Bioconductor - Packages: GIT Log

Home
Developers
Packages: GIT Log

Bioconductor has moved to GIT for contributed packages; the subversion logs are no longer active. The following are the git logs.

GIT Logs

This is a list of recent commits to git.bioconductor.org, the devel(development) branch of the Bioconductor GIT repository.

This list is also available as an RSS feed (devel branch), and RSS feed (release branch)

Package: HoloFoodR
Commit: 077f835ba94fa7f36d5e12d611670b4d5f29d2e5
Author: Tuomas Borman <60338854+TuomasBorman@users.noreply.github.com>
Date: 2025-04-03 19:57:49 +0300
Commit message:

 Fix error caused by httr2::url_parse (#41)

Package: msa
Commit: a7b5ecd0f1f98bc8d024bb152eada2a2149d6cbc
Author: UBod <ulrich@bodenhofer.com>
Date: 2025-04-03 18:54:46 +0200
Commit message:

 update of gc; some fixes; version number bumped to 1.39.3

Package: annotation
Commit: 7b6b920e90973f20dbe723225182496ebefddfe7
Author: lshep <lori.shepherd@roswellpark.org>
Date: 2025-04-03 12:52:36 -0400
Commit message:

 Update hub code that is incorrect

Package: ExpressionAtlas
Commit: 9c3cc424f4cc3b9b228b26a1424e827bf9af2122
Author: Pedro Madrigal <pmadrigal@ebi.ac.uk>
Date: 2025-04-03 17:33:24 +0100
Commit message:

 Merge remote-tracking branch 'upstream/master'

# Conflicts:
#	DESCRIPTION

Package: ExpressionAtlas
Commit: f848f43639e8ed260311b9d9a10b8ee58a59c152
Author: Pedro Madrigal <8195212+pmb59@users.noreply.github.com>
Date: 2025-04-03 17:25:23 +0100
Commit message:

 Add functionality to search, retrieve and visualise data from SC Expression Atlas (#12)

* add support functions for SCEA

* add function 'getAtlasSCExperiment'

* add temp comments for development

* adds getExperimentType function to determine experiment type

* changes getExperimentType function to internal function

* adds function getNormalisedAtlasExpression to retrieve normalised data (TPMs and FPKMs) for rna-seq baseline experiments

* fixing R Bioconductor test fix

* fixes var name

* replaces assay id with assay labels

* adds heatmapAtlasExperiment function

* removing unwanted variable

* adds supporting information for heatmapAtlasExperiment

* updates documentation for heatmapAtlasExperiment

* getNormalisedAtlasExpression function now supports downloading CPM

* adds example for CPM data download and plotting

* comments

* adds vignette

* Calcuates CPM and returns mean values for replicate

* add functions getAtlasSCExperiment( experimentAccession ) and .retryDownload /.downloadExpressionFile due to file download random fails from ftp. Also implement similar logic in getAtlasExperiment()

* add getAtlasSCExperiment.Rd

* add getAtlasSCExperiment() to vignette, add authors and edit structure

* add plotDimRedSCAtlasExperiment() and plotDimRedSCAtlasExperiment.Rd

* Major restructuring on how experiment search is performed. Added support for SCXA

* edit Title of the package; rm unnecessary comments

* add examples of single-cell exp search to the package Vignette

* renaming function and argument appropriately for wider use, changing warning message

* adds getAnalysticsDifferentialAtlasExpression function to fetch analytics for differential expreiments

* Implement a simple retry mechanism for anndata download

* few improvements to package vignette

* rename internal function to .download_anndata_with_retry

* adds functionality to replace contrasts id with names/description

* add ontology-based query search against the SCXA cell-type wheel

* adds volcanoDifferentialAtlasExperiment to create volcano plots

* fix heatmapAtlasExperiment() and edit vignette

* fix volcanoDifferentialAtlasExperiment; fix Warnings; improve vignette

* add function heatmapSCAtlasExperiment(...)

* add function dotPlotSCAtlasExperiment(...)

* add reshape2 to imports

* add GTEX vignette

* add single-cell vignette, edit other vignettes and man help.

* As a special case, any package with version x.99.z is bumped to (x+1) . 0 . (z-z) in release, and (x+1) . 1 . 0 in devel. Thus authors wishing to signify a major change to their package should set y to 99 in their devel package.

* Add detailed search functionality through Atlas Experiment Metadata

---------

Co-authored-by: Anil Thanki <thanki.anil@gmail.com>

Package: spatialLIBD
Commit: 5a2e570cc56dfab437ec8e893dd5955b6ad1de71
Author: lcolladotor <lcolladotor@gmail.com>
Date: 2025-04-03 11:54:07 -0400
Commit message:

 v1.19.12 -- added guide_point_size in vis_clus() by @lahuuki

Package: spatialLIBD
Commit: 049678fb6314ed4d1749a6db90b044eaab4a942d
Author: lcolladotor <lcolladotor@gmail.com>
Date: 2025-04-03 11:52:08 -0400
Commit message:

 Reformat with Air

Package: spatialLIBD
Commit: 864158692b3b0c6b1d16c420099e2f92f9e75d51
Author: lcolladotor <lcolladotor@gmail.com>
Date: 2025-04-03 11:51:25 -0400
Commit message:

 Add support to vis_clus(guide_point_size) on the shiny apps

Package: spatialLIBD
Commit: 30b39fa14068bbb06cb4862f4a02d163d229f80f
Author: lcolladotor <lcolladotor@gmail.com>
Date: 2025-04-03 11:41:56 -0400
Commit message:

 Also use guide_point_size in vis_grid_clus()

Co-authored-by: Louise Huuki <lahuuki@gmail.com>

Package: spatialLIBD
Commit: 9bceef62d0f4ceb64aa94a539ebb62c3db58ed65
Author: Leonardo Collado-Torres <lcolladotor@gmail.com>
Date: 2025-04-03 11:40:26 -0400
Commit message:

 Merge pull request #104 from LieberInstitute/vis_clus_change_guide_point_size

Add guide_point_size as an arg in vis_clus

Package: spatialLIBD
Commit: e55dd2e0d4354bb231d3b76cf428a98887235766
Author: Louise Huuki <lahuuki@gmail.com>
Date: 2025-03-25 09:55:20 -0400
Commit message:

 Add guide_point_size as an arg in vis_clus

Package: imageTCGA
Commit: f97cf426759eef6802b0876251e2f268c023577e
Author: billila <ilaria.billato@studenti.unipd.it>
Date: 2025-04-03 17:15:59 +0200
Commit message:

 bump version

Package: imageTCGA
Commit: 02e344f2e9c51cb9b6a17b464b451f5119f883ab
Author: billila <ilaria.billato@studenti.unipd.it>
Date: 2025-04-03 17:11:18 +0200
Commit message:

 image vignette

Package: imageTCGA
Commit: 7c4877740596835dff5324bfdad54a8674da1ddf
Author: billila <ilaria.billato@studenti.unipd.it>
Date: 2025-04-03 15:38:30 +0200
Commit message:

 fix vignette

Package: imageTCGA
Commit: f19006b740ca686525b428040322d20c45ef8eb4
Author: billila <ilaria.billato@studenti.unipd.it>
Date: 2025-04-03 12:43:47 +0200
Commit message:

 wide img in vignette

Package: imageTCGA
Commit: ba8f2ff9a5bdb6d29b74e0a49130f03b98296d7d
Author: billila <ilaria.billato@studenti.unipd.it>
Date: 2025-04-03 12:04:36 +0200
Commit message:

 change in generate code text

Package: imageTCGA
Commit: dc29ae6fbfd9fb137feca7b0f3dfa7222f890ab3
Author: billila <ilaria.billato@studenti.unipd.it>
Date: 2025-04-03 11:46:07 +0200
Commit message:

 heatmap -> dotplot

Package: imageTCGA
Commit: 213aaaad5541c2fac0f67c80fbfe711454a3003b
Author: billila <ilaria.billato@studenti.unipd.it>
Date: 2025-04-03 10:32:26 +0200
Commit message:

 fix db

Package: imageTCGA
Commit: 4d085055fed2dc9a601c7f068586808f9c8c41d8
Author: billila <ilaria.billato@studenti.unipd.it>
Date: 2025-04-03 09:24:07 +0200
Commit message:

 add toc to the vignette

Package: imageTCGA
Commit: d0c8fafe8029b02f6d40feba2cc33861482cd667
Author: billila <ilaria.billato@studenti.unipd.it>
Date: 2025-04-03 09:14:11 +0200
Commit message:

 update README.md

Package: imageTCGA
Commit: e032ebe68ab209276471f05712b288043f6a2480
Author: billila <ilaria.billato@studenti.unipd.it>
Date: 2025-04-03 09:12:49 +0200
Commit message:

 update README.md and man/imageTCGA.Rd

Package: imageTCGA
Commit: fce45e93caf116c82f84def030744f1a2a1e4ebb
Author: billila <ilaria.billato@studenti.unipd.it>
Date: 2025-04-03 09:04:24 +0200
Commit message:

 fix example imageTCGA

Package: imageTCGA
Commit: e5f828893f51f094cd9d712cb1c6a2373385407b
Author: billila <ilaria.billato@studenti.unipd.it>
Date: 2025-04-03 09:01:47 +0200
Commit message:

 remove app.R

Package: LegATo
Commit: 6007ea33705829f40f556f05ead9562f2fce0583
Author: Aubrey Odom <aodom@bu.edu>
Date: 2025-04-03 11:13:05 -0400
Commit message:

 Fix minor issues

Package: HoloFoodR
Commit: 5df02eb8492a576ec3fabd4e87c257aede3624aa
Author: Tuomas Borman <60338854+TuomasBorman@users.noreply.github.com>
Date: 2025-04-03 17:15:03 +0300
Commit message:

 Improve support for MetaboLights (#40)

Package: SmartPhos
Commit: 063d0077fa43b0ae0e98f54c57f5d73d4fdbfd47
Author: shubh2565 <catchshubham2565@gmail.com>
Date: 2025-04-03 16:20:10 +0200
Commit message:

 code update added match.arg

Package: scBubbletree
Commit: 2f76668d5f0f400ea00385281b8762ea13181b2d
Author: snaketron <simo.kitanovski@uni-due.de>
Date: 2025-04-03 15:05:41 +0200
Commit message:

 bump readme updated

Package: scBubbletree
Commit: 81044b8cd41a2411de19b7bf5de74328e036ff2a
Author: snaketron <simo.kitanovski@uni-due.de>
Date: 2025-04-03 15:00:52 +0200
Commit message:

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

Package: scBubbletree
Commit: 1a3da3345be5b4c101fa2d8fb18f572632ee252e
Author: snaketron <simo.kitanovski@uni-due.de>
Date: 2025-04-03 14:38:03 +0200
Commit message:

 bump

Package: scBubbletree
Commit: 2a739b1ee3930b4f6e4b7c3288c8aaf409d2c629
Author: snaketron <snaketron@users.noreply.github.com>
Date: 2025-04-03 14:37:31 +0200
Commit message:

 Update README.md

pubmed of paper

Package: GBScleanR
Commit: 5014c7cfdd37c6597bf91841c7c69e3d4f8575b8
Author: tomoyukif <f.tomoyuki@okayama-u.ac.jp>
Date: 2025-04-03 19:57:00 +0900
Commit message:

 Fix scripts to meet Bioconductor's guide lines

Package: GBScleanR
Commit: 5bd2dd6ac0a79bfa247274b1dc046a3998d39c6c
Author: tomoyukif <f.tomoyuki@okayama-u.ac.jp>
Date: 2025-04-03 19:21:26 +0900
Commit message:

 version bump

Package: GBScleanR
Commit: f90193e6e6399a7dad76319e987f0d69ab25d4a7
Author: tomoyukif <f.tomoyuki@okayama-u.ac.jp>
Date: 2025-04-03 19:19:37 +0900
Commit message:

 fix conflict.

Merge branch 'devel'

# Conflicts:
#	DESCRIPTION
#	inst/NEWS.md

Package: GBScleanR
Commit: 7f95f1fc73354ab6f3f5b9472050282fe2798649
Author: tomoyukif <f.tomoyuki@okayama-u.ac.jp>
Date: 2025-03-19 18:36:05 +0900
Commit message:

 bug fix in .getValidPat()

Package: GBScleanR
Commit: 0f74056826739bf618fcf6e405bfafede5aa5e95
Author: tomoyukif <f.tomoyuki@okayama-u.ac.jp>
Date: 2025-04-03 19:18:00 +0900
Commit message:

 Update manuals of setPloidy(), getPloidy(), setFixedParamter(), and getFixedParameter(), and deleted unnecessary descriptions in AllGenerics.R.

Package: SeqArray
Commit: 4d076e39a472d92a2174c70c17327eb459114bab
Author: Xiuwen Zheng <zhengxwen@gmail.com>
Date: 2025-04-02 22:32:36 -0500
Commit message:

 update seqListVarData()

Package: OSCA.advanced
Commit: 77d2c629e57f88d34071bb7ea8472a86047da844
Author: Peter Hickey <peter.hickey@gmail.com>
Date: 2025-04-03 14:28:39 +1100
Commit message:

 Merge pull request #20 from OSCA-source/emptyDrops-changes

Accommodate changes from DropletUtils::emptyDrops()

Package: OSCA.advanced
Commit: 8a4f9b4a13e354c20bf0ac128c9ee21ddc0e4681
Author: PeteHaitch <peter.hickey@gmail.com>
Date: 2025-03-31 18:43:42 +1100
Commit message:

 Version bump

Package: OSCA.advanced
Commit: 19910f745b3a29581ce77fe14e9507a7d091798c
Author: PeteHaitch <peter.hickey@gmail.com>
Date: 2025-03-31 16:52:50 +1100
Commit message:

 Tweak sanity check

- Not directly related to emptyDrops changes, but perhaps indirectly?

Package: OSCA.advanced
Commit: f8ddbcfd5026cbb280aa35297bd92cbf7f8cd457
Author: PeteHaitch <peter.hickey@gmail.com>
Date: 2025-03-31 10:07:35 +1100
Commit message:

 Merge branch 'devel' into emptyDrops-changes

Package: OSCA.advanced
Commit: 8b6a9afd23b79bda775e10247224d1e81483f3b4
Author: Peter Hickey <peter.hickey@gmail.com>
Date: 2025-01-10 17:03:33 +1100
Commit message:

 Further accommodations for changes from DropletUtils::emptyDrops()

- Details of changes: MarioniLab/DropletUtils#118
- For this chunk, the new default of `alpha=Inf` gives poor results. Some quick comparisons given below
  - BioC 3.21
    - 39,028 non-empty droplets with `emptyDrops(counts(hto.sce), by.rank=40000)`
    - 21,374 non-empty droplets with `emptyDrops(counts(hto.sce), by.rank=40000, alpha=NULL)
    - 29,673 non-empty droplets with `emptyDrops(counts(hto.sce), by.rank=30000)`
  - BioC 3.20
    - 21780 on-empty droplets with `emptyDrops(counts(hto.sce), by.rank=40000) (i.e. former default of `alpha = NULL`)
- Added some explanation/justification cribbed from that removed in 76a88c599a15c2d1197d49c084ddb3217a958c34

Package: OSCA.advanced
Commit: 76a88c599a15c2d1197d49c084ddb3217a958c34
Author: Peter Hickey <peter.hickey@gmail.com>
Date: 2025-01-10 16:24:17 +1100
Commit message:

 Accommodate changes from DropletUtils::emptyDrops()

- Details of changes: MarioniLab/DropletUtils#118
- Since the default is now `alpha=Inf`, the claims around `alpha` values and sanity check no longer make sense, so just remove them.

Package: MetaScope
Commit: ea22448ea84cd30011162bb2506f0c3cb2ff4bb7
Author: Aubrey Odom <aodom@bu.edu>
Date: 2025-04-02 22:52:51 -0400
Commit message:

 Fix minor check errors

Package: MetaScope
Commit: 70845f6535cd768a0876af78df2e06abb2cb35e3
Author: Aubrey Odom <aodom@bu.edu>
Date: 2025-01-16 17:05:56 -0500
Commit message:

 Update site

Package: MetaScope
Commit: f555f5160c6919796861a0dfee32cd3aaea89f8b
Author: Aubrey Odom <aodom@bu.edu>
Date: 2025-01-16 16:24:30 -0500
Commit message:

 Update SILVA instructions

Package: TBSignatureProfiler
Commit: 9a5f9ac008978edbc2d615101921efd81bf7f364
Author: Aubrey Odom <aodom@bu.edu>
Date: 2025-04-02 22:30:38 -0400
Commit message:

 Update Shiny app upload limit

Package: nullranges
Commit: 5de859fa20f23a7374bee462feed6d6f3077c493
Author: Mike Love <mikelove@users.noreply.github.com>
Date: 2025-04-02 20:50:26 -0400
Commit message:

 version bump

Package: nullranges
Commit: c9aa4690b630bfcaddcfa2ea705833b27e44c226
Author: Michael Love <mikelove@users.noreply.github.com>
Date: 2025-04-02 20:48:12 -0400
Commit message:

 Merge pull request #24 from nullranges/matchitToMatched

matchitToMatched function

Package: nullranges
Commit: f9f43dacd8b26a830d2af946d26b7d0dc0983994
Author: EricSDavis <ericscottdavis@outlook.com>
Date: 2025-04-02 11:42:42 -0400
Commit message:

 Fix note in package check.

Package: nullranges
Commit: fc7ea76e041974c33e785e2a160b9086ff685f4b
Author: EricSDavis <ericscottdavis@outlook.com>
Date: 2025-04-02 11:41:54 -0400
Commit message:

 Add matchitToMatched coercion and related methods for compatibility with Matched classes

Package: nullranges
Commit: 20a8f972144743f4bdf47983c0672676fcb6ef4d
Author: Eric Davis <ericscottdavis@outlook.com>
Date: 2022-12-23 23:42:14 -0500
Commit message:

 matchitToMatched function

Package: shinyDSP
Commit: 5bf78a1a7033fc3e78ae84a4a01b80c89b1d2255
Author: kimsjune <skim823@uwo.ca>
Date: 2025-04-02 20:27:09 -0400
Commit message:

 Bump to 0.99.13. Moved svglite to Suggests

Package: geomeTriD
Commit: 895bfc6b8e87a16f62ada757ca6efd08c978bea9
Author: Jianhong Ou <jou@JNXKY095H1.local>
Date: 2025-04-02 15:48:02 -0400
Commit message:

 add pointCluster.

Package: CytoGLMM
Commit: d8f1c695d3c6c1e456aa2742854c1ff8929a2190
Author: ChristofSeiler <christof.seiler@gmail.com>
Date: 2025-04-02 19:13:09 +0200
Commit message:

 removed mbest pkg

Package: nondetects
Commit: 710612246c4fe0f777587e1ecf3441e5dc109989
Author: lshep <lori.shepherd@roswellpark.org>
Date: 2025-04-02 12:43:53 -0400
Commit message:

 un-deprecate

Package: HTqPCR
Commit: dcea751247de208cf098d5ea0a07ceb98b7c8b1f
Author: lshep <lori.shepherd@roswellpark.org>
Date: 2025-04-02 12:43:05 -0400
Commit message:

 Un-deprecate

Package: singleCellTK
Commit: ecffb8aeb6e06bdaf4495f45f5dba3a3ab8f05df
Author: Josh Campbell <joshua-d-campbell@gmail.com>
Date: 2025-04-02 11:58:51 -0400
Commit message:

 version bump

Package: singleCellTK
Commit: eeda1ca9887eb19689feedace89bbf99e97da557
Author: Joshua D. Campbell <joshua.d.campbell@gmail.com>
Date: 2025-03-29 12:04:50 -0400
Commit message:

 Merge pull request #784 from salzcamino/master

Update import msigdbr function

Package: singleCellTK
Commit: f653da45575202b66cf0fde964bc4242cb94ac07
Author: Salam AlAbdullatif <salamha@bu.edu>
Date: 2025-03-27 15:45:42 -0400
Commit message:

 importGeneSetsFromMsigDB documentation update

Package: singleCellTK
Commit: 632fdbb561a8f2fe1c696b7082fd4dfeae3c4cf4
Author: Salam AlAbdullatif <salamha@bu.edu>
Date: 2025-03-26 13:08:52 -0400
Commit message:

 Update importGeneSets.R

fix error caused by msigdbr v10.0.0

Package: bandle
Commit: 6e06dbe8f93748a0ef0e166edb08404a93490054
Author: Oliver M. Crook <ococrook@gmail.com>
Date: 2025-04-02 16:43:57 +0100
Commit message:

 bump package number

Package: bandle
Commit: 099b2eadb3a94c1b04fe13a059639c900c57c5bc
Author: Lisa Breckels <lms79@cam.ac.uk>
Date: 2025-04-02 14:03:05 +0100
Commit message:

 Merge branch 'devel'

Package: bandle
Commit: e1a41b36dc21576699a205cd4ae5aabc2eaa4662
Author: Lisa Breckels <lms79@cam.ac.uk>
Date: 2025-04-02 14:02:59 +0100
Commit message:

 update version and news

Package: bandle
Commit: e8137f65548495a5061764a8ab650e167c931af2
Author: Lisa Breckels <lms79@cam.ac.uk>
Date: 2025-04-02 12:47:12 +0100
Commit message:

 Merge pull request #31 from ococrook/main

merge for Bioc

Package: bandle
Commit: a829c5124b76486a2a27c2e4cd6dfdae05d4bab6
Author: Lisa Breckels <lms79@cam.ac.uk>
Date: 2025-04-02 12:44:47 +0100
Commit message:

 Merge pull request #30 from ococrook/devel

update to C++14

Package: bandle
Commit: 83dce0cce22e0a42a9a5527fd3a02850a77a549f
Author: Lisa Breckels <lms79@cam.ac.uk>
Date: 2025-04-02 12:43:49 +0100
Commit message:

 update news

Package: bandle
Commit: 4ae89b46d475dd25abcdefe960d0a3255e918722
Author: Oliver M. Crook <ococrook@gmail.com>
Date: 2025-01-14 15:36:05 +0000
Commit message:

 Update check-bioc.yml

Package: bandle
Commit: 4c79f294bb0a78010cda69d9c00d7899b54d4258
Author: Oliver M. Crook <ococrook@gmail.com>
Date: 2024-11-01 17:01:16 +0000
Commit message:

 Merge pull request #28 from ococrook/devel

Devel

Package: GSVA
Commit: 28d3ec0c91e2c990171412478720ac0a7a26fe64
Author: Robert Castelo <robert.castelo@upf.edu>
Date: 2025-04-02 16:36:00 +0200
Commit message:

 Bump version

Package: GSVA
Commit: 8b9d67cd0fc6a863efe30aeb75357d459ed8da06
Author: Axel Klenk <72612834+axelklenk@users.noreply.github.com>
Date: 2025-04-02 14:10:48 +0200
Commit message:

 Merge pull request #238 from rcastelo/235-r-cmd-check-notes-caused-by-documentation

235 r cmd check notes caused by documentation

Package: GSVA
Commit: ab6e80610be74f0b98ffa340c73301f0fa61635d
Author: Axel Klenk <axel.klenk@gmail.com>
Date: 2025-04-02 13:56:19 +0200
Commit message:

 Merge branch 'devel' into 235-r-cmd-check-notes-caused-by-documentation

Package: GSVA
Commit: 85f82196c12a05c0a0ed68dccbc0e89a4d895412
Author: Axel Klenk <axel.klenk@gmail.com>
Date: 2025-04-02 13:55:54 +0200
Commit message:

 fix documentation links to other non-base packages, part 2

Package: GSVA
Commit: f5494cc88cf010c3460efd2719a6ba6f22bdccce
Author: Axel Klenk <axel.klenk@gmail.com>
Date: 2025-04-02 11:21:57 +0200
Commit message:

 fix documentation links to other non-base packages, part 1

Package: GSVA
Commit: c7577427cffaaa5021e8dc026ec767ab5011156c
Author: Axel Klenk <72612834+axelklenk@users.noreply.github.com>
Date: 2025-04-02 11:04:08 +0200
Commit message:

 Merge pull request #237 from rcastelo/236-remove-old-api

236 remove old api

Package: GSVA
Commit: b1bfce9232746c5f1fb96ca1331d1b881edad749
Author: Axel Klenk <axel.klenk@gmail.com>
Date: 2025-04-01 17:11:30 +0200
Commit message:

 fix URLs in vignette and DOI refs in documentation

Package: GSVA
Commit: ecd9ba5025a1703fa0cda97fc45bb4c990b71ac1
Author: Axel Klenk <axel.klenk@gmail.com>
Date: 2025-04-01 10:17:27 +0200
Commit message:

 removed former usage of 'gsva()' from code and docs

Package: GSVA
Commit: f54e25e8c4195005847417a32af3259314251239
Author: Axel Klenk <axel.klenk@gmail.com>
Date: 2025-04-01 09:36:39 +0200
Commit message:

 Revert "first attempt; to be tested more thoroughly"

This reverts commit 6cd5b3d9c0c71964f7a861056222c276e725a35b.

Package: GSVA
Commit: 6cd5b3d9c0c71964f7a861056222c276e725a35b
Author: Axel Klenk <axel.klenk@gmail.com>
Date: 2025-03-26 18:34:15 +0100
Commit message:

 first attempt; to be tested more thoroughly

Package: nullranges
Commit: 3a0f5687988a53d098d0f884b45af267b2e95d63
Author: Mike Love <mikelove@users.noreply.github.com>
Date: 2025-04-02 07:48:03 -0400
Commit message:

 try a new GHA

Package: nullranges
Commit: 6ffa16f9bfd31bacf6f1ee4af0e2f70796938b05
Author: Mike Love <mikelove@users.noreply.github.com>
Date: 2025-04-02 07:41:56 -0400
Commit message:

 update suggests

Package: nullranges
Commit: 74da9ef61a4821414823a662717a6fb35623ed70
Author: Mike Love <mikelove@users.noreply.github.com>
Date: 2025-04-02 07:29:27 -0400
Commit message:

 GHA try cache v4

Package: nullranges
Commit: d335b7244c8c42c756b79aba87c5935e9f31129b
Author: Mike Love <mikelove@users.noreply.github.com>
Date: 2025-04-02 07:25:52 -0400
Commit message:

 removing uneval code in vignette

Package: SmartPhos
Commit: 7ca386c8085c88cbfe919034f68d3300c3fb7f29
Author: shubh2565 <catchshubham2565@gmail.com>
Date: 2025-04-02 13:06:06 +0200
Commit message:

 code format

Package: mitology
Commit: d3729287232a4e602a7d365e58f88833afb5c9be
Author: Stefania Pirrotta <s.pirrotta.sp@gmail.com>
Date: 2025-04-02 10:13:14 +0200
Commit message:

 solve last notes and bump version

Package: pathMED
Commit: f290ab4a4e7c6bcc1289a06076757120c4e957f8
Author: jordimartorell <jmartorellm@gmail.com>
Date: 2025-04-02 09:22:51 +0200
Commit message:

 Bioconductor review

Package: barbieQ
Commit: e512f53bdb390a224d6e08c7ef7af05b2932173a
Author: Liyang Fei <fei.liyang@outlook.com>
Date: 2025-04-02 17:08:48 +1100
Commit message:

 adjust logit trans

Package: extraChIPs
Commit: 4c6dbd2a76fbc07f9cf943c114108cb881cccc6c
Author: Stevie Ped <stephen.pederson.au@gmail.com>
Date: 2025-04-02 16:40:30 +1030
Commit message:

 Version bump after modifying plot functions

Package: extraChIPs
Commit: f8a216b9914af790526dd82206019ac90b3a7d10
Author: Stevie Ped <stephen.pederson.au@gmail.com>
Date: 2025-04-02 16:21:13 +1030
Commit message:

 Modified plotting argument handling

Package: extraChIPs
Commit: bbfdc2094f8fccf5b55988048fe4bea7c981744d
Author: Stevie Ped <stephen.pederson.au@gmail.com>
Date: 2025-04-02 10:56:57 +1030
Commit message:

 Minor linefix

Package: extraChIPs
Commit: 9056526f0a1b6290a79db51e5c06f4d49ea94698
Author: Stevie Ped <stephen.pederson.au@gmail.com>
Date: 2025-04-02 02:45:34 +1030
Commit message:

 Improved parameters for plotAssayPCA

Package: extraChIPs
Commit: 19eaa08b50a5d19a376b21caf73590630533450c
Author: Stevie Ped <stephen.pederson.au@gmail.com>
Date: 2025-04-02 00:25:56 +1030
Commit message:

 Improved parameters for plotAssayDensities

Package: linkSet
Commit: 4e8a2b64d4f1d2cbf72697bb140ab4bfcc705600
Author: GilbertHan <GilbertHan1011@gmail.com>
Date: 2025-04-02 05:09:59 +0000
Commit message:

20250402

Package: linkSet
Commit: eab418fc71fa527b0b5425309bb1ec5a83e05214
Author: GilbertHan <GilbertHan1011@gmail.com>
Date: 2025-04-02 05:09:41 +0000
Commit message:

20250402

Package: linkSet
Commit: 926b77f509e09defe746aaaedb3ebaeb46e43f3c
Author: GilbertHan1011 <GilbertHan1011@gmail.com>
Date: 2025-04-02 12:41:54 +0800
Commit message:

 20250401_3

Package: pairedGSEA
Commit: 900d76d1fc3fc1bfe10a8d949c3a6aa2f44db904
Author: Søren Helweg Dam <49019552+shdam@users.noreply.github.com>
Date: 2025-04-02 06:31:48 +0200
Commit message:

 rm msigdbdf

Package: linkSet
Commit: 6de0fe3c04a8d49fd2417039eb31791f5a5883ce
Author: GilbertHan1011 <GilbertHan1011@gmail.com>
Date: 2025-04-02 11:18:07 +0800
Commit message:

 20250401_2

Package: linkSet
Commit: a8afa3f264c8fb0a191ca44568b3bcabeb796395
Author: GilbertHan1011 <GilbertHan1011@gmail.com>
Date: 2025-04-02 10:50:58 +0800
Commit message:

20250401

Package: shinyDSP
Commit: c63e576fdc6b782674f5ea8099cc1b2b45fd2625
Author: kimsjune <skim823@uwo.ca>
Date: 2025-04-01 22:15:29 -0400
Commit message:

 Bumped to 0.99.12

Package: SeqArray
Commit: d6efeeb64642e0734e95dd4e989d5c62760d73f3
Author: Xiuwen Zheng <zhengxwen@gmail.com>
Date: 2025-04-01 20:45:42 -0500
Commit message:

 recent update before release

Package: TENET
Commit: 1461f4e7409dda1c70c70811f12b2c7142e652f2
Author: Ethan Nelson-Moore <nelsonmo@usc.edu>
Date: 2025-04-01 18:35:15 -0700
Commit message:

 v0.99.7: Fix TCGADownloader by defaulting to fewer files per chunk via an option to TCGAbiolinks. Allow the user to pass in the files per chunk and method (API/GDC client) to TCGAbiolinks so they can use whatever works best for them; use AnnotationHub::query for ExperimentHub since it doesn't have its own method; remove outdated comment

Package: ClassifyR
Commit: 26e0236448d8af90e3a416cea1e1d628b66978ff
Author: Dario Strbenac <dario@maths.usyd.edu.au>
Date: 2025-04-02 11:15:11 +1100
Commit message:

 - Regression introduced into calcExternalPerformance fixed.
- flowchart gains orientation parameter.

Package: rWikiPathways
Commit: eca95a1acae344e4e7ef4b8b6e1702b708cb1ca5
Author: Alexander Pico <apico@gladstone.ucsf.edu>
Date: 2025-04-01 15:56:43 -0700
Commit message:

 Update DESCRIPTION

update for release

Package: rWikiPathways
Commit: 84f2da5e3f1c8ccc926d4d5cd1ea0fd43f135387
Author: Alexander Pico <apico@gladstone.ucsf.edu>
Date: 2025-04-01 15:56:17 -0700
Commit message:

 Update NEWS

update for release

Package: sparrow
Commit: 52ba36735d1550b40d197d6d7caace3af72e38cc
Author: Steve Lianoglou <slianoglou@gmail.com>
Date: 2025-04-01 13:42:40 -0700
Commit message:

 skip msigdb unit tests if msigdfdb is not installed

Package: sparrow
Commit: 9cd95a5751fde65db6e1efd93c4589289a1f4408
Author: Steve Lianoglou <slianoglou@gmail.com>
Date: 2025-04-01 13:07:26 -0700
Commit message:

 Changes to fix R CMD check isseus to do updated msigdbr package.

Package: sparrow
Commit: eb998af344cd627b66ed864cbdd7787febd90314
Author: Steve Lianoglou <slianoglou@gmail.com>
Date: 2025-03-20 07:53:34 -0700
Commit message:

 minor msigdbr updates

Package: Rigraphlib
Commit: 1be0932851365f2ba60051eaf3f9177e7f2007ab
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2025-04-01 10:27:56 -0700
Commit message:

 Added cleanup script to remove binaries after R CMD BUILD.

Otherwise they get sucked into the tarball and this prevents a (correct) build
from source on machines that don't expect binary distributions.

We also nest the installation directory within 'inst' to avoid potential
conflicts with R's expected package directory structure.

Package: ComplexHeatmap
Commit: 57dbacef341729254436f19149dd21d7c516d2df
Author: Zuguang Gu <jokergoo@gmail.com>
Date: 2025-04-01 18:51:21 +0200
Commit message:

 change anno_background_col

Package: ComplexHeatmap
Commit: 73c14557e39829c3f22ec6b5a14f93e747b3c3d4
Author: Zuguang Gu <jokergoo@gmail.com>
Date: 2025-04-01 18:31:31 +0200
Commit message:

 merge

Package: ComplexHeatmap
Commit: 0628404dcd44e4da74232fa3a71d91e519ad24a5
Author: Zuguang Gu <jokergoo@gmail.com>
Date: 2025-04-01 18:30:04 +0200
Commit message:

 add background to anno functions

Package: ComplexHeatmap
Commit: 3398d2157df844f4acd5202148dd87a54ca7cb62
Author: Zuguang Gu <jokergoo@gmail.com>
Date: 2024-12-19 13:52:56 +0100
Commit message:

 anno_barplot(): add_numbers and reversed direction

Package: zellkonverter
Commit: 06fe811fb8452099f0dab77dd3c020ce510013cd
Author: Luke Zappia <lazappi@users.noreply.github.com>
Date: 2025-04-01 18:30:52 +0200
Commit message:

 Merge pull request #138 from mcmero/spatialexp

Add spatial coordinates to Anndata when converting from SpatialExperiment

Package: zellkonverter
Commit: a213c2b5f7949bc4b7a986f2acad1e9d60bb3b03
Author: Luke Zappia <lazappi@users.noreply.github.com>
Date: 2025-04-01 18:29:34 +0200
Commit message:

 Bump dev version

Package: zellkonverter
Commit: 5e7e97ff1cee8fea54fd0bf55d4f060b94d828c7
Author: Luke Zappia <lazappi@users.noreply.github.com>
Date: 2025-03-20 20:57:52 +0100
Commit message:

 Add test that writeH5AD() keeps dimnames

Package: zellkonverter
Commit: 279214778187320e488befea8eda8733bc1a0643
Author: Luke Zappia <lazappi@users.noreply.github.com>
Date: 2025-03-20 20:51:09 +0100
Commit message:

 Handle reducedDims without colnames in SCE2AnnData

Package: zellkonverter
Commit: 0fb2b02aaa8902d90578ca07091224b7ed9f1e4a
Author: Luke Zappia <lazappi@users.noreply.github.com>
Date: 2025-03-20 17:45:19 +0100
Commit message:

 Merge remote-tracking branch 'origin/devel' into spatialexp

* origin/devel:
  Fix GHA badge in README.md

Package: zellkonverter
Commit: ce44c280da909ac535f0131893f3b82345b3556d
Author: mcmero <7799828+mcmero@users.noreply.github.com>
Date: 2025-03-20 10:43:32 +1100
Commit message:

 Throw error when attempting to set_axis without colnames in the sce object

Package: zellkonverter
Commit: b1e034b4b36afd966a2ec853a128f0774985a56a
Author: Luke Zappia <lazappi@users.noreply.github.com>
Date: 2025-03-19 18:52:55 +0100
Commit message:

 Add test for spatial coords without names

Package: zellkonverter
Commit: 6dde700dbf70d499bf76a2f1c4f8c7765cf4c638
Author: Luke Zappia <lazappi@users.noreply.github.com>
Date: 2025-03-19 18:43:20 +0100
Commit message:

 Add headings to AnnData-Conversion details

Package: zellkonverter
Commit: 41861c688218c23a44da20ee7d97cddc7a1985b0
Author: Luke Zappia <lazappi@users.noreply.github.com>
Date: 2025-03-19 18:29:13 +0100
Commit message:

 Fix GHA badge in README.md

Package: zellkonverter
Commit: fd0ba1c9c7d4864ef5e09fdf5e5f37d680bba3d4
Author: mcmero <7799828+mcmero@users.noreply.github.com>
Date: 2025-03-17 11:58:26 +1100
Commit message:

 Update documentation

Package: zellkonverter
Commit: c7d5c9a24df3004900a8cc0475954c1dec002935
Author: mcmero <7799828+mcmero@users.noreply.github.com>
Date: 2025-03-17 11:48:49 +1100
Commit message:

 Move SpatialExperiment handling to SCE2AnnData

Package: zellkonverter
Commit: 30dfda34fd07d90e3e5d926c6bd08e311cd439b5
Author: mcmero <7799828+mcmero@users.noreply.github.com>
Date: 2025-03-17 10:09:12 +1100
Commit message:

 Merge branch 'devel' into spatialexp

Package: zellkonverter
Commit: bb7be1feab3a7c261ed499496884677e83761635
Author: Luke Zappia <lazappi@users.noreply.github.com>
Date: 2025-03-16 17:52:23 +0100
Commit message:

 Install rsync for pkgdown job

Also set git user in deploy step

Package: zellkonverter
Commit: 850ab0504423d6fbaf44ef631bac8511950efe9a
Author: Luke Zappia <lazappi@users.noreply.github.com>
Date: 2025-03-16 17:47:18 +0100
Commit message:

 Add colnames to coords in SpatialExperiment test

Package: zellkonverter
Commit: ba1f746b30fb38d2835c67306fbf5841812e9670
Author: Luke Zappia <lazappi@users.noreply.github.com>
Date: 2025-03-16 17:35:45 +0100
Commit message:

 Merge remote-tracking branch 'origin/devel' into spatialexp

* origin/devel:
  Fix handling of missing rowData/colData

Package: zellkonverter
Commit: 03ab944dc5ba35e7a4a9cf25ff73afa1cd4c3f35
Author: Luke Zappia <lazappi@users.noreply.github.com>
Date: 2025-03-16 17:34:34 +0100
Commit message:

 Fix handling of missing rowData/colData

Fixes #105

Package: zellkonverter
Commit: 4b0f23c23fe6e6f7166df10e6a3cce04ebb600ee
Author: Luke Zappia <lazappi@users.noreply.github.com>
Date: 2025-03-13 19:27:25 +0100
Commit message:

 Merge remote-tracking branch 'origin/devel' into spatialexp

* origin/devel:
  Update when GHA actions are run
  Update GitHub Actions bot user config
  Move set git credentials step in pkgdown job

Package: zellkonverter
Commit: 23fc192a8ccdcd9150662f8db2e7f40c2bf78951
Author: Luke Zappia <lazappi@users.noreply.github.com>
Date: 2025-03-13 19:25:50 +0100
Commit message:

 Merge pull request #139 from theislab/actions

Update CI

Package: zellkonverter
Commit: d38aec555dd7c8581c117d72a9648ee782bd613c
Author: Luke Zappia <lazappi@users.noreply.github.com>
Date: 2025-03-13 18:43:40 +0100
Commit message:

 Update when GHA actions are run

Package: zellkonverter
Commit: a59523b4e1133bd3789fe5149e91127acaf961c6
Author: Luke Zappia <lazappi@users.noreply.github.com>
Date: 2025-03-13 17:36:54 +0100
Commit message:

 Update GitHub Actions bot user config

Package: zellkonverter
Commit: 765e1ae848a5fb5db86b3666c22dea9ed7dddb3a
Author: Luke Zappia <lazappi@users.noreply.github.com>
Date: 2025-03-13 17:35:16 +0100
Commit message:

 Move set git credentials step in pkgdown job

Package: zellkonverter
Commit: 793661646645d512318793357b02b301c477aca3
Author: Luke Zappia <lazappi@users.noreply.github.com>
Date: 2025-03-13 17:22:17 +0100
Commit message:

 Merge branch 'devel' into spatialexp

Package: zellkonverter
Commit: 861df4163fbcbf57ddf8fb78089e1af4e26dcd7b
Author: mcmero <7799828+mcmero@users.noreply.github.com>
Date: 2025-03-11 11:51:56 +1100
Commit message:

 Clear colnames from coords

If coords has colnames, this causes isses with rd$set_axis(colnames(sce))

Package: zellkonverter
Commit: 022d0407458db27e8f7fbd03423d8c3063eaecc3
Author: mcmero <7799828+mcmero@users.noreply.github.com>
Date: 2025-03-11 11:33:58 +1100
Commit message:

 Add contributor information

Package: zellkonverter
Commit: 61ef0da7dcee86a3be745103afa935e50a3d05b9
Author: Luke Zappia <lazappi@users.noreply.github.com>
Date: 2025-03-09 10:50:21 +0100
Commit message:

 Clean up check GHA

Package: zellkonverter
Commit: f8af5994bdffbd33d3dc8a6506d7f0ea1699ec8b
Author: Luke Zappia <lazappi@users.noreply.github.com>
Date: 2025-03-09 10:49:09 +0100
Commit message:

 Update check GHA

Package: zellkonverter
Commit: 050fdb4a003e2e145b415d9560248132f125a5bf
Author: Luke Zappia <lazappi@users.noreply.github.com>
Date: 2025-03-08 13:31:22 +0100
Commit message:

 Simplify SpatialExperiment test

Package: zellkonverter
Commit: a7dad36c4b312acd37ce7a0fc1c6d4a5cde0cac6
Author: Luke Zappia <lazappi@users.noreply.github.com>
Date: 2025-03-08 13:30:53 +0100
Commit message:

 Adjust how spatial coords are stored

Package: zellkonverter
Commit: 12004662ba3791461bb0d2c4210972df68099b08
Author: Luke Zappia <lazappi@users.noreply.github.com>
Date: 2025-03-08 13:27:08 +0100
Commit message:

 Adjust dependencies

Package: zellkonverter
Commit: 35d9c42dfe5ecb777b56d53e14ba00847dfb3a0a
Author: mcmero <7799828+mcmero@users.noreply.github.com>
Date: 2025-03-03 13:39:33 +1100
Commit message:

 Add test for writing SpatialExperiment

Package: zellkonverter
Commit: dc7d4a8dd6ee3f52c4055acc04e6febf76cf6897
Author: mcmero <7799828+mcmero@users.noreply.github.com>
Date: 2025-02-27 10:59:53 +1100
Commit message:

 Add spatial coords to reducedDims instead of modifying conversion code

Package: zellkonverter
Commit: c38af0eb48220f37b26ca45bb3f3c6f393309819
Author: mcmero <7799828+mcmero@users.noreply.github.com>
Date: 2025-02-26 09:33:37 +1100
Commit message:

 Add coords when converting SpatialExperiment objects

Package: mitology
Commit: 062dc8a6f97ff37091271f1b52ffed5ddefcf308
Author: Stefania Pirrotta <s.pirrotta.sp@gmail.com>
Date: 2025-04-01 16:02:42 +0200
Commit message:

 version bump

Package: mitology
Commit: 2367558a46103215ea4256aeb09d00941a2cfb3a
Author: Stefania Pirrotta <s.pirrotta.sp@gmail.com>
Date: 2025-04-01 16:01:57 +0200
Commit message:

 adjust code and tests

Package: mitology
Commit: 031536ac8886fe221c29800a0b0221a3a123a0d1
Author: Stefania Pirrotta <s.pirrotta.sp@gmail.com>
Date: 2025-04-01 16:00:40 +0200
Commit message:

 reduce vignette size

Package: ClustIRR
Commit: da10c02087261aa278a94e983f9b9e3a6fd3050d
Author: snaketron <simo.kitanovski@proton.me>
Date: 2025-04-01 16:10:55 +0200
Commit message:

 Merge branch 'main' of github.com:snaketron/ClustIRR

Package: ClustIRR
Commit: 371b1f47d9c5e04a97895171204b2d02f43b068c
Author: snaketron <simo.kitanovski@proton.me>
Date: 2025-04-01 16:10:04 +0200
Commit message:

 minor clarification

Package: ClustIRR
Commit: 317312cf77adfd43d9a37f4d8dd79bce7f64f967
Author: snaketron <simo.kitanovski@proton.me>
Date: 2025-04-01 16:05:08 +0200
Commit message:

 cleanup, now clustirr is the main method: it does clust_irr + get_graph/get_joint graph

Package: RUCova
Commit: 054e87de05eafcb5ea503a90dfb6dff621262979
Author: Rosario Astaburuaga-García <rosario.astaburuaga@charite.de>
Date: 2025-04-01 15:15:24 +0200
Commit message:

 new compare_corr function

Package: RUCova
Commit: b8da91509c29178dc33eb2a42530de386acd40f2
Author: Rosario Astaburuaga-García <rosario.astaburuaga@charite.de>
Date: 2025-04-01 14:55:51 +0200
Commit message:

 new compare_corr function

Package: mia
Commit: feb15de993bba361e822e1147a82432751e907c4
Author: Tuomas Borman <60338854+TuomasBorman@users.noreply.github.com>
Date: 2025-04-01 15:18:32 +0300
Commit message:

 Fix phyloseq converter (#723)

Package: QFeatures
Commit: 1b2c1a6cd9500202c969ac30bb422fee89b4ed81
Author: Laurent Gatto <laurent.gatto@gmail.com>
Date: 2025-04-01 14:08:29 +0200
Commit message:

 Merge pull request #232 from rformassspectrometry/issue231

fix issue231

Package: QFeatures
Commit: c41ef77f3c706013a11fc1336b81d505f89fe69b
Author: Laurent Gatto <laurent.gatto@uclouvain.be>
Date: 2025-03-22 15:16:20 +0100
Commit message:

 update readme

Package: QFeatures
Commit: ca8e24cfb19cbf056ba42fc3bbaf95300cbf1086
Author: Laurent Gatto <laurent.gatto@uclouvain.be>
Date: 2025-03-22 15:00:22 +0100
Commit message:

 use pkgdown logo

Package: QFeatures
Commit: 7f5216c0f5e17e3d5aa5eee33c2b29906680f5c0
Author: Laurent Gatto <laurent.gatto@uclouvain.be>
Date: 2025-03-22 14:39:23 +0100
Commit message:

 use bootstrap 5 (on master)

Package: QFeatures
Commit: cb3254ed5e11105ed1c3c9bef10c010f347d757e
Author: Laurent Gatto <laurent.gatto@uclouvain.be>
Date: 2025-03-22 14:38:41 +0100
Commit message:

 remove last change

Package: QFeatures
Commit: 119c619b523e4b95c5b29f72c32cc85a7d88416f
Author: Laurent Gatto <laurent.gatto@uclouvain.be>
Date: 2025-03-22 14:38:00 +0100
Commit message:

 use bootstrap 5

Package: QFeatures
Commit: ab7ce80658bd53e9636cfd68f182e62d8b1cc0ad
Author: Laurent Gatto <laurent.gatto@gmail.com>
Date: 2025-03-22 14:20:04 +0100
Commit message:

 Merge pull request #217 from rformassspectrometry/lgatto-patch-1

get preprocessCore source from bioconductor git

Package: QFeatures
Commit: c7bb1e3bae49d1bde92f97313b3bc1738d1a6fb9
Author: Laurent Gatto <laurent.gatto@uclouvain.be>
Date: 2025-03-22 12:48:34 +0100
Commit message:

 fix version

Package: QFeatures
Commit: 86af4b0b4efa3982424431d576160184778a0d40
Author: Laurent Gatto <laurent.gatto@uclouvain.be>
Date: 2025-03-22 12:28:34 +0100
Commit message:

 adapt tests to new keep argument

Package: QFeatures
Commit: 81baae8ed8fa0e6cdc7678c8897dc179cb5f8469
Author: Laurent Gatto <laurent.gatto@uclouvain.be>
Date: 2025-03-22 11:01:03 +0100
Commit message:

 adapt tests to new messages

Package: QFeatures
Commit: 094a48f08d85292a0c2639147a03bb3faf7781bb
Author: Laurent Gatto <laurent.gatto@uclouvain.be>
Date: 2025-03-21 22:18:33 +0100
Commit message:

 bump version and update news

Package: QFeatures
Commit: 2cf3eb6906d8ccb3c23586f1fec6866e70d81a87
Author: Laurent Gatto <laurent.gatto@uclouvain.be>
Date: 2025-03-21 22:09:02 +0100
Commit message:

 fix issue231

Package: QFeatures
Commit: f178bd99a1dff551f6c0d8d3ea1c1a1f95d4ae5e
Author: Laurent Gatto <laurent.gatto@uclouvain.be>
Date: 2025-03-21 10:32:15 +0100
Commit message:

 fix workflow_dispatch

Package: QFeatures
Commit: 0251b7136f1987d9f75e24184bc87e910d4c684e
Author: Laurent Gatto <laurent.gatto@uclouvain.be>
Date: 2025-03-21 10:31:13 +0100
Commit message:

 add workflowdispatch to run gha manually on any branch

Package: QFeatures
Commit: b0f6cffdf5697f2871707e9fe74c30ca2b2a18e1
Author: Laurent Gatto <laurent.gatto@gmail.com>
Date: 2025-03-04 11:38:28 +0100
Commit message:

 Merge pull request #225 from rformassspectrometry/lgatto-patch-2

Update check-bioc.yml

Package: QFeatures
Commit: 6e41566cff52d8dbd50eba657f2823c34d18ec4e
Author: Laurent Gatto <laurent.gatto@gmail.com>
Date: 2025-03-04 11:38:05 +0100
Commit message:

 Update check-bioc.yml

Package: QFeatures
Commit: 9299c7bf86b9598a4db49e04f76e999cdfdd4952
Author: Laurent Gatto <laurent.gatto@uclouvain.be>
Date: 2025-03-04 11:29:28 +0100
Commit message:

 new devel version

Package: QFeatures
Commit: 97cb6440d5110cbf10fbf70cbb16805c1b641890
Author: Laurent Gatto <laurent.gatto@gmail.com>
Date: 2024-10-09 12:08:57 +0200
Commit message:

 use https instead of git

Package: QFeatures
Commit: 048ba07272ca6bab49f9e47a0b77d7bceb902afd
Author: Laurent Gatto <laurent.gatto@gmail.com>
Date: 2024-10-09 11:58:15 +0200
Commit message:

 fix git clone

Package: QFeatures
Commit: 23a785facc27e05e164418d428e3f7a7d8b6639a
Author: Laurent Gatto <laurent.gatto@gmail.com>
Date: 2024-10-09 11:45:46 +0200
Commit message:

 get preprocessCore source from bioconductor git

Package: stPipe
Commit: a7d005aecd0495977decb5a55ca6e4a94dc686f2
Author: YangXuuu <xuyang1121wws@gmail.com>
Date: 2025-04-01 20:02:05 +1100
Commit message:

 Edit DESCRIPTION, add demo data

Package: stPipe
Commit: 068fbd2022f303cd6049a234d5a5b8cf414f7a22
Author: YangXuuu <xuyang1121wws@gmail.com>
Date: 2025-04-01 18:34:52 +1100
Commit message:

 Edit DESCRIPTION

Package: scHiCcompare
Commit: 8cb99b705af919da49476a6c8dacb39a5007ccba
Author: hamy12398 <hamy.12398@gmail.com>
Date: 2025-04-01 03:03:01 -0400
Commit message:

 update package

Package: scHiCcompare
Commit: 6b0df5b817246af1637bdf37d31a7135c507ae26
Author: hamy12398 <hamy.12398@gmail.com>
Date: 2025-04-01 00:35:38 -0400
Commit message:

 update

Package: scHiCcompare
Commit: 6b98765ac37d75b8a53c3be392fd71c7065a9488
Author: hamy12398 <hamy.12398@gmail.com>
Date: 2025-04-01 00:35:18 -0400
Commit message:

 Merge branch 'main' of https://github.com/dozmorovlab/scHiCcompare

Package: scHiCcompare
Commit: af8fae702850ce9459d320e2a25420cb9bb5bc01
Author: hamy12398 <hamy.12398@gmail.com>
Date: 2025-04-01 00:35:10 -0400
Commit message:

 update

Package: scHiCcompare
Commit: c7e3d63e6e5727983b249492fac026d100dc1df5
Author: hamy12398 <93464589+hamy12398@users.noreply.github.com>
Date: 2025-04-01 00:10:21 -0400
Commit message:

 Merge pull request #24 from dozmorovlab/devel

Merge pull request #23 from dozmorovlab/main

Package: scHiCcompare
Commit: 6bb9efd14f30b63c8ba84f8a0fff0145465221ef
Author: hamy12398 <hamy.12398@gmail.com>
Date: 2025-03-31 23:59:43 -0400
Commit message:

try

Package: scHiCcompare
Commit: 408d907dbd827c0f0bcc8eeee837c8f31c71793f
Author: hamy12398 <hamy.12398@gmail.com>
Date: 2025-03-31 23:54:17 -0400
Commit message:

 update

Package: scHiCcompare
Commit: d98697d8286e262d3a95677e38b49ddab84f4b20
Author: hamy12398 <hamy.12398@gmail.com>
Date: 2025-03-31 23:42:34 -0400
Commit message:

 try update

Package: scHiCcompare
Commit: af62863ee7de3424ea59eecc188ceeb41fb613b1
Author: hamy12398 <hamy.12398@gmail.com>
Date: 2025-03-31 23:38:57 -0400
Commit message:

 update

Package: scHiCcompare
Commit: d507e0f469778d30af76cb1ecb5d4bdcef43f421
Author: hamy12398 <hamy.12398@gmail.com>
Date: 2025-03-31 23:32:34 -0400
Commit message:

 update

Package: scHiCcompare
Commit: 05eee3fe8e3302a6bd20a58dcd8662030d5159b2
Author: hamy12398 <hamy.12398@gmail.com>
Date: 2025-03-31 23:27:14 -0400
Commit message:

 update

Package: scHiCcompare
Commit: 214881a36bbe6a2f0af38b04b504810ab1d9cfde
Author: hamy12398 <93464589+hamy12398@users.noreply.github.com>
Date: 2025-03-31 23:24:09 -0400
Commit message:

 Merge pull request #23 from dozmorovlab/main

push

Package: scHiCcompare
Commit: 0f3098535f5e5236465107e82f1c722891fa7100
Author: hamy12398 <hamy.12398@gmail.com>
Date: 2025-03-31 23:23:24 -0400
Commit message:

 update

Package: stPipe
Commit: 53a9b6e2ad972c486e5534d12aa8b9dd382e7959
Author: YangXuuu <xuyang1121wws@gmail.com>
Date: 2025-04-01 17:54:26 +1100
Commit message:

 Remove unnecessary system and compiled files, update documentation, and edit DESCRIPTION

Package: barbieQ
Commit: 91409a95a0659416dfb15768717a1ea811402f52
Author: Liyang Fei <fei.liyang@outlook.com>
Date: 2025-04-01 14:28:26 +1100
Commit message:

 update documentation

Package: barbieQ
Commit: 36be8a0fc60a35ed220d6b1e8067efa51e6ed975
Author: Liyang Fei <fei.liyang@outlook.com>
Date: 2025-04-01 13:05:22 +1100
Commit message:

 update vignette

Package: barbieQ
Commit: d00cc61c1dea861c4d2730488ea0e103dab4d8e1
Author: Liyang Fei <fei.liyang@outlook.com>
Date: 2025-04-01 12:51:17 +1100
Commit message:

 fix plot testing

Package: barbieQ
Commit: 0301cc9fa501c9315bd52b402b5a4ccb28dfe023
Author: Liyang Fei <fei.liyang@outlook.com>
Date: 2025-04-01 11:22:14 +1100
Commit message:

 update documentayion

Package: barbieQ
Commit: 38d26f1e57d00aebbaaa0093215e8b47b3485085
Author: Liyang Fei <fei.liyang@outlook.com>
Date: 2025-03-27 02:27:45 +1100
Commit message:

 update vignette

Package: barbieQ
Commit: c297f307382b6edbc4aa480eb69794b42ca9d0b8
Author: Liyang Fei <fei.liyang@outlook.com>
Date: 2025-03-27 02:17:55 +1100
Commit message:

 delete accessors

Package: barbieQ
Commit: b9b2fc0da86efaa7b9904f3b8951a96f1bf203a7
Author: Liyang Fei <fei.liyang@outlook.com>
Date: 2025-03-27 02:04:40 +1100
Commit message:

 update data

Package: barbieQ
Commit: caadd2950c5ad1087f478d6c95d8b62635072585
Author: Liyang Fei <fei.liyang@outlook.com>
Date: 2025-03-27 01:39:02 +1100
Commit message:

 pivot to SE

Package: barbieQ
Commit: 02157f4901f576be9b438d811f7bc8d117f3d7c6
Author: Liyang Fei <fei.liyang@outlook.com>
Date: 2025-03-17 15:48:55 +1100
Commit message:

 update readme

Package: barbieQ
Commit: 5679538e786c4ca59606703237f3271c8f3ed5b6
Author: Liyang Fei <fei.liyang@outlook.com>
Date: 2025-03-17 15:25:29 +1100
Commit message:

 fix rev comments

Package: barbieQ
Commit: b1539363e86176bcfbfe7eda99a7b21e14f14ce6
Author: Liyang Fei <fei.liyang@outlook.com>
Date: 2025-03-17 14:45:56 +1100
Commit message:

 document monkey HSPC data

Package: barbieQ
Commit: b426be809c645e1f4a1422416f5926d26ca0604a
Author: Liyang Fei <fei.liyang@outlook.com>
Date: 2025-03-17 14:43:50 +1100
Commit message:

 document monkey HSPC data

Package: barbieQ
Commit: 4b6c676cda8125a35b3e514bfb446f679d45a80c
Author: Liyang Fei <fei.liyang@outlook.com>
Date: 2025-03-17 14:40:03 +1100
Commit message:

 document monkeyHSPC data

Package: barbieQ
Commit: c08412fe63f61e136a396c1632663f19387af19f
Author: Liyang Fei <fei.liyang@outlook.com>
Date: 2025-02-27 19:48:24 +1100
Commit message:

 add data ZG66

Package: barbieQ
Commit: 2c7dbbf2133639d2cabf8f829783dc6a77f8dc12
Author: Liyang Fei <feiliyang@ma59096.petermac.org.au>
Date: 2025-02-25 18:16:06 +1100
Commit message:

 rename parameters

Package: stPipe
Commit: 103a82a0700a741fdb80ce528e4f80a39cfad9aa
Author: YangXuuu <xuyang1121wws@gmail.com>
Date: 2025-04-01 17:14:23 +1100
Commit message:

 Version bump: 0.99.4 -> 0.99.5

Package: stPipe
Commit: abe36531cd8a31a26f8bea6f77e73e72ed796df1
Author: YangXuuu <xuyang1121wws@gmail.com>
Date: 2025-04-01 17:12:51 +1100
Commit message:

 Remove unnecessary system and compiled files, update documentation

Package: pairedGSEA
Commit: 74e30d488459433f122c91ef86e8c0e3640e8e0f
Author: Søren Helweg Dam <49019552+shdam@users.noreply.github.com>
Date: 2025-04-01 07:55:13 +0200
Commit message:

 S4Vectors::subset

Package: stPipe
Commit: d907ab9d6ef3e841c252f20bb534781d75f64885
Author: YangXuuu <xuyang1121wws@gmail.com>
Date: 2025-04-01 16:17:04 +1100
Commit message:

 Version bump: update DESCRIPTION and R/Run_Visualization.R R/Run_Create_Obj.R R/Run_Clustering.R R/Run_ST.R R/Run_HTML.R R/Run_QC.R R/Run_Interactive.R R/Run_Loc_Match.R

Package: mitch
Commit: 8f142aeae14f56afdb4c26ae2fd6f9f681c7f777
Author: markziemann <markziemann@gmail.com>
Date: 2025-04-01 15:31:48 +1100
Commit message:

 fix Jaccard legend

Package: scHiCcompare
Commit: 886c2b7a021542da68c1128ead8c4e58f0d24c4e
Author: hamy12398 <93464589+hamy12398@users.noreply.github.com>
Date: 2025-03-31 22:56:43 -0400
Commit message:

 Merge pull request #22 from dozmorovlab/devel

Merge pull request #21 from dozmorovlab/main

Package: scHiCcompare
Commit: ce8c645f45fa5f3feb31fd89960b5e54e525bdb2
Author: hamy12398 <93464589+hamy12398@users.noreply.github.com>
Date: 2025-03-31 22:56:01 -0400
Commit message:

 Merge pull request #21 from dozmorovlab/main

merge

Package: scHiCcompare
Commit: 855fd010859b8fce99bfb5d99e8a7bd728a9bf3c
Author: hamy12398 <hamy.12398@gmail.com>
Date: 2025-03-31 22:54:57 -0400
Commit message:

 fix R version

Package: BiocParallel
Commit: f290670edda3b6203959c4ed457deaeb237ef195
Author: Martin Morgan <mtmorgan.xyz@gmail.com>
Date: 2025-03-31 16:23:55 -0400
Commit message:

 add Boost license for source code inclusion

Package: HTqPCR
Commit: eea5c6d484cf9c1c0787cc800e979d4bd28b5898
Author: Matthew N. McCall <mccallm@gmail.com>
Date: 2025-03-31 14:41:09 -0400
Commit message:

 Fix vignette errors

Package: BiocParallel
Commit: ff5f39238f27a0a3dafc35e025bd3ff9902b4adc
Author: Martin Morgan <mtmorgan.xyz@gmail.com>
Date: 2025-03-31 13:20:11 -0400
Commit message:

 add local include path to Makevars.ucrt

Package: mitch
Commit: ebe1af01cec82126137c8cad3a0c4861aac69f1f
Author: markziemann <markziemann@gmail.com>
Date: 2025-04-01 01:45:17 +1100
Commit message:

 added a new network plot

Package: ngsReports
Commit: c3e6e30033ed0529a89c5900cb44f5eb46dc317d
Author: Stevie Ped <stephen.pederson.au@gmail.com>
Date: 2025-03-31 11:28:55 +1030
Commit message:

 Minor man edits

Package: strandCheckR
Commit: f298b3d1575f041e4771dedc8607aa3cc49deaff
Author: Stevie Ped <stephen.pederson.au@gmail.com>
Date: 2025-03-22 01:25:50 +1030
Commit message:

 Fixed BioCheck warnings

Package: strandCheckR
Commit: 08105922ba87b245e741ec82a40ca3aca2f6ce4e
Author: Stevie Ped <stephen.pederson.au@gmail.com>
Date: 2025-03-22 00:42:01 +1030
Commit message:

 Minor edits

Package: strandCheckR
Commit: a1975fb933e8dd936424d84b77fdde70a23465f8
Author: Stevie Ped <stephen.pederson.au@gmail.com>
Date: 2025-03-21 23:55:25 +1030
Commit message:

 Added NULL handling to statFile

Package: strandCheckR
Commit: d7f615a3fd05e5b332a514cb686ee3761217b372
Author: Stevie Ped <stephen.pederson.au@gmail.com>
Date: 2025-03-19 16:00:15 +1030
Commit message:

 Recompiled README

Package: strandCheckR
Commit: 22eca4c70f778cca81e757b26951514af787780f
Author: Stevie Ped <stephen.pederson.au@gmail.com>
Date: 2025-03-19 15:54:27 +1030
Commit message:

 Updated imports, details & added CITATION

Package: sechm
Commit: a65ac97d82072da12a3076928aead578c1955f3d
Author: plger <pl.germain@gmail.com>
Date: 2025-03-31 15:15:06 +0200
Commit message:

 fixed missing colnames

Package: sechm
Commit: 6729ab7af92a385fc8e50c7c5e11181c10fc4888
Author: plger <pl.germain@gmail.com>
Date: 2025-03-31 14:45:23 +0200
Commit message:

 changed to bioc action

Package: sechm
Commit: 5a2534be4ee9029b77d1636bacd272c6966635d5
Author: plger <pl.germain@gmail.com>
Date: 2025-03-31 14:39:20 +0200
Commit message:

 version bump

Package: sechm
Commit: 074a35b1311b10eabd77b9482146f44b23277450
Author: plger <pl.germain@gmail.com>
Date: 2025-03-31 14:38:36 +0200
Commit message:

 fixed bug with invalid column names

Package: UPDhmm
Commit: ecc72c5d53cfe33aa0bc7a44551961c4d37610cb
Author: martasevilla <martasevillaporras@gmail.com>
Date: 2025-03-31 14:11:09 +0200
Commit message:

 Added knitr to Suggests and VignetteBuilder in DESCRIPTION

Package: spatialFDA
Commit: 7415a2eae82abe2fdff6a24d7b24524c662154a6
Author: mjemons <martin.emons@gmail.com>
Date: 2025-03-31 14:10:33 +0200
Commit message:

 changed vignette example

Package: mia
Commit: b2d09f6ed8bb432e5c669c15137a42eec51fa477
Author: Tuomas Borman <60338854+TuomasBorman@users.noreply.github.com>
Date: 2025-03-31 11:16:49 +0300
Commit message:

 Add example for ignoring zeroes in cross correlation (#720)

Package: mia
Commit: 5603d0b988cb6be50dcbaa3e5d832edd0df0f94d
Author: ake <40662956+ake123@users.noreply.github.com>
Date: 2025-03-27 16:00:02 +0200
Commit message:

 Update bug_report.md (#719)

Package: MOSim
Commit: 73d32a9afa7b37e9140a740d37958288cc225893
Author: Sonia Tarazona Campos <sotacam@upv.edu.es>
Date: 2025-03-31 13:14:10 +0200
Commit message:

 version update

Package: MOSim
Commit: 565a5975e2dfc93a7d4c93657693f5e5b0c0c866
Author: Carolina Monzó <carolmonzoc@gmail.com>
Date: 2025-03-27 10:25:36 +0100
Commit message:

 updating engine to rmarkdown

Package: MOSim
Commit: 7123c28561b1e9dba0381fd727d2df54999b15f8
Author: Carolina Monzó <carolmonzoc@gmail.com>
Date: 2025-03-25 14:53:24 +0100
Commit message:

 updating citation and vignette formatting

Package: MOSim
Commit: cf29ee48fa9bc00d4ba73f20ff990845620e36e0
Author: Carolina Monzó <carolmonzoc@gmail.com>
Date: 2025-03-25 13:05:16 +0100
Commit message:

 update reference to published article

Package: MOSim
Commit: cb3e84164c79b8fa8fca8ae196364a30233cdbd8
Author: Carolina Monzó <carolmonzoc@gmail.com>
Date: 2024-12-15 20:34:56 +0100
Commit message:

 Update MOSim.Rmd with MOSim applications

Package: MOSim
Commit: d4f3eb40ac6978806026a94b798f641dd347051e
Author: Carolina Monzó <carolmonzoc@gmail.com>
Date: 2024-12-15 20:33:59 +0100
Commit message:

 Update README.md with MOSim applications

Package: gDRcore
Commit: ffb74ac35fd2995cf819c095db297028acaf2108
Author: Bartek <32614650+bczech@users.noreply.github.com>
Date: 2025-03-31 11:13:04 +0200
Commit message:

 Merge pull request #172 from gdrplatform/GDR-2941

Gdr 2941

Package: gDRcore
Commit: 8c6d4187f982ff9432acc3a1663506f5ccedf26f
Author: Bartek Czech <bartosz.w.czech@gmail.com>
Date: 2025-03-31 09:13:21 +0200
Commit message:

 test: add unit tests

Package: gDRcore
Commit: ee42dbde3d03427decd13f7b1c8ba2942c24dec9
Author: Bartek Czech <bartosz.w.czech@gmail.com>
Date: 2025-03-31 09:10:50 +0200
Commit message:

 chore: bump version and update NEWS.md

Package: gDRcore
Commit: be42295fe0bdd7981266500148a0318698f249a9
Author: Bartek Czech <bartosz.w.czech@gmail.com>
Date: 2025-03-31 09:09:37 +0200
Commit message:

 refactor: extend the logic for getting annotation from dt

Package: pairedGSEA
Commit: 3c060be2bf86d913b7fb1e235deff17578c20b3a
Author: Søren Helweg Dam <49019552+shdam@users.noreply.github.com>
Date: 2025-03-31 11:06:52 +0200
Commit message:

 add fix in vignette

Package: pairedGSEA
Commit: d886a0fef338cacfe94394fa7ab0df932c912d3a
Author: Søren Helweg Dam <49019552+shdam@users.noreply.github.com>
Date: 2025-03-31 10:47:57 +0200
Commit message:

 suggest plotly

Package: COTAN
Commit: 2a8638ae6300ba09bd02f2e29332d4c04643e47e
Author: trinetra75 <marco.fantozzi@gmail.com>
Date: 2025-03-12 18:10:58 +0100
Commit message:

 Bumped-up version and updated NEWS.md

Package: COTAN
Commit: 217f80ddee194afa7697441091845089f31e5679
Author: Marco Fantozzi <57561972+trinetra75@users.noreply.github.com>
Date: 2025-03-12 17:36:47 +0100
Commit message:

 Smaller vignette size (#104)

* Made compiled vignette file smaller

* Fixed typo in documentation

Package: COTAN
Commit: 3884ef776cdf322249ecb533810874af9897f818
Author: Marco Fantozzi <57561972+trinetra75@users.noreply.github.com>
Date: 2025-03-12 17:30:10 +0100
Commit message:

 Added fall-back method for distance calculations (#105)

* Added fall-back method for distance calculations

Wrapped all calls to the `parDist()` function into a local utility
function `calcDist()`. In this way it will be possible to recover
in case parDist() has troubles running n the architecture

* Updated NEWS.md

Package: FLAMES
Commit: 67e4189d0f17f01dee29f9ac1df26c1f5cf487ec
Author: Changqing Wang <wang.ch@wehi.edu.au>
Date: 2025-03-31 15:06:23 +1100
Commit message:

 version bump

Package: FLAMES
Commit: b89365058089fafd727b7418f9e9187d66ab9b64
Author: Changqing Wang <wang.ch@wehi.edu.au>
Date: 2025-03-27 18:53:28 +1100
Commit message:

 remove non-ASCII chars; move warnings to check_args; allow rownames as transcript_id argument for plot_isoform_heatmap

Package: FLAMES
Commit: db2ec3652d562538c96e413789a727483b550458
Author: ChangqingW <87298334+ChangqingW@users.noreply.github.com>
Date: 2025-03-27 18:20:26 +1100
Commit message:

 Merge pull request #56 from Sefi196/master

Sefi pull request - FLAMES Improved speed, clarity & config file

Package: FLAMES
Commit: c83e0769451c2c30b86b398e6aa9d1216d04dda1
Author: Sefi_(Yair)_Prawer <69101574+Sefi196@users.noreply.github.com>
Date: 2025-03-26 19:24:28 +1100
Commit message:

 Update sc_long_multisample_pipeline.R

remove troubleshooting comments

Package: FLAMES
Commit: 73b8f3b6b259e6b6d04637edaa7e3a359f7c810b
Author: Sefi Prawer <yairp@student.unimelb.edu.au>
Date: 2025-03-20 18:49:56 +1100
Commit message:

 bug fix in sc_long_pipeline

Package: FLAMES
Commit: c2b89e1845ae36bf8387e7c03f4b5b2d3c2a4f7f
Author: Sefi Prawer <yairp@student.unimelb.edu.au>
Date: 2025-03-20 17:37:56 +1100
Commit message:

 fix typos in readme

Package: FLAMES
Commit: 9a7e5e9ac0c536b90f2b211b9eb3f3c277af9e27
Author: Sefi Prawer <yairp@student.unimelb.edu.au>
Date: 2025-03-20 17:34:24 +1100
Commit message:

 update readme

Package: FLAMES
Commit: 49b19a92abe562a130571c40982cfd7538305e96
Author: Sefi Prawer <yairp@student.unimelb.edu.au>
Date: 2025-03-20 17:31:01 +1100
Commit message:

 Add multithreading to bam sorting

Package: scHiCcompare
Commit: a3e8cb134fd024499ad582f72d4a53d9bc95eb39
Author: hamy12398 <93464589+hamy12398@users.noreply.github.com>
Date: 2025-03-30 23:28:10 -0400
Commit message:

 Merge pull request #20 from dozmorovlab/devel

Devel

Package: scHiCcompare
Commit: 74d8bb37f2efe532c5edeffb93555a33e59cab1c
Author: hamy12398 <93464589+hamy12398@users.noreply.github.com>
Date: 2025-03-30 23:27:08 -0400
Commit message:

 Merge pull request #19 from dozmorovlab/main

update

Package: scHiCcompare
Commit: df85150a7452909696a35045e8205efc2b304897
Author: hamy12398 <hamy.12398@gmail.com>
Date: 2025-03-30 23:24:39 -0400
Commit message:

 update github README

Package: scHiCcompare
Commit: 1d2c424e975bb73980dcc717e8c5e40ebdfc8e83
Author: hamy12398 <hamy.12398@gmail.com>
Date: 2025-03-30 23:20:05 -0400
Commit message:

 Merge branch 'main' of https://github.com/dozmorovlab/scHiCcompare

Package: scHiCcompare
Commit: d194fea575c2bdb5ebceb23e78ab4e25d28000a5
Author: hamy12398 <hamy.12398@gmail.com>
Date: 2025-03-30 23:19:49 -0400
Commit message:

 update

Package: scHiCcompare
Commit: a12b24bdd29d349ddaeb4b1ab813e9528db09abb
Author: hamy12398 <93464589+hamy12398@users.noreply.github.com>
Date: 2025-03-30 23:18:23 -0400
Commit message:

 Merge pull request #18 from dozmorovlab/main

merge

Package: scHiCcompare
Commit: 9b1c9ae16b520590b429e0c4943e247f307f4da3
Author: hamy12398 <93464589+hamy12398@users.noreply.github.com>
Date: 2025-03-30 23:17:42 -0400
Commit message:

 Merge pull request #17 from dozmorovlab/devel

Merge pull request #16 from dozmorovlab/main

Package: scHiCcompare
Commit: 2417459a4b7a60a1c4860d5f1ca5518837b3f74b
Author: hamy12398 <hamy.12398@gmail.com>
Date: 2025-03-30 23:16:12 -0400
Commit message:

 update checkNumber class

Package: scHiCcompare
Commit: 49311a3f869c035b01a59b8b0c1420cffc68b60d
Author: hamy12398 <93464589+hamy12398@users.noreply.github.com>
Date: 2025-03-30 22:03:01 -0400
Commit message:

 Merge pull request #16 from dozmorovlab/main

merge

Package: scHiCcompare
Commit: d1250da4522b0132d36a6d1cb964f8fb1f0f1dd9
Author: hamy12398 <hamy.12398@gmail.com>
Date: 2025-03-30 21:38:08 -0400
Commit message:

 update vers

Package: scHiCcompare
Commit: aeca7a0d946a4d55dfd7d635f58452be50498827
Author: hamy12398 <93464589+hamy12398@users.noreply.github.com>
Date: 2025-03-30 21:07:30 -0400
Commit message:

 Merge pull request #15 from dozmorovlab/devel

Merge pull request #14 from dozmorovlab/main

Package: scHiCcompare
Commit: bf1c82676203e4570030ff4deb1dfca4c00c4522
Author: hamy12398 <93464589+hamy12398@users.noreply.github.com>
Date: 2025-03-30 21:07:05 -0400
Commit message:

 Merge pull request #14 from dozmorovlab/main

merge

Package: motifTestR
Commit: de15f8c1b24c48d7537c29851328aa3aa165c13e
Author: Stevie Ped <stephen.pederson.au@gmail.com>
Date: 2025-03-11 01:20:17 +1030
Commit message:

 Tidied up mcols for simSeq

Package: motifTestR
Commit: 7c893b79e22f35f7c2b4e18ee53a01b4132d0759
Author: Stevie Ped <stephen.pederson.au@gmail.com>
Date: 2025-03-10 23:49:19 +1030
Commit message:

 Added Poisson & NB capabilities when simulating sequences

Package: motifTestR
Commit: 271bbeb8f356e89a2a0c1904d2bf741a569b2bba
Author: Stevie Ped <stephen.pederson.au@gmail.com>
Date: 2025-03-09 01:45:44 +1030
Commit message:

 Added prior counts to hypergeometric

Package: motifTestR
Commit: f12a5ae5109b29ef364bffd53498f6d3728e7ec6
Author: Stevie Ped <stephen.pederson.au@gmail.com>
Date: 2025-03-09 01:32:27 +1030
Commit message:

 Enabled prior counts for poisson, quasipoisson and iterative enrichment testing

Package: BatchSVG
Commit: f0d7b6147bd057f3922521ecbbd94d9b1a656166
Author: christinehou11 <chou11@jh.edu>
Date: 2025-03-30 20:13:51 -0400
Commit message:

new

Package: TreeSummarizedExperiment
Commit: ee1204e0e044c67b420b5d981ef5df788da11a88
Author: Mark Robinson <mark.robinson@mls.uzh.ch>
Date: 2025-03-11 23:01:29 +0100
Commit message:

 Merge pull request #87 from TuomasBorman/master

Update cache action

Package: TreeSummarizedExperiment
Commit: 66d732986a46c3957f334b4fd0b121fc5419ab0e
Author: TuomasBorman <tvborm@utu.fi>
Date: 2025-03-10 21:12:07 +0200
Commit message:

 Update cache action

Package: TreeSummarizedExperiment
Commit: dd628ee0e88067d321e32a434ad2e5aaccf68cff
Author: Mark Robinson <mark.robinson@mls.uzh.ch>
Date: 2025-03-10 16:02:32 +0100
Commit message:

 fix version conflict

Package: TreeSummarizedExperiment
Commit: 84b8243db8b564990c76c1021afa649d529b4c02
Author: Mark Robinson <mark.robinson@mls.uzh.ch>
Date: 2025-03-10 15:52:29 +0100
Commit message:

 bump version

Package: TreeSummarizedExperiment
Commit: c9ea18093e780f73a2571b0fd928b315a3f95952
Author: Ruizhu HUANG <ruizhuRH@gmail.com>
Date: 2025-03-10 15:47:34 +0100
Commit message:

 Merge pull request #86 from TuomasBorman/master

Bugfix to subsetByLeaf

Package: TreeSummarizedExperiment
Commit: f5335a07f4575ddbf7b2670a77ed0e4685d2287b
Author: TuomasBorman <tvborm@utu.fi>
Date: 2025-03-06 10:56:53 +0200
Commit message:

 Bugfix to subsetByLeaf

Package: PureCN
Commit: 956277bf52388cb7790d5b5735778bad1864054f
Author: Markus Riester <markus.riester@novartis.com>
Date: 2025-03-30 15:05:57 -0400
Commit message:

 Another attempt in fixing build errors.

Package: PureCN
Commit: 7101598bfb2cea01e953f2ac402bc49fb2159e4c
Author: Markus Riester <markus.riester@novartis.com>
Date: 2025-03-30 14:34:28 -0400
Commit message:

 Attempt in fixing build errors.

Package: notame
Commit: ed74b6b3e17905a29e4c61ba0ac2f35677636cd1
Author: vsuksi <vsuksi@abo.fi>
Date: 2025-03-30 22:20:46 +0300
Commit message:

 Bump submission version

Package: notame
Commit: d37525982280b9cc3dad2f0c59eeef61f180e5dc
Author: vsuksi <vsuksi@abo.fi>
Date: 2025-03-30 22:18:24 +0300
Commit message:

 Example for scale method added

Example for scale method added to address BiocCheck NOTE (not sure why 
scale methods require example but log methods do not).

Package: notame
Commit: 0f31d5c8b094b3cb9e5d563e5732f73e8cb55e7f
Author: vsuksi <vsuksi@abo.fi>
Date: 2025-03-30 22:16:52 +0300
Commit message:

 Fix examples with long run time

Doing less repeats of cross-validation in mixOmics wrappers. Also 
included nrepeat parameter in call to mixOmics::perf(), believing there 
was formerly a mistake here with 50 repeats hard-coded. Only need to 
shave off seconds or so for R CMD check (max 10 minutes), here goes a 
minute or so. Further reduction of check time is not trivial.

Package: BiocParallel
Commit: c722890ecae4201337bcd28f0e3030601cf355bd
Author: Martin Morgan <mtmorgan.xyz@gmail.com>
Date: 2025-03-30 10:01:03 -0400
Commit message:

 Merge branch 'boost-patch-template-arg' into devel

- closes #271

Package: BiocParallel
Commit: 73c479567ff279b937b8dde405f084079b0e829c
Author: Martin Morgan <mtmorgan.xyz@gmail.com>
Date: 2025-03-30 10:00:15 -0400
Commit message:

 version bump and NEWS entry

- update R dependency for use of `|>`

Package: BiocParallel
Commit: 5d4bedbddaa4cebaa008491dbf3dac3b73aa482c
Author: Martin Morgan <mtmorgan.xyz@gmail.com>
Date: 2025-03-29 17:37:11 -0400
Commit message:

 `from_first_header` is not a templated member of block_header_t

Package: BiocParallel
Commit: 8239b257076223fd92d977cc128f53399597b0ab
Author: Martin Morgan <mtmorgan.xyz@gmail.com>
Date: 2025-03-29 12:28:40 -0400
Commit message:

 arrange to use 'boost_patch_1_87/interprocess/segment_manager.hpp'

Package: BiocParallel
Commit: 1b463dcd2bae67c002253ce7a7f0bfb632de3069
Author: Martin Morgan <mtmorgan.xyz@gmail.com>
Date: 2025-03-29 12:23:57 -0400
Commit message:

 add boost files requiring modification

Package: cfTools
Commit: e148f8e01d851d12fa81f8c1baafa47c40088941
Author: RoseHuRan <huran@ucla.edu>
Date: 2025-03-29 22:32:57 -0400
Commit message:

 add function

Package: PloidyPeaks
Commit: f077f418a18053829aa1a3ee9eb3daf2c0e93ebc
Author: ckostna <caitlinkostna@shaw.ca>
Date: 2025-03-29 16:41:50 -0500
Commit message:

 new documentation

Package: PloidyPeaks
Commit: 28bc07b97b1da1aa1b9a4d6034c56ae71209fe3a
Author: ckostna <caitlinkostna@shaw.ca>
Date: 2025-03-29 16:14:00 -0500
Commit message:

 remove html

Package: PloidyPeaks
Commit: 8da4d9f4bc0459b1d5f9ed8976dd0b35f9589a07
Author: ckostna <caitlinkostna@shaw.ca>
Date: 2025-03-29 16:13:18 -0500
Commit message:

 update

Package: PloidyPeaks
Commit: 99e2bfa9bc3a24642bb69ec784a6ff60263d8a38
Author: ckostna <caitlinkostna@shaw.ca>
Date: 2025-03-29 15:45:36 -0500
Commit message:

 remove html

Package: PloidyPeaks
Commit: 54914a898f550c42459e84914a7ade89db768862
Author: ckostna <caitlinkostna@shaw.ca>
Date: 2025-03-29 15:45:11 -0500
Commit message:

 update

Package: omXplore
Commit: 45244310f836521b35b388aec3ac0635c78a33c4
Author: Samuel Wieczorek <samuel.wieczorek@cea.fr>
Date: 2025-03-29 17:11:40 +0100
Commit message:

 Update

Package: omXplore
Commit: fec6c938bbdf34f740aba15f05cd738876a663c7
Author: ARIZTEGUI Cyril <CA281109@intra.cea.fr>
Date: 2025-03-28 14:59:29 +0100
Commit message:

 Modifications ACP

Package: omXplore
Commit: 761b9952685b9c5fa5b5804d7f16708a28dd7b7d
Author: Samuel Wieczorek <samuel.wieczorek@cea.fr>
Date: 2025-03-29 16:13:51 +0100
Commit message:

 Update

Package: omXplore
Commit: 9597c89621a5d997fe706d9cdad16f03cf71bb2c
Author: Samuel Wieczorek <samuel.wieczorek@cea.fr>
Date: 2025-03-29 16:12:01 +0100
Commit message:

 Update

Package: limma
Commit: 28b157e9ce4482e7053fe9b970cd399740206e9a
Author: Gordon Smyth <smyth@wehi.edu.au>
Date: 2025-03-29 20:47:58 +1100
Commit message:

 limma 3.63.11

- Update NEWS.Rd for Bioc 3.21 release. Add dates for historical releases.

Package: edgeR
Commit: b0b5e2b277a42da129a5297c9e594dba8456f7d4
Author: Gordon Smyth <smyth@wehi.edu.au>
Date: 2025-03-29 19:50:21 +1100
Commit message:

 edgeR 4.5.10
- In diffSplice.DGEGLM, `robust` now defaults to same setting as for the original exon-level fit.

Package: pathview
Commit: affd4b6aba54ffd2aed0436e18b1161336c7e087
Author: Weijun Luo <luo_weijun@yahoo.com>
Date: 2025-03-28 22:40:20 -0400
Commit message:

 version 1.47.1

Package: PloidyPeaks
Commit: 9b12acd4476d19c2d56208af6674388ba89a3d25
Author: ckostna <caitlinkostna@shaw.ca>
Date: 2025-03-28 19:11:38 -0500
Commit message:

 remove html

Package: PloidyPeaks
Commit: d0cb24f591ee52354714081f1a44e3e8ccfd6e99
Author: ckostna <caitlinkostna@shaw.ca>
Date: 2025-03-28 19:11:04 -0500
Commit message:

 desc

Package: PloidyPeaks
Commit: 9a599af8421677a1a378cf9c56b8f3692d88ed71
Author: ckostna <caitlinkostna@shaw.ca>
Date: 2025-03-28 19:10:08 -0500
Commit message:

 Remove html

Package: PloidyPeaks
Commit: d20843c2c654c953354c38a5b37caf7afbb32139
Author: ckostna <caitlinkostna@shaw.ca>
Date: 2025-03-28 19:09:32 -0500
Commit message:

 update

Package: PloidyPeaks
Commit: 148ae0f143b5fe814baa0bcf388f536df2ccd19f
Author: ckostna <caitlinkostna@shaw.ca>
Date: 2025-03-28 18:15:55 -0500
Commit message:

 remove html

Package: PloidyPeaks
Commit: b8b1b113a3f707f105140feacacb42cb47627822
Author: ckostna <caitlinkostna@shaw.ca>
Date: 2025-03-28 18:14:52 -0500
Commit message:

 update

Package: PloidyPeaks
Commit: b798ce738522f741b714d032f119ad37b4c06ac4
Author: ckostna <caitlinkostna@shaw.ca>
Date: 2025-03-28 17:44:28 -0500
Commit message:

 Remove html

Package: PloidyPeaks
Commit: 2fc8acba3bd6b033079393150b7fe5571bd7fa97
Author: ckostna <caitlinkostna@shaw.ca>
Date: 2025-03-28 17:43:24 -0500
Commit message:

 Update

Package: PloidyPeaks
Commit: 4056f402ea8c9eaf873c81d9aa17f7bb7646c73e
Author: ckostna <caitlinkostna@shaw.ca>
Date: 2025-03-28 17:36:53 -0500
Commit message:

 Remove html

Package: PloidyPeaks
Commit: b684bb8bec1c2d9d6bc89025fea119aa813bfdc5
Author: ckostna <caitlinkostna@shaw.ca>
Date: 2025-03-28 17:36:16 -0500
Commit message:

 Update

Package: QRscore
Commit: 5f7b2bc212e96bdd885bf2b3eb9b05c5bcc34d44
Author: Fanding-Zhou <97563019+Fanding-Zhou@users.noreply.github.com>
Date: 2025-03-28 13:10:08 -0700
Commit message:

 Update package and documentation

Package: QRscore
Commit: 3672fadbafbf48363f10b3ccf976494308356c04
Author: Fanding-Zhou <97563019+Fanding-Zhou@users.noreply.github.com>
Date: 2025-03-28 13:08:11 -0700
Commit message:

 Update package and documentation

Package: PureCN
Commit: 7ed7c90c8bab4acabd3c03c8f97e7184c8aace03
Author: Markus Riester <markus.riester@novartis.com>
Date: 2025-03-28 14:31:40 -0400
Commit message:

 Merge branch 'devel' of https://github.com/lima1/PureCN into devel

Package: PureCN
Commit: f117e0616463f98a7d5942c8dc46d3461da1a1fb
Author: Markus Riester <markus.riester@novartis.com>
Date: 2025-03-28 14:31:08 -0400
Commit message:

 Version bump.

Package: PureCN
Commit: 55905e78ab2da14b8a23d9fdd622ad4f85d36585
Author: Markus Riester <markus.riester@novartis.com>
Date: 2025-03-28 14:27:48 -0400
Commit message:

 Merge pull request #384 from lima1/issue_342

Issue 342

Package: PureCN
Commit: 69f0492e9d827516b0acb38448de897d1a36f39e
Author: Markus Riester <markus.riester@novartis.com>
Date: 2025-03-28 14:23:32 -0400
Commit message:

 Merge branch 'devel' into issue_342

Package: PureCN
Commit: bc70644168918b60090420840ad60393e01e9901
Author: Markus Riester <markus.riester@novartis.com>
Date: 2025-03-28 13:53:58 -0400
Commit message:

 Merge branch 'devel' into issue_342

Package: PureCN
Commit: f14ac867274178c068b0d94b5a81d59eeb7fea03
Author: Markus Riester <markus.riester@novartis.com>
Date: 2024-09-13 10:36:22 -0400
Commit message:

 Merge branch 'devel' into issue_342

Package: PureCN
Commit: f1530d5d1bb873eba37a3908ba1d6901ff23e8c9
Author: Markus Riester <markus.riester@novartis.com>
Date: 2024-03-28 14:50:25 -0400
Commit message:

 Keep allosome log ratio.

Package: HTqPCR
Commit: 3c817bb342387c3a41d42a203060ddd60c615027
Author: McCall <mmccall@mmcall3osx.urmc-sh.rochester.edu>
Date: 2025-03-28 13:31:21 -0400
Commit message:

 change maintainer and version bump in devel

Package: qpgraph
Commit: d9808da692afcbf18b5c511c1efbb2d26f5318ef
Author: Robert Castelo <robert.castelo@upf.edu>
Date: 2025-03-28 16:44:50 +0100
Commit message:

 Restore original code in the vignette now that Rgraphviz seems to have fixed the problems that where breaking it

Package: DESpace
Commit: 3ec00b4fe658795df70e42fc7c631fce84296ff1
Author: peicai <peiying.cai@gmail.com>
Date: 2025-03-28 16:26:35 +0100
Commit message:

 reduce package size

Package: DESpace
Commit: ac95b439900212fef2d5cf0775da6726eb087597
Author: peicai <55488976+peicai@users.noreply.github.com>
Date: 2025-03-25 18:43:28 +0100
Commit message:

 Update README.md

Package: DESpace
Commit: 83f3689d44d8e09eb55122c7b577378a5376a195
Author: peicai <peiying.cai@gmail.com>
Date: 2025-03-25 18:03:44 +0100
Commit message:

 r version for pkgdown

Package: DESpace
Commit: 9102ddf462abb5e4a61482ef3d684c916d450dca
Author: peicai <peiying.cai@gmail.com>
Date: 2025-03-25 16:25:15 +0100
Commit message:

 update r version

Package: DESpace
Commit: d7a48f9df3149fd22e04ae3cd1b80327a319a5cb
Author: peicai <peiying.cai@gmail.com>
Date: 2025-03-25 15:33:25 +0100
Commit message:

 change r version to devel

Package: DESpace
Commit: b1d99054373190bb23fe101feb3d19b3ec7b04b2
Author: peicai <peiying.cai@gmail.com>
Date: 2025-03-25 13:44:52 +0100
Commit message:

 fix sosta fct and build pkgdown

Package: Lheuristic
Commit: 239fa1d66d440a6f2e4dcbcdebebc93676439fb3
Author: ASPteaching <asanchez@ub.edu>
Date: 2025-03-28 16:18:50 +0100
Commit message:

 solved warnig with Aviso: replacing previous import 'MultiAssayExperiment::complete.cases' by 'stats::complete.cases' when loading 'Lheuristic'

Package: CCAFE
Commit: 9f60ddb5336d6e6809320fe4a0b3f0323f8e7ea8
Author: Hayley Wolff <150075196+wolffha@users.noreply.github.com>
Date: 2025-03-28 08:25:17 -0600
Commit message:

 Update NEWS

Package: CCAFE
Commit: 7b51d55d9a119756534673fcc9ec707dd62a63d1
Author: Hayley Wolff <150075196+wolffha@users.noreply.github.com>
Date: 2025-03-28 08:24:41 -0600
Commit message:

 Bump version

Package: CCAFE
Commit: 7cec305517b00e37128ab327a97f24555102f705
Author: wolffha <150075196+wolffha@users.noreply.github.com>
Date: 2025-03-28 08:23:21 -0600
Commit message:

 Delete intermediate files in vignettes folder

Package: snpStats
Commit: c8d871945d6ff169e7319fa7b674634a07a93e0e
Author: vjcitn <stvjc@channing.harvard.edu>
Date: 2025-03-27 22:25:24 +0000
Commit message:

 repair a problem in ld when depth is not set in R but passed as NULL to
C

Package: RiboCrypt
Commit: baae084618022b028edad287ff19b41b21adfd79
Author: Roleren <hauken_heyken@hotmail.com>
Date: 2025-03-28 12:30:05 +0100
Commit message:

 bump version

Package: RiboCrypt
Commit: 44bf1afe70a4e7fd54e4c64ff75199a894431f5f
Author: Roleren <hauken_heyken@hotmail.com>
Date: 2025-03-28 12:28:47 +0100
Commit message:

 Made animate plot work again

Package: RiboCrypt
Commit: 0446db4f41f8a89b7122771160cccaf7c124ee5a
Author: Roleren <hauken_heyken@hotmail.com>
Date: 2025-03-28 11:47:43 +0100
Commit message:

 Improved docs for multiomics

Package: RiboCrypt
Commit: 126d3b4eb7853ec1f278e30f2cc40bf3626c91d6
Author: Roleren <hauken_heyken@hotmail.com>
Date: 2025-03-28 11:44:20 +0100
Commit message:

 Fixed R call functions to multiomics

Package: RiboCrypt
Commit: 4b5e5a40d7194742c1edee65cae2f4dd27c8e46b
Author: Roleren <hauken_heyken@hotmail.com>
Date: 2025-03-26 09:53:42 +0100
Commit message:

 Now allows to not have bam files present

Package: RiboCrypt
Commit: 51e338048c4726e442c07cd37e7589df027956ee
Author: Roleren <hauken_heyken@hotmail.com>
Date: 2025-03-25 15:58:58 +0100
Commit message:

 Fixed bug in DEG selectize clicking and browser now has better Y coordinates

Package: IntEREst
Commit: d1e5d0150959671659c0d567e1aff7afcf1fae03
Author: gacatag <ali.oghabian@helsinki.fi>
Date: 2025-03-28 12:25:25 +0200
Commit message:

 Correcting limitRanges setting. Removing unnecessary codes.

Package: Lheuristic
Commit: 780c31445560837cec1d46b845241608c4d70d80
Author: ASPteaching <asanchez@ub.edu>
Date: 2025-03-28 11:10:20 +0100
Commit message:

 Update with changes required by reviewer

Package: MSA2dist
Commit: dcadc7af4b0ef83bf8d264e85d0513896eb71579
Author: Kristian Ullrich <ullrich@evolbio.mpg.de>
Date: 2025-03-28 09:07:37 +0100
Commit message:

 update DESCRIPTION

Package: spacexr
Commit: 48081abe9acdb485e54090794fc60987089d3e08
Author: ggrajeda <gabriel.grajeda@gmail.com>
Date: 2025-03-28 04:02:38 -0400
Commit message:

 Bump package version to 0.99.2

Package: spacexr
Commit: 64c2b447bc09050eff25f803de2a72573b97b8e3
Author: ggrajeda <gabriel.grajeda@gmail.com>
Date: 2025-03-27 16:20:56 -0400
Commit message:

 Export createRctd again

Users are now able to see the pre-processed data again.

Package: SimBu
Commit: a7c13d21ffb53a9034c6878c0c2fc0bdeb0568a2
Author: alex-d13 <dietrich.alexander1310@gmail.com>
Date: 2025-03-28 08:50:10 +0100
Commit message:

 Fix YAML boolean values and vignette title warnings

Package: stPipe
Commit: e271a01594fad9b572fdb92eb73ddbf0bb1ae229
Author: YangXuuu <xuyang1121wws@gmail.com>
Date: 2025-03-28 17:27:46 +1100
Commit message:

 Version bump: 0.99.2 -> 0.99.3

Package: mixOmics
Commit: 6319ff6665c34f46f10d636251b72f372d783abb
Author: Kim-Anh Lê Cao <mixomicsdeveloper@gmail.com>
Date: 2025-03-28 14:47:44 +1100
Commit message:

 Merge remote-tracking branch 'bioc/devel' into HEAD

Package: mixOmics
Commit: 7525ec27a7a2707eafa12d9d64340df6bcd2f1d7
Author: Eva Hamrud <50098063+evaham1@users.noreply.github.com>
Date: 2025-03-28 14:03:28 +1100
Commit message:

 Merge pull request #360 from mixOmicsTeam/357-plotindiv-pch-order

357 plotindiv pch order

Package: mixOmics
Commit: c9e32592ad17d68dd4d70a52e0af0f675b167224
Author: Eva Hamrud <50098063+evaham1@users.noreply.github.com>
Date: 2025-03-28 12:32:38 +1100
Commit message:

 updated deprecated 'size' to 'linewidth'

Package: mixOmics
Commit: 40347570f8cbbd9d357c849ee8c2adb1761193d6
Author: Eva Hamrud <50098063+evaham1@users.noreply.github.com>
Date: 2025-03-28 12:23:23 +1100
Commit message:

 update deprecated 'size' to 'linewidth'

Package: mixOmics
Commit: bf5a62db510342709aaa4a85a12b7af6d1fbdc0f
Author: Eva Hamrud <50098063+evaham1@users.noreply.github.com>
Date: 2025-03-28 12:17:13 +1100
Commit message:

 add unit tests for biplot

Package: mixOmics
Commit: a95f98e4960ccdc3e9818351c4e4c76f0ab62ebc
Author: Eva Hamrud <50098063+evaham1@users.noreply.github.com>
Date: 2025-03-28 12:09:19 +1100
Commit message:

 add examples and fix pch issues with biplot

Package: mixOmics
Commit: f540dc459f43292b0a893344729550aebfcb5874
Author: Eva Hamrud <50098063+evaham1@users.noreply.github.com>
Date: 2025-03-28 11:46:57 +1100
Commit message:

 plot arrow unit testing

Package: mixOmics
Commit: 3bf1ec69d39820ab7e48c8e2fcbb7ea2c993bdc3
Author: Eva Hamrud <50098063+evaham1@users.noreply.github.com>
Date: 2025-03-28 11:41:17 +1100
Commit message:

 updated plotArrow docs so pch customisable

Package: mixOmics
Commit: 751e9f7359ece5fb319c3529a655c27276123c62
Author: Eva Hamrud <50098063+evaham1@users.noreply.github.com>
Date: 2025-03-21 16:30:59 +1100
Commit message:

 reduce biocparallel workers to 2 for all processes

Package: mixOmics
Commit: bad76b9781be28542f22e01acf58c23b448d2cdd
Author: Eva Hamrud <50098063+evaham1@users.noreply.github.com>
Date: 2025-03-21 16:11:29 +1100
Commit message:

 force bpparam to 2 to not exceed cpus on github runner

Package: mixOmics
Commit: 2b2a4e2bf6b2af5d52d17245b887f2261d15a0d1
Author: Eva Hamrud <50098063+evaham1@users.noreply.github.com>
Date: 2025-03-21 15:53:41 +1100
Commit message:

 built vignette locally

Package: mixOmics
Commit: 464e69c86454d200958a3f294823c671adfb4c27
Author: Eva Hamrud <50098063+evaham1@users.noreply.github.com>
Date: 2025-03-21 15:46:36 +1100
Commit message:

 add mime to suggests package

Package: mixOmics
Commit: b0da17fba0e93e1f23f787c89f1184370c95749b
Author: Eva Hamrud <50098063+evaham1@users.noreply.github.com>
Date: 2025-03-21 15:44:07 +1100
Commit message:

 debug rcmd check errors

Package: mixOmics
Commit: afefabfc64aff9625ec37b856238eb87bf650416
Author: Eva Hamrud <50098063+evaham1@users.noreply.github.com>
Date: 2025-03-21 15:06:27 +1100
Commit message:

 typo in plotarrow example

Package: mixOmics
Commit: 66c7ab370b1061f0f8d485ec036db983a18d21bb
Author: Eva Hamrud <50098063+evaham1@users.noreply.github.com>
Date: 2025-03-21 14:52:36 +1100
Commit message:

 update docs

Package: mixOmics
Commit: 31af70b0b77fa4f66d95a90139387d1bb99189fe
Author: Eva Hamrud <50098063+evaham1@users.noreply.github.com>
Date: 2025-03-21 14:52:21 +1100
Commit message:

 remove col.per.group from biplot function

Package: mixOmics
Commit: 87765abeab4500d0c24474572faad47a690b13ff
Author: Eva Hamrud <50098063+evaham1@users.noreply.github.com>
Date: 2025-03-21 14:44:23 +1100
Commit message:

 update docs

Package: mixOmics
Commit: d55cdd18a0233f6a4716a4d7b1e12c7620f0ad1e
Author: Eva Hamrud <50098063+evaham1@users.noreply.github.com>
Date: 2025-03-21 14:44:17 +1100
Commit message:

 remov col.per.group from plotArrow

Package: mixOmics
Commit: e19070711c5dc9124300beb9119cc99299e023d7
Author: Eva Hamrud <50098063+evaham1@users.noreply.github.com>
Date: 2025-03-21 14:37:56 +1100
Commit message:

 trying to pass rcmdcheck locally

Package: mixOmics
Commit: 7cd33407409e705bf7989fdcd1e137f74ea4b2de
Author: Eva Hamrud <50098063+evaham1@users.noreply.github.com>
Date: 2025-03-21 13:51:01 +1100
Commit message:

 test plots

Package: mixOmics
Commit: 4f329b838fb64ee52641fe33f33deeb6817b764a
Author: Eva Hamrud <50098063+evaham1@users.noreply.github.com>
Date: 2025-03-21 13:50:50 +1100
Commit message:

 update unit tests so they work on both R4.4 and R4.5

Package: mixOmics
Commit: ee53695b0dd2a4c50d042ebb94aba1e43909c6a2
Author: Eva Hamrud <50098063+evaham1@users.noreply.github.com>
Date: 2025-03-21 12:06:59 +1100
Commit message:

 update plotIndiv docs and examples

Package: mixOmics
Commit: 387b594c009cdf54c263b2d35e1a9b7e93ad2b33
Author: Eva Hamrud <50098063+evaham1@users.noreply.github.com>
Date: 2025-03-19 15:08:38 +1100
Commit message:

 update docs for plotIndiv new args

Package: mixOmics
Commit: fcdb4ca20d1bdca9ac5305f73f43837b2a44b3d5
Author: Eva Hamrud <50098063+evaham1@users.noreply.github.com>
Date: 2025-03-19 14:43:12 +1100
Commit message:

 fixed warnings and tests

Package: mixOmics
Commit: 7b4e51a026ecd56eea5d5c043eebb8e69b59bd5b
Author: Eva Hamrud <50098063+evaham1@users.noreply.github.com>
Date: 2025-03-19 14:33:41 +1100
Commit message:

 add unit tests for argument checking

Package: mixOmics
Commit: dbaca0ec2615dc8f5caf6d42bcc7a40637696de3
Author: Eva Hamrud <50098063+evaham1@users.noreply.github.com>
Date: 2025-03-19 13:23:51 +1100
Commit message:

 cleanup plotIndiv.sgcca args

Package: mixOmics
Commit: 9cca5bd6a36488e287b50f7ffff2e7b5c55c5309
Author: Eva Hamrud <50098063+evaham1@users.noreply.github.com>
Date: 2025-03-19 13:21:16 +1100
Commit message:

 cleanup plotIndiv.pca args

Package: mixOmics
Commit: d7db45fa99349778f816a359d20a353aa0c7649a
Author: Eva Hamrud <50098063+evaham1@users.noreply.github.com>
Date: 2025-03-19 13:17:56 +1100
Commit message:

 clean up plotIndiv mint args

Package: mixOmics
Commit: d467f8842febb1d8b48ba6c3a9191d07bdc45377
Author: Eva Hamrud <50098063+evaham1@users.noreply.github.com>
Date: 2025-03-19 11:56:21 +1100
Commit message:

 make plotIndiv unit testing silent

Package: mixOmics
Commit: ee5b705b5a3998192e617f1a0ff51d4c6eda786c
Author: Eva Hamrud <50098063+evaham1@users.noreply.github.com>
Date: 2025-03-19 11:43:49 +1100
Commit message:

 add unit tests for mint.pls objs

Package: mixOmics
Commit: caa68a046a2615416804c871b21da232bbe113fb
Author: Eva Hamrud <50098063+evaham1@users.noreply.github.com>
Date: 2025-03-19 11:41:23 +1100
Commit message:

 add plotIndiv.mint tests for mint plsda objs

Package: mixOmics
Commit: d75d84672d2e7d74981e919b5d1e24829de1bab5
Author: Eva Hamrud <50098063+evaham1@users.noreply.github.com>
Date: 2025-03-19 11:31:05 +1100
Commit message:

 add unit test for background plotIndiv on plsda obj

Package: mixOmics
Commit: e038c938c0b89bd516010110eeb9736c51dd539f
Author: Eva Hamrud <50098063+evaham1@users.noreply.github.com>
Date: 2025-03-19 10:49:09 +1100
Commit message:

 unit tests for plotIndiv.sgccda

Package: mixOmics
Commit: 0e248bbedba616d390d133d9e82ce2d45a842b71
Author: Eva Hamrud <50098063+evaham1@users.noreply.github.com>
Date: 2025-03-18 16:46:14 +1100
Commit message:

 started on unit tests for plotIndiv.sgcca

Package: mixOmics
Commit: e79d4f1f0332e87cc5789356500cb6add14e439d
Author: Eva Hamrud <50098063+evaham1@users.noreply.github.com>
Date: 2025-03-18 16:46:00 +1100
Commit message:

 unit tests for plotIndiv.pls function (rcc, pls, plsda objs)

Package: mixOmics
Commit: b81470a37acde6a137ab3fc3346030e424c9b4b2
Author: Eva Hamrud <50098063+evaham1@users.noreply.github.com>
Date: 2025-03-18 14:45:46 +1100
Commit message:

 update plotIndiv.pca unit testing using vdiffr

Package: mixOmics
Commit: 5f4f5f998765cde958aedf0e981a58e6e0daf196
Author: Eva Hamrud <50098063+evaham1@users.noreply.github.com>
Date: 2025-03-18 12:25:17 +1100
Commit message:

 see if the failing unit test is ignored when run CI

Package: mixOmics
Commit: 9bb9daccc41fdf6878514c06dfb7d5908a22f4fe
Author: Eva Hamrud <50098063+evaham1@users.noreply.github.com>
Date: 2025-03-18 11:57:43 +1100
Commit message:

 add vdiffr package to suggested packages

Package: mixOmics
Commit: 51d48f0b89175c227d02939bb8da2fcaea76d4aa
Author: Eva Hamrud <50098063+evaham1@users.noreply.github.com>
Date: 2025-03-18 10:52:53 +1100
Commit message:

 comment out other tests for now

Package: mixOmics
Commit: 45917a20451c4c1a631a353782a768fef4ec83d1
Author: Eva Hamrud <50098063+evaham1@users.noreply.github.com>
Date: 2025-03-18 10:33:31 +1100
Commit message:

 add vdiffr installation to rcmd check workflow

Package: mixOmics
Commit: 7e38ac57fdb2dfd79aaf65a7c451b6b28217668d
Author: Eva Hamrud <50098063+evaham1@users.noreply.github.com>
Date: 2025-03-18 10:31:45 +1100
Commit message:

 update docs for pch arg

Package: mixOmics
Commit: 3b27a8e8c5dc7739f8662fd5b0b3df48da1c9dc0
Author: Eva Hamrud <50098063+evaham1@users.noreply.github.com>
Date: 2025-03-17 17:06:02 +1100
Commit message:

 fix error in plotIndiv.mint in vignette

Package: mixOmics
Commit: bf6e7e05750d9d862c3a2bb0f321083b9d284bb8
Author: Eva Hamrud <50098063+evaham1@users.noreply.github.com>
Date: 2025-03-17 16:40:53 +1100
Commit message:

 update plotIndiv examples

Package: mixOmics
Commit: 74f12e1850023b85012e770f66b3d9563044c810
Author: Eva Hamrud <50098063+evaham1@users.noreply.github.com>
Date: 2025-03-17 16:21:02 +1100
Commit message:

 output of local testing

Package: mixOmics
Commit: c10f835d956b0941f6f660b1e0faef940c10af63
Author: Eva Hamrud <50098063+evaham1@users.noreply.github.com>
Date: 2025-03-17 16:20:49 +1100
Commit message:

 testing vdiffr package for plot testing - works when run all tests locally

Package: mixOmics
Commit: 41095c5d1d8c0841d861907085e7bd804c5a22bf
Author: Eva Hamrud <50098063+evaham1@users.noreply.github.com>
Date: 2025-03-17 15:21:52 +1100
Commit message:

 tidy pch.levels arg

Package: mixOmics
Commit: df5425600e58128f98b9175b9de49aeca2cb0eb3
Author: Eva Hamrud <50098063+evaham1@users.noreply.github.com>
Date: 2025-03-17 14:57:20 +1100
Commit message:

 runs all tests

Package: mixOmics
Commit: 3a2791475564b62047649b0ca2ff3e9c502c0f3d
Author: Eva Hamrud <50098063+evaham1@users.noreply.github.com>
Date: 2025-03-17 14:29:35 +1100
Commit message:

 dont set pch  as default, but create inside function if not set

Package: mixOmics
Commit: 6ca70083bfab5fe11630eba621fb55919f2745f7
Author: Eva Hamrud <50098063+evaham1@users.noreply.github.com>
Date: 2025-03-17 14:16:11 +1100
Commit message:

 fixed plotindiv.sgcca with default pch value

Package: mixOmics
Commit: bf37de8876f7ef0be71e05b0b17e1c5daad9fb3e
Author: Eva Hamrud <50098063+evaham1@users.noreply.github.com>
Date: 2025-03-17 14:14:40 +1100
Commit message:

 fixed plotindiv.pls tests for colours and default colours

Package: mixOmics
Commit: b468e881fa719eb8b0ed62672fec79f9a1ce59c9
Author: Eva Hamrud <50098063+evaham1@users.noreply.github.com>
Date: 2025-03-17 13:10:18 +1100
Commit message:

 set default pch

Package: mixOmics
Commit: 17601ce43fe4c5c1aab65368cc219ce9b6c50882
Author: Eva Hamrud <50098063+evaham1@users.noreply.github.com>
Date: 2025-03-17 13:06:52 +1100
Commit message:

 plotIndiv.pca tests run

Package: mixOmics
Commit: bec9e9f26635e291559b03bd5f53e6c2146de854
Author: Eva Hamrud <50098063+evaham1@users.noreply.github.com>
Date: 2025-03-17 13:05:35 +1100
Commit message:

 fix plotindiv.pca cols

Package: mixOmics
Commit: 8161a2aaa036a02784f0e43431df6ad3bf987384
Author: Eva Hamrud <50098063+evaham1@users.noreply.github.com>
Date: 2025-03-17 12:01:05 +1100
Commit message:

 split plotIndiv tests by specific functions

Package: mixOmics
Commit: 186705cc60a08acc9dcca1cb4261015be8ef7704
Author: Eva Hamrud <50098063+evaham1@users.noreply.github.com>
Date: 2025-03-14 17:07:55 +1100
Commit message:

 clean up plotting args

Package: mixOmics
Commit: eadef37dffb3b610b02d996f985cfdfe3b967562
Author: Eva Hamrud <50098063+evaham1@users.noreply.github.com>
Date: 2025-03-14 16:55:04 +1100
Commit message:

 remove pch.levels arg and col.per.group args as they are redundant

Package: mixOmics
Commit: 9f113fab73c88e78132e2f504c88e2cb2fd0ba50
Author: Eva Hamrud <50098063+evaham1@users.noreply.github.com>
Date: 2025-03-14 16:10:19 +1100
Commit message:

 go back to old r and bioc version which works for cmd testing

Package: mixOmics
Commit: c7a9e3946613aaa9f583bf0bb984a86daabb7b74
Author: Eva Hamrud <50098063+evaham1@users.noreply.github.com>
Date: 2025-03-14 15:56:50 +1100
Commit message:

 fix pch order for lattice style

Package: mixOmics
Commit: f796ccd7dfbb9d3fe369e35f3e4b5b2952582574
Author: Eva Hamrud <50098063+evaham1@users.noreply.github.com>
Date: 2025-03-14 15:54:31 +1100
Commit message:

 fix pch relevelling error with graphics style

Package: mixOmics
Commit: dd252447c1927b9bde4a4ca73fde8e71beb5070e
Author: Eva Hamrud <50098063+evaham1@users.noreply.github.com>
Date: 2025-03-14 14:48:15 +1100
Commit message:

 fixed reordering of pch levels when colour groups are different

Package: stPipe
Commit: 45b125dfa2192f7f6616a3fc92db12c5b5b82123
Author: YangXuuu <xuyang1121wws@gmail.com>
Date: 2025-03-28 13:43:45 +1100
Commit message:

 Version bump: 0.99.1 -> 0.99.2

Package: stPipe
Commit: e1e6b1840c850fa6c409641f55000c6f25e14c28
Author: YangXuuu <xuyang1121wws@gmail.com>
Date: 2025-03-28 12:43:19 +1100
Commit message:

 Version bump: update src/Makevars

Package: stPipe
Commit: 122f4695cfb49ad09be281639b16525d7f5bef07
Author: YangXuuu <xuyang1121wws@gmail.com>
Date: 2025-03-28 12:29:35 +1100
Commit message:

 Version bump: update DESCRIPTION and src/Makevars

Package: dmGsea
Commit: 3e41bf1a711960b1e6599e1cb5b78b676de0be6e
Author: xuz1 <xuz@niehs.nih.gov>
Date: 2025-03-27 20:35:52 -0400
Commit message:

 bugfix

Signed-off-by: xuz1 <xuz@niehs.nih.gov>

Package: dmGsea
Commit: c756ca3dc0ba74f4e49d3d75cb5b636771cce938
Author: xuz1 <xuz@niehs.nih.gov>
Date: 2025-03-27 20:17:16 -0400
Commit message:

 Bug fix

Package: gDRutils
Commit: d8be1464998cad365e36b32da2f9960c793449d1
Author: darsoo <daro.scig@gmail.com>
Date: 2025-03-28 00:43:25 +0100
Commit message:

 Merge pull request #155 from gdrplatform/GDR-2896

Gdr 2896

Package: gDRutils
Commit: b2b32d2134ee3ac7f252cad4cc945daf2bfdf878
Author: Dariusz Scigocki <daro.scig@gmail.com>
Date: 2025-03-27 13:56:06 +0100
Commit message:

 Merge branch 'GDR-2896' of github.com:gdrplatform/gDRutils into GDR-2896

Package: gDRutils
Commit: 05edba38d45c6d43204490e5550e632ea934ac11
Author: darsoo <daro.scig@gmail.com>
Date: 2025-03-27 13:55:27 +0100
Commit message:

 Update R/utils.R

Co-authored-by: j-smola <31825957+j-smola@users.noreply.github.com>

Package: gDRutils
Commit: eba675afc99bbb6e4199b0e26ad41adf2f126394
Author: darsoo <daro.scig@gmail.com>
Date: 2025-03-27 13:55:18 +0100
Commit message:

 Update R/utils.R

Co-authored-by: j-smola <31825957+j-smola@users.noreply.github.com>

Package: gDRutils
Commit: 361153e91ad02fca8f24a1f6ed04dee1b19d1047
Author: Dariusz Scigocki <daro.scig@gmail.com>
Date: 2025-03-27 13:54:53 +0100
Commit message:

 added test for default param in get_settings_from_json

Package: gDRutils
Commit: 216115e8df8df22e56faab5608f7cb20f03e134d
Author: Dariusz Scigocki <daro.scig@gmail.com>
Date: 2025-03-27 10:11:14 +0100
Commit message:

 updated docs

Package: gDRutils
Commit: 32298bacc901e45695a7bf0b253edd6fab05d8a7
Author: Dariusz Scigocki <daro.scig@gmail.com>
Date: 2025-03-26 09:15:27 -0700
Commit message:

 fixed issue with wrong format of output in split_big_table_for_xlsx

Package: gDRutils
Commit: 2ddca04ee96be164840fed452a0de3220d83c575
Author: Dariusz Scigocki <daro.scig@gmail.com>
Date: 2025-03-26 10:03:08 +0000
Commit message:

 bump version

Package: gDRutils
Commit: f8c1980ccdd46bddaab0e84b392b3d91a53c84bb
Author: Dariusz Scigocki <daro.scig@gmail.com>
Date: 2025-03-26 10:02:10 +0000
Commit message:

 fixed default parameter in get_settings_from_json

Package: TENET.ExperimentHub
Commit: ca75dd72881ace8a5a4e4afa2a2043898ddbbe7d
Author: Ethan Nelson-Moore <nelsonmo@usc.edu>
Date: 2025-03-27 14:39:56 -0700
Commit message:

 Add LICENSE file

Package: TENET.AnnotationHub
Commit: 14bccd5e6b8ce8189e7e13c5616fe64bba62c9a9
Author: Ethan Nelson-Moore <nelsonmo@usc.edu>
Date: 2025-03-27 14:38:16 -0700
Commit message:

 Add LICENSE file

Package: groHMM
Commit: b15ceadf7bf3304a729030a2776034f026d638a9
Author: Pariksheet Nanda <pan79@pitt.edu>
Date: 2025-03-27 15:34:07 -0400
Commit message:

 DEV: Synchronize noisy doxygen updates

Package: groHMM
Commit: a245a05c55e762f7e6ba9733f5d63958e9d43563
Author: Pariksheet Nanda <pan79@pitt.edu>
Date: 2025-03-27 15:33:05 -0400
Commit message:

 DOC: Add runnable examples for >=80% exported functions

Package: groHMM
Commit: bdf3eedd5a2b25b37b54d2ac59c478741d9b0d73
Author: Pariksheet Nanda <pan79@pitt.edu>
Date: 2025-03-27 15:25:29 -0400
Commit message:

 DEV: Fix BiocCheck improper author, maintainer errors

Package: groHMM
Commit: 5752698373578e1575918a8d4ac71508d296fbc2
Author: Pariksheet Nanda <pan79@pitt.edu>
Date: 2025-03-27 15:20:04 -0400
Commit message:

 MAINT: Migrate to strict headers of R 4.5

Related discussion on the bioc-devel mailing list:
https://stat.ethz.ch/pipermail/bioc-devel/2025-January/020807.html

Package: PloidyPeaks
Commit: 08d1ab9a8c0f68dfdfb7701c7051de1dcf7f42b5
Author: ckostna <caitlinkostna@shaw.ca>
Date: 2025-03-27 12:48:37 -0500
Commit message:

 Remove HTML

Package: PloidyPeaks
Commit: 618d56eb9816fd0c3db862c9ddd683d2fb23c1b0
Author: ckostna <caitlinkostna@shaw.ca>
Date: 2025-03-27 12:47:27 -0500
Commit message:

 Updated DESCRIPTION

Package: pRoloc
Commit: 6647c2f19377e07f20118b7a6a811afb99ff52cd
Author: Lisa Breckels <lms79@cam.ac.uk>
Date: 2025-03-27 15:14:06 +0000
Commit message:

 Merge pull request #154 from lgatto/prettymaps

Updates to plot2D

Package: pRoloc
Commit: eb5ac9f692cc9f91fd2a2adb07c678e9e84e97ab
Author: Lisa Breckels <lms79@cam.ac.uk>
Date: 2025-03-27 15:12:19 +0000
Commit message:

 fix figure size

Package: pRoloc
Commit: 15906e57a1f0f697844d1be85f8fe1871ef9a844
Author: Lisa Breckels <lms79@cam.ac.uk>
Date: 2025-03-27 15:03:23 +0000
Commit message:

 fix typos and doc/code mismatches

Package: pRoloc
Commit: 1cd68bb774e545585f659b2b075289a544a26b6f
Author: Lisa Breckels <lms79@cam.ac.uk>
Date: 2025-03-27 11:28:05 +0000
Commit message:

 Remove Author/Maintainer field as per BiocCheck

Package: pRoloc
Commit: 4f5150f23e4b6c9967d9396a2ed62d2bbc594ed1
Author: Lisa Breckels <lms79@cam.ac.uk>
Date: 2025-03-26 17:09:45 +0000
Commit message:

 update vignette typos, news and bump version

Package: pRoloc
Commit: d95b1038eb76a35ed07a8367c570ba7de855060b
Author: Lisa Breckels <lms79@cam.ac.uk>
Date: 2025-03-26 17:09:18 +0000
Commit message:

 update documentation for allowing unknowns to another character/name

Package: pRoloc
Commit: acf1315d2667361ac6f8b4f958e01af8cab7f3cb
Author: Lisa Breckels <lms79@cam.ac.uk>
Date: 2025-03-26 17:08:53 +0000
Commit message:

 Remove hardcoding of unknown

Package: pRoloc
Commit: 50b0225926394643b0f02a593892243c3bbf9a9f
Author: Lisa Breckels <lms79@cam.ac.uk>
Date: 2025-03-26 12:35:43 +0000
Commit message:

 Resolve merge conflicts

Package: pRoloc
Commit: 35cee07562cfb02a422bc77bdc9b2477544cf421
Author: Lisa Breckels <lms79@cam.ac.uk>
Date: 2025-03-26 11:44:26 +0000
Commit message:

 Merge pull request #157 from lgatto/cleanup

Cleanup

Package: pRoloc
Commit: f8a1ed1a8db587346848340dbc85d7bce309672a
Author: Lisa Breckels <lms79@cam.ac.uk>
Date: 2025-03-26 11:43:34 +0000
Commit message:

 remove call to local file

Package: pRoloc
Commit: 4b91c7527508f3cdbfe640ad51ad82d2df00f26b
Author: Lisa Breckels <lms79@cam.ac.uk>
Date: 2025-03-26 10:17:59 +0000
Commit message:

 update unit tests regarding GO term functions

Package: pRoloc
Commit: 9a5a573f904791e507de54f8d05bb1bc7770fb58
Author: Lisa Breckels <lms79@cam.ac.uk>
Date: 2025-03-25 14:35:30 +0000
Commit message:

 update TL vignette

Package: pRoloc
Commit: c7b0575c3173af40bc85eb15f99af16d27db8cea
Author: Lisa Breckels <lms79@cam.ac.uk>
Date: 2025-03-14 16:39:36 +0000
Commit message:

 update documentation

Package: pRoloc
Commit: 0697ef139842f479ef6eaa8eaf71ddf2abf8cde0
Author: Lisa Breckels <lms79@cam.ac.uk>
Date: 2025-03-14 10:14:17 +0000
Commit message:

 deprecate GO annotation functions

Package: pRoloc
Commit: f441bce3ddd7bf1b2a63e3f91884e472a5b42f47
Author: Lisa Breckels <lms79@cam.ac.uk>
Date: 2025-03-14 10:13:52 +0000
Commit message:

 fix typo

Package: pRoloc
Commit: 972fd6abdb0b0cfafeba1fbdb7bcfc136761a006
Author: Lisa Breckels <lms79@cam.ac.uk>
Date: 2025-03-14 09:39:28 +0000
Commit message:

 remove GO term code in clustDist functions

Package: pRoloc
Commit: b4847e6465226dabbc35981cd0e95a2d1b7fa0b9
Author: Lisa Breckels <lms79@cam.ac.uk>
Date: 2025-03-14 09:02:43 +0000
Commit message:

 update clustdist documentation

Package: pRoloc
Commit: e3d1be6c2fd5dfd800f515af4078a35d020e552b
Author: Lisa Breckels <lms79@cam.ac.uk>
Date: 2025-03-14 07:44:22 +0000
Commit message:

 remove v04 GO vignette and add clustDist to v01 vignette

Package: pRoloc
Commit: 4a8d5bddc3c580c45d3b7a03bc3f0ab324420b61
Author: Lisa Breckels <lms79@cam.ac.uk>
Date: 2025-03-14 07:27:14 +0000
Commit message:

 add option to plot method to plot raw distances

Package: pRoloc
Commit: 193c8dea797cc65d6e10e00365af8bf3f36a9b96
Author: Lisa Breckels <lms79@cam.ac.uk>
Date: 2025-03-14 07:26:47 +0000
Commit message:

 fix bug in clustdist function

Package: pRoloc
Commit: 70bbe0548d31f8c88390e78ed25d81fd0552dd82
Author: Lisa Breckels <lms79@cam.ac.uk>
Date: 2025-03-11 14:48:16 +0000
Commit message:

 remove phenodisco example from vignette and add details on class imbalance

Package: pRoloc
Commit: bd5e66196e22b813c921b9eb948fc4e941c22387
Author: Lisa Breckels <lms79@cam.ac.uk>
Date: 2024-10-24 16:36:51 +0100
Commit message:

 update news see issue #111

Package: pRoloc
Commit: f967b4e6d24c527b76ceb5fb273b58670556da20
Author: Lisa Breckels <lms79@cam.ac.uk>
Date: 2024-10-24 16:36:00 +0100
Commit message:

 add umap CRAN package to suggests

Package: pRoloc
Commit: 9f636219a2446e2bdafbcd69fdc91fbe42b8c8c0
Author: Lisa Breckels <lms79@cam.ac.uk>
Date: 2024-10-24 16:35:32 +0100
Commit message:

 add UMAP method

Package: pRoloc
Commit: 54013394d809f2b82c2ef071c3a56747d6cc6bb9
Author: Lisa Breckels <lms79@cam.ac.uk>
Date: 2024-10-24 16:35:11 +0100
Commit message:

 add section on UMAP in vignette v01 and update outdated figs

Package: pRoloc
Commit: c86e4e91ad9dc9570bc3337c706609f9516ca33c
Author: Lisa Breckels <lms79@cam.ac.uk>
Date: 2024-10-24 16:34:24 +0100
Commit message:

 add UMAP method to plot2D

Package: pRoloc
Commit: 3dfc6e4e64ab57a7d5916926b3ac9a06be3bfa35
Author: Lisa Breckels <lms79@cam.ac.uk>
Date: 2024-10-24 14:34:57 +0100
Commit message:

 update news as per issue #152

Package: pRoloc
Commit: 638810e04231f439df01247a8baa3cc4009748ff
Author: Lisa Breckels <lms79@cam.ac.uk>
Date: 2024-10-24 14:34:38 +0100
Commit message:

 add getStockbg and friends

Package: pRoloc
Commit: cc038cfde3b2f4397208bf25a5dbbe919a4a600b
Author: Lisa Breckels <lms79@cam.ac.uk>
Date: 2024-10-24 14:33:41 +0100
Commit message:

 add colorspace to depends

Package: pRoloc
Commit: cd6c8eb5a2619e64ebc78d59fd56073493808dc9
Author: Lisa Breckels <lms79@cam.ac.uk>
Date: 2024-10-24 14:32:25 +0100
Commit message:

 update vignette following #152

Package: pRoloc
Commit: 106552d37aec37c81df4d07381cef62fcfd8fd2e
Author: Lisa Breckels <lms79@cam.ac.uk>
Date: 2024-10-24 14:32:01 +0100
Commit message:

 update documentation for issue #152

Package: pRoloc
Commit: d377e9461a81a48db2738f9c3c1157f2892b3d7f
Author: Lisa Breckels <lms79@cam.ac.uk>
Date: 2024-10-24 14:31:21 +0100
Commit message:

 update plot2D as per issue #152

Package: pRoloc
Commit: 98d443c75c36b4986c34da68833d93e4893f95b9
Author: Lisa Breckels <lms79@cam.ac.uk>
Date: 2024-10-24 14:30:49 +0100
Commit message:

 add new functions getStockbg and friends

Package: gwascat
Commit: 8252998acda3a9032911b8bb590a2724f886667a
Author: vjcitn <stvjc@channing.harvard.edu>
Date: 2025-03-27 13:15:00 -0400
Commit message:

 blocking a core dumping test

Package: QRscore
Commit: cb5507f4c17a90b2806594ee4efec319849e4547
Author: Fanding-Zhou <97563019+Fanding-Zhou@users.noreply.github.com>
Date: 2025-03-27 09:13:32 -0700
Commit message:

 Address Bioconductor suggestions

Package: omXplore
Commit: 7adf05d1fafacd0f1714f6d337e8fdf6852aa92d
Author: Samuel Wieczorek <samuel.wieczorek@cea.fr>
Date: 2025-03-27 17:09:33 +0100
Commit message:

 Update #5.

Package: CARDspa
Commit: 97e9e57c668f9300c12b3bd50df8310b17905173
Author: Jing Fu <167481871+JINGFU9912@users.noreply.github.com>
Date: 2025-03-27 11:18:33 -0400
Commit message:

 new build for kunpeng2

Package: trackViewer
Commit: 70f23157f3a6d821e87f49405c1a8e488d33b63f
Author: Jianhong Ou <jou@JNXKY095H1.local>
Date: 2025-03-27 10:15:56 -0400
Commit message:

 Fix a bug in reading sparse cool file.

Package: omXplore
Commit: 3fec13581e97bcb6ffdca545a34e131a2d582ce8
Author: Samuel Wieczorek <samuel.wieczorek@cea.fr>
Date: 2025-03-27 14:38:34 +0100
Commit message:

 Update #5. Need to be tested

Package: omXplore
Commit: b8f7d276577a3e5f3b1413efae1ac610c1c377e0
Author: Samuel Wieczorek <samuel.wieczorek@cea.fr>
Date: 2025-03-27 06:18:45 +0100
Commit message:

 Update #5. Need to be tested

Package: miaDash
Commit: 487d3a2bbef24dafa2409b3980c57efaa3783a44
Author: Giulio Benedetti <giuliobene2000@gmail.com>
Date: 2025-03-27 11:58:56 +0200
Commit message:

 Merge pull request #20 from microbiome/fix

Update iSEEtree compat requirements

Package: miaDash
Commit: 439be2e755cc0e1795db4c8b5e34e22bd9dfbdce
Author: Giulio Benedetti <giuliobene2000@gmail.com>
Date: 2025-03-27 11:42:54 +0200
Commit message:

 philr fix

Package: miaDash
Commit: e5d353bdd6d4ba6f85ae7b26c608726b1c5dcb2f
Author: Giulio Benedetti <giuliobene2000@gmail.com>
Date: 2025-03-27 11:30:24 +0200
Commit message:

 Add philr to Suggests

Package: miaDash
Commit: 4871221abfdddf54c71aa5593ce0d968239a3656
Author: Giulio Benedetti <giuliobene2000@gmail.com>
Date: 2025-03-27 11:23:04 +0200
Commit message:

 Add more constants

Package: miaDash
Commit: cd835ce84372ee1edce08cdd6685abb5d051ebb5
Author: Giulio Benedetti <giuliobene2000@gmail.com>
Date: 2025-03-27 10:18:05 +0200
Commit message:

 Update iSEEtree compat requirements

Package: SmartPhos
Commit: 3c2c1c1ca9868338209a111c972be4e48e2afc40
Author: shubh2565 <catchshubham2565@gmail.com>
Date: 2025-03-27 12:43:07 +0100
Commit message:

 minor fixes and version bump

Package: HoloFoodR
Commit: 1f9b3fb177c3050016da0419267afdd10b917df1
Author: Tuomas Borman <60338854+TuomasBorman@users.noreply.github.com>
Date: 2025-02-24 16:46:47 +0200
Commit message:

 Update document (#39)

Package: MGnifyR
Commit: 69dc18f5cf4b053837029f853fb96f2d67c968aa
Author: Tuomas Borman <60338854+TuomasBorman@users.noreply.github.com>
Date: 2025-03-27 10:54:31 +0200
Commit message:

 Update README.md (#51)

Package: MGnifyR
Commit: ff250f808ee33d499b42e380bab391dc0d151c96
Author: Tuomas Borman <60338854+TuomasBorman@users.noreply.github.com>
Date: 2024-12-02 17:57:00 +0200
Commit message:

 Update biocViews (#50)

* Update DESCRIPTION

* Update DESCRIPTION

* Update DESCRIPTION

Package: HoloFoodR
Commit: 38bb3d8b4d1290754a372ba0d4b57d47c028fe53
Author: Tuomas Borman <60338854+TuomasBorman@users.noreply.github.com>
Date: 2024-12-02 16:24:54 +0200
Commit message:

 Update biocViews (#38)

Package: HoloFoodR
Commit: c4371aff30b58fc49a0a2d71634eb91b6650c64a
Author: Tuomas Borman <60338854+TuomasBorman@users.noreply.github.com>
Date: 2024-12-01 15:51:06 +0200
Commit message:

 Suppress pkg loading messages (#37)

Package: HoloFoodR
Commit: 2fc99f28a6ae669adfd9caf9a013ad0b3b85583e
Author: Tuomas Borman <60338854+TuomasBorman@users.noreply.github.com>
Date: 2024-11-25 18:06:22 +0200
Commit message:

 Update case_study.Rmd (#36)

Package: HoloFoodR
Commit: 32ca69c9c12aa97a0279dd819fe65c67f95bf2cc
Author: Tuomas Borman <60338854+TuomasBorman@users.noreply.github.com>
Date: 2024-11-25 16:41:57 +0200
Commit message:

 Update rworkflows.yml (#35)

Package: HoloFoodR
Commit: 479c02bd316ddd1de705432a73cedb889724229e
Author: Tuomas Borman <60338854+TuomasBorman@users.noreply.github.com>
Date: 2024-11-25 14:27:42 +0200
Commit message:

 Add case study vignette (#33)

Co-authored-by: Artur Sannikov <40318410+artur-sannikov@users.noreply.github.com>

Package: mia
Commit: 6c9ceb2eec35d6c0fdd011f7329d86c372603c1c
Author: Tuomas Borman <60338854+TuomasBorman@users.noreply.github.com>
Date: 2025-03-27 12:01:18 +0200
Commit message:

 Default alpha diversity indices (#713)

Package: mia
Commit: 59147520024a1716a62c26b12bcbb8e3c58adafd
Author: Tuomas Borman <60338854+TuomasBorman@users.noreply.github.com>
Date: 2025-03-25 11:59:02 +0200
Commit message:

 addPrevalentAbundance (#716)

Package: mia
Commit: 570ac1490256354df78b54e560af8f8c51032f21
Author: Tuomas Borman <60338854+TuomasBorman@users.noreply.github.com>
Date: 2025-03-25 10:43:56 +0200
Commit message:

 Add pseudocount as method (#715)

Package: mia
Commit: 3b6ce6bf07a54635e7241daf4fcb3b65bf19a964
Author: Giulio Benedetti <giuliobene2000@gmail.com>
Date: 2025-03-19 16:20:23 +0200
Commit message:

 Add Tito2024QMP to mia dataset vignettes (#714)

Package: mia
Commit: 172c19311e3b09e0238c548cb903a8dffd5056ff
Author: jepasan <148062058+jepasan@users.noreply.github.com>
Date: 2025-03-17 21:34:47 +0200
Commit message:

 C++ implementation of the Stacked Faith algorithm (#697)

Co-authored-by: Leo Lahti <leo.lahti@iki.fi>
Co-authored-by: TuomasBorman <tvborm@utu.fi>

Package: clustSIGNAL
Commit: 143c2f58315e8c6c7fdec3bf6f4ddfb0c908b80b
Author: PratibhaPanwar <pratibhapanwar.4@gmail.com>
Date: 2025-03-27 19:49:17 +1100
Commit message:

 Minor fix of the author affiliations in vignette.

Package: clustSIGNAL
Commit: b1709d406a3e48449fcb0846c046806db5a4483b
Author: PratibhaPanwar <pratibhapanwar.4@gmail.com>
Date: 2025-03-27 19:28:25 +1100
Commit message:

 Minor updates to vignette.

Package: clustSIGNAL
Commit: 1b4d95a0d5211ba38b8717144ac634651d32f852
Author: PratibhaPanwar <pratibhapanwar.4@gmail.com>
Date: 2025-03-27 18:24:06 +1100
Commit message:

 Updated author affiliations.

Package: clustSIGNAL
Commit: 63e18aa07a2e8506260c38ace773bec114eb6dcb
Author: PratibhaPanwar <pratibhapanwar.4@gmail.com>
Date: 2025-03-27 17:37:54 +1100
Commit message:

 Updated package version to 0.99.9

Package: clustSIGNAL
Commit: 40a8108f612faba7a188d39a6d2c7b749fff7817
Author: PratibhaPanwar <pratibhapanwar.4@gmail.com>
Date: 2025-03-27 17:37:37 +1100
Commit message:

 Added list of main changes made to package.

Package: clustSIGNAL
Commit: 87effd6b84187c579259be29ce076d080e7300a1
Author: PratibhaPanwar <pratibhapanwar.4@gmail.com>
Date: 2025-03-27 17:37:01 +1100
Commit message:

 Minor update to package description.

Package: clustSIGNAL
Commit: 6b3f4caa8f25d4e2f536499f4fc26a4539a304d0
Author: PratibhaPanwar <pratibhapanwar.4@gmail.com>
Date: 2025-03-27 17:36:12 +1100
Commit message:

 Updated the overview section of the vignette. Also, updated the author information by adding affiliations.

Package: gDRimport
Commit: ec3a733582f2095ac1eb83c7bc7381b958a545f2
Author: j-smola <31825957+j-smola@users.noreply.github.com>
Date: 2025-03-27 08:16:23 +0100
Commit message:

 Merge pull request #101 from gdrplatform/GDR-2940

[GDR-2940] Implement PRISM change in report

Package: gDRimport
Commit: 60489315f301941d04e2c9eca7c683504f96c631
Author: Janina Smola <janina.smola@contractors.roche.com>
Date: 2025-03-26 08:23:32 -0700
Commit message:

 chore: unify support for using OncotreeLineage

Package: gDRimport
Commit: 43e254961eca3cb53955705bc393858091804cb6
Author: Janina Smola <janina.smola@contractors.roche.com>
Date: 2025-03-26 00:44:49 -0700
Commit message:

 chore: unify support for using OncotreeLineage

Package: gDRimport
Commit: 4cb8a26adc24459be87cb74ef70ced2177c6faae
Author: Janina Smola <janina.smola@contractors.roche.com>
Date: 2025-03-26 00:44:27 -0700
Commit message:

 chore: unify support for using OncotreeLineage

Package: RCy3
Commit: ce5b6ca8b55734ca69e100be76ac65a263f4f528
Author: Yihang Xin <46608109+yihangx@users.noreply.github.com>
Date: 2025-03-26 16:47:53 -0700
Commit message:

 Update DESCRIPTION

Package: RCy3
Commit: c8a510712e175322987793688772bc2cabc2d27b
Author: Yihang Xin <46608109+yihangx@users.noreply.github.com>
Date: 2025-03-26 16:47:27 -0700
Commit message:

 Update NEWS

Package: PloidyPeaks
Commit: a995bcc3cbf5ac4ac8b9709d761d5da59b058686
Author: ckostna <caitlinkostna@shaw.ca>
Date: 2025-03-26 18:47:57 -0500
Commit message:

 Trigger Bioconductor build

Package: openCyto
Commit: 1968c83083aaff60dc9037de06a7c7e872b35c9a
Author: Andrew McDavid <andrew.n.mcdavid@gmail.com>
Date: 2025-03-26 14:37:15 -0700
Commit message:

 Merge pull request #270 from amcdavid/fix-markdown

markdown 2.0 doesn't like yes/no for boolean

Package: openCyto
Commit: 29a7f7f545c1d371c1bcc1c2c08e4a3fa03d44ed
Author: Andrew McDavid <andrew@ozette.com>
Date: 2025-03-26 14:02:43 -0700
Commit message:

 we are using boost