      Commit: f98eb45ece96c9b69db4e9ef86ff7200af1ebf1b

      Author:  Muckenhuber, Markus <markus.muckenhuber@novartis.com> 

      Date: 2025-07-22 16:52:51 +0200

      Commit message:


	  
		
 Add the output_format as option and the required code to check input and output
 

    

  
    

      Package: peakCombiner

      Commit: dea24fe2c82f3487cd27922ef1d5ae677028bcc1

      Author:  Muckenhuber, Markus <markus.muckenhuber@novartis.com> 

      Date: 2025-07-22 16:52:41 +0200

      Commit message:


	  
		
 Add the output_format as option and the required code to check input and output
 

    

  
    

      Package: peakCombiner

      Commit: a0c23cf768e363ca645efea9edf112939bf0d2f6

      Author:  Muckenhuber, Markus <markus.muckenhuber@novartis.com> 

      Date: 2025-07-22 15:13:29 +0200

      Commit message:


	  
		
 Added to change the strand when transforming into a tibble
 

    

  
    

      Package: peakCombiner

      Commit: 113f394ea375330c7dddb4d0a27614429449928b

      Author:  Muckenhuber, Markus <markus.muckenhuber@novartis.com> 

      Date: 2025-07-22 15:12:58 +0200

      Commit message:


	  
		
 Added the new option to define output file format
 

    

  
    

      Package: peakCombiner

      Commit: 2a363c38ac7105d56442652104004bf2cc1f2938

      Author:  Muckenhuber, Markus <markus.muckenhuber@novartis.com> 

      Date: 2025-07-22 15:12:34 +0200

      Commit message:


	  
		
 Adjusted manual how midpoint is now calculated
 

    

  
    

      Package: peakCombiner

      Commit: 18b75a8793b897ffbc87048c5c05995e8b55101d

      Author:  Muckenhuber, Markus <markus.muckenhuber@novartis.com> 

      Date: 2025-07-22 15:12:15 +0200

      Commit message:


	  
		
 Remove the blacklisted files from ENCODE
 

    

  
    

      Package: peakCombiner

      Commit: 23b570e10a3df4d904099c9f65d9ef3294228ec3

      Author:  Muckenhuber, Markus <markus.muckenhuber@novartis.com> 

      Date: 2025-07-22 15:11:30 +0200

      Commit message:


	  
		
 Format adjusted
 

    

  
    

      Package: peakCombiner

      Commit: f5bbba553a61859699e1db3fa81331fb4e22664b

      Author:  Muckenhuber, Markus <markus.muckenhuber@novartis.com> 

      Date: 2025-07-22 15:11:15 +0200

      Commit message:


	  
		
 Removed Encode black list reference
 

    

  
    

      Package: peakCombiner

      Commit: c2b290892ffea9da85e5621eb9df7c0bc219afb0

      Author:  Muckenhuber, Markus <markus.muckenhuber@novartis.com> 

      Date: 2025-07-22 15:10:47 +0200

      Commit message:


	  
		
 Added option to define output format in prepare intput
 

    

  
    

      Package: peakCombiner

      Commit: 8ab7561b8aa75404797fcffc5e7409169014562f

      Author:  Muckenhuber, Markus <markus.muckenhuber@novartis.com> 

      Date: 2025-07-21 18:02:30 +0200

      Commit message:


	  
		
 Fixed an error witthin the if else
 

    

  
    

      Package: peakCombiner

      Commit: d9e4c654e22bbb9fba009d405f08819ceceeaf65

      Author:  Muckenhuber, Markus <markus.muckenhuber@novartis.com> 

      Date: 2025-07-21 18:02:08 +0200

      Commit message:


	  
		
 Removed blacklist files
 

    

  
    

      Package: peakCombiner

      Commit: b750086cd2883ca95b5c232ed72db0ada198c471

      Author:  Muckenhuber, Markus <markus.muckenhuber@novartis.com> 

      Date: 2025-07-21 17:37:55 +0200

      Commit message:


	  
		
 Fix test filtering after updating blacklist
 

    

  
    

      Package: peakCombiner

      Commit: 1a1c64cda7f0ae9385e681fb2bce7ca14d61d333

      Author:  Muckenhuber, Markus <markus.muckenhuber@novartis.com> 

      Date: 2025-07-21 17:37:38 +0200

      Commit message:


	  
		
 Delete package provided blacklists
 

    

  
    

      Package: peakCombiner

      Commit: 4721255f0836eac6aa965d4d8feeed53d63da762

      Author:  Muckenhuber, Markus <markus.muckenhuber@novartis.com> 

      Date: 2025-07-21 17:37:23 +0200

      Commit message:


	  
		
 Removed encode blacklists for file
 

    

  
    

      Package: peakCombiner

      Commit: 9e62bc2c59875e8274e3667c02b2cdbaf8c4a2e0

      Author:  Muckenhuber, Markus <markus.muckenhuber@novartis.com> 

      Date: 2025-07-21 17:37:01 +0200

      Commit message:


	  
		
 Update text how midpoint is calculated
 

    

  
    

      Package: peakCombiner

      Commit: 2be3958154f6a7b62a7ccfd31a18b49b1a8f5662

      Author:  Muckenhuber, Markus <markus.muckenhuber@novartis.com> 

      Date: 2025-07-21 17:36:41 +0200

      Commit message:


	  
		
 Add Rporj to ignor
 

    

  
    

      Package: peakCombiner

      Commit: 8a1069e30626c79b11c8007efbd4e373b1ddffe1

      Author:  Muckenhuber, Markus <markus.muckenhuber@novartis.com> 

      Date: 2025-07-21 16:10:36 +0200

      Commit message:


	  
		
 Remove value "hg38" from tests
 

    

  
    

      Package: peakCombiner

      Commit: f98b89f8aaa7874c99e2197e5985285f9ee8ad0f

      Author:  Muckenhuber, Markus <markus.muckenhuber@novartis.com> 

      Date: 2025-07-21 16:08:34 +0200

      Commit message:


	  
		
 Remove hg38 from test for blacklist
 

    

  
    

      Package: peakCombiner

      Commit: 2db7fd9a32ccae62eefa154d76588e97423d1eb7

      Author:  Muckenhuber, Markus <markus.muckenhuber@novartis.com> 

      Date: 2025-07-21 16:07:29 +0200

      Commit message:


	  
		
 Added package to make Genomic Ranges object
 

    

  
    

      Package: peakCombiner

      Commit: d7e694a223ecff6bcdadc12bec71d23d9b644a97

      Author:  Muckenhuber, Markus <markus.muckenhuber@novartis.com> 

      Date: 2025-07-21 16:05:46 +0200

      Commit message:


	  
		
 Use resite instead of calculation of midpoint
 

    

  
    

      Package: peakCombiner

      Commit: 089996907c8a7f0073a6828d2ba5833f441a3d57

      Author:  Muckenhuber, Markus <markus.muckenhuber@novartis.com> 

      Date: 2025-07-21 14:45:34 +0200

      Commit message:


	  
		
 Add excluderanges to vignette
 

    

  
    

      Package: peakCombiner

      Commit: f5fc440a92c233457e5269eb1776f9f8d0479867

      Author:  Muckenhuber, Markus <markus.muckenhuber@novartis.com> 

      Date: 2025-07-21 14:43:01 +0200

      Commit message:


	  
		
 Update the test to run with the new script by not providing the encode blacklists
 

    

  
    

      Package: peakCombiner

      Commit: 0c807ba1e61faadbf210f375f0f219d7984bc20e

      Author:  Muckenhuber, Markus <markus.muckenhuber@novartis.com> 

      Date: 2025-07-21 14:42:36 +0200

      Commit message:


	  
		
 Changed the refernces to the encode blacklists
 

    

  
    

      Package: peakCombiner

      Commit: f8ad296b329bfcf153ad8c0963aeb5c804296ef6

      Author:  Muckenhuber, Markus <markus.muckenhuber@novartis.com> 

      Date: 2025-07-21 14:36:35 +0200

      Commit message:


	  
		
 Remove pre-loading of HG38 and mm10 from ENCODE
 

    

  
    

      Package: peakCombiner

      Commit: dea402d99705a661958ea8fecd4e99f2f1814ba5

      Author:  Muckenhuber, Markus <markus.muckenhuber@novartis.com> 

      Date: 2025-07-21 11:54:05 +0200

      Commit message:


	  
		
 Added a new RProject
 

    

  
    

      Package: Spectra

      Commit: 0afa29917e224747e8c4e20af4e056e3d2ed5ce6

      Author:  Johannes Rainer <5506112+jorainer@users.noreply.github.com> 

      Date: 2025-08-28 10:10:43 +0200

      Commit message:


	  
		
 Merge pull request #364 from rformassspectrometry/jomain

Add longForm methods 

    

  
    

      Package: Spectra

      Commit: f3ca46552859df814cbe5f2f9e300617ec3b2cd9

      Author:  Johannes Rainer <johannes.rainer@gmail.com> 

      Date: 2025-08-28 10:10:09 +0200

      Commit message:


	  
		
 address Phili's comments
 

    

  
    

      Package: Spectra

      Commit: fbfdc6a8a117905d297b9e3a2fccd4583a2267c8

      Author:  Johannes Rainer <johannes.rainer@gmail.com> 

      Date: 2025-08-27 14:36:14 +0200

      Commit message:


	  
		
 feat: add longForm,Spectra (issue 360)
 

    

  
    

      Package: Spectra

      Commit: 82bf71ec9555e39bc9de1f691251b4fe497c31de

      Author:  Johannes Rainer <johannes.rainer@gmail.com> 

      Date: 2025-08-27 13:55:34 +0200

      Commit message:


	  
		
 feat: add longForm,MsBackend method (issue #360)
 

    

  
    

      Package: Ularcirc

      Commit: 8cd13d1d073af53fdb3ff935e5c68e5c8a46d11a

      Author:  David Humphreys <dth569@gadi-login-07.gadi.nci.org.au> 

      Date: 2025-08-28 14:33:28 +1000

      Commit message:


	  
		
 Remove mirBase.db dependency
 

    

  
    

      Package: SeqArray

      Commit: 6e66555b817378a5b3e964a3843fceaeda12c2f7

      Author:  Xiuwen Zheng <zhengxwen@gmail.com> 

      Date: 2025-08-27 23:30:36 -0500

      Commit message:


	  
		
 version bump
 

    

  
    

      Package: punKEGGer

      Commit: 8967c7a9aac52fbb8fece4eb2200ff21d9057729

      Author:  gdj <gdeanda@inmegen.edu.mx> 

      Date: 2025-08-27 18:05:09 -0600

      Commit message:


	  
		
 Bump version to 0.99.5
 

    

  
    

      Package: basilisk

      Commit: 9942970f6957217a867f7fee0c60188781f38fcb

      Author:  LTLA <infinite.monkeys.with.keyboards@gmail.com> 

      Date: 2025-08-27 14:46:34 -0700

      Commit message:


	  
		
 Remove references to Conda in the README.
 

    

  
    

      Package: basilisk.utils

      Commit: 112f90d25fd6b41041ef2f310869d411e616c515

      Author:  LTLA <infinite.monkeys.with.keyboards@gmail.com> 

      Date: 2025-08-27 14:50:54 -0700

      Commit message:


	  
		
 Updated README for the new purpose of this package, added badges.
 

    

  
    

      Package: BiocPkgTools

      Commit: 68dd50d5b75f07a3fe99f29eddbdb0b71d0491a8

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

      Date: 2025-08-27 16:14:54 -0400

      Commit message:


	  
		
 version bump 1.27.12
 

    

  
    

      Package: BiocPkgTools

      Commit: 3eedadca944f28dff16810b7dab4489d8cce8054

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

      Date: 2025-08-27 15:47:15 -0400

      Commit message:


	  
		
 use \code{} for type specs in docs
 

    

  
    

      Package: BiocPkgTools

      Commit: 910b4a9f314b1b5d745d1e5770bb90a0e1f1af2e

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

      Date: 2025-08-27 15:40:26 -0400

      Commit message:


	  
		
 minor remove spaces
 

    

  
    

      Package: BiocPkgTools

      Commit: c302ed2902d8de90a49cc686d903f75f849fcfb0

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

      Date: 2025-08-27 15:40:18 -0400

      Commit message:


	  
		
 use markdown for roxygen2 cross-refs
 

    

  
    

      Package: BiocPkgTools

      Commit: d4e93c293f096a2581947e1d1d91a9a20f3ca01c

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

      Date: 2025-08-27 15:36:04 -0400

      Commit message:


	  
		
 use markdown in roxygen2 blocks
 

    

  
    

      Package: BiocPkgTools

      Commit: f71a2ca3d14886e3853ab9fbb58401465b0570ee

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

      Date: 2025-08-27 14:52:29 -0400

      Commit message:


	  
		
 version bump 1.27.11
 

    

  
    

      Package: BiocPkgTools

      Commit: dadaeab2ec4d56fe48499bd74d9b94d33220d1d7

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

      Date: 2025-08-27 14:52:20 -0400

      Commit message:


	  
		
 update arg in examples
 

    

  
    

      Package: BiocPkgTools

      Commit: ae1b13b4f986a8a2a76f9bc3ae3190c4afcfd662

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

      Date: 2025-08-27 14:51:14 -0400

      Commit message:


	  
		
 exclude soon to be deprecated rorcid package
 

    

  
    

      Package: DropletUtils

      Commit: d85890b5222828f6fbb288cf372a1dd613d0ddee

      Author:  LTLA <infinite.monkeys.with.keyboards@gmail.com> 

      Date: 2025-08-27 10:53:10 -0700

      Commit message:


	  
		
 Bugfix for two-pass Matrix Market parsing.
 

    

  
    

      Package: plyxp

      Commit: d9d960c6eac7e0c4eab89aff588a0aa05fee9a23

      Author:  jtlandis <jtlandis314@gmail.com> 

      Date: 2025-08-27 13:38:05 -0400

      Commit message:


	  
		
 some unneeded code
 

    

  
    

      Package: plyxp

      Commit: 1f73ff763b1a8b81e0caed7726aed3fb0b33603f

      Author:  jtlandis <jtlandis314@gmail.com> 

      Date: 2025-08-26 22:57:38 -0400

      Commit message:


	  
		
 had a typo in argument
 

    

  
    

      Package: plyxp

      Commit: 7cd34d6bd9461acf38f5e5bac50fc9a15f11f091

      Author:  jtlandis <jtlandis314@gmail.com> 

      Date: 2025-08-26 22:52:26 -0400

      Commit message:


	  
		
 Update PlySummarizedExperiment-methods.Rd
 

    

  
    

      Package: plyxp

      Commit: 9bd2849eb66eeb4904d90615409942f5bc3ee93e

      Author:  jtlandis <jtlandis314@gmail.com> 

      Date: 2025-08-26 22:52:03 -0400

      Commit message:


	  
		
 fixing errors
 

    

  
    

      Package: plyxp

      Commit: cf95700faba397ebaf94b52969c08f3e969a39f9

      Author:  jtlandis <jtlandis314@gmail.com> 

      Date: 2025-08-26 17:42:50 -0400

      Commit message:


	  
		
 writing docs
 

    

  
    

      Package: plyxp

      Commit: e124fdf1e0f533663a66ef41d1c1d36863d665dc

      Author:  jtlandis <jtlandis314@gmail.com> 

      Date: 2025-08-26 17:42:05 -0400

      Commit message:


	  
		
 accidently removed this method...
 

    

  
    

      Package: plyxp

      Commit: be1ce2e78e281dbdd1d6dfd88ab493c8b19e4451

      Author:  jtlandis <jtlandis314@gmail.com> 

      Date: 2025-08-26 17:39:48 -0400

      Commit message:


	  
		
 adding docs
 

    

  
    

      Package: plyxp

      Commit: 28389c984a2db21d6e1a527ec28dcd128d4ca042

      Author:  jtlandis <jtlandis314@gmail.com> 

      Date: 2025-08-26 17:39:41 -0400

      Commit message:


	  
		
 trying to align with dplyr in that results are now grouped if object is
grouped
 

    

  
    

      Package: plyxp

      Commit: 077b95944db211e708d5544c0787b89f8119c5c0

      Author:  jtlandis <jtlandis314@gmail.com> 

      Date: 2025-08-26 17:38:51 -0400

      Commit message:


	  
		
 refactor manager to use an apply function. exposing a "get_chop()"
function for plyxp_mask
 

    

  
    

      Package: plyxp

      Commit: ad5a332f4fb5eeb7cdad7ffc0722f27d0946985e

      Author:  jtlandis <jtlandis314@gmail.com> 

      Date: 2025-08-26 15:10:12 -0400

      Commit message:


	  
		
 making an assignment function
 

    

  
    

      Package: plyxp

      Commit: d689cb77f4c15fd7c73aa7da93e9e7e81becff2f

      Author:  jtlandis <jtlandis314@gmail.com> 

      Date: 2025-08-26 15:08:46 -0400

      Commit message:


	  
		
 formatting
 

    

  
    

      Package: plyxp

      Commit: c5945ab69afe70aaf5a0a2015b9a9276422a81ab

      Author:  jtlandis <jtlandis314@gmail.com> 

      Date: 2025-08-26 15:07:42 -0400

      Commit message:


	  
		
 Update test_dplyr_group_by.R
 

    

  
    

      Package: plyxp

      Commit: f6d7698453d9c7cc59415b489cbabc851031a9c4

      Author:  jtlandis <jtlandis314@gmail.com> 

      Date: 2025-08-26 15:07:03 -0400

      Commit message:


	  
		
 Add result method to plyxp_mask and plyxp_manager classes. Using the
`result` method to pull ony specific values from mask within slice
method
 

    

  
    

      Package: plyxp

      Commit: c4b7a6feee6c3f9197cd2709088a796fdbb7f7c1

      Author:  jtlandis <jtlandis314@gmail.com> 

      Date: 2025-08-26 15:05:00 -0400

      Commit message:


	  
		
 Update connect_masks.R
 

    

  
    

      Package: plyxp

      Commit: 2104086fb5877f74256d2d5c32faf6e50fa2e01d

      Author:  jtlandis <jtlandis314@gmail.com> 

      Date: 2025-08-26 14:22:10 -0400

      Commit message:


	  
		
 deleting browser()
 

    

  
    

      Package: plyxp

      Commit: 0b917ae36ac4e47e910659e929f22812b1df3454

      Author:  jtlandis <jtlandis314@gmail.com> 

      Date: 2025-08-26 10:04:08 -0400

      Commit message:


	  
		
 Update NEWS
 

    

  
    

      Package: plyxp

      Commit: fed69e4854356f73d891b980d9ca650e1d3a1a6a

      Author:  jtlandis <jtlandis314@gmail.com> 

      Date: 2025-08-25 15:01:19 -0400

      Commit message:


	  
		
 Condensing down logic revolving around slicing the summarized Experiment
with `[`. Now `plyxp_slice_se()` will handle this case appropriately for
these opperations (even with groups)
 

    

  
    

      Package: plyxp

      Commit: 1ff3813772f8e41108c211c6ecd84f999c172af5

      Author:  jtlandis <jtlandis314@gmail.com> 

      Date: 2025-08-25 14:21:22 -0400

      Commit message:


	  
		
 Implement missing methods for PlySummarizedExperiment objects
 

    

  
    

      Package: punKEGGer

      Commit: 2d8e292a78946ddc4538448ac0282db6476d5ca0

      Author:  gdj <gdeanda@inmegen.edu.mx> 

      Date: 2025-08-27 10:47:39 -0600

      Commit message:


	  
		
 Bump version to 0.99.4
 

    

  
    

      Package: punKEGGer

      Commit: 2d01158b36aee17ae9d4712b973ad84f0aaf93f6

      Author:  gdj <gdeanda@inmegen.edu.mx> 

      Date: 2025-08-27 10:47:39 -0600

      Commit message:


	  
		
 Stop tracking IDE files
 

    

  
    

      Package: punKEGGer

      Commit: 3419ff5ac5f15a1573b1cf1908a8c41325fb6da7

      Author:  gdj <gdeanda@inmegen.edu.mx> 

      Date: 2025-08-27 10:13:10 -0600

      Commit message:


	  
		
 Add KEGG biocView, URL/BugReports, ORCID; bump to 0.99.3
 

    

  
    

      Package: punKEGGer

      Commit: e0259e6ceba256d5d10838976552ff31b54f501d

      Author:  gdj <gdeanda@inmegen.edu.mx> 

      Date: 2025-08-27 10:12:51 -0600

      Commit message:


	  
		
 Add KEGG biocView, URL/BugReports, ORCID; bump to 0.99.1
 

    

  
    

      Package: punKEGGer

      Commit: 0f6fad7fe3c02b36b6821163e6824644585b9f6e

      Author:  gdj <gdeanda@inmegen.edu.mx> 

      Date: 2025-08-27 10:12:14 -0600

      Commit message:


	  
		
 Add KEGG biocView, URL/BugReports, ORCID; bump to 0.99.1
 

    

  
    

      Package: punKEGGer

      Commit: 560d85e19af96d0706c145f5df2e2683ec6b25ca

      Author:  gdj <gdeanda@inmegen.edu.mx> 

      Date: 2025-08-27 10:10:58 -0600

      Commit message:


	  
		
 Add provenance script for extdata (KEGG + BioMart sources)
 

    

  
    

      Package: punKEGGer

      Commit: 5330bfac0adbe36d85a99fd9f736db2829dac7e4

      Author:  gdj <gdeanda@inmegen.edu.mx> 

      Date: 2025-08-27 10:05:18 -0600

      Commit message:


	  
		
 Fix LICENSE DCF stub for MIT license
 

    

  
    

      Package: punKEGGer

      Commit: caeab784ba194fc0f93757af2312e5a63dfa25be

      Author:  gdj <gdeanda@inmegen.edu.mx> 

      Date: 2025-08-27 10:04:43 -0600

      Commit message:


	  
		
 Stop tracking RStudio project files; keep locally via .gitignore
 

    

  
    

      Package: immunotation

      Commit: 8fdfeecc0dbc44e6af97414b648b0d2d397d63eb

      Author:  Katharina Imkeller <ag.imkeller@gmail.com> 

      Date: 2025-08-27 16:09:25 +0200

      Commit message:


	  
		
 fix decoding check
 

    

  
    

      Package: immunotation

      Commit: 21116bd1d5eb33748222fdf20adae6a193a5ef65

      Author:  Katharina Imkeller <ag.imkeller@gmail.com> 

      Date: 2025-08-25 13:22:18 +0200

      Commit message:


	  
		
 version correct 2
 

    

  
    

      Package: immunotation

      Commit: 0663fe32118ad981f15d0dfeae891f1947fc7777

      Author:  Katharina Imkeller <ag.imkeller@gmail.com> 

      Date: 2025-08-25 13:21:47 +0200

      Commit message:


	  
		
 version correct
 

    

  
    

      Package: immunotation

      Commit: 72931ca1c664a1e8a9c8405deef73a26366bb1bf

      Author:  Katharina Imkeller <ag.imkeller@gmail.com> 

      Date: 2025-08-25 13:14:57 +0200

      Commit message:


	  
		
 version 1.17.2
 

    

  
    

      Package: biomaRt

      Commit: f11e024327aab53d10e7e9c0b76d716c948f5fc0

      Author:  Hugo Gruson <10783929+Bisaloo@users.noreply.github.com> 

      Date: 2025-08-27 15:49:48 +0200

      Commit message:


	  
		
 Recognize ENSEMBL_MART_ENSEMBL as ensembl in martCheck() (#131)

 

    

  
    

      Package: Pigengene

      Commit: 126d6fd9eaaa2d0e12eb4a1cc0ae40eab975bc22

      Author:  Habil Zare <zare@uthscsa.edu> 

      Date: 2025-08-27 08:50:33 -0500

      Commit message:


	  
		
 Move
 

    

  
    

      Package: biomaRt

      Commit: e93e00b00509e3b92e2d1628d6112c93acba6057

      Author:  Hugo Gruson <10783929+Bisaloo@users.noreply.github.com> 

      Date: 2025-08-26 16:32:58 +0200

      Commit message:


	  
		
 Convert roxygen documentation to markdown syntax (#135)

 

    

  
    

      Package: Rarr

      Commit: c4c61c4de85ee1aa57b9c12723084c44761b3206

      Author:  Hugo Gruson <10783929+Bisaloo@users.noreply.github.com> 

      Date: 2025-08-27 13:22:52 +0200

      Commit message:


	  
		
 Remove unused stringr dependency (#34)

 

    

  
    

      Package: Rarr

      Commit: 63932ea88fffed39a168b13b082c1acef796fa59

      Author:  Hugo Gruson <10783929+Bisaloo@users.noreply.github.com> 

      Date: 2025-08-27 13:21:35 +0200

      Commit message:


	  
		
 Support "other" numeric datatype

 

    

  
    

      Package: Rarr

      Commit: 1c36508071fd7354efeff26eba62db969e8be0e0

      Author:  Hugo Gruson <10783929+Bisaloo@users.noreply.github.com> 

      Date: 2025-08-27 13:16:12 +0200

      Commit message:


	  
		
 Use pretty = 4 rather than pretty = TRUE

Default is 2 spaces.
4 spaces is consistent with python and previous versions of this package.
 

    

  
    

      Package: Rarr

      Commit: 6dc676877f9b193c965853ce20058f4545c9385b

      Author:  Hugo Gruson <10783929+Bisaloo@users.noreply.github.com> 

      Date: 2025-08-26 17:23:27 +0200

      Commit message:


	  
		
 Use curl directly rather than httr (#31)

 

    

  
    

      Package: Rarr

      Commit: 5acac5541bf110927bdfa8674992dd08053f3e9b

      Author:  Hugo Gruson <10783929+Bisaloo@users.noreply.github.com> 

      Date: 2025-08-26 16:25:17 +0200

      Commit message:


	  
		
 Document lintr changes in NEWS
 

    

  
    

      Package: Rarr

      Commit: fc4bdeea9ea844adc547d3eccd5cc8e6d6437c8b

      Author:  Hugo Gruson <10783929+Bisaloo@users.noreply.github.com> 

      Date: 2025-08-26 14:43:03 +0200

      Commit message:


	  
		
 Import selectively from jsonlite namespace
 

    

  
    

      Package: Rarr

      Commit: d48b0a2efb98baa42f99fa502618a04390d86934

      Author:  Hugo Gruson <10783929+Bisaloo@users.noreply.github.com> 

      Date: 2025-08-26 12:53:19 +0200

      Commit message:


	  
		
 Use write_json() directly and rm .format_json()
 

    

  
    

      Package: Rarr

      Commit: ab23ae5d775cfac24a70b4802bb8970cf9ed9388

      Author:  Hugo Gruson <10783929+Bisaloo@users.noreply.github.com> 

      Date: 2025-08-26 13:41:52 +0200

      Commit message:


	  
		
 Add lintr config file and GitHub Action
 

    

  
    

      Package: Rarr

      Commit: 0d8529421209a1114866caff2991c1fc644b2b58

      Author:  Hugo Gruson <10783929+Bisaloo@users.noreply.github.com> 

      Date: 2025-08-26 13:39:43 +0200

      Commit message:


	  
		
 Reduce nesting
 

    

  
    

      Package: Rarr

      Commit: 5c75d4088c61ade1961836ce147c1bdb6fec7171

      Author:  Hugo Gruson <10783929+Bisaloo@users.noreply.github.com> 

      Date: 2025-08-26 13:39:26 +0200

      Commit message:


	  
		
 Add nolint comments for false positives
 

    

  
    

      Package: Rarr

      Commit: 46a63b80c0e237e8b799197ec392b07cc5a4899b

      Author:  Hugo Gruson <10783929+Bisaloo@users.noreply.github.com> 

      Date: 2025-08-26 14:03:52 +0200

      Commit message:


	  
		
 Use stop() early in the function
 

    

  
    

      Package: Rarr

      Commit: d165fd50bbf26b55462b26885814c476cd2b9a98

      Author:  Hugo Gruson <10783929+Bisaloo@users.noreply.github.com> 

      Date: 2025-08-26 14:15:12 +0200

      Commit message:


	  
		
 Use paste() where appropriate
 

    

  
    

      Package: Rarr

      Commit: b753a4fc025db460a2d561a471b91dafb517fe08

      Author:  Hugo Gruson <10783929+Bisaloo@users.noreply.github.com> 

      Date: 2025-08-26 13:26:44 +0200

      Commit message:


	  
		
 Remove commented code
 

    

  
    

      Package: Rarr

      Commit: fa25b0ba221ac298d0a8267cb5775f515e1b0805

      Author:  Hugo Gruson <10783929+Bisaloo@users.noreply.github.com> 

      Date: 2025-08-26 13:10:16 +0200

      Commit message:


	  
		
 Fix whitespace in Rmd documents
 

    

  
    

      Package: Rarr

      Commit: 603f507b275447582dd02aaf4e37eb27a6bc88dd

      Author:  Hugo Gruson <10783929+Bisaloo@users.noreply.github.com> 

      Date: 2025-08-26 12:43:13 +0200

      Commit message:


	  
		
 Avoid exists() approach
 

    

  
    

      Package: Rarr

      Commit: 51a6ed40b14af0fab0c1c5a08549db8f3df62c43

      Author:  Hugo Gruson <10783929+Bisaloo@users.noreply.github.com> 

      Date: 2025-08-26 12:42:48 +0200

      Commit message:


	  
		
 Set on.exit() next to connection opening step
 

    

  
    

      Package: Rarr

      Commit: f5494c5fe4a5fbc60990daf891398d6ba340b732

      Author:  Hugo Gruson <10783929+Bisaloo@users.noreply.github.com> 

      Date: 2025-08-26 11:44:13 +0200

      Commit message:


	  
		
 Simplify raw vector initialization
 

    

  
    

      Package: Rarr

      Commit: 9738a20ae5d0ae82cde4de14a8492a5256975378

      Author:  Hugo Gruson <10783929+Bisaloo@users.noreply.github.com> 

      Date: 2025-08-26 11:43:58 +0200

      Commit message:


	  
		
 Fix typo
 

    

  
    

      Package: Rarr

      Commit: 4ff3273e5ce9166482b58ac1408e267023ac7093

      Author:  Hugo Gruson <10783929+Bisaloo@users.noreply.github.com> 

      Date: 2025-08-25 10:13:58 +0200

      Commit message:


	  
		
 Use %||% where appropriate
 

    

  
    

      Package: Rarr

      Commit: 00d5a210190d17f1820d17e20f4d9daee264f12c

      Author:  Hugo Gruson <10783929+Bisaloo@users.noreply.github.com> 

      Date: 2025-08-23 20:40:17 +0200

      Commit message:


	  
		
 Simplify zarray creation
 

    

  
    

      Package: Rarr

      Commit: 586ee23833ad988d3d15bb408cf6ce2bec53c473

      Author:  Hugo Gruson <10783929+Bisaloo@users.noreply.github.com> 

      Date: 2025-08-23 20:26:10 +0200

      Commit message:


	  
		
 Get boolean directly without ifelse()
 

    

  
    

      Package: Rarr

      Commit: b4f9b537c98e2ac6dd555ccf9c16f27472cc04a4

      Author:  Hugo Gruson <10783929+Bisaloo@users.noreply.github.com> 

      Date: 2025-08-23 20:25:53 +0200

      Commit message:


	  
		
 Use fixed = TRUE in regexes where relevant
 

    

  
    

      Package: Rarr

      Commit: d34cbd6d63a3b1a6b15d10f2d498b80f931a01a0

      Author:  Hugo Gruson <10783929+Bisaloo@users.noreply.github.com> 

      Date: 2025-08-18 10:47:06 +0200

      Commit message:


	  
		
 Remove unnecessary c()
 

    

  
    

      Package: Rarr

      Commit: 61d5a1697a27ce204ae3bdf78b1d2f54fd583e35

      Author:  Hugo Gruson <10783929+Bisaloo@users.noreply.github.com> 

      Date: 2025-08-18 10:46:54 +0200

      Commit message:


	  
		
 Use lengths()
 

    

  
    

      Package: Rarr

      Commit: 28cf5969e411debd8248417852b907901430763c

      Author:  Hugo Gruson <10783929+Bisaloo@users.noreply.github.com> 

      Date: 2025-08-15 15:32:56 +0200

      Commit message:


	  
		
 Remove unused variable
 

    

  
    

      Package: Rarr

      Commit: 0b1c9debdbcff9cea352191858074521fa37b83e

      Author:  Hugo Gruson <10783929+Bisaloo@users.noreply.github.com> 

      Date: 2025-07-25 19:08:55 +0200

      Commit message:


	  
		
 Fix variable initialization

rep() doesn't have an n= argument and this call currently always returns FALSE (length 1)
 

    

  
    

      Package: Rarr

      Commit: c834110002eb354e278f67cda17c66adbb3c4b7d

      Author:  Hugo Gruson <10783929+Bisaloo@users.noreply.github.com> 

      Date: 2025-07-18 19:40:12 +0200

      Commit message:


	  
		
 Use double logical operators in if
 

    

  
    

      Package: Rarr

      Commit: a307ad9151f62e6635d1802360311375df78e249

      Author:  Hugo Gruson <10783929+Bisaloo@users.noreply.github.com> 

      Date: 2025-08-26 14:32:03 +0200

      Commit message:


	  
		
 Convert to upper or lower only once
 

    

  
    

      Package: Rarr

      Commit: f439833f58dad0b4647adcf20c50981099bebb83

      Author:  Hugo Gruson <10783929+Bisaloo@users.noreply.github.com> 

      Date: 2025-08-26 12:43:59 +0200

      Commit message:


	  
		
 Set R CMD check to a stricter setting and fix NOTEs and WARNINGs (#27)

 

    

  
    

      Package: Rarr

      Commit: 1118f8cb1bfbafb2323591e7010fb818be838719

      Author:  Hugo Gruson <10783929+Bisaloo@users.noreply.github.com> 

      Date: 2025-08-26 10:58:30 +0200

      Commit message:


	  
		
 Consolidate NEWS under a single version header (#29)

 

    

  
    

      Package: Rarr

      Commit: c4766950ecda0a526ebed6fb5a3df0a7cce4a841

      Author:  Artür Manukyan <artur-man@hotmail.com> 

      Date: 2025-08-25 17:11:10 +0200

      Commit message:


	  
		
 add support for reading, writing and updating attributes (#19)

Co-authored-by: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
 

    

  
    

      Package: Rarr

      Commit: 78c8cc05201aea2be05eee861d0b5bc21c112220

      Author:  Hugo Gruson <10783929+Bisaloo@users.noreply.github.com> 

      Date: 2025-08-25 11:41:14 +0200

      Commit message:


	  
		
 Add air commit to git-blame-ignore-revs

To keep git blame simple and clean
 

    

  
    

      Package: Rarr

      Commit: 18cdd7b4142a9485127b71c384aac69556025a47

      Author:  Hugo Gruson <10783929+Bisaloo@users.noreply.github.com> 

      Date: 2025-08-22 16:50:15 +0200

      Commit message:


	  
		
 Set up and run air (#26)

 

    

  
    

      Package: Rarr

      Commit: 47d52da77ac581d3357b8faac852cb3949f10905

      Author:  Hugo Gruson <10783929+Bisaloo@users.noreply.github.com> 

      Date: 2025-08-22 14:47:36 +0200

      Commit message:


	  
		
 Expand .normalize_zarr_path() tests and fix edge cases (#25)

 

    

  
    

      Package: smoppix

      Commit: adeab581d5f43b6a30dc6444b293a30e38265e79

      Author:  stijn <stijn.hawinkel@psb.ugent.be> 

      Date: 2025-08-27 11:16:45 +0200

      Commit message:


	  
		
 export loadbalancebplapply in news and description
 

    

  
    

      Package: smoppix

      Commit: 3a54c8dfef75423f400219e5c7aab9dabacc1279

      Author:  stijn <stijn.hawinkel@psb.ugent.be> 

      Date: 2025-08-27 11:15:27 +0200

      Commit message:


	  
		
 export loadBalanceBplapply for use in other packages
 

    

  
    

      Package: gDRimport

      Commit: 9a5a6dda54f7d8182dfb27a275b5f30b4791c91a

      Author:  Bartek <32614650+bczech@users.noreply.github.com> 

      Date: 2025-08-27 11:07:35 +0200

      Commit message:


	  
		
 Merge pull request #107 from gdrplatform/GDR-771

Gdr 771 

    

  
    

      Package: gDRimport

      Commit: 8564d3fd7a02b3eb9dfc09239f9ab94565f09e44

      Author:  Bartek Czech <bartosz.w.czech@gmail.com> 

      Date: 2025-08-27 10:06:56 +0200

      Commit message:


	  
		
 ci: trigger build
 

    

  
    

      Package: gDRimport

      Commit: dd64ed881ea0abeb66c09f876747ec529d4803cd

      Author:  Bartek Czech <bartosz.w.czech@gmail.com> 

      Date: 2025-08-26 16:08:51 +0200

      Commit message:


	  
		
 ci: trigger build
 

    

  
    

      Package: gDRimport

      Commit: a6d8b2a3d9348536cbb4e7ce0f682fa556673a5c

      Author:  Bartek Czech <bartosz.w.czech@gmail.com> 

      Date: 2025-08-26 16:08:21 +0200

      Commit message:


	  
		
 ci: trigger build
 

    

  
    

      Package: gDRimport

      Commit: ff1e1bb2e04c511b7233e62137e4aad0b6d46a4f

      Author:  Bartek <32614650+bczech@users.noreply.github.com> 

      Date: 2025-08-21 09:24:22 +0200

      Commit message:


	  
		
 refactor: Update load_files.R 

    

  
    

      Package: gDRimport

      Commit: c02dd6c5af03d935485a1e31c62d7e6aabbd261c

      Author:  Bartek Czech <bartosz.w.czech@gmail.com> 

      Date: 2025-08-12 08:20:32 +0200

      Commit message:


	  
		
 chore: bump version and update NEWS.md
 

    

  
    

      Package: gDRimport

      Commit: 860d1a541b89190651d711c0ba45980d48d44bbd

      Author:  Bartek Czech <bartosz.w.czech@gmail.com> 

      Date: 2025-08-12 08:20:28 +0200

      Commit message:


	  
		
 fix: usage of ifelse
 

    

  
    

      Package: gDRutils

      Commit: 7911c112086d0b92c1267261153b0fefcc567dfa

      Author:  Bartek <32614650+bczech@users.noreply.github.com> 

      Date: 2025-08-27 11:07:29 +0200

      Commit message:


	  
		
 Merge pull request #172 from gdrplatform/GDR-771

Gdr 771 

    

  
    

      Package: gDRutils

      Commit: 35b969c8bf5d2176709b8ecfc57d040ed293792b

      Author:  Bartek Czech <bartosz.w.czech@gmail.com> 

      Date: 2025-08-27 10:09:00 +0200

      Commit message:


	  
		
 ci: trigger build
 

    

  
    

      Package: gDRutils

      Commit: 90cdac64a238fba9c74725909b399bd8e84eeb72

      Author:  Bartek Czech <bartosz.w.czech@gmail.com> 

      Date: 2025-08-26 16:09:20 +0200

      Commit message:


	  
		
 ci: trigger build
 

    

  
    

      Package: gDRutils

      Commit: f7bf7c70df30c567ca26407703504888bccc49ad

      Author:  Bartek <32614650+bczech@users.noreply.github.com> 

      Date: 2025-08-21 09:18:50 +0200

      Commit message:


	  
		
 refactor: Update fit_curves.R 

    

  
    

      Package: gDRutils

      Commit: 3d36b43c1ffb2948f6fc8666d22876a063d14af4

      Author:  Bartek Czech <bartosz.w.czech@gmail.com> 

      Date: 2025-08-12 07:46:11 +0200

      Commit message:


	  
		
 chore: bump version and update NEWS.md
 

    

  
    

      Package: gDRutils

      Commit: 071e05fab457b4451881a3cf4f1dec67bc93c98a

      Author:  Bartek Czech <bartosz.w.czech@gmail.com> 

      Date: 2025-08-12 07:45:35 +0200

      Commit message:


	  
		
 refactor: fix usage of ifelse
 

    

  
    

      Package: scGraphVerse

      Commit: 0b6084409f0a7ea950bbe0fe257fcf60c340bd44

      Author:  francescoc <francesco.cecerengs@gmail.com> 

      Date: 2025-08-27 10:22:13 +0200

      Commit message:


	  
		
 fix count_matrices to 2
 

    

  
    

      Package: scGraphVerse

      Commit: 4539d637b39c545634ca787a59f1a988905d6f8e

      Author:  francescoc <francesco.cecerengs@gmail.com> 

      Date: 2025-08-27 09:49:08 +0200

      Commit message:


	  
		
 fix WARN time
 

    

  
    

      Package: SeqArray

      Commit: 4cc25c2cf8ac710174c922c0acf099b86d2beb6f

      Author:  Xiuwen Zheng <zhengxwen@gmail.com> 

      Date: 2025-08-26 23:27:11 -0500

      Commit message:


	  
		
 improved workload balancing
 

    

  
    

      Package: EnrichmentBrowser

      Commit: 2ce1126725e4d694e2e377aebd84e628cdd4b5d4

      Author:  lgeistlinger <ludwig.geistlinger@gmail.com> 

      Date: 2025-08-26 22:46:53 -0400

      Commit message:


	  
		
 getGenesets: fix msigdb mouse collections
 

    

  
    

      Package: EnrichmentBrowser

      Commit: 700e85006f7dee6b98bd0ff5dbefd5d1208e1d7e

      Author:  lgeistlinger <ludwig.geistlinger@gmail.com> 

      Date: 2025-08-26 22:34:56 -0400

      Commit message:


	  
		
 getGenesets: fix msigdb mouse collections
 

    

  
    

      Package: EnrichmentBrowser

      Commit: aa9388bbf540528de1b928479e737c8893f10ef4

      Author:  lgeistlinger <ludwig.geistlinger@gmail.com> 

      Date: 2025-08-18 16:30:24 -0400

      Commit message:


	  
		
 pull upstream changes
 

    

  
    

      Package: EnrichmentBrowser

      Commit: bec2c849fcd40bfc542ba82238af1a6cbb706a58

      Author:  lgeistlinger <ludwig.geistlinger@gmail.com> 

      Date: 2025-07-10 11:15:01 -0400

      Commit message:


	  
		
 Bump version and update date
 

    

  
    

      Package: EnrichmentBrowser

      Commit: d081f32513ec5f63689999edf2f83484060f2960

      Author:  lgeistlinger <ludwig.geistlinger@gmail.com> 

      Date: 2025-07-10 10:49:24 -0400

      Commit message:


	  
		
 Bump version and update date
 

    

  
    

      Package: scRNAseqApp

      Commit: 0b21d81422b0b64c2d31d27d9fc6452cb226dd99

      Author:  Jianhong Ou <jianhong.ou@gmail.com> 

      Date: 2025-08-26 20:59:40 -0400

      Commit message:


	  
		
 add support for dark mode.
 

    

  
    

      Package: scGraphVerse

      Commit: ff7668fcede03a98655b7e04a87c7ad69e4a9c59

      Author:  francescoc <francesco.cecerengs@gmail.com> 

      Date: 2025-08-27 00:47:59 +0200

      Commit message:


	  
		
 fix compare_consensus example
 

    

  
    

      Package: scGraphVerse

      Commit: 10e47e984922fb2365a4fdef66d533ac4c466dd6

      Author:  francescoc <francesco.cecerengs@gmail.com> 

      Date: 2025-08-27 00:07:30 +0200

      Commit message:


	  
		
 fix time WARN
 

    

  
    

      Package: cellmig

      Commit: c94f7bcfcbcdda6cc50bf07714b78444b72eaae1

      Author:  snaketron <simo.kitanovski@uni-due.de> 

      Date: 2025-08-26 23:38:24 +0200

      Commit message:


	  
		
 more tests, dev-cov >80%
 

    

  
    

      Package: scGraphVerse

      Commit: db29f1e9d52a0769561bc76ffcd765b41e88aefc

      Author:  francescoc <francesco.cecerengs@gmail.com> 

      Date: 2025-08-26 23:36:09 +0200

      Commit message:


	  
		
 fix selgene example
 

    

  
    

      Package: SETA

      Commit: aab1357007bec58b198f2127dcaa719f7f24b903

      Author:  kylekimler <kylejkimler@gmail.com> 

      Date: 2025-08-26 14:02:58 -0400

      Commit message:


	  
		
 version bump and remote setup
 

    

  
    

      Package: SETA

      Commit: 98606b59a3149c4c3f54a8b5dc2d207b30c81746

      Author:  kylekimler <kylejkimler@gmail.com> 

      Date: 2025-08-22 17:56:22 -0400

      Commit message:


	  
		
 special char cleanup
 

    

  
    

      Package: SETA

      Commit: df14ec4069feb9cba43ab685d2760a54a8a5e71f

      Author:  kylekimler <kylejkimler@gmail.com> 

      Date: 2025-08-22 17:48:29 -0400

      Commit message:


	  
		
 ubuntu latex ERROR updates and other notes from bioconductor
 

    

  
    

      Package: scRNAseqApp

      Commit: 7e14a8f87825cc387581ec3da2bdccb59cf0efaa

      Author:  Jianhong Ou <jianhong.ou@gmail.com> 

      Date: 2025-08-26 10:55:22 -0400

      Commit message:


	  
		
 update search table when updateGeneExprPlot.
 

    

  
    

      Package: scRNAseqApp

      Commit: db52296c907ed758fa76f7f9ef802c91dbfcff65

      Author:  Jianhong Ou <jianhong.ou@gmail.com> 

      Date: 2025-08-26 09:53:26 -0400

      Commit message:


	  
		
 remove duplicated removeModal()
 

    

  
    

      Package: scRNAseqApp

      Commit: bed2dd71b121b39af6bbd5d447020c5538190046

      Author:  Jianhong Ou <jianhong.ou@gmail.com> 

      Date: 2025-08-26 09:42:32 -0400

      Commit message:


	  
		
 Add support for config.dcf file
 

    

  
    

      Package: gDRcore

      Commit: 440ba6de8647b91b268f061cb20e8de0d2a8c7cb

      Author:  Bartek <32614650+bczech@users.noreply.github.com> 

      Date: 2025-08-26 16:47:20 +0200

      Commit message:


	  
		
 Merge pull request #182 from gdrplatform/GDR-771

Gdr 771 

    

  
    

      Package: gDRcore

      Commit: 7c301bdef1f640b41ee2d64fd864505f0652785f

      Author:  Bartek Czech <bartosz.w.czech@gmail.com> 

      Date: 2025-08-26 16:09:04 +0200

      Commit message:


	  
		
 ci: trigger build
 

    

  
    

      Package: gDRcore

      Commit: 39b49720229d4465e7c883adfede59d8cb85a3ff

      Author:  Bartek <32614650+bczech@users.noreply.github.com> 

      Date: 2025-08-21 09:34:52 +0200

      Commit message:


	  
		
 refactor: Update normalize_SE.R 

    

  
    

      Package: gDRcore

      Commit: 13aca1e789dfa1826e03fa0330d77b9745b4b075

      Author:  Bartek <32614650+bczech@users.noreply.github.com> 

      Date: 2025-08-21 09:32:42 +0200

      Commit message:


	  
		
 refactor: Update fit_SE.combinations.R 

    

  
    

      Package: gDRcore

      Commit: 19fdb4619b0980c5c04f9ec2469805d560798837

      Author:  Bartek Czech <bartosz.w.czech@gmail.com> 

      Date: 2025-08-12 08:00:18 +0200

      Commit message:


	  
		
 chore: bump version and update NEWS.md
 

    

  
    

      Package: gDRcore

      Commit: abf92d4c798ee73277b3ec4796fb631a8b5efa36

      Author:  Bartek Czech <bartosz.w.czech@gmail.com> 

      Date: 2025-08-12 07:59:37 +0200

      Commit message:


	  
		
 fix: usage of ifelse
 

    

  
    

      Package: MSstatsShiny

      Commit: fdef91afbfac6637ca78197bb37ea898b502a0fa

      Author:  tonywu1999 <anthonywu92@gmail.com> 

      Date: 2025-08-26 10:28:04 -0400

      Commit message:


	  
		
 Bump version from 1.11.3 to 1.11.4 

    

  
    

      Package: MSstatsShiny

      Commit: 882ff3fdf10e1fed6e4ee562f28791d61eaf8566

      Author:  tonywu1999 <anthonywu92@gmail.com> 

      Date: 2025-08-26 10:27:06 -0400

      Commit message:


	  
		
 fix(download-button): Add error handling for download button (#112)

 

    

  
    

      Package: MSstatsShiny

      Commit: a3205e305e0f7a1769cf64590895532d49d6fa8b

      Author:  tonywu1999 <anthonywu92@gmail.com> 

      Date: 2025-08-26 10:10:58 -0400

      Commit message:


	  
		
 feat(network-interpretation): Add button to download network analysis code (#111)

 

    

  
    

      Package: damidBind

      Commit: 15fe5a105d38572382d284cc71c3102050b3eb48

      Author:  Owen Marshall <owen.marshall@utas.edu.au> 

      Date: 2025-08-26 11:58:23 +0000

      Commit message:


	  
		
 Added data provenance markdown detailing generation pipeline for files in inst/extdata
 

    

  
    

      Package: spatialFDA

      Commit: fc15443378ea7c2ca7e42b1b0b0cd320b8fc544a

      Author:  mjemons <martin.emons@gmail.com> 

      Date: 2025-08-26 13:30:06 +0200

      Commit message:


	  
		
 new weighting, bubble plot
 

    

  
    

      Package: MSnbase

      Commit: ec1e05c5e1b87d323bc4bbd70f0538ad4ab93952

      Author:  Laurent Gatto <lgatto@protonmail.ch> 

      Date: 2025-08-26 13:16:43 +0200

      Commit message:


	  
		
 fix PSMatch dependency version
 

    

  
    

      Package: Pedixplorer

      Commit: 34518cb7f59a244a3b0e1cc892e5db5b80cbde03

      Author:  Louis Le Nézet <58640615+LouisLeNezet@users.noreply.github.com> 

      Date: 2025-08-26 12:40:01 +0200

      Commit message:


	  
		
 Add Ggplot legend (#36)

* Simplify message kindepth error

* Try fix legend ggplot

* Fix ggplot legend

* Update documentation and tests

* Update test plot legend

* Update version and News

* Add missing new line

* Fix vignettte

* Fix vignette

---------

Co-authored-by: Louis Le Nezet <louislenezet@gamil.com> 

    

  
    

      Package: Pedixplorer

      Commit: b21a6dcbf80300575c308982e82bde0dcc516067

      Author:  Louis Le Nézet <58640615+LouisLeNezet@users.noreply.github.com> 

      Date: 2025-07-24 10:19:43 +0200

      Commit message:


	  
		
 Update to Bioconductor (#35)

Co-authored-by: Louis Le Nezet <louislenezet@gamil.com> 

    

  
    

      Package: SpectriPy

      Commit: e09cc13033857fb2ace2350af0fbdd05fed06e1a

      Author:  Johannes Rainer <5506112+jorainer@users.noreply.github.com> 

      Date: 2025-08-26 07:56:00 +0200

      Commit message:


	  
		
 Merge pull request #82 from rformassspectrometry/py_require

Use reticulate's py_require() to manage the Python installation and environment 

    

  
    

      Package: SpectriPy

      Commit: 8a8c9b23b5f063b822906e3f84b3e0c86b306035

      Author:  jorainer <johannes.rainer@gmail.com> 

      Date: 2025-08-26 07:36:10 +0200

      Commit message:


	  
		
 Address Marilyn's comments
 

    

  
    

      Package: SpectriPy

      Commit: 6096093611c0397f25e6a8b8ad8c25a4a5aa512c

      Author:  jorainer <johannes.rainer@gmail.com> 

      Date: 2025-08-25 15:17:48 +0200

      Commit message:


	  
		
 Remove links to BioC release
 

    

  
    

      Package: SpectriPy

      Commit: 93b4fe60a5f4325882a99ed2a999291601a5547e

      Author:  jorainer <johannes.rainer@gmail.com> 

      Date: 2025-08-22 08:49:13 +0200

      Commit message:


	  
		
 Merge remote-tracking branch 'origin/main' into py_require
 

    

  
    

      Package: SpectriPy

      Commit: 81004544045e3e6c7084cec0f157ca6257e4a4d5

      Author:  jorainer <johannes.rainer@gmail.com> 

      Date: 2025-08-22 08:02:09 +0200

      Commit message:


	  
		
 docs: complete installation and troubleshooting
 

    

  
    

      Package: SpectriPy

      Commit: eb653805d13ebf7fff625f12d1d607cab9007193

      Author:  jorainer <johannes.rainer@gmail.com> 

      Date: 2025-08-22 07:19:12 +0200

      Commit message:


	  
		
 docs: add/expand installation instructions
 

    

  
    

      Package: SpectriPy

      Commit: 47f3f38c8f864e154d0b5c0995962d0fdfb09e2e

      Author:  jorainer <johannes.rainer@gmail.com> 

      Date: 2025-08-21 07:38:53 +0200

      Commit message:


	  
		
 tests: add unit tests for package loading
 

    

  
    

      Package: SpectriPy

      Commit: d435ffc7e94b4af7c547f1b59b9aff6137a58942

      Author:  Johannes Rainer <5506112+jorainer@users.noreply.github.com> 

      Date: 2025-07-09 10:21:26 +0200

      Commit message:


	  
		
 Merge pull request #80 from rformassspectrometry/jomain

Add support for `setBackend` 

    

  
    

      Package: SpectriPy

      Commit: d442b7865002c8ac19d17dfc2dd23219a3f42e9b

      Author:  jorainer <johannes.rainer@gmail.com> 

      Date: 2025-06-18 16:42:47 +0200

      Commit message:


	  
		
 feat: add support for parameter data to backendInitialize

- Add support for parameter `data` to `backendInitialize,MsBackendPy`: enables
  changing the backend of a `Spectra` object with `setBackend()` to a
  `MsBackendPy`.
 

    

  
    

      Package: SpectriPy

      Commit: 572b41dfee75e84583e15a6729d79d598da0ac3d

      Author:  jorainer <johannes.rainer@gmail.com> 

      Date: 2025-06-18 06:25:48 +0200

      Commit message:


	  
		
 Merge branch 'main' into jomain
 

    

  
    

      Package: SpectriPy

      Commit: d3cb4b398b58b4e7beb2fb4ce9715e87b76eb842

      Author:  jorainer <johannes.rainer@gmail.com> 

      Date: 2025-05-22 07:40:42 +0200

      Commit message:


	  
		
 tests: refactor zzz.R and add unit tests
 

    

  
    

      Package: SpectriPy

      Commit: b6d0297448f9426fe73d43793f92812a01286e11

      Author:  jorainer <johannes.rainer@gmail.com> 

      Date: 2025-05-21 16:23:49 +0200

      Commit message:


	  
		
 Merge branch 'bioc_submission' into jomain
 

    

  
    

      Package: SpectriPy

      Commit: 41f965baf58542faf92dcb2ab3f377ea88fccb51

      Author:  jorainer <johannes.rainer@gmail.com> 

      Date: 2025-05-21 08:19:11 +0200

      Commit message:


	  
		
 refactor: package loading
 

    

  
    

      Package: SpectriPy

      Commit: 7d6456d18887ce1c1dfc2e12fb48f1bd330c877a

      Author:  jorainer <johannes.rainer@gmail.com> 

      Date: 2025-05-20 08:19:25 +0200

      Commit message:


	  
		
 tests: add more unit tests
 

    

  
    

      Package: SpectriPy

      Commit: ac0d0b0c521c590aff452a17ce16d6e8d6aa883e

      Author:  jorainer <johannes.rainer@gmail.com> 

      Date: 2025-05-05 07:38:34 +0200

      Commit message:


	  
		
 tests: add unit tests for zzz.R
 

    

  
    

      Package: SpectriPy

      Commit: 3e8d07bc88fd9d524f9580ad31228f5b6cad75a4

      Author:  jorainer <johannes.rainer@gmail.com> 

      Date: 2025-05-05 06:44:01 +0200

      Commit message:


	  
		
 Merge branch 'main' into jomain
 

    

  
    

      Package: SpectriPy

      Commit: 22d5f81a89f976179a051896ed3b19b7028b38f9

      Author:  jorainer <johannes.rainer@gmail.com> 

      Date: 2025-04-22 07:50:04 +0200

      Commit message:


	  
		
 feat: add support for data parameter in backendInitialize()
 

    

  
    

      Package: SpectriPy

      Commit: cee534239964a6d2ac60a988d59e64f5c2f8f667

      Author:  jorainer <johannes.rainer@gmail.com> 

      Date: 2025-04-18 08:47:36 +0200

      Commit message:


	  
		
 feat: backendInitialize to support data parameter
 

    

  
  


</div>

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