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GIT Logs

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

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Package: geomeTriD
Commit: c73add9d4f4604d67b6ac4e688c2282a751a49df
Author: Jianhong Ou <jianhong.ou@gmail.com>
Date: 2025-10-02 12:43:09 -0400
Commit message:

 update the documentation.
Package: fgsea
Commit: 393628080141098672272b11659fc64532bf8726
Author: Alexey Sergushichev <alsergbox@gmail.com>
Date: 2025-10-02 10:21:35 -0500
Commit message:

 version bump 1.35.8
Package: fgsea
Commit: 7cce9ff6849328db5f80c6268f758b9007081257
Author: Alexey Sergushichev <alsergbox@gmail.com>
Date: 2025-10-01 13:00:28 -0500
Commit message:

 Update README.md
Package: fgsea
Commit: 5b43cc99a1b29a36e8230c94dd2cca5e25afac14
Author: Alexey Sergushichev <alsergbox@gmail.com>
Date: 2025-10-01 12:55:07 -0500
Commit message:

 fix stats=0 and gseaParam=0 in plotEnrichment
Package: CalibraCurve
Commit: c903d97610e273987bc9ca3b0695379dcd4a2b50
Author: KarinSchork <karin.schork@rub.de>
Date: 2025-10-02 17:09:22 +0200
Commit message:

 version bumb
Package: CalibraCurve
Commit: e9b7c216441b2c7dae5fe69fd501ecfdda753121
Author: KarinSchork <karin.schork@rub.de>
Date: 2025-10-02 17:07:56 +0200
Commit message:

 line width
Package: CalibraCurve
Commit: 22e5f83de7c3b34d0005f7cd109f9e6c9767d840
Author: KarinSchork <karin.schork@rub.de>
Date: 2025-10-02 17:07:45 +0200
Commit message:

 add importFroms
Package: CalibraCurve
Commit: 2d74fe1b9102580b376e2a07f3b8d464b215831a
Author: KarinSchork <karin.schork@rub.de>
Date: 2025-10-02 16:16:43 +0200
Commit message:

 change filepaths so that they work on different OS
Package: CalibraCurve
Commit: cbb925ec19d0ac4c8ea33c65b2dbc4bbfc15fb86
Author: KarinSchork <karin.schork@rub.de>
Date: 2025-10-02 15:27:33 +0200
Commit message:

 add possibility to import SummarizedExperiment objects directly
Package: CalibraCurve
Commit: 144e7bb1f8338c4264721297e84ebc1efd075de5
Author: KarinSchork <karin.schork@rub.de>
Date: 2025-10-02 14:24:18 +0200
Commit message:

 add missing content to vignette
Package: CalibraCurve
Commit: e292767ea2fff7baa579769d52c23164c7056014
Author: KarinSchork <karin.schork@rub.de>
Date: 2025-10-02 09:58:38 +0200
Commit message:

 rename main package vignette
Package: CalibraCurve
Commit: c7de324bc4e3732e126e359874a9b62b54a60d89
Author: KarinSchork <karin.schork@rub.de>
Date: 2025-10-02 09:58:25 +0200
Commit message:

 increase roxygen version
Package: spatialFDA
Commit: d61fb947874029e51a085c236fa8262353988d74
Author: mjemons <martin.emons@gmail.com>
Date: 2025-10-02 16:43:15 +0200
Commit message:

 small change to naming of calcMetric plots
Package: DOtools
Commit: 3c95d1ad9fd1ce5d0d2f20288267a682bbb30a19
Author: MarianoRuzJurado <mariani95@gmx.de>
Date: 2025-10-02 16:36:30 +0200
Commit message:

 test changes
Package: DOtools
Commit: f63b9e6b0088b211c2a68b353341358570ab8a83
Author: MarianoRuzJurado <mariani95@gmx.de>
Date: 2025-10-02 14:13:04 +0200
Commit message:

 - Fix test
Package: MetMashR
Commit: 38b08fedfca55a32bb155d60b6138df5cf9e588a
Author: Gavin Rhys Lloyd <grlloyd@users.noreply.github.com>
Date: 2025-10-02 15:11:10 +0100
Commit message:

 update upset_filters documentation

use rdname to include helper functions in the combined helper documentation
Package: MetMashR
Commit: 5857fb1685737b03dfd9d1a6a84d8f47d83a85a5
Author: Gavin Rhys Lloyd <grlloyd@users.noreply.github.com>
Date: 2025-10-02 14:23:47 +0100
Commit message:

 fix GO.db see also
Package: CytoPipeline
Commit: 5390b8a23f5d342d5952a8e98f22f6f975cd51f1
Author: phauchamps <philippehauchamps@hotmail.com>
Date: 2025-10-02 15:51:58 +0200
Commit message:

 - bumped to version 1.9.4
- improved `aggregateAndSample()` added a `setup` parameter, such that when
it is equal to "forceNEvent", the nb of events selected per flow frame is not
always balanced, to always obtain `nTotalEvents`
(except when the total nb of available events, taking all flowFrames,
is less than `nTotalEvents`).
Package: CytoPipelineGUI
Commit: 3c4d44a29782354322d4dcbdaeb9f64734b197c7
Author: phauchamps <philippehauchamps@hotmail.com>
Date: 2025-10-02 15:56:51 +0200
Commit message:

 Merge branch 'main' into devel
Package: CytoPipelineGUI
Commit: b9a7603e68097303457c01ddc5fb70b3488775b2
Author: phauchamps <philippehauchamps@hotmail.com>
Date: 2025-09-29 17:16:59 +0200
Commit message:

 - using sample display names instead of base names or full paths,
as provided from CytoPipeline 1.9.3
- bumped version to 1.7.2
Package: CytoPipelineGUI
Commit: 0cb099bfaedb85d37033cec071802be1cb8c55c0
Author: phauchamps <philippehauchamps@hotmail.com>
Date: 2025-08-19 12:07:34 +0200
Commit message:

 updated LICENSE file to 2025
Package: CytoPipelineGUI
Commit: 4f79fb84b7932e335d70ca588104db82d2d647f4
Author: phauchamps <philippehauchamps@hotmail.com>
Date: 2025-08-19 11:52:02 +0200
Commit message:

 - updated @seealso link to CytoPipeline package to avoid NOTE in R CMD CHECK
- updated license statement to 2025
Package: CytoPipelineGUI
Commit: 134b51bd8e3969dd9db66592b2f91cca99a82c2c
Author: phauchamps <philippehauchamps@hotmail.com>
Date: 2025-05-15 11:33:36 +0200
Commit message:

 GHA: migrated workflow to Bioconductor 3.22
Package: CytoPipelineGUI
Commit: b31d9f643a078563bf57d45ed64b2f0008010341
Author: phauchamps <philippehauchamps@hotmail.com>
Date: 2025-05-15 11:17:27 +0200
Commit message:

 - migrated to GHA cache v4
- bumped version to 1.7.1
Package: CytoPipelineGUI
Commit: cd1db853a67d0c1556717a97154d15cca7575cda
Author: phauchamps <philippehauchamps@hotmail.com>
Date: 2024-11-04 13:13:21 +0100
Commit message:

 - bumped devel version to 1.5.1
Package: NanoMethViz
Commit: b617bc71cf51a280ba74b11d768c301c7c7cd0e9
Author: shians <registertonysu@gmail.com>
Date: 2025-10-02 23:36:38 +1000
Commit message:

 Version bump to 3.5.6
Package: NanoMethViz
Commit: 9a9807946be389dd0d125f26cf11216837576a1f
Author: shians <registertonysu@gmail.com>
Date: 2025-10-02 23:35:00 +1000
Commit message:

 Fixed gene annotation symbols breaking for factor columns
Package: NanoMethViz
Commit: 622101eda98b3480f3114eed9bcc0b9627655d2a
Author: shians <registertonysu@gmail.com>
Date: 2025-10-02 23:34:35 +1000
Commit message:

 Updated T2T exon data
Package: NanoMethViz
Commit: 0b9a26adf18dcc9ba717a7fd40bdbc5d8ebb29d4
Author: shians <registertonysu@gmail.com>
Date: 2025-08-11 14:06:23 +1000
Commit message:

 Updated codecov action
Package: NanoMethViz
Commit: b1a3381433c9de729635c8d630a3c62c32dfb244
Author: shians <registertonysu@gmail.com>
Date: 2025-08-11 11:16:28 +1000
Commit message:

 Updated tests
Package: NanoMethViz
Commit: 27ed7fb67d99d44e1753326449664c53688e84cc
Author: shians <registertonysu@gmail.com>
Date: 2025-08-11 11:14:26 +1000
Commit message:

 Updated validation and error mesages
Package: NanoMethViz
Commit: d87eadbb058fc6e70b2042131adfece171c6a2b6
Author: shians <registertonysu@gmail.com>
Date: 2025-08-11 11:11:31 +1000
Commit message:

 Added new asserts
Package: NanoMethViz
Commit: edeaa4cea5c234c89a6004aa88aa5726760ce7ac
Author: shians <registertonysu@gmail.com>
Date: 2025-08-11 10:31:21 +1000
Commit message:

 Updated gitignore
Package: NanoMethViz
Commit: 6083e2f1344a5afccfc73a0eed640d7dd8f5eb19
Author: shians <registertonysu@gmail.com>
Date: 2025-08-11 09:15:30 +1000
Commit message:

 Updated test coverage action
Package: DOtools
Commit: c1cfe1b58a6aaa539ee443b830ccb6943d31be9a
Author: MarianoRuzJurado <mariani95@gmx.de>
Date: 2025-10-02 14:13:04 +0200
Commit message:

 - Fix bug due to ggplot 4.0.0
Package: DOtools
Commit: 744a9cc5fd4162a487d13be8ab3d1b44c17d2fae
Author: MarianoRuzJurado <mariani95@gmx.de>
Date: 2025-10-02 13:56:42 +0200
Commit message:

 Merge branch 'master' into devel
Package: DOtools
Commit: 0ff82c487a8df526e6224c06d70d58f8a0e0f1ea
Author: MarianoRuzJurado <mariani95@gmx.de>
Date: 2025-10-02 12:55:55 +0200
Commit message:

 -docs rebuild, fix bug
Package: DOtools
Commit: 48d01dbb83a09034ccb47654898d9861ce42cacc
Author: MarianoRuzJurado <mariani95@gmx.de>
Date: 2025-10-02 12:55:55 +0200
Commit message:

 -docs rebuild
Package: DOtools
Commit: bc83d2a319eb0bd252e526c7a7ae5c1c3e16558d
Author: MarianoRuzJurado <mariani95@gmx.de>
Date: 2025-10-02 12:30:07 +0200
Commit message:

 -Runtime improvements, moving long unit tests to longtest directory
Package: DuplexDiscovereR
Commit: 56b637086543ee377d17bf0b9f0524afd9649d88
Author: Egors01 <yegor.smb@gmail.com>
Date: 2025-10-02 15:14:11 +0200
Commit message:

 version bump
Package: DuplexDiscovereR
Commit: 68157e1828035115196b4022e743648c33ef4b3f
Author: Egors01 <yegor.smb@gmail.com>
Date: 2025-10-02 15:03:08 +0200
Commit message:

 added vcstrs::vec_cast import to the pkg imports
Package: MetMashR
Commit: d01b8dab8562b7b2e98cee0850afcc5fe982a625
Author: Gavin Rhys Lloyd <grlloyd@users.noreply.github.com>
Date: 2025-10-02 13:47:29 +0100
Commit message:

 fix broken BiocFileCache download

- verbose is no longer an input
Package: BgeeDB
Commit: 07aa210eda962464f020e08dcdb53f3b7707120b
Author: Julien Wollbrett <julien.wollbrett@unil.ch>
Date: 2025-10-02 14:43:52 +0200
Commit message:

 Merge branch 'bioc_devel' into develop
Package: BgeeDB
Commit: 2e64799d24215bf3a2a8730d2ce80818a49093d7
Author: smoretti <smoretti@users.noreply.github.com>
Date: 2025-02-03 15:00:44 +0100
Commit message:

 Update Bluesky badge
Package: BgeeDB
Commit: e91eb474268d7312baf8b3f84a132673120e4ac5
Author: smoretti <smoretti@users.noreply.github.com>
Date: 2025-02-03 14:20:11 +0100
Commit message:

 Add Bluesky badge
Package: BgeeDB
Commit: 7295288945f2ab893be00cea4730ce467dac4bd6
Author: jwollbrett <julien.wollbrett@unil.ch>
Date: 2024-08-16 14:53:33 +0200
Commit message:

 manage bug when pathToData is provided using a tilde
Package: BgeeDB
Commit: 3bb20975e84f08c87c93f4689cfe65e07e4ec2dc
Author: jwollbrett <julien.wollbrett@unil.ch>
Date: 2024-08-16 14:58:40 +0200
Commit message:

 Merge branch 'devel' into develop
Package: BgeeDB
Commit: 4c9e962ad7d6f730ea4adedc4c81942180515756
Author: Julien <julien.wollbrett@gmail.com>
Date: 2023-05-15 17:01:22 +0200
Commit message:

 update documentation
Package: MetMashR
Commit: bbf6c1464c5c00158c4c5efbef46a9c4b6341d89
Author: Gavin Rhys Lloyd <grlloyd@users.noreply.github.com>
Date: 2025-10-02 11:46:41 +0100
Commit message:

 version bump
Package: MetMashR
Commit: 5cc8066f98d92ae78b87b88bb314fcaa030813b3
Author: Gavin Rhys Lloyd <grlloyd@users.noreply.github.com>
Date: 2025-10-02 10:49:41 +0100
Commit message:

 tweak appearance of annotation_bar_chart
Package: MetMashR
Commit: 0834129b0c4b984a97b200579054e0cfe19ec7af
Author: Gavin Rhys Lloyd <grlloyd@users.noreply.github.com>
Date: 2025-10-01 15:38:24 +0100
Commit message:

 update upset plots

- use ggVennDiagram instead of ComplexUpset
- update filter_venn to use filters reuse code with annotation upset
Package: MetMashR
Commit: 90fbf7220fe3e3435cc6b74d18a385388b030e63
Author: Gavin Rhys Lloyd <grlloyd@users.noreply.github.com>
Date: 2025-10-01 10:15:38 +0100
Commit message:

 update documentation
Package: MetMashR
Commit: cbe0f5b6c80f45a89e1e58f534d95b78f40396a3
Author: Gavin Rhys Lloyd <grlloyd@users.noreply.github.com>
Date: 2025-10-01 10:15:26 +0100
Commit message:

 remove RVenn

using ggVennDiagram instead
Package: MetMashR
Commit: eb5268c55ae2b66c397ffa96b5c0f4f10d00aa66
Author: Gavin Rhys Lloyd <grlloyd@users.noreply.github.com>
Date: 2025-10-01 10:15:02 +0100
Commit message:

 remove openbabel_structure

Removes dependency on ChemmineOB
- update vignettes
- rebuild
Package: imcRtools
Commit: 0c0cdbc8dc5d613c4b041a48417525a0932df29f
Author: SchulzDan <shooltz@gmx.de>
Date: 2025-09-29 10:48:22 +0200
Commit message:

 Merge pull request #140 from chiarasch/interaction_add_zscore_cozi

Add zscore to testInteractions()
Package: imcRtools
Commit: 81eee90da1dbcd745faf6998f61f2979642bf81c
Author: chiarasch <chiara_schiller@t-online.de>
Date: 2025-09-26 17:35:07 +0200
Commit message:

 update NEWS
Package: imcRtools
Commit: e76f092f909b13b5b0dee082583ad25d5dd3b4ed
Author: chiarasch <chiara_schiller@t-online.de>
Date: 2025-09-26 17:30:04 +0200
Commit message:

 remove dev comment
Package: imcRtools
Commit: 498eabd13fbd12d4dd07159a55bcbf9c1d2093ee
Author: chiarasch <chiara_schiller@t-online.de>
Date: 2025-09-26 17:29:06 +0200
Commit message:

 remove cozi plot markdown
Package: imcRtools
Commit: a5fa3b132f916e375bff4f97a0774b3c7c20328b
Author: chiarasch <chiara_schiller@t-online.de>
Date: 2025-09-26 17:27:55 +0200
Commit message:

 add histocat error message
Package: imcRtools
Commit: 342cc591e166097a36c01d2373613095a315c2df
Author: chiarasch <chiara_schiller@t-online.de>
Date: 2025-09-26 17:26:48 +0200
Commit message:

 highlight method renaming
Package: imcRtools
Commit: f19f6b8a4632a12d9dee2aeaebbb813527b2520e
Author: chiarasch <chiara_schiller@t-online.de>
Date: 2025-09-26 17:24:58 +0200
Commit message:

 add cond_ratio to vignette
Package: imcRtools
Commit: 66170f7046919448a7d4e88e7c2b2228dcadb7a3
Author: chiarasch <chiara_schiller@t-online.de>
Date: 2025-09-26 17:23:50 +0200
Commit message:

 remove cond_ratio from package
Package: imcRtools
Commit: b56ffc9c335dc1a54f5e8606a3c9e276bfe26124
Author: chiarasch <chiara_schiller@t-online.de>
Date: 2025-09-04 11:18:06 +0200
Commit message:

 add cond_ratio NA
Package: imcRtools
Commit: 5286afd216c69940341e262ee9f2685ec44b95f2
Author: chiarasch <chiara_schiller@t-online.de>
Date: 2025-09-04 11:14:23 +0200
Commit message:

 add zscore vector in test
Package: imcRtools
Commit: 7b404a254b76d76c8d3261701aa789a4bc864318
Author: chiarasch <chiara_schiller@t-online.de>
Date: 2025-09-04 11:02:53 +0200
Commit message:

 add plotting to vignette
Package: imcRtools
Commit: 3eec3c6440b3f4de5435dd5ce926fa48fccb911f
Author: chiarasch <chiara_schiller@t-online.de>
Date: 2025-09-04 11:02:22 +0200
Commit message:

 remove plotInteractionsCozi
Package: imcRtools
Commit: 0999b830710ffb95ca712c4e163d53fa15d0a8a4
Author: chiarasch <chiara_schiller@t-online.de>
Date: 2025-08-27 15:35:00 +0200
Commit message:

 fix vignette library loading
Package: imcRtools
Commit: c7838f57467cf6daabba7eabebb1bea8f8fa1433
Author: chiarasch <chiara_schiller@t-online.de>
Date: 2025-08-27 09:32:12 +0200
Commit message:

 fix bracket
Package: imcRtools
Commit: be5169875c953f918073bc9a36c84f999f20f4e3
Author: chiarasch <chiara_schiller@t-online.de>
Date: 2025-08-27 09:31:38 +0200
Commit message:

 fix typo
Package: imcRtools
Commit: c9a6b1bcf9aa1cb67fa1ba4bcd8681365f44fd9c
Author: chiarasch <chiara_schiller@t-online.de>
Date: 2025-08-27 09:31:03 +0200
Commit message:

 correct test
Package: imcRtools
Commit: 89905b768dc9fb9afa9db21e2f7d43eb494ba787
Author: chiarasch <chiara_schiller@t-online.de>
Date: 2025-08-27 09:28:59 +0200
Commit message:

 deal with NA and Inf
Package: imcRtools
Commit: 84fbeabc4946d6af6f9889d5b6c8ab70b9fef9d3
Author: chiarasch <chiara_schiller@t-online.de>
Date: 2025-08-26 19:46:58 +0200
Commit message:

 adapt tests to conditional
Package: imcRtools
Commit: 742196a50282f597a9c16bc501bccd9056257162
Author: chiarasch <chiara_schiller@t-online.de>
Date: 2025-08-26 19:30:39 +0200
Commit message:

 fix typo
Package: imcRtools
Commit: 5faa27d30fc9b925702f4f5ac283cce141132d47
Author: chiarasch <chiara_schiller@t-online.de>
Date: 2025-08-26 19:28:42 +0200
Commit message:

 add cond_ratio tests
Package: imcRtools
Commit: d506bc3325399962464f04b514591f9b53305ecb
Author: chiarasch <chiara_schiller@t-online.de>
Date: 2025-08-26 19:21:32 +0200
Commit message:

 add zscore and cond_ratio tests
Package: imcRtools
Commit: 0f6fa270c83d45f6f723abf8e2ab497e25578e8c
Author: chiarasch <chiara_schiller@t-online.de>
Date: 2025-08-26 18:36:32 +0200
Commit message:

 add tests
Package: imcRtools
Commit: 5b04b03217a169c15d59ef1b983e0b9257dbf3d6
Author: chiarasch <chiara_schiller@t-online.de>
Date: 2025-08-26 18:16:17 +0200
Commit message:

 add roxygen2 documentation
Package: imcRtools
Commit: 443e32f8be5d90448cc9d3d9b5d781970187063a
Author: chiarasch <chiara_schiller@t-online.de>
Date: 2025-08-26 17:49:01 +0200
Commit message:

 adapt documentation
Package: imcRtools
Commit: 0c9945f780823281a0168b7a2760a223f71e18b5
Author: chiarasch <chiara_schiller@t-online.de>
Date: 2025-08-26 17:44:37 +0200
Commit message:

 add validity checks
Package: imcRtools
Commit: 8315c303f145592cc71feea3eca42062311a2fa4
Author: chiarasch <chiara_schiller@t-online.de>
Date: 2025-08-26 17:27:37 +0200
Commit message:

 describe changes in NEWS
Package: imcRtools
Commit: c9d0a35b4430fec9e3a15fd7422171e0c140ca52
Author: chiarasch <chiara_schiller@t-online.de>
Date: 2025-08-26 17:26:52 +0200
Commit message:

 adapt NAMESPACE to changes
Package: imcRtools
Commit: f5446bb88fa8d1bf40c77de5d38a638bc2ac0840
Author: chiarasch <chiara_schiller@t-online.de>
Date: 2025-08-26 17:25:35 +0200
Commit message:

 add cozi dotplot to vignette
Package: imcRtools
Commit: fafcd62922212fe6b7a31902153657b1a7a7e475
Author: chiarasch <chiara_schiller@t-online.de>
Date: 2025-08-26 17:13:32 +0200
Commit message:

 rename histocat to conditional method
Package: imcRtools
Commit: 115762fedeee8fb0c4dc9c8abead154f999922d2
Author: chiarasch <chiara_schiller@t-online.de>
Date: 2025-08-26 16:04:04 +0200
Commit message:

 add zscore and CCR plot
Package: imcRtools
Commit: cf9f3db70dabfa3492afb36464d9ab78b735a37b
Author: chiarasch <chiara_schiller@t-online.de>
Date: 2025-08-26 15:23:56 +0200
Commit message:

 add cond_ratio
Package: imcRtools
Commit: ca53aaed0a6cc4257a2eb494f533c06966ed1f01
Author: chiarasch <chiara_schiller@t-online.de>
Date: 2025-08-26 14:08:34 +0200
Commit message:

 add zscore
Package: gemma.R
Commit: 8d58f1876265e402c4933497d46e52009fadacd6
Author: OganM <ogan.mancarcii@gmail.com>
Date: 2025-10-01 18:04:17 -0700
Commit message:

 version bump
Package: gemma.R
Commit: e8e82b20fdbd8dfd9bfb3121bfb01d8241365f46
Author: OganM <ogan.mancarcii@gmail.com>
Date: 2025-10-01 18:03:57 -0700
Commit message:

 internalize processing function
Package: gemma.R
Commit: 4ef12dd4c5598891e4ca5216a3dd8110ccfbf21c
Author: OganM <ogan.mancarcii@gmail.com>
Date: 2025-10-01 17:49:55 -0700
Commit message:

 version bump
Package: gemma.R
Commit: 24bfd11f696d9b8a219170157f823dc2e4ec2a21
Author: OganM <ogan.mancarcii@gmail.com>
Date: 2025-10-01 17:49:29 -0700
Commit message:

 documentation bump
Package: gemma.R
Commit: 193e87983066f1a32cb4225206f74699ba024df1
Author: OganM <ogan.mancarcii@gmail.com>
Date: 2025-10-01 16:44:12 -0700
Commit message:

 version bump
Package: gemma.R
Commit: 93592c89ff98a056ff46b7df0d73e1a36933bd1d
Author: OganM <ogan.mancarcii@gmail.com>
Date: 2025-10-01 15:52:01 -0700
Commit message:

 search_annotation results are currently non deterministic. don't test for identical results
Package: gemma.R
Commit: 134a9f6fa274490f272da63d3d42906490743233
Author: OganM <ogan.mancarcii@gmail.com>
Date: 2025-09-04 16:32:06 -0700
Commit message:

 version bump
Package: gemma.R
Commit: 569d765937a16d616d83180f583cb415ed7aeec5
Author: OganM <ogan.mancarcii@gmail.com>
Date: 2025-09-04 16:31:47 -0700
Commit message:

 add get_dataset_publications
Package: DominoEffect
Commit: fad563c1ac04e18aefbb0d20a501d64efc8bfe76
Author: Peter Blattmann <peter_blattmann@bluewin.ch>
Date: 2025-10-02 00:14:40 +0200
Commit message:

 Merge branch 'devel' of git.bioconductor.org:packages/DominoEffect into devel
Package: DominoEffect
Commit: cb4013c38ff6b82dac55fadb554098f81aacdfd6
Author: Peter Blattmann <peter_blattmann@bluewin.ch>
Date: 2025-10-01 23:53:12 +0200
Commit message:

 Moved pattern function from Biostrings to pwalign
Package: tximeta
Commit: d3536992e555cbcdc731784600536223f6e2b53b
Author: Mike Love <mikelove@users.noreply.github.com>
Date: 2025-10-01 18:04:13 -0400
Commit message:

 adding linkedTxpData to bfc
Package: tximeta
Commit: dd22bac8afe89f9c617c2b771ce1d61c144e9e75
Author: Mike Love <mikelove@users.noreply.github.com>
Date: 2025-09-30 19:45:39 -0400
Commit message:

 version bump, trigger GHA
Package: tximeta
Commit: f162b404e45b7b8c30be41ae0d1f92f78c7c000d
Author: Mike Love <mikelove@users.noreply.github.com>
Date: 2025-09-30 13:52:44 -0400
Commit message:

 initial function def for makeLinkedTxpData
Package: DominoEffect
Commit: 80e1fc6c1b46256cefa69d06a7ca777a6f9eb497
Author: Peter Blattmann <peter_blattmann@bluewin.ch>
Date: 2025-10-01 23:53:12 +0200
Commit message:

 Moved pattern function from Biostrings to pwalign
Package: Pirat
Commit: ec6446fd9784f42cceb66de522b5915066a0cefc
Author: Lucas Etourneau <lucas.etourneau@berkeley.edu>
Date: 2025-10-01 12:30:28 -0700
Commit message:

 Version upgrade
Package: rhinotypeR
Commit: 19a4c3b9b3ad5b41c4845daa76a733911e536195
Author: marthaluka <mawia.martha@gmail.com>
Date: 2025-10-01 18:41:52 +0100
Commit message:

 update workflow
Package: rhinotypeR
Commit: 4595d06ba5821613a0b2b58c695b23ea90e75542
Author: marthaluka <mawia.martha@gmail.com>
Date: 2025-10-01 18:40:43 +0100
Commit message:

 manuscript revisions
Package: Moonlight2R
Commit: 976b6a1cbc221b3738a357fbf7d4b03c51454f73
Author: AlessiaCampo <59013682+AlessiaCampo@users.noreply.github.com>
Date: 2025-10-01 19:20:38 +0200
Commit message:

 Fix143 dmaplot crash (#148)

* Fixes in GLS function to work with easyPubMed updates and new functions; Updates of the NEWS, DESCRIPTION and reference dataGLS accordingly

* removed unused print in Moonlight.rmd file

* Fix on plotDMA, plotGMA, plotMoonlight and plotMoonlightMet for updates on tiles and bars creation from tidyHeatmap package; updated images in vignettes accordingly

* Updates of the version in DESCRIPTION AND NEWS.md files

* Fixed wrong file extension for plot images in Moonlight2R.Rmd

---------

Co-authored-by: Alessia Campo <acampo@kb-bioinfo01.cancer.dk>
Package: markeR
Commit: ed5e4828fd47f6aaf77ad953ad51e7ff8ed816a1
Author: Rita Silva <ritamtbsilva@gmail.com>
Date: 2025-10-01 17:23:37 +0100
Commit message:

 version bump in devel
Package: markeR
Commit: d08ed01b6528eb498ebe4b17ac8701a218c26f5e
Author: Rita Silva <ritamtbsilva@gmail.com>
Date: 2025-10-01 17:20:53 +0100
Commit message:

 bug fix: change version to new bumped version in readme file
Package: markeR
Commit: 380b681b1c0c6f549be217aba96222d77cb425ce
Author: Rita Silva <ritamtbsilva@gmail.com>
Date: 2025-10-01 17:20:08 +0100
Commit message:

 bug fix: change description to better reflect the package's current functionalities
Package: markeR
Commit: 988fb12de9c656169d1b0551c97ea0504e539203
Author: Rita Silva <ritamtbsilva@gmail.com>
Date: 2025-10-01 17:15:36 +0100
Commit message:

 change back version
Package: markeR
Commit: 504139ac98516348023ff2ec5e8810ea6afb6546
Author: Rita Silva <ritamtbsilva@gmail.com>
Date: 2025-10-01 17:13:23 +0100
Commit message:

 Update package description to reflect current functionalities
Package: markeR
Commit: 2b431f6efde167af871a020b20ff44fa82e4748e
Author: Rita Silva <ritamtbsilva@gmail.com>
Date: 2025-09-17 16:45:38 +0100
Commit message:

 Revert "Merge branch 'default' into main"

This reverts commit d8961f5048d1f4ab43c2ef90473fa3c05fbb06c0, reversing
changes made to c9aaf4e359783f2b647cbd4e53ec8c3e0e253246.
Package: markeR
Commit: d8961f5048d1f4ab43c2ef90473fa3c05fbb06c0
Author: Rita Silva <55759937+ritamtbsilva@users.noreply.github.com>
Date: 2025-09-17 16:37:54 +0100
Commit message:

 Merge branch 'default' into main
Package: markeR
Commit: f6335ca6817d5e7ef3a17844e7c5b997e310283f
Author: Rita Silva <ritamtbsilva@gmail.com>
Date: 2025-08-21 16:56:16 +0100
Commit message:

 update vignette to be more useful
Package: markeR
Commit: 81a46dfbd9cbada63c38ef6b06150ceb6ad3660f
Author: Rita Silva <ritamtbsilva@gmail.com>
Date: 2025-08-21 12:29:44 +0100
Commit message:

 Merge branch 'default' of https://github.com/DiseaseTranscriptomicsLab/markeR into default
Package: markeR
Commit: edc007a6577eaf66b256ded698d7bc3127feacb1
Author: Rita Silva <ritamtbsilva@gmail.com>
Date: 2025-08-21 12:29:36 +0100
Commit message:

 update vignette default branch to not include bioconductor instructions
Package: markeR
Commit: 839ab040476af1b689e1ed96565a2c9c1ac36892
Author: Rita Silva <55759937+ritamtbsilva@users.noreply.github.com>
Date: 2025-08-21 12:27:07 +0100
Commit message:

 Update pkgdown.yaml
Package: markeR
Commit: 8d7dc6d80458a5be165c317e3d7d18d09f338308
Author: Rita Silva <ritamtbsilva@gmail.com>
Date: 2025-08-21 12:24:53 +0100
Commit message:

 Merge branch 'default' of https://github.com/DiseaseTranscriptomicsLab/markeR into default
Package: markeR
Commit: 0d62bdc52acdb73724354fe4a7987906a1a26581
Author: Rita Silva <ritamtbsilva@gmail.com>
Date: 2025-08-21 12:24:45 +0100
Commit message:

 update notes with release 0.99.3
Package: blase
Commit: 59f88c1fc4074e06a9e54c136fd6d9e44b90db88
Author: Andrew McCluskey <andrew@cluskii.com>
Date: 2025-10-01 17:07:26 +0100
Commit message:

 bump version to 0.99.3
Package: blase
Commit: 955991d8e594b53a20868cf6d34df7f81650f7e9
Author: Andrew McCluskey <andrew@cluskii.com>
Date: 2025-10-01 17:07:01 +0100
Commit message:

 tidying up documentation
Package: blase
Commit: 002c3109b57430d35106d505dda7228e8daf16c0
Author: Andrew McCluskey <andrew@cluskii.com>
Date: 2025-10-01 16:51:45 +0100
Commit message:

 bump version to 0.99.2
Package: blase
Commit: 746690a1ace9d228809b1a229846a2b4819eb066
Author: Andrew McCluskey <andrew@cluskii.com>
Date: 2025-10-01 16:51:23 +0100
Commit message:

 Move vignette data into package
Package: OSTA
Commit: 94405d9ffa426196b989164f2a6eec94470ef84f
Author: Lukas Weber <lmweb012@gmail.com>
Date: 2025-10-01 11:10:29 -0400
Commit message:

 version and date
Package: OSTA
Commit: 622b23ed613f1f8f793c9a72903a84a135eab9d8
Author: Lukas Weber <lmweb012@gmail.com>
Date: 2025-09-28 19:03:56 -0400
Commit message:

 Merge pull request #220 from HelenaLC/sandbox

fixed refs; hide ecosystems printing
Package: OSTA
Commit: 1c74b9090208da6215329cd46d05af14cc89e518
Author: HelenaLC <helena@crowell.eu>
Date: 2025-09-28 12:39:57 +0200
Commit message:

 code-fold instead of echo=FALSE
Package: OSTA
Commit: 580464aac89602a65fbd854a53ed747eaf8503e1
Author: HelenaLC <helena@crowell.eu>
Date: 2025-09-28 12:35:31 +0200
Commit message:

 fix method of year refs
Package: OSTA
Commit: 95b41b6fc5ede61945632ecccc4aa9dfd5575bba
Author: HelenaLC <helena@crowell.eu>
Date: 2025-09-28 12:24:08 +0200
Commit message:

 hide upwanted outputs
Package: OSTA
Commit: e00ec597d72f6c482b582924f8dadb2b3145b752
Author: Helena L. Crowell <helena@crowell.eu>
Date: 2025-09-28 12:14:47 +0200
Commit message:

 revision of multi-* chapters; fixed OSTA sticker
Package: OSTA
Commit: 474a5d6738174dce4c1514e4dee6e16246698597
Author: Helena L. Crowell <helena@crowell.eu>
Date: 2025-09-28 12:11:12 +0200
Commit message:

 Merge pull request #35 from HelenaLC/mul

update OSTA sticker & reactivate all chapters
Package: OSTA
Commit: 5dcf2a29df6d6250a68e4f7befe081daf4931078
Author: HelenaLC <helena@crowell.eu>
Date: 2025-09-28 12:10:24 +0200
Commit message:

 reactivate all chapters
Package: OSTA
Commit: 060dacb18dade192e5b88c341330494c96d90f74
Author: HelenaLC <helena@crowell.eu>
Date: 2025-09-28 11:57:10 +0200
Commit message:

 update OSTA sticker (hline removed)
Package: OSTA
Commit: 3ff953303a89d8d82cb3b9d67e483025ff0bbff3
Author: Helena L. Crowell <helena@crowell.eu>
Date: 2025-09-28 11:48:22 +0200
Commit message:

 Merge pull request #34 from HelenaLC/mul

differential colocalization revision
Package: OSTA
Commit: 937cb86ee56dfd13bb288e65bfba8ba1191f5075
Author: HelenaLC <helena@crowell.eu>
Date: 2025-09-28 11:47:36 +0200
Commit message:

 deactivate all but mult-* chapters for testing
Package: OSTA
Commit: 6ff4ab4859110046e9d13f55f00f1aadddc8c717
Author: HelenaLC <helena@crowell.eu>
Date: 2025-09-28 11:47:16 +0200
Commit message:

 multi-coloc revision
Package: OSTA
Commit: 9344be3b0131f17c77b9f959636b015824495bfd
Author: Helena L. Crowell <helena@crowell.eu>
Date: 2025-09-28 10:36:32 +0200
Commit message:

 Merge pull request #33 from HelenaLC/mul

spatial patterns revision
Package: OSTA
Commit: 9135f981f353a9bd99f8cd4c824cf15596814a92
Author: HelenaLC <helena@crowell.eu>
Date: 2025-09-28 10:35:37 +0200
Commit message:

 spatial patterns revision
Package: OSTA
Commit: b31a3889c524ede744eadd0a5475e02cec50abe8
Author: Helena L. Crowell <helena@crowell.eu>
Date: 2025-09-28 09:53:12 +0200
Commit message:

 Merge pull request #32 from HelenaLC/mul

structure-based analysis revision
Package: OSTA
Commit: b618e701392748ab56b6c1ea72c16cce2504e4ab
Author: HelenaLC <helena@crowell.eu>
Date: 2025-09-28 09:52:24 +0200
Commit message:

 merge mod <- and summary(mod) code chunks
Package: OSTA
Commit: c2b75246d7d6142cbbc536cce19daefe31f75968
Author: HelenaLC <helena@crowell.eu>
Date: 2025-09-28 09:47:00 +0200
Commit message:

 structure-based analysis revision
Package: OSTA
Commit: fc82494cb18ede142437c2f0c2524e190c1f9c85
Author: Lukas Weber <lmweb012@gmail.com>
Date: 2025-09-25 14:47:13 -0400
Commit message:

 minor typos and spell out CSR
Package: OSTA
Commit: 8c9e28e5b67a6facab7a3fc71e8fc7ce91dc366e
Author: Lukas Weber <lmweb012@gmail.com>
Date: 2025-09-25 14:40:35 -0400
Commit message:

 Merge pull request #217 from lmweber/spatstat

ind-spatstat revision
Package: OSTA
Commit: a40079b25c1fcbef5850a71ec97c074c325e1814
Author: HelenaLC <helena@crowell.eu>
Date: 2025-09-25 19:48:35 +0200
Commit message:

 code styling; up lgd key size; figure sizes
Package: OSTA
Commit: ff3b5d547feb8ab2bb61cb600fe00e1e50187360
Author: Lukas Weber <lmweb012@gmail.com>
Date: 2025-09-25 13:10:32 -0400
Commit message:

 endothelial
Package: OSTA
Commit: 10c4cbc2f4390b7ea08827059a92a3712dc614f8
Author: Lukas Weber <lmweb012@gmail.com>
Date: 2025-09-25 12:47:01 -0400
Commit message:

 update order of carousel images
Package: OSTA
Commit: 7edd9eed18f0c5f5ddaf4f9d14bebd68ce0c05ad
Author: Lukas Weber <lmweb012@gmail.com>
Date: 2025-09-25 12:38:28 -0400
Commit message:

 references formatting
Package: OSTA
Commit: a62acad620c916dbeeb67522eff4baece6a7625f
Author: Lukas Weber <lmweb012@gmail.com>
Date: 2025-09-25 12:35:33 -0400
Commit message:

 Merge pull request #216 from lmweber/vishd

seq-workflow-visium-hd revision
Package: OSTA
Commit: ff3c5d3ef0959d468c2c560659844480275ebc06
Author: Lukas Weber <lmweb012@gmail.com>
Date: 2025-09-25 12:27:09 -0400
Commit message:

 minor typos and wording
Package: OSTA
Commit: 9a557815144abfe054d97d4798512f34b721aea4
Author: Lukas Weber <lmweb012@gmail.com>
Date: 2025-09-25 12:26:56 -0400
Commit message:

 references formatting
Package: OSTA
Commit: 6ed1d8cbea74160ebb61a3b182194c81845850d6
Author: Lukas Weber <lmweb012@gmail.com>
Date: 2025-09-25 12:14:15 -0400
Commit message:

 Merge pull request #214 from HelenaLC/tbl

bkg-ecosystem
Package: OSTA
Commit: c03dde330ac87bb581d6f61762455fe99157f0fa
Author: Lukas Weber <lmweb012@gmail.com>
Date: 2025-09-25 12:10:21 -0400
Commit message:

 Merge branch 'sandbox' into tbl
Package: OSTA
Commit: d16ce361b119835a8c16ebcb40301835533098dd
Author: Lukas Weber <lmweb012@gmail.com>
Date: 2025-09-25 12:01:12 -0400
Commit message:

 minor formatting and typos
Package: OSTA
Commit: 6ea99ee9a3a5e35b25f99342b4101c9a458b1ff4
Author: Lukas Weber <lmweb012@gmail.com>
Date: 2025-09-25 12:01:00 -0400
Commit message:

 references formatting
Package: OSTA
Commit: 6b9184d47a1449c127a3a4e024e48b4ab8ec0bf6
Author: Lukas Weber <lmweb012@gmail.com>
Date: 2025-09-25 11:25:42 -0400
Commit message:

 Merge pull request #212 from HelenaLC/viz

+ alabaster, iSEE
Package: OSTA
Commit: d2f66b2222c054b452868095c512cfa81778b83e
Author: HelenaLC <helena@crowell.eu>
Date: 2025-09-25 17:25:26 +0200
Commit message:

 code revision for readability and consistency
Package: OSTA
Commit: e8b017890b3b4af6dc6713693e0d76aa0fb1bd7e
Author: HelenaLC <helena@crowell.eu>
Date: 2025-09-25 17:24:54 +0200
Commit message:

 update 'pasta' reference
Package: OSTA
Commit: 705318caadf3c0acfedc8a98a30518525cfad4b1
Author: HelenaLC <helena@crowell.eu>
Date: 2025-09-25 16:09:09 +0200
Commit message:

 code formatting; added banksy+rcdt references
Package: OSTA
Commit: 421e1960078f194092a569ed0dafcafe7381d912
Author: HelenaLC <helena@crowell.eu>
Date: 2025-09-25 15:57:20 +0200
Commit message:

 revise heatmap description
Package: OSTA
Commit: 155458d0e8f10d1c1ec84d0daacf963721bb6a96
Author: HelenaLC <helena@crowell.eu>
Date: 2025-09-25 15:51:30 +0200
Commit message:

 remove workaround
Package: OSTA
Commit: 272fff64a22cdf4d3db1057e3bc42e9c2f4324dd
Author: HelenaLC <helena@crowell.eu>
Date: 2025-09-25 15:49:54 +0200
Commit message:

 Visium HD workflow revision; add 'Statial' reference
Package: OSTA
Commit: 2e0f12914f622bab0c9de982763b6df924946d90
Author: HelenaLC <helena@crowell.eu>
Date: 2025-09-25 12:51:30 +0200
Commit message:

 chp rnm: data infrastructure -> infrastructure
Package: OSTA
Commit: cf69a2d849be65fc99a6d281638f0f907b73fa03
Author: HelenaLC <helena@crowell.eu>
Date: 2025-09-25 09:52:29 +0200
Commit message:

 add subterms analysis
Package: OSTA
Commit: 2c3991d104b2e3faf22a48135cd73be6a3e1bf10
Author: HelenaLC <helena@crowell.eu>
Date: 2025-09-25 09:05:12 +0200
Commit message:

 revise intro
Package: OSTA
Commit: d85f368c23e8b0e07de4e540c8b55a781e3afa5d
Author: HelenaLC <helena@crowell.eu>
Date: 2025-09-25 09:02:01 +0200
Commit message:

 fix typos
Package: OSTA
Commit: a2ba59f5e26c03b350b65ee2739e59a0f84464fc
Author: HelenaLC <helena@crowell.eu>
Date: 2025-09-24 18:32:23 +0200
Commit message:

 add ecosys draft
Package: OSTA
Commit: 628f3a405d2e9d3fa17d3496cb25e3a073bf41fe
Author: HelenaLC <helena@crowell.eu>
Date: 2025-09-24 10:14:11 +0200
Commit message:

 consistent citations; rephrasing
Package: OSTA
Commit: 08e64421fc703992ced629f085bfd766aa7f458e
Author: HelenaLC <helena@crowell.eu>
Date: 2025-09-24 10:05:00 +0200
Commit message:

 +napari
Package: OSTA
Commit: 95740b48799c2ce0b27958f1d8a2150e8c2a2d6d
Author: HelenaLC <helena@crowell.eu>
Date: 2025-09-24 09:46:54 +0200
Commit message:

 + alabaster, iSEE
Package: OSTA
Commit: 510d2aec94a196843e19aec838c8f359612e83f7
Author: Lukas Weber <lmweb012@gmail.com>
Date: 2025-09-21 21:03:45 -0400
Commit message:

 slightly adjust width
Package: OSTA
Commit: aa2c6587571263ff5b0756e0d3350d6867aac332
Author: Lukas Weber <lmweb012@gmail.com>
Date: 2025-09-21 18:24:36 -0400
Commit message:

 fix welcome heading after adding carousel
Package: OSTA
Commit: 63f717d485926b0207fcac646044145b22217754
Author: Lukas Weber <lmweb012@gmail.com>
Date: 2025-09-21 13:14:53 -0400
Commit message:

 Merge pull request #211 from lmweber/misc

misc
Package: OSTA
Commit: 57544d35da4b6dcd447fe0ffac9dc11f1d76a84e
Author: HelenaLC <helena@crowell.eu>
Date: 2025-09-21 12:13:55 +0200
Commit message:

 add sticker to readme
Package: OSTA
Commit: ed0ad4a7b2d9608378e8f3d1c28a12062a7fbec4
Author: HelenaLC <helena@crowell.eu>
Date: 2025-09-21 12:13:42 +0200
Commit message:

 add flags to contributors
Package: OSTA
Commit: 43c3611848f76ff1672707f22b3f1454b8faefe0
Author: HelenaLC <helena@crowell.eu>
Date: 2025-09-21 12:13:27 +0200
Commit message:

 add image carousel to landing page
Package: OSTA
Commit: 0155bda93274397fa8b2ab5d750bc9d75b113929
Author: Lukas Weber <lmweb012@gmail.com>
Date: 2025-09-17 18:14:24 -0400
Commit message:

 editing, fix filtering
Package: OSTA
Commit: b2af297c17d949fdb054d5f9332b7d641d9cf935
Author: Lukas Weber <lmweb012@gmail.com>
Date: 2025-09-16 21:15:56 -0400
Commit message:

 edits, formatting, add reference
Package: OSTA
Commit: b9774ad3acfbcc909fda0584ac2dc8af09c4ff80
Author: Lukas Weber <lmweb012@gmail.com>
Date: 2025-09-15 00:59:43 -0400
Commit message:

 remove CCC chapter until Python envs fixed
Package: OSTA
Commit: 291844d328760bb0cc27455e30a4cd2ce9fa51d6
Author: Lukas Weber <lmweb012@gmail.com>
Date: 2025-09-15 00:57:28 -0400
Commit message:

 partial update and fix python envs in CCC chapter - not working
Package: OSTA
Commit: 675b9b60963a6392882b0ad2ad61d690813c8835
Author: Lukas Weber <lmweb012@gmail.com>
Date: 2025-09-14 19:52:39 -0400
Commit message:

 various minor edits and formatting
Package: OSTA
Commit: 04802c163847806e4a4903e12d2bad1127a93430
Author: Lukas Weber <lmweb012@gmail.com>
Date: 2025-09-14 18:31:19 -0400
Commit message:

 match updated section ordering
Package: OSTA
Commit: b94a9d6158950b16d284bbaeba9abed24eb7cdd9
Author: Lukas Weber <lmweb012@gmail.com>
Date: 2025-09-13 00:30:20 -0400
Commit message:

 test build new ggplot
Package: OSTA
Commit: 5c6b76e81854f4e765cbabf85312b32513c4cabb
Author: Lukas Weber <lmweb012@gmail.com>
Date: 2025-09-10 09:04:51 -0400
Commit message:

 fix typo - from @vjcitn
Package: OSTA
Commit: af2812fcce4beaa3eff05ea73eff7f58ded5a882
Author: Lukas Weber <lmweb012@gmail.com>
Date: 2025-09-09 23:09:27 -0400
Commit message:

 change order of bkg chapters - from @Artur-man
Package: OSTA
Commit: 11d1d67b57f34306e017fa93d79182ec2f2cfd5f
Author: Lukas Weber <lmweb012@gmail.com>
Date: 2025-09-09 22:56:14 -0400
Commit message:

 remove dependencies section
Package: OSTA
Commit: cc2f71a061c303b49577cc0fab0e848114697913
Author: Lukas Weber <lmweb012@gmail.com>
Date: 2025-09-09 22:55:39 -0400
Commit message:

 minor edits and updates
Package: OSTA
Commit: 13334def32047e5207e189d482d87747bb05b442
Author: Lukas Weber <lmweb012@gmail.com>
Date: 2025-09-09 22:34:04 -0400
Commit message:

 fix Madabhushi reference
Package: OSTA
Commit: d1c4cbbfe3c468af9083e803f7d3d04500849251
Author: Lukas Weber <lmweb012@gmail.com>
Date: 2025-09-09 22:22:58 -0400
Commit message:

 consistent references formatting for ind-image-analysis
Package: OSTA
Commit: 3973c38e5f22855f07fced99cb0d3d85a183c7eb
Author: Helena L. Crowell <helena@crowell.eu>
Date: 2025-09-09 15:05:09 +0200
Commit message:

 Merge pull request #206 from lmweber/image

reduce image size
Package: OSTA
Commit: e9a870a491ef26c1b6ccaa7ba57882c62510488d
Author: HelenaLC <helena@crowell.eu>
Date: 2025-09-09 15:04:26 +0200
Commit message:

 reduce image size
Package: OSTA
Commit: 363e76e5dac34cd49c91ddf31c46de4ea1c19a19
Author: Helena L. Crowell <helena@crowell.eu>
Date: 2025-09-09 14:53:37 +0200
Commit message:

 Merge pull request #205 from lmweber/image

+ind-image-analysis
Package: OSTA
Commit: ecbf65ac7a4632774cf9c0528de7ad5c72614437
Author: HelenaLC <helena@crowell.eu>
Date: 2025-09-09 14:52:30 +0200
Commit message:

 uncapitalize header for consistency
Package: OSTA
Commit: 3923ede4d747b5eacf4a3ef0eec254d025a97aed
Author: HelenaLC <helena@crowell.eu>
Date: 2025-09-09 14:51:14 +0200
Commit message:

 hlc revision: added subsections, fixed references, added hyperlinks
Package: OSTA
Commit: 8fdd82f1a05181976eb283008b888254d3e101a2
Author: HelenaLC <helena@crowell.eu>
Date: 2025-09-09 14:50:59 +0200
Commit message:

 add missing ind-image-analysis ref
Package: OSTA
Commit: d2fbe3ddc560a2cb76267c88870cd20f20da7a68
Author: HelenaLC <helena@crowell.eu>
Date: 2025-09-09 14:50:47 +0200
Commit message:

 update ind-image-analysis pyramid image
Package: OSTA
Commit: 122fdb44d90dcc26ef5b8a1a61087001ccdc1d34
Author: HelenaLC <helena@crowell.eu>
Date: 2025-09-09 10:49:41 +0200
Commit message:

 fix ind-image-analysis references
Package: OSTA
Commit: 139ea80c683dce5632fbed8cc99ec9704a6691b9
Author: HelenaLC <helena@crowell.eu>
Date: 2025-09-09 10:49:24 +0200
Commit message:

 acknowledge Ilaria Billato
Package: OSTA
Commit: d5c02d35caa5a73008f697302764f6921ae0d40c
Author: Lukas Weber <lmweb012@gmail.com>
Date: 2025-09-04 10:24:24 -0400
Commit message:

 try without ome-zarr version specification
Package: OSTA
Commit: 3d2e7349eccf8008cd9565de4b2cb1102bcb99d9
Author: Lukas Weber <lmweb012@gmail.com>
Date: 2025-09-03 22:04:59 -0400
Commit message:

 use Zarr v2 to fix BaseStore error from Zarr v3
Package: OSTA
Commit: 9231e285499ef69137822d3f929793e89ae47659
Author: Lukas Weber <lmweb012@gmail.com>
Date: 2025-09-03 17:40:57 -0400
Commit message:

 reverse a few additional things
Package: OSTA
Commit: 95260206d841718af1dcdd68edcd4ac938548f74
Author: Lukas Weber <lmweb012@gmail.com>
Date: 2025-09-03 17:20:39 -0400
Commit message:

 Merge pull request #204 from markrobinsonuzh/img-mark-edits

mark edits on imaging chapters
Package: OSTA
Commit: 748d2ed62394b398b7a5e303940d146a57fc1e2a
Author: Mark Robinson <mark.robinson@mls.uzh.ch>
Date: 2025-09-03 08:52:52 +0200
Commit message:

 roll back a couple things
Package: OSTA
Commit: b29091f3a4e5e1ac41d75223a5fc6365ac54a642
Author: Mark Robinson <mark.robinson@mls.uzh.ch>
Date: 2025-08-21 08:22:50 +0200
Commit message:

 edits to workflow
Package: OSTA
Commit: 9c236b901f2abe6f9a35162b9d0851b6c8960f8a
Author: Mark Robinson <mark.robinson@mls.uzh.ch>
Date: 2025-08-20 19:52:17 +0200
Commit message:

 trying to wrange a basilisk env; but it's eval=FALSE anyways
Package: OSTA
Commit: 114ae38d87cea46ad23ef9deec9866f1405236af
Author: Mark Robinson <mark.robinson@mls.uzh.ch>
Date: 2025-08-20 19:43:15 +0200
Commit message:

 modified env to use older zarr/ome-zarr b/c squidpy needs that
Package: OSTA
Commit: d4fbb4fb0c7979d4c70479249e1856b2bddae88c
Author: Mark Robinson <mark.robinson@mls.uzh.ch>
Date: 2025-08-20 12:55:44 +0200
Commit message:

 edits
Package: OSTA
Commit: 61a959f6df350c885386d530dc9ee45b1e5fdeb8
Author: Mark Robinson <mark.robinson@mls.uzh.ch>
Date: 2025-08-20 12:12:59 +0200
Commit message:

 edits to intermed proc
Package: OSTA
Commit: a075ad928f28b7285adf76295532959ffa1d6b82
Author: Mark Robinson <mark.robinson@mls.uzh.ch>
Date: 2025-08-20 11:50:34 +0200
Commit message:

 edits
Package: OSTA
Commit: c55a3b705ca49a473b5a2cc365c07af95862e265
Author: Mark Robinson <mark.robinson@mls.uzh.ch>
Date: 2025-08-19 17:09:45 +0200
Commit message:

 some edits
Package: OSTA
Commit: 0a01fd75254b5292247b565d624b92bc0a7fa816
Author: billila <ilaria.billato@studenti.unipd.it>
Date: 2025-08-19 17:07:44 +0200
Commit message:

 fix minor
Package: OSTA
Commit: 85e726c5f1f9350eb2c04605fc989629f2d5a074
Author: billila <ilaria.billato@studenti.unipd.it>
Date: 2025-08-19 16:25:55 +0200
Commit message:

 add feature extraction part
Package: OSTA
Commit: a5158c0ea73ce9c30f25e9dc7ddb5c7376e675c6
Author: Mark Robinson <mark.robinson@mls.uzh.ch>
Date: 2025-08-19 16:11:52 +0200
Commit message:

 edits for img-segmentation
Package: OSTA
Commit: 26af9406b6fb81a8d3d3ada2abe3c7be6c0e1d0f
Author: Mark Robinson <mark.robinson@mls.uzh.ch>
Date: 2025-08-19 15:24:05 +0200
Commit message:

 harmonizing link structure
Package: OSTA
Commit: 7f4df78c3661ae706d5f8a40963af332a9066917
Author: billila <ilaria.billato@studenti.unipd.it>
Date: 2025-08-19 12:34:24 +0200
Commit message:

 add png images
Package: OSTA
Commit: 7a70b3e0a4f9ab588bb256a82056a30871ede0f4
Author: billila <ilaria.billato@studenti.unipd.it>
Date: 2025-08-19 12:31:32 +0200
Commit message:

 add ind-image-analysis
Package: OSTA
Commit: bd9945621976659bdd574e2dc1d39c0bf57e42b7
Author: billila <ilaria.billato@studenti.unipd.it>
Date: 2025-08-19 12:29:48 +0200
Commit message:

 ind-image-analysis bib
Package: OSTA
Commit: e020c6b2ab52f635ac133393b3a56f73865a83c0
Author: billila <ilaria.billato@studenti.unipd.it>
Date: 2025-08-19 12:25:29 +0200
Commit message:

 add ind-image-analysis.qmd
Package: SPOTlight
Commit: 4f27474c8cc8e9f734838a50fec1b8841980cef3
Author: MarcElosua <elosua.marc@gmail.com>
Date: 2025-10-01 11:06:24 -0400
Commit message:

 Makevars update
Package: SPOTlight
Commit: 928e845bb764788fd4f5bca8a753acbbe3b43c1c
Author: MarcElosua <elosua.marc@gmail.com>
Date: 2025-10-01 11:06:02 -0400
Commit message:

 test updates ggplot v4.0.0
Package: looking4clusters
Commit: 812475fe0d8bd5188274bc8af35b00e68fb6060e
Author: BioinfoUSAL <bioinfo@usal.es>
Date: 2025-10-01 16:59:28 +0200
Commit message:

 json download added
Package: UCell
Commit: 6bf47c683de42c51efbaedcc47fd4ba01336612d
Author: mass-a <massimo.andreatta@unige.ch>
Date: 2025-10-01 16:49:22 +0200
Commit message:

 changelog
Package: UCell
Commit: e8989395c46c4e288c2f021c475d780a4d9d288c
Author: mass-a <massimo.andreatta@unige.ch>
Date: 2025-10-01 16:44:51 +0200
Commit message:

 Add new vignette to discuss important parameters
Package: SmartPhos
Commit: 38bf3ded7c18c04c8ac27645c31c019c4455d68d
Author: shubh2565 <catchshubham2565@gmail.com>
Date: 2025-10-01 15:40:06 +0200
Commit message:

 update namespace
Package: scRepertoire
Commit: bbd600dc265bade166fe9cdb10c9f849a65df403
Author: theHumanBorch <ncborch@gmail.com>
Date: 2025-10-01 08:12:49 -0500
Commit message:

 Merge pull request #539 from BorchLab/combineBCR-grouping

Fix combineBCR() group.by
Package: scRepertoire
Commit: 5ba2e67ac76b6e24be86cab8d476e2fe15ba1ee8
Author: theHumanBorch <ncborch@gmail.com>
Date: 2025-10-01 07:59:45 -0500
Commit message:

 Readding remotes immApex

This will be changed once dev branch is moved to production on bioconductor
Package: scRepertoire
Commit: de1498a16c2b2c134a3c52e184049bd4abf61f65
Author: theHumanBorch <ncborch@gmail.com>
Date: 2025-10-01 07:52:19 -0500
Commit message:

 Merge pull request #538 from BorchLab/devel

Combine devel and combineBCR fix
Package: scRepertoire
Commit: c140b2dc6eccbabb8edd8e8c0c16969f6b24b3a7
Author: theHumanBorch <ncborch@gmail.com>
Date: 2025-10-01 07:52:09 -0500
Commit message:

 Merge branch 'combineBCR-grouping' into devel
Package: scRepertoire
Commit: ceab0ec0079cafa8a7dacd0fbeca73682a9b13a0
Author: theHumanBorch <ncborch@gmail.com>
Date: 2025-10-01 07:47:38 -0500
Commit message:

 Fix combineBCR

Add contigent group.by per issue #537
Package: SmartPhos
Commit: 2f1e4be40906ff20da58ea823bb2aaa6f48a430b
Author: shubh2565 <catchshubham2565@gmail.com>
Date: 2025-10-01 15:02:56 +0200
Commit message:

 replace DEP functions and update some tests
Package: DOtools
Commit: 32f14584e5a329c83f0e7541e67387f4e97f634a
Author: MarianoRuzJurado <mariani95@gmx.de>
Date: 2025-10-01 13:51:55 +0200
Commit message:

 Merge remote-tracking branch 'origin/devel' into devel
Package: DOtools
Commit: 1f53744e6d796182bd0fa610bb98b5147a2fb4ad
Author: MarianoRuzJurado <mariani95@gmx.de>
Date: 2025-10-01 13:01:30 +0200
Commit message:

 -minor adjustments in test running time
Package: SingleCellSignalR
Commit: 417c87a09f4974f502621e9ab3ebd2cc16f2a13a
Author: jcolinge <65902924+jcolinge@users.noreply.github.com>
Date: 2025-10-01 13:13:36 +0200
Commit message:

 commit 1.99.1 to switch to 2.0.0
Package: DOtools
Commit: e84d7ab2361731cc117faf9c6b00d7cc8828eed1
Author: MarianoRuzJurado <mariani95@gmx.de>
Date: 2025-10-01 13:01:30 +0200
Commit message:

 -warning handling
Package: DOtools
Commit: ef80e1eb1dfbfa123cc80d0901f2ffad01524daa
Author: MarianoRuzJurado <mariani95@gmx.de>
Date: 2025-10-01 12:16:14 +0200
Commit message:

 Merge remote-tracking branch 'origin/devel' into devel
Package: DOtools
Commit: 9f13739461e9917b7de349eb67d7a1de0e9f4ffa
Author: MarianoRuzJurado <mariani95@gmx.de>
Date: 2025-09-30 14:02:20 +0200
Commit message:

 -Adjustemnts for warnings
Package: DOtools
Commit: 582bf383f93dded2e29aaec6447f71fb3cc7db5d
Author: MarianoRuzJurado <mariani95@gmx.de>
Date: 2025-09-30 14:02:20 +0200
Commit message:

 -Pre ggplot update
Package: DOtools
Commit: c147238a8c174f17ae4fbbc8f80f7ec93a26f3ca
Author: MarianoRuzJurado <mariani95@gmx.de>
Date: 2025-09-30 11:45:22 +0200
Commit message:

 -Major adjustments in coding style
Package: DOtools
Commit: 34a874bf0b9e71dc42e84b5194533cf0cd75a86c
Author: MarianoRuzJurado <mariani95@gmx.de>
Date: 2025-09-19 15:23:47 +0200
Commit message:

 Merge remote-tracking branch 'origin/devel' into devel
Package: DOtools
Commit: c8c0ef37b6be61c3719181a04e37c259a9d10817
Author: MarianoRuzJurado <mariani95@gmx.de>
Date: 2025-09-19 13:13:07 +0200
Commit message:

 Merge remote-tracking branch 'origin/devel' into devel
Package: DOtools
Commit: 9fa640f9c098d5063ef1efb403587c352db9e972
Author: MarianoRuzJurado <mariani95@gmx.de>
Date: 2025-09-19 13:13:07 +0200
Commit message:

 Merge remote-tracking branch 'origin/devel' into devel
Package: DOtools
Commit: 6edb7426d011e629888558ae46f44ac605f284a9
Author: MarianoRuzJurado <mariani95@gmx.de>
Date: 2025-09-17 14:04:32 +0200
Commit message:

 Merge remote-tracking branch 'origin/devel' into devel
Package: DOtools
Commit: 092687b7050d5ab4e391fbe0c6032274fbc37cf0
Author: MarianoRuzJurado <mariani95@gmx.de>
Date: 2025-09-17 14:04:32 +0200
Commit message:

 Merge remote-tracking branch 'origin/devel' into devel
Package: DOtools
Commit: 98ec814a8a8383f6d894a6197d0250e429df9cab
Author: MarianoRuzJurado <mariani95@gmx.de>
Date: 2025-09-17 10:08:48 +0200
Commit message:

 Merge remote-tracking branch 'origin/devel' into devel
Package: DOtools
Commit: 82c7098ac5e639e85546759e516d3ea49e8be4ce
Author: MarianoRuzJurado <mariani95@gmx.de>
Date: 2025-09-17 10:08:48 +0200
Commit message:

 Merge remote-tracking branch 'origin/devel' into devel
Package: DOtools
Commit: bc5d36a8fab72d142724f8cc689022cdefbfe3e6
Author: MarianoRuzJurado <mariani95@gmx.de>
Date: 2025-09-16 15:00:05 +0200
Commit message:

 Merge remote-tracking branch 'origin/devel' into devel
Package: DOtools
Commit: e443c8f6e281aa1a71f319dbbcf28fb90ef40698
Author: MarianoRuzJurado <mariani95@gmx.de>
Date: 2025-09-16 15:00:05 +0200
Commit message:

 Merge remote-tracking branch 'origin/devel' into devel
Package: DOtools
Commit: 67db6d24bda68e124f989214449f16b21dcf03bf
Author: MarianoRuzJurado <mariani95@gmx.de>
Date: 2025-09-16 14:42:33 +0200
Commit message:

 - Extensive modifications to DO.Heatmap, implemented FC visualisation
Package: DOtools
Commit: 0d0fd6dbbf75a59e72e9c3038587e8d2a6e0d5e1
Author: MarianoRuzJurado <mariani95@gmx.de>
Date: 2025-09-16 14:42:33 +0200
Commit message:

 - Extensive modifications to DO.Heatmap, implemented FC visualisation
Package: DOtools
Commit: fc3a9a77193d2a5fd5a974fa2e2629942609178f
Author: MarianoRuzJurado <mariani95@gmx.de>
Date: 2025-09-11 12:55:51 +0200
Commit message:

 - Some adjustments for DO.Heatmap function
Package: DOtools
Commit: 2ec5b7ba6080f7656f2aecdda166d0a2d214c9b0
Author: MarianoRuzJurado <mariani95@gmx.de>
Date: 2025-09-11 10:57:22 +0200
Commit message:

 - Coding structure
Package: DOtools
Commit: 164b9c9f87dd10df293fcfb48ce1264a660500de
Author: MarianoRuzJurado <mariani95@gmx.de>
Date: 2025-09-09 16:16:19 +0200
Commit message:

 Merge remote-tracking branch 'origin/devel' into devel
Package: DOtools
Commit: 89b7516b9e3ae138efa5535d1fdbd35c6a0a53ca
Author: MarianoRuzJurado <mariani95@gmx.de>
Date: 2025-09-09 15:55:43 +0200
Commit message:

 - Consolidating vignettes
Package: DOtools
Commit: 32c2b8c2ceb46838dc508d7e93d08d7a199fed04
Author: MarianoRuzJurado <mariani95@gmx.de>
Date: 2025-09-09 15:55:43 +0200
Commit message:

 - Consolidating vignettes
Package: DOtools
Commit: aff28328da9bb6295e8d9cd8ca424e9873d3df49
Author: MarianoRuzJurado <mariani95@gmx.de>
Date: 2025-09-09 14:16:50 +0200
Commit message:

 - Warning resolvement
Package: DOtools
Commit: a689ce92444a16e4033de7f91a2687be8caed687
Author: MarianoRuzJurado <mariani95@gmx.de>
Date: 2025-09-09 13:48:58 +0200
Commit message:

 Merge remote-tracking branch 'origin/devel' into devel
Package: DOtools
Commit: 40697acba2048a26842ad1b56d5a923179834256
Author: MarianoRuzJurado <mariani95@gmx.de>
Date: 2025-09-09 13:25:35 +0200
Commit message:

 - minor fix for warnings
Package: DOtools
Commit: d052cd6e210801969e3e6f7cc72ebf0581179535
Author: MarianoRuzJurado <mariani95@gmx.de>
Date: 2025-09-09 13:25:35 +0200
Commit message:

 - minor fix for warnings
Package: DOtools
Commit: 58f2f302840508a99ecb71b103e822097275bc0d
Author: MarianoRuzJurado <mariani95@gmx.de>
Date: 2025-09-09 13:13:54 +0200
Commit message:

 Merge remote-tracking branch 'origin/devel' into devel
Package: DOtools
Commit: f6268bbf7b077da3dcc9847e55aa7cb23acbf7fd
Author: MarianoRuzJurado <mariani95@gmx.de>
Date: 2025-09-09 10:41:54 +0200
Commit message:

 -Update script descritptions
Package: DOtools
Commit: 824060cc0b88f622196ffe4ba5b0b2acab65fc87
Author: MarianoRuzJurado <mariani95@gmx.de>
Date: 2025-09-09 10:41:54 +0200
Commit message:

 Merge remote-tracking branch 'origin/devel' into devel
Package: DOtools
Commit: 3d1be914c366141676f0e7d639cd886bd31d9882
Author: MarianoRuzJurado <mariani95@gmx.de>
Date: 2025-08-20 13:03:42 +0200
Commit message:

 - Script splitting for better readibility
Package: DOtools
Commit: c2f97ff0d2cccc9d2774b88c007127dc234f61c6
Author: MarianoRuzJurado <mariani95@gmx.de>
Date: 2025-08-20 13:03:42 +0200
Commit message:

 Merge remote-tracking branch 'upstream/devel' into devel
Package: DOtools
Commit: 64c7da7c79fe1dd4add1996e87e25d6848cd9c8e
Author: MarianoRuzJurado <mariani95@gmx.de>
Date: 2025-08-06 15:02:00 +0200
Commit message:

 -add significance testing in dotplot
Package: MetaboDynamics
Commit: 33fe345bc46169c2b5d43ac081ed87cbdcb71faa
Author: ada697e <katja.danielzik@uni-due.de>
Date: 2025-10-01 10:55:18 +0200
Commit message:

 bug fix
Package: MetaboDynamics
Commit: a80b4d8607850a74aafb0eeb02913ac30eb1650a
Author: ada697e <katja.danielzik@uni-due.de>
Date: 2025-10-01 10:15:33 +0200
Commit message:

 bug fix
Package: MetaboDynamics
Commit: aab3d12719496afb174811c93c89fcdaf51a5af4
Author: ada697e <katja.danielzik@uni-due.de>
Date: 2025-10-01 10:14:47 +0200
Commit message:

 error fix in installation code
Package: SpaceTrooper
Commit: e723f66d29e879a68aa297345eb9fc39aedd8314
Author: dario righelli <dario.righelli@gmail.com>
Date: 2025-10-01 10:17:39 +0200
Commit message:

 Merge pull request #39 from drighelli/copilot/fix-b77606fa-5a0a-4979-babe-b651087114cf

Fix qcFlagPlots crash when polygon data filtering returns empty results
Package: SpaceTrooper
Commit: 91d51c3cb51059b3b739faf7aca978966bfaf3f0
Author: dario righelli <dario.righelli@gmail.com>
Date: 2025-09-30 17:31:27 +0200
Commit message:

 Enhance bioc_submit.yml for better CI/CD management

Updated GitHub Actions workflow to include new jobs and environment variables for Bioconductor version handling, dependency installation, and test coverage.
Package: SpaceTrooper
Commit: 616e3d27d152faf35bde1a1ef2291fe98c2021f0
Author: dario righelli <dario.righelli@gmail.com>
Date: 2025-09-26 16:54:37 +0200
Commit message:

 Update bioc_submit.yml
Package: SpaceTrooper
Commit: c09b7cdaf38f68d26228ac6ea5703189e5e31058
Author: dario righelli <dario.righelli@gmail.com>
Date: 2025-09-26 14:57:53 +0200
Commit message:

 Update Bioconductor version to 'devel'
Package: SpaceTrooper
Commit: fee75aabc0dc05ae8ef7cf66038aec1377d9753b
Author: dario righelli <dario.righelli@gmail.com>
Date: 2025-09-26 14:54:15 +0200
Commit message:

 Fix Bioconductor version format in workflow
Package: SpaceTrooper
Commit: 99100f4f1f5252b97735dd975a122b25e63b79ee
Author: dario righelli <dario.righelli@gmail.com>
Date: 2025-09-26 14:52:43 +0200
Commit message:

 Change Bioconductor version to devel_R_4.5.1

Update Bioconductor version for workflow matrix.
Package: SpaceTrooper
Commit: 84e938e16bdb70ad635835c311e7cb74fae0bee4
Author: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Date: 2025-09-25 17:12:30 +0000
Commit message:

 Remove build artifact and update .gitignore

Co-authored-by: drighelli <22836149+drighelli@users.noreply.github.com>
Package: SpaceTrooper
Commit: 9b5336d3b1081218c46beb0de0e4f1acead958fe
Author: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Date: 2025-09-25 17:12:06 +0000
Commit message:

 Final validation completed - qcFlagPlots fix ready

Co-authored-by: drighelli <22836149+drighelli@users.noreply.github.com>
Package: SpaceTrooper
Commit: ba373acc354213fe3a2ecc523c47d341d612f907
Author: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Date: 2025-09-25 17:07:39 +0000
Commit message:

 Fix NULL data error in qcFlagPlots by adding data validation in .make_outlier_plot

Co-authored-by: drighelli <22836149+drighelli@users.noreply.github.com>
Package: SpaceTrooper
Commit: 52883d8454c517ee766a0341caaf69cb78f3183a
Author: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Date: 2025-09-25 16:59:57 +0000
Commit message:

 Initial plan
Package: scrapper
Commit: c4f0a55f9e2197cf3d8ef5d484e8dd15cd8f17ec
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2025-10-01 01:23:42 -0700
Commit message:

 Don't sanitize the colnames of the levels DF from combineFactors.
Package: scrapper
Commit: 9a2a6efa3bfe32cc84147a954ec1114f701a5344
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2025-09-30 13:48:50 -0700
Commit message:

 Propagate the row names into the dimnames of the PCA output.
Package: pathMED
Commit: c3b8af74adee472dd17009b9d915536637019455
Author: jordimartorell <jmartorellm@gmail.com>
Date: 2025-10-01 09:46:25 +0200
Commit message:

 Minor changes
Package: limma
Commit: cc097121eedcafec85c46170d1204c87a42708d1
Author: Gordon Smyth <smyth@wehi.edu.au>
Date: 2025-10-01 16:49:59 +1000
Commit message:

 - Add "differential usage" concept tags to appropriate help pages.
Package: limma
Commit: bbd90ea4abc049a00edab3652969d0348b802391
Author: Gordon Smyth <smyth@wehi.edu.au>
Date: 2025-10-01 16:43:28 +1000
Commit message:

 limma 3.65.5

- Bug fix to contrastAsCoef() when the `contrast` matrix is not of
  full column rank.
Package: DMRcaller
Commit: 3121818bd93daf52829e9f8b6cfc8a1901ea83ee
Author: nrzabet <r.zabet@qmul.ac.uk>
Date: 2025-10-01 07:31:01 +0100
Commit message:

 added support for ONT methylation data
Package: SeqArray
Commit: f7c4cdc1462f4bdc1806d1cb985354c11da3351c
Author: Xiuwen Zheng <zhengxwen@gmail.com>
Date: 2025-09-30 22:38:21 -0500
Commit message:

 seqGDS2VCF with indexing
Package: IRanges
Commit: 52ffddd59be59946d919456fb3066d68103a1d39
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2025-09-30 17:03:22 -0700
Commit message:

 IRanges 2.43.5: Fix misplaced closing brace
Package: GenomicSuperSignature
Commit: 3455c036ecfee86fae96b0c108f3b18eb8713992
Author: Sehyun Oh <shbrief@gmail.com>
Date: 2025-09-30 17:18:50 -0400
Commit message:

 allow users to choose the number of PCs to validate against (with default)
Package: geomeTriD
Commit: 2c4611cd86e881431ed4c2acc05cc9a817e091fa
Author: Jianhong Ou <jianhong.ou@gmail.com>
Date: 2025-09-30 17:11:21 -0400
Commit message:

 update the author list.
Package: ExploreModelMatrix
Commit: 472cec6c43aebbd26f5ff84b58620c7b5db7fc12
Author: Charlotte Soneson <charlottesoneson@gmail.com>
Date: 2025-09-30 20:34:42 +0200
Commit message:

 Avoid use of deprecated aes_string
Package: BatchQC
Commit: 3db79cb703550d6894fa18b6a4d94c7acd45677b
Author: Jessica <102758461+jessmcc22@users.noreply.github.com>
Date: 2025-09-30 13:41:56 -0400
Commit message:

 Merge pull request #128 from jessmcc22/devel

Added covar as a shape variable in umap
Package: BatchQC
Commit: 4c9dde7384e4eea4934d19f27678429b4b392e33
Author: jessmcc22Mac <jessmcc@bu.edu>
Date: 2025-09-29 15:58:06 -0400
Commit message:

 Merge branch 'devel' of https://github.com/jessmcc22/BatchQC into devel
Package: BatchQC
Commit: 89ef4f3a4482645d4a09568c167933ea5b2b0ed0
Author: jessmcc22Mac <jessmcc@bu.edu>
Date: 2025-09-29 15:58:02 -0400
Commit message:

 Add covar as shape to umap plots
Package: curatedMetagenomicData
Commit: d23e87627560c64c955d7d87078149eb0263cbaa
Author: Sehyun Oh <shbrief@gmail.com>
Date: 2025-09-26 09:24:39 -0400
Commit message:

 missing dependency + version bump
Package: blase
Commit: 2cde01c79317036028019dd2e00045cfb47d0fee
Author: Andrew McCluskey <andrew@cluskii.com>
Date: 2025-09-30 17:21:01 +0100
Commit message:

 bump version to 0.99.1
Package: blase
Commit: 291f000525e4cfff37a01f2d9a3ac0072f81bdcf
Author: Andrew McCluskey <andrew@cluskii.com>
Date: 2025-09-30 17:18:16 +0100
Commit message:

 Save vignette data in package
Package: blase
Commit: 67f250fca2c9e30abee03eda35cb5694ffada973
Author: Andrew McCluskey <andrew@cluskii.com>
Date: 2025-09-30 16:49:01 +0100
Commit message:

 vignette review comments
Package: blase
Commit: 291ebf85d5dfc3697236a6693f57fa87fd2c9f90
Author: Andrew McCluskey <andrew@cluskii.com>
Date: 2025-09-30 16:27:09 +0100
Commit message:

 Use BiocStyle for vignettes and fix markdown table
Package: blase
Commit: 7b4c9ab19608a3eda7fd317d219d150dbdc7d435
Author: Andrew McCluskey <andrew@cluskii.com>
Date: 2025-09-30 16:13:55 +0100
Commit message:

 tests
Package: blase
Commit: 46477575b511c7ff566c0adf45122c39f7bd0e8b
Author: Andrew McCluskey <andrew@cluskii.com>
Date: 2025-09-30 16:04:07 +0100
Commit message:

 more tests
Package: blase
Commit: 2109b00b050cbdf03aab8b94d751ec843a958c67
Author: Andrew McCluskey <andrew@cluskii.com>
Date: 2025-09-30 13:01:25 +0100
Commit message:

 additional tests
Package: blase
Commit: 29576efaa04aab82dba4c0df7ea47a80a8addeb5
Author: Andrew McCluskey <andrew@cluskii.com>
Date: 2025-09-30 10:39:29 +0100
Commit message:

 expanding tests
Package: blase
Commit: 2dd3afa8ca79d2b6fecceab87089df2cb2bf1a34
Author: Andrew McCluskey <andrew@cluskii.com>
Date: 2025-09-29 17:41:37 +0100
Commit message:

 Use constructor for MappingResults
Package: blase
Commit: eaf388f07a3b31db7b5523326d2c9f9f165a4880
Author: Andrew McCluskey <andrew@cluskii.com>
Date: 2025-09-29 16:43:28 +0100
Commit message:

 using accessor functions
Package: blase
Commit: b59feb82b2ed301c93d5a7d85c6dc501040af682
Author: Andrew McCluskey <andrew@cluskii.com>
Date: 2025-09-29 15:57:36 +0100
Commit message:

 Add types to function parameter documentation.
Package: blase
Commit: 912075ad92bcd61f26554184b6bcbb8737558cfa
Author: Andrew McCluskey <andrew@cluskii.com>
Date: 2025-09-29 14:40:02 +0100
Commit message:

 Fix citation and NAMESPACE suggestions from review
Package: blase
Commit: 0a7a5c4029321a6fb716760742c5a9518877e72e
Author: Andrew McCluskey <andrew@cluskii.com>
Date: 2025-09-26 11:14:38 +0100
Commit message:

 add citation and move news and pkgdown files to inst
Package: blase
Commit: dca1a8aa7eed47329401783dce30ed48b31939d6
Author: Andrew McCluskey <andrew@cluskii.com>
Date: 2025-09-26 11:05:49 +0100
Commit message:

 Remove tools dir
Package: blase
Commit: 75ae245fdb7d18b25cd8f7273d922e46278dd86a
Author: Andrew McCluskey <andrew@cluskii.com>
Date: 2025-09-26 10:57:05 +0100
Commit message:

 DESCRIPTION review comments
Package: tximeta
Commit: 49f200cadc6d10ba6ff908ab4e5e99f4fd078261
Author: Mike Love <mikelove@users.noreply.github.com>
Date: 2025-09-30 11:47:16 -0400
Commit message:

 version bump for bioc
Package: tximeta
Commit: eb4c66b1e3082e43681941d6271306fd65c59ab5
Author: Mike Love <mikelove@users.noreply.github.com>
Date: 2025-09-30 11:46:16 -0400
Commit message:

 updates to vignette
Package: tximeta
Commit: df40dc4af6bf14b9d38b5e5728b3fd52419f5bf3
Author: Mike Love <mikelove@users.noreply.github.com>
Date: 2025-09-29 14:17:08 -0400
Commit message:

 avoid download via linkedTxome
Package: UCell
Commit: b49c69a2211833fe9410d96e1d4711c8f56375a1
Author: Massimo Andreatta <massimo.andreatta@unil.ch>
Date: 2025-09-30 16:47:37 +0200
Commit message:

 Implement missing_genes option. Refactor scoring function
Package: Moonlight2R
Commit: 69c6c4fcb92f37190aeb345424379f85d9ff6ee0
Author: Matteo Tiberti <matteo.tiberti@gmail.com>
Date: 2025-09-30 15:42:27 +0200
Commit message:

 Merge remote-tracking branch 'upstream/devel' into devel
Package: Moonlight2R
Commit: 406e27fe68ba822169d56ccb2e71f32d0d162840
Author: AlessiaCampo <59013682+AlessiaCampo@users.noreply.github.com>
Date: 2025-09-30 15:26:02 +0200
Commit message:

 Fixes in GLS function to work with easyPubMed updates. (#145)

* Fixes in GLS function to work with easyPubMed updates and new functions; Updates of the NEWS, DESCRIPTION and reference dataGLS accordingly

* removed unused print in Moonlight.rmd file

---------

Co-authored-by: Alessia Campo <acampo@kb-bioinfo01.cancer.dk>
Package: Moonlight2R
Commit: d734f5eeaa7c629e9e7fd37a0add40148bd5f159
Author: Matteo Tiberti <matteo.tiberti@gmail.com>
Date: 2025-04-23 16:35:57 +0200
Commit message:

 Updates repo upon BioC 3.21 release (#139)

* bump x.y.z version to even y prior to creation of RELEASE_3_21 branch

* bump x.y.z version to odd y following creation of RELEASE_3_21 branch

* increased R version requirement

* added update in NEWS

---------

Co-authored-by: A Wokaty <andres.wokaty@sph.cuny.edu>
Package: anansi
Commit: 4f3121846ccc135e55ec72a93d6a769bc06fd9c4
Author: thomaz <thomazbastiaanssen@gmail.com>
Date: 2025-09-30 14:55:10 +0200
Commit message:

 version bump to build - fix support site issue
Package: GenomeInfoDb
Commit: c9f851729c647e10665b370e053d49e4f84a06f7
Author: lshep <lori.shepherd@roswellpark.org>
Date: 2025-09-30 08:48:00 -0400
Commit message:

 Update genomeMappingTbl for release
Package: PhyloProfile
Commit: 50ee66382727bdf9cb9d5fc0c1b9055d0092158a
Author: AnnamTran <trvinh@gmail.com>
Date: 2025-09-30 13:38:24 +0200
Commit message:

 moved detailed and domain plot to modalDialog
Package: PhyloProfile
Commit: 924a117d0c19edfcc900069bdd9353bb32b9647b
Author: AnnamTran <trvinh@gmail.com>
Date: 2025-09-30 13:35:43 +0200
Commit message:

 removed extrafont
Package: PhyloProfile
Commit: 37b8a6970e01e4968ec3486665bbbe8e9aa9e08d
Author: Vinh Tran <trvinh@gmail.com>
Date: 2025-07-10 09:17:56 +0200
Commit message:

 Update README.md
Package: cageminer
Commit: 954b427b8fd4e13ad12fa93b4efb47e7a37347b7
Author: almeidasilvaf <fabricio_almeidasilva@hotmail.com>
Date: 2025-09-30 13:18:30 +0200
Commit message:

 Version bump in devel
Package: cageminer
Commit: ffd3609248c097ec9d1e92b3697615092e08ffb2
Author: almeidasilvaf <fabricio_almeidasilva@hotmail.com>
Date: 2025-09-30 13:17:21 +0200
Commit message:

 Fixed unit tests after ggplot update
Package: anansi
Commit: 56d36eda2fc633304f626362a84309075a4cc8af
Author: thomaz <thomazbastiaanssen@gmail.com>
Date: 2025-09-30 12:53:05 +0200
Commit message:

 Version bump
- update R, RoxygenNote versions in DESCRIPTION
- fix Support Site issue
Package: cageminer
Commit: 484f1aabdde7c35b89416f325a51beb02505b1b2
Author: almeidasilvaf <fabricio_almeidasilva@hotmail.com>
Date: 2025-09-30 12:41:53 +0200
Commit message:

 Updated GHA workflow
Package: ggbio
Commit: 245af340658f79ab7177546fc428da2f9c376522
Author: Michael Lawrence <lawremi@gmail.com>
Date: 2025-09-30 03:27:31 -0700
Commit message:

 remove dependency on GGally
Package: cageminer
Commit: 69a12a5d49fa16e7894344ca8e1d51734e5d62d0
Author: almeidasilvaf <fabricio_almeidasilva@hotmail.com>
Date: 2025-09-30 12:11:58 +0200
Commit message:

 Version bump in devel
Package: cageminer
Commit: c819f4f0450e2da874d617863fbf38c2c2b08307
Author: almeidasilvaf <fabricio_almeidasilva@hotmail.com>
Date: 2025-09-30 12:11:29 +0200
Commit message:

 Fixed ggplot unit tests after switch to S6
Package: UCell
Commit: d26c7ff0ba0863dc7646fc0a5edfc2f36efbfc49
Author: Massimo Andreatta <massimo.andreatta@unil.ch>
Date: 2025-09-30 11:30:22 +0200
Commit message:

 Update README.md
Package: UCell
Commit: 5311c4b490679545c3059661f56e9f925828c71d
Author: Massimo Andreatta <massimo.andreatta@unil.ch>
Date: 2025-09-26 13:34:40 +0200
Commit message:

 Update README.md
Package: ggkegg
Commit: 9668270d08fa603ceccb9ffea0d23757348a559e
Author: noriakis <nori@hgc.jp>
Date: 2025-09-30 12:09:00 +0900
Commit message:

 v1.7.2 in devel
Package: ggkegg
Commit: f6d8835a498fb8456b116fa93f36bc6a9a338d02
Author: noriakis <nori@hgc.jp>
Date: 2025-09-30 12:06:27 +0900
Commit message:

 v1.6.2
Package: ggkegg
Commit: 4a6647d095faddb5b48cf1e3f0939012e728b0ec
Author: nsato <nori@hgc.jp>
Date: 2025-09-30 11:31:40 +0900
Commit message:

 readable edge problem (3)
Package: ggkegg
Commit: 72c2f2af6575dc14e45139578c3a2115cc8d80be
Author: nsato <nori@hgc.jp>
Date: 2025-09-30 11:15:31 +0900
Commit message:

 readable edge problem (2)
Package: ggkegg
Commit: a8335d7b766150d93517f2f03842e756315c0ea0
Author: noriakis <nori@hgc.jp>
Date: 2025-09-30 10:57:48 +0900
Commit message:

 readable edge problem
Package: ggkegg
Commit: 9bf164ccbf4db168de0eb211fd801b0ab5a76077
Author: noriakis <nori@hgc.jp>
Date: 2025-09-24 10:43:08 +0900
Commit message:

 v1.6.1
Package: ggkegg
Commit: 389f2d81b014b3115764e33af60970babe1f02b4
Author: noriakis <nori@hgc.jp>
Date: 2025-09-24 10:42:03 +0900
Commit message:

 Merge branch 'devel'

# Conflicts:
#	DESCRIPTION
Package: ggkegg
Commit: 2bc9c3b3217b3fc63e790e35e50ef76a233eb303
Author: noriakis <nori@hgc.jp>
Date: 2025-09-16 10:13:29 +0900
Commit message:

 Merge remote-tracking branch 'origin/devel' into devel
Package: ggkegg
Commit: 76ab4f662bca5279cf19367478a2d19c3b5d24d2
Author: noriakis <31095487+noriakis@users.noreply.github.com>
Date: 2025-03-29 10:36:46 +0900
Commit message:

 new function: add_readable_edge_label
Package: ggkegg
Commit: a9e00aa875a2b8bd46630f505274e8c4f24560cf
Author: noriakis <nori@hgc.jp>
Date: 2025-01-29 14:16:18 +0900
Commit message:

 v1.4.1 release
Package: qsvaR
Commit: 3cab57c35fc6f9281b036b7b1a65d1f75a21e663
Author: lcolladotor <lcolladotor@gmail.com>
Date: 2025-09-29 21:57:34 -0400
Commit message:

 v1.13.3 -- list Nick as the maintainer
Package: scruff
Commit: e1c69304b5b080e5ffeec840f03f80e8d03ed657
Author: Josh Campbell <joshua-d-campbell@gmail.com>
Date: 2025-09-29 21:23:41 -0400
Commit message:

 Merge branch 'master' into devel
Package: scruff
Commit: a610e440dc6fdf76b7966288bb799a31ae1df20e
Author: Zhe Wang <zhe@bu.edu>
Date: 2024-03-27 21:40:55 -0400
Commit message:

 Merge pull request #188 from zhewa/master

Update Master
Package: scruff
Commit: afc9efe372087eb769da165f6bafe0442174b004
Author: zhewa <zhe@bu.edu>
Date: 2024-03-27 21:35:03 -0400
Commit message:

 Merge branch 'master' of github.com:campbio/scruff
Package: scruff
Commit: 26f260e8c43fc6d825670595b468b1b42f421eb0
Author: Zhe Wang <zhe@bu.edu>
Date: 2021-11-13 11:05:15 -0500
Commit message:

 Merge pull request #182 from zhewa/master

fix #181. remove "width" in .getGeneAnnotation
Package: Pirat
Commit: a512d83c3e8807405ead887a31c746fc14640c7e
Author: Lucas Etourneau <lucas.etourneau@berkeley.edu>
Date: 2025-09-29 16:24:54 -0700
Commit message:

 Package version change
Package: MetabolomicsPipeline
Commit: 6b91b2676991cadcacd79bab023fd115ecaa8642
Author: joelparkeruofa <joelparker@arizona.edu>
Date: 2025-09-29 15:34:18 -0700
Commit message:

 removing reactivity in vignette
Package: MetaDICT
Commit: 2f68b8fa517e08a9b04948d69b64e48eea795db4
Author: Bo Yuan <boyuan5@illinois.edu>
Date: 2025-09-29 17:25:32 -0500
Commit message:

 update suggests
Package: MetaDICT
Commit: 61be00464ed63d22e2a6e9b7c193af878ffc49f8
Author: BoYuan07 <97987151+BoYuan07@users.noreply.github.com>
Date: 2025-09-03 15:58:26 -0500
Commit message:

 Update README.md
Package: MetabolomicsPipeline
Commit: 764b996cc03af4cc5ddf0d75b87714591b234987
Author: joelparkeruofa <joelparker@arizona.edu>
Date: 2025-09-29 15:17:50 -0700
Commit message:

 version bump
Package: MetabolomicsPipeline
Commit: 0a36c6be4314c18519780666383d91e37cab8c18
Author: joelparkeruofa <joelparker@arizona.edu>
Date: 2025-09-29 15:01:20 -0700
Commit message:

 updating desctiption
Package: BUSpaRse
Commit: d204f22207e470e148d25b24d83eefa740e589f9
Author: Lambda Moses <dlu2@caltech.edu>
Date: 2025-09-29 17:39:24 -0400
Commit message:

 Really deal with Ensembl not archiving version 99 anymore
Package: notame
Commit: df288971107f70b98ea1f3a09fb4b22302716b72
Author: vsuksi <vsuksi@abo.fi>
Date: 2025-09-29 23:37:50 +0300
Commit message:

 Version bump

Bump needed to get notame built with notameStats and notameViz 
dependencies on server.
Package: wompwomp
Commit: 8adc6c69c65025e7e2dc7c0639d5a2587b9e4d11
Author: josephrich98 <josephrich98@gmail.com>
Date: 2025-09-29 11:42:19 -0700
Commit message:

 version bump
Package: wompwomp
Commit: ce2a0f928ddd56296d4db47144ef2db6c1f12d04
Author: josephrich98 <josephrich98@gmail.com>
Date: 2025-09-28 19:44:01 -0700
Commit message:

 small string change
Package: wompwomp
Commit: b4a5bdbe9794bdef37f568467017e22a75beb8f1
Author: josephrich98 <josephrich98@gmail.com>
Date: 2025-09-28 19:40:08 -0700
Commit message:

 minor string change
Package: NanoStringNCTools
Commit: d043c645cd5045b44663944629ffced831bc8f2a
Author: Maddy Griswold <mgriswold@nanostring.com>
Date: 2025-09-29 14:09:40 -0400
Commit message:

 dev version
Package: NanoStringNCTools
Commit: cd6d05b6ca288729d31c86e9038efef06614898e
Author: Maddy Griswold <40255151+maddygriz@users.noreply.github.com>
Date: 2025-09-29 14:06:55 -0400
Commit message:

 Merge pull request #42 from Nanostring-Biostats/dev

Bioc 3.21
Package: NanoStringNCTools
Commit: 2a12f215b20596a5a34c11e305aad7ed5665d2aa
Author: Maddy Griswold <40255151+maddygriz@users.noreply.github.com>
Date: 2025-09-29 11:22:43 -0400
Commit message:

 Merge pull request #41 from Nanostring-Biostats/plottingIssue

Plotting issue
Package: NanoStringNCTools
Commit: a54c3fc2125034009fc8f1fbe259502d4a5aab48
Author: Maddy Griswold <40255151+maddygriz@users.noreply.github.com>
Date: 2025-09-26 14:40:11 -0400
Commit message:

 boxplot default

Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>
Package: NanoStringNCTools
Commit: 90873782f6eb70033b9a5a04fac62c72fa85832a
Author: Maddy Griswold <40255151+maddygriz@users.noreply.github.com>
Date: 2025-09-26 14:39:29 -0400
Commit message:

 Merge branch 'dev' into plottingIssue
Package: NanoStringNCTools
Commit: efe824ecce34ec74ac0e67c1613f1adc403a92f9
Author: Maddy Griswold <mgriswold@nanostring.com>
Date: 2025-09-26 17:47:03 +0000
Commit message:

 version update
Package: NanoStringNCTools
Commit: e27c01adc457c5a75470d605dca2b395afc3970f
Author: Maddy Griswold <mgriswold@nanostring.com>
Date: 2025-09-26 17:43:20 +0000
Commit message:

 use ggplot defaults instead of ggiraph
Package: universalmotif
Commit: 26a42b33c72084d48e655c8de466cf9bc864a0dd
Author: bjmt <benjmtremblay@gmail.com>
Date: 2025-09-29 18:57:00 +0100
Commit message:

 quiet rcpp warning in test
Package: SpatialOmicsOverlay
Commit: 9c1b7c8286dfe483c1aef82e43867bddcfa20129
Author: Maddy Griswold <40255151+maddygriz@users.noreply.github.com>
Date: 2025-09-29 11:27:47 -0400
Commit message:

 Package Version
Package: SpatialOmicsOverlay
Commit: 1e85803d6901fe0c998f3a352baf28193a63cf17
Author: Maddy Griswold <40255151+maddygriz@users.noreply.github.com>
Date: 2025-09-26 15:21:59 -0400
Commit message:

 Merge pull request #61 from Nanostring-Biostats/ggplot2Checks

update ggplot checks in tests
Package: SpatialOmicsOverlay
Commit: e5430c41059d6f46099a9c4c6a74979d29ea2bf4
Author: Maddy Griswold <mgriswold@nanostring.com>
Date: 2025-07-22 21:22:03 +0000
Commit message:

 update ggplot checks in tests
Package: scDesign3
Commit: dec8acb2f54c2498f005ab0fce9781b7654562ef
Author: Dongyuan Song <dongyuansong@ucla.edu>
Date: 2025-09-29 10:51:50 -0700
Commit message:

 Move rvinecopulib to Suggests
Package: tximportData
Commit: 0da95c16663cfb53b9f2f4471a0abfedf4faf184
Author: Mike Love <mikelove@users.noreply.github.com>
Date: 2025-09-29 13:48:53 -0400
Commit message:

 version bump
Package: tximportData
Commit: 4d0eec0e1727e856430a237b1475b7119110238c
Author: Mike Love <mikelove@users.noreply.github.com>
Date: 2025-09-29 13:46:14 -0400
Commit message:

 adding gencode gtf to avoid ftp issues in tximeta
Package: universalmotif
Commit: c6bb747803761bff26c6f6028c00121d00aee78f
Author: bjmt <benjmtremblay@gmail.com>
Date: 2025-09-29 18:35:40 +0100
Commit message:

 bugfix v1.26.3
Package: universalmotif
Commit: 03be0e226156b724c76a021c0dbe50793db570db
Author: Benjamin Jean-Marie Tremblay <benjmtremblay@gmail.com>
Date: 2025-09-20 09:16:12 +0100
Commit message:

 Merge pull request #31 from smped/master

Quick bugfix
Package: universalmotif
Commit: 11580adc994ea6bcc4cb3ac9c3ad26355c6fae75
Author: Stevie Ped <stephen.pederson.au@gmail.com>
Date: 2025-09-18 00:56:22 +0930
Commit message:

 Quick bugfix
Package: tximeta
Commit: 1e29d7cf311ed40eb475a95949dbf4b5654a8aee
Author: Mike Love <mikelove@users.noreply.github.com>
Date: 2025-09-29 13:22:51 -0400
Commit message:

 avoid download from ftp entirely
Package: tximeta
Commit: 5f6d7ec3dab9415d975231f606c29858cc8bd2e9
Author: Mike Love <mikelove@users.noreply.github.com>
Date: 2025-09-29 12:01:38 -0400
Commit message:

 attempt to fix GHA and download from ftp
Package: tximeta
Commit: dd2549ca5a6774dafe8e1d408ac7a93c9442f2da
Author: Mike Love <mikelove@users.noreply.github.com>
Date: 2025-09-29 08:39:40 -0400
Commit message:

 monday morning update
Package: tximeta
Commit: 3149ad018a0ad3eb84e222d6ad5c94904ef3c746
Author: Mike Love <mikelove@users.noreply.github.com>
Date: 2025-09-28 11:29:35 -0400
Commit message:

 run pkgdown for real this time
Package: CytoPipeline
Commit: 0bc310a5e9028298b6c58572f345a586e31d2ebb
Author: phauchamps <philippehauchamps@hotmail.com>
Date: 2025-09-29 19:17:28 +0200
Commit message:

 Merge branch 'devel' of git.bioconductor.org:packages/CytoPipeline into devel
Package: CytoPipeline
Commit: 58bbdcbc67e3dd0f4e256cdc089cd93f9bb40403
Author: phauchamps <philippehauchamps@hotmail.com>
Date: 2025-09-29 16:05:51 +0200
Commit message:

 - added sampleDisplayNames()
- bumped version to 1.9.3
Package: CytoPipeline
Commit: 2ba3c80cf474f5c0710db4c29cc314bd47106b5a
Author: phauchamps <philippehauchamps@hotmail.com>
Date: 2025-09-29 13:40:31 +0200
Commit message:

 additional bug corrections for :
'sample files can now have duplicate base names (provided full paths are different)'
Package: CytoPipeline
Commit: 295f893f5c8b742b790e35717395abc8e983caf5
Author: phauchamps <philippehauchamps@hotmail.com>
Date: 2025-09-28 12:28:00 +0200
Commit message:

 `pData<-` can now accept new pData containing more rows than existing sample names
(the corresponding subset of pData is taken).
Package: CytoPipeline
Commit: f681e990eaadddbfd40440ec12631235e318f2bd
Author: phauchamps <philippehauchamps@hotmail.com>
Date: 2025-09-26 17:08:22 +0200
Commit message:

 - sample files can now have duplicate base names
(provided full paths are different)
- bumped version to 1.9.2
Package: CytoPipeline
Commit: 77cd7047aad10df80d811b3894affc5e53ab10c8
Author: phauchamps <philippehauchamps@hotmail.com>
Date: 2025-08-19 12:09:27 +0200
Commit message:

 updated LICENSE file to 2025
Package: CytoPipeline
Commit: dade4854a9347a540aa1508020c1788ae248b70a
Author: phauchamps <philippehauchamps@hotmail.com>
Date: 2025-08-19 11:59:16 +0200
Commit message:

 updated license statements in R files to 2025
Package: CytoPipeline
Commit: 0835c53c006e0df7cc991d38f649afc6f7d500ff
Author: phauchamps <philippehauchamps@hotmail.com>
Date: 2025-05-15 13:13:25 +0200
Commit message:

 Corrected typo in NEWS.md
Package: CytoPipeline
Commit: 11d301acff8a316ed1789faa0fbf1824eb5f8131
Author: phauchamps <philippehauchamps@hotmail.com>
Date: 2025-05-15 11:59:45 +0200
Commit message:

 GHA migrated to Bioc 3.22
Package: CytoPipeline
Commit: efe22ab87ceae2f0d15a91b759ad9523a072a0f4
Author: phauchamps <philippehauchamps@hotmail.com>
Date: 2025-05-15 11:20:00 +0200
Commit message:

 - upgraded to GHA cache v4
- bumped version to 1.9.1
Package: CytoPipeline
Commit: 785712f21323a387c4448b6442200752e250f8ab
Author: phauchamps <philippehauchamps@hotmail.com>
Date: 2025-05-15 11:08:07 +0200
Commit message:

 bumped version to 1.9.0 (Bioc 3.22)
Package: CytoPipeline
Commit: 29a8591c596effc41f208c5056d89800811e3e06
Author: phauchamps <philippehauchamps@hotmail.com>
Date: 2024-11-04 13:09:15 +0100
Commit message:

 bumped devel version to 1.7.1
Package: ggbio
Commit: ae5ad9961280ee75b723fa6408215945eae0fb61
Author: Michael Lawrence <lawremi@gmail.com>
Date: 2025-09-29 10:07:12 -0700
Commit message:

 clean up the ggplot2 class definitions, fixes #178
Package: smoppix
Commit: 359b01b746ddc10c5d5f2f79ac97c4838c88f0b4
Author: stijn <stijn.hawinkel@psb.ugent.be>
Date: 2025-09-29 11:14:58 +0200
Commit message:

 Mention vignette in readme
Package: Rarr
Commit: 94a4b4b6c68a152748cb42b57c468d75b142a7ab
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-09-05 12:53:49 +0200
Commit message:

 Bump version
Package: Rarr
Commit: b91883ff38b4b317a08c8f94a1fb76d918a83a77
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-09-05 12:53:34 +0200
Commit message:

 Document changes
Package: Rarr
Commit: 4c78154183ded811484a1beaed77720ff7b85879
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-09-05 15:06:11 +0200
Commit message:

 Update s3 test with latest metadata df
Package: Rarr
Commit: 68605b96bb8bb8f9fb763873242ac99a53289b70
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-09-05 12:50:00 +0200
Commit message:

 Update documentation with changes for v3 support
Package: Rarr
Commit: 83f713a76d228cd4985075fe0654ce3199330b10
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-09-05 09:29:32 +0200
Commit message:

 Customize error message for missing metadata
Package: Rarr
Commit: 89dc01a94029442f053785d8a99cd093e1f6006c
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-09-04 18:07:40 +0200
Commit message:

 Reduce code duplication between .rbind_array_metadata and .print_array_metadata
Package: Rarr
Commit: 19241bafaf6eb059734be71b303e5ed2470f2a82
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-09-04 17:34:51 +0200
Commit message:

 Move v3 conversion step to metadata printing exclusive functions

Since we still need to update all the places where we extract, e.g., the chunk shape in the data reading/writing portions of the code.
Package: Rarr
Commit: 5c708d6b46c181e0b8489c2bd0ec39419272bd28
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-09-04 17:10:19 +0200
Commit message:

 Set metadata_file arg to ".zarray" in data read/write functions for now
Package: Rarr
Commit: 4c2e9253fbf9e6a13e535b8d48730198ebf0c05e
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-09-04 17:04:37 +0200
Commit message:

 Add error message when trying to read v3 array
Package: Rarr
Commit: 9a503dfc8467e223cc5ea97af4e1db3dad934f99
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-09-04 17:02:06 +0200
Commit message:

 Support v3 metadata dataframing
Package: Rarr
Commit: 0facd83a401fefac96795789978f2830adbce871
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-09-04 16:51:00 +0200
Commit message:

 Support v3 metadata printing
Package: Rarr
Commit: 4677bf4235d8863037553e14b488ea1f1fb96ea1
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-09-04 16:20:49 +0200
Commit message:

 Add version 2 to 3 metadata mapping
Package: Rarr
Commit: e02f2ed634769cfe341efb8f5540eaba2f3bf54f
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-09-04 16:01:34 +0200
Commit message:

 Avoid calling .parse_datatype twice in .read_array_metadata()
Package: Rarr
Commit: 01a70b13bb8a26d7ff8808e60672c0e4076fccc5
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-09-04 15:11:07 +0200
Commit message:

 Use bool for boolean

For consistency with v3 spec
Package: Rarr
Commit: 204b153ed73f0f56c2d766e4455bf662d28da28a
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-09-04 13:12:03 +0200
Commit message:

 Add test for v3 metadata
Package: Rarr
Commit: 524625ac6ed2f840f20acd6e75ac51b3d077150f
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-09-05 10:51:29 +0200
Commit message:

 Add snapshot tests for metadata printing
Package: Rarr
Commit: 68777574f8b3899ea688b50b73787c905f66b11d
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-09-04 11:27:29 +0200
Commit message:

 Add comment about why we check for existence again
Package: Rarr
Commit: 348bad4bdb4817a794f1ed15d200fe2a6e45a2dd
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-09-04 11:24:43 +0200
Commit message:

 Move metadata file existence checking at the start of `zarr_overview()`
Package: Rarr
Commit: 2eacf480db227b07a479e11d8c0c5e0888fa5992
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-09-26 11:22:08 +0200
Commit message:

 Fix GHA indentation
Package: Rarr
Commit: 0d1390317d934887917b23b0c7d401cb790a0eb7
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-09-26 11:20:15 +0200
Commit message:

 Restore running continuous benchmarks on all PR
Package: Rarr
Commit: 20fac42a1cb0404fda4462468742d19b06bd66e0
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-09-26 11:16:36 +0200
Commit message:

 Reduce number of runs for (de)compress benchmarks
Package: Rarr
Commit: 90a50696db5d404fdee72e1c5889052c66f585dc
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-09-25 20:21:39 +0200
Commit message:

 Set up touchstone (#51)
Package: Rarr
Commit: 17bfb1866a295c391ba4c5acfbaf3f3d4f54fd3e
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-09-22 18:09:13 +0200
Commit message:

 Rename read/write_zattrs() to read/write_zarr_attributes()

To prepare for v3 attributes support
Package: Rarr
Commit: 4e610fa9840524a2413fbea6bb24312322f95ed8
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-09-22 15:40:42 +0000
Commit message:

 Render pkgdown on devel
Package: Rarr
Commit: 5f14cc08359c88e1aa4fcc6df6b048b5148f2975
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-09-22 14:42:30 +0200
Commit message:

 Add NEWS
Package: Rarr
Commit: b422cc37fbe52195d4f57a3bd4706bce532fa7e5
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-09-22 14:34:30 +0200
Commit message:

 Fix children chunks path
Package: Rarr
Commit: bd1d0892580ea9e00c9f7b9c64c64c54557a4f99
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-09-22 14:21:00 +0200
Commit message:

 Create custom reference index
Package: Rarr
Commit: 4f7db099ac4f047e6e791102ee72d92bd94c15d4
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-09-22 14:20:22 +0200
Commit message:

 Mark .parse_datatype() as internal
Package: Rarr
Commit: 3bb5aa0da97751f28e1a61c2271f88b36dbd6a29
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-09-22 13:28:37 +0200
Commit message:

 Run devtools::document()
Package: Rarr
Commit: b68143ce6515b317cc4f821e9168f81f355e5fd8
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-09-22 13:27:51 +0200
Commit message:

 Use lowercase 'internal' roxygen keyword

So the topics are properly ignored by pkgdown
Package: Rarr
Commit: 5686de81ba606eafe9533bcb86fd70b887179f5e
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-09-22 13:24:30 +0200
Commit message:

 Run usethis::use_pkgdown_github_pages()
Package: SETA
Commit: 020938def14b55289a5e9320a840422016929d88
Author: kylekimler <kylejkimler@gmail.com>
Date: 2025-09-28 22:25:50 -0400
Commit message:

 add SCE as dependency
Package: DuplexDiscovereR
Commit: a71dd2d820ce2bc391e5e8331df634b21c0e662e
Author: Egors01 <38434635+Egors01@users.noreply.github.com>
Date: 2025-09-29 16:25:27 +0200
Commit message:

 Merge pull request #15 from Egors01/release_bioc_3_21

fixed the argument descriptions in documentation
Package: DuplexDiscovereR
Commit: 7acdc9fecaa667027123550c6f7012982e4199ef
Author: Egors01 <yegor.smb@gmail.com>
Date: 2025-09-29 16:22:36 +0200
Commit message:

 fixed the argument descriptions in documentation
Package: DuplexDiscovereR
Commit: 8be7eebb167d70f1221ef292dcf449f7cff487dc
Author: Egors01 <yegor.smb@gmail.com>
Date: 2025-09-29 15:07:47 +0200
Commit message:

 New annotate function. Change the veccast warning
Package: BANDITS
Commit: 06a68fa5c8e3c19cfa1d57a2fabf8368e83d7eb6
Author: Simone Tiberi <simone.tiberi@unibo.it>
Date: 2025-09-29 16:10:00 +0200
Commit message:

 Update
Package: BANDITS
Commit: 6812ef35d4623b084a3d5ab256eb5a1a1b8d2b39
Author: Simone Tiberi <simone.tiberi@unibo.it>
Date: 2025-09-29 16:06:44 +0200
Commit message:

 create_data updated
Package: biomaRt
Commit: 4741f8a39e9e4654dc65e8a13b96b0864b0cc0fe
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-09-29 15:07:21 +0200
Commit message:

 Bump version
Package: biomaRt
Commit: fc281b0f928a12e90a1be0ec1e3f882220a37a0f
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-09-29 15:07:02 +0200
Commit message:

 Add NEWS
Package: biomaRt
Commit: 9ebdc9e04b0a8e966528279850c6b552095fe292
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-09-01 10:35:29 +0200
Commit message:

 Repeat request if redirected
Package: biomaRt
Commit: 51aa6ada780323529bbde10cd143466921dec925
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-09-01 10:35:11 +0200
Commit message:

 Let httr2 handle separator before POST data
Package: biomaRt
Commit: bef8404b506a6975296fb8c5a55ccab824569f1c
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-09-29 15:09:43 +0200
Commit message:

 Fix old URL to biomart.org in vignette
Package: biomaRt
Commit: 45e7bc1ca49fb92415e11ebdc97cddacea950ee8
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-09-29 15:08:59 +0200
Commit message:

 Send users to https pages only
Package: notameViz
Commit: a39ee1cec28d928111dc3e3fe51d42753a6815a8
Author: vsuksi <vsuksi@abo.fi>
Date: 2025-09-29 16:15:03 +0300
Commit message:

 Version bump

Made no progress on unavailable igraph package after a bunch of 
troubleshooting and suggestions, so simply commenting example out for 
now.
Package: nmrdata
Commit: 27cb4431b8da251d904dabc410043d680bc14439
Author: tk <tkimhofer@gmail.com>
Date: 2025-09-29 15:01:09 +0200
Commit message:

 added runnable example for fct getRawExpDir
Package: nmrdata
Commit: 568beb1a73bc8bc455100d95191214a8be8ca6b3
Author: tk <tkimhofer@gmail.com>
Date: 2025-09-29 08:50:52 +0200
Commit message:

 added runnable example
Package: biodb
Commit: 0b0ffc757e2f716b48dcaecb2de69fb385efaf93
Author: Pierrick Roger <pk.roger@icloud.com>
Date: 2025-09-29 14:57:15 +0200
Commit message:

 Resolve "Remove wizard connector generator"
Package: biodb
Commit: 6e98d3bb74244f7812ea87276adf6cf7ffdb749f
Author: Pierrick Roger <pk.roger@icloud.com>
Date: 2025-09-29 13:00:23 +0200
Commit message:

 Resolve "Remove new connector vignette"
Package: biodb
Commit: 673771662fe7ef48d714ddaa2498fcb5ff57d35c
Author: Pierrick Roger <pierrick.rogermele@cea.fr>
Date: 2025-09-29 10:42:41 +0200
Commit message:

 Update doc
Package: rtracklayer
Commit: 8268289f35ca0658ccacf0c92d80bb113c120e40
Author: Michael Lawrence <michafla@gene.com>
Date: 2025-09-29 05:29:33 -0700
Commit message:

 Merge pull request #144 from sanchit-saini/big_format_fix

refactor(bigBed): use bigBedAsOrDefault for AutoSQL parsing
Package: rtracklayer
Commit: 5ad089d3dc5e08b487e13eacc2b69d021b010549
Author: Sanchit Saini <sanchitsaini14@gmail.com>
Date: 2025-09-23 15:45:44 +0530
Commit message:

 BigBed: fix coordinate handling to be 1-based

- Use IRanges(start, end) instead of manual width calculation for clarity.
- Adjust thickStart, blockStarts, and ranges(x) to subtract 1L where UCSC uses 0-based coordinates.
- Update unit tests (test_bb.R, test_ucsc.R) to account for 1-based starts and corrected widths.
- Remove unnecessary elementMetadata reset in tests.
Package: rtracklayer
Commit: ef66dc3956ebb07bd1d666fb0516d2c2c70d3ce8
Author: Sanchit Saini <sanchitsaini14@gmail.com>
Date: 2025-09-12 23:44:09 +0530
Commit message:

 Enhance BigBed import to support full BED12 and custom fields

- Expanded default `colnames` in `BigBedSelection` to include all standard
  BED12 fields (`chrom`, `chromStart`, `chromEnd`, `name`, `score`, `strand`,
  `thickStart`, `thickEnd`, `itemRgb`, `blockCount`, `blockSizes`,
  `blockStarts`).
- Added support for dynamically using field names from the BigBed file when
  no custom `colnames` are specified.
- Implemented automatic construction of a `GRanges` covering all sequences
  when `which = NULL`.
- Improved handling of unavailable fields by issuing user warnings.
- Updated documentation (`BigBedSelection.rd`) to clarify that default
  columns follow BED12 conventions, and to explain support for file-provided
  or custom non-standard fields.
Package: rtracklayer
Commit: 5ca3063a7f8aa6ed8e7927b90e4f754883bec33f
Author: Sanchit Saini <sanchitsaini14@gmail.com>
Date: 2025-09-05 22:26:36 +0530
Commit message:

 refactor(bigBed): simplify BBDFile_query API to use column selection by names

- Changed BBDFile_query signature from taking `r_defaultindex` and
  `r_extraindex` arguments to a single `r_colnames` argument for
  explicit column selection.
- Refactored query logic into smaller helper functions:
  - queryIntervals(): performs range-based interval queries.
  - mapAsTypeToRType(): maps bigBed autosql types to R SEXPTYPE.
  - prepareFieldContainers(): allocates result containers for selected fields.
  - fillResults(): populates result vectors from query hits.
  - wrapResults(): constructs final return SEXP with field values and n_qhits.
- Removed legacy helpers `isPresent()` and `isSelected()` (now obsolete).
Package: rtracklayer
Commit: f3e22cb567a99d06991feefe94f8e21ecbecd87f
Author: Sanchit Saini <sanchitsaini14@gmail.com>
Date: 2025-08-28 15:40:43 +0530
Commit message:

 refactor(bigBed): use bigBedAsOrDefault for AutoSQL parsing

With bigBedAsOrDefault() that returns either the parsed AutoSQL schema
or a default BED12 schema if no AutoSQL is present.
Package: Chromatograms
Commit: f1fceaf31ce836635d2e9f6f1379a0fa035e9025
Author: Philippine Louail <philippine.louail@outlook.com>
Date: 2025-09-29 13:29:57 +0200
Commit message:

 Merge pull request #41 from rformassspectrometry/bioconductor

fix spectra dependency
Package: Chromatograms
Commit: 29870e2ac20dcda50c6634b60c2e7e6bd6c3451a
Author: Philippine Louail <127301965+philouail@users.noreply.github.com>
Date: 2025-09-29 09:57:46 +0200
Commit message:

 fix spectra dep
Package: rhdf5
Commit: 6e48b78972b4759b476019b8ada8722dea29e1b0
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-09-29 12:53:17 +0200
Commit message:

 Bump patch version
Package: rhdf5
Commit: 69a1a6a627dde87f6cdb41598265a9d337504af5
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-09-29 12:52:45 +0200
Commit message:

 Update package maintainer
Package: rhdf5
Commit: 0663f7551db75b4b6a78147850ddfff4f5363ef7
Author: Hugo Gruson <10783929+Bisaloo@users.noreply.github.com>
Date: 2025-08-29 16:03:01 +0200
Commit message:

 Set up rhub GHA workflow for more advanced checks
Package: rhdf5
Commit: 430f55b0f7f75b49ff0586b5e798ab88b6635820
Author: Michael R. Crusoe <crusoe@debian.org>
Date: 2024-12-11 12:24:56 +0100
Commit message:

 Fix typo
Package: MetMashR
Commit: 075a8a1f79710a38ef3ac8a1d44ea1925831752e
Author: Gavin Rhys Lloyd <grlloyd@users.noreply.github.com>
Date: 2025-09-29 09:10:39 +0100
Commit message:

 remove RVenn

it has been deprecated; no longer on cran
Package: IRanges
Commit: 0dfa0610317003686b00fef021b258af5c23954a
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2025-09-28 22:29:59 -0700
Commit message:

 one more test in test_NCList-class.R
Package: OSCA.workflows
Commit: 9edae1e161f8385f7781a9ebbbaca32be48c5815
Author: Peter Hickey <peter.hickey@gmail.com>
Date: 2025-09-29 14:53:41 +1000
Commit message:

 Version bump
Package: OSCA.workflows
Commit: c11e89193790e68ac63e5ba0030a803b00f88326
Author: Peter Hickey <peter.hickey@gmail.com>
Date: 2025-09-29 14:53:30 +1000
Commit message:

 Update hce-bone-marrow.Rmd

- Update highlighted cluster
- Correct description of plot
Package: notameViz
Commit: e4dc778b325de168955bc800b06976d70e3aaf97
Author: vsuksi <vsuksi@abo.fi>
Date: 2025-09-29 06:30:08 +0300
Commit message:

 Version bump without changes for interlinked notame builds on Bioc server.
Package: OSCA.basic
Commit: b18d43b1ffdfefa6790d37c666ff5d542e5f2906
Author: PeteHaitch <peter.hickey@gmail.com>
Date: 2025-09-29 13:13:47 +1000
Commit message:

 Version bump
Package: OSCA.workflows
Commit: d874bb8f7f7d4f6e7d8ebf68552cd1a8daa10c28
Author: PeteHaitch <peter.hickey@gmail.com>
Date: 2025-09-29 13:13:13 +1000
Commit message:

 Version bump
Package: OSCA.workflows
Commit: 3121bab8c94885f23cf00183a05bb87f69df61e3
Author: PeteHaitch <peter.hickey@gmail.com>
Date: 2025-09-29 13:10:47 +1000
Commit message:

 Update tenx-unfiltered-pbmc4k.Rmd

- Update highlighted clusters
Package: OSCA.basic
Commit: 8809cc5239340bc7a4a74be1c94857f6cdcf6cb2
Author: PeteHaitch <peter.hickey@gmail.com>
Date: 2025-09-29 12:10:12 +1000
Commit message:

 Update marker-detection.Rmd

- Update highlighted clusters
Package: OSCA.basic
Commit: 0ce9c9a31af450374804125c8b62c5763bf7ab3b
Author: PeteHaitch <peter.hickey@gmail.com>
Date: 2025-09-29 11:24:45 +1000
Commit message:

 Update clustering.Rmd

- Update memory T cell cluster
Package: IRanges
Commit: 247ed4e6982322304880f7069c3835477ccad9b9
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2025-09-28 16:39:36 -0700
Commit message:

 IRanges 2.43.4: Reduce findOverlaps() memory footprint

Switch "Auto-Extending buffers" used in findOverlaps() for temporary
storage of the hits from R_alloc-based buffers (transient memory) to
malloc-based buffers (user-controlled memory). This significantly
reduces memory usage (typically by about 20% to 55%) and it slightly
improves speed (typically by about 3% and 10%).

Note that using malloc-based buffers is also a prerequisite for safe
multithreading because R_alloc() is not thread safe (this is due to
R's garbage collector not being thread safe).
Package: SingleCellSignalR
Commit: e2002f3fd7fd019d270b8778fd497ff522206d33
Author: jcolinge <65902924+jcolinge@users.noreply.github.com>
Date: 2025-09-28 22:50:17 +0200
Commit message:

 commit 1.99.1 to switch to 2.0.0
Package: scrapper
Commit: c666fdf4d05885398d5273d194672f367d3d1362
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2025-09-28 10:47:45 -0700
Commit message:

 Report the overlap and set size from testEnrichment.

We already compute it, so we might as well let the user know about it.
Package: immApex
Commit: 17216cf2748d944599ab798808abb78e6828d128
Author: theHumanBorch <ncborch@gmail.com>
Date: 2025-09-28 10:43:30 -0500
Commit message:

 Merge branch 'main' into devel
Package: immApex
Commit: 100a5e7443657f30d04c1670fdbe3dec8dba23d1
Author: theHumanBorch <ncborch@gmail.com>
Date: 2025-09-28 10:42:16 -0500
Commit message:

 Merge pull request #12 from BorchLab/buldNetwork-symmetric

Force symmetry in buildNetwork
Package: immApex
Commit: 95c90697ea4ad93b3de9be81d669b04b96e8c629
Author: theHumanBorch <ncborch@gmail.com>
Date: 2025-09-28 10:20:59 -0500
Commit message:

 Force symmetry
Package: immApex
Commit: c6eafae42428984ed851d87ed25b61e72f7c8515
Author: theHumanBorch <ncborch@gmail.com>
Date: 2025-08-18 03:14:10 -0500
Commit message:

 Update immApex_hex.png
Package: scRepertoire
Commit: 097357974890a014ea9c88f08f154ea55a810dd4
Author: theHumanBorch <ncborch@gmail.com>
Date: 2025-09-28 10:22:51 -0500
Commit message:

 Update DESCRIPTION
Package: DMRcaller
Commit: ac4d9f28aab81bc982e0242729406d5df603e05e
Author: nrzabet <r.zabet@qmul.ac.uk>
Date: 2025-09-28 15:12:19 +0100
Commit message:

 added support for ONT methylation data
Package: DMRcaller
Commit: 5079a9910061bc2a8de25a767153971e6fe22e29
Author: nrzabet <r.zabet@qmul.ac.uk>
Date: 2025-09-28 15:08:05 +0100
Commit message:

 added support for ONT methylation data
Package: tximeta
Commit: 25712fc97bd82f1cf0723226c1d296ee888eb93c
Author: Mike Love <mikelove@users.noreply.github.com>
Date: 2025-09-27 23:33:15 -0400
Commit message:

 cleaning up some docs
Package: tximeta
Commit: d2673f1b0d8ef68a7a6e79ed36cb076ed226174a
Author: Mike Love <mikelove@users.noreply.github.com>
Date: 2025-09-27 23:28:23 -0400
Commit message:

 fix example code
Package: tximeta
Commit: fe10db17ca4b26c4f919d44c8ad34d93684c2751
Author: Mike Love <mikelove@users.noreply.github.com>
Date: 2025-09-27 22:22:57 -0400
Commit message:

 fix error in vignette
Package: tximeta
Commit: 1b32d28a612b1af91d3303a949102425795af053
Author: Mike Love <mikelove@users.noreply.github.com>
Date: 2025-09-27 10:10:59 -0400
Commit message:

 updating vignette
Package: tximeta
Commit: f273b51ebcd571fd8965102a1c687596c4c17af2
Author: Mike Love <mikelove@users.noreply.github.com>
Date: 2025-09-26 17:13:50 -0400
Commit message:

 no bioc check
Package: tximeta
Commit: 3af39655e0e919673547be1bb704d86b80bc29df
Author: Mike Love <mikelove@users.noreply.github.com>
Date: 2025-09-26 15:47:37 -0400
Commit message:

 remove mac and windows builders
Package: tximeta
Commit: 10a10d50818b6e1906d81ecb040876f82f4006d7
Author: Mike Love <mikelove@users.noreply.github.com>
Date: 2025-09-26 15:45:04 -0400
Commit message:

 update to biocthis GHA workflow
Package: tximeta
Commit: 552bfb6f822a308e11c2d1985e438ee406ebd5b6
Author: Mike Love <mikelove@users.noreply.github.com>
Date: 2025-09-26 14:16:02 -0400
Commit message:

 renaming update and startign vignette
Package: tximeta
Commit: dd7e54dc3589f8b361ddb6aabf83a87372ccac1c
Author: Mike Love <mikelove@users.noreply.github.com>
Date: 2025-09-26 11:51:45 -0400
Commit message:

 update tximix docs
Package: tximeta
Commit: 2631f991a95c8ef574b4d5af0be386f9e28eac5d
Author: Mike Love <mikelove@users.noreply.github.com>
Date: 2025-09-25 16:29:09 -0400
Commit message:

 work on inspect man page
Package: tximeta
Commit: 98d5c29973bb5fc027ddcc26c985aebadd9a6402
Author: Mike Love <mikelove@users.noreply.github.com>
Date: 2025-09-25 11:06:35 -0400
Commit message:

 updating man pages
Package: tximeta
Commit: f797021869e4dde49976aa249e2cb939ebd290ac
Author: Mike Love <mikelove@users.noreply.github.com>
Date: 2025-09-24 17:05:03 -0400
Commit message:

 adding to the function reference
Package: tximeta
Commit: 7382d4c6ae553d46c5e152d4b03b39a13ba2b6e7
Author: Mike Love <mikelove@users.noreply.github.com>
Date: 2025-09-24 15:51:54 -0400
Commit message:

 update to devel GHA, Seqinfo package is new
Package: tximeta
Commit: 9b13ed8dca18750585bc4ef2ea39f674ccd2b543
Author: Michael Love <mikelove@users.noreply.github.com>
Date: 2025-09-24 12:58:32 -0400
Commit message:

 Merge pull request #90 from thelovelab/tximix

tximix - new function for import using multiple reference transcriptomes
Package: tximeta
Commit: cde55824cdb95fb0ee919fce83cc22b2feee7750
Author: Mike Love <mikelove@users.noreply.github.com>
Date: 2025-09-24 12:52:25 -0400
Commit message:

 ready to merge back into devel branch
Package: tximeta
Commit: f911f9a9fe5b45b5fa66051177e224845e3f52e7
Author: Mike Love <mikelove@users.noreply.github.com>
Date: 2025-09-23 14:29:20 -0400
Commit message:

 plus documentation
Package: tximeta
Commit: f7a70df6ca993296c79e0a38cad2fd89040bcabb
Author: Mike Love <mikelove@users.noreply.github.com>
Date: 2025-09-23 14:29:06 -0400
Commit message:

 add counting txps to indices
Package: tximeta
Commit: 66f090695d158bea4aa563d295a463d00edd11e2
Author: Mike Love <mikelove@users.noreply.github.com>
Date: 2025-09-23 14:02:09 -0400
Commit message:

 inspect, update working demo with manual txpData
Package: tximeta
Commit: 32966038e983e187acde86ba017dda8920d1675e
Author: Mike Love <mikelove@users.noreply.github.com>
Date: 2025-09-22 15:33:05 -0400
Commit message:

 more work on update txpdata
Package: tximeta
Commit: 1f7091b16153d846f6f997dc4cc95a97125420b8
Author: Mike Love <mikelove@users.noreply.github.com>
Date: 2025-09-19 11:56:16 -0400
Commit message:

 add and update metadata functions
Package: tximeta
Commit: f5e9210b2078099d58194c11baa03151f24fd6e5
Author: Mike Love <mikelove@users.noreply.github.com>
Date: 2025-09-18 16:14:21 -0400
Commit message:

 inspect digests
Package: tximeta
Commit: 241006570b23691da0633956f9a4e88b4ed47042
Author: Mike Love <mikelove@users.noreply.github.com>
Date: 2025-09-15 13:03:20 -0400
Commit message:

 inspection works
Package: tximeta
Commit: f8aeb12188473572b0327cb7ce84b7deacecb3f4
Author: Mike Love <mikelove@users.noreply.github.com>
Date: 2025-09-12 11:50:36 -0400
Commit message:

 some more work on mix
Package: tximeta
Commit: af10f8478e6c4dc555cf9e92ac262d0bee481fdb
Author: Mike Love <mikelove@users.noreply.github.com>
Date: 2025-09-09 15:44:23 -0400
Commit message:

 GENCODE 49 (H.s.), M38 (M.m), and Ensembl 115
Package: tximeta
Commit: 0b8e4b8bdaaf8d086488d324c07893e4a1b34652
Author: Mike Love <mikelove@users.noreply.github.com>
Date: 2025-08-28 12:44:58 -0400
Commit message:

 working on tximix step 1
Package: tximeta
Commit: be78c3fb0e5bab7cebb80c518de100acf21c1e98
Author: Mike Love <mikelove@users.noreply.github.com>
Date: 2025-08-27 13:10:04 -0400
Commit message:

 tximeta working on oarfish
Package: tximeta
Commit: 6b40dbf2c0371ee3982b6a5e73bd1862acb4d83b
Author: Mike Love <mikelove@users.noreply.github.com>
Date: 2025-08-26 13:56:43 -0400
Commit message:

 fixing bugs and updating tests
Package: tximeta
Commit: 3190e5a798780991bb1dca08ca0fbbc24b53d6fa
Author: Mike Love <mikelove@users.noreply.github.com>
Date: 2025-08-25 14:16:19 -0400
Commit message:

 bug fix and function tweaks
Package: tximeta
Commit: 6e90a0ae93a0d6ff5742eb9e505c1fc47399c488
Author: Mike Love <mikelove@users.noreply.github.com>
Date: 2025-08-25 14:04:29 -0400
Commit message:

 comments and small tweaks
Package: tximeta
Commit: 0767fce703858d962c22712c622ae59339f78189
Author: Mike Love <mikelove@users.noreply.github.com>
Date: 2025-08-25 13:40:12 -0400
Commit message:

 reorg all of alevin code
Package: tximeta
Commit: 477d7cd03c5dab355e293c2988e7ab5186f70107
Author: Mike Love <mikelove@users.noreply.github.com>
Date: 2025-08-25 10:58:34 -0400
Commit message:

 add missing file
Package: tximeta
Commit: c2cd8c5dc2cae6f2502e4c20ffb6c26f60ca3ffe
Author: Mike Love <mikelove@users.noreply.github.com>
Date: 2025-08-22 15:01:30 -0400
Commit message:

 more work on tixmix, reorganize R a bit
Package: tximeta
Commit: 3cb6d503f2effc873c4348d5ff76db70c3872ec8
Author: Mike Love <mikelove@users.noreply.github.com>
Date: 2025-08-22 11:15:31 -0400
Commit message:

 beginning work on tximix
Package: tximeta
Commit: e5e34429808ce8759faa77d76525ef3dcce16f73
Author: Mike Love <mikelove@users.noreply.github.com>
Date: 2025-06-25 13:48:28 -0400
Commit message:

 first commit to tximix
Package: MDSvis
Commit: 791bb59e2d05692ef4f4a1b5b64c030921a28e74
Author: phauchamps <philippehauchamps@hotmail.com>
Date: 2025-09-28 14:56:30 +0200
Commit message:

 - moved shiny app code to main package R directory instead of install directory
- bumped version to 0.99.3