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Bioconductor has moved to GIT for contributed packages; the subversion logs are no longer active.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

GIT Logs

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

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

Package: edgeR
Commit: 691a96e42a5d143fcaeb272a8af44c46a91b3489
Author: Gordon Smyth <smyth@wehi.edu.au>
Date: 2024-09-01 18:30:10 +1000
Commit message:

 edgeR 4.3.14
- Edit several help pages
- Simplify code in some internal R files
- Consistent use of tab indents in R code files

Package: velociraptor
Commit: 08a5447af0e436646fdd8e36627839512f89af70
Author: Kevin Rue-Albrecht <kevinrue67@gmail.com>
Date: 2024-09-01 06:20:26 +0100
Commit message:

 macos fix for github action: downgrade freetype to install 'ragg' and install binary 'units' (#85)

* upgrade freetype

* misunderstood fix

* option --cask

* install file directly

* freetype 2.13.2

* remove --cask option

* disable faulty line

* unlink

* change path to xml2-config

* udunits?

* udunits2

* install units binary

Package: systemPipeRdata
Commit: 39c2a2660a634773c8c4dc2eaa9454992f9aae32
Author: tgirke <tgirke@citrus.ucr.edu>
Date: 2024-08-31 19:06:10 -0700
Commit message:

 updated new vignette

Package: systemPipeRdata
Commit: d23b48fb8bce3cab6d06f452780c53950d34383d
Author: Thomas Girke <tgirke@citrus.ucr.edu>
Date: 2024-08-31 18:36:05 -0700
Commit message:

 Merge pull request #18 from systemPipeR/devel

fix: revert blast wf cmd tool mis-change

Package: systemPipeRdata
Commit: 80f9b5cd4353a9e742197b792e081e3a284c3751
Author: Le Zhang <35240440+lz100@users.noreply.github.com>
Date: 2024-08-08 18:32:27 -0700
Commit message:

 fix: revert blast wf cmd tool mis-change

Package: systemPipeR
Commit: ed05f83e6928607e7f04265b3fd0f9ac7822f0b5
Author: tgirke <tgirke@citrus.ucr.edu>
Date: 2024-08-31 18:10:23 -0700
Commit message:

 vignette edits

Package: rhinotypeR
Commit: 7e2d7efc1f6779826541e739e8edde1fd1e2f30d
Author: marthaluka <mawia.martha@gmail.com>
Date: 2024-08-31 22:43:11 +0100
Commit message:

 updated datae on DESC

Package: rhinotypeR
Commit: cf6e6a95b97943784a8d3b29976a54035264ab35
Author: marthaluka <mawia.martha@gmail.com>
Date: 2024-08-31 22:19:53 +0100
Commit message:

 Removed readFasta.Rd and updated DESCRIPTION, NAMESPACE, README.Rmd, and vignette.

Package: rhinotypeR
Commit: fc98fb8f76fdabcca66630d38c12fea4969084d8
Author: marthaluka <mawia.martha@gmail.com>
Date: 2024-08-31 22:17:26 +0100
Commit message:

 add unit tests

Package: rhinotypeR
Commit: b4a5aa53b7039016c6adda45013810a14aa5a177
Author: marthaluka <mawia.martha@gmail.com>
Date: 2024-08-31 22:16:27 +0100
Commit message:

 update man pages

Package: rhinotypeR
Commit: 42fa015509e468444c693e8d1cc71acef5a814e6
Author: marthaluka <mawia.martha@gmail.com>
Date: 2024-08-31 22:15:32 +0100
Commit message:

 minimize code repetition and vectorize

Package: igvShiny
Commit: 5a83495c875f5314e6a699d00e39e88becde1d73
Author: Arkadiusz Gladki <arkadiusz.gladki@contractors.roche.com>
Date: 2024-08-31 22:07:27 +0200
Commit message:

 Merge branch 'master' into devel

Package: igvShiny
Commit: 648a469c24c0810879067317c8e897ef7f8fa610
Author: Arek Gladki <41166437+gladkia@users.noreply.github.com>
Date: 2024-08-30 13:00:21 +0200
Commit message:

 Merge pull request #89 from parv-sachdeva/master

Update loadBedTrackFromFile function to ignore shiny query strings #88

Package: igvShiny
Commit: 550e39a09331fb11474cb5a0fee56c4cbde8c25e
Author: parv-sachdeva <parv.sachdeva@sonomabio.com>
Date: 2024-08-29 18:19:13 -0400
Commit message:

 Update NEWS.md with notes for v1.0.5 - #88

Package: igvShiny
Commit: c56c5d767b6e4843851c9efdb8327635cb99b75a
Author: parv-sachdeva <parv.sachdeva@sonomabio.com>
Date: 2024-08-29 18:18:38 -0400
Commit message:

 Update version to 1.0.5 for #88

Package: igvShiny
Commit: 109bf61acedfce0eb36953d5a0f86a5f0005d40a
Author: parv-sachdeva <parv.sachdeva@sonomabio.com>
Date: 2024-08-27 16:23:17 -0400
Commit message:

 Fixes gladkia/igvShiny#88

Package: scMultiSim
Commit: fd9a74da81f3f044bd7a5ab8a25dffba140a892a
Author: Hechen Li <lhc199652@gmail.com>
Date: 2024-08-31 15:38:28 -0400
Commit message:

 Fix building warnings by importing BiocParallel

Package: Rcollectl
Commit: ad9dc5ff45695469cca2be6fb918073c61f2b8d8
Author: vjcitn <stvjc@channing.harvard.edu>
Date: 2024-08-31 08:15:00 -0400
Commit message:

 added arg to rescale memory consumption report, and weakened test to find five clicks with 8 seconds sleep

Package: rhinotypeR
Commit: 28a04ec966c0e64ad67aae96767457deee241a63
Author: marthaluka <mawia.martha@gmail.com>
Date: 2024-08-31 10:59:32 +0100
Commit message:

 use Biostrings to read fasta

Package: nipalsMCIA
Commit: c1bf9f2e9810bcd078fdd92145d6b4cc2e134bcb
Author: muunraker <24959832+Muunraker@users.noreply.github.com>
Date: 2024-08-31 14:35:36 +0700
Commit message:

 v1.3.1 commit

Package: scMultiSim
Commit: 961ea0afb2247441f2699c64b0536f335a754ba0
Author: Hechen Li <lhc199652@gmail.com>
Date: 2024-08-30 21:57:27 -0400
Commit message:

 Update CCI docs

Package: Rcpi
Commit: 3bf7903a8292ec852f958ba1287fbb32891edc37
Author: Nan Xiao <me@nanx.me>
Date: 2024-08-30 17:54:28 -0400
Commit message:

 v1.41.2

Package: chevreul
Commit: c61dc7dcfe2232ac98ed080cc431da9681ff1c14
Author: whtns <kevin.stachelek@gmail.com>
Date: 2024-08-30 14:44:14 -0700
Commit message:

 trigger rebuild

Package: SVMDO
Commit: a10cc82cf4c6cc413935325f6d091d3f44a3fccc
Author: robogeno <erhanozer18@gmail.com>
Date: 2024-08-31 00:33:50 +0300
Commit message:

 Update DESCRIPTION

Package: SVMDO
Commit: 97e144e99972808ca9d31ee44505dd68d9a99879
Author: robogeno <erhanozer18@gmail.com>
Date: 2024-08-31 00:26:07 +0300
Commit message:

 Update svmdo_fig_1.png

Package: SVMDO
Commit: 0d2755333604b1c6b3db2b72037e63b235e4ac42
Author: robogeno <erhanozer18@gmail.com>
Date: 2024-08-31 00:23:01 +0300
Commit message:

 update

Package: SVMDO
Commit: 1f4ed0ebf08df62193dc526cd0613f7640a6af3b
Author: robogeno <erhanozer18@gmail.com>
Date: 2024-08-31 00:22:30 +0300
Commit message:

 Update NEWS.md

Package: SVMDO
Commit: d899c362ec97bf0f983c38c3d32cbdac38748c2e
Author: robogeno <erhanozer18@gmail.com>
Date: 2024-08-31 00:06:19 +0300
Commit message:

 Merge branch 'devel' of https://github.com/robogeno/SVMDO into devel

Package: SVMDO
Commit: 4f719c60ddc85eacb5945ea072baa74c9f7cc978
Author: robogeno <erhanozer18@gmail.com>
Date: 2024-08-31 00:05:35 +0300
Commit message:

 UPDATE

Package: SVMDO
Commit: 91de15cd5f1694d1727f1f8d09d45d3cb17d9129
Author: J Wokaty <jwokaty@users.noreply.github.com>
Date: 2024-04-30 11:49:19 -0400
Commit message:

 bump x.y.z version to odd y following creation of RELEASE_3_19 branch

Package: SVMDO
Commit: e8a839f22dab70201e136d1165ef1572290e99b7
Author: robogeno <erhanozer18@gmail.com>
Date: 2024-08-26 22:26:37 +0300
Commit message:

 update

Package: SVMDO
Commit: 44dccc6c4550491942d6fc5bead0dae8d5b62b99
Author: robogeno <erhanozer18@gmail.com>
Date: 2024-08-26 19:01:01 +0300
Commit message:

 update

Package: SVMDO
Commit: 147a03c20b5632e71622af26a4a221839ccc65dd
Author: robogeno <erhanozer18@gmail.com>
Date: 2024-08-26 07:12:46 +0300
Commit message:

 updated branch for enrichDO

Package: SVMDO
Commit: 188793bdf38c67e8f8d3618d4f733fdc4c6db14d
Author: robogeno <erhanozer18@gmail.com>
Date: 2024-08-30 17:20:56 +0300
Commit message:

 UPDATE

Package: SVMDO
Commit: f839af4193bf4548f7f711e33072942bc7706b38
Author: robogeno <erhanozer18@gmail.com>
Date: 2024-08-30 17:16:48 +0300
Commit message:

 update

Package: SVMDO
Commit: 4eb5b9bd11e3269623a17b7df651bd5ccf47f97c
Author: robogeno <erhanozer18@gmail.com>
Date: 2024-08-30 16:45:40 +0300
Commit message:

 Update DESCRIPTION

Package: SVMDO
Commit: 4ffae9988114aaf4320ced0c0b81ce13e01cba06
Author: robogeno <erhanozer18@gmail.com>
Date: 2024-08-26 22:22:26 +0300
Commit message:

 update

Package: SVMDO
Commit: 4fc3c338c379a1bb24349dd12d0e3c93be3c8cde
Author: robogeno <erhanozer18@gmail.com>
Date: 2024-08-30 23:53:09 +0300
Commit message:

 UPDATE

Package: velociraptor
Commit: 13f40d237fa2cb840ddf6fd284104774c58133b4
Author: Kevin Rue-Albrecht <kevinrue67@gmail.com>
Date: 2024-08-30 20:29:30 +0100
Commit message:

 Fix environment using micromamba for macosx Arm (#84)

* first attempt at macos m1 environment using micromamba

* scipy==1.13.1 (theislab/scvelo#1260)

* fix switch between environments

* add news

Package: TENxIO
Commit: 40844df12cf78dc4b909201cae09e4e9001b0d67
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2024-08-30 15:27:33 -0400
Commit message:

 version bump 1.7.3

Package: TENxIO
Commit: d98190d3d33afb036e42fb87665c634cb8cdbd22
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2024-08-30 15:00:33 -0400
Commit message:

 add *_cache to .Rbuildignore

Package: TENxIO
Commit: 99f995541f499f946b199c3f8208f8ad95dbe718
Author: LiNk-NY <marcel.ramos@roswellpark.org>
Date: 2024-08-29 18:05:11 -0400
Commit message:

 import rowData for version 3 datasets

Package: rSWeeP
Commit: a17986595e4db32a6d1c1813191b943733c71326
Author: Camila Pereira Perico <camilapp94@gmail.com>
Date: 2024-08-30 15:41:40 -0300
Commit message:

 update

Package: DNEA
Commit: 8f3cde437da340add7ffc16531f3638fa5490015
Author: chrispatsalis <patsalis@umich.edu>
Date: 2024-08-30 13:53:53 -0400
Commit message:

 vignette was modified so it would knit faster:

package was timing out during bioconductor build stage due to vignette run time. dnw results object is now loaded in and used instead of actually evaluating the stability selection code chunk, which takes the most time

Package: DNEA
Commit: c8e34371217814943dd99985e204f400fec3915f
Author: chrispatsalis <patsalis@umich.edu>
Date: 2024-08-30 13:52:43 -0400
Commit message:

 version bump

Package: DNEA
Commit: 36fa5bd39971367cb661855d2d551d0930b9182d
Author: chrispatsalis <patsalis@umich.edu>
Date: 2024-08-30 13:38:03 -0400
Commit message:

 Revert "modified vignette to knit faster:"

This reverts commit c637b2293f24d8db4f47798fd7a35942993bb553.

Package: DNEA
Commit: 4bae08c91fb778136b39ed39156bba02e8cc99a9
Author: chrispatsalis <patsalis@umich.edu>
Date: 2024-08-30 13:30:46 -0400
Commit message:

 Revert "bump version"

This reverts commit c6a450f6a159d79bb1a03ce803d96b10838c047f.

revert version bump

Package: DNEA
Commit: c6a450f6a159d79bb1a03ce803d96b10838c047f
Author: chrispatsalis <patsalis@umich.edu>
Date: 2024-08-30 13:14:37 -0400
Commit message:

 bump version

Package: DNEA
Commit: c637b2293f24d8db4f47798fd7a35942993bb553
Author: chrispatsalis <patsalis@umich.edu>
Date: 2024-08-30 13:09:44 -0400
Commit message:

 modified vignette to knit faster:

The vignette was changed so that the stability selection code chunk is not actually evaluated, rather the code chunk is shown but the vignette pulls the dnw results data stored in the package and continues with that instead.

Additionally, FALSE parameter was spelled wrong in the load processed data code chunk that loads in the stored results

Package: SVMDO
Commit: a1e14566ba9dd6f99e0ff426cdfdb774b3fdd79c
Author: robogeno <erhanozer18@gmail.com>
Date: 2024-08-30 16:39:34 +0300
Commit message:

 update

Package: gDRstyle
Commit: 5b40c45ac6dd9ab03871b8c310adf6533de17838
Author: marcin-kam <marcin.kamianowski@gmail.com>
Date: 2024-08-30 14:33:38 +0200
Commit message:

 Merge pull request #82 from gdrplatform/GDR-2675

fix: improve pkgdown action

Package: gDRstyle
Commit: 2ab6158075c32807ead6775c03f8ee539a49bcec
Author: Marcin Kamianowski <marcin.kamianowski@contractors.roche.com>
Date: 2024-08-29 14:53:36 +0200
Commit message:

 fix: improve pkgdown action

Package: OmnipathR
Commit: da9dee03fe3e751255876141b4b0b69a53ad593e
Author: deeenes <turei.denes@gmail.com>
Date: 2024-08-29 16:04:08 +0200
Commit message:

 Bump version: 3.13.20 → 3.13.21

Package: OmnipathR
Commit: 2801131fb14b7621886cf41889a8a223499cb323
Author: deeenes <turei.denes@gmail.com>
Date: 2024-08-29 16:04:03 +0200
Commit message:

 name updates in vignettes

Package: OmnipathR
Commit: 21be1515a945731e6f2c140d34e5d095bb11140e
Author: deeenes <turei.denes@gmail.com>
Date: 2024-08-22 23:03:17 +0200
Commit message:

 removed `slow_doctest` from `all_uniprots` (required for vignette builds)

Package: OmnipathR
Commit: b32b6a030aafb1cceeadd23ae069dda1ea97e7e0
Author: deeenes <turei.denes@gmail.com>
Date: 2024-08-22 19:42:21 +0200
Commit message:

 Bump version: 3.13.19 → 3.13.20

Package: OmnipathR
Commit: c2530d1b3ae748ca8be9f7f15444e866682c5e2d
Author: deeenes <turei.denes@gmail.com>
Date: 2024-08-22 19:42:15 +0200
Commit message:

 docs rebuild

Package: OmnipathR
Commit: 11bf1dc5328a403daa9d521925d68cb404185cee
Author: deeenes <turei.denes@gmail.com>
Date: 2024-08-22 19:41:29 +0200
Commit message:

 `logging` and `options`: made the whole thing independent from OmnipathR, suitable for other packages

Package: velociraptor
Commit: 71cca0898d0b789a564736b3e91bf89d5c804f9a
Author: Kevin Rue-Albrecht <kevinrue67@gmail.com>
Date: 2024-08-30 11:06:35 +0100
Commit message:

 Fix conda environment using micromamba for windows (#82)

* update environment for windows using micromamba

* try Windows environment resolved using micromamba

* add pip dependencies

* downgrade matplotlib to 3.7.3 (https://stackoverflow.com/questions/77128061/ydata-profiling-profilereport-attributeerror-module-matplotlib-cbook-has-no)

* downgrade pandas (https://github.com/theislab/scvelo/issues/811#issuecomment-1026555408)

* remove pip section

* https://github.com/kevinrue/velociraptor/issues/80#issuecomment-2320454366

* woops updated env in R code too

* downgrade python (https://github.com/theislab/scvelo/issues/1124#issuecomment-1802261666)

* matplotlib 3.6.3

* pandas 1.5.2

* numpy 1.21.1

* fix version bump

* remove useless pip

---------

Co-authored-by: Kevin Rue <kevinrue@users.noreply.github.com>

Package: ropls
Commit: b9db1a7e1e28e4d2874e3ea86f7afe6151c85000
Author: THEVENOT Etienne <ET207099@intra.cea.fr>
Date: 2024-08-30 11:42:02 +0200
Commit message:

 v1.37.4: 'plot_score' method described in the vignette

Package: ropls
Commit: 0ea7429b9980044d5e75004420318c5083c44968
Author: THEVENOT Etienne <ET207099@intra.cea.fr>
Date: 2024-08-29 14:35:24 +0200
Commit message:

 gg_scoreplot: guessing color factor from the model.c parameter

Package: ropls
Commit: 6f85589e4551fccfffcf77516f1e48c5dbbf6403
Author: THEVENOT Etienne <ET207099@intra.cea.fr>
Date: 2024-08-29 13:36:26 +0200
Commit message:

 v1.37.2: gg_scoreplot: now handling 1D and empty models

Package: BgeeDB
Commit: 17b2db4fac83b78f6ba4a73e436eececd01296ec
Author: Julien Wollbrett <julien.wollbrett@unil.ch>
Date: 2024-08-30 11:26:04 +0200
Commit message:

 update getCellProcessedData() example to avoid loading to much data during R CMD CHECK

Package: BgeeDB
Commit: 740db7fd7525c777663fd846293c87f3dc9df192
Author: Julien Wollbrett <julien.wollbrett@unil.ch>
Date: 2024-08-30 10:02:22 +0200
Commit message:

 update URL to download gene to annotation mapping

Package: BgeeDB
Commit: 8c714ba224234967b217cb93f8bd7f25cb719093
Author: Julien Wollbrett <julien.wollbrett@unil.ch>
Date: 2024-08-30 09:53:30 +0200
Commit message:

 improved management of time needed to generate the gene to annotation mapping file for topAnat

Package: MouseFM
Commit: 5cf6e94ec7d3c816e579b4501741a952a49b6c04
Author: Matthias Munz <matthias.munz@gmx.de>
Date: 2024-08-30 09:43:06 +0200
Commit message:

 bugfix and version bump

Package: scMultiSim
Commit: 876c385e21d3dbc26b8a17e92d01f0c0111434df
Author: Hechen Li <lhc199652@gmail.com>
Date: 2024-08-29 21:56:34 -0400
Commit message:

 Update vignette titles

Package: scMultiSim
Commit: 7b5a62a1ae8d13ce9f80a1f3cc9a2378ccf9fee7
Author: Hechen Li <lhc199652@gmail.com>
Date: 2024-08-29 21:33:26 -0400
Commit message:

 Bump version to 1.1.4

Package: phenomis
Commit: ce0e718e87f09608cec08e4bca44edee09814029
Author: THEVENOT Etienne <ET207099@intra.cea.fr>
Date: 2024-08-29 22:04:46 +0200
Commit message:

 v1.7.4: writing: bug fix when writing MAE with single colData column

Package: raer
Commit: 248f100b805a1ff21db1266d5047a3190c40468f
Author: Kent Riemondy <kent.riemondy@gmail.com>
Date: 2024-08-29 12:06:52 -0600
Commit message:

 roxygen update and version bump

Package: raer
Commit: 8f71546f3721427e96efc0e60a72ba643e481129
Author: Kent Riemondy <kent.riemondy@gmail.com>
Date: 2024-08-29 12:04:08 -0600
Commit message:

 update workflow figure

Package: raer
Commit: 243952f3a6c1fe6f652b4e2658359358b4b40b73
Author: Kent Riemondy <kent.riemondy@gmail.com>
Date: 2024-08-29 11:40:11 -0600
Commit message:

 Merge branch 'devel' of github.com:rnabioco/raer into devel

Package: raer
Commit: 681bbddfa0b74f440f770b3dc0d073f9a84111e5
Author: Jay Hesselberth <jay.hesselberth@gmail.com>
Date: 2024-07-10 08:18:30 -0600
Commit message:

 add workflow figure to readme

closes #53

Package: raer
Commit: 7a72a0d2dfea50ea4c027c0f0ade58c7377e773d
Author: Kent Riemondy <kent.riemondy@gmail.com>
Date: 2024-05-29 13:44:33 -0600
Commit message:

 check for missing bamnames

Package: clustifyr
Commit: b67b34b443cf15e2d9c1fd2fa7d959a5e890da60
Author: raysinensis <raysinensis@gmail.com>
Date: 2024-08-29 13:26:22 -0400
Commit message:

 readme update

Package: gDRimport
Commit: 7f02e7a257a9aa6e9914a813ef6d90fdbc7a3534
Author: j-smola <31825957+j-smola@users.noreply.github.com>
Date: 2024-08-29 17:39:09 +0200
Commit message:

 Merge pull request #89 from gdrplatform/GDR-2675

[GDR-2675] Fix failing github page

Package: gDRimport
Commit: a21a3f451db7d500165da69bb43740257134f0c7
Author: Janina Smola <janina.smola@contractors.roche.com>
Date: 2024-08-29 16:57:21 +0200
Commit message:

 doc: fix failing github page

Package: koinar
Commit: 961e3990cb9033c9be52743c09a8683d945030c3
Author: Ludwig Lautenbacher <Ludwig.Lautenbacher@tum.de>
Date: 2024-08-29 15:56:04 +0200
Commit message:

 Bump version

Package: koinar
Commit: 55a8788db02aa4bb91e2106e6e21af753c6860c1
Author: Ludwig Lautenbacher <Ludwig.Lautenbacher@tum.de>
Date: 2024-08-29 15:53:15 +0200
Commit message:

 Manually shorten paths.

Package: koinar
Commit: 6343cca244609a15b03b725248fbc32eee3829e2
Author: Ludwig Lautenbacher <Ludwig.Lautenbacher@tum.de>
Date: 2024-08-29 15:43:04 +0200
Commit message:

 Update mockapi_batching.zip

Package: koinar
Commit: 06fcc095873dff61dd11b227fcd046a852605508
Author: Ludwig Lautenbacher <Ludwig.Lautenbacher@tum.de>
Date: 2024-08-29 15:37:11 +0200
Commit message:

 Hide configuration part in vignette.

Package: koinar
Commit: 441cae994fd0eec7be435396b1a05c51b7faafe1
Author: Ludwig Lautenbacher <Ludwig.Lautenbacher@tum.de>
Date: 2024-08-29 15:20:04 +0200
Commit message:

 Shorten api paths

Package: rSWeeP
Commit: c1d896c5ce2023a04447c5abc93d614c10007b58
Author: Camila Pereira Perico <camilapp94@gmail.com>
Date: 2024-08-29 10:24:33 -0300
Commit message:

 PMPG output update

Package: gDRimport
Commit: c2310dc0555dd3242893916f83b2f63965892a8f
Author: Bartek <32614650+bczech@users.noreply.github.com>
Date: 2024-08-29 15:21:07 +0200
Commit message:

 Merge pull request #88 from gdrplatform/GDR-2638

Gdr 2638

Package: gDRimport
Commit: dfd4c7bc4f5a409fcee3e27c7e9af764e4538fcc
Author: bczech <bartosz.czech@contractors.roche.com>
Date: 2024-08-12 07:50:40 -0700
Commit message:

 chore: bump version and update NEWS.md

Package: gDRimport
Commit: cd476dacdf7b02c6b3b1e2c5b51706e209f486f8
Author: bczech <bartosz.czech@contractors.roche.com>
Date: 2024-08-12 07:50:33 -0700
Commit message:

 refactor: update the function for importing public PRISM data

Package: EnrichDO
Commit: b32752ee5ad51643a88ff820a7bf293413bbc9ff
Author: CHENGliang!@#123 <liangcheng@hrbmu.edu.cn>
Date: 2024-08-29 21:14:05 +0800
Commit message:

 modification

Package: EnrichDO
Commit: c316d2024a1930b675fd8fd480e522ed95d5c86e
Author: CHENGliang!@#123 <liangcheng@hrbmu.edu.cn>
Date: 2024-08-29 21:12:02 +0800
Commit message:

 modification

Package: EnrichDO
Commit: 39150c1d545ddcbf2bde46b340637e7d9f680a22
Author: CHENGliang!@#123 <liangcheng@hrbmu.edu.cn>
Date: 2024-08-29 21:11:44 +0800
Commit message:

 modification

Package: EnrichDO
Commit: 7054625cb4ed41b76434c63d5a45cbd26cd88d77
Author: CHENGliang!@#123 <liangcheng@hrbmu.edu.cn>
Date: 2024-08-29 21:11:25 +0800
Commit message:

 modification

Package: EnrichDO
Commit: a514515149fc9ce33a651af5e7b637e92b30b3bc
Author: CHENGliang!@#123 <liangcheng@hrbmu.edu.cn>
Date: 2024-08-29 21:10:53 +0800
Commit message:

 modification

Package: EnrichDO
Commit: 0467e093ae0b73a7e287195fcda080e848ac8ccf
Author: CHENGliang!@#123 <liangcheng@hrbmu.edu.cn>
Date: 2024-08-29 21:10:38 +0800
Commit message:

 modification

Package: PhyloProfile
Commit: aca3ac1c2d2b364ef29e28f2af6ba74f48c55ae3
Author: trvinh <trvinh@gmail.com>
Date: 2024-08-29 14:25:08 +0200
Commit message:

 group labels umap

Package: koinar
Commit: 9f129e1a9297bc4c98d943619e532d0db9c92936
Author: Ludwig Lautenbacher <Ludwig.Lautenbacher@tum.de>
Date: 2024-08-29 13:45:13 +0200
Commit message:

 Update gitignore.

Package: koinar
Commit: b1f54a0762cc5e0a6e572f41d77fcded4d15373c
Author: Ludwig Lautenbacher <Ludwig.Lautenbacher@tum.de>
Date: 2024-08-29 13:34:39 +0200
Commit message:

 Bump version

Package: koinar
Commit: 1314dc943b9ec33d48d0d4afc49b8e3dc56b4838
Author: Ludwig Lautenbacher <Ludwig.Lautenbacher@tum.de>
Date: 2024-08-29 13:30:26 +0200
Commit message:

 Fix batchsize to adhere to bioconductor 5MB file limit.

Package: koinar
Commit: 7ff8b88336edaa52faae4d10829edab42700f5ea
Author: Ludwig Lautenbacher <Ludwig.Lautenbacher@tum.de>
Date: 2024-08-29 13:14:38 +0200
Commit message:

 Fix id so hash calculation of mockapi works.

Package: koinar
Commit: 4f3a6a3c96f92ef7b8c7de9df428865054005ce6
Author: Ludwig Lautenbacher <Ludwig.Lautenbacher@tum.de>
Date: 2024-08-28 18:38:56 +0200
Commit message:

 Mock api with httptest.

Package: edgeR
Commit: 260d2fb852dbd63f03a847f6dc1380f886859259
Author: Gordon Smyth <smyth@wehi.edu.au>
Date: 2024-08-29 21:24:06 +1000
Commit message:

 edgeR 4.3.13
- Update NEWS.Rd for changes that will be in the Bioc 3.20 release.

Package: velociraptor
Commit: febb53b97cf7936d094ef72c4be30664ebb1d1f4
Author: Kevin Rue-Albrecht <kevinrue67@gmail.com>
Date: 2024-08-29 11:32:15 +0100
Commit message:

 Add anaconda to channels for Linux (#81)

* update linux environment

* add new yaml env

* try another micromamba env resolved inside the biocdevel container

* replace env in R code

* try an environment using anaconda

* version bump and update main branch name in github action

Package: edgeR
Commit: 3d9fda2e463cfad2e9a2400d6f3614ed715f9d7a
Author: Gordon Smyth <smyth@wehi.edu.au>
Date: 2024-08-29 18:12:03 +1000
Commit message:

 edgeR 4.3.12
- Fix compilation error for Apple clang and old versions of gcc

Package: smoppix
Commit: 00a712fd238e3e79d1a3f2dfc5d182d2e9a783b5
Author: stijn <stijn.hawinkel@psb.ugent.be>
Date: 2024-08-29 09:33:01 +0200
Commit message:

 Version bump for addnculei

Package: smoppix
Commit: ce991c016a16598a1d1f0b55ea70dcd75b3ce194
Author: stijn <stijn.hawinkel@psb.ugent.be>
Date: 2024-08-29 09:20:06 +0200
Commit message:

 Aloow for nuclei to be added

Merge branch 'nuclei'
# Please enter a commit message to explain why this merge is necessary,
# especially if it merges an updated upstream into a topic branch.
#
# Lines starting with '#' will be ignored, and an empty message aborts
# the commit.

Package: smoppix
Commit: bb4dc60ca74b96c853bd88728ad8c32406dade5e
Author: stijn <stijn.hawinkel@psb.ugent.be>
Date: 2024-08-29 09:16:43 +0200
Commit message:

 doc for addcell

Package: smoppix
Commit: a843b600086d8f049326353bd93c1d40ae0aa2b3
Author: stijn <stijn.hawinkel@psb.ugent.be>
Date: 2024-08-29 08:48:08 +0200
Commit message:

 Update docu on addcell

Package: smoppix
Commit: 627ec03f235b0f47d14afa94f43bbf614a190f14
Author: stijn <stijn.hawinkel@psb.ugent.be>
Date: 2024-08-28 17:28:52 +0200
Commit message:

 AddCell in parallel

Package: smoppix
Commit: 8912786eec09894a69382ec707f8b2c77c55ff95
Author: stijn <stijn.hawinkel@psb.ugent.be>
Date: 2024-08-28 17:16:00 +0200
Commit message:

 Mention addnuclei in vignette

Package: smoppix
Commit: c44161a9c84fb245e342bb5e7434657e18b01c30
Author: stijn <stijn.hawinkel@psb.ugent.be>
Date: 2024-08-28 17:07:48 +0200
Commit message:

 Version bump for nuclei

Package: smoppix
Commit: 5b122fe38f66522af33265fc78f5bc5213c74127
Author: stijn <stijn.hawinkel@psb.ugent.be>
Date: 2024-08-28 17:05:26 +0200
Commit message:

 Missing documentation

Package: smoppix
Commit: 699ce7595bd99bae002aeeb08431f8e4b3c1eef9
Author: stijn <stijn.hawinkel@psb.ugent.be>
Date: 2024-08-28 16:50:55 +0200
Commit message:

 Adjusting getppvars to get rid of error messages

Package: smoppix
Commit: 3e0f389792333c1558040b3a33883fcf928d900e
Author: stijn <stijn.hawinkel@psb.ugent.be>
Date: 2024-08-28 13:26:55 +0200
Commit message:

 Adding nuclei works

Package: smoppix
Commit: 85cf56b82fb7b463cae8c439495d4658b9880df5
Author: stijn <stijn.hawinkel@psb.ugent.be>
Date: 2024-08-28 11:52:08 +0200
Commit message:

 Adding and plotting nuclei with the right checks

Package: smoppix
Commit: 1407ee755886eb7795b55edaffe7d2877bd9b27b
Author: stijn <stijn.hawinkel@psb.ugent.be>
Date: 2024-08-28 11:41:51 +0200
Commit message:

 Add plotting nuclei

Package: smoppix
Commit: 5e308cb18c902e13ea502096e25e59f60cec7e1a
Author: stijn <stijn.hawinkel@psb.ugent.be>
Date: 2024-08-28 11:15:59 +0200
Commit message:

 Function for adding nuclei

Package: simona
Commit: 26a679f670595c2dde643441e7ade2445ec790e2
Author: Zuguang Gu <jokergoo@gmail.com>
Date: 2024-08-29 08:58:06 +0200
Commit message:

 Merge branch 'master' into devel

Package: simona
Commit: 560197d14dc537d0bfce4cb89fbf8342428a7229
Author: Zuguang Gu <jokergoo@gmail.com>
Date: 2024-08-29 08:55:44 +0200
Commit message:

 Merge branch 'master' of github.com:jokergoo/ontsim

Package: simona
Commit: fe47a43c6389f8dd11e36a909e0ea64b83d2099d
Author: Zuguang Gu <jokergoo@gmail.com>
Date: 2024-08-29 08:55:30 +0200
Commit message:

 paper revision version

Package: simona
Commit: ba43529e622e6af8e21e70dba38cdf9949c4b347
Author: Zuguang Gu <jokergoo@gmail.com>
Date: 2024-07-16 22:29:21 +0200
Commit message:

 Merge pull request #7 from cmungall/patch-1

Update README.md

Package: simona
Commit: e5d8853697c94f490d135aa601a5da5b4c5a6811
Author: Zuguang Gu <jokergoo@gmail.com>
Date: 2024-06-11 13:49:58 +0200
Commit message:

 ignore gci_filter keyword

Package: simona
Commit: 1771ecb7422ca0a583c55ac9241d9cced573c77d
Author: Chris Mungall <cjm@berkeleybop.org>
Date: 2024-04-04 18:40:17 -0400
Commit message:

 Update README.md

Use a PURL for the location of the plant ontology

Package: scMultiSim
Commit: e09144c87ddfbd40cf059dc88525c4476874208c
Author: Hechen Li <lhc199652@gmail.com>
Date: 2024-08-28 23:10:12 -0400
Commit message:

 Update documentation

# Conflicts:
#	README.md

Package: scMultiSim
Commit: 7fb95f3c2f5f7e3d9a30c0c828ce67ce6b9e2495
Author: Hechen Li <lhc199652@gmail.com>
Date: 2024-08-25 02:20:38 -0400
Commit message:

 Update documentation

Package: scMultiSim
Commit: 77a2d5beda3d24f5a083e5621a358f9fb25c1c0e
Author: Hechen Li <lhc199652@gmail.com>
Date: 2024-08-25 02:03:50 -0400
Commit message:

 Update version info

# Conflicts:
#	DESCRIPTION
#	NEWS.md

Package: scMultiSim
Commit: 56ecadc83872fff971025f10aee9c74de6b245e1
Author: Hechen Li <lhc199652@gmail.com>
Date: 2024-08-25 01:33:42 -0400
Commit message:

 Use pkgdown

# Conflicts:
#	.gitignore
#	README.md

Package: GBScleanR
Commit: f4fcdb2ae230d3fd1417649c057c9d98c72ade6d
Author: tomoyukif <f.tomoyuki@okayama-u.ac.jp>
Date: 2024-08-29 11:47:59 +0900
Commit message:

 version bump

Package: GBScleanR
Commit: b6a97ae88f944a846771ae81947d03ae2198be34
Author: tomoyukif <f.tomoyuki@okayama-u.ac.jp>
Date: 2024-08-29 11:46:44 +0900
Commit message:

 Replace set/getDominantMarkers() to set/getFixedBias().

Package: GBScleanR
Commit: 219d8b79a0886d2c1a3f1fe179ef2525bbc302e2
Author: tomoyukif <f.tomoyuki@okayama-u.ac.jp>
Date: 2024-08-29 01:59:33 +0900
Commit message:

 version bump

Package: BiocBaseUtils
Commit: 19d5e316289dd0e94d5ab428527de3bc03b9e2f8
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2024-08-28 17:02:08 -0400
Commit message:

 version bump 1.7.3

Package: BiocBaseUtils
Commit: 42f40555a488ee1235725d2186cc548e2def93f2
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2024-08-28 17:01:17 -0400
Commit message:

 add more tests

Package: BiocBaseUtils
Commit: a70076bd5de82e0eb813309e427a1934f2ccabec
Author: LiNk-NY <marcel.ramosperez@roswellpark.org>
Date: 2024-08-12 11:04:54 -0400
Commit message:

 add lifeCycle helper

Package: tidyCoverage
Commit: d2f5e792641f0f37970710e026ba1ae3903a06e4
Author: js2264 <jacquesserizay@gmail.com>
Date: 2024-08-28 22:55:48 +0200
Commit message:

 bump to v1.1.2

Package: tidyCoverage
Commit: d039c967c85a19b9cc2dcf6f3738bad1ec72d1f3
Author: js2264 <jacquesserizay@gmail.com>
Date: 2024-08-28 22:55:34 +0200
Commit message:

 doc: add badges and citation material

Package: tidyCoverage
Commit: a408d48f55a96608796a35aba240632fece219f0
Author: js2264 <jacquesserizay@gmail.com>
Date: 2024-07-31 22:46:16 +0200
Commit message:

 fix: move paper figure vignette to package root

Package: multiMiR
Commit: b452b4cc623e8b3909f950f59f61c4c05f990ada
Author: Spencer Mahaffey <Spencer.Mahaffey@ucdenver.edu>
Date: 2024-08-28 14:53:10 -0600
Commit message:

 update README

Package: HiCExperiment
Commit: 1ea442fbe1bf1ef7da13e7d95ab128eb8b511123
Author: js2264 <jacquesserizay@gmail.com>
Date: 2024-08-28 22:44:03 +0200
Commit message:

 bump to 1.5.1

Package: HiCExperiment
Commit: 0d5f34fe584ce2ed59c871970366774fa6811422
Author: js2264 <jacquesserizay@gmail.com>
Date: 2024-08-28 22:41:59 +0200
Commit message:

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

Package: HiCExperiment
Commit: 1a2f5e0b8ab9440bc9174784dfe35185b3c38679
Author: js2264 <jacquesserizay@gmail.com>
Date: 2024-08-28 22:41:36 +0200
Commit message:

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

Package: HiCExperiment
Commit: 890ca857a09a30c7ce7dbe6af7b6387d194cafc6
Author: js2264 <jacquesserizay@gmail.com>
Date: 2024-08-28 22:33:38 +0200
Commit message:

 bump to 1.5.0

Package: HiCExperiment
Commit: d5702078746526df5157192f2960d1cec42b5e81
Author: js2264 <jacquesserizay@gmail.com>
Date: 2024-06-03 16:31:30 +0200
Commit message:

 add CITATION and DOI badge

Package: HiCExperiment
Commit: 246ace8ef68eaf861d39fd9847d5bb56ea9f2f22
Author: js2264 <jacquesserizay@gmail.com>
Date: 2024-01-26 11:25:19 +0100
Commit message:

 bump to v1.3.1

Package: HiCExperiment
Commit: e9af1513ec9aa085ce8cb059e77e3e707f1c123f
Author: js2264 <jacquesserizay@gmail.com>
Date: 2024-01-26 11:24:57 +0100
Commit message:

 fix: missing pair_type.field definition

Package: VisiumIO
Commit: 1573cf11b1a5798bc0ab8d4e19d77e66017a61ad
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2024-08-28 16:27:21 -0400
Commit message:

 version bump 1.1.3

Package: VisiumIO
Commit: 089efbbf7e31483809ddf386a307b45a6b8f8eaa
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2024-08-28 16:04:32 -0400
Commit message:

 update TENxSpatialList constructor for TENxFileList resources inputs

- add aligned_fiducials

Package: VisiumIO
Commit: e4269850abff0d766875169ef2615c4e9865575e
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2024-08-28 12:23:18 -0400
Commit message:

 fix bin_size in spatial path

Package: VisiumIO
Commit: 4191aecff5ede2df8675262599a547ec638293dd
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2024-08-26 17:15:17 -0400
Commit message:

 add resolution parser and slot to TENxSpatialList

Package: VisiumIO
Commit: afc0529f41149a5074de2316e33cb46ade097b6c
Author: LiNk-NY <marcel.ramosperez@roswellpark.org>
Date: 2024-08-19 16:27:39 -0400
Commit message:

 fix typo in SElist

Package: VisiumIO
Commit: 6bfbc67fddf6b8555233e6a22708d427d6fa1327
Author: LiNk-NY <marcel.ramosperez@roswellpark.org>
Date: 2024-08-19 13:25:04 -0400
Commit message:

 support colData import as tbl_df from parquet read in

Package: VisiumIO
Commit: 01a79added6d7f704153992fcd7d2ea6a2b1abed
Author: LiNk-NY <marcel.ramosperez@roswellpark.org>
Date: 2024-08-16 17:32:51 -0400
Commit message:

 initial support for VisiumHD

Package: multiMiR
Commit: 1bdabdae48c466ff9a8ad85a8ba0d6c41b25f5c7
Author: Spencer Mahaffey <Spencer.Mahaffey@ucdenver.edu>
Date: 2024-08-28 13:31:01 -0600
Commit message:

 fixed version bump error.  Back to 1.27.2

Package: multiMiR
Commit: 5eac0e882fb21ad16f4dffcb48f6640551aee350
Author: Spencer Mahaffey <Spencer.Mahaffey@ucdenver.edu>
Date: 2024-08-28 13:28:02 -0600
Commit message:

 bumped the version.

Package: multiMiR
Commit: 52747cd4abae96d89243a7b4e290bb4f9e024a95
Author: Spencer Mahaffey <Spencer.Mahaffey@ucdenver.edu>
Date: 2024-08-28 13:27:51 -0600
Commit message:

 attempted to alter the connection timeout throughout the package.

Package: multiMiR
Commit: a97e9c2f55304517b7dd10b54c6a4598f91464f7
Author: Spencer Mahaffey <Spencer.Mahaffey@ucdenver.edu>
Date: 2024-08-28 13:27:11 -0600
Commit message:

 Fixed empty summary error

Package: multiMiR
Commit: 4faa45bf4bb223d6ef6259a9540519b4f31c3fca
Author: Spencer Mahaffey <Spencer.Mahaffey@ucdenver.edu>
Date: 2024-08-28 10:30:54 -0600
Commit message:

 replaced as_data_frame -> as_tibble()

Package: multiMiR
Commit: 8f5327d49fe32b7437d9b810dbf23f581e2d65ff
Author: Spencer Mahaffey <Spencer.Mahaffey@ucdenver.edu>
Date: 2024-08-28 10:24:20 -0600
Commit message:

 Extended timeout for RCurl

Package: multiMiR
Commit: 6373e07fd8ead8b0fef00a269d1555dad25b4c30
Author: Spencer Mahaffey <Spencer.Mahaffey@ucdenver.edu>
Date: 2024-08-28 10:17:38 -0600
Commit message:

 update .gitignore

Package: GBScleanR
Commit: 1a3424da37ebee5413c6936a6b1935e8f75c884f
Author: tomoyukif <f.tomoyuki@okayama-u.ac.jp>
Date: 2024-08-29 01:58:48 +0900
Commit message:

 Fix a bug in .transitionProb() to support polyploids.

Package: gDRutils
Commit: a179666cb3f017480380b42e3152e15c803b9876
Author: Bartek <32614650+bczech@users.noreply.github.com>
Date: 2024-08-28 18:21:19 +0200
Commit message:

 Merge pull request #129 from gdrplatform/GDR-2668

Gdr 2668

Package: gDRutils
Commit: 9c9280b095841f90f204154a50d44baa4d25b0a1
Author: czechb3 <bartosz.w.czech@gmail.com>
Date: 2024-08-28 14:14:28 +0200
Commit message:

 chore: bump version and update NEWS.md

Package: gDRutils
Commit: 44fb4ff182d33a2ebf3996553bc497bf9c1ecd43
Author: czechb3 <bartosz.w.czech@gmail.com>
Date: 2024-08-28 14:14:23 +0200
Commit message:

 test: update unit tests

Package: gDRutils
Commit: c8478d4fa5fbeeed64701bcf0482301f6e237bbe
Author: czechb3 <bartosz.w.czech@gmail.com>
Date: 2024-08-28 14:14:10 +0200
Commit message:

 refactor get_additional_variables

Package: GBScleanR
Commit: cf83f4387de658cc20a4377b8ad04756f2d21b95
Author: tomoyukif <f.tomoyuki@okayama-u.ac.jp>
Date: 2024-08-29 01:19:54 +0900
Commit message:

 fix conflicts

Merge branch 'main' into devel

# Conflicts:
#	DESCRIPTION
#	inst/NEWS.md

Package: GBScleanR
Commit: 90b941b800fa68c29f5d97b5f76ba958a1d04e71
Author: tomoyukif <f.tomoyuki@okayama-u.ac.jp>
Date: 2024-08-29 01:19:05 +0900
Commit message:

 Fix a bug in .getValidPat()

Package: GBScleanR
Commit: d8cf80772df01f07b20c5f8e66f21600e0b9af30
Author: tomoyukif <f.tomoyuki@okayama-u.ac.jp>
Date: 2024-08-29 01:09:29 +0900
Commit message:

 version bump

Package: GBScleanR
Commit: 868d0e82b6503424e42946389739d8389a46bbcb
Author: tomoyukif <f.tomoyuki@okayama-u.ac.jp>
Date: 2024-08-29 01:08:14 +0900
Commit message:

 version bump

Package: GBScleanR
Commit: bea071d87ee73297014a181ceb46e28e5e90ee98
Author: tomoyukif <f.tomoyuki@okayama-u.ac.jp>
Date: 2024-08-29 01:08:49 +0900
Commit message:

 version bump

Package: GBScleanR
Commit: ae47016bb75f1aeff2c6c380848cf5ad7b9baf01
Author: tomoyukif <f.tomoyuki@okayama-u.ac.jp>
Date: 2024-08-29 01:06:56 +0900
Commit message:

 update estGeno()

Package: GBScleanR
Commit: ff84c8fa03d04d8209e867fd1076bd7149fdb9b6
Author: tomoyukif <f.tomoyuki@okayama-u.ac.jp>
Date: 2024-08-29 00:42:56 +0900
Commit message:

 Fix a bug in .transitionProb() to support polyploids.

Merge branch 'main' into devel

# Conflicts:
#	DESCRIPTION
#	inst/NEWS.md

Package: GBScleanR
Commit: 650377b690e166599ea5dff5a2df177d95e5cd85
Author: tomoyukif <f.tomoyuki@okayama-u.ac.jp>
Date: 2024-08-29 00:42:16 +0900
Commit message:

 Fix a bug in .transitionProb() to support polyploids.

Package: koinar
Commit: 59f8fbda78b21a2e62a5414ed76493e2d905903c
Author: Ludwig Lautenbacher <Ludwig.Lautenbacher@tum.de>
Date: 2024-08-28 17:28:32 +0200
Commit message:

 Replace default url.

Package: koinar
Commit: 19a0e9636f2798f20ebb14c5f2c767c352d598e4
Author: Ludwig Lautenbacher <Ludwig.Lautenbacher@tum.de>
Date: 2024-08-28 17:22:11 +0200
Commit message:

 Replace Koina$new with Koina.

Package: GBScleanR
Commit: 3875f7dba76b9678de361b76100aa388f6544bc0
Author: tomoyukif <f.tomoyuki@okayama-u.ac.jp>
Date: 2024-08-29 00:14:34 +0900
Commit message:

 Update .getValidPat() and change the timing when .makePattern() run in estGeno().

Merge branch 'main' into devel

# Conflicts:
#	DESCRIPTION
#	inst/NEWS.md

Package: GBScleanR
Commit: a7c0744d95067edb202bf7fbb3e72555bd65ae44
Author: tomoyukif <f.tomoyuki@okayama-u.ac.jp>
Date: 2024-08-29 00:13:46 +0900
Commit message:

 Update .getValidPat() and change the timing when .makePattern() run in estGeno().

Package: koinar
Commit: 7e844dafbec469f5b0dfb028680edce8af80a046
Author: Ludwig Lautenbacher <Ludwig.Lautenbacher@tum.de>
Date: 2024-08-28 16:51:43 +0200
Commit message:

 Trigger bioconductor build again.

Package: koinar
Commit: 1ccf67a557088f3c4e3fb2fb44e1c83c31564857
Author: Ludwig Lautenbacher <Ludwig.Lautenbacher@tum.de>
Date: 2024-08-28 16:42:57 +0200
Commit message:

 Trigger bioconductor build again.

Package: koinar
Commit: 47ff31dc708a2868d82c73c1d523d96cee5ce265
Author: Ludwig Lautenbacher <Ludwig.Lautenbacher@tum.de>
Date: 2024-08-28 16:00:17 +0200
Commit message:

 Trigger bioconductor build again.

Package: koinar
Commit: 3ddf58367855388ced505ed4741944856e321217
Author: Ludwig Lautenbacher <Ludwig.Lautenbacher@tum.de>
Date: 2024-08-28 15:25:13 +0200
Commit message:

 Add introduction to README.

Package: MouseFM
Commit: e04a2b7f255cc76972c5c152a4451cdca1c80fbe
Author: Matthias Munz <matthias.munz@gmx.de>
Date: 2024-08-28 15:51:01 +0200
Commit message:

 version bump and roxygen

Package: transmogR
Commit: 75eb43680196a81709878e2e16fda89c38eaf773
Author: Stevie Ped <stephen.pederson.au@gmail.com>
Date: 2024-08-28 23:09:10 +0930
Commit message:

 Removed requirement for cmd_info.json

Package: transmogR
Commit: 3e3edfe311d242b259c13cf832e890e8144ccaa6
Author: Stevie Ped <stephen.pederson.au@gmail.com>
Date: 2024-08-01 21:30:14 +0930
Commit message:

 Minor improvement to tests

Package: transmogR
Commit: d47d86c62d4bc6de64ba1620b1261e96a7cf0c33
Author: Stevie Ped <stephen.pederson.au@gmail.com>
Date: 2024-08-01 19:09:17 +0930
Commit message:

 Added digestSalmon to pkgdown

Package: transmogR
Commit: 3aecb51f4e8877df8d65778f9caaa8c4d3482237
Author: Stevie Ped <stephen.pederson.au@gmail.com>
Date: 2024-08-01 19:07:06 +0930
Commit message:

 Added digestSalmon

Package: koinar
Commit: 9ade84af689d0896a93ef0a565db95250c63b54f
Author: Ludwig Lautenbacher <Ludwig.Lautenbacher@tum.de>
Date: 2024-08-28 15:05:00 +0200
Commit message:

 Merge branch 'main' of github.com:wilhelm-lab/koinar

Package: koinar
Commit: a488c2e06edf19ca47408b51097d991b7860df18
Author: Ludwig Lautenbacher <Ludwig.Lautenbacher@tum.de>
Date: 2024-08-28 15:02:13 +0200
Commit message:

 Update documentation.

Package: koinar
Commit: 0aa9af7c5b82f3df68b9f5a85bca40fce5ea4e45
Author: Ludwig Lautenbacher <Ludwig.Lautenbacher@tum.de>
Date: 2024-08-28 15:02:13 +0200
Commit message:

 Update documentation.

Package: koinar
Commit: 4430ff2a499e10ddeb00dda8ce019e0e7738de4c
Author: Ludwig Lautenbacher <Ludwig.Lautenbacher@tum.de>
Date: 2024-08-28 14:52:37 +0200
Commit message:

 Add predictWithKoinaModel helper function.

Package: koinar
Commit: 649bb6a61d09769d86ed0cfe6eb28d759ada6d04
Author: Ludwig Lautenbacher <Ludwig.Lautenbacher@tum.de>
Date: 2024-08-21 18:49:29 +0200
Commit message:

 Update Title and Description.

Package: koinar
Commit: c7c1b5d7b6f2c539793820f2d3190dae4dc21a1b
Author: Ludwig Lautenbacher <Ludwig.Lautenbacher@tum.de>
Date: 2024-08-21 17:18:14 +0200
Commit message:

 Update documentation.

Package: koinar
Commit: 64ef55d8bef7af248dcf1fcc3fa1c74b340781e5
Author: Ludwig Lautenbacher <Ludwig.Lautenbacher@tum.de>
Date: 2024-08-20 16:46:47 +0200
Commit message:

 Replace for loop with apply.

Package: koinar
Commit: 07ef43b9576878cabc92ad9680e00cbc80eb2017
Author: Ludwig Lautenbacher <Ludwig.Lautenbacher@tum.de>
Date: 2024-08-20 14:44:50 +0200
Commit message:

 Add testcase for bioconductor DataFrame.

Package: koinar
Commit: 65c997f65cb454cc1b75cb4e4989c185de2a7229
Author: Ludwig Lautenbacher <Ludwig.Lautenbacher@tum.de>
Date: 2024-08-20 14:16:35 +0200
Commit message:

 Add support for bioconductor DataFrame.

Package: koinar
Commit: 9f476e41d1b4ee2e1342c6f81ed16ba335ed0f5e
Author: Ludwig Lautenbacher <Ludwig.Lautenbacher@tum.de>
Date: 2024-08-20 14:16:06 +0200
Commit message:

 Implement show method.

Package: MouseFM
Commit: 7312b31001cbbc55c4b4338aad546034e12726a5
Author: Matthias Munz <matthias.munz@gmx.de>
Date: 2024-08-28 15:02:21 +0200
Commit message:

 version bump

Package: MouseFM
Commit: 329dbf29fdc06ed7b0326e9f00ccc10187e9e944
Author: Matthias Munz <matthias.munz@gmx.de>
Date: 2024-08-28 14:58:44 +0200
Commit message:

 Change in set/getURL

Package: CatsCradle
Commit: cd706584ff2c5bbb7491499c806e543e67582961
Author: Michael Shapiro <michael.shapiro@crick.ac.uk>
Date: 2024-08-28 13:19:57 +0100
Commit message:

 updated to R 4.4.0 and attendant changes
further responses to requests for revisions

Package: CatsCradle
Commit: 67a0b9f8eb140004a6d04e32072dd09f7f275090
Author: Michael Shapiro <michael.shapiro@crick.ac.uk>
Date: 2024-08-16 15:53:20 +0100
Commit message:

 fidgetting line lengths

Package: CatsCradle
Commit: 86c43cf75624e6173236e8ae11e003019ef14e53
Author: Michael Shapiro <michael.shapiro@crick.ac.uk>
Date: 2024-08-16 15:04:11 +0100
Commit message:

 Broke up code into files with related functions.

Additional fidgetting with imports.

Package: CatsCradle
Commit: b571a93899fff376ba170495069a821c78a68b8b
Author: Michael Shapiro <michael.shapiro@crick.ac.uk>
Date: 2024-08-15 12:33:40 +0100
Commit message:

 In revisions for resubmission.  Major changes so far:
- quicker conversion from sce to seurat
- SCE vignette
- renamed object and functions
- largely wrangled imports

Onwards!

Package: mia
Commit: 2d52298c998e86601c03fa884503c1b58c372341
Author: Danielle Callan <53306535+d-callan@users.noreply.github.com>
Date: 2024-08-28 04:56:01 -0400
Commit message:

 smaller test file for type-less taxpasta biom (#631)

Package: mia
Commit: dcaa110131162d48d82081d1da3a74da18268a3b
Author: Muluh <127390183+Daenarys8@users.noreply.github.com>
Date: 2024-08-17 16:15:06 +0100
Commit message:

 remove authors from fxns (#629)

Signed-off-by: Daena Rys <rysdaena8@gmail.com>

Package: mia
Commit: 0eb0ebc9a8ecb4fe0a2724d7dc609ba642304be8
Author: Théotime Pralas <151254073+thpralas@users.noreply.github.com>
Date: 2024-08-13 19:10:00 +0200
Commit message:

 New dissimilarity functions (#609)

Co-authored-by: TuomasBorman <tvborm@utu.fi>
Co-authored-by: Leo Lahti <leo.lahti@iki.fi>
Co-authored-by: Tuomas Borman <60338854+TuomasBorman@users.noreply.github.com>

Package: mia
Commit: dcb48dc89fad2fd8c5c0c5a53d8ad22184a995a0
Author: Muluh <127390183+Daenarys8@users.noreply.github.com>
Date: 2024-08-11 15:31:58 +0100
Commit message:

 spell checker (#625)

Signed-off-by: Daena Rys <rysdaena8@gmail.com>
Co-authored-by: Leo Lahti <leo.lahti@iki.fi>

Package: mia
Commit: 5282a72e13e677f65b7bec01ce5f776685ad07cd
Author: Danielle Callan <53306535+d-callan@users.noreply.github.com>
Date: 2024-08-09 14:39:05 -0400
Commit message:

 Fix importTaxpasta (#619)

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

Package: mia
Commit: 552a9521c19dae07df11c6887a67f730bbe830a4
Author: Théotime Pralas <151254073+thpralas@users.noreply.github.com>
Date: 2024-08-09 13:25:41 +0200
Commit message:

 NMF ordination with feature loadings computation (#616)

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

Package: mia
Commit: c00541b64042219a099c9373b374f7ca625ab4d1
Author: Muluh <127390183+Daenarys8@users.noreply.github.com>
Date: 2024-08-06 18:02:25 +0100
Commit message:

 typo in summary example (#620)

Signed-off-by: Daena Rys <rysdaena8@gmail.com>

Package: mia
Commit: f193173bf0eaecf1b5fb560106b6c486dac01be7
Author: Muluh <127390183+Daenarys8@users.noreply.github.com>
Date: 2024-08-05 09:30:21 +0100
Commit message:

 ignore NAs when pseudocount is TRUE (#615)

Signed-off-by: Daena Rys <rysdaena8@gmail.com>

Package: mia
Commit: b75207ad64e5dc73f2e46576cccf4610fd36f9a6
Author: ake <40662956+ake123@users.noreply.github.com>
Date: 2024-07-30 14:57:10 +0300
Commit message:

 #601 and OMA issue #482 (#602)

Co-authored-by: Tuomas Borman <60338854+TuomasBorman@users.noreply.github.com>
Co-authored-by: Leo Lahti <leo.lahti@iki.fi>

Package: mia
Commit: 056ad480c122ba7e2241679318d8781cacc09746
Author: Tuomas Borman <60338854+TuomasBorman@users.noreply.github.com>
Date: 2024-07-30 00:10:55 +0300
Commit message:

 Package loading message (#608)

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

Package: GBScleanR
Commit: c594a0eed25b7071fbfe73e4eada3bfdec247ae0
Author: tomoyukif <f.tomoyuki@okayama-u.ac.jp>
Date: 2024-08-28 18:50:56 +0900
Commit message:

 Fix a bug in .summarizeEst() to support polyploids.

Merge branch 'main' into devel

# Conflicts:
#	DESCRIPTION
#	inst/NEWS.md

Package: GBScleanR
Commit: 8c6a08ac35420f6637580210915e8f23313ba3c1
Author: tomoyukif <f.tomoyuki@okayama-u.ac.jp>
Date: 2024-08-28 18:49:52 +0900
Commit message:

 Fix a bug in .summarizeEst() to support polyploids.

Package: GBScleanR
Commit: 197a2073ffb9735106ad5e486688f5813e60bf7e
Author: tomoyukif <f.tomoyuki@okayama-u.ac.jp>
Date: 2024-08-28 18:33:48 +0900
Commit message:

 Minor bug gix in getGenotype()

Merge branch 'main' into devel

# Conflicts:
#	DESCRIPTION
#	inst/NEWS.md

Package: GBScleanR
Commit: 6cf6678e0a4b5154adff39df0e425856d46c52a7
Author: tomoyukif <f.tomoyuki@okayama-u.ac.jp>
Date: 2024-08-28 18:32:34 +0900
Commit message:

 Minor bug fix in getGenotype()

Package: GBScleanR
Commit: 420f96eb664d46f7eec494e4617621b989833f62
Author: tomoyukif <f.tomoyuki@okayama-u.ac.jp>
Date: 2024-08-28 18:27:54 +0900
Commit message:

 fix version bump

Merge branch 'main' into devel

# Conflicts:
#	DESCRIPTION
#	inst/NEWS.md

Package: GBScleanR
Commit: 8982126507f5f409d199fea310b87e2ce75671aa
Author: tomoyukif <f.tomoyuki@okayama-u.ac.jp>
Date: 2024-08-28 18:26:54 +0900
Commit message:

 Modify getRead() and getGenotype() to make them work with the modified .filtData().

Package: GBScleanR
Commit: bb2959cc1f7874f1c14b5063c0bbf44d09f29fdf
Author: tomoyukif <f.tomoyuki@okayama-u.ac.jp>
Date: 2024-08-28 16:43:34 +0900
Commit message:

 fix conflicts

Merge branch 'main' into devel

# Conflicts:
#	DESCRIPTION
#	inst/NEWS.md

Package: GBScleanR
Commit: 6cc38812d4cdd203cf885098af2beb7b5b0e6558
Author: tomoyukif <f.tomoyuki@okayama-u.ac.jp>
Date: 2024-08-28 16:41:57 +0900
Commit message:

 version bump

Package: GBScleanR
Commit: e2916379ec877c0861f416b154ccd33724750589
Author: tomoyukif <f.tomoyuki@okayama-u.ac.jp>
Date: 2024-08-28 16:40:21 +0900
Commit message:

 moidfy .filtData() because seqGetData cannot work on the data for polyploids

Package: smoppix
Commit: e9b6f29234776c92fb6aa2b3ac18b38dc16b352c
Author: stijn <stijn.hawinkel@psb.ugent.be>
Date: 2024-08-28 09:56:44 +0200
Commit message:

 Problems with git clone

Package: MouseFM
Commit: 2ef71a31c9898da85ead568c3d35e616b9e2ca23
Author: Matthias Munz <matthias.munz@gmx.de>
Date: 2024-08-28 09:35:29 +0200
Commit message:

 2024-08-28

Package: scDiagnostics
Commit: dbfc2e5cf1656506243ce4d969c2b611cf166c87
Author: Anthony Christidis <anthony.christidis@stat.ubc.ca>
Date: 2024-08-28 00:33:53 -0400
Commit message:

 Trigger new Bioconductor build.

Package: scDiagnostics
Commit: b462aa2312dd8d2a9275ef04ccd00e1ea4c143f6
Author: Anthony Christidis <34141555+AnthonyChristidis@users.noreply.github.com>
Date: 2024-08-28 00:30:51 -0400
Commit message:

 Merge pull request #68 from AnthonyChristidis/main

Tidy up anomaly detection vignette.

Package: scDiagnostics
Commit: f57bf7bdf53a4124d2ce9e62e762911e17d60feb
Author: Anthony Christidis <anthony.christidis@stat.ubc.ca>
Date: 2024-08-28 00:30:31 -0400
Commit message:

 Tidy up anomaly detection vignette.

Package: scDiagnostics
Commit: f74ce56d9f62144d0d51f4e120a6ee730336568e
Author: Anthony Christidis <34141555+AnthonyChristidis@users.noreply.github.com>
Date: 2024-08-28 00:07:58 -0400
Commit message:

 Merge pull request #67 from AnthonyChristidis/main

Update README file.

Package: scDiagnostics
Commit: 4258ff4b2340ba3f9451ba4bf7d449dfab34f9aa
Author: Anthony Christidis <anthony.christidis@stat.ubc.ca>
Date: 2024-08-28 00:07:42 -0400
Commit message:

 Update README file.

Package: scDiagnostics
Commit: 604b7a6a611c295cf62e9d2be32d9a087e0c0081
Author: Anthony Christidis <34141555+AnthonyChristidis@users.noreply.github.com>
Date: 2024-08-27 23:47:21 -0400
Commit message:

 Merge pull request #66 from AnthonyChristidis/main

Improve README and tidy up vignettes.

Package: scDiagnostics
Commit: e39bf2810f42afa2c39c2829aa3cb8c5b7bb6e3a
Author: Anthony Christidis <34141555+AnthonyChristidis@users.noreply.github.com>
Date: 2024-08-27 23:46:44 -0400
Commit message:

 Merge branch 'ccb-hms:main' into main

Package: scDiagnostics
Commit: 139b60ed2c379960f0337f559cb8b651c8eabcd9
Author: Anthony Christidis <anthony.christidis@stat.ubc.ca>
Date: 2024-08-27 23:46:33 -0400
Commit message:

 Update Getting Started vignette.

Package: scDiagnostics
Commit: 4f54f663f86f712d546b06ea5d68d0801523c304
Author: Anthony Christidis <anthony.christidis@stat.ubc.ca>
Date: 2024-08-27 23:42:54 -0400
Commit message:

 Merge branch 'main' of github.com:AnthonyChristidis/scDiagnostics

Package: scDiagnostics
Commit: 8398b9f49862dc9150a3cec533efd440181f2243
Author: Anthony Christidis <anthony.christidis@stat.ubc.ca>
Date: 2024-08-27 23:42:16 -0400
Commit message:

 Improve README file.

Package: scDiagnostics
Commit: 495b50d2dcb56f3820d3af640a192b3d661d664d
Author: Anthony Christidis <34141555+AnthonyChristidis@users.noreply.github.com>
Date: 2024-08-27 23:33:00 -0400
Commit message:

 Merge pull request #65 from AnthonyChristidis/main

Update README file with vignette links.

Package: scDiagnostics
Commit: 6be217026e31d3e26bc18be901dc75c212639da3
Author: Anthony Christidis <34141555+AnthonyChristidis@users.noreply.github.com>
Date: 2024-08-27 23:32:32 -0400
Commit message:

 Merge branch 'ccb-hms:main' into main

Package: scDiagnostics
Commit: 401ec5528db9887ac2423a7ff34cbc3b6758a72a
Author: Anthony Christidis <anthony.christidis@stat.ubc.ca>
Date: 2024-08-27 23:31:25 -0400
Commit message:

 Add vignette links to README file.

Package: scDiagnostics
Commit: 2dcc8a3b8417c954ccb5c2ffa3518c9bb7fa810e
Author: Anthony Christidis <anthony.christidis@stat.ubc.ca>
Date: 2024-08-27 22:03:45 -0400
Commit message:

 Remove quantpng documentation.

Package: scDiagnostics
Commit: 7c7e76557870f999d9c769b87a5bd7ef21693b1b
Author: Anthony Christidis <anthony.christidis@stat.ubc.ca>
Date: 2024-08-27 21:19:23 -0400
Commit message:

 Remove pngquant compression functionality.

Package: scDiagnostics
Commit: 19ddee19371136b6d0b09dad8a248d512f284ce9
Author: Anthony Christidis <anthony.christidis@stat.ubc.ca>
Date: 2024-08-27 21:11:30 -0400
Commit message:

 Test automated quantpng compression function.

Package: scDiagnostics
Commit: f9c545646a59eeb72115f321c57c2dae725720ed
Author: Anthony Christidis <34141555+AnthonyChristidis@users.noreply.github.com>
Date: 2024-08-27 19:54:09 -0400
Commit message:

 Merge pull request #64 from AnthonyChristidis/main

Update vignettes and pkgdown site.

Package: scDiagnostics
Commit: 0e5249d7f13469bbe4453e0737e0935cbe19c2e5
Author: Anthony Christidis <anthony.christidis@stat.ubc.ca>
Date: 2024-08-27 19:24:22 -0400
Commit message:

 Update .Rbuildignore file.

Package: scDiagnostics
Commit: 027c34bc6714ee764fa955eb75e09e1fea0229e1
Author: Anthony Christidis <anthony.christidis@stat.ubc.ca>
Date: 2024-08-27 19:14:37 -0400
Commit message:

 Fix vignette metadata.

Package: scDiagnostics
Commit: d6d16a8600f8eb2bef2d2d1d56aeda523e4a17c3
Author: Anthony Christidis <anthony.christidis@stat.ubc.ca>
Date: 2024-08-27 18:54:02 -0400
Commit message:

 Add inst folder for compressed images, and hide figures in vignette code.

Package: scDiagnostics
Commit: 94c912568f25a1b4e6b58e8baa8d81d67d74ee46
Author: Anthony Christidis <anthony.christidis@stat.ubc.ca>
Date: 2024-08-27 16:47:37 -0400
Commit message:

 Decrease size of vignettes again.

Package: scDiagnostics
Commit: d659a9590dfed301f0a9be8dd97265b82726884f
Author: Anthony Christidis <anthony.christidis@stat.ubc.ca>
Date: 2024-08-27 15:56:37 -0400
Commit message:

 Reduce size of vignettes further.

Package: scDiagnostics
Commit: d23d94f1b8b705b0514f07eb1571df60b69db73d
Author: Anthony Christidis <anthony.christidis@stat.ubc.ca>
Date: 2024-08-27 15:23:16 -0400
Commit message:

 Reduce size of vignettes.

Package: scDiagnostics
Commit: b28097c0f3c821dcb9413909bb90d12c214fd44c
Author: Anthony Christidis <anthony.christidis@stat.ubc.ca>
Date: 2024-08-26 01:55:20 -0400
Commit message:

 Fix unit test error.

Package: scDiagnostics
Commit: 82c78bf6ab624a71f84973918ec6afc7b9507d99
Author: Anthony Christidis <anthony.christidis@stat.ubc.ca>
Date: 2024-08-26 01:42:45 -0400
Commit message:

 Update unit test error in calcualteCellDistancesSimilarity.

Package: scDiagnostics
Commit: 45d9da2bbe728ba82f865a425df2517434419c4c
Author: Anthony Christidis <anthony.christidis@stat.ubc.ca>
Date: 2024-08-26 01:27:26 -0400
Commit message:

 Remove unnecessary pkgdown files.

Package: scDiagnostics
Commit: a609272a88da4d4c1dd0fe62f895a9a2e9bd97a0
Author: Anthony Christidis <anthony.christidis@stat.ubc.ca>
Date: 2024-08-26 01:26:24 -0400
Commit message:

 Remove unnecessary files.

Package: scDiagnostics
Commit: 19614896650b5a79a101b7c2ef8dd61599f35257
Author: Anthony Christidis <anthony.christidis@stat.ubc.ca>
Date: 2024-08-26 01:11:42 -0400
Commit message:

 Merge branch 'main' of github.com:AnthonyChristidis/scDiagnostics

Package: scDiagnostics
Commit: d4bf582fdaddc43eb5a933989d3152e891931f71
Author: Anthony Christidis <anthony.christidis@stat.ubc.ca>
Date: 2024-08-26 01:11:31 -0400
Commit message:

 Add all the new vignettes.

Package: scDiagnostics
Commit: c2494e8b1e27f6179f14a0011f998416c875f0b1
Author: Anthony Christidis <34141555+AnthonyChristidis@users.noreply.github.com>
Date: 2024-08-24 22:05:54 -0400
Commit message:

 Merge pull request #63 from AnthonyChristidis/main

Update Get Started vignette.

Package: scDiagnostics
Commit: 2cf0c58490e0dd8f7c99f55e7a3bb4ec9d062661
Author: Anthony Christidis <anthony.christidis@stat.ubc.ca>
Date: 2024-08-24 21:38:38 -0400
Commit message:

 Update Get Started vignette.

Package: scDiagnostics
Commit: 64af97818f65cb8299f9efcf22e8ea28c3509724
Author: Anthony Christidis <34141555+AnthonyChristidis@users.noreply.github.com>
Date: 2024-08-24 16:11:33 -0400
Commit message:

 Merge pull request #62 from AnthonyChristidis/main

Change anomaly threshold for isolation forest.

Package: scDiagnostics
Commit: d9fe7b1e84a0e12710eecae759ee7c8091bec894
Author: Anthony Christidis <anthony.christidis@stat.ubc.ca>
Date: 2024-08-24 14:30:10 -0400
Commit message:

 Change anomaly threshold for isolation forest.

Package: scDiagnostics
Commit: 4ee29b94a17c79785940217f30dc0308325a5b39
Author: Anthony Christidis <34141555+AnthonyChristidis@users.noreply.github.com>
Date: 2024-07-21 17:18:44 -0400
Commit message:

 Merge pull request #60 from AnthonyChristidis/main

Update affiliations.

Package: scDiagnostics
Commit: 00fbdb86d7233989fbdec2042428c3e51f0b469d
Author: Anthony Christidis <anthony.christidis@stat.ubc.ca>
Date: 2024-07-21 17:06:09 -0400
Commit message:

 Merge branch 'main' of github.com:AnthonyChristidis/scDiagnostics

Package: scDiagnostics
Commit: cef59ee240ff04e32588d56af31d0f69b2dc353e
Author: Anthony Christidis <anthony.christidis@stat.ubc.ca>
Date: 2024-07-21 17:05:58 -0400
Commit message:

 Update affiliations.

Package: scDiagnostics
Commit: 1bc1ed867697af7119e45777cf2ddadef5003b3b
Author: Anthony Christidis <34141555+AnthonyChristidis@users.noreply.github.com>
Date: 2024-07-21 16:33:36 -0400
Commit message:

 Merge pull request #59 from AnthonyChristidis/main

Tidy up the documentation of functions, and add package documentation.

Package: scDiagnostics
Commit: 2c22d095c3914bd0354a62dcb5e31bf1195f536b
Author: Anthony Christidis <anthony.christidis@stat.ubc.ca>
Date: 2024-07-21 15:53:05 -0400
Commit message:

 Tidy up the documentation of functions, and add package documentation.

Package: scDiagnostics
Commit: 7975c44724791575a020a98c9becf725d3bc5172
Author: Anthony Christidis <34141555+AnthonyChristidis@users.noreply.github.com>
Date: 2024-07-16 17:50:46 -0400
Commit message:

 Merge pull request #58 from AnthonyChristidis/main

Bioconductor Review Update

Package: scDiagnostics
Commit: b812641e8b4e5e7287b4fc8eba4eb5879582401c
Author: Anthony Christidis <anthony.christidis@stat.ubc.ca>
Date: 2024-07-16 17:32:48 -0400
Commit message:

 Further image compression for the vignette.

Package: scDiagnostics
Commit: cbc7c5fc35ab82d56693e8922ef8a1a063d205f0
Author: Anthony Christidis <anthony.christidis@stat.ubc.ca>
Date: 2024-07-16 17:02:45 -0400
Commit message:

 Add pngquant for image compression.

Package: scDiagnostics
Commit: a312b25db10dae441c3a3471cb61bfdfd1d76ce5
Author: Anthony Christidis <anthony.christidis@stat.ubc.ca>
Date: 2024-07-16 16:14:18 -0400
Commit message:

 Fix vignette code.

Package: scDiagnostics
Commit: 62c63bdeb5e220b20863e2bc99d5735ff8d9bb07
Author: Anthony Christidis <anthony.christidis@stat.ubc.ca>
Date: 2024-07-16 16:07:59 -0400
Commit message:

 Fix vignette code.

Package: scDiagnostics
Commit: 0d404a138eb66fac801d2ada21177cbecee58c04
Author: Anthony Christidis <anthony.christidis@stat.ubc.ca>
Date: 2024-07-16 15:37:15 -0400
Commit message:

 Fix vignette code.

Package: scDiagnostics
Commit: 25b557e0d1c779c7e0161fa2fede5efb6275cb76
Author: Anthony Christidis <anthony.christidis@stat.ubc.ca>
Date: 2024-07-16 15:31:20 -0400
Commit message:

 Fix vignette code.

Package: scDiagnostics
Commit: 81fb834da10ac23ce46293ed8d791f06df7fe3d7
Author: Anthony Christidis <anthony.christidis@stat.ubc.ca>
Date: 2024-07-16 15:23:09 -0400
Commit message:

 Update NEWS.md file and DESCRIPTION for Bioconductor review.

Package: scDiagnostics
Commit: c81dc2de6768e5068ef32078fa5d0a4d9409a084
Author: Anthony Christidis <anthony.christidis@stat.ubc.ca>
Date: 2024-07-16 13:12:48 -0400
Commit message:

 Add remaining unit tests (S3 plot methods).

Package: scDiagnostics
Commit: 2959fd6ea5fc0750cb97ba2357e13d87929d4da9
Author: Anthony Christidis <anthony.christidis@stat.ubc.ca>
Date: 2024-07-16 01:46:43 -0400
Commit message:

 Tidy up the documentation of functions and remove usage of sapply.

Package: scDiagnostics
Commit: 587fd39519287e8be9652be3a26ba337b43d3e9b
Author: Anthony Christidis <anthony.christidis@stat.ubc.ca>
Date: 2024-07-16 00:58:16 -0400
Commit message:

 Update package for Bioconductor review.

Package: scDiagnostics
Commit: 49dd4d587224ad4ee39d850ba3169a04f2e2359e
Author: Anthony Christidis <34141555+AnthonyChristidis@users.noreply.github.com>
Date: 2024-06-23 15:49:25 -0400
Commit message:

 Merge pull request #16 from ccb-hms/main

PR from ccb-hms version.

Package: Damsel
Commit: 7da606480d7b21113b2ed4988aac7ed8ffa358a4
Author: Caitlin Page <caitlin.page@petermac.org>
Date: 2024-08-28 11:57:12 +1000
Commit message:

 version bump in devel

Package: Damsel
Commit: f6a265ebda55f7a87234b58e960a4085f53f0357
Author: Caitlin Page <caitlin.page@petermac.org>
Date: 2024-08-28 11:56:26 +1000
Commit message:

 bug fix: factor problem

Package: AnVIL
Commit: 2ce465ed2dbce90a2f7ffb49d1d3c2bd43e08ff8
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2024-08-27 17:17:12 -0400
Commit message:

 version bump 1.17.14

Package: AnVIL
Commit: b9af50794f3521d5d8b9a6b1b7376065c1112978
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2024-08-27 17:16:39 -0400
Commit message:

 update email in Rd

Package: Biobase
Commit: 40c9d1bc35c18fed99ddddb86e0a3f0ec15ca930
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2024-08-27 14:15:09 -0700
Commit message:

 bump version to 2.65.1

Package: Biobase
Commit: e792eb85e468d967a9dac0d16b0b63fdfaf5490f
Author: Kevin Ushey <kevin@posit.co>
Date: 2024-08-27 14:13:15 -0700
Commit message:

 adapt to STRICT_R_HEADERS requirement (#22)

Package: BiocBaseUtils
Commit: f8662d807f80994975cab4d8a9ab28a86202a753
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2024-08-27 17:12:35 -0400
Commit message:

 version bump 1.7.2

Package: BiocBaseUtils
Commit: bc815e6ed8e944c6bd8b5c99c69758af7af169de
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2024-08-27 17:12:31 -0400
Commit message:

 update email in Rd

Package: RaggedExperiment
Commit: d6980d1383033fddb8c8e48f99010eb061ab065f
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2024-08-27 17:11:51 -0400
Commit message:

 version bump 1.29.3

Package: RaggedExperiment
Commit: 7b330ec11a58e0d62a114651c8a2f66c542f010d
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2024-08-27 17:11:47 -0400
Commit message:

 update email in Rd

Package: AnVILBase
Commit: d6e3d82ed1c84355eac99e6d397738f7d3ea890d
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2024-08-27 17:10:27 -0400
Commit message:

 version bump 0.99.27

Package: AnVILBase
Commit: a3e87267bc8c473a856f9459ec4fce8b37d65e5e
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2024-08-27 17:10:23 -0400
Commit message:

 udpate email in Rd

Package: GenomicDataCommons
Commit: a40f46602ecf190ca712356abc7244b7f09c716e
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2024-08-27 17:09:20 -0400
Commit message:

 version bump 1.29.4

Package: GenomicDataCommons
Commit: 2d4ff3462f2a15828cb782e4ec22ae5fee3f0cf5
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2024-08-27 17:09:18 -0400
Commit message:

 change email in Rd

Package: GenomicDataCommons
Commit: 82dc5ed57b6cd91e2ba6a891d351827cd0dd9665
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2024-08-27 12:43:10 -0400
Commit message:

 update email

Package: AnVILAz
Commit: 89ae1559f14311c0cd38313e997f8de12f35e64d
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2024-08-27 16:59:14 -0400
Commit message:

 version bump 0.99.19

Package: AnVILAz
Commit: 99db7bc80104cadb57cdc38637fff6122be4c93f
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2024-08-27 16:59:07 -0400
Commit message:

 update email in vignette

Package: AnVILAz
Commit: 3fb44c48928081b077aa94aa0755abe4af5bbdf6
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2024-08-27 16:58:27 -0400
Commit message:

 version bump 0.99.18

Package: AnVILAz
Commit: 159f603e499a3fff95b92347e5c792810e7a50a7
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2024-08-27 16:58:25 -0400
Commit message:

 update email in Rd

Package: AnVILAz
Commit: d0d015468f8c2de47103c6c57f553a13a7e49207
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2024-08-27 16:56:30 -0400
Commit message:

 version bump 0.99.17

Package: AnVILAz
Commit: fdcb281010164403c710ea6d4fea1c6359f8595f
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2024-08-27 16:56:24 -0400
Commit message:

 update email

Package: clustifyr
Commit: d33cd200f807a0fb428ffd1288de58a5d9204fe5
Author: Kent Riemondy <kent.riemondy@gmail.com>
Date: 2024-08-27 14:48:41 -0600
Commit message:

 pass maintenance back to Rui, and redoc

Package: scRNAseqApp
Commit: 595857a2936ea422cc6aabf3b76bd5a06fec3a05
Author: JIANHONG OU <jianhong@users.noreply.github.com>
Date: 2024-08-27 16:42:53 -0400
Commit message:

 remove disabled = FALSE from updateActionButton

Package: alabaster.base
Commit: 484111131748dcabb00d4bb1b636559964dff50d
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2024-08-27 13:24:14 -0700
Commit message:

 Bumped version and date for new release, plus minor fixes.

- Added Encoding so that roxygen stops complaining.
- Fix LICENSE so that R CMD check stops complaining.

Package: alabaster.base
Commit: b62a60d05978bbda0f6c5c9a33ae0e95d76de829
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2024-08-27 13:20:00 -0700
Commit message:

 Updated validateDirectory to work with files created by saveObject.

Package: escape
Commit: 4c51261c2024d541a3a3e014f814cd6552eac5ce
Author: theHumanBorch <ncborch@gmail.com>
Date: 2024-08-27 13:36:33 -0500
Commit message:

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

Package: escape
Commit: ecbb120ea1b8a577ed1ed152d03a55ffb6e4911c
Author: theHumanBorch <ncborch@gmail.com>
Date: 2024-08-27 13:35:08 -0500
Commit message:

 Update DESCRIPTION

Package: escape
Commit: 91e0f16a28aace727eebce5322bb23a591471c06
Author: theHumanBorch <ncborch@gmail.com>
Date: 2024-08-27 13:33:48 -0500
Commit message:

 Merge pull request #117 from ncborcherding/master

merging into devel

Package: escape
Commit: 82dd54c8e6817d09b83e2f1741e7dd32020151a3
Author: theHumanBorch <ncborch@gmail.com>
Date: 2024-05-23 13:08:19 -0500
Commit message:

 Merge pull request #98 from neanderthalensis/devel

minor changes to getGeneSet

Package: escape
Commit: 48d77414dcd69a1aef78339a38e889ce0f3d6645
Author: neanderthalensis <atyrlik@terpmail.umd.edu>
Date: 2024-05-21 19:20:22 -0400
Commit message:

 minor changes to getGeneSet

Package: escape
Commit: 8b738a291cc3d52eb964dd33bbdadaf1225704d6
Author: theHumanBorch <ncborch@gmail.com>
Date: 2024-08-27 13:14:05 -0500
Commit message:

 Resolved merge conflicts between main and devel

Package: escape
Commit: b5307d028401878da621291a21a99974c3ac3b53
Author: theHumanBorch <ncborch@gmail.com>
Date: 2024-08-22 14:29:28 -0500
Commit message:

 Merge pull request #111 from LinearParadox/LinearParadox-patch-1

Update performNormalization.R

Package: escape
Commit: a3116ff5fdab4b4c03ceae9fb412fdd7b8ce6382
Author: Alexei Martsinkovskiy <alexei.martsinkovskiy@gmail.com>
Date: 2024-08-21 17:23:10 -0700
Commit message:

 Update densityEnrichment.R

rolled back function renaming

Package: escape
Commit: cb97c24067302b0d793f3d546d790f72b0fd35df
Author: Alexei Martsinkovskiy <alexei.martsinkovskiy@gmail.com>
Date: 2024-08-20 15:54:59 -0700
Commit message:

 minor refactor

removed redundant split matrix function (already present). added matrix dependency to imports.

Package: escape
Commit: 46541f252d196f2e8106a8742993cd405f81a719
Author: Alexei Martsinkovskiy <alexei.martsinkovskiy@gmail.com>
Date: 2024-08-20 13:42:21 -0700
Commit message:

 documentation. minor code cleanup

added documentation for groups. added ucell split data matrix since it is an internal function and can't be imported. minor code cleanup.

Package: escape
Commit: 44e7faffc32956d28cc4d505fd31a222a385bad8
Author: Alexei Martsinkovskiy <alexei.martsinkovskiy@gmail.com>
Date: 2024-08-19 14:59:50 -0700
Commit message:

 updated to pass chunking, fixing bug with scale factors

Package: escape
Commit: 1245b1d51fac235e62185fe40f91a4d6556f85db
Author: Alexei Martsinkovskiy <alexei.martsinkovskiy@gmail.com>
Date: 2024-08-16 17:25:43 -0700
Commit message:

 added contributor name

Package: escape
Commit: c4d3996471e4927f720c05099825b6f03da077a0
Author: Alexei Martsinkovskiy <alexei.martsinkovskiy@gmail.com>
Date: 2024-08-16 17:16:20 -0700
Commit message:

 rewrote normalize to be vectorized.

Package: escape
Commit: 26e935ced2fe121b2a7ebee812812269af11edac
Author: Alexei Martsinkovskiy <alexei.martsinkovskiy@gmail.com>
Date: 2024-08-15 16:13:34 -0700
Commit message:

 Update performNormalization.R

significantly speed up calculating scale factors

Package: escape
Commit: 41d079897b7d9e34f199789d22efaefe355b8a2d
Author: theHumanBorch <ncborch@gmail.com>
Date: 2024-08-14 09:06:31 -0500
Commit message:

 Update performNormalization.R

Adding bpvec to importfrom

Package: escape
Commit: 685a12c64a77fc7cd09e2fc62f94b675e1c98300
Author: Alexei Martsinkovskiy <alexei.martsinkovskiy@gmail.com>
Date: 2024-08-13 16:09:12 -0700
Commit message:

 Update performNormalization.R

improved efficiency in the case of a provided scale factor, fixed for cases where scale factor is not provided

Package: escape
Commit: 77ffb9cdeaba4b78c8318e583e475271a9758eb0
Author: Alexei Martsinkovskiy <alexei.martsinkovskiy@gmail.com>
Date: 2024-08-13 14:00:51 -0700
Commit message:

 Update performNormalization.R

added parallelization to normalize function. This might be memory intensive, but still would offer a speed benefit over a strictly single threaded approach. Under the hood, bpvec splits the vector into the number of workers and then executes the function on them, before joining it back together. 

I tested it against the equivalent single thread method and got an identical result.

Package: escape
Commit: 44f083e3162781bb8c52d5dd9bade042133d4300
Author: theHumanBorch <ncborch@gmail.com>
Date: 2024-08-02 08:00:31 -0500
Commit message:

 Merge pull request #109 from ncborcherding/dev

updating scale.factor for normalizatrion

Package: escape
Commit: 20a23d2ed71648666e87b987bd694697c233c343
Author: theHumanBorch <ncborch@gmail.com>
Date: 2024-08-02 08:00:24 -0500
Commit message:

 Merge branch 'master' into dev

Package: escape
Commit: 600bee8af5a2694c196263fc17535d3afc18d18d
Author: theHumanBorch <ncborch@gmail.com>
Date: 2024-08-02 07:54:54 -0500
Commit message:

 pushing updated testthat

Package: escape
Commit: 7e4b065a8f0381abef6c60d00f30d6b1d795892e
Author: theHumanBorch <ncborch@gmail.com>
Date: 2024-07-31 09:36:13 -0500
Commit message:

 Normalization fix

#107 Normalization error when only using a input matrix - split input.data into sc.data and enrichment.data

Package: escape
Commit: c301476431efcd2d8d017c12e247ff20e97d3374
Author: theHumanBorch <ncborch@gmail.com>
Date: 2024-07-26 08:25:25 -0500
Commit message:

 News and Version update

Package: escape
Commit: 774905b64a68ec735a1810cd6f3a9c947f45bb05
Author: theHumanBorch <ncborch@gmail.com>
Date: 2024-07-26 08:23:05 -0500
Commit message:

 Pass parallel to runEscape

#105 Issue fix

Package: escape
Commit: 8d4ec7a821e86f211fdf221dc52f53d6dd988077
Author: theHumanBorch <ncborch@gmail.com>
Date: 2024-07-26 08:08:26 -0500
Commit message:

 Merge branch 'master' of https://github.com/ncborcherding/escape

Package: escape
Commit: 1487b1ce72a08db168efa1ce5f497dd14d56c9d2
Author: theHumanBorch <ncborch@gmail.com>
Date: 2024-05-12 14:01:03 -0500
Commit message:

 Update README.md

Package: escape
Commit: bc244dadeedf8db3587fb9cdaf9fb586deea0dab
Author: theHumanBorch <ncborch@gmail.com>
Date: 2024-05-12 13:54:28 -0500
Commit message:

 Update README.md

Package: escape
Commit: d4ecb0b75db0454ada611bd1c5e64cd3996b63c9
Author: theHumanBorch <ncborch@gmail.com>
Date: 2024-05-12 13:53:50 -0500
Commit message:

 Update README.md

Package: escape
Commit: 4b75c160ed185913ac6e4b3389c29ce5870387d6
Author: theHumanBorch <ncborch@gmail.com>
Date: 2024-05-03 07:26:40 -0500
Commit message:

 3.19 release readme update

Package: escape
Commit: 30c551efb7e02d95b0afa3366d208386551f9ed5
Author: theHumanBorch <ncborch@gmail.com>
Date: 2024-05-01 08:48:02 -0500
Commit message:

 modulate testthat

Package: escape
Commit: 42b4c201699d3a67ff71295e37d3d9e6bb02552b
Author: theHumanBorch <ncborch@gmail.com>
Date: 2024-05-01 08:14:26 -0500
Commit message:

 update testthat

Package: escape
Commit: f825958373c2e818717c95e91cbca0570ad8e286
Author: theHumanBorch <ncborch@gmail.com>
Date: 2024-04-25 13:25:38 -0500
Commit message:

 Update R-CMD-check.yaml

Package: escape
Commit: 7fbb45829160dc4564c7d122866d01fbec0b40a9
Author: theHumanBorch <ncborch@gmail.com>
Date: 2024-04-25 10:33:52 -0500
Commit message:

 Update test-coverage.yaml

Package: escape
Commit: ed8df641a0ba11b4ceaf39c91fc445124daf122c
Author: theHumanBorch <ncborch@gmail.com>
Date: 2024-04-04 08:40:27 -0500
Commit message:

 Update test-coverage.yaml

Package: escape
Commit: d5baeaebc9d7932e6cac4d58137b2272dd52f395
Author: theHumanBorch <ncborch@gmail.com>
Date: 2024-04-04 08:39:54 -0500
Commit message:

 fix break caused by GSVA version

Package: escape
Commit: c067057d980c9a5a27e03fe41280f034d050ce1b
Author: theHumanBorch <ncborch@gmail.com>
Date: 2024-04-04 07:22:12 -0500
Commit message:

 Update test-coverage.yaml

Package: escape
Commit: d8b75d1921e3768eee6104c11e390cfc7b380f81
Author: theHumanBorch <ncborch@gmail.com>
Date: 2024-04-04 07:21:14 -0500
Commit message:

 update r-cmd-check after PR

Package: escape
Commit: 9c631ec0e344ea52ff7bf66aef98a1400c89167a
Author: theHumanBorch <ncborch@gmail.com>
Date: 2024-04-04 05:42:47 -0500
Commit message:

 update hex sticker location

Package: escape
Commit: 336f7ee240b7ba4b86acb08c5b9156b66d447e95
Author: theHumanBorch <ncborch@gmail.com>
Date: 2024-03-25 06:28:22 -0500
Commit message:

 Merge remote-tracking branch 'upstream/devel'
Silencing teststhat for later package update.

Package: escape
Commit: e5ee9bf2c9c46aba444eecb6cf2c18e391c1f721
Author: theHumanBorch <ncborch@gmail.com>
Date: 2024-03-25 06:27:57 -0500
Commit message:

 silence some tests

Package: smoppix
Commit: 83a47a3581fcc9c6e5543278cc36c8138e872937
Author: stijn <stijn.hawinkel@psb.ugent.be>
Date: 2024-08-27 17:38:05 +0200
Commit message:

 Version bump for bugfixes

Package: smoppix
Commit: a101f40f790314cbcb62f22170af4912014c75d1
Author: stijn <stijn.hawinkel@psb.ugent.be>
Date: 2024-08-27 17:37:40 +0200
Commit message:

 typo

Package: smoppix
Commit: 53f301b00a340705dcab8ce55c5117222cb10a85
Author: stijn <stijn.hawinkel@psb.ugent.be>
Date: 2024-08-27 17:28:16 +0200
Commit message:

 Another bug due to weird subsetting behaviour

Package: smoppix
Commit: 3a57929972389d1be67a45039ccc81b1867f0c21
Author: stijn <stijn.hawinkel@psb.ugent.be>
Date: 2024-08-27 16:31:18 +0200
Commit message:

 Now with thr real bugfix

Package: smoppix
Commit: d630fa8ca682c52d3d9573d41e2b75542c2d5aea
Author: stijn <stijn.hawinkel@psb.ugent.be>
Date: 2024-08-27 16:27:16 +0200
Commit message:

 bugfix for builddataframe

Package: SynExtend
Commit: 32bee239dc8fe845571979656a4e609a35304a8a
Author: Nicholas Cooley <39340402+npcooley@users.noreply.github.com>
Date: 2024-08-27 10:39:20 -0400
Commit message:

 Merge pull request #53 from ahl27/master

feat: allow users to set inflation in `ExoLabel`

Package: SynExtend
Commit: 7f56cc87245a06d1c88534e40dfb0cf03d49d9aa
Author: Aidan Lakshman <ahl27@pitt.edu>
Date: 2024-08-27 10:34:06 -0400
Commit message:

 update news and description

Package: SynExtend
Commit: b446f1990de87bf9507cfc49764f0d71b6fc15e7
Author: Aidan Lakshman <ahl27@pitt.edu>
Date: 2024-08-27 10:32:56 -0400
Commit message:

 Merge branch 'npcooley:devel' into master

Package: SynExtend
Commit: 424cba42319ea6630a0ed4e5219cf082eb3fb3bd
Author: ahl27 <ahl27@pitt.edu>
Date: 2024-08-27 10:32:01 -0400
Commit message:

 updates ExoLabel to allow users to set the inflation parameter

Package: scRNAseqApp
Commit: 1b96b2b69d53f30bec3950bbb060e16afb9124de
Author: JIANHONG OU <jianhong@users.noreply.github.com>
Date: 2024-08-26 14:13:45 -0400
Commit message:

 add cell info editor functions.

Package: scRNAseqApp
Commit: 2ab0d880d11925dfdac551cec5cc3cb33439c765
Author: JIANHONG OU <jianhong@users.noreply.github.com>
Date: 2024-08-21 17:37:22 -0400
Commit message:

 add more download format

Package: msa
Commit: c3ecf2928aa56b6071f6bf5fbdce3417b8e8596e
Author: UBod <ulrich@bodenhofer.com>
Date: 2024-08-23 13:01:22 +0200
Commit message:

 Change of msaPrettyPrint() interface to allow for workaround around texi2dvi() problems; version number bumped to 1.37.4

Package: GSVA
Commit: 6808922117f5eb4ac7481916a6140848160ccac1
Author: Robert Castelo <robert.castelo@upf.edu>
Date: 2024-08-27 12:14:42 +0200
Commit message:

 Bump version

Package: GBScleanR
Commit: a5ec485795ebfbb4f108e211940faaaeead60539
Author: tomoyukif <f.tomoyuki@okayama-u.ac.jp>
Date: 2024-08-27 19:14:26 +0900
Commit message:

 version bump

Package: GBScleanR
Commit: 7c273e1c404368f2db5c08e174db329aad75078b
Author: tomoyukif <f.tomoyuki@okayama-u.ac.jp>
Date: 2024-08-27 18:56:33 +0900
Commit message:

 Change update dates

Package: GBScleanR
Commit: 144a3961789688a537f5e2db9261484754e720f9
Author: tomoyukif <f.tomoyuki@okayama-u.ac.jp>
Date: 2024-08-27 17:27:56 +0900
Commit message:

 Update the vignette.

Package: GBScleanR
Commit: 2d75f0b632b318043abc048de0d36170bd77060b
Author: tomoyukif <f.tomoyuki@okayama-u.ac.jp>
Date: 2024-08-26 18:38:50 +0900
Commit message:

 Minor bug fix in ParGenoProb

Package: GBScleanR
Commit: 79f3468d2a35d75a721d05e71797b077aa3e57ad
Author: tomoyukif <f.tomoyuki@okayama-u.ac.jp>
Date: 2024-08-26 16:59:20 +0900
Commit message:

 Minor bug fix in calcMissmap

Package: GBScleanR
Commit: 8c11b06056299aff622e5bbfd952d8c655f6a058
Author: tomoyukif <f.tomoyuki@okayama-u.ac.jp>
Date: 2024-08-26 16:34:18 +0900
Commit message:

 Minor bug fix in calcMismapp

Package: GBScleanR
Commit: c783183ace6fd549edb6578e44c200cc7c356422
Author: tomoyukif <f.tomoyuki@okayama-u.ac.jp>
Date: 2024-08-26 16:07:17 +0900
Commit message:

 Minor bug fix in calcMissmap

Package: GBScleanR
Commit: 462f810277646f83af3a46cdcf804045cc8dbbc0
Author: tomoyukif <f.tomoyuki@okayama-u.ac.jp>
Date: 2024-08-26 15:57:12 +0900
Commit message:

 Minor bug fix in calcPemit

Package: GBScleanR
Commit: 98766ef123396b94b00f33c70709b378ac3bc455
Author: tomoyukif <f.tomoyuki@okayama-u.ac.jp>
Date: 2024-08-26 14:55:23 +0900
Commit message:

 Bug fix in .transitionProb()

Package: GBScleanR
Commit: abf75a3fc4798ee33301fab4151b5fdc9d401af7
Author: tomoyukif <f.tomoyuki@okayama-u.ac.jp>
Date: 2024-08-26 13:38:43 +0900
Commit message:

 Bug fix in .makeGenoParents()

Package: GBScleanR
Commit: ba40f17057ae52dc67f20bf778ad245d591abf8d
Author: tomoyukif <f.tomoyuki@okayama-u.ac.jp>
Date: 2024-08-23 16:09:07 +0900
Commit message:

 minor update in gbsrIPO.cpp

Package: GBScleanR
Commit: 0215b3e62f1d4880a6bc0ce0d0c962c1791e15fc
Author: tomoyukif <f.tomoyuki@okayama-u.ac.jp>
Date: 2024-08-21 23:51:25 +0900
Commit message:

 Minor update in Cpp codes for making it run faster

Package: GBScleanR
Commit: bb04a5e7f3dfe01c0dd699ed926ffeb166f00bb2
Author: tomoyukif <f.tomoyuki@okayama-u.ac.jp>
Date: 2024-08-21 22:45:07 +0900
Commit message:

 Minor update in the Vigerbi algorithm

Package: GBScleanR
Commit: 8bb1e91e84a1704f7ec250f3363292dfdefadca2
Author: tomoyukif <f.tomoyuki@okayama-u.ac.jp>
Date: 2024-08-21 21:38:28 +0900
Commit message:

 Fix a minor bug in counting up chromosomes in .sumUpBias().

Package: GBScleanR
Commit: 0da77b4d5d9d230471679d975cc558b82f77a9a1
Author: tomoyukif <f.tomoyuki@okayama-u.ac.jp>
Date: 2024-08-21 21:37:10 +0900
Commit message:

 Fix a minor bug in counting up chromosomes in .sumUpBias()

Package: GBScleanR
Commit: 766d57e960b222bd25e4068783b27c33a6eb6c39
Author: tomoyukif <f.tomoyuki@okayama-u.ac.jp>
Date: 2024-08-21 00:16:22 +0900
Commit message:

 Modify scripts to support polyploid populations.
Update to GBScleanR version 2

Package: GSVA
Commit: 07d85bacc6ed1bceccfaad82474898aeacb8b751
Author: Axel Klenk <axel.klenk@gmail.com>
Date: 2024-08-27 09:40:36 +0200
Commit message:

 export gsvaAnnotation() methods; add and export gsvaAnnotation<-() replacement methods

Package: GBScleanR
Commit: 9ad57d8633536143ff5578c2eb1168bab88c850c
Author: tomoyukif <f.tomoyuki@okayama-u.ac.jp>
Date: 2024-08-27 18:32:07 +0900
Commit message:

 version bump

Package: GBScleanR
Commit: ee53f8c119717a90bbfed1dfa4c710f77a5eb22f
Author: tomoyukif <f.tomoyuki@okayama-u.ac.jp>
Date: 2024-08-27 18:30:22 +0900
Commit message:

 Update in gbsrGDS2VCF() to solve the issue that an open GDS file cannot be copied on a Windows machine

Package: GBScleanR
Commit: 8c6e6df6e9f721247775f9b6ee65d1d5e159b590
Author: tomoyukif <f.tomoyuki@okayama-u.ac.jp>
Date: 2024-08-27 17:33:10 +0900
Commit message:

 Version bump

Package: GBScleanR
Commit: 9ddd706b359c7bbe15fce8191fcf5a5cd509c271
Author: tomoyukif <f.tomoyuki@okayama-u.ac.jp>
Date: 2024-08-27 17:29:04 +0900
Commit message:

 Fix a minor bug in getGenotype()

Package: GBScleanR
Commit: e21ffe1e421e1e6bb4aac974b1489fba7ce824e8
Author: tomoyukif <f.tomoyuki@okayama-u.ac.jp>
Date: 2024-08-07 20:06:43 +0900
Commit message:

 minor bug fix in getGenotype() to use the function in the GenovisR package.

Package: assorthead
Commit: 32478eb8cb858e9ea8582755eaf200dc367af297
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2024-08-26 22:11:21 -0700
Commit message:

 Updated all tatami libraries, added tatami_hdf5 library.

Package: assorthead
Commit: 9ab7ca956d5d4076884722082e89da129468ef29
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2024-08-26 21:02:26 -0700
Commit message:

 Added the subpar library.

Package: assorthead
Commit: f4f4b80744ed03f671ed5c14f342dca9ace402a9
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2024-08-21 21:36:10 -0700
Commit message:

 Vendored in the mumosa library.

Package: rawDiag
Commit: 3b96786a2b9975e2bdc7a9fa2a63a09aa0d71a98
Author: Christian Panse <cp@fgcz.ethz.ch>
Date: 2024-08-27 07:43:57 +0200
Commit message:

 add check in man page

Package: ggkegg
Commit: 88a401b5ef6e11be5e43688a72b4e4878c0ced8f
Author: noriakis <nori@hgc.jp>
Date: 2024-08-27 09:21:42 +0900
Commit message:

 v1.3.5 directory param in highlight_entities

Package: ggkegg
Commit: 042b0f35f7930654884d132a77b7ef10d249a105
Author: noriakis <nori@hgc.jp>
Date: 2024-08-27 09:19:51 +0900
Commit message:

 directory param in highlight_entities

Package: BiocSklearn
Commit: 6fe6348249371e8499b7c663a635f2362dbb8793
Author: vjcitn <stvjc@channing.harvard.edu>
Date: 2024-08-26 19:04:39 -0400
Commit message:

 Merge branch 'RELEASE_3_19' into devel

Package: BiocSklearn
Commit: 0ff22935c0cd0f8719c800846cbb44ed9b3d7791
Author: vjcitn <stvjc@channing.harvard.edu>
Date: 2024-08-26 14:29:34 -0400
Commit message:

 version bump and elimination of deprecated restfulSE dependence

Package: CARDspa
Commit: d18fb3946a39689ba798c0a79b4e72c2a4d5c83e
Author: Jing Fu <167481871+JINGFU9912@users.noreply.github.com>
Date: 2024-08-26 17:35:22 -0400
Commit message:

 update.version.number

Package: MouseFM
Commit: bfc5de14f504db728e5efae3c53eafd74512e2eb
Author: Matthias Munz <matthias.munz@gmx.de>
Date: 2024-08-27 00:55:49 +0200
Commit message:

 2024-08-27

Package: MouseFM
Commit: eb7e638e056c1123c0f7dffcd8563a59fe166db2
Author: Matthias Munz <matthias.munz@gmx.de>
Date: 2024-08-27 00:25:26 +0200
Commit message:

 2024-08-27

Package: MouseFM
Commit: 0f2c2aeaea0552ea24984b9aaa50459759ce1025
Author: Matthias Munz <matthias.munz@gmx.de>
Date: 2024-08-27 00:23:02 +0200
Commit message:

 2024-08-27

Package: MouseFM
Commit: 10be168bb5c27730fea54896586f75ac51a69a52
Author: Matthias Munz <matthias.munz@gmx.de>
Date: 2024-08-27 00:18:35 +0200
Commit message:

 2024-08-27

Package: PhyloProfile
Commit: d0a4e5fb560d8d2ef179092602429b22d490a7bb
Author: trvinh <trvinh@gmail.com>
Date: 2024-08-26 23:59:10 +0200
Commit message:

 more opts for umap

Package: PhyloProfile
Commit: e38772395f1738da629afb8a6931da59092a41c2
Author: trvinh <trvinh@gmail.com>
Date: 2024-08-01 16:52:34 +0200
Commit message:

 group label umap by taxa freq

Package: SVMDO
Commit: cbdf5dcdabccfd4fc65ef8b6327c2363692a0da2
Author: robogeno <erhanozer18@gmail.com>
Date: 2024-08-26 22:28:54 +0300
Commit message:

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

Package: SVMDO
Commit: d077904a7f4c9929748a7ff0dfce76e74574d0e8
Author: robogeno <erhanozer18@gmail.com>
Date: 2024-08-26 22:26:37 +0300
Commit message:

 update

Package: SVMDO
Commit: fbd0cf01a93bf522bcdc938b1bd91b1687891487
Author: robogeno <erhanozer18@gmail.com>
Date: 2024-08-26 19:01:01 +0300
Commit message:

 update

Package: SVMDO
Commit: 06f6e2685e8152bb898baea0376c4bb4c881c710
Author: robogeno <erhanozer18@gmail.com>
Date: 2024-08-26 07:12:46 +0300
Commit message:

 updated branch for enrichDO

Package: AnVIL
Commit: 72f102fc27cc588a888c13e76e5638fb2f2b9838
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2024-08-26 12:35:32 -0400
Commit message:

 version bump 1.17.13

Package: AnVIL
Commit: d864bb47fb0d6e9a95f95e4610a335ff4d84d13e
Author: LiNk-NY <marcel.ramos@roswellpark.org>
Date: 2024-07-31 13:06:11 -0400
Commit message:

 use native pipe over magrittr pipe

Package: AnVIL
Commit: 7404e2cd5c7b83af5576a7d00a2c95c154a1499c
Author: LiNk-NY <marcel.ramosperez@roswellpark.org>
Date: 2024-08-22 04:16:07 +0000
Commit message:

 update to changes in rapiclient

Package: AnVIL
Commit: 65550a49c054d3f35d385e7da20eedc728992ee4
Author: LiNk-NY <marcel.ramosperez@roswellpark.org>
Date: 2024-08-22 14:37:48 -0400
Commit message:

 version bump 1.17.12

Package: rawDiag
Commit: 082265b381abed6cbb1543c60b8caa30ed64a834
Author: Christian Panse <cp@fgcz.ethz.ch>
Date: 2024-08-26 16:29:12 +0200
Commit message:

 doc: beiing more verbose

Package: gDRcore
Commit: 211c1ec81b5ec21f5388490d582e1b25bafa969b
Author: Bartek <32614650+bczech@users.noreply.github.com>
Date: 2024-08-26 12:50:25 +0200
Commit message:

 Merge pull request #161 from gdrplatform/GDR-2643

Gdr 2643

Package: gDRcore
Commit: 73997b508c7c5e23b5985e8b3a57422da5a7d7d0
Author: czechb3 <bartosz.w.czech@gmail.com>
Date: 2024-08-26 10:44:26 +0200
Commit message:

 test: update unit tests

Package: gDRcore
Commit: 614b74864d99ec5624940b62b9f7c641c6d8507c
Author: czechb3 <bartosz.w.czech@gmail.com>
Date: 2024-08-26 08:49:22 +0200
Commit message:

 refactor: update as per review (III)

Package: gDRcore
Commit: 66f3ce425f97dbd6f2b3bf2ce3632a3f5b43cf01
Author: czechb3 <bartosz.w.czech@gmail.com>
Date: 2024-08-23 10:17:41 +0200
Commit message:

 refactor: update as per review

Package: gDRcore
Commit: 0955e32e16d4591fe657c6c0d7e59528568afbc6
Author: czechb3 <bartosz.w.czech@gmail.com>
Date: 2024-08-22 18:02:11 +0200
Commit message:

 ci: trigger build

Package: gDRcore
Commit: 1ebf34d2a17eb7c79d9e50e2fb6c98ed1e107085
Author: czechb3 <bartosz.w.czech@gmail.com>
Date: 2024-08-22 14:34:27 +0200
Commit message:

 refactor: update as per review

Package: gDRcore
Commit: 3a67c321e7cea22bff0a9e29cbdcb743c93661d2
Author: czechb3 <bartosz.w.czech@gmail.com>
Date: 2024-08-22 07:03:31 +0200
Commit message:

 refactor: update as per review

Package: gDRcore
Commit: 1ef7ff217510764f8f397d3ab6313358ebf795a6
Author: czechb3 <bartosz.w.czech@gmail.com>
Date: 2024-08-21 17:36:24 +0200
Commit message:

 ci: trigger build

Package: gDRcore
Commit: 9d677a321d15c382587cae1e52eccae97f52464b
Author: czechb3 <bartosz.w.czech@gmail.com>
Date: 2024-08-21 11:44:07 +0200
Commit message:

 refactor: update fun

Package: gDRcore
Commit: 874ffffcea3ee236da1503c9fbb2649f2428f6ac
Author: czechb3 <bartosz.w.czech@gmail.com>
Date: 2024-08-21 11:06:36 +0200
Commit message:

 refactor: fix identifiers

Package: gDRcore
Commit: 3ca6a648f4939b53e1e3053b5d0146f833af7528
Author: czechb3 <bartosz.w.czech@gmail.com>
Date: 2024-08-21 10:38:37 +0200
Commit message:

 ci: trigger build

Package: gDRcore
Commit: ed853e132743d1e11fd1f2260b677a65b9586e6b
Author: czechb3 <bartosz.w.czech@gmail.com>
Date: 2024-08-21 10:15:06 +0200
Commit message:

 refactor: restore identifier

Package: gDRcore
Commit: 023b96dfee2f5af8e5e6af881a650980284dfad6
Author: czechb3 <bartosz.w.czech@gmail.com>
Date: 2024-08-21 09:38:00 +0200
Commit message:

 chore: bump version and update NEWS.md

Package: gDRcore
Commit: a5e316066c626b6dc1023e8276e013b9ef3ebea8
Author: czechb3 <bartosz.w.czech@gmail.com>
Date: 2024-08-21 09:37:03 +0200
Commit message:

 test: add unit tests

Package: gDRcore
Commit: a90fdc4cbc08d253c5daed95eb04ef194267cda6
Author: czechb3 <bartosz.w.czech@gmail.com>
Date: 2024-08-21 09:36:58 +0200
Commit message:

 refactor: reoxygenate

Package: gDRcore
Commit: 395473e94bdd8c57e030dc2e3bf7221aba70571c
Author: czechb3 <bartosz.w.czech@gmail.com>
Date: 2024-08-21 09:36:46 +0200
Commit message:

 refactor: identify additional perturbations hidden in the secondary drug

Package: DOSE
Commit: 6fc5ecbcefbe0d470d5c9ce0f225ac014e27c794
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2024-08-26 18:24:17 +0800
Commit message:

 bump version

Package: DOSE
Commit: 585825b46d05bdbb2cef7ec6783024a45971fd59
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2024-08-26 18:09:47 +0800
Commit message:

 return NULL in GSEA if not genes can be mapped (2024-08-26, Mon, ReactomePA#43)

Package: ReactomePA
Commit: 3511f29ae6fd010e9d61805e1f35af733bde3c1e
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2024-08-26 18:12:14 +0800
Commit message:

 update url

Package: ReactomePA
Commit: 1936c2318f4449fa513cb7c4fe47db92ec3774c6
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2024-08-26 18:00:59 +0800
Commit message:

 bump version

Package: ReactomePA
Commit: 5034c0da76026b9e21c6f991b3848f9c22a320e6
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2024-08-20 17:15:26 +0800
Commit message:

 restore citation

Package: ReactomePA
Commit: 04899fcfd7128f68c4333cd1f36317c9d01aa30f
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2024-07-26 17:34:51 +0800
Commit message:

 update

Package: ReactomePA
Commit: de0f8d3728992caef488a2656fb5d88f5594df41
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2024-05-15 09:40:51 +0800
Commit message:

 update bioc version

Package: Pirat
Commit: 28cc73edfbeae483734b5ca8cc0b0c8ba9c82b55
Author: Samuel Wieczorek <samuel.wieczorek@cea.fr>
Date: 2024-08-26 11:00:07 +0200
Commit message:

 try to fix build error on Bioconductor

Package: rhinotypeR
Commit: de84cfd5b166894ef730b7571ada408c77705723
Author: marthaluka <mawia.martha@gmail.com>
Date: 2024-08-26 09:10:55 +0100
Commit message:

 change maintainer and remove redundant code

Package: GSVA
Commit: 49563e6a6f93c75539e215387318e88f028c2b98
Author: Robert Castelo <robert.castelo@upf.edu>
Date: 2024-08-26 08:26:46 +0200
Commit message:

 Fix documentation in vignette

Package: EnrichDO
Commit: 439befc54ce91f96eeca4bb13a341cfdb93a5002
Author: CHENGliang!@#123 <liangcheng@hrbmu.edu.cn>
Date: 2024-08-26 14:20:25 +0800
Commit message:

 modification

Package: EnrichDO
Commit: 3ee67e52ec6fc7922e138fdb05596cb1feadeec4
Author: CHENGliang!@#123 <liangcheng@hrbmu.edu.cn>
Date: 2024-08-26 14:20:06 +0800
Commit message:

 modification

Package: EnrichDO
Commit: 5bdc18b58a2354edfbb2cd5aeb6b70a6c4c6f04e
Author: CHENGliang!@#123 <liangcheng@hrbmu.edu.cn>
Date: 2024-08-26 14:18:32 +0800
Commit message:

 modification

Package: EnrichDO
Commit: e468c771a97788724c82e9b8a39260324589a040
Author: CHENGliang!@#123 <liangcheng@hrbmu.edu.cn>
Date: 2024-08-26 14:17:18 +0800
Commit message:

 modification

Package: EnrichDO
Commit: 419b98a0466b5967f08590b6970a9e6efdc7aeac
Author: CHENGliang!@#123 <liangcheng@hrbmu.edu.cn>
Date: 2024-08-26 14:16:19 +0800
Commit message:

 modification

Package: EnrichDO
Commit: 889fcd384919fd4f0347a8048247bf538a1a9a65
Author: CHENGliang!@#123 <liangcheng@hrbmu.edu.cn>
Date: 2024-08-26 14:14:45 +0800
Commit message:

 modification

Package: EnrichDO
Commit: 9720933b3b56fcd6d0860066920abb87a7709c5f
Author: CHENGliang!@#123 <liangcheng@hrbmu.edu.cn>
Date: 2024-08-26 14:06:00 +0800
Commit message:

 modification

Package: GSVA
Commit: 27a21fe12fd83c52dccfb9c135d2cb4e497cba18
Author: Robert Castelo <robert.castelo@upf.edu>
Date: 2024-08-26 08:18:26 +0200
Commit message:

 Setting default sparse=TRUE in the GSVA parameter object constructor. Updating documentation accordingly

Package: GSVA
Commit: 688b9507916ec14f074b421bbbeb88363a6f4fde
Author: Robert Castelo <robert.castelo@upf.edu>
Date: 2024-08-26 08:14:07 +0200
Commit message:

 Bump version

Package: GSVA
Commit: 3b065b1d35d3b2d5944063f48829d59e29172d09
Author: Robert Castelo <robert.castelo@upf.edu>
Date: 2024-08-26 08:13:29 +0200
Commit message:

 Merge pull request #195 from rcastelo/193-add-a-new-default-auto-argument-to-the-kcdf-parameter-in-the-gsva-method

New default auto argument to the kcdf parameter in the gsva method

Package: GSVA
Commit: 103f99b81b00e0685c15be3869d9cb8e90dd2fcb
Author: Robert Castelo <robert.castelo@upf.edu>
Date: 2024-08-26 07:50:07 +0200
Commit message:

 Implement logic behind kcdf="auto"

Package: GSVA
Commit: d6df7b3796f90a85e39cd4e10d39afa7efb69b7f
Author: Robert Castelo <robert.castelo@upf.edu>
Date: 2024-08-26 05:11:19 +0200
Commit message:

 Merge remote-tracking branch 'origin/devel' into 193-add-a-new-default-auto-argument-to-the-kcdf-parameter-in-the-gsva-method

Package: GSVA
Commit: 6e4f2e31c04301090b97301c5d6f7659115b5981
Author: Robert Castelo <robert.castelo@upf.edu>
Date: 2024-08-24 21:06:50 +0200
Commit message:

 Added "auto" as new default value to kcdf. Added new slot kcdfNoneMinSampleSize to the gsvaParam class and the corresponding parameter to the constructor function

Package: GSVA
Commit: 3c1ca9c02e0247c959a475aa1212a3168b6e7ea1
Author: Robert Castelo <robert.castelo@upf.edu>
Date: 2024-08-26 05:10:35 +0200
Commit message:

 Version bump

Package: GSVA
Commit: 0e2b69fed6068f5b60244fbc9578402df295826b
Author: Axel Klenk <72612834+axelklenk@users.noreply.github.com>
Date: 2024-08-25 23:29:39 +0200
Commit message:

 Merge pull request #194 from rcastelo/177-improve-annotation-mapping-through-readgmt

add annotation mapping for SummarizedExperiment and subclasses

Package: GSVA
Commit: fea96e36855bf06ae454fb21a0c4de3436bd83ba
Author: Axel Klenk <axel.klenk@gmail.com>
Date: 2024-08-25 23:09:18 +0200
Commit message:

 add annotation mapping for SummarizedExperiment and subclasses

Package: enrichplot
Commit: 1c5e810af4771833eaaf414b041c30ecb64c5a2c
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2024-08-26 09:24:24 +0800
Commit message:

 update example and bump version

Package: enrichplot
Commit: c7d162c84ef7fc6ac9942fee10ef4f7f50be43ca
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2024-08-19 20:33:35 +0800
Commit message:

 bug fixed

Package: clusterProfiler
Commit: 22fcc51de9763b8d7b9377772a2bc3e216c35d06
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2024-08-26 09:16:27 +0800
Commit message:

 bump version

Package: clusterProfiler
Commit: 04d651065127d4f7b028775aeb5212da2d75db0b
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2024-08-22 15:55:17 +0800
Commit message:

 update

Package: clusterProfiler
Commit: 27529b2777656e779ebfbcac20c40ddfc1b00956
Author: Guangchuang Yu <guangchuangyu@gmail.com>
Date: 2024-08-20 17:22:49 +0800
Commit message:

 update

Package: tidytof
Commit: ace89c75b5a2a64971cc206b0c3e8401881434a0
Author: Timothy Keyes <tkeyes@stanford.edu>
Date: 2024-08-25 16:12:33 -0700
Commit message:

 vignette bug fixes

Package: tidytof
Commit: cd770dc51ee54d1a464cf5f43500b6f973ac5d54
Author: Timothy Keyes <tkeyes@stanford.edu>
Date: 2024-08-25 15:53:28 -0700
Commit message:

 Update vignettes

Package: igvShiny
Commit: 3ff4472815a7df7340d6568e6e1221d1365e2287
Author: Arkadiusz Gladki <arkadiusz.gladki@contractors.roche.com>
Date: 2024-08-25 22:17:06 +0200
Commit message:

 Merge branch 'master' into devel

Package: igvShiny
Commit: 188c4557bc5cef614706325d32b882250b296f21
Author: Arek Gladki <41166437+gladkia@users.noreply.github.com>
Date: 2024-08-25 22:15:21 +0200
Commit message:

 Merge pull request #87 from gladkia/86-fix-bioc-builds-on-windows

86 fix bioc builds on windows

Package: igvShiny
Commit: e3d93f45cf56daac06c9b37f61bfe002b1120d12
Author: Arkadiusz Gladki <arkadiusz.gladki@contractors.roche.com>
Date: 2024-08-25 21:54:37 +0200
Commit message:

 chore: bump v+c

Package: igvShiny
Commit: 877007f95baf97ed17a2480aa5ae642c27fcbe3c
Author: Arkadiusz Gladki <arkadiusz.gladki@contractors.roche.com>
Date: 2024-08-25 21:54:18 +0200
Commit message:

 refactor: switch from Rcurl::url.exists to httr::http_error (Windows compatibility)

Package: igvShiny
Commit: cdee014ac56e5a1b298d65980270ec6d9fed8a55
Author: Arkadiusz Gladki <arkadiusz.gladki@contractors.roche.com>
Date: 2024-08-25 20:48:02 +0200
Commit message:

 Merge branch 'master' into devel

Package: igvShiny
Commit: 425cda0aa2b3eada3aafb5f38912ebaf5159b4b7
Author: Arek Gladki <41166437+gladkia@users.noreply.github.com>
Date: 2024-08-25 20:19:15 +0200
Commit message:

 Merge pull request #85 from gladkia/84-fix-bioc-errors-amazon-s3-url-unreachable

84 fix bioc errors amazon s3 url unreachable

Package: igvShiny
Commit: 6a5b02812fbab1d54fdc07d550a49910571a77d3
Author: Arkadiusz Gladki <arkadiusz.gladki@contractors.roche.com>
Date: 2024-08-25 20:01:45 +0200
Commit message:

 chore: update urls

Package: igvShiny
Commit: 60dc57f6fc232ccf0c35eb7606cd4facc5634d1a
Author: Arkadiusz Gladki <arkadiusz.gladki@contractors.roche.com>
Date: 2024-08-25 19:03:01 +0200
Commit message:

 chore: bump v+c

Package: igvShiny
Commit: 215aa3a485d79fe7b03e32e09a0f24d7f1e0190d
Author: Arkadiusz Gladki <arkadiusz.gladki@contractors.roche.com>
Date: 2024-08-25 19:02:48 +0200
Commit message:

 bugfix: stop using Amazon S3 URLs by default

Package: clustifyr
Commit: 7db8ab62895a91ee38495ffe47deaeac4466579f
Author: Kent Riemondy <kent.riemondy@gmail.com>
Date: 2024-08-25 09:30:01 -0600
Commit message:

 bump patch version

Package: SparseArray
Commit: 25ca66d1a685ff1677d3ff8eac48245d5d195e3d
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2024-08-25 05:46:33 -0700
Commit message:

 more tweaks to C code base

Package: sketchR
Commit: 86792d6fa973e96c00472350a3181818187bba76
Author: Charlotte Soneson <charlottesoneson@gmail.com>
Date: 2024-08-25 10:10:12 +0200
Commit message:

 Add environment for LinuxAarch64

Package: miRSM
Commit: ce35d0638c57efcaa78025d39077e1246a3a57fc
Author: zhangjunpeng411 <zhangjunpeng_411@yahoo.com>
Date: 2024-08-25 14:48:02 +0800
Commit message:

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

Package: miRSM
Commit: e86dad66fdf128fc9c95f0951da945a69b61e3ef
Author: zhangjunpeng411 <zhangjunpeng_411@yahoo.com>
Date: 2024-08-25 13:52:01 +0800
Commit message:

 Update

Package: miRspongeR
Commit: 7541548412c9fb72da2a011145d1835e69a34cfb
Author: zhangjunpeng411 <zhangjunpeng_411@yahoo.com>
Date: 2024-08-25 14:01:06 +0800
Commit message:

 Update

Package: miRspongeR
Commit: 10b145e5a98f389f1917aaffd1a98a994c8ad934
Author: zhangjunpeng411 <zhangjunpeng_411@yahoo.com>
Date: 2024-08-25 10:45:23 +0800
Commit message:

 Update

Package: miRSM
Commit: 5502518f4578bbb4aaef8c5ee79454dac609e8f7
Author: zhangjunpeng411 <zhangjunpeng_411@yahoo.com>
Date: 2024-08-25 13:52:01 +0800
Commit message:

 Update

Package: miRSM
Commit: 93dc329b67743393cbd000894a3d4dbb8f1d1262
Author: zhangjunpeng411 <zhangjunpeng_411@yahoo.com>
Date: 2024-08-25 13:50:32 +0800
Commit message:

 Merge branch 'devel' of github.com:zhangjunpeng411/miRSM into devel

Package: miRSM
Commit: 6f75e892b5cd33869b6b3b887ce055b55489ac4f
Author: zhangjunpeng411 <zhangjunpeng_411@yahoo.com>
Date: 2024-04-05 11:42:29 +0800
Commit message:

 Update

Package: miRspongeR
Commit: 66c468b48c84dc1bd4702ebe114d483f5dbfd7a3
Author: zhangjunpeng411 <zhangjunpeng_411@yahoo.com>
Date: 2024-08-25 10:45:23 +0800
Commit message:

 Update

Package: miRspongeR
Commit: 64124cff5decb8ab7afcd83978452bd71dfbc601
Author: J Wokaty <jwokaty@users.noreply.github.com>
Date: 2024-04-30 10:59:49 -0400
Commit message:

 Update

Package: biotidy
Commit: fa55944cc81f28917f93996af83478448fa935ae
Author: yun <yunyunpp96@outlook.com>
Date: 2024-08-25 06:01:24 +0800
Commit message:

 update

Package: biotidy
Commit: c9f21840b203c6013741bff9dbad192f332ba050
Author: yun <yunyunpp96@outlook.com>
Date: 2024-08-25 05:59:24 +0800
Commit message:

 try to fix much example verbose

Package: biotidy
Commit: 39c391a919459fa1fac653751916ff5a8af5f53e
Author: yun <yunyunpp96@outlook.com>
Date: 2024-08-25 05:54:45 +0800
Commit message:

 reduce verbose example messages

Package: rSWeeP
Commit: c21fcbd6a0fb19a167b9a5044855e12f7b926024
Author: Camila Pereira Perico <camilapp94@gmail.com>
Date: 2024-08-24 18:01:35 -0300
Commit message:

 adding a check

Package: GSVA
Commit: 8078ba1db1908d92004722dbad063b67615c26b2
Author: Robert Castelo <robert.castelo@upf.edu>
Date: 2024-08-24 16:31:57 +0200
Commit message:

 removed obsolete unit test on HDF5Array input

Package: BG2
Commit: b451283471b73d658b660d8315f873fca2d09e5a
Author: jwilliams10 <jwilliams_winona@hotmail.com>
Date: 2024-08-24 09:37:14 -0400
Commit message:

 Updated Documentation

Package: scMultiSim
Commit: 72b25f79dd3419db2924c28bac49db1cf3293410
Author: Hechen Li <lhc199652@gmail.com>
Date: 2024-08-23 23:52:14 -0400
Commit message:

 Remove devtools::load_all call

Package: miRBaseConverter
Commit: f0992ee76028712ba91d4612fbb432803a7eda80
Author: taoshengxu <taosheng.x@gmail.com>
Date: 2024-08-24 09:46:37 +0800
Commit message:

 fix errors in 20240824_ok

Package: chevreul
Commit: 2ab03397c103960e00e7111861d9b2a2e3d7c374
Author: whtns <kevin.stachelek@gmail.com>
Date: 2024-08-23 15:26:41 -0700
Commit message:

 trigger rebuild

Package: chevreul
Commit: 000857d8589cdaf4e9fc44417810d713418c5501
Author: whtns <kevin.stachelek@gmail.com>
Date: 2024-08-23 15:26:23 -0700
Commit message:

 remove bad examples

Package: chevreul
Commit: c9cbffe669e65d097f3ef73959b104ab27180a92
Author: whtns <kevin.stachelek@gmail.com>
Date: 2024-08-23 15:25:44 -0700
Commit message:

 trigger rebuild

Package: chevreul
Commit: ea7bdcbc2ca4d1b44a7b9193d6fe0808f60f2859
Author: whtns <kevin.stachelek@gmail.com>
Date: 2024-08-23 15:23:33 -0700
Commit message:

 remove exports of long-running examples

Package: visiumStitched
Commit: edda4cb14f9ef1746069b03ea121c5371a3b4755
Author: Nick-Eagles <nick.eagles@libd.org>
Date: 2024-08-23 16:46:21 -0400
Commit message:

 Increment version number to 0.99.7

Package: visiumStitched
Commit: 77ffe10d05ae487402f4cf573e1f6eb8caeef6e9
Author: Nick-Eagles <nick.eagles@libd.org>
Date: 2024-08-23 16:45:22 -0400
Commit message:

 Make a test shorter to run by using smaller data

Package: visiumStitched
Commit: 46bc9d5c7dff78d0f0eb34f0e5f3e6a404634f50
Author: Nick-Eagles <nick.eagles@libd.org>
Date: 2024-08-23 16:24:59 -0400
Commit message:

 Make 'spe_to_seurat()' example faster by running on smaller subsets of data

Package: isomiRs
Commit: 463fad98d07e253ef65efdb4b36404b25578ea24
Author: Lorena Pantano <lorena.pantano@gmail.com>
Date: 2024-08-23 15:23:18 -0400
Commit message:

 merge

Merge branch 'main' into devel

# Conflicts:
#	DESCRIPTION
#	NEWS

Package: isomiRs
Commit: 45df1aa559784df63d00354e2dfcd563225d7a35
Author: Lorena Pantano <lorena.pantano@gmail.com>
Date: 2024-08-23 15:17:34 -0400
Commit message:

 fix https://github.com/lpantano/isomiRs/issues/18

Package: miRBaseConverter
Commit: 604739212f0a665c4f7a1e02408addccc072fe52
Author: taoshengxu <taosheng.x@gmail.com>
Date: 2024-08-24 01:33:16 +0800
Commit message:

 fix error2 in 20240824

Package: miRBaseConverter
Commit: d6e4b69d62f91ad13a728dac5184da063c5b3034
Author: taoshengxu <taosheng.x@gmail.com>
Date: 2024-08-24 01:17:10 +0800
Commit message:

 fix error in 20240824

Package: visiumStitched
Commit: 79b3a1494ead849add6f4e062444d9f531135c3b
Author: Nick-Eagles <nick.eagles@libd.org>
Date: 2024-08-23 13:17:13 -0400
Commit message:

 Increment version number to 0.99.6

Package: visiumStitched
Commit: 68221dd0d0870004abcc4533924cb872559c7750
Author: Nick-Eagles <nick.eagles@libd.org>
Date: 2024-08-23 13:00:21 -0400
Commit message:

 Use temporary files to simulate persistence of objects across examples and tests

Package: visiumStitched
Commit: 4e5e6ad4b40d233413c9cc80b19bcd8fd2f7ee74
Author: Nick-Eagles <nick.eagles@libd.org>
Date: 2024-08-23 12:18:09 -0400
Commit message:

 Experiment with using temporary files to have objects persist across examples

Package: visiumStitched
Commit: 4233f47e3f2c1267633bff4ba4ddd30c5abb4403
Author: Nick-Eagles <nick.eagles@libd.org>
Date: 2024-08-23 11:43:09 -0400
Commit message:

 Try 'dontrun' instead of conditional code (sanity check)

Package: visiumStitched
Commit: a4739b5442d7bea357e8d53f093f0d99ae2f7d64
Author: Nick-Eagles <nick.eagles@libd.org>
Date: 2024-08-23 10:44:13 -0400
Commit message:

 Cache 'sample_info' in memory to reduce time for examples and tests to run

Package: visiumStitched
Commit: 35a8f0e888c6a5958b0331352459b955e04fecb3
Author: Nick-Eagles <nick.eagles@libd.org>
Date: 2024-08-23 10:16:34 -0400
Commit message:

 Cache the 'spe' object in memory to reduce R CMD CHECK time

Package: ontoProc
Commit: f6f2039c5ab9b9e1d85583e2fae6a4601e2a5a2c
Author: vjcitn <stvjc@channing.harvard.edu>
Date: 2024-08-23 12:59:59 -0400
Commit message:

 add ignore

Package: ontoProc
Commit: 4d9baeac35a5cd35686333ae5070fb9816f28522
Author: vjcitn <stvjc@channing.harvard.edu>
Date: 2024-08-23 12:58:58 -0400
Commit message:

 drop the .github folder for bioc git repo

Package: ontoProc
Commit: 1ebbaa2a5b5a81f3646fc97c43ea9a45057a2e76
Author: vjcitn <stvjc@channing.harvard.edu>
Date: 2024-08-03 07:47:42 -0400
Commit message:

 dropping docker and pages action components (pages doesn't seem to work)

Package: ontoProc
Commit: acbab0331de40829a474b154e08ef4b6d9f8b1ef
Author: vjcitn <stvjc@channing.harvard.edu>
Date: 2024-08-03 06:57:01 -0400
Commit message:

 fiddle with python

Package: ontoProc
Commit: 0008b051f5ebf3b3cc6cbf0e571b2218cffe2789
Author: vjcitn <stvjc@channing.harvard.edu>
Date: 2024-08-03 06:41:16 -0400
Commit message:

 reposition owlready2 installation via py_install

Package: ontoProc
Commit: 8f20a5b32d34ae527ca680e5967c27b044494807
Author: vjcitn <stvjc@channing.harvard.edu>
Date: 2024-08-03 06:23:48 -0400
Commit message:

 use py_install in action

Package: ontoProc
Commit: 7f9c952f26eed55c04b5d98b8b79b0e9e53aac32
Author: vjcitn <stvjc@channing.harvard.edu>
Date: 2024-07-14 15:28:43 -0400
Commit message:

 trying to get owlready2 for vignette

Package: ontoProc
Commit: 80cd04114517a61ee3e8edcb58c974be9a451b90
Author: vjcitn <stvjc@channing.harvard.edu>
Date: 2024-07-13 04:35:11 -0400
Commit message:

 Merge branch 'devel' of https://github.com/vjcitn/ontoProc into devel

Package: ontoProc
Commit: edf6e91c9c850d6293fd37a4b8fc39662d442c2b
Author: Vince Carey <stvjc@channing.harvard.edu>
Date: 2024-07-12 22:29:36 -0400
Commit message:

 Update owlents.Rmd

Package: chevreul
Commit: 86ab12548fe88c90b3b58d0079584c3c25992e9a
Author: whtns <kevin.stachelek@gmail.com>
Date: 2024-08-23 09:58:12 -0700
Commit message:

 move data loading to helper file; trigger rebuild

Package: clustifyr
Commit: 8224ebc85c6edc1a8b7ca9a407cbf1770e29281c
Author: Kent Riemondy <kent.riemondy@gmail.com>
Date: 2024-08-23 09:09:40 -0600
Commit message:

 Upkeep (#407)

* update email

* unexport object_loc_lookup

* T -> TRUE

* add value info

* add sessioninfo

* fix more notes

* run styler

* test against devel container

* forgot to save

Package: AnVILGCP
Commit: 96d450877b904eb94bccc44c8580387895d2c52f
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2024-08-23 12:05:19 -0400
Commit message:

 version bump 0.99.34

Package: AnVILGCP
Commit: 0587a67468aa08a9c25195c7eb7c813297258f26
Author: LiNk-NY <marcel.ramosperez@roswellpark.org>
Date: 2024-08-20 16:18:53 -0400
Commit message:

 add lifeCycle function to defunct functions and document

Package: rtracklayer
Commit: 32cd3c296c7609c44cad40eb38ff5e51a7dc95fa
Author: Michael Lawrence <michafla@gene.com>
Date: 2024-08-23 08:05:39 -0700
Commit message:

 Merge pull request #130 from sanchit-saini/ubuntu-libcurl-1

Add checks for remaining MACROS to handle older libcurl