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GIT Logs

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

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Package: scrapper
Commit: d006bee162a6e02313b1dc9f473a6c81402d300c
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2025-05-13 13:05:58 -0700
Commit message:

 Bugfix for runAllNeighborSteps when no steps are actually requested.
Package: biocmake
Commit: f8f33508aa2564d47babade8a0fdcc950040faa1
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2025-05-13 09:34:34 -0700
Commit message:

 Sanitize weird Cmake version strings (and fail gracefully otherwise).
Package: anglemania
Commit: a2b9d34df9f1a01f5dcaffd968293f1ac06fb672
Author: kollo97 <aaron.kollo@gmail.com>
Date: 2025-05-13 16:41:46 +0200
Commit message:

 Fix bioconductor build report comments
Package: BiocFileCache
Commit: 945d9900d07009618cbfcd3becb911599b44e773
Author: lshep <lori.shepherd@roswellpark.org>
Date: 2025-05-13 08:33:48 -0400
Commit message:

 Merge pull request #63 from lshep/progressBar

Progress bar
Package: BiocFileCache
Commit: 0051921ef239882241593fd20d3cf6cbb4139176
Author: lshep <lori.shepherd@roswellpark.org>
Date: 2025-05-13 08:26:37 -0400
Commit message:

 Consistency and clean up
Package: BiocFileCache
Commit: 2cc73dc5fabb94c764cb53b2e44139c3c1806e8e
Author: lshep <lori.shepherd@roswellpark.org>
Date: 2025-05-12 13:48:16 -0400
Commit message:

 Merge branch 'progressBar' of github.com:lshep/BiocFileCache into progressBar
Package: BiocFileCache
Commit: 1079a7ce74d531fd121ac831ed6623e35d72b45a
Author: lshep <lori.shepherd@roswellpark.org>
Date: 2025-05-12 13:34:33 -0400
Commit message:

 Add progress argument to control progress bar during interactive session
Package: BiocFileCache
Commit: 7897afb09ccabb4723c1bf7fc9c27d5697a3918b
Author: lshep <lori.shepherd@roswellpark.org>
Date: 2025-05-12 13:34:33 -0400
Commit message:

 Add progress argument to control progress bar during interactive session
Package: DNAfusion
Commit: 2308eec2b44b44154095c705eb23e89a300877ab
Author: Christoffer Trier Månsson <ctm@clin.au.dk>
Date: 2025-05-13 13:26:04 +0200
Commit message:

 Increasing speed of find_variants()
Package: anglemania
Commit: f27399fb947adfa0de6134493e737658ca591af5
Author: kollo97 <aaron.kollo@gmail.com>
Date: 2025-04-16 15:57:08 +0200
Commit message:

 make variable_genes_overlap use SelectIntegrationFeatures
Package: anglemania
Commit: 8052de59deae277d8941493bd72e026f04c5d854
Author: kollo97 <aaron.kollo@gmail.com>
Date: 2025-04-15 14:55:35 +0200
Commit message:

 fix select_genes when no genes passed thresholds
Package: anglemania
Commit: 7e9fffc200903b3cffa413336f7ecc761f626f99
Author: kollo97 <aaron.kollo@gmail.com>
Date: 2025-04-09 12:34:38 +0200
Commit message:

 bump version for Bioconductor package check
Package: anglemania
Commit: 6bbf8ca2b326521204d6390af0779d79301e399b
Author: kollo97 <aaron.kollo@gmail.com>
Date: 2025-04-09 12:17:09 +0200
Commit message:

 Fix error when dataset_key = NULL
Package: anglemania
Commit: f7a6391f322863eec8f9f3354e98214f5dfb9187
Author: kollo97 <aaron.kollo@gmail.com>
Date: 2025-04-08 11:45:27 +0200
Commit message:

 remove renv stuff
Package: anglemania
Commit: ea2e9e00b365dd318edcabe4fbf16a23bac3444d
Author: kollo97 <aaron.kollo@gmail.com>
Date: 2025-04-08 11:44:34 +0200
Commit message:

 update tests after modifying extract_angles and factorise
Package: anglemania
Commit: ac08210272ed99a23738a180f5bbe4572a16e233
Author: kollo97 <aaron.kollo@gmail.com>
Date: 2025-04-08 11:40:13 +0200
Commit message:

 Test whether there are cells in the matrix with 0 counts
Package: anglemania
Commit: 2ec56d769f40b9e4650959f0affabf424e9f5a8e
Author: kollo97 <aaron.kollo@gmail.com>
Date: 2025-04-08 11:39:46 +0200
Commit message:

 Update documentation. After adding normalization_method.
Package: anglemania
Commit: 2fbcc45f33c0bc6f2dc875a8038216847be4628a
Author: vfranke <vedran.franke@gmail.com>
Date: 2025-04-04 18:20:27 +0200
Commit message:

 Corrected denominator and imroved styling
Package: anglemania
Commit: 6d592d3f9893116fa63b6b9a7c41924d38b38749
Author: vfranke <vedran.franke@gmail.com>
Date: 2025-04-04 18:19:10 +0200
Commit message:

 normalization -permutation correction

normalization was done before permutation, which is ok for column permutation
but breaks row permuation

also added normalization through regression
Package: anglemania
Commit: 7c9f0ba9118f419a40e7d0b743b1045b462c24c0
Author: vfranke <vedran.franke@gmail.com>
Date: 2025-03-19 15:48:54 +0100
Commit message:

 Assays -> Seurat::Assays
Package: anglemania
Commit: 19aff5d01bacc3b7d78f4cabf49e0aba5de54feb
Author: vfranke <vedran.franke@gmail.com>
Date: 2025-03-11 12:03:30 +0100
Commit message:

 permutation function expansion

factorise:
    - can take row and column permutations
    - enabled non-zero value permutation
Package: anglemania
Commit: 7483154d5e8ca3f2a70e3e068d3d5fe15f454e9e
Author: kollo97 <aaron.kollo@gmail.com>
Date: 2025-04-02 16:55:01 +0200
Commit message:

 exchange load_all() for library()
Package: anglemania
Commit: 57271e1cbd08fff4c0ef042048660641df1dc990
Author: kollo97 <aaron.kollo@gmail.com>
Date: 2025-04-02 16:37:40 +0200
Commit message:

 add matrixStats to suggests, remove from imports
Package: anglemania
Commit: dddd8f508afa1d489f2bc5f7893f75961a286e92
Author: kollo97 <aaron.kollo@gmail.com>
Date: 2025-04-02 16:02:51 +0200
Commit message:

 devtools::document
Package: anglemania
Commit: 516cfc0f94d0a4057c64c4a7d3df5da624e148f9
Author: kollo97 <aaron.kollo@gmail.com>
Date: 2025-04-02 16:02:33 +0200
Commit message:

 change license to gpl-3 to accommodate bigstatsr functions
Package: anglemania
Commit: a5f1ea134d3d916845322a7e754c42890e23d838
Author: kollo97 <aaron.kollo@gmail.com>
Date: 2025-04-02 16:02:12 +0200
Commit message:

 add matrixStats as dependency for tests
Package: anglemania
Commit: 558e8c97a78c05f6f4c5f65103066e8d43827cad
Author: kollo97 <aaron.kollo@gmail.com>
Date: 2025-04-02 16:01:17 +0200
Commit message:

 remove unnecessary cpp functions. add scaleK from bigstatsr
Package: anglemania
Commit: 4168d4717abf1439cbe4730df1b0c1ab3d07306e
Author: kollo97 <aaron.kollo@gmail.com>
Date: 2025-04-02 16:00:45 +0200
Commit message:

 update tests
Package: anglemania
Commit: b418f14cf37643cd998045f7bb44caa223cae01f
Author: kollo97 <aaron.kollo@gmail.com>
Date: 2025-04-02 16:00:31 +0200
Commit message:

 update documentation2
Package: anglemania
Commit: 825de2a766816f9e7e8ced7ff952e56ff91de909
Author: kollo97 <aaron.kollo@gmail.com>
Date: 2025-04-02 15:59:36 +0200
Commit message:

 update documentation
Package: anglemania
Commit: f60dee11f6482dda998bd9fec104d59ca324eeaf
Author: kollo97 <aaron.kollo@gmail.com>
Date: 2025-04-02 15:59:26 +0200
Commit message:

 update example
Package: anglemania
Commit: 695003d8bcbbc1e0ab28bea85a71271017ea9c53
Author: kollo97 <aaron.kollo@gmail.com>
Date: 2025-04-02 15:59:07 +0200
Commit message:

 remove DIEM
Package: anglemania
Commit: 19b569964a24dfd5018fc95db655fc9d3f7b08d4
Author: kollo97 <aaron.kollo@gmail.com>
Date: 2025-04-02 15:58:52 +0200
Commit message:

 add support for missing features in samples by adapting bigstatsr functions
Package: anglemania
Commit: 809a949bc07b26b3ec3a9ad6cfd48d8f541c840d
Author: kollo97 <aaron.kollo@gmail.com>
Date: 2025-04-02 15:57:48 +0200
Commit message:

 update vignettes
Package: anglemania
Commit: e020276ae4559abdfb2957551869cead7924da2e
Author: kollo97 <aaron.kollo@gmail.com>
Date: 2025-04-02 15:57:31 +0200
Commit message:

 Refactor create_anglemania_objects. re-implement support for SCE and lists of SCE and Seurat objects.
Package: anglemania
Commit: c06868423c8387fb021f8ae227295c5a59f1866e
Author: vfranke <vedran.franke@gmail.com>
Date: 2025-03-07 16:39:27 +0100
Commit message:

 reversal to bigstatsr::big_cor

commented out angl_cor for  bigstatsr::big_cor calculation
Package: anglemania
Commit: a96cd64afe6d56aa9cd1d6bd70897ce60c017a32
Author: vfranke <vedran.franke@gmail.com>
Date: 2025-03-07 16:36:05 +0100
Commit message:

 anglemanise_utils.R: updated select_genes + handling NAN

select_genes:
	updated to prefiltered table - not checked completely

mat_sn_zscore calculation added replace_with_na
Package: anglemania
Commit: 7729aa9cbcf6dbf02042b1f202ac38c5077142d3
Author: vfranke <vedran.franke@gmail.com>
Date: 2025-03-07 16:31:57 +0100
Commit message:

 prefilter threshold + comment code

anglemania:
	added prefilter threshold to the
	params

commented out:
	list_stats(angl)$sn_zscore[list_stats(angl)$sds_zscore == 0] = 0
This should be covered now in the get_list_stats function
Package: anglemania
Commit: 05b784f81f4663f10a16219cae1a1e1a5d10dd24
Author: vfranke <vedran.franke@gmail.com>
Date: 2025-03-05 10:41:18 +0100
Commit message:

 argument typos
Package: anglemania
Commit: 96fd561f802c857cc754a4a2c95c07b6b609535e
Author: vfranke <vedran.franke@gmail.com>
Date: 2025-03-05 09:44:22 +0100
Commit message:

 anglemania_object -> angl
Package: anglemania
Commit: 17ffa09d7bae96ac85cf8204c569b33790dc35fc
Author: vfranke <vedran.franke@gmail.com>
Date: 2025-03-05 09:27:42 +0100
Commit message:

 making variables uniform
Package: anglemania
Commit: 1ee261493942fc2713f2b0da2ef3d26b617a508c
Author: vfranke <vedran.franke@gmail.com>
Date: 2025-02-27 17:39:11 +0100
Commit message:

 objects.R: support for nonuniform features

supports features that are not present in all cells
Package: anglemania
Commit: 26eeb40edd7998441642c2153c7195c61deee20e
Author: vfranke <vedran.franke@gmail.com>
Date: 2025-02-21 14:59:08 +0100
Commit message:

 support for nonuniform features accross samples

The package supports features that are not present
in all samples.

Datasets weighting has been set to mean of 1 for
all samples
Package: anglemania
Commit: 33dc2ee64f686ec51184c8c6523caff4f7a762a1
Author: vfranke <vedran.franke@gmail.com>
Date: 2024-12-11 20:01:23 +0100
Commit message:

 create_anglemaniaObject: typo
Package: anglemania
Commit: 29276e9dc859df30c089b2ffacb2380e8e7dd3f0
Author: vfranke <vedran.franke@gmail.com>
Date: 2024-12-11 19:58:49 +0100
Commit message:

 objects.R: assay as param and weights only if datasets > 1

create_anglemaniaObject:
    - added assay as a paramter
    - assay also saved as a slot

matrix_list:
    - calculates weights only if dataset number is
    greater than 1
Package: anglemania
Commit: 94759a7cd0f3e1f61f7a2c39d735e9d203b83b3a
Author: vfranke <vedran.franke@gmail.com>
Date: 2024-12-09 17:56:17 +0100
Commit message:

 permutation function expansion

factorise:
    - can take row and column permutations
    - enabled non-zero value permutation
Package: anglemania
Commit: f93901659be8c0426c01791988221ffaea107499
Author: vfranke <vedran.franke@gmail.com>
Date: 2024-12-09 17:53:58 +0100
Commit message:

 anglemanise_utils: mean calculation and list_stats

get_list_stats:
    - calculates per gene mean and variance
    - uses unbiased weighted variance calculation

get_dstat:
    - per gene mean and variance calculation
Package: anglemania
Commit: 5cc2c28d3b57fd839efedae9acb05d11c39be466
Author: vfranke <vedran.franke@gmail.com>
Date: 2024-12-04 16:52:45 +0100
Commit message:

 select_genes: added possibility to select positive or negative zscore
Package: rigvf
Commit: 646bc71e57d433ea69e7c8287627b565128f4e29
Author: Mike Love <mikelove@users.noreply.github.com>
Date: 2025-05-12 14:29:15 -0400
Commit message:

 version bump
Package: rigvf
Commit: e11bff1ca568ca6eecdd0b5cd0d548482db9a53d
Author: Mike Love <mikelove@users.noreply.github.com>
Date: 2025-05-12 14:28:57 -0400
Commit message:

 fix for IGVF Catalog API changes
Package: GenomicDataCommons
Commit: b59db7b7a5c08b90bb06caf6f800e6fe5b2b25c4
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-05-12 14:24:20 -0400
Commit message:

 version bump 1.33.1
Package: GenomicDataCommons
Commit: 7876d434121cfa02e5e818ecdc17c8cca154d0a3
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-05-12 14:24:12 -0400
Commit message:

 relax strictness in clinical_data checks
Package: doppelgangR
Commit: c539a22adb687d2046a799b849e7784cb2ce611c
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-05-12 12:27:22 -0400
Commit message:

 version bump 1.37.3
Package: doppelgangR
Commit: c112b6d1b2e5384a5cb6fd1e20b0d2101a594abf
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-05-12 12:25:48 -0400
Commit message:

 add fig.cap to single pair plot
Package: doppelgangR
Commit: 04d9265ecd63d20801702e4b961cac814a7f79df
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-05-12 12:25:27 -0400
Commit message:

 update README.md
Package: doppelgangR
Commit: 06a19036bd997f8ccc6b5e1bb18e4709cda8ff7b
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-05-12 12:15:49 -0400
Commit message:

 version bump 1.37.2
Package: doppelgangR
Commit: 7e8f9009e9de6f8d7c300f2090b4e14a96574bb0
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-05-12 12:15:37 -0400
Commit message:

 add abstract to vignette
Package: doppelgangR
Commit: 2501c3bdf053d8036cef0fb10f214fc50fb47ac1
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-05-12 12:15:19 -0400
Commit message:

 move scripts to inst/scripts
Package: doppelgangR
Commit: 596ff2c54917dd87e5cc23f7fe95a45d491de96f
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-05-12 12:10:09 -0400
Commit message:

 add pkgdown website to DESCRIPTION
Package: doppelgangR
Commit: 3cba9ad55c73a17b326670467dcb9f8719e66751
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-05-12 12:09:55 -0400
Commit message:

 move paper to waldronlab/doppelgangR_paper
Package: doppelgangR
Commit: 625ea9d11ce53f4ed78c5294189048fe02d34810
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-05-12 11:48:51 -0400
Commit message:

 version bump 1.37.1
Package: doppelgangR
Commit: 6a6df9064b07650da17fa553c56335952f99aeac
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-05-12 11:48:44 -0400
Commit message:

 rename and reformat CHANGELOG to NEWS.md
Package: doppelgangR
Commit: e7ef00e28c5e755621984054e418eac01ab9f9b9
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-05-12 11:44:27 -0400
Commit message:

 remove old GHA check.yml
Package: doppelgangR
Commit: 87c1b73e0f25cb3cd91069c9ae9350c3b8b5d776
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-05-12 11:43:16 -0400
Commit message:

 add _pkgdown.yml and .github/workflows/pr_check.yml GHA
Package: doppelgangR
Commit: 7f24cadf1d1864b1a98e8ecce9097d4c16813f42
Author: Marcel Ramos Pérez <LiNk-NY@users.noreply.github.com>
Date: 2025-01-06 16:26:50 -0500
Commit message:

 set actions/cache to v4
Package: regioneR
Commit: 0ac9d2a75775bbc87aec0353ac3c9ad557075fff
Author: Bernat <bernatgel@gmail.com>
Date: 2025-05-12 18:07:52 +0200
Commit message:

 Version Bump
Package: regioneR
Commit: c73f5883c53e2a9cf3f00851be20818224b4121a
Author: Bernat <bernatgel@gmail.com>
Date: 2025-05-12 18:05:34 +0200
Commit message:

 Merge commit '1d3f0977654987c398eb60fea0485dd45113c40e' into devel
Package: regioneR
Commit: 1d3f0977654987c398eb60fea0485dd45113c40e
Author: Bernat <bernatgel@gmail.com>
Date: 2025-05-12 18:05:20 +0200
Commit message:

 removed scipen

Removed scipen from plotLocalZScoreResults, since it was throwing an error in Bioc machines
Package: BenchHub
Commit: 9f1e602f81c4a576713b6378de08ff4dc08ecb5f
Author: Nicholas Robertson <nickrrrr@gmail.com>
Date: 2025-05-12 16:51:49 +0200
Commit message:

 bump version
Package: GSAR
Commit: 7bf48e7aaab1c639e43fb1758aa5149751d79e11
Author: yrahmatallah <yrahmatallah@uams.edu>
Date: 2025-05-12 09:50:21 -0500
Commit message:

 commit1-12-May-2025
Package: BenchHub
Commit: 5f820e630ed5a84f920ad6e518ca6f3c053e88e9
Author: Yue Cao <yue.cao@sydney.edu.au>
Date: 2025-05-08 14:49:46 +1000
Commit message:

 add more explanation of Trio to vignette 1
Package: BenchHub
Commit: 505ec0fbb926c7634b5fb3a99d090b0981c9fe7c
Author: Yue Cao <yue.cao@sydney.edu.au>
Date: 2025-05-08 14:32:26 +1000
Commit message:

 update name from TrioR to trio  in vignette 2
Package: tximeta
Commit: a4604bd10b4dbeb9cc247dc67b6fb16e05039efd
Author: Mike Love <mikelove@users.noreply.github.com>
Date: 2025-05-12 09:40:15 -0400
Commit message:

 version bump
Package: tximeta
Commit: 84b63d13e4000e165295d6f9b9b3bf795a09baa7
Author: Mike Love <mikelove@users.noreply.github.com>
Date: 2025-05-12 09:39:33 -0400
Commit message:

 merge
Package: tximeta
Commit: 81e2042c0a8823c2a3480ec93470a5380af544fd
Author: Mike Love <mikelove@users.noreply.github.com>
Date: 2025-05-12 09:39:15 -0400
Commit message:

 Merge branch 'devel' of git.bioconductor.org:packages/tximeta into devel
Package: tximeta
Commit: 25f78c33bae2ee739872cd450c9b3f8131af4ca2
Author: Mike Love <mikelove@users.noreply.github.com>
Date: 2025-05-12 09:38:29 -0400
Commit message:

 GENCODE 48 (H.s.), M37 (M.m), and Ensembl 114
Package: fastreeR
Commit: 99c939c007c9ffd79226a6cc27e8b090650d8695
Author: Anestis Gkanogiannis <ganoyan@gmail.com>
Date: 2025-05-12 16:14:48 +0400
Commit message:

 Update backend and CLI
Package: MOSClip
Commit: 77d7d96f63289dd0b23e1851fe7edf261745da5f
Author: Anna Bortolato <anna.bortolato@unipd.it>
Date: 2025-05-12 11:44:45 +0200
Commit message:

 version bump in devel
Package: MOSClip
Commit: e5de40191644138bb24a25ca341a09a205ded08e
Author: Anna Bortolato <anna.bortolato@unipd.it>
Date: 2025-05-12 11:43:38 +0200
Commit message:

 bug fix: correct pathway names in test Supertest
Package: scviR
Commit: 5dd474c03e91e8cbab6515442b8d361f71f75ec6
Author: vjcitn <stvjc@channing.harvard.edu>
Date: 2025-05-12 05:55:48 -0400
Commit message:

 passing check on linux, extirpation of events using obsolete pytorch model object
Package: scviR
Commit: 47c22949d7e564e8a2e2b32a7f31eca0f9b309c9
Author: vjcitn <stvjc@channing.harvard.edu>
Date: 2025-05-11 17:32:24 -0400
Commit message:

 remove swap file
Package: scviR
Commit: c1603fa35be6e1926ff10562b4fb406584a2778d
Author: vjcitn <stvjc@channing.harvard.edu>
Date: 2025-05-11 17:31:26 -0400
Commit message:

 various changes including deprecation and light dependency spec in basilisk.R
Package: ggspavis
Commit: 6f36d812735a7db617025b0ea80e5057f7ab069a
Author: Lukas Weber <lmweb012@gmail.com>
Date: 2025-05-11 14:30:03 -0400
Commit message:

 version
Package: ggspavis
Commit: d2407aaa3a575a127ce8a422ea13130fa29bb2d3
Author: Lukas Weber <lmweb012@gmail.com>
Date: 2025-05-11 14:29:56 -0400
Commit message:

 update NEWS for function name changes
Package: ggspavis
Commit: ff8e3906e0d0ea6bae5b5b3284fc53974f768cc3
Author: Lukas Weber <lmweb012@gmail.com>
Date: 2025-05-11 14:29:30 -0400
Commit message:

 update function names in vignette
Package: ggspavis
Commit: f1bc24654da3cf08af2828fe3c4d4ebca17dffc1
Author: Lukas Weber <lmweb012@gmail.com>
Date: 2025-05-11 14:29:10 -0400
Commit message:

 rename functions to plotCoords() and plotObsQC()
Package: fastreeR
Commit: 73dae73240e25e6f20953830dc6c5168b962046a
Author: Anestis Gkanogiannis <ganoyan@gmail.com>
Date: 2025-05-11 18:10:45 +0400
Commit message:

 Update backend and CLI
Package: basilisk
Commit: 955d71dcf1175cc259b004e62252778a026e966d
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2025-05-10 19:13:31 -0700
Commit message:

 Actually use the specified python when creating a new venv.
Package: basilisk
Commit: 742fbfda974ac179ebd69dd3b0f982671b0191fa
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2025-05-10 19:00:15 -0700
Commit message:

 Remove python specification from packages= before making the venv.
Package: scviR
Commit: d367a65a36d7cfdc07cc8a3cc781a9ae13073307
Author: vjcitn <stvjc@channing.harvard.edu>
Date: 2025-05-10 10:07:56 -0400
Commit message:

 added timing for GPU vs CPU runs
Package: scviR
Commit: f6b8752a19f1672e3d9b19ff140f1d43048d73eb
Author: vjcitn <stvjc@channing.harvard.edu>
Date: 2025-05-09 09:02:22 -0400
Commit message:

 Merge branch 'newvince' of https://github.com/vjcitn/scviR into devel
Package: scviR
Commit: 5f4f68aec025a5d152186c253363249602aa7dff
Author: vjcitn <stvjc@channing.harvard.edu>
Date: 2025-05-09 13:00:15 +0000
Commit message:

 improve cuda/gpu detection, remove v from version setting for session_info
Package: DEqMS
Commit: 664a95f019498e6a14f24ea9f98826c9ac4181cd
Author: Yafeng_MacPro <yafeng.zhu@outlook.com>
Date: 2025-05-10 14:53:09 +0800
Commit message:

 add version bump
Package: DEqMS
Commit: 5c5bcf77b43a5ba1f00bfe2ac6d7d46689ad83f4
Author: Yafeng_MacPro <yafeng.zhu@outlook.com>
Date: 2025-05-10 14:50:12 +0800
Commit message:

 add dplyr dependency
Package: DEqMS
Commit: 7c6b075be8259bb9138aefb26140be406265d8dd
Author: Yafeng_MacPro <yafeng.zhu@outlook.com>
Date: 2025-05-10 14:42:42 +0800
Commit message:

 add pseudocount 1 automatically if min(count) is 0
Package: DEqMS
Commit: e96b53b68695724db659854285716d49f9346175
Author: Yafeng_MacPro <yafeng.zhu@outlook.com>
Date: 2025-05-10 14:29:26 +0800
Commit message:

 add dplyr dependency
Package: OrganismDbi
Commit: 1d155137ae263aa0e4b5273933dfd04c1b882928
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2025-05-09 19:13:46 -0700
Commit message:

 OrganismDbi 1.51.2: Move txdbmaker from Imports to Suggests
Package: txdbmaker
Commit: ca25803e8e42c64a9ccfb41db103cb7ca4299f9b
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2025-05-09 18:32:24 -0700
Commit message:

 txdbmaker 1.5.3: Small tweaks
Package: GenomicFeatures
Commit: 181025e15e5b3528ee39632f3fd49540bb81ee22
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2025-05-09 18:28:47 -0700
Commit message:

 GenomicFeatures 1.61.2: Small tweaks
Package: cBioPortalData
Commit: 913d48a15948ac2d244b384c1bc9f9f5c56b8d7f
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-05-09 16:35:39 -0400
Commit message:

 version bump 2.21.2
Package: cBioPortalData
Commit: b3d022e334e098a0843b66b381f2645c23c27e15
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-05-09 16:35:33 -0400
Commit message:

 remove removeDataCache examples
Package: cBioPortalData
Commit: d9423f49137d65d5438a7c11e9a7cab1ee04bd48
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-05-09 16:35:23 -0400
Commit message:

 update .Rbuildignore and .gitignore
Package: dmrseq
Commit: bd5187a759c362927344a6e049b4924fa0d5368a
Author: kdkorthauer <kdkorthauer@gmail.com>
Date: 2025-05-09 10:38:04 -0700
Commit message:

 version bump in devel
Package: dmrseq
Commit: 4500e6adcc34b1f3f5d87c9528d5f9f1fc6f4b84
Author: kdkorthauer <kdkorthauer@gmail.com>
Date: 2025-05-09 10:37:40 -0700
Commit message:

 Fix for #69: check for NA in covariates
Package: basilisk
Commit: 17e1092a18002e3ef81df7b54d43d81088a7275e
Author: Aaron Lun <infinite.monkeys.with.keyboards@gmail.com>
Date: 2025-05-09 09:50:03 -0700
Commit message:

 Switch to PyEnv + virtualenv for Python management, environment creation. (#52)

The aim is to eliminate the reliance on conda so that we avoid GLIBCXX version
errors from mismatches in system libraries between conda and R. We achieve this
by using Pyenv (via reticulate) to natively install the desired Python, and
then creating virtualenvs instead of conda.

For developers, the basilisk interface does not change, though the various
pinned versions of packages= will likely need to be updated to use PyPi
versions instead of their conda counterparts. Also channels= no longer has any
effect, obviously. Developers can supply more functions to basiliskStart()
without worrying about whether it will work with the fallback environment.

For administrators, it is trivial to instruct basilisk to use one or more
custom Pythons instead of installing a new version via Pyenv. This is probably
more friendly than forcing everyone to use conda. 

We no longer perform system installs of Python in basilisk itself, as basilisk
doesn't know anything about which Python versions are required in downstream
packages. This allows us to eliminate the dependency on basilisk.utils.
Package: basilisk.utils
Commit: 943832def03c3ffde2fa02ea4b9c4692f2d76e38
Author: Aaron Lun <infinite.monkeys.with.keyboards@gmail.com>
Date: 2025-05-09 09:38:22 -0700
Commit message:

 Refactor this package to serve as a conda-provisioning system. (#14)

The idea is to provide a central conda instance for all BioC packages, in the
same vein as biocmake. We inherit some of the environment creation +
configuration utilities from the old conda-based basilisk, to make it easier
for downstream packages to create and cache environments. However, we don't
mandate the use of reticulate here due to GLIBCXX version discrepancies.
Package: scRNAseqApp
Commit: 524e3e8b616bb3d16e4d893519be2f85bd561eaa
Author: Jianhong Ou <jou@JNXKY095H1.local>
Date: 2025-05-09 11:48:58 -0400
Commit message:

 Allow single gene heatmap plot.
Package: BiocFileCache
Commit: 7bad0eff945297cc155b01c588018c88d8004ea4
Author: lshep <lori.shepherd@roswellpark.org>
Date: 2025-05-09 11:26:02 -0400
Commit message:

 Fix Bugs:

1. soft failure if HEAD does not work. Instead of hard fail, will proceed with
download and adding to cache but without caching information to check for
updates

2. Be able to pass config information for head/download for bfcadd,
bfcneedsupdate, bfcrpath
Package: spatialLIBD
Commit: aff00dbd3c8deebf377190817f06b2e8ffe03bff
Author: lcolladotor <lcolladotor@gmail.com>
Date: 2025-05-09 11:38:42 -0400
Commit message:

 v1.21.5 -- depend on R 4.1 due to the use of the native R pipe
Package: smoppix
Commit: 3e21644b2a13dbbcd29aa85a526a5de5e042b27d
Author: stijn <stijn.hawinkel@psb.ugent.be>
Date: 2025-05-09 14:54:28 +0200
Commit message:

 avoid id confusion
Package: smoppix
Commit: 06babcb036ee484747cce306045e3bb46cacaf2c
Author: stijn <stijn.hawinkel@psb.ugent.be>
Date: 2025-05-09 14:53:25 +0200
Commit message:

 mOve the parentehsis with big consequences
Package: smoppix
Commit: 91d16dde5ea1e88512f64f5aa3604553c721b52a
Author: stijn <stijn.hawinkel@psb.ugent.be>
Date: 2025-05-09 14:03:58 +0200
Commit message:

 make sure to loop over required features only
Package: smoppix
Commit: 3e6f115b9bcd12aa650085ea921e4ec409cfb968
Author: stijn <stijn.hawinkel@psb.ugent.be>
Date: 2025-05-09 12:20:05 +0200
Commit message:

 Limit analysis to features with actually estimated PIs
Package: GeneTonic
Commit: 666ed577c6c9428deb5aa503c1d3647f9b10579f
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2025-05-09 13:17:35 +0200
Commit message:

 updated news
Package: GeneTonic
Commit: 8e593a78df9d457929b3f6d7d118f795beecee5c
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2025-05-09 13:16:20 +0200
Commit message:

 version bump, 3.3.2
Package: GeneTonic
Commit: 7c599a7fcff8012a52b6f5c08deeadb3b45cfd04
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2025-05-09 13:15:46 +0200
Commit message:

 Merge pull request #66 from NajlaAbassi/devel

fixing tiny typos in gs_shaker
Package: GeneTonic
Commit: 96ecbad4d12e83579dc9ddf125a8c9ef658cf50d
Author: Najla Abassi <abassi.nejla96@gmail.com>
Date: 2025-05-08 16:53:59 +0200
Commit message:

 fixing tiny typos
Package: iSEEtree
Commit: f60296d514e1d937dd556b19f485944cc05312c0
Author: Giulio Benedetti <giuliobene2000@gmail.com>
Date: 2025-05-09 13:49:37 +0300
Commit message:

 Update citation
Package: smoppix
Commit: 32db7c00537301a96d81247ef533bc2977972a20
Author: stijn <stijn.hawinkel@psb.ugent.be>
Date: 2025-05-09 11:35:03 +0200
Commit message:

 Remove commented code
Package: smoppix
Commit: 003229e7ba25d1a7d26189d7c17fbad1ccefb18d
Author: stijn <stijn.hawinkel@psb.ugent.be>
Date: 2025-05-02 13:55:10 +0200
Commit message:

 Typo in extractresults
Package: MetaboCoreUtils
Commit: d7c7b8ba6906281c06e3b1a74ee963014e5fb782
Author: Johannes Rainer <johannes.rainer@gmail.com>
Date: 2025-05-09 11:28:24 +0200
Commit message:

 Merge remote-tracking branch 'upstream/devel'
Package: MetaboCoreUtils
Commit: 45c8d416a53083372f1c869366f8955878b29b30
Author: Johannes Rainer <5506112+jorainer@users.noreply.github.com>
Date: 2025-05-09 11:25:42 +0200
Commit message:

 Merge pull request #85 from rformassspectrometry/phili

fix adductFormula for negative polarity
Package: MetaboCoreUtils
Commit: 0ad240c5fa607b8bb60ffe428c4971bbccdd57ee
Author: Philippine Louail <127301965+philouail@users.noreply.github.com>
Date: 2025-05-09 11:06:51 +0200
Commit message:

 Update check-bioc.yml
Package: MetaboCoreUtils
Commit: 5b4ba9b80238e314c75b95f3111af0dbaa0a43ae
Author: Philippine Louail <127301965+philouail@users.noreply.github.com>
Date: 2025-05-09 11:05:08 +0200
Commit message:

 Update check-bioc.yml
Package: MetaboCoreUtils
Commit: 27e6541d32c16fa45e1806799325e60a871bba33
Author: Philippine Louail <127301965+philouail@users.noreply.github.com>
Date: 2025-05-09 11:02:30 +0200
Commit message:

 Update check-bioc.yml
Package: MetaboCoreUtils
Commit: 7d30c08f2591fcb39a5dc38e9724b68c52e39c57
Author: Philippine Louail <127301965+philouail@users.noreply.github.com>
Date: 2025-05-09 10:58:39 +0200
Commit message:

 bump version
Package: MetaboCoreUtils
Commit: 4046750577ab3f084effbbe354cc8554dd1a2c34
Author: Philippine Louail <127301965+philouail@users.noreply.github.com>
Date: 2025-05-09 10:57:22 +0200
Commit message:

 merge with main
Package: MetaboCoreUtils
Commit: 2d2e0f9b2a8cbbee8bc76902a806c94a15c92e01
Author: Philippine Louail <127301965+philouail@users.noreply.github.com>
Date: 2025-05-09 10:55:23 +0200
Commit message:

 small fix on adductFormula()
Package: MetaboCoreUtils
Commit: 0f9f33f48d479e862501ef4adb7db04d1b130678
Author: Johannes Rainer <johannes.rainer@gmail.com>
Date: 2025-04-08 08:46:36 +0200
Commit message:

 Update editorconfig
Package: MetaboCoreUtils
Commit: fa030f17892d5148fa79540378d72bd60d718d7a
Author: jorainer <johannes.rainer@gmail.com>
Date: 2024-09-27 21:46:48 +0200
Commit message:

 ci: fix GHA
Package: MetaboCoreUtils
Commit: 3530932143f902d940f46a02eab197fc2993b799
Author: jorainer <johannes.rainer@gmail.com>
Date: 2024-09-27 21:41:03 +0200
Commit message:

 ci: add CODECOV
Package: MetaboCoreUtils
Commit: a9017d2d6de94de256d671fa408ed315d322a0fc
Author: Johannes Rainer <johannes.rainer@gmail.com>
Date: 2024-09-27 17:06:52 +0200
Commit message:

 ci: update to BioC 3.20
Package: MetaboCoreUtils
Commit: a431382f9c94fbb4d178274a5dc29cf1194e201c
Author: Johannes Rainer <johannes.rainer@gmail.com>
Date: 2024-09-27 17:06:14 +0200
Commit message:

 tests: complete unit tests
Package: CAMERA
Commit: 43df5410b76fff61ce393dc38b961602f905ebe4
Author: Steffen Neumann <sneumann@ipb-halle.de>
Date: 2025-05-09 10:56:41 +0200
Commit message:

 Fix a few more logic expressions causing the condition has length > 1 type issues
Package: Biostrings
Commit: 5a36f2f49c181b4fc635ccc8fc2a55c9b89dc138
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2025-05-08 22:38:16 -0700
Commit message:

 Biostrings 2.77.1

- All the functions that went to pwalign in BioC 3.19 and got formally
  deprecated in Biostrings in BioC 3.21 are now defunct.

- After being deprecated in BioC 3.19, XStringPartialMatches objects
  and matchprobes() are now defunct.

- Remove needwunsQS() (was defunct in BioC 3.19).
Package: CircSeqAlignTk
Commit: a6c35fd57172c5566736e9f18b58d8631e8aafe9
Author: jsun <sun@bitdessin.dev>
Date: 2025-05-09 14:46:13 +0900
Commit message:

 [change] change default aligners and update documentation.
Package: GenomicFeatures
Commit: 7dfa249c4a728ed283ec8fed6d05b12957001aae
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2025-05-08 19:57:14 -0700
Commit message:

 GenomicFeatures 1.61.1

All the functions that went to txdbmaker in BioC 3.19 and got formally
deprecated in GenomicFeatures in BioC 3.21 are now defunct.
Package: txdbmaker
Commit: a1440689b3e95cfef2d4a7152a3ab5b07f470d61
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2025-05-08 17:09:27 -0700
Commit message:

 txdbmaker 1.5.2

Argument 'port' in functions makeTxDbPackageFromBiomart(),
makeTxDbFromBiomart(), and getChromInfoFromBiomart() is now defunct.

Also make makeTxDbFromEnsembl() man page example more robust to
new Ensembl releases. See '?makeTxDbFromEnsembl'.
Package: biocmake
Commit: 51eba0c0ad1576d2f1b6625231baa476f5591bf2
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2025-05-08 16:15:26 -0700
Commit message:

 Tidied up some of the wording in the vignette, README.
Package: BiocPkgTools
Commit: 9b766cdd0b01613c9bd292480b31c91cfcd15de0
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-05-08 16:48:22 -0400
Commit message:

 version bump 1.27.4
Package: BiocPkgTools
Commit: 195513a637bf7b4cc0c537f8c9183ce9dfa527e6
Author: Marcel Ramos Pérez <LiNk-NY@users.noreply.github.com>
Date: 2025-05-08 16:37:49 -0400
Commit message:

 update status badge in README.md
Package: BiocPkgTools
Commit: 11661c9c58ab29aea91d1c278f241fafc88d9cc7
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-05-08 15:47:07 -0400
Commit message:

 update branches in GHAs
Package: ProteinGymR
Commit: c17b6f8b640814d3cb4233a6990e2f7c53badfba
Author: tram-nguyen-n <tram_nguyen@hms.harvard.edu>
Date: 2025-05-08 19:33:32 +0000
Commit message:

 fixed bug for plot_structure
Package: ProteinGymR
Commit: 9094d42cae745a4ac793cff89490a410e4c96027
Author: tram-nguyen-n <tram_nguyen@hms.harvard.edu>
Date: 2025-05-08 17:52:17 +0000
Commit message:

 col_fun() as helper
Package: ProteinGymR
Commit: 46b13a765f1779b25033fa871aa3acd5366ef014
Author: tram-nguyen-n <tram_nguyen@hms.harvard.edu>
Date: 2025-05-07 17:50:59 +0000
Commit message:

 update news
Package: ProteinGymR
Commit: fa669d65549b313c6e0833f6f11413caf7922df5
Author: tram-nguyen-n <tram_nguyen@hms.harvard.edu>
Date: 2025-05-07 17:38:34 +0000
Commit message:

 col_fun() scoping issue
Package: ProteinGymR
Commit: ee5dd0bb9c2db146920fea4297ef2366e877d7ae
Author: tram-nguyen-n <tram_nguyen@hms.harvard.edu>
Date: 2025-05-07 17:24:39 +0000
Commit message:

 pair down vignette examples
Package: ProteinGymR
Commit: bb931a220b3e815fabaa547d92f6ec4d6e8c9791
Author: tram-nguyen-n <tram_nguyen@hms.harvard.edu>
Date: 2025-05-07 17:24:19 +0000
Commit message:

 add color scale bar and EVE color_scheme
Package: ProteinGymR
Commit: 872a3b826f2b95a6c4a08f7398d5e5649859c624
Author: tram-nguyen-n <tram_nguyen@hms.harvard.edu>
Date: 2025-05-05 18:46:02 +0000
Commit message:

 htmltools and pals to dependencies
Package: MSstatsBioNet
Commit: eb83b30b0d82e00343448b1c14a340145aa9dd37
Author: tonywu1999 <wu.anthon@northeastern.edu>
Date: 2025-05-08 15:08:55 -0400
Commit message:

 version bump
Package: MSstatsBioNet
Commit: 6080c94e4801aaf3de89f19e111fbb679327296c
Author: tonywu1999 <wu.anthon@northeastern.edu>
Date: 2025-05-08 15:07:58 -0400
Commit message:

 Add additional functionality to extract CHEBI networks (#44)
Package: TrIdent
Commit: 98cc8e3f70bc63a579f759c0e9dec9d5a11a0d2d
Author: jlmaier <jlmaier@ncsu.edu>
Date: 2025-05-08 14:31:32 -0400
Commit message:

 Fixed conflicts in version change
Package: TrIdent
Commit: 13f98ef1e8c758512ac135f9ef6a05f6d5949414
Author: jlmaier <jlmaier@ncsu.edu>
Date: 2025-05-08 13:35:49 -0400
Commit message:

 Bug fixes and minor updates
Package: ggspavis
Commit: 59e0ec5e1b37b4d95828faf608a805fdccabddf1
Author: Lukas Weber <lmweb012@gmail.com>
Date: 2025-05-08 14:30:26 -0400
Commit message:

 version
Package: ggspavis
Commit: dc19aa8bf2f0caa58a51e670ff9ed920d0fdff91
Author: Lukas Weber <lmweb012@gmail.com>
Date: 2025-05-08 14:27:32 -0400
Commit message:

 fix broken link in docs
Package: ggspavis
Commit: 5ea61c9d4b1742901890201ab52920cc8ae9be67
Author: Lukas Weber <lmweb012@gmail.com>
Date: 2025-05-08 14:22:52 -0400
Commit message:

 version
Package: ggspavis
Commit: 69e614620cc7a41aaecd131715aa2bb9a538b164
Author: Lukas Weber <lmweb012@gmail.com>
Date: 2025-05-08 14:22:43 -0400
Commit message:

 add NEWS
Package: ggspavis
Commit: 8c99c3e1352b69056ce63faa47449d4bbbbda974
Author: Lukas Weber <lmweb012@gmail.com>
Date: 2025-05-08 14:18:27 -0400
Commit message:

 rename functions to plotSpa() and plotSpaQC() to avoid name clash with plotSpatial() from imcRtools package
Package: TENxIO
Commit: 2f684b16bb8e382f837746658fbc9f4d7fd82e5c
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-05-08 14:22:10 -0400
Commit message:

 version bump 1.11.4
Package: TENxIO
Commit: 50b12aa7b0ec98554c60754ff87c4e438328f24f
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-05-06 19:17:29 -0400
Commit message:

 use integrated HTML sessionInfo
Package: MSstatsBioNet
Commit: fb1bc39545868fbf6571621b7dcb9614dc039ce9
Author: tonywu1999 <wu.anthon@northeastern.edu>
Date: 2025-05-08 13:33:08 -0400
Commit message:

 version bump
Package: MSstatsBioNet
Commit: 45991166c679e8e48e247f9e935e81896980ff24
Author: tonywu1999 <wu.anthon@northeastern.edu>
Date: 2025-05-08 13:32:41 -0400
Commit message:

 update scoring function to include phosphorylation and complexes (#43)
Package: GSEABenchmarkeR
Commit: c520218ae428083ea2dc2f8552028372dea29fb0
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-05-08 12:44:31 -0400
Commit message:

 version bump 1.29.1
Package: GSEABenchmarkeR
Commit: 2cb5fb56ac7c24238b6005a3f309a8643268012d
Author: lgeistlinger <ludwig.geistlinger@gmail.com>
Date: 2025-05-07 18:12:33 -0400
Commit message:

 Merge pull request #17 from waldronlab/build_site_gha

Add .github/workflows for building GHA pkgdown site
Package: GSEABenchmarkeR
Commit: 0e46f4b5b1f13ace6487a84a57b8b66f822c0b25
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-05-07 15:32:24 -0400
Commit message:

 add _pkgdown.yml and .github/workflows/pr_check.yml GHA
Package: GSEABenchmarkeR
Commit: 44804cd1979991a6f9675011d4a49a0c6a76c572
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-05-07 15:39:59 -0400
Commit message:

 resolve build warning and note
Package: GSEABenchmarkeR
Commit: 432effa9398ad4d852756375f794282685f3463c
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-05-07 15:35:46 -0400
Commit message:

 use Authors@R
Package: GSEABenchmarkeR
Commit: 1f3b7a12bcc81ccf14beda66400ec84f4e75d7a1
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-05-07 15:32:56 -0400
Commit message:

 remove old CI files
Package: GSEABenchmarkeR
Commit: 1b22242b73aa26dc49d069ef822ee0381d0cd61b
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-05-07 15:32:09 -0400
Commit message:

 update .Rbuildignore and .gitignore .Rproj
Package: CNVRanger
Commit: 82ec0eab97e532e907a535d4d8540308477883ff
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-05-08 12:17:16 -0400
Commit message:

 version bump 1.25.4
Package: CNVRanger
Commit: 5bbe13fa14bc9d7c15f7567c511329ce8533e418
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-05-08 12:17:11 -0400
Commit message:

 fix references
Package: CNVRanger
Commit: 175c2d1f0c6563765f5be0be74b0b019db110b6d
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-05-08 11:04:54 -0400
Commit message:

 version bump 1.25.3
Package: CNVRanger
Commit: ce91e6ad832586135c12dca258f0b47f2b88b974
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-05-07 19:56:38 -0400
Commit message:

 use bibliography
Package: CNVRanger
Commit: ef20c16453b965e636f26951617d346abe8cbd5e
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-05-07 18:46:10 -0400
Commit message:

 move png files to man/figures
Package: ggspavis
Commit: eb069106881b829f5336ba1aa87373f6fc981996
Author: Lukas Weber <lmweb012@gmail.com>
Date: 2025-05-08 10:29:19 -0400
Commit message:

 version
Package: ggspavis
Commit: 45c36536bd4724a201ef16829c68581777164a50
Author: Lukas Weber <lmweb012@gmail.com>
Date: 2025-05-08 10:29:06 -0400
Commit message:

 bug fix to check assay names correctly if multiple assay names have overlapping sub-strings (e.g. 'counts' and 'logcounts') - bug reported by @nilseling
Package: MSstatsBioNet
Commit: 94c49ec8912fe172ba00ccf5cac74859ee373caa
Author: tonywu1999 <wu.anthon@northeastern.edu>
Date: 2025-05-08 10:22:14 -0400
Commit message:

 version bump
Package: MSstatsBioNet
Commit: efd65ef5d09738d052fc370a4d189d198d0eff6c
Author: tonywu1999 <wu.anthon@northeastern.edu>
Date: 2025-05-08 10:15:00 -0400
Commit message:

 Add getPathwaysFromIndra function (#42)
Package: SpatialExperiment
Commit: 0b2953777e17bd031b693315102787afa0f252c8
Author: Lukas Weber <lmweb012@gmail.com>
Date: 2025-05-08 10:03:51 -0400
Commit message:

 Merge pull request #167 from lmweber/devel

Sync version bumps and previous updates
Package: SpatialExperiment
Commit: a8fc00f931fce6b0e31ae58fede5f4488ff4e8e5
Author: Lukas Weber <lmweb012@gmail.com>
Date: 2025-05-07 18:28:21 -0400
Commit message:

 version
Package: SpatialExperiment
Commit: 8fabc05270c66d850694d5b3b6b58b284e54eca1
Author: Lukas Weber <lmweb012@gmail.com>
Date: 2025-05-07 18:27:24 -0400
Commit message:

 update GHA
Package: SpatialExperiment
Commit: 3fa5af24083b30b0845a63658913451e14a44da4
Author: Lukas Weber <lmweb012@gmail.com>
Date: 2025-05-07 18:26:51 -0400
Commit message:

 update email
Package: SpatialExperiment
Commit: 1e55cde8eb2ce9a73bac157b318e2aaa0c18aa66
Author: Lukas Weber <lmweb012@gmail.com>
Date: 2025-05-07 18:22:38 -0400
Commit message:

 Merge remote-tracking branch 'upstream/devel' into devel
Package: SpatialExperiment
Commit: 0e6fcadab3f235eab9615c976429cbb4ea653e53
Author: Helena L. Crowell <helena@crowell.eu>
Date: 2024-06-24 12:53:16 +0200
Commit message:

 Merge pull request #155 from drighelli/deprecate_read10xVisium

Deprecate read10xVisium()
Package: SpatialExperiment
Commit: cf1c4f707ca869d760e88b54c436a0ba3f991ad4
Author: Lukas Weber <lmweberedu@gmail.com>
Date: 2024-06-22 10:20:22 +0800
Commit message:

 update LMW email address
Package: SpatialExperiment
Commit: c7d58c44ddd088b51d0d440663fecf052ef4777d
Author: HelenaLC <helena@crowells.eu>
Date: 2024-06-21 19:31:34 +0200
Commit message:

 fix example
Package: SpatialExperiment
Commit: 9a063b5547a86027c2797cd27629ed98a54f9acb
Author: HelenaLC <helena@crowells.eu>
Date: 2024-06-21 18:55:52 +0200
Commit message:

 drop VisiumIO link (can't link the function from suggested pkgs)
Package: SpatialExperiment
Commit: a996f8c114c37936b1c46c3c9e22fd1b73758af2
Author: HelenaLC <helena@crowells.eu>
Date: 2024-06-21 11:29:41 +0200
Commit message:

 deprecate read10xVisium in favor of VisiumIO functions
Package: SpatialExperiment
Commit: f7422690a04713a1f8fa1c4d22eb36e3eea8e748
Author: HelenaLC <helena@crowells.eu>
Date: 2024-06-21 11:29:21 +0200
Commit message:

 +ORCID iDs; version bump 1.15.1>.2
Package: SpatialExperiment
Commit: fdd6ba0287ddd25cd39b8df273774bb64318072c
Author: HelenaLC <helena@crowells.eu>
Date: 2024-06-21 11:28:42 +0200
Commit message:

 update NEWS
Package: DNAfusion
Commit: b5bd9a00cb20585303d94673fd6fc56c009cbf80
Author: Christoffer Trier Månsson <ctm@clin.au.dk>
Date: 2025-05-08 15:59:49 +0200
Commit message:

 Merge remote-tracking branch 'upstream/devel'
Package: DNAfusion
Commit: 1fd6dec3cf0e7aa249747792ddf5db3ddda02a38
Author: Christoffer Trier Månsson <ctm@clin.au.dk>
Date: 2025-05-08 15:20:09 +0200
Commit message:

 Update README.md
Package: DNAfusion
Commit: 35354428868659b0e236e3ba71506faa426cb2a6
Author: Christoffer Trier Månsson <ctm@clin.au.dk>
Date: 2025-05-08 15:16:56 +0200
Commit message:

 Update DNAfusion_functions.R
Package: DNAfusion
Commit: 07cadcb0705b6e34e6449f1878fdf39ed6757c66
Author: Christoffer Trier Månsson <ctm@clin.au.dk>
Date: 2025-05-08 14:52:17 +0200
Commit message:

 Update DESCRIPTION
Package: DNAfusion
Commit: ddb0aa45b47fc03790237e32e2c4b7a77e7fee3b
Author: Christoffer Trier Månsson <ctm@clin.au.dk>
Date: 2025-05-08 14:22:42 +0200
Commit message:

 Updating NAMESPACE for 1.11.1
Package: DNAfusion
Commit: 87b9596255b7a4bb2ce643ae2f75d7e1d6a7b219
Author: Christoffer Trier Månsson <ctm@clin.au.dk>
Date: 2025-05-08 13:58:57 +0200
Commit message:

 1.11.1 - Removing bamsignals dependency and using Rsamtools for depth estimation
Package: DNAfusion
Commit: 666e87f2bfc6a49a249772edff95467dfc3e8d3a
Author: Christoffer Trier Månsson <ctm@clin.au.dk>
Date: 2023-10-25 09:44:05 +0200
Commit message:

 Merge branch 'devel'
Package: DNAfusion
Commit: 9d45cb4fe01ac2dc2fb9a9582d0f34a2400ce261
Author: Christoffer Trier Månsson <ctm@clin.au.dk>
Date: 2023-05-02 09:26:26 +0200
Commit message:

 Update README.md
Package: DNAfusion
Commit: a68ed2f9b333ac9ab992309699bb0925f432b34f
Author: Christoffer Trier Månsson <ctm@clin.au.dk>
Date: 2023-05-02 09:26:07 +0200
Commit message:

 Update README.md
Package: DNAfusion
Commit: 48584c822c5b3cce0dba8136bad89771a807cf3e
Author: Christoffer Trier Månsson <ctm@clin.au.dk>
Date: 2023-05-02 09:25:33 +0200
Commit message:

 Update README.md
Package: DNAfusion
Commit: 3feba92dd046f3b3ad4090532cf194496fe486af
Author: Christoffer Trier Månsson <ctm@clin.au.dk>
Date: 2023-05-02 09:22:35 +0200
Commit message:

 Update README.md
Package: DNAfusion
Commit: 6a568d96d8643c1338229074ddfa4edd750c47e7
Author: Christoffer Trier Månsson <ctm@clin.au.dk>
Date: 2023-05-02 09:18:11 +0200
Commit message:

 Update README.md
Package: DNAfusion
Commit: afa74a7566a7bd5d8b74b19119942b2c9294b547
Author: Christoffer Trier Månsson <ctm@clin.au.dk>
Date: 2023-05-02 09:16:47 +0200
Commit message:

 Update README.md
Package: DNAfusion
Commit: 1ca2e231317c7ac23d62923b51694c5b4da34900
Author: Christoffer Trier Månsson <ctm@clin.au.dk>
Date: 2023-05-02 09:16:00 +0200
Commit message:

 Update README.md
Package: DNAfusion
Commit: d6b580a204d93a8cc11e07346addbc4b2dd8ffc0
Author: Christoffer Trier Månsson <ctm@clin.au.dk>
Date: 2023-05-02 09:07:38 +0200
Commit message:

 Create CITATION
Package: DNAfusion
Commit: df9e10be487e0e75b85a2aa85d504d269e3a3159
Author: Christoffer Trier Månsson <ctm@clin.au.dk>
Date: 2023-05-02 08:46:27 +0200
Commit message:

 Update README.md
Package: DNAfusion
Commit: 82b33e54f7c1b21d9ab1194a5b76a043e118f5d2
Author: Christoffer Trier Månsson <ctm@clin.au.dk>
Date: 2023-05-02 08:44:15 +0200
Commit message:

 Update README.md
Package: scviR
Commit: cb1efb2082912389fd75310d2beb5c4d483d596a
Author: vjcitn <stvjc@channing.harvard.edu>
Date: 2025-05-08 06:37:07 -0400
Commit message:

 adding GPU_reliance: optional to .BBS options and removing the denial of attempt on windows
Package: scviR
Commit: 0d68d1790a7e511f17570c9448cf6e9057fb8d07
Author: vjcitn <stvjc@channing.harvard.edu>
Date: 2025-05-07 07:53:20 -0400
Commit message:

 indicate citeseq_tut vignette is obsolete, scotch a problem with pandas deprecation
Package: scviR
Commit: ea5466b721682beaf2dc3c4a3670a54283b603f7
Author: vjcitn <stvjc@channing.harvard.edu>
Date: 2025-05-06 07:34:50 -0400
Commit message:

 adding scripts
Package: scviR
Commit: 4f3dc7d7abc3a2c8c23c2c6997ca7226fe6b6083
Author: vjcitn <stvjc@channing.harvard.edu>
Date: 2025-05-05 22:11:29 -0400
Commit message:

 use proper caching function for data to read
Package: scviR
Commit: af752ad721dd4fd815bf5ab611477d9d93855c61
Author: vjcitn <stvjc@channing.harvard.edu>
Date: 2025-05-05 22:10:49 -0400
Commit message:

 adding timing script
Package: scviR
Commit: ae9c10c32864fe018ac00438a9efdea69757b20d
Author: vjcitn <stvjc@channing.harvard.edu>
Date: 2025-05-04 13:29:24 +0000
Commit message:

 added cuda check in vignette
Package: scviR
Commit: 862a64bd935eabac625e5b50188cc6dc67d51194
Author: vjcitn <stvjc@channing.harvard.edu>
Date: 2025-05-04 09:13:44 -0400
Commit message:

 new citeseq vignette that checks for MPS on mac with torch
Package: scviR
Commit: 251648a0651facb4fbaa854c296a1a8f9b5dd189
Author: vjcitn <stvjc@channing.harvard.edu>
Date: 2025-05-03 11:38:40 +0000
Commit message:

 save some scripts
Package: scviR
Commit: 9d5bdacd6de2009b0c150813cb93e04d1b50722d
Author: vjcitn <stvjc@channing.harvard.edu>
Date: 2025-05-03 11:36:48 +0000
Commit message:

 this setup led to successful training on E44
Package: scviR
Commit: 3509ebac8f84bfc7ea53fa0d2acb325190ef2a00
Author: vjcitn <stvjc@channing.harvard.edu>
Date: 2025-05-03 05:53:19 -0400
Commit message:

 updating to match current scvi tutorial notebook, including large citeseq protein panel example
Package: HilbertVis
Commit: 6f5dca6784f6439f96236f384d67cd253e41ac20
Author: Simon Anders <sanders@fs.tum.de>
Date: 2025-05-08 08:28:36 +0200
Commit message:

 fixed remaining calls to error
Package: biocmake
Commit: ab7ccb768665485c4b9451411ddeee485e897245
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2025-05-07 21:17:04 -0700
Commit message:

 Remember and return the result of the last call in find().

This saves some time by skipping repeated queries of the version or the cache,
especially when neither of those things usually change during an R session.
Package: CircSeqAlignTk
Commit: 2a2a1f283c802c7ca6781a5e153a124c46755e94
Author: jsun <sun@bitdessin.dev>
Date: 2025-05-08 13:09:35 +0900
Commit message:

 [update] update documentation.
Package: ggspavis
Commit: ffe75958d6f500d3a42b75d7af67e215121af2e7
Author: Lukas Weber <lmweb012@gmail.com>
Date: 2025-05-07 23:04:26 -0400
Commit message:

 version
Package: ggspavis
Commit: 8ef57ef67fc36f6b4446fa720511ad715f269759
Author: Lukas Weber <lmweb012@gmail.com>
Date: 2025-05-07 23:03:07 -0400
Commit message:

 handle NULL values in 'annotate' when using get()
Package: ggspavis
Commit: 353aa663208cbb4fe8606f762dfaf3849767819a
Author: Lukas Weber <lmweb012@gmail.com>
Date: 2025-05-07 17:33:39 -0400
Commit message:

 update NEWS
Package: ggspavis
Commit: 30f385348ecb4f1cdb5b9e3b5daa1e5ae64107b8
Author: Lukas Weber <lmweb012@gmail.com>
Date: 2025-05-07 17:26:55 -0400
Commit message:

 update email
Package: ggspavis
Commit: 9c4e607ec11b73ce8aa8e1d9a87e25a144a2fe22
Author: Lukas Weber <lmweb012@gmail.com>
Date: 2025-05-07 17:26:31 -0400
Commit message:

 version
Package: ggspavis
Commit: 53c706b7f8dc1852c8c4201cfadece6171a61203
Author: Lukas Weber <lmweb012@gmail.com>
Date: 2025-05-07 17:26:12 -0400
Commit message:

 put back .Rproj
Package: ggspavis
Commit: 2d069e49f94dd321f667e05c8aa471c53008daf6
Author: Lukas Weber <lmweb012@gmail.com>
Date: 2025-05-07 17:22:04 -0400
Commit message:

 Merge pull request #17 from estellad/estellad

VisiumHD compatible and some small things
Package: ggspavis
Commit: 334c58e144ded9d52f08cac2b8b4e0529bf72c51
Author: Lukas Weber <lmweb012@gmail.com>
Date: 2025-05-07 17:12:39 -0400
Commit message:

 various minor updates; rename 'shape' argument to 'point_shape'
Package: ggspavis
Commit: ff7116d01f52bfc96875715e898b98a0d70dd5a1
Author: Lukas Weber <lmweb012@gmail.com>
Date: 2025-05-07 14:34:51 -0400
Commit message:

 update GHA
Package: ggspavis
Commit: 3e979d54398b05d7cc95de3546f6f74cf3534da6
Author: estellad <estelladong729@gmail.com>
Date: 2025-04-12 14:49:22 +0200
Commit message:

 update to plotSpatial and plotVisium
Package: ggspavis
Commit: 89469175bfa27c2d98739fbf7d4c27a6df4e07cf
Author: estellad <estelladong729@gmail.com>
Date: 2025-04-11 19:34:32 +0200
Commit message:

 rename spot to spatial, add hd shape, palette rainbow rename, default facet null, check.name=FALSE in data.frame() and aes_string to aes(get())
Package: ggspavis
Commit: 5c628da93c729e93db64abbf17e3bf0203879f1d
Author: estellad <estelladong729@gmail.com>
Date: 2025-04-11 18:36:21 +0200
Commit message:

 new addition
Package: ggspavis
Commit: 9488130789acd299002936b8009ccda42fd998d4
Author: Estella Yixing Dong <estelladong729@gmail.com>
Date: 2025-04-11 16:30:31 +0200
Commit message:

 Merge branch 'lmweber:devel' into estellad
Package: ggspavis
Commit: b888b4b4477595cdc56c26347518c347fad88999
Author: Dong Yixing <yi4173@hos79595.wifi.intranet.chuv>
Date: 2024-06-23 12:33:13 +0200
Commit message:

 test
Package: CNVRanger
Commit: 18d3216e24a93f03373d2aa5aace5f104da6bde7
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-05-07 12:26:36 -0400
Commit message:

 version bump 1.25.2
Package: CNVRanger
Commit: 0c993dd6a3af3aa1ecaca63a85ceb6be4f89347b
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-05-07 12:26:27 -0400
Commit message:

 use Authors@R

- add ORCID
Package: CNVRanger
Commit: c97871fa17671ed780cd2000c60a25989c00611e
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-05-07 11:33:05 -0400
Commit message:

 version bump 1.25.1
Package: CNVRanger
Commit: 51785d9e3c7c40fc614cbc953745d0acddcd0cc8
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-05-07 11:31:41 -0400
Commit message:

 add _pkgdown.yml and .github/workflows/pr_check.yml GHA
Package: CNVRanger
Commit: fa94ea3d18ca133ccee8a644bb8151d474beabc7
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-05-07 11:30:50 -0400
Commit message:

 update branch in README.md
Package: CNVRanger
Commit: ec1a46478f5cd771fb072b34d51e2a75c364fb7c
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-05-07 11:30:34 -0400
Commit message:

 update .Rbuildignore and .gitignore
Package: HilbertVis
Commit: 3194a86c5f08bf311f3dd3aa83c0f0712ff060c7
Author: Simon Anders <sanders@fs.tum.de>
Date: 2025-05-07 17:58:11 +0200
Commit message:

 fixed format error due to Rf_error
Package: circRNAprofiler
Commit: 0e1b53455ba0c06f5848c64def80fbb5b616d8b8
Author: Aufiero <simo.aufiero@gmail.com>
Date: 2025-05-06 18:30:34 +0200
Commit message:

 From Version 1.23.0 to version 1.23.1
Package: circRNAprofiler
Commit: ac0d3054d5d654db4f95d22dd3935a1302d654c2
Author: Aufiero <simo.aufiero@gmail.com>
Date: 2025-05-06 18:29:59 +0200
Commit message:

 added a check to gettMotifs function in case the connection with the db does not work
Package: scRNAseqApp
Commit: 4e7e9b920b37648909219bd1b0d1c57464bcd371
Author: Jianhong Ou <jou@JNXKY095H1.local>
Date: 2025-05-07 11:41:22 -0400
Commit message:

 fix the melt issue
Package: VisiumIO
Commit: 0ffa1d44442a5af032702f9514ed5ae161082e5e
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-05-07 11:07:34 -0400
Commit message:

 version bump 1.5.6
Package: VisiumIO
Commit: d856e70231953d64ac4a66b35fc267580f155d79
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-05-07 11:07:26 -0400
Commit message:

 update .Rbuildignore
Package: UCell
Commit: e31e956cff841c26195de543902946c18b41c39c
Author: Massimo Andreatta <massimo.andreatta@unil.ch>
Date: 2025-05-07 17:02:53 +0200
Commit message:

 Update README.md
Package: AnnotationHub
Commit: 2cccc0b516eb3031ab844eb4f8af863e82f8247e
Author: lshep <lori.shepherd@roswellpark.org>
Date: 2025-05-07 09:04:44 -0400
Commit message:

 Fix bug with removeResource that prevent message from displaying
Package: Coralysis
Commit: 652e7cccc51c4b692574fd3add08c8b92cf6ae65
Author: antonioggsousa <antonioggsousa@gmail.com>
Date: 2025-05-07 15:24:08 +0300
Commit message:

 Adding scrapper as suggests for SingleR
Package: iSEEtree
Commit: 06f1a52123edcf7049a0852ba2f2c3bbd1334c74
Author: Giulio Benedetti <giuliobene2000@gmail.com>
Date: 2025-05-06 15:24:35 +0300
Commit message:

 Merge pull request #47 from microbiome/fix_warn

Fix warning related to tabTitle arg
Package: iSEEtree
Commit: 90e6ae8a2f8533c192bc278c0c015b0710e36a6b
Author: Giulio Benedetti <giuliobene2000@gmail.com>
Date: 2025-05-06 14:36:51 +0300
Commit message:

 Bump version
Package: iSEEtree
Commit: d145d738e4b8fc140aa85664c761dc0873fa17d2
Author: Giulio Benedetti <giuliobene2000@gmail.com>
Date: 2025-05-06 14:29:58 +0300
Commit message:

 Align args to iSEE 2.19.4
Package: XAItest
Commit: 28fbd268cd5604e2c70d7a9fd9ba787d07a2bf66
Author: GhislainFievet <ghislain.fievet@gmail.com>
Date: 2025-05-07 06:53:41 +0200
Commit message:

 Remove obsolete vignette and bump patch version to 1.1.1
Package: HVP
Commit: fc4a1890b2cd565ceb0e27e5ee7f65efddb34187
Author: Wei Xin Chan <cweixin@gmail.com>
Date: 2025-05-07 11:01:37 +0800
Commit message:

 docs: add installation instructions from bioconductor
Package: Biostrings
Commit: 44e8aa36353658a53a8ff7141082c024b6b39b9c
Author: Aidan Lakshman <ahl27@pitt.edu>
Date: 2025-05-06 21:26:56 -0400
Commit message:

 Fix: minor bug with input verification in `write.phylip`; clean up formatting (#124)
Package: TENET
Commit: 52aa25df091f355bdc6442694350f3d3ee0b641d
Author: Ethan Nelson-Moore <nelsonmo@usc.edu>
Date: 2025-05-06 17:14:17 -0700
Commit message:

 Bump version after merging survival bug fix from Bioconductor 3.21 release branch
Package: TENET
Commit: 3783ad4e040a9f97cd5fa0ab1a54d68c52f7a0c8
Author: Ethan Nelson-Moore <nelsonmo@usc.edu>
Date: 2025-05-06 17:04:15 -0700
Commit message:

 Update news for survival bug fix
Package: TENET
Commit: eca025725739fc8c07758a66c796df2fe8e6fe2c
Author: Ethan Nelson-Moore <nelsonmo@usc.edu>
Date: 2025-05-06 16:57:52 -0700
Commit message:

 Fix typo in survival calculation code which made the number of case samples with intermediate expression/methylation levels always 0
Package: VisiumIO
Commit: ca428e7d17c9bb791991413d44c9a64290d9224c
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-05-06 19:00:43 -0400
Commit message:

 version bump 1.5.5
Package: VisiumIO
Commit: a047d6430be0715b65ee2f5e30a623f425b54c56
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-05-06 19:00:32 -0400
Commit message:

 remove HTML from .Rbuildignore
Package: scRNAseqApp
Commit: 93eca7a75b9aeaa91ea06c75ce23a08caa8a82b3
Author: Jianhong Ou <jou@JNXKY095H1.local>
Date: 2025-05-06 18:52:13 -0400
Commit message:

 fix the group name issue for aes.
Package: VisiumIO
Commit: fa0e469148bcada0f9ee8bb9afa2c002696b78df
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-05-06 18:50:54 -0400
Commit message:

 version bump 1.5.4
Package: VisiumIO
Commit: e7c450ec9a95dadb5a7c414e65cbf66330efaa2f
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-05-06 18:50:46 -0400
Commit message:

 use HTML integrated sessionInfo
Package: VisiumIO
Commit: fdba5868f47c73681364d5936ab822cef06c223a
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-05-06 18:50:32 -0400
Commit message:

 resolve codoc mismatches warning
Package: scRNAseqApp
Commit: 7851b32d475f1963d9fa52b3be47d0b99bb894d2
Author: Jianhong Ou <jou@JNXKY095H1.local>
Date: 2025-05-06 18:47:07 -0400
Commit message:

 add progress bar for atac signal plot.
Package: XeniumIO
Commit: 302b3c8df75785903fbdd7c230ae241264854c25
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-05-06 18:23:23 -0400
Commit message:

 version bump 1.1.2
Package: XeniumIO
Commit: 1eadb5570d00d123536a720555d2ba4f51b494ef
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-05-06 18:23:02 -0400
Commit message:

 update README.md
Package: XeniumIO
Commit: a24595040426f1117bdc5f1bb1bad4ba59651f63
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-05-06 18:22:50 -0400
Commit message:

 add expandable sessionInfo in HTML
Package: XeniumIO
Commit: 2124b370d403ff0ed0c9c1c574462437419dc818
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-05-06 18:01:18 -0400
Commit message:

 update Installation section
Package: XeniumIO
Commit: 5d241ce4ac32d5f5e48419e9ca54405e96c6a408
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-05-06 17:58:24 -0400
Commit message:

 add _pkgdown.yml and .github/workflows/pr_check.yml GHA
Package: VisiumIO
Commit: 7c929b8c78389196adb9011a4a5a98dee2d58f76
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-05-06 17:54:32 -0400
Commit message:

 version bump 1.5.3
Package: VisiumIO
Commit: 4ff6e9cbdad6ae6b8e1a33be2c275818b68e13dd
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-05-06 17:54:07 -0400
Commit message:

 add expandable sessionInfo to README.md
Package: VisiumIO
Commit: 69d7604de4fe63a6bf14385e031cb8dd8f152ec5
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-05-06 17:44:17 -0400
Commit message:

 add _pkgdown.yml and .github/workflows/pr_check.yml GHA
Package: VisiumIO
Commit: e3ad587e896742be36fd5c748983ea264b6b2107
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-05-06 17:41:54 -0400
Commit message:

 version bump 1.5.2
Package: VisiumIO
Commit: 732a28bbe885142fd6070d1962bcf3159b564ca7
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-05-06 17:41:31 -0400
Commit message:

 update README.md
Package: VisiumIO
Commit: 8aa17d0af1b801105282d47f18c12f85364d8da3
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-05-06 17:41:19 -0400
Commit message:

 add clickable sessionInfo
Package: VisiumIO
Commit: ff7560791b9f96d447e6038cbb75216007648639
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-05-06 17:36:26 -0400
Commit message:

 update .gitignore add .Rbuildignore
Package: TENxIO
Commit: 27617012b1b64df6a402697e058269f77feabbff
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-05-06 17:29:03 -0400
Commit message:

 version bump 1.11.3
Package: TENxIO
Commit: 3350fd40582a59788fb99989e6ec5bcabb135af7
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-05-06 17:27:10 -0400
Commit message:

 add _pkgdown.yml and .github/workflows/pr_check.yml GHA
Package: TENxIO
Commit: d2ecffbf934a1fd98d209bb0525392becf6508c4
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-05-06 17:25:17 -0400
Commit message:

 version bump 1.11.2
Package: TENxIO
Commit: fda59ec3ac52f001bd105764359e2c7e0317991c
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-05-06 17:25:11 -0400
Commit message:

 update README.md
Package: TENxIO
Commit: d3de443ffdf1ca40e0eabf644dca6e03375bfecf
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-05-06 17:25:03 -0400
Commit message:

 add clickable sessionInfo section
Package: AnVIL
Commit: 008053494c249d16e36a661871d32be9f83356a0
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-05-06 17:11:14 -0400
Commit message:

 version bump 1.21.3
Package: AnVIL
Commit: bff5e708024b79a753ac2f33f1f6a1d71c1d37cd
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-05-06 17:10:47 -0400
Commit message:

 add ... to Service constructor
Package: SingleCellMultiModal
Commit: ccecd624f2e149ad974650ed202ee5addd63fb3c
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-05-06 16:21:33 -0400
Commit message:

 version bump 1.21.2
Package: SingleCellMultiModal
Commit: bcb3cb9c589fbf0df60608de3e8e96e0e9edf18a
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-05-06 16:21:25 -0400
Commit message:

 add sticker to README.md
Package: msigdbeh
Commit: 1a81498fe46f3d7c59dabcf006e5d144e981955d
Author: igor <6363505+igordot@users.noreply.github.com>
Date: 2025-05-06 14:23:48 -0400
Commit message:

 Update GitHub Actions
Package: msigdbeh
Commit: 61aa0293958335b314ac171e6f6930c1769b862a
Author: igor <6363505+igordot@users.noreply.github.com>
Date: 2025-05-06 14:19:38 -0400
Commit message:

 Update documentation
Package: msigdbeh
Commit: 1d9b81aaeba2233ac0876a22d41f3dca77fe42ae
Author: igor <6363505+igordot@users.noreply.github.com>
Date: 2025-05-06 14:16:43 -0400
Commit message:

 Update DESCRIPTION
Package: msigdbeh
Commit: 214c600c29ac28a9f224d324f5055cba02ee5445
Author: igor <6363505+igordot@users.noreply.github.com>
Date: 2025-05-06 12:35:20 -0400
Commit message:

 Update GitHub Actions
Package: msigdbeh
Commit: a054940e20675d426352ab5ed1e40ebe61327413
Author: igor <6363505+igordot@users.noreply.github.com>
Date: 2025-05-05 13:42:12 -0400
Commit message:

 Clean up code
Package: msigdbeh
Commit: d820a1ac7213a0bf564cfdb1158fb8204cb3eb66
Author: igor <6363505+igordot@users.noreply.github.com>
Date: 2025-05-05 13:40:17 -0400
Commit message:

 Update GitHub Actions
Package: msigdbeh
Commit: 18bb496e5c8b959241676c696455ca324f45fb8e
Author: igor <6363505+igordot@users.noreply.github.com>
Date: 2025-05-05 13:24:02 -0400
Commit message:

 Update DESCRIPTION
Package: msigdbeh
Commit: 6a96cc15547178380511c41a370d9ed4699517b8
Author: igor <6363505+igordot@users.noreply.github.com>
Date: 2025-04-12 23:39:51 -0400
Commit message:

 Update README.md
Package: AnVIL
Commit: 4e6589db8ca5a57770fea53e0d4ef22dd068a0c6
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-05-06 14:20:55 -0400
Commit message:

 version bump 1.21.2
Package: AnVIL
Commit: 78df41694dde3392844c949d1d877d1713df2573
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-05-06 14:20:48 -0400
Commit message:

 fix notes with imports
Package: AnVIL
Commit: 1f86c84134b3fd74fdcc3481e10a8ea5d8726330
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-05-06 14:20:37 -0400
Commit message:

 update AnVILBase imports
Package: AnVIL
Commit: ea4e9266c6668a87fabb29aa245f4bb22ba9ce90
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-05-06 14:19:57 -0400
Commit message:

 use checkInstalled throughout
Package: AnVIL
Commit: ac9243c10d06ac03a1cfb747c31999eda2e44815
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-05-06 14:18:33 -0400
Commit message:

 remove defunct functionality from AnVIL
Package: scRNAseqApp
Commit: 43ce374f9e08ef395bad10a43c1dab57ba96c9f0
Author: Jianhong Ou <jou@JNXKY095H1.local>
Date: 2025-05-06 13:03:53 -0400
Commit message:

 fix a bug introduced by 1.9.2.
Package: scRNAseqApp
Commit: b8086a3cbe816e7beffb39b1c05c33051085570b
Author: Jianhong Ou <jou@JNXKY095H1.local>
Date: 2025-05-06 12:30:51 -0400
Commit message:

 adjust the atac peak links plot region.
Package: MultiAssayExperiment
Commit: 30c4a732cd1e8d19a862afde2e2866005f42268a
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-05-06 11:45:00 -0400
Commit message:

 version bump 1.35.3
Package: MultiAssayExperiment
Commit: 8a13d135c68996c736a5441c26aa8b7fe9089746
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-05-06 11:43:26 -0400
Commit message:

 update NEWS.md
Package: MultiAssayExperiment
Commit: bd0d8df10fcc292fc98e34dc7e2ba75e97791626
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-05-06 11:40:29 -0400
Commit message:

 defunct longFormat
Package: cBioPortalData
Commit: 53774d7ee1e7de0e62b151ed8a614f9696a1af5e
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-05-06 11:30:11 -0400
Commit message:

 version bump 2.21.1
Package: cBioPortalData
Commit: e373266cca2b6f75cd93d57c3ff6f7b184199474
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-05-06 11:30:04 -0400
Commit message:

 update action check for dockerfile
Package: cBioPortalData
Commit: b07a5df4e8bfba3ba7e75ddd565b987a61663dfb
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-05-06 11:28:34 -0400
Commit message:

 update NEWS.md
Package: cBioPortalData
Commit: 982678f1419a05940e4b08fa82d0da8fd8711c62
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-05-06 11:24:33 -0400
Commit message:

 defunct removeDataCache; caching not used for cBioPortalData
Package: cBioPortalData
Commit: 2e4927c171e000ffb7a3e268c4f6148eee86b589
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-04-22 14:41:41 -0400
Commit message:

 add _pkgdown.yml file
Package: cBioPortalData
Commit: 171b66b87e9a2b691cc2f4c0f09955accb658a56
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-04-22 14:38:16 -0400
Commit message:

 add GPG to devel builds
Package: cBioPortalData
Commit: 63f8f88a92a0ae0d427e5d8aede89f0f6d56a45f
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-04-21 17:47:08 -0400
Commit message:

 combine test-coverage.yml and devel_check_dock.yml into pr_check.yml
Package: scRNAseqApp
Commit: d88198288736bd35c8b189c9f57b00f76967445a
Author: Jianhong Ou <jou@JNXKY095H1.local>
Date: 2025-05-06 10:48:52 -0400
Commit message:

 try to fix the list dataset issue.
add edge links.
Package: ORFik
Commit: c354336ed971d421fbb391863d7a09e37eac5266
Author: Roleren <hauken_heyken@hotmail.com>
Date: 2025-05-06 10:50:12 +0200
Commit message:

 merge with master
Package: ORFik
Commit: ed015f8edf73265a2ed47c6d43371a873459e2cd
Author: Roleren <hauken_heyken@hotmail.com>
Date: 2025-05-06 10:49:13 +0200
Commit message:

 Merge branch 'master' into devel
Package: ORFik
Commit: 75cf756776c5768eaf23997137f004a7a71d4dc8
Author: Roleren <hauken_heyken@hotmail.com>
Date: 2025-05-06 10:48:53 +0200
Commit message:

 added GenomeInfoDbData to master branch also
Package: ORFik
Commit: d8c01ee84dfd96f9bf5826393a12265a16084dc5
Author: Roleren <hauken_heyken@hotmail.com>
Date: 2025-05-06 10:09:05 +0200
Commit message:

 Implemented pseudoIntronsPerGroup
Package: ORFik
Commit: cb96af05fc115046df56bf09e23eb46db5968536
Author: Roleren <hauken_heyken@hotmail.com>
Date: 2025-05-06 09:07:41 +0200
Commit message:

 synced to RELEASE_3_21 with GenomeInfoDbData in suggest
Package: ORFik
Commit: 41c61cfd6b489a3a455a4a5d774ddf06a22e9638
Author: Roleren <hauken_heyken@hotmail.com>
Date: 2025-05-06 09:05:40 +0200
Commit message:

 added GenomeInfoDbData to suggest
Package: ORFik
Commit: 8caf20a4f0c36500dfb4fac2622f388d7cc997fa
Author: Roleren <hauken_heyken@hotmail.com>
Date: 2025-05-06 09:03:08 +0200
Commit message:

 synced to master
Package: ORFik
Commit: 370ea12f921b67fbcfbbfe955f3129b106516f75
Author: Roleren <hauken_heyken@hotmail.com>
Date: 2025-05-06 08:54:12 +0200
Commit message:

 Added gene summary search through sra.
Improved count table qc
Package: ORFik
Commit: 6cbf3d0a49bf94ebc81c67280e5108a4f358b9bc
Author: Roleren <hauken_heyken@hotmail.com>
Date: 2025-04-03 14:33:56 +0200
Commit message:

 Fixed star bug
Package: ORFik
Commit: 92dae1df50d4a6bed59876b34353417eb5fdbe04
Author: Roleren <hauken_heyken@hotmail.com>
Date: 2025-04-03 12:45:31 +0200
Commit message:

 Improved system usage
Package: ORFik
Commit: 0de26f62f56cc1757737443786a422ce072d5712
Author: Roleren <hauken_heyken@hotmail.com>
Date: 2025-04-03 12:22:55 +0200
Commit message:

 Fixed bug in star index
Package: ORFik
Commit: 8a705b34380d52cb061de5617e46434f904359b3
Author: Roleren <hauken_heyken@hotmail.com>
Date: 2025-03-31 14:47:09 +0200
Commit message:

 T to TRUE fix
Package: ORFik
Commit: 72b33b5e86e2d18ad2ca1006dc9b3992b08f4431
Author: Roleren <hauken_heyken@hotmail.com>
Date: 2025-03-31 13:16:27 +0200
Commit message:

 Improved docs
Package: ORFik
Commit: 5a54993461fdc74dd00bf0eaedb8a604b9fe4466
Author: Roleren <hauken_heyken@hotmail.com>
Date: 2025-03-31 12:44:27 +0200
Commit message:

 Fixed bug in STAR.align.single
Package: ORFik
Commit: d2145b44fc62b6c3ffb78955250ad0626f716d6e
Author: Roleren <hauken_heyken@hotmail.com>
Date: 2025-03-28 11:26:51 +0100
Commit message:

 Added more docs to codon usage
Package: ORFik
Commit: 8578bac5a7c642c0f17e841824652c57f1328dc5
Author: Roleren <hauken_heyken@hotmail.com>
Date: 2025-03-28 11:25:32 +0100
Commit message:

 Split up vignettes to human and yeast ribo-seq pipeline
Package: ORFik
Commit: ffa44f31fd6c298583c3608e6078deeea79a237c
Author: Roleren <hauken_heyken@hotmail.com>
Date: 2025-03-27 11:54:06 +0100
Commit message:

 Improved overall STAR usage, and now have check for system usage.
Package: ORFik
Commit: 73aee7608e31436874a43e3d539293f76732a5a8
Author: Roleren <hauken_heyken@hotmail.com>
Date: 2025-03-26 09:55:34 +0100
Commit message:

 Improved SRA and now allows to outputLibs without existing default files (bam usually)
Package: ORFik
Commit: 1f896b3805928ff064de5098c5ba3f49933e366b
Author: Roleren <hauken_heyken@hotmail.com>
Date: 2025-03-17 21:06:54 +0100
Commit message:

 Added additional input col for DEG model simple
Package: ORFik
Commit: 16f350be553a02db71caba7183711b407ccd9009
Author: Roleren <hauken_heyken@hotmail.com>
Date: 2025-03-10 18:04:50 +0100
Commit message:

 Improved list.experiments()
Package: ORFik
Commit: e6e85dd238014ccdc88e220b36846b47e71944d7
Author: Roleren <hauken_heyken@hotmail.com>
Date: 2025-03-09 23:03:41 +0100
Commit message:

 Small bugfix star
Package: ORFik
Commit: ac1e4a37f77df984f27465c0a5f772bce9070fe7
Author: Roleren <hauken_heyken@hotmail.com>
Date: 2025-03-09 22:59:56 +0100
Commit message:

 Small bugfix star
Package: ORFik
Commit: 107436e5a7aba06ffb4b53320d0c087fc02f160c
Author: Roleren <hauken_heyken@hotmail.com>
Date: 2025-03-09 22:57:48 +0100
Commit message:

 Added trim tail to star call
Package: ORFik
Commit: 37896b4c7fa3d35ae8c06c080a4ffe6fd7fac300
Author: Roleren <hauken_heyken@hotmail.com>
Date: 2025-03-07 00:01:03 +0100
Commit message:

 Improved ebi url finder
Package: ORFik
Commit: 07e6f00bb78c346661132f8187539693f0358ac1
Author: Roleren <hauken_heyken@hotmail.com>
Date: 2025-03-06 20:52:16 +0100
Commit message:

 Added adapter check for trimming.table
Package: HMP16SData
Commit: 95b7a6d2005d3561f65af583ed4b70813ec4b8a4
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-05-05 17:58:46 -0400
Commit message:

 version bump 1.29.1
Package: HMP16SData
Commit: 36dfc67b244cef6e510df62fb9a4c5b71fc494a2
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-05-05 17:56:34 -0400
Commit message:

 add _pkgdown.yml and .github/workflows/pr_check.yml GHA
Package: SingleCellMultiModal
Commit: ee797b5da4b43b07d44e01e3d001b77290fe9240
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-05-05 17:43:20 -0400
Commit message:

 version bump 1.21.1
Package: SingleCellMultiModal
Commit: b3a6a637c79192e3ec7d6b01af6d340d5b733373
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-05-05 17:42:49 -0400
Commit message:

 add _pkgdown.yml and .github/workflows/pr_check.yml GHA
Package: SingleCellMultiModal
Commit: 4b52cd0a6a1b1c77f1302ad702e1f8963b8a4672
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-05-05 17:41:04 -0400
Commit message:

 delete old check-bioc.yml
Package: TCGAutils
Commit: e8fec500766a44fb0a25555c465603554e7745c6
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-05-05 17:38:54 -0400
Commit message:

 version bump 1.29.2
Package: TCGAutils
Commit: 06fa819d16b3cdbe01a7a1030e140534826770ad
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-05-05 17:37:35 -0400
Commit message:

 add _pkgdown.yml and .github/workflows/pr_check.yml GHA
Package: TCGAutils
Commit: 2f98d1087819964259aae21bba19c68c25216aa0
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-05-05 17:34:35 -0400
Commit message:

 remove old CI yml
Package: curatedTCGAData
Commit: 28d4601ebdd0fe997df5c688fc81c55d51de92d0
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-05-05 17:32:41 -0400
Commit message:

 version bump 1.31.1
Package: curatedTCGAData
Commit: a13b6ab5acf8787846b9279cb1247ce24c955e88
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-05-05 17:31:52 -0400
Commit message:

 update CI in .Rbuildignore
Package: curatedTCGAData
Commit: 6c7ebb677a8c2e50374ab0b6f37f0529e3d492b0
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-05-05 17:23:26 -0400
Commit message:

 add _pkgdown.yml and .github/workflows/pr_check.yml GHA
Package: curatedOvarianData
Commit: e5f2a11befda9cb0499238d91cbff9972e03a4ed
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-05-05 16:56:03 -0400
Commit message:

 version bump 1.47.2
Package: curatedOvarianData
Commit: 1c4c95fec616edcc147eac64b142af2938d9f4b2
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-05-05 16:55:56 -0400
Commit message:

 rename CHANGELOG and reformat NEWS.md
Package: curatedOvarianData
Commit: 790fc5ad975f2002613b62f0171b5bc9a9bbfa6d
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-05-05 16:55:37 -0400
Commit message:

 update .Rbuildignore and .gitignore
Package: curatedOvarianData
Commit: 12f0dc9efe79ecfd4dadfff3825285531301d896
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-05-05 16:41:13 -0400
Commit message:

 add R version to fix NOTE
Package: curatedOvarianData
Commit: dbadfc3faee902534a9f65765c25892d43ba9ce2
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-05-05 16:41:03 -0400
Commit message:

 fix URL in _pkgdown.yml
Package: RaggedExperiment
Commit: 00f871113eeec986cfd96e8fed17e50f5850de5a
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-05-05 16:38:11 -0400
Commit message:

 version bump 1.33.2
Package: RaggedExperiment
Commit: 93fb46fc7c79cd5d659484cbf6e10befbb581376
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-05-05 16:37:37 -0400
Commit message:

 fix typo
Package: RaggedExperiment
Commit: 1bd0436479d16a3b77b53a838e914a0bf50a984c
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-05-01 16:23:11 -0400
Commit message:

 skip dock step when Dockerfile not present
Package: curatedOvarianData
Commit: 34a478dd60802446a95a1193f348dd4c62695e25
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-05-05 16:31:01 -0400
Commit message:

 version bump 1.47.1
Package: curatedOvarianData
Commit: cbeb7ff75b7e272652889a675b0176d398a8c537
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-05-05 16:22:33 -0400
Commit message:

 use Authors@R field
Package: curatedOvarianData
Commit: 35c353b2489241039256c6bf74dcd8e2b7f64be0
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-05-05 15:46:55 -0400
Commit message:

 convert Rnw to Rmd
Package: curatedOvarianData
Commit: 5c92aa7b46b025d43e72866c7c20b7433da6597c
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-05-05 15:44:10 -0400
Commit message:

 format DESCRIPTION
Package: curatedOvarianData
Commit: e2dd4d7ce4491a5d296b8e8a2a7c37530f924c90
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-05-05 13:40:40 -0400
Commit message:

 remove check.yml
Package: curatedOvarianData
Commit: dd4d8491ec18a03f3f122cfef03de9659e69f14a
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-05-05 13:38:47 -0400
Commit message:

 add _pkgdown.yml and .github/workflows/pr_check.yml GHA

Co-authored-by: bd4everyone <199158181+bd4everyone@users.noreply.github.com>
Package: curatedOvarianData
Commit: 9c0da919927cfae868cd11f94fe9516d06ca492f
Author: Marcel Ramos Pérez <LiNk-NY@users.noreply.github.com>
Date: 2025-01-06 16:25:17 -0500
Commit message:

 set actions/cache to v4
Package: MultiAssayExperiment
Commit: 0a48ee132c35f6eafd014933a029b232d797ce24
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-05-05 13:28:19 -0400
Commit message:

 version bump 1.35.2
Package: MultiAssayExperiment
Commit: e56ff7f1c6f4ab9b2207a9c457d0e2431559ece1
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-05-05 13:27:07 -0400
Commit message:

 update R ver dep
Package: ProteinGymR
Commit: a07b2cb3a11bad99eb4cfd162ee2b0d5668a157c
Author: tram-nguyen-n <tram_nguyen@hms.harvard.edu>
Date: 2025-05-05 17:04:06 +0000
Commit message:

 - transform aggregated model scores by normalized quantile scale in `plot_structure()`
- change model color palette
Package: CleanUpRNAseq
Commit: e977f16f04fcfa12683d7241dd4f1f5693766038
Author: Liu <haibo.liu@umassmed.edu>
Date: 2025-05-05 11:52:37 -0400
Commit message:

 merge with bioc devel
Package: CleanUpRNAseq
Commit: fc4bda94bcf0439cc17d3a5aba519cf6c3da0894
Author: Liu <haibo.liu@umassmed.edu>
Date: 2025-05-05 11:37:14 -0400
Commit message:

 fix a bug in get_saf() and bump to version 1.3.1
Package: CleanUpRNAseq
Commit: 0e6eced172dd57aa2b7a3bb5be80b71109f2a818
Author: Haibo Liu <48487183+haibol2016@users.noreply.github.com>
Date: 2025-05-05 10:59:53 -0400
Commit message:

 Update misc.R

make setdiff() ingore the strand info for getting intergenic regions
Package: CleanUpRNAseq
Commit: 9d792beb41349d35f654500d52d29ce348f00293
Author: Haibo Liu <48487183+haibol2016@users.noreply.github.com>
Date: 2025-05-05 10:52:51 -0400
Commit message:

 bump to version 1.1.2 after fix a bug in the get_saf()

originally, Genomic ranges representing the intergenic regions were not correct because setdiff() considers the strand information of genomic ranges.
Package: CleanUpRNAseq
Commit: 684eb4a5ec911ce9e2dd8a6bde1af33404bd5688
Author: Haibo Liu <48487183+haibol2016@users.noreply.github.com>
Date: 2025-05-05 10:46:48 -0400
Commit message:

 Merge pull request #2 from AnisMerabet/devel

Update get_saf() function in misc.R
Package: CleanUpRNAseq
Commit: 130d36199e6899ffa015f7a15fcb25338a1f2fb4
Author: AnisMerabet <143795484+AnisMerabet@users.noreply.github.com>
Date: 2025-05-03 20:57:44 +0200
Commit message:

 Update get_saf() function in misc.R

Correct a bug in get_saf() function: setdiff() behavior affected by strand inconsistency.
Package: ATACseqQC
Commit: 3e4fc42d1d320c2b57284901a30f9802d77c0e75
Author: Jianhong Ou <jou@JNXKY095H1.local>
Date: 2025-05-05 09:53:40 -0400
Commit message:

 add option 'ATACseqQC.bigFile'
Package: MIRit
Commit: d896a5b53f68bf05875bd11f81fc921dcca233fe
Author: jacopo-ronchi <jacopo.ronchi@unimib.it>
Date: 2025-05-05 13:30:32 +0000
Commit message:

 The README and the NEWS files for the development version have been updated accordingly.
Package: MIRit
Commit: e0ea5f5bebd44731b62c7013e91506a0e168978e
Author: jacopo-ronchi <jacopo.ronchi@unimib.it>
Date: 2025-05-05 13:14:06 +0000
Commit message:

 Version bump in devel after fixing the url for downloading miRTarBase.
Package: MIRit
Commit: d71b42e9884423e1f559a04143147b53043534b9
Author: jacopo-ronchi <jacopo.ronchi@unimib.it>
Date: 2025-05-05 13:10:12 +0000
Commit message:

 Bug Fix: the url for downloading miRTarBase v10 has been updated.
Package: BenchHub
Commit: ec72278377e74e800e7d983b2b982a73636e599a
Author: Nicholas Robertson <nickrrrr@gmail.com>
Date: 2025-05-05 14:40:46 +0200
Commit message:

 bump version
Package: BenchHub
Commit: d8c186407bb6856e53c6cdb1f77efa4d4e91058d
Author: Nicholas Robertson <nickrrrr@gmail.com>
Date: 2025-05-05 14:40:20 +0200
Commit message:

 fix issues for review
Package: BenchHub
Commit: ecc8e1b76065d30f3b2785542cc5473b88adc7b4
Author: Yue Cao <yue.cao.au@gmail.com>
Date: 2025-04-24 17:42:48 +1000
Commit message:

 Create benchhubstudy_design.R
Package: Pedixplorer
Commit: d77b51b643453a93f42665d506d15e7a8f946d51
Author: Louis Le Nézet <58640615+LouisLeNezet@users.noreply.github.com>
Date: 2025-05-05 11:52:30 +0200
Commit message:

 Update alignment vignette (#27)

* Update alignment vignette

* Update lint workflow

* Add back local

---------

Co-authored-by: Louis Le Nezet <louislenezet@gamil.com>
Package: MetaScope
Commit: cc591d64488293ca9a4126142c3b8a57b9c7c7bc
Author: Aubrey Odom <aodom@bu.edu>
Date: 2025-05-04 01:55:54 -0400
Commit message:

 Update version number
Package: MetaScope
Commit: 3f813e28669a00769e5ad7bd68e04c216ee004f5
Author: Aubrey Odom <aodom@bu.edu>
Date: 2025-05-04 01:32:44 -0400
Commit message:

 Updated issue with convert_animalcules and overaccounting of present reads
Package: MassSpecWavelet
Commit: 486cc2b7d076c8ec0189fbafa043e0a8af4476bb
Author: Sergio Oller <sergioller@gmail.com>
Date: 2025-05-04 02:55:37 +0200
Commit message:

 Update NEWS
Package: MassSpecWavelet
Commit: b2dceebdf62725d42fa2747798fc000ddbd34538
Author: Sergio Oller <sergioller@gmail.com>
Date: 2025-05-04 01:19:00 +0200
Commit message:

 Provide more details on identified peaks to better optimize parameters
Package: MassSpecWavelet
Commit: 9f77e22006579ed285fe1cfda0d2686975962062
Author: Sergio Oller <sergioller@gmail.com>
Date: 2025-05-04 00:28:52 +0200
Commit message:

 Methods to display prepared_wavelets objects
Package: ProteinGymR
Commit: e41f98a8fa75ab9db1b57540e7559625f4c8ac66
Author: Tram Nguyen <tram_nguyen@hms.harvard.edu>
Date: 2025-05-03 14:49:51 -0400
Commit message:

 Merge pull request #42 from ccb-hms/model_corr_plots

merge `model_corr_plots` branch
Package: ProteinGymR
Commit: ef6f747a08a4753b8323f7eead0bb54837c14a9d
Author: tram-nguyen-n <tram_nguyen@hms.harvard.edu>
Date: 2025-05-03 18:48:08 +0000
Commit message:

 deprecated `alphamissense_table` argument documentation
Package: ProteinGymR
Commit: d05dd1dbe1b92c16a3dbddb1a7b9bbc8afd678f1
Author: tram-nguyen-n <tram_nguyen@hms.harvard.edu>
Date: 2025-05-03 14:16:12 +0000
Commit message:

 added dependencies
Package: ProteinGymR
Commit: cdaad156abe79cb4f870f1a27e7771cd5a762cf5
Author: tram-nguyen-n <tram_nguyen@hms.harvard.edu>
Date: 2025-05-03 13:10:56 +0000
Commit message:

 additional dependencies
Package: ProteinGymR
Commit: 02a2bce88a80a9a75d4ec8b4de7958b03f088e02
Author: tram-nguyen-n <tram_nguyen@hms.harvard.edu>
Date: 2025-05-03 13:09:19 +0000
Commit message:

 replace correlation code with functions
Package: ProteinGymR
Commit: eb6ec1810aba447485f79a2af96ede513e8c63f1
Author: tram-nguyen-n <tram_nguyen@hms.harvard.edu>
Date: 2025-05-03 13:08:21 +0000
Commit message:

 allow two model comparison with `model_corr_plot()`
Package: ProteinGymR
Commit: 26ef2750891b7a98996ef1ff0805a968d9aefa80
Author: tram-nguyen-n <tram_nguyen@hms.harvard.edu>
Date: 2025-04-30 19:50:52 +0000
Commit message:

 updated examples in documentation
Package: ProteinGymR
Commit: be6a2761512c9c05d709482e99a72a8bd029aa31
Author: tram-nguyen-n <tram_nguyen@hms.harvard.edu>
Date: 2025-04-30 19:28:42 +0000
Commit message:

 add model score plotting to `plot_structure()`
Package: ProteinGymR
Commit: e4082b7bdd84cfb9e1e346882e754675f2c0fd91
Author: tram-nguyen-n <tram_nguyen@hms.harvard.edu>
Date: 2025-04-30 16:44:39 +0000
Commit message:

 add unit test for updated `dms_corr_plot()`
Package: ProteinGymR
Commit: af27ea1e3a92fabd2976962b33d24c5387f37df2
Author: tram-nguyen-n <tram_nguyen@hms.harvard.edu>
Date: 2025-04-29 16:24:59 +0000
Commit message:

 generalize `dms_corr_plot()` to any model, not just AM.
- deprecated `alphamissense_table` arg
- replace with `model` arg
Package: MassSpecWavelet
Commit: d08ce4c1e85f2804a8fea099ad93fec8e9982427
Author: Sergio Oller <sergioller@gmail.com>
Date: 2025-05-03 15:45:18 +0200
Commit message:

 Bump version
Package: MassSpecWavelet
Commit: 9b1577d57ab306464df6848c2c2c9cce418f4f61
Author: Sergio Oller <sergioller@gmail.com>
Date: 2025-05-03 15:30:00 +0200
Commit message:

 Update NEWS
Package: MassSpecWavelet
Commit: 0f3e6b51751573099543f9996c684d6ebbb80d68
Author: Sergio Oller <sergioller@gmail.com>
Date: 2025-05-03 15:28:56 +0200
Commit message:

 devtools::document()
Package: MassSpecWavelet
Commit: 8c6fdccdb663b92d0378d9edd18ab6c7cc8191eb
Author: Sergio Oller <sergioller@gmail.com>
Date: 2025-05-03 15:28:45 +0200
Commit message:

 Improve documentation of identifyMajorPeaks
Package: MassSpecWavelet
Commit: 7f7dc1f250a27bc920a08c622a0447021b44f744
Author: Sergio Oller <sergioller@gmail.com>
Date: 2025-05-03 15:28:12 +0200
Commit message:

 Properly handle SNR.Th=0 and excludeBoundariesSize=0
Package: MassSpecWavelet
Commit: 072135d8da03b5a06f8444a10509ec17bc58cb95
Author: Sergio Oller <sergioller@gmail.com>
Date: 2025-05-03 15:27:28 +0200
Commit message:

 Error on invalid SNR.method value
Package: MassSpecWavelet
Commit: 5471daec768b6f1ffa9f85d77021e2ee60d729fd
Author: Sergio Oller <sergioller@gmail.com>
Date: 2025-05-03 13:46:06 +0200
Commit message:

 devtools::document()
Package: MassSpecWavelet
Commit: b6623247c4b16979a57fa50c7d890b1bf951af51
Author: Sergio Oller <sergioller@gmail.com>
Date: 2025-05-03 13:45:53 +0200
Commit message:

 Fix NOTE on special latex characters
Package: edgeR
Commit: fbb43b78051f27f06cb5e6f8c7190cbe5a5d35b6
Author: Gordon Smyth <smyth@wehi.edu.au>
Date: 2025-05-03 12:51:53 +1000
Commit message:

 edgeR 4.7.2
- Update edgeR-Tests.Rout.save to reflect bug fix to limma::diffSplice last month
Package: edgeR
Commit: c0637b9b2eaa1545aed7aef71374bc7eeddc069c
Author: Gordon Smyth <smyth@wehi.edu.au>
Date: 2025-05-03 12:43:42 +1000
Commit message:

 edgeR 4.7.1
- Update User's Guide
Package: AWAggregatorData
Commit: 7f10b951ea0a1fd72a155b302ada6d248c018770
Author: Jiahua Tan <jiahuatan@chem.ubc.ca>
Date: 2025-05-02 19:04:45 -0700
Commit message:

 Trigger Bioconductor Report & Fix Potential Package Rd Warning

1. Incremented version ID to trigger a new Bioconductor build/report
2. Edited files in "R/" and "man/" directories to resolve a potential warning due to a missing "\value" section in the "AWAggregatorData-package.Rd" documentation.
Package: GSAR
Commit: ddc997eb370b79cd09df712c34b6566b995295b5
Author: yrahmatallah <yrahmatallah@uams.edu>
Date: 2025-05-02 21:07:31 -0500
Commit message:

 updateRef2-5-2-2025
Package: GSAR
Commit: 0d390ebfa1b4382a19aa55033598b471e8b52766
Author: Rahmatallah <RahmatallahYasir@uams.edu>
Date: 2025-05-02 21:02:15 -0500
Commit message:

 updateRef-5-2-2025
Package: GeneTonic
Commit: 2ab39c1b5ff4dfa00d0b8692cf0d5096a594b808
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2025-05-03 01:04:43 +0200
Commit message:

 version bump, 3.3.1
Package: GeneTonic
Commit: 503dc4b7432067d26575d7cbf98c1f6787243c2e
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2025-05-03 01:04:33 +0200
Commit message:

 updated news
Package: GeneTonic
Commit: 4d47e1ab77cb2684cc724218137d2a233e56d2a8
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2025-05-02 16:28:57 +0200
Commit message:

 enrichment_map carries along the information on the value it should color by (as a favor to the gg-world)
Package: GeneTonic
Commit: 97ffd232b434ba3b3b5c73a0563ef4fae118acaa
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2025-05-02 09:04:21 +0200
Commit message:

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

# Conflicts:
#	DESCRIPTION
Package: GeneTonic
Commit: c5f2fef165e3f9cd5994538f82100caa8150039d
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2025-03-07 14:36:46 +0100
Commit message:

 updating GHA to a more recent cache version
Package: GeneTonic
Commit: 2cebd920d6a94e87c7ffc4bdfdddb45beebbae64
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2025-03-05 18:48:06 +0100
Commit message:

 version bump, 3.1.5
Package: GeneTonic
Commit: 1dcef33e9b46ba705152bef1725cc377161f1f9b
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2025-03-05 18:47:57 +0100
Commit message:

 rerendered manpage of the pkg itself
Package: GeneTonic
Commit: 25a0cc0ecd30f36df44a360b465be26e735afd15
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2025-03-05 18:47:19 +0100
Commit message:

 more informative message returned upon loading in the data
Package: GeneTonic
Commit: e1a08675d3ef1e87c419637f69726b2da688c451
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2025-03-05 18:46:49 +0100
Commit message:

 fixing capitalization of bibtex entry
Package: GeneTonic
Commit: 0732bfc6dcbde3250cc279c1ef665f3a83ad4eae
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2025-02-18 12:11:56 +0100
Commit message:

 fixing DESCRIPTION extra parenthesis
Package: GeneTonic
Commit: e7ce5d24e95605644c8a94df02ae9f0d98cd58b6
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2025-02-18 08:10:34 +0100
Commit message:

 added Edo as contributor
Package: GeneTonic
Commit: 37b94b969bde567faf2ff128256c0f090efc1be9
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2025-02-18 08:10:24 +0100
Commit message:

 updated Annekathrin's surname, it was due time
Package: GeneTonic
Commit: ddf579aca2f577d90b9ff0a2dd4f9fadeecd884e
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2025-02-17 18:52:24 +0100
Commit message:

 updated news
Package: GeneTonic
Commit: 889f4a669a5b206eae287ee6b8fb8d68372ee6fd
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2025-02-17 18:51:01 +0100
Commit message:

 version bump, 3.1.4
Package: GeneTonic
Commit: 0e4d337f5706c02a60eea283afbca75a9dca6505
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2025-02-17 18:50:08 +0100
Commit message:

 ref to #63 PR
Package: GeneTonic
Commit: dc23b5b92f50dd52a8719df60505b2304a6b900a
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2025-02-17 18:36:41 +0100
Commit message:

 fixing the typo
Package: GeneTonic
Commit: 99c5edf188b35e64919ffbe04109a2c5b017c6c0
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2025-02-17 18:36:41 +0100
Commit message:

 fixing the typo
Package: GeneTonic
Commit: 8a180535b057c40aaab7b1276bc149df7cf69e6a
Author: “edo98811” <“filippie@uni-mainz.de”>
Date: 2025-02-10 13:53:33 +0100
Commit message:

 gs_heatmap: if there is only one gene to be plotted in the heatmap it creates a warning, it avoid collapsing the dataframe
Package: GeneTonic
Commit: 2d4e4d277cc4a2b28060ddd103b588d41436bf88
Author: “edo98811” <“filippie@uni-mainz.de”>
Date: 2025-02-10 11:40:53 +0100
Commit message:

 added check for error message and creating a temporary res_enrich table table
Package: GeneTonic
Commit: c41ba65bca449c67514170d8079cbfee5a1072da
Author: Edoardo Filippi <63752787+edo98811@users.noreply.github.com>
Date: 2025-02-10 11:30:58 +0100
Commit message:

 Merge branch 'federicomarini:devel' into devel
Package: GeneTonic
Commit: 493637ccd447abc0c0be9e9d2106bdafe2a1fdd2
Author: “edo98811” <“filippie@uni-mainz.de”>
Date: 2025-02-10 11:30:13 +0100
Commit message:

 gs_heatamp: handled case there is only one gene to plot in the heatmap
Package: GeneTonic
Commit: 4fb79766f39bb334367f8cc62485814e39f23dc2
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2025-01-29 22:17:01 +0100
Commit message:

 version bump, 3.1.3
Package: GeneTonic
Commit: 23033361450edb0d47215bd5bb3466e55971a0c4
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2025-01-29 22:16:20 +0100
Commit message:

 tiny but potentially impactful change ("fixing" gs_heatmap), with inverted order of the arguments to the calls to `intersect`
Package: BiocCheck
Commit: d1618aaead8387cedcd5e6707c1ee7b835481eb5
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-05-02 18:39:04 -0400
Commit message:

 version bump 1.45.6
Package: BiocCheck
Commit: 7f8f671e73d19812bee472fe9a0a2a645f09c962
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-05-02 18:13:34 -0400
Commit message:

 update checkNEWS section, closes #73

- return error when news() result is null or not news_db class
Package: BiocCheck
Commit: d46f2d01bfe8ad505637d878ac8f311209200fed
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-05-02 16:50:53 -0400
Commit message:

 version bump 1.45.5
Package: BiocCheck
Commit: 762b2e9ad76241dc3a7a37042d4e51f1d72c5395
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-05-02 16:50:39 -0400
Commit message:

 fix coordinate line numbers for vignette checks, closes #226
Package: gemma.R
Commit: a58a49164385d38509a44eb687bbfbaa9e0b311a
Author: OganM <ogan.mancarcii@gmail.com>
Date: 2025-05-02 13:42:01 -0700
Commit message:

 measurements has summaries too
Package: gemma.R
Commit: 0edd26ef2bc6aee4d6f7a26a8c418fc8fdab399a
Author: OganM <ogan.mancarcii@gmail.com>
Date: 2025-05-02 13:38:15 -0700
Commit message:

 Merge branch 'devel' of github.com:PavlidisLab/gemma.R into devel
Package: gemma.R
Commit: 1350b1c8855b6a47c8a21ccadd052320f1a0a20b
Author: A Wokaty <andres.wokaty@sph.cuny.edu>
Date: 2025-04-15 12:56:36 -0400
Commit message:

 bump x.y.z version to odd y following creation of RELEASE_3_21 branch
Package: gemma.R
Commit: 1f0164f8cc7846f9660eca4c68b344fe6c33bf54
Author: A Wokaty <andres.wokaty@sph.cuny.edu>
Date: 2025-04-15 12:56:36 -0400
Commit message:

 bump x.y.z version to even y prior to creation of RELEASE_3_21 branch
Package: gemma.R
Commit: 733c2294ec1a291ff3a822b95b4e60df8b34ac08
Author: OganM <ogan.mancarcii@gmail.com>
Date: 2025-05-02 13:18:08 -0700
Commit message:

 better support for measurements when accessing differential expression data
Package: pgxRpi
Commit: cdad3bb44757b422737f060b42affd19a2cd8fcd
Author: hangjiaz <zhaohj314@gmail.com>
Date: 2025-05-02 11:51:47 -0400
Commit message:

 version bump in devel
Package: pgxRpi
Commit: 05bfd7f13fa5fc7cb7e5182d74010ca01471dc08
Author: hangjiaz <zhaohj314@gmail.com>
Date: 2025-05-02 11:50:44 -0400
Commit message:

 v1.5.2: add more tests; change cancercellline example in vignettes
Package: ribosomeProfilingQC
Commit: fabbd112a5e4b2322d19ff02444085e6ba4ecbfb
Author: Jianhong Ou <jou@JNXKY095H1.local>
Date: 2025-05-02 10:47:39 -0400
Commit message:

 update the documents.
Package: ribosomeProfilingQC
Commit: 009f6e261d15f10efe084ac8f814bee71f44e749
Author: JIANHONG OU <jianhong@users.noreply.github.com>
Date: 2025-05-02 10:13:01 -0400
Commit message:

 Merge pull request #12 from hpages/devel

ribosomeProfilingQC 1.21.1 -- add GenomeInfoDbData to Suggests
Package: ribosomeProfilingQC
Commit: 272e0ae12a49736dd1cae21bbc5827f1e977a817
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2025-04-30 17:29:29 -0700
Commit message:

 ribosomeProfilingQC 1.21.1 -- add GenomeInfoDbData to Suggests

The ribosomeProfilingQC package uses txdbmaker::makeTxDbFromGFF() in
various places, which relies on the GenomeInfoDbData package.

Also all the makeTxDb*() functions were moved from GenomicFeatures to
txdbmaker about 1 year ago (in BioC 3.19), so library(txdbmaker) now
needs to be used instead of library(GenomicFeatures) before calling
makeTxDbFromGFF() in the vignette and examples.
Package: BiocCheck
Commit: 0b397d049773f3b738443cb6b0d54b0f04f0120c
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-05-02 10:13:12 -0400
Commit message:

 version bump 1.45.4
Package: BiocCheck
Commit: 358a4346d71a7c7074a4f24da81f840678161304
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-04-24 16:58:42 -0400
Commit message:

 update vignette to changes
Package: BiocCheck
Commit: 5722a3d4f7a448c2b429fa25b12e3ff200a3a24e
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-04-24 16:53:36 -0400
Commit message:

 update unit tests
Package: BiocCheck
Commit: 8efe69455adcbf8ac642e21e3c8ec649f1e32f63
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-04-24 16:53:11 -0400
Commit message:

 Set warning for grep install.* calls instead of error, closes #227
Package: BiocCheck
Commit: 53b677dfc211fed15740b82174808f9b6ef542e6
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-04-24 16:51:46 -0400
Commit message:

 set checkPkgInstallCalls to error for .BAD_INSTALL_CALLS
Package: BiocCheck
Commit: 2d71c1309812b08afb2686bc409f024db246fea8
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-04-24 16:50:47 -0400
Commit message:

 remove duplicate check for .BAD_INSTALL_CALLS in R files
Package: bsseq
Commit: c112942973696d1d4392c3f56d3054d415708d60
Author: Kasper Daniel Hansen <kasperdanielhansen@gmail.com>
Date: 2025-05-01 17:18:50 -0400
Commit message:

 Merge pull request #146 from SrenBlikdal/version-update-1.45.1

Add function to read bedMethyl files from modkit and filter using likelihoods
Package: bsseq
Commit: ba382c169c597f775c709750002fc951f842a068
Author: SrenBlikdal <vrt191@alumni.ku.dk>
Date: 2025-05-01 00:34:56 +0200
Commit message:

 Fixed warning by changing proper import from matrixStats to DelayedMatrixStats
Package: bsseq
Commit: b89d19e30a12ce3bd3fdc81d6d6caca084827d31
Author: SrenBlikdal <vrt191@alumni.ku.dk>
Date: 2025-04-29 21:12:51 +0200
Commit message:

 Add function to read bedMethyl files from modkit along with the functions to compute and filter using scaled likelihoods CpG status
Package: pgxRpi
Commit: 4ef4d12cc9c032604fd5764bd49cf89bb7a34e94
Author: hangjiaz <zhaohj314@gmail.com>
Date: 2025-05-02 00:23:17 -0400
Commit message:

 version bump in devel
Package: pgxRpi
Commit: 7198c5f7c0421c0a14e78c6860a646fbe565ecdf
Author: hangjiaz <zhaohj314@gmail.com>
Date: 2025-05-02 00:21:04 -0400
Commit message:

 1.5.1 update: add bioc version requirement to readme; add limit in variant query to reutn all variants; bug fix for optimising warning
Package: NanoMethViz
Commit: bed7908ae0d30d2a941a585af73e40b7c83e320c
Author: shians <registertonysu@gmail.com>
Date: 2025-05-02 12:08:48 +1000
Commit message:

 Version bump
Package: NanoMethViz
Commit: 28cbcef26270c1ee690b46994ead5e7aebf75e2d
Author: shians <registertonysu@gmail.com>
Date: 2025-05-02 12:08:29 +1000
Commit message:

 Added t2t exons and CGI
Package: NanoMethViz
Commit: 564800578b4439361987d5415646169037955e5a
Author: shians <registertonysu@gmail.com>
Date: 2025-04-18 22:09:39 +1000
Commit message:

 Changed annotation plot spacing
Package: NanoMethViz
Commit: 84df59303758f22007d6e6b3675ccf1f1e382609
Author: shians <registertonysu@gmail.com>
Date: 2025-04-18 21:48:22 +1000
Commit message:

 Refactored annotation plot
Package: CPSM
Commit: 2044bc8531a79a7003c71681f0ea4418d71082b0
Author: Harpreet Kaur <hks04180@gmail.com>
Date: 2025-05-01 19:15:53 -0400
Commit message:

 Update R/MTLR_pred_model_f.R , R/surv_curve_plots_f.R , R/ Lasso_PI_scores_f.R , R/mean_median_surv_barplot_f.R , R/Nomogram_generate_f.R  files to remove any undesired package
Package: SplineDV
Commit: 16d71a5d2ebbf2d9d45c7ee19a672589411f30cb
Author: xenon8778 <xenon8778@tamu.edu>
Date: 2025-05-01 15:49:20 -0500
Commit message:

 v1.1.1: Citation update
Package: RaggedExperiment
Commit: 818e0ae3e21c8ce1d569dce16ad3af334f276450
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-05-01 16:08:18 -0400
Commit message:

 version bump 1.33.1
Package: RaggedExperiment
Commit: 65ae5e217b4866589161bf4642c0dad182d991db
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-05-01 16:07:12 -0400
Commit message:

 move svg to man/figures/ for pkgdown
Package: RaggedExperiment
Commit: 988683522bb7d7730c1d5f4a8756e20ccecca71f
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-05-01 16:05:47 -0400
Commit message:

 add URL field to DESCRIPTION
Package: RaggedExperiment
Commit: b288dc8fcac01f28ff5ca8c5f32897b1b6225a80
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-05-01 14:59:58 -0400
Commit message:

 add _pkgdown.yml and .github/workflows/pr_check.yml GHA

Co-authored-by: bd4everyone <199158181+bd4everyone@users.noreply.github.com>
Package: Rigraphlib
Commit: ae7ce6708d9fc38bb154aafc8c09a5241bb3ec44
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2025-05-01 12:03:06 -0700
Commit message:

 Stop installation if the system2() commands have non-zero exit.
Package: igblastr
Commit: fc2c45cd385eb4b69d8caf8f4234b7fd2efe65ad
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2025-05-01 11:14:21 -0700
Commit message:

 igblastr 0.99.3

Use only 2 cores for parallel execution when environment variable
_R_CHECK_LIMIT_CORES_ is set to TRUE.
Package: miaDash
Commit: 5d409864a06f44f4dda725e1d3e625923cbef323
Author: Giulio Benedetti <giuliobene2000@gmail.com>
Date: 2025-05-01 20:40:35 +0300
Commit message:

 Bump version
Package: miaDash
Commit: 5c86d75dd2b3ff7ef49f64c8d367ad484a70bda0
Author: Giulio Benedetti <giuliobene2000@gmail.com>
Date: 2025-04-23 10:13:08 +0300
Commit message:

 Merge pull request #21 from microbiome/tab_title

Tab title
Package: miaDash
Commit: 13fdf6318273476c4bf46655473e0d4e73b35d64
Author: Giulio Benedetti <giuliobene2000@gmail.com>
Date: 2025-04-22 18:53:32 +0200
Commit message:

 Update NEWS
Package: miaDash
Commit: 1a5bbead8d36723d25fa9d14333a1bee083af6c7
Author: Giulio Benedetti <giuliobene2000@gmail.com>
Date: 2025-04-22 18:52:47 +0200
Commit message:

 Bump version
Package: miaDash
Commit: bf5944573a75c2760f03c5ec7819edb451a496f3
Author: Giulio Benedetti <giuliobene2000@gmail.com>
Date: 2025-04-22 18:50:57 +0200
Commit message:

 Add tabTitle support
Package: mosdef
Commit: 0964a99d45fa4a5bccac056ae78e61a0f3906a2c
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2025-05-01 15:15:36 +0200
Commit message:

 Merge pull request #17 from imbeimainz/magmafix

Magmafix
Package: mosdef
Commit: f6336cab5ca7f649e4b527203abca47685372a86
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2025-05-01 15:08:57 +0200
Commit message:

 version bump, 1.5.1 - hotfix to volcano functions
Package: mosdef
Commit: 4c9661f361c2815b040a0af78159c59753c2e4b2
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2025-05-01 15:08:23 +0200
Commit message:

 updated news
Package: mosdef
Commit: 594b077ebee47328237bf5e677d9ca258807ab0d
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2025-05-01 15:06:17 +0200
Commit message:

 manpage redone
Package: mosdef
Commit: 5311ecaa7116162846f1e685ff2c18b39aa14f86
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2025-05-01 15:06:08 +0200
Commit message:

 carrying over the edits to the generic volcano plot function onto the go_volcano function
Package: mosdef
Commit: 427011eb9a0853150fa5249a674bef7876af41b1
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2025-05-01 14:47:27 +0200
Commit message:

 Merge branch 'devel' into magmafix
Package: mosdef
Commit: 39e8fd9c8bcd245c8a7583e2eb81c9531beaccf1
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2025-05-01 14:45:28 +0200
Commit message:

 re-rendering manpages
Package: mosdef
Commit: deb96e793b32bbacf9e89e9a17f59cd769d35782
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2025-05-01 14:45:10 +0200
Commit message:

 correctly forcing the values of the legend (relevant if not all three categories would show up)
Package: mosdef
Commit: 14aa79577e57b9e1fa60f198e0c903d51ab679ad
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2025-05-01 14:44:32 +0200
Commit message:

 lfc cutoff defaulting to 0 to avoid "mental thresholding"
Package: mosdef
Commit: d00fe2d6a5c4b98e01dd0e05f63741a53bf28a70
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2025-05-01 14:44:09 +0200
Commit message:

 making horizontal line optional
Package: mosdef
Commit: 35a4f011006182ecefd113e5e9638b70ab7e0b20
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2025-05-01 14:43:28 +0200
Commit message:

 filtering on adj pvalues to have correct coloring
Package: mosdef
Commit: 216bc3e70eda329594c3a5bfcc23ecba8430eff2
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2025-05-01 14:46:48 +0200
Commit message:

 Merge remote-tracking branch 'upstream/devel' into devel
Package: mosdef
Commit: 972127cbf8e8502a9f7705532f7257218dd58e3a
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2025-03-07 15:10:46 +0100
Commit message:

 updating GHA to a more recent cache version
Package: QuasR
Commit: cbb6408bb335c7452c0cd1b7a594c768e57d735b
Author: mbstadler <stadler.michael@gmail.com>
Date: 2025-05-01 10:53:36 +0200
Commit message:

 add GenomeInfoDbData to Suggests to adapt to recent changes in GenomeInfoDb (https://github.com/Bioconductor/GenomeInfoDb/commit/c4126c181c97a0914f52066c716958a08c797d81)
Package: biocmake
Commit: 46e90f99cf721ea8745342028ca985398fb4e96d
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2025-05-01 00:16:54 -0700
Commit message:

 Provide filepaths for CMAKE_AR and CMAKE_RANLIB, not just commands.

Otherwise they seem to be treated as local paths in the working directory.
Package: BiocFHIR
Commit: 6a27e5df959d851fb001ccb7fa33436c7898225a
Author: vjcitn <stvjc@channing.harvard.edu>
Date: 2025-04-30 20:48:46 -0400
Commit message:

 Merge branch 'devel' of git.bioconductor.org:packages/BiocFHIR into devel
Package: BiocFHIR
Commit: a54a32dc2527e7c1b56a31a7ef05fe4de38a6397
Author: vjcitn <stvjc@channing.harvard.edu>
Date: 2025-04-30 20:47:05 -0400
Commit message:

 minor changes
Package: BiocPkgTools
Commit: bc9f597e489f4678b7dd3e4516c566fc24e57e83
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-04-30 18:23:12 -0400
Commit message:

 version bump 1.27.3
Package: BiocPkgTools
Commit: 3d913469d5e3f6bce804e1bbbe0ec5745eadce12
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-04-30 18:08:19 -0400
Commit message:

 remove rtype="web" from bfcdownload
Package: beachmat.hdf5
Commit: a0b7ff1945d05e4a260ad47417c5fd3fb368efa7
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2025-04-30 14:26:26 -0700
Commit message:

 Merge remote-tracking branch 'upstream/devel'
Package: beachmat.hdf5
Commit: deee4d9918142df47307c4673c7a1b317a647387
Author: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: 2024-11-14 21:41:22 -0800
Commit message:

 Add links to the BioC landing pages in the README.
Package: BiocCheck
Commit: dfb1e7ab36270c8ac6962f8ab8708b8bceeb36e4
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-04-30 15:18:23 -0400
Commit message:

 version bump 1.45.3
Package: BiocCheck
Commit: 46acc8e7588302b9e7c78f3e2220f3f0d8ffa079
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2025-04-30 15:18:01 -0400
Commit message:

 remove rtype="web" from bfcdownload call
Package: proBAMr
Commit: c2450bbadda13b1f766ca32872db809fdc91620f
Author: Hervé Pagès <hpages.on.github@gmail.com>
Date: 2025-04-30 12:07:53 -0700
Commit message:

 proBAMr 1.43.1 -- add GenomeInfoDbData to Suggests

proBAMr makes calls to txdbmaker::makeTxDbFromGFF() internally, which
relies on the GenomeInfoDbData package.
Package: TBSignatureProfiler
Commit: 2d27ac32b448d3c899a1a30feaed6a24799d7355
Author: Aubrey Odom <aodom@bu.edu>
Date: 2025-04-30 13:57:23 -0400
Commit message:

 Merge branch 'main' of https://github.com/wejlab/tbsignatureprofiler
Package: TBSignatureProfiler
Commit: 5f20e60047d8c8690324cde21cb36a3e2565a3cb
Author: Aubrey Odom <aodom@bu.edu>
Date: 2025-04-30 13:41:55 -0400
Commit message:

 Update version number
Package: TBSignatureProfiler
Commit: 76ca7995f909513544649e7c3c0455d278c12693
Author: Aubrey Odom <aodom@bu.edu>
Date: 2025-04-30 13:34:00 -0400
Commit message:

 Implement fix to convert gene names with unaccepted encoding