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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: iClusterPlus
Commit: 954aabde7ed69942d3e85f56ef845339b4ef6cb0
Author: qianxing.mo <qianxing.mo@moffitt.org>
Date: 2026-03-20 15:34:31 -0400
Commit message:

 change Integrative clustering to iCluster for consistency in Tutorial_iCluster2b_singleCell.Rmd
Package: omicsViewer
Commit: bfd7dd713e1312070e1fd61361b8c1c86df226bd
Author: Chen Meng <mengchen18@gmail.com>
Date: 2026-03-20 18:43:34 +0100
Commit message:

 feat: complete snapshot status save/restore for all modules

- Fix na2null crash on vector inputs during snapshot restore
  (is.na on vector + || requires scalar logical)
- Add status save/restore for ORA triselector selection
- Add status save/restore for PTM motif triselector selection
- Add Bees/Curve plot type save/restore in feature_general
- Include cor heatmap and dynamic heatmap status in data space return
- Restore feature/sample selection from snapshots in L0_module_app
- Fix WebGL detection timing (shiny:connected vs document.ready)
- Wrap PTM/ORA status in tryCatch for modules without data

Bump version to 1.15.4.

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
Package: omicsViewer
Commit: ac050cb6c9cd2aa6be13322b3fa3dc5e594cb900
Author: Chen Meng <mengchen18@gmail.com>
Date: 2026-03-20 16:58:21 +0100
Commit message:

 fix: scatter plot regression line crash on NA/Inf and WebGL fallback

- Replace !is.na() filter with is.finite() to also exclude Inf/-Inf
  values that cause lm() and cor.test() to fail
- Use cleaned df$x/df$y in cor.test() instead of raw input vectors
- Move toWebGL() from plotly_scatter() into renderPlotly with
  browser-side WebGL detection, falling back to standard plotly
  when WebGL is not supported
- Add CLAUDE.md with developer notes

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
Package: DMRsegaldata
Commit: 8a7ee2dc0eebcc5deb12ba647b526b20922c4c91
Author: vaslem <vaslemonidis@hotmail.com>
Date: 2026-03-20 18:21:20 +0100
Commit message:

 Bump package version to 0.99.6 in DESCRIPTION and documentation
Package: DMRsegaldata
Commit: 0df93a023b1a4511dcbfabe079b115b28373db2f
Author: vaslem <vaslemonidis@hotmail.com>
Date: 2026-03-20 18:12:26 +0100
Commit message:

 Add ExperimentHub to package dependencies in DESCRIPTION to conform with at least one Bioconductor dependency
Package: DMRsegaldata
Commit: 62d1e9b900e83fb2f90fc54f5ab4bceb855fb15e
Author: vaslem <vaslemonidis@hotmail.com>
Date: 2026-03-20 18:07:24 +0100
Commit message:

 Extended the /dontrun in the example
Package: DMRsegaldata
Commit: 4eb3c0a8308b739a0f5f4dc11b7058c28772edb2
Author: vaslem <vaslemonidis@hotmail.com>
Date: 2026-03-20 18:02:20 +0100
Commit message:

 Updated tags on bioconductor site
Package: DMRsegaldata
Commit: b9cca4bce3ebb2ec5774fe65f8ea55db18e890c8
Author: vaslem <vaslemonidis@hotmail.com>
Date: 2026-03-20 17:55:23 +0100
Commit message:

 Removed future package and updatd pattern matching in .Rbuildignore
Package: DMRsegaldata
Commit: 42a42969298bd9a8f77ba006bafe4ecd0e4ce5bc
Author: vaslem <vaslemonidis@hotmail.com>
Date: 2026-03-20 17:39:57 +0100
Commit message:

 Minor fixes, regarding formatting
Package: DMRsegaldata
Commit: 803dc488ac430dba7c6fe6c3d8bc96c0415b829d
Author: vaslem <vaslemonidis@hotmail.com>
Date: 2026-03-02 17:53:27 +0100
Commit message:

 Update .Rbuildignore to include .lintr and data directories
Package: DMRsegaldata
Commit: 99cac17fbcc8502efe722a849031ec1fc5779c4f
Author: vaslem <vaslemonidis@hotmail.com>
Date: 2026-03-02 17:48:47 +0100
Commit message:

 Update .gitignore to include .lintr and remove .lintr file; modify make-data.R to delete temporary files after data download
Package: DMRsegaldata
Commit: 63f3066af51baf8c320e360145842e43b650e004
Author: vaslem <vaslemonidis@hotmail.com>
Date: 2026-03-02 17:40:52 +0100
Commit message:

 Update .gitignore to exclude the parent directory of Rcheck
Package: DMRsegaldata
Commit: f1aa9238cb7e5eb04fc54acc0171af50dd4a1efa
Author: vaslem <vaslemonidis@hotmail.com>
Date: 2026-03-02 17:39:20 +0100
Commit message:

 Fix .gitignore to correctly include DMRsegaldata.Rcheck directory
Package: signatureSearch
Commit: 971fc48def05c1bf9cf803dced46c6e6df5d624c
Author: brendangongol <brengong@gmail.com>
Date: 2026-03-20 08:53:47 -0700
Commit message:

 Addresseing warning messages
Package: Chromatograms
Commit: 4bd208631edc0b5e14b80968dbd834e4dace05a9
Author: Philippine Louail <philippine.louail@outlook.com>
Date: 2026-03-20 16:27:07 +0100
Commit message:

 Merge pull request #49 from rformassspectrometry/phili

feat: add peakBoundary()
Package: Chromatograms
Commit: fc438cb648165c5147ab43b6034b8685b943cd6e
Author: Philippine Louail <127301965+philouail@users.noreply.github.com>
Date: 2026-03-20 16:09:53 +0100
Commit message:

 fix: use valleys()
Package: Chromatograms
Commit: f6943b3560cb0061888b015a16265b16ca98edbc
Author: Philippine Louail <127301965+philouail@users.noreply.github.com>
Date: 2026-03-20 15:07:59 +0100
Commit message:

 feat: add peakBoundary()
Package: scater
Commit: ec4264a15da1ab41fb2173d1093e87644b2760ca
Author: Alan O'Callaghan <alan.ocallaghan@outlook.com>
Date: 2026-03-20 15:06:29 +0000
Commit message:

 Relax tests and import stats::quantile
Package: hipathia
Commit: b9c057b309479c921bde971f57ad770e412fa1d9
Author: Marta Hidalgo <marta.hidalgo@outlook.es>
Date: 2026-03-20 15:15:53 +0100
Commit message:

 Merge branch 'master' into devel
Package: hipathia
Commit: 9c238198099c38bdfbe006099b096f942d47e3e5
Author: Marta Hidalgo <marta.hidalgo@outlook.es>
Date: 2026-03-20 15:11:59 +0100
Commit message:

 bumping to version 3.11.1
Package: hipathia
Commit: 849d00930f0f51f533ed5dee7921608c90f1a219
Author: Marta Hidalgo <marta.hidalgo@outlook.es>
Date: 2026-03-20 15:11:32 +0100
Commit message:

 updating to hpAnnot version 3
Package: hipathia
Commit: 7486aceacc5e06077a391207dac200174095f4c3
Author: Marta R. Hidalgo <marta.hidalgo@outlook.es>
Date: 2025-09-29 22:50:15 +0200
Commit message:

 commenting figures in vignette
Package: hipathia
Commit: adde3c8da719e6c9481603aabf024e97d96c297d
Author: Marta R. Hidalgo <marta.hidalgo@outlook.es>
Date: 2023-05-22 11:40:47 +0200
Commit message:

 changing plotVisGraphDE output options
Package: hipathia
Commit: d2b7516af93967f2bf08142ab4045939c8a724a0
Author: Marta R. Hidalgo <marta.hidalgo@outlook.es>
Date: 2025-09-29 22:50:15 +0200
Commit message:

 commenting figures in vignette
Package: hipathia
Commit: e95649fa5b1cbbc6cf5406a72b272830328e85e4
Author: Marta R. Hidalgo <marta.hidalgo@outlook.es>
Date: 2023-05-22 11:40:47 +0200
Commit message:

 changing plotVisGraphDE output options
Package: cellNexus
Commit: 67ef23be5cc59104a07a5ece88623c7baeb3dea8
Author: Mengyuan Shen <129487421+myushen@users.noreply.github.com>
Date: 2026-03-20 21:48:05 +1100
Commit message:

 Merge pull request #95 from myushen/bioconductor

get_metadata grabs populated columns only
Package: cellNexus
Commit: 557c01760cf579ba3db413fe6b80788864353fad
Author: myushen <mengyuan.shen@outlook.com>
Date: 2026-03-20 21:25:47 +1100
Commit message:

 version up
Package: cellNexus
Commit: f1e05db9297f27c5f5e1a582e2617d4cb9a3e02c
Author: myushen <mengyuan.shen@outlook.com>
Date: 2026-03-20 21:06:02 +1100
Commit message:

 Merge branch 'master' into bioconductor
merge master
Package: cellNexus
Commit: 496a0ba02ae83513558f4c4714a5410908a7b074
Author: myushen <mengyuan.shen@outlook.com>
Date: 2026-03-20 20:34:36 +1100
Commit message:

 update docs
Package: cellNexus
Commit: ff8943c51bb8c630fc187181d5a94dbc3bb00eb2
Author: myushen <mengyuan.shen@outlook.com>
Date: 2026-03-20 17:22:33 +1100
Commit message:

 get_metadata only returns cellnexus annotations. join_census_table append census annotations
Package: cellNexus
Commit: 98d083bd23e1dc5728d4db9573bebc872e9c8887
Author: myushen <mengyuan.shen@outlook.com>
Date: 2026-03-20 16:22:25 +1100
Commit message:

 pull from master, solve conflicts

Merge branch 'master' into bioconductor

# Conflicts:
#	NAMESPACE
#	R/data.R
#	R/metadata.R
#	R/utils.R
#	R/zzz.R
#	README.md
#	man/duckdb_read_parquet.Rd
#	man/get_metacell.Rd
#	man/get_metadata.Rd
#	man/keep_updated_metadata.Rd
#	tests/testthat/test-query.R
Package: cellNexus
Commit: 031aa8f232c89a3252e9c4a1c8d76e570384eb00
Author: myushen <mengyuan.shen@outlook.com>
Date: 2026-03-20 16:08:40 +1100
Commit message:

 put metacell function as internal. every man page should have example. every internal should not generate Rd
Package: cellNexus
Commit: c4ee3d5ae0016da8abd9f7e627803e010ecfff3a
Author: Stefano Mangiola <mangiolastefano@gmail.com>
Date: 2026-03-20 13:48:17 +1030
Commit message:

 update renv for website
Package: cellNexus
Commit: 825113b29248663cbff090744f26f8ceae7c8488
Author: Mengyuan Shen <129487421+myushen@users.noreply.github.com>
Date: 2026-03-20 12:44:01 +1100
Commit message:

 Merge pull request #91 from myushen/master

update deployment manifest
Package: cellNexus
Commit: 0c0bdf1a4f8bf00713d77433cebf0b20eccbe41c
Author: myushen <mengyuan.shen@outlook.com>
Date: 2026-03-20 12:25:07 +1100
Commit message:

 use org name
Package: cellNexus
Commit: 464f22052a3580ef99250f4bca0e5cbe869c7bfe
Author: myushen <mengyuan.shen@outlook.com>
Date: 2026-03-20 11:29:12 +1100
Commit message:

 version bump
Package: cellNexus
Commit: 7fd0ce70d3df5863508790313a3100f1ea6cabc7
Author: myushen <mengyuan.shen@outlook.com>
Date: 2026-03-20 10:40:23 +1100
Commit message:

 fix deployment manifest and url
Package: goatea
Commit: f0ceaf50d6457ec65d23534a8192638430f82836
Author: Maurits Unkel <mauritsunkel@gmail.com>
Date: 2026-03-20 11:39:39 +0100
Commit message:

 Fix clusterProfiler::enricher(universe = NULL) to universe = as.character(all_genes_background) for mv to enrichit package
Package: Chromatograms
Commit: 95cb9d4c381797854d427ae051a2db6c7d97b525
Author: Philippine Louail <philippine.louail@outlook.com>
Date: 2026-03-13 14:33:15 +0100
Commit message:

 Merge pull request #48 from rformassspectrometry/phili

refactor: efficiency update for data access and .process_peaks_data()
Package: Chromatograms
Commit: 6c8ea54a44639c60ea5e19b7b64cce2902af5ec3
Author: Philippine Louail <127301965+philouail@users.noreply.github.com>
Date: 2026-03-13 14:13:13 +0100
Commit message:

 force data.table install
Package: Chromatograms
Commit: b150a1d1baded8a97e473f6ac65db20de43a3745
Author: Philippine Louail <127301965+philouail@users.noreply.github.com>
Date: 2026-03-13 14:10:44 +0100
Commit message:

 fix cache
Package: Chromatograms
Commit: 641a3f9f7a789829d91babf71078ace14e8a9554
Author: Philippine Louail <127301965+philouail@users.noreply.github.com>
Date: 2026-03-13 13:57:54 +0100
Commit message:

 refactor small codes parts based on jo's comments
Package: Chromatograms
Commit: 3c231d39cf9228d399fe98713e073a0663032767
Author: Philippine Louail <127301965+philouail@users.noreply.github.com>
Date: 2026-03-11 18:29:31 +0100
Commit message:

 Code clean and fix based on jo comments
Package: Chromatograms
Commit: 1f81de2ee8dc6358564bde367ca8a9c995ac0594
Author: Philippine Louail <127301965+philouail@users.noreply.github.com>
Date: 2026-03-10 12:09:28 +0100
Commit message:

 Update helpers.R
Package: Chromatograms
Commit: 61446a113c792e13085e153808f9f9ab8c4fb4f2
Author: Philippine Louail <127301965+philouail@users.noreply.github.com>
Date: 2026-03-10 12:05:52 +0100
Commit message:

 efficiency update
Package: Chromatograms
Commit: 52783acc934c44fe11117a50758f32b5270d37fc
Author: Philippine Louail <philippine.louail@outlook.com>
Date: 2026-03-05 14:25:26 +0100
Commit message:

 Merge pull request #46 from rformassspectrometry/phili

feature c() and filterEmptyChromatograms() methods.
Package: Chromatograms
Commit: 8acc80f88e88a592107cd75febc3db9f0e235c6c
Author: Philippine Louail <127301965+philouail@users.noreply.github.com>
Date: 2026-03-05 13:44:35 +0100
Commit message:

 feature: add filterEmptyChromatograms()
Package: Chromatograms
Commit: 6f7b0c3c3913841be31e69be40dd065e553bc2af
Author: Philippine Louail <127301965+philouail@users.noreply.github.com>
Date: 2026-02-26 14:50:37 +0100
Commit message:

 feature: concatenate and extrapolation
Package: Chromatograms
Commit: d3219c2e4c789fe0a5a6b1543d013483051e575b
Author: Philippine Louail <127301965+philouail@users.noreply.github.com>
Date: 2026-02-05 16:44:04 +0100
Commit message:

 refactor: order or returned peaksData for chromBackendSpectra
Package: imageTCGAutils
Commit: 57ea13cfd704a5009aa5b59ca80e11712c0f7f0c
Author: billila <ilaria.billato@studenti.unipd.it>
Date: 2026-03-20 10:59:06 +0100
Commit message:

 version bump 0.99.21
Package: imageTCGAutils
Commit: 8f19b143dbed7870cb59a82ccf752dc055143bd0
Author: billila <ilaria.billato@studenti.unipd.it>
Date: 2026-03-20 10:56:52 +0100
Commit message:

 add remotes package for GHA
Package: scECODA
Commit: 35c1068aa375c567eb40efed17c75ea850fc0d08
Author: halterc <chalterbio@gmail.com>
Date: 2026-03-20 10:19:45 +0100
Commit message:

 Version bump
Package: scECODA
Commit: 9b26caa4f9fd7456dcd8e0a25d9d0fb5ed210c9a
Author: halterc <chalterbio@gmail.com>
Date: 2026-03-20 10:19:38 +0100
Commit message:

 plot_pca: changed anosim_parallel = 1 (default) (update documentation)
Package: msdata
Commit: 9e1a3d5e1e76dcf0c430b3cda6a34975a39c7974
Author: Laurent Gatto <lgatto@protonmail.ch>
Date: 2026-03-20 09:46:56 +0100
Commit message:

 remove files
Package: SeqArray
Commit: 3f3d0dcef37096a9c1277b992171a023ecdd8755
Author: Xiuwen Zheng <zhengxwen@gmail.com>
Date: 2026-03-19 22:56:44 -0500
Commit message:

 new 'ploidy' in seqVCF2GDS()
Package: SpiecEasi
Commit: e1a8004db8ce30707ad5a39555ad7a72c19aa0b2
Author: Zachary Kurtz <zdkurtz@gmail.com>
Date: 2026-03-19 20:32:21 -0400
Commit message:

 bump patch
Package: SpiecEasi
Commit: a596224f0931a7f1a8867cd0a950122fc759158e
Author: Zachary Kurtz <zdkurtz@gmail.com>
Date: 2026-03-19 20:27:59 -0400
Commit message:

 fix parallel vignette for Windows builds
Package: glmSparseNet
Commit: 29cbab5ffcbf58317fa1f598af7c3d3abafdb50f
Author: André Veríssimo <211358+averissimo@users.noreply.github.com>
Date: 2026-03-20 00:09:47 +0000
Commit message:

 fix: linter errors
Package: OmicsMLRepoR
Commit: b9df1d6ff0899a1d14de9c2eb4ebe6bf46c33016
Author: Sehyun Oh <shbrief@gmail.com>
Date: 2026-03-19 20:06:31 -0400
Commit message:

 version bump
Package: OmicsMLRepoR
Commit: 868c8afec42af172dbb390a6b64263513f21fbec
Author: Sehyun Oh <shbrief@gmail.com>
Date: 2026-03-19 20:03:50 -0400
Commit message:

 Merge branch 'devel' of https://github.com/shbrief/OmicsMLRepoR into devel
Package: OmicsMLRepoR
Commit: 53cec52550ff5720a7d13927474765696c8f2657
Author: Sehyun Oh <shbrief@gmail.com>
Date: 2026-03-19 19:53:06 -0400
Commit message:

 remove synonym search test due to inconsistency in OLS
Package: OmicsMLRepoR
Commit: 83e3f857fdd2cc6a7d20cd48152ae4cdfa86a8ff
Author: Sehyun Oh <shbrief@gmail.com>
Date: 2026-03-13 11:24:08 -0400
Commit message:

 version bump
Package: OmicsMLRepoR
Commit: a11ed795393cdaeffc32406f2915aaa43ce5c3f9
Author: Sehyun Oh <shbrief@gmail.com>
Date: 2026-02-02 12:26:07 -0500
Commit message:

 version bump
Package: OmicsMLRepoR
Commit: db4405a61700c558209303deae0a545e1d6c6b92
Author: Sehyun Oh <shbrief@gmail.com>
Date: 2026-03-13 11:13:21 -0400
Commit message:

 version bump
Package: OmicsMLRepoR
Commit: b2c43a51051a6dece8e0cc3dcf1ca7878c3cb9e6
Author: Sehyun Oh <shbrief@gmail.com>
Date: 2026-03-13 11:13:11 -0400
Commit message:

 update rols API endpoint
Package: OmicsMLRepoR
Commit: 1edeb0349a20d28e39f8e8905a2b7a5f2f07f703
Author: Sehyun Oh <shbrief@gmail.com>
Date: 2026-03-04 09:15:38 -0500
Commit message:

 Fix bfcdownload() parameter name and version bump

Use 'rid' instead of 'rids' in bfcdownload() call to fix
vignette build error: "!missing(rid) is not TRUE"

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
Package: OmicsMLRepoR
Commit: 232810b540054488d6b75492c56971a8ce46dbdc
Author: Sehyun Oh <shbrief@gmail.com>
Date: 2026-02-11 16:09:36 -0500
Commit message:

 version bump
Package: OmicsMLRepoR
Commit: 1ea55b06b3315f6470be2b920ad25b13960721d3
Author: Sehyun Oh <shbrief@gmail.com>
Date: 2026-02-11 16:09:12 -0500
Commit message:

 Stop tracking test vignettes
Package: OmicsMLRepoR
Commit: e578f8cbe7b4989cabeb55569e2534adb34bb941
Author: Sehyun Oh <shbrief@gmail.com>
Date: 2026-02-02 12:24:32 -0500
Commit message:

 version bump
Package: clusterExperiment
Commit: 884dd90fbfe99d7a9dcf73370c9958f19b155280
Author: Elizabeth Purdom <epurdom@stat.berkeley.edu>
Date: 2026-03-19 14:14:25 -0700
Commit message:

 bump up version
Package: clusterExperiment
Commit: 794d20ed2ae109c404bca7433b3677dacb3dff8a
Author: Elizabeth Purdom <epurdom@stat.berkeley.edu>
Date: 2026-03-19 14:10:40 -0700
Commit message:

 fix malformed \item braces in makeConsensus docs

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
Package: clusterExperiment
Commit: d7b065941a35e427519f4129117df40996f2d231
Author: Elizabeth Purdom <epurdom@stat.berkeley.edu>
Date: 2026-03-19 14:08:20 -0700
Commit message:

 fix \itemize -> \describe in getClusterIndex docs

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
Package: imageFeatureTCGA
Commit: 9cf2e5a1b17f54e3c2ca04f8a8211861418f51eb
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2026-03-19 17:11:57 -0400
Commit message:

 version bump 0.99.65
Package: imageFeatureTCGA
Commit: ef730cc8a5c7d94cd4fc5c77b98c73acec922861
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2026-03-19 17:11:54 -0400
Commit message:

 fill locals vector only for those not cached and redownloaded
Package: imageFeatureTCGA
Commit: fe56701c52d31b2a971e1b1fa3e1f5690e4f503d
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2026-03-19 17:10:44 -0400
Commit message:

 create urls_to_download vector for clarity
Package: imageFeatureTCGA
Commit: 43db360a26e6b6f568b7b17a37addb4a79990ec9
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2026-03-19 17:09:10 -0400
Commit message:

 use .move_file to fallback to file.copy when file.rename fails
Package: imageFeatureTCGA
Commit: 168e9f37f53c47c41fec9b846e7086d466296bc6
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2026-03-19 16:04:40 -0400
Commit message:

 version bump 0.99.64
Package: imageFeatureTCGA
Commit: cd99343e61a864404b322dc4508464ff891ac915
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2026-03-19 16:04:31 -0400
Commit message:

 minor clean up
Package: imageFeatureTCGA
Commit: 81b7a8bf2f77476cd1fe04f42c9444204cf2a5f3
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2026-03-19 16:04:20 -0400
Commit message:

 combine base URLs for catalog and resources
Package: glmSparseNet
Commit: e861615408415e80822b2d69ff2e718c87bf5421
Author: André Veríssimo <211358+averissimo@users.noreply.github.com>
Date: 2026-03-19 19:08:31 +0000
Commit message:

 fix: message from logger not being caught
Package: HiCool
Commit: 0f6ba8e9a37edd9faa559085a53d34dbcb811bc4
Author: js2264 <jacquesserizay@gmail.com>
Date: 2026-03-19 18:54:03 +0100
Commit message:

 bump to 1.11.3
Package: HiCool
Commit: 00b3f6f9d4e1174950b17cabcef1711b813132a5
Author: Jacques <jacquesserizay@gmail.com>
Date: 2026-03-19 18:48:57 +0100
Commit message:

 fix: set KMP_DUPLICATE_LIB_OK to TRUE to prevent double-init of OpenMP runtime
Package: imageTCGAutils
Commit: 79cb7dd2e1538ef301f74e683713e2cbbac09e0a
Author: billila <ilaria.billato@studenti.unipd.it>
Date: 2026-03-19 18:03:40 +0100
Commit message:

 version bump 0.99.20
Package: imageTCGAutils
Commit: 3d6d8e0420a19303fc9cbd200b49ab2109fb499d
Author: billila <ilaria.billato@studenti.unipd.it>
Date: 2026-03-19 17:59:00 +0100
Commit message:

 restructure matchHoverNetToTiles function
Package: RCX
Commit: ee9b8612d3d99fe0d5dc67d2ddf2fd3eb9917465
Author: Florian J. Auer <florian.auer@informatik.uni-augsburg.de>
Date: 2026-03-19 17:23:34 +0100
Commit message:

 fix: toIgraph now can handle edgeless networks
Package: RCX
Commit: a3f7bf366055194b53f4bbf52aa1fe305fd2027a
Author: Florian J. Auer <florian.auer@informatik.uni-augsburg.de>
Date: 2026-03-19 17:20:41 +0100
Commit message:

 fix: toIgraph now can handle edgeless networks
Package: RCX
Commit: 2f3da7746c81188d728593418c76d1dc659d8d99
Author: Florian J. Auer <florian.auer@informatik.uni-augsburg.de>
Date: 2026-03-19 17:13:59 +0100
Commit message:

 fix: toIgraph now can handle edgeless networks
Package: RCX
Commit: 6cdc2411cb122611631364f8e040c92183e63e6a
Author: Florian J. Auer <florian.auer@informatik.uni-augsburg.de>
Date: 2026-01-20 13:11:19 +0100
Commit message:

 Fix: cyGroups follows a different naming structure in the JSON export. Updated the export function accordingly. Also the CyGroup ids have to be present in RCX object, a check for those references has been added.
Package: BiocPkgDash
Commit: 61a14a0db6bb3b717e34ae2c75f788d082109eb2
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2026-03-19 11:01:38 -0400
Commit message:

 version bump 0.99.48
Package: BiocPkgDash
Commit: f2425db690da6bb1451daf2a4498e64c3fe36a5c
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2026-03-18 18:17:35 -0400
Commit message:

 conditionally show or hide the content with is_email_provided()
Package: scECODA
Commit: 0edd3f5bf353d482a1c42b54ba65f366fac3b14c
Author: halterc <chalterbio@gmail.com>
Date: 2026-03-19 15:13:21 +0100
Commit message:

 Version bump
Package: scECODA
Commit: 50fd402ab5761af69ca44f4345f6d9b298238dec
Author: halterc <chalterbio@gmail.com>
Date: 2026-03-19 15:11:50 +0100
Commit message:

 Merge branch 'main' of https://github.com/carmonalab/scECODA
Package: scECODA
Commit: 025871e19dda47be9e3cec473102cc2397704000
Author: halterc <chalterbio@gmail.com>
Date: 2026-03-19 15:10:02 +0100
Commit message:

 plot_pca: changed anosim_parallel = 1 (default)
Package: scECODA
Commit: 2298172ce3f8996a486e419c8c9dfc4da4c381a3
Author: halterc <chalterbio@gmail.com>
Date: 2026-03-19 15:10:02 +0100
Commit message:

 plot_pca: changed anosim_parallel = 1 (default)
Package: variancePartition
Commit: 16e114ff973d966d1d8ad74a9218b67c74022585
Author: Gabriel Hoffman <gabriel.hoffman@gmail.com>
Date: 2026-03-19 09:20:03 -0400
Commit message:

 1.41.5
Package: variancePartition
Commit: 15d79e68c62bc65d39516e650cf34883ade5547e
Author: Gabriel Hoffman <gabriel.hoffman@gmail.com>
Date: 2026-03-19 09:18:00 -0400
Commit message:

 1.41.4
Package: CAGEfightR
Commit: 26802e1fe0485fd60abd7280a627a30befb3ad1d
Author: Malte Thodberg <maltethodberg@gmail.com>
Date: 2026-03-19 12:22:35 +0100
Commit message:

 Removed pryr dependency and replaced it with lobstr and purrr. Updated DESCRIPTION in the process.
Package: CompoundDb
Commit: 7daa5754dffffde823e42268a9bd3dc6a1a9ddd8
Author: Johannes Rainer <5506112+jorainer@users.noreply.github.com>
Date: 2026-03-19 09:10:35 +0100
Commit message:

 Merge pull request #124 from rformassspectrometry/jomain

fix: support filling missing spectra variables in HMDB import
Package: CompoundDb
Commit: 268d02823fdc49b194dc95945e944eb1e4be4e24
Author: Johannes Rainer <johannes.rainer@gmail.com>
Date: 2026-03-19 08:57:37 +0100
Commit message:

 fix: support filling missing spectra variables in HMDB import
Package: MetaboAnnotation
Commit: 34e5ba4bdeb5d2fe021dac40d50bbfbadd566c8d
Author: Johannes Rainer <5506112+jorainer@users.noreply.github.com>
Date: 2026-03-19 09:10:28 +0100
Commit message:

 Merge pull request #131 from rformassspectrometry/jomain

refactor: use rbindlistWithRownames
Package: MetaboAnnotation
Commit: b9e5ea16f6201e72173df382b2b5566e2f54f909
Author: Johannes Rainer <johannes.rainer@gmail.com>
Date: 2026-03-19 08:51:17 +0100
Commit message:

 fix: addMatches allows filling
Package: MetaboAnnotation
Commit: f0ac37c2f24fb73c35a9268d16b177a2c2e1aa1e
Author: Johannes Rainer <johannes.rainer@gmail.com>
Date: 2026-03-19 07:26:40 +0100
Commit message:

 ci: fix namespace and use R devel
Package: MetaboAnnotation
Commit: 04b81666020fc043406f57f779603096071c22de
Author: Johannes Rainer <johannes.rainer@gmail.com>
Date: 2026-03-18 15:33:16 +0100
Commit message:

 refactor: use rbindlistWithRownames
Package: SMTrackR
Commit: 6533c78358a13e2e84a7527aa842b4aff9138669
Author: satyanarayan-rao <satyanarayan.rao@cuanschutz.edu>
Date: 2026-03-19 13:13:53 +0530
Commit message:

 added BiocStyle in Imports and Suggests
Package: cellNexus
Commit: ad1fdbc6b893161ee1d6591fa5a8cc65190905be
Author: Mengyuan Shen <129487421+myushen@users.noreply.github.com>
Date: 2026-03-19 16:02:06 +1100
Commit message:

 Merge pull request #90 from myushen/master

Load RShiny data correctly and show vignettes output
Package: cellNexus
Commit: b8519ace0b14f49bfcb3edd6b68613ee135bd329
Author: Mengyuan Shen <mengyuan.shen@outlook.com>
Date: 2026-03-19 15:40:09 +1100
Commit message:

 Update query builder assay selection box
Solve conflicts, rebase
Package: cellNexus
Commit: b0daa74cffae975dbeceeababfd1cb20193cbe87
Author: myushen <mengyuan.shen@outlook.com>
Date: 2026-03-19 15:24:30 +1100
Commit message:

 dependency
Package: cellNexus
Commit: c7af92ba895055bd70f973ebe7efecd138bf6fb6
Author: myushen <mengyuan.shen@outlook.com>
Date: 2026-03-19 15:16:13 +1100
Commit message:

 show vignettes output. load rshiny data correctly
Package: cellNexus
Commit: 913b749c8c69ba9421892a59b4ea112093db48f0
Author: Mengyuan Shen <129487421+myushen@users.noreply.github.com>
Date: 2026-03-19 14:02:47 +1100
Commit message:

 Merge pull request #63 from myushen/read_files_progress_bar

Read files progress bar
Package: cellNexus
Commit: 31ac8e2b182ce3bb15c21cfcfd51d039b89a6110
Author: myushen <mengyuan.shen@outlook.com>
Date: 2026-03-19 12:32:23 +1100
Commit message:

 Merge master and solve conflicts. Add progress bar for reading each assay

Merge branch 'master' into read_files_progress_bar

# Conflicts:
#	DESCRIPTION
#	R/counts.R
#	dev/split_census_anndata_base_on_sample_id.R
Package: cellNexus
Commit: e0d1542823a0919ace61029b791f6ec6622f9f7f
Author: myushen <mengyuan.shen@outlook.com>
Date: 2026-03-19 11:09:01 +1100
Commit message:

 update vignettes
Package: cellNexus
Commit: 4091432e26cc5d4395acf647abb5a73877fff9e5
Author: myushen <mengyuan.shen@outlook.com>
Date: 2026-03-19 09:59:03 +1100
Commit message:

 fix warning messages in check
Package: cellNexus
Commit: 0c7ba62188073a8a426450752c11a4a15df184d2
Author: myushen <mengyuan.shen@outlook.com>
Date: 2026-03-18 17:00:23 +1100
Commit message:

 merge devel

Merge branch 'devel'

# Conflicts:
#	DESCRIPTION
#	NAMESPACE
#	R/counts.R
#	R/data.R
#	R/interface_app.R
#	R/metadata.R
#	R/utils.R
#	dev/5_unify_and_update_sce_metadata.R
#	man/create_interface_app.Rd
#	man/get_SingleCellExperiment.Rd
#	man/get_metadata.Rd
#	man/get_metadata_url.Rd
#	man/get_pseudobulk.Rd
#	man/get_seurat.Rd
#	man/get_single_cell_experiment.Rd
#	vignettes/cellNexus.Rmd
Package: cellNexus
Commit: b9bc93bf4644597fadcba5e5d2c8f550547fd26d
Author: myushen <mengyuan.shen@outlook.com>
Date: 2026-03-18 13:04:10 +1100
Commit message:

 Merge branch 'master' of https://github.com/myushen/cellNexus
Package: cellNexus
Commit: c40ff7e814a73d6d7d802c49270e48fbf4c5ec68
Author: Stefano Mangiola <mangiolastefano@gmail.com>
Date: 2026-03-17 18:16:13 +1030
Commit message:

 Merge pull request #89 from MangiolaLaboratory/pseudobulk-SE

Update version to 0.99.10; enhance get_pseudobulk() with as_Summarize…
Package: cellNexus
Commit: ac3e896dde6057ac0699d5bfce5349175ff6bbf0
Author: Stefano Mangiola <mangiolastefano@gmail.com>
Date: 2026-03-17 17:36:16 +1030
Commit message:

 Potential fix for pull request finding

Co-authored-by: Copilot Autofix powered by AI <175728472+Copilot@users.noreply.github.com>
Package: cellNexus
Commit: 6ba57e8656abff68c6955ee009651a44a4c06855
Author: Stefano Mangiola <mangiolastefano@gmail.com>
Date: 2026-03-17 17:23:04 +1030
Commit message:

 Update version to 0.99.10; enhance get_pseudobulk() with as_SummarizedExperiment parameter to optionally return a SummarizedExperiment while preserving feature rownames. Add corresponding tests.
Package: cellNexus
Commit: d250a3ba5199f4ec83110817b08f2f918e16b87b
Author: myushen <mengyuan.shen@outlook.com>
Date: 2026-03-17 17:29:48 +1100
Commit message:

 merge solve conflict
Package: cellNexus
Commit: 7b09f7ec05a503483a1f39050be3dab0ee1c0c1b
Author: myushen <mengyuan.shen@outlook.com>
Date: 2026-03-13 14:17:47 +1100
Commit message:

 update data release
Package: cellNexus
Commit: f0b6f6944a8c54dfcc38e388ff27ee9ffe51ebbe
Author: Mengyuan Shen <129487421+myushen@users.noreply.github.com>
Date: 2026-03-17 17:15:58 +1100
Commit message:

 Merge pull request #86 from myushen/bioconductor

Bioconductor
Package: cellNexus
Commit: 1639e03d5f4a4a787793ef40a574e45c13694908
Author: myushen <mengyuan.shen@outlook.com>
Date: 2026-03-17 16:17:57 +1100
Commit message:

 version bump
Package: cellNexus
Commit: d7ec13c11a6772937173c5c7df9a611ed35505af
Author: Mengyuan Shen <129487421+myushen@users.noreply.github.com>
Date: 2026-03-17 15:46:26 +1100
Commit message:

 Merge branch 'master' into bioconductor
Package: cellNexus
Commit: 51dddf2f80103181adf70146e2f961bb8f8b436e
Author: Mengyuan Shen <129487421+myushen@users.noreply.github.com>
Date: 2026-03-17 15:33:02 +1100
Commit message:

 Merge pull request #85 from j-andrews7/app_updates

App updates
Package: cellNexus
Commit: 11af7021476ec38cfbed255e3e42f333e4449f5c
Author: Mengyuan Shen <mengyuan.shen@outlook.com>
Date: 2026-03-17 15:19:02 +1100
Commit message:

 rclipboard dep issue, try remove
Package: cellNexus
Commit: 725d9f6c94ff9f43036cba0b8e3883f178566fce
Author: Mengyuan Shen <mengyuan.shen@outlook.com>
Date: 2026-03-17 13:51:15 +1100
Commit message:

 suggest rclipboard
Package: cellNexus
Commit: 87f38756392a703c40df79220af24b2a4ee0f139
Author: Mengyuan Shen <mengyuan.shen@outlook.com>
Date: 2026-03-17 11:45:47 +1100
Commit message:

 sync_assay_file to download files without relying on reading metadata
Package: cellNexus
Commit: f118dca360ad2de67f3c43998444ec17a3a3a282
Author: myushen <mengyuan.shen@outlook.com>
Date: 2026-03-17 09:47:20 +1100
Commit message:

 Stop tracking dev scripts, ignore dev/
Package: cellNexus
Commit: 6fcc3ac2a9dd7414ee37e6542d5d89636bcf027c
Author: myushen <mengyuan.shen@outlook.com>
Date: 2026-03-17 09:38:09 +1100
Commit message:

 update metadata release version
Package: cellNexus
Commit: ba769372169555fb35727859c8fbbf63a8b58571
Author: Mengyuan Shen <mengyuan.shen@outlook.com>
Date: 2026-03-16 18:25:35 +1100
Commit message:

 fix = to <-; use zellkonverter::writeH5AD for internal save anndata function
Package: cellNexus
Commit: 06f2b789b9ded296d06e345461daadee2bb57a5e
Author: myushen <mengyuan.shen@outlook.com>
Date: 2026-03-16 16:36:53 +1100
Commit message:

 Merge branch 'bioconductor' of https://github.com/myushen/cellNexus into bioconductor
Package: cellNexus
Commit: 4b698bec365720300e20fc1d9cef5d19468a89a9
Author: myushen <mengyuan.shen@outlook.com>
Date: 2026-03-16 16:35:57 +1100
Commit message:

 update system requirement
Package: cellNexus
Commit: e0611caad5ec2b190d971d94b96e486eac68e974
Author: Mengyuan Shen <mengyuan.shen@outlook.com>
Date: 2026-03-16 16:35:10 +1100
Commit message:

 refactor get_sce, get_pseudobulk, get_metacell. avoid code repetition
Package: cellNexus
Commit: 95f63308c340147f9a6536bee64d4c943b7cc5f2
Author: Mengyuan Shen <mengyuan.shen@outlook.com>
Date: 2026-03-16 16:34:44 +1100
Commit message:

 systemrequire
Package: cellNexus
Commit: da5d32d2d145ad8b40303038ac53bf084bfacba3
Author: myushen <mengyuan.shen@outlook.com>
Date: 2026-03-13 14:17:47 +1100
Commit message:

 update data release
Package: cellNexus
Commit: ce8c6535da36bf44c16ef621413f60d5a514c08c
Author: myushen <mengyuan.shen@outlook.com>
Date: 2026-03-09 17:20:33 +1100
Commit message:

 merge from master

Merge branch 'master' into bioconductor

# Conflicts:
#	R/counts.R
#	R/utils.R
#	man/get_pseudobulk.Rd
#	man/save_sce_as_h5ad.Rd
Package: cellNexus
Commit: 465f79eb932b57119220e5ad66e748b12c47577e
Author: myushen <mengyuan.shen@outlook.com>
Date: 2026-03-09 17:16:34 +1100
Commit message:

 update:
get_metacell() to use numeric internally.
get_sce() converts numeric to character to slice anndata.
save_sce inherit ... from `anndataR`
Package: cellNexus
Commit: b6e3ae9d3ccb050face829eb19711e020470d798
Author: myushen <mengyuan.shen@outlook.com>
Date: 2026-03-03 17:25:39 +1100
Commit message:

 remove internal functions Rds. add unit test for get_CPM()
Package: cellNexus
Commit: 2b96918de911722764ec22bd4f309ab78702fcb4
Author: myushen <mengyuan.shen@outlook.com>
Date: 2026-03-03 15:42:39 +1100
Commit message:

 fix write_h5ad
Package: cellNexus
Commit: a8748fd33e4368efd9c09f5432944bdf760b0946
Author: myushen <mengyuan.shen@outlook.com>
Date: 2026-03-03 15:37:07 +1100
Commit message:

 fix check warnings and errors
Package: cellNexus
Commit: fc3f83d3dc43aac9160e3ed7d751c8e51913911e
Author: Mengyuan Shen <mengyuan.shen@outlook.com>
Date: 2026-02-27 17:52:08 +1100
Commit message:

 fix check warnings and errors
Package: cellNexus
Commit: dd4bd96c3074b32e8abd8b935fc4c92d32971835
Author: myushen <mengyuan.shen@outlook.com>
Date: 2026-02-27 17:36:10 +1100
Commit message:

 import zellkonverter
Package: cellNexus
Commit: c57d3dd9c277ee6371bccb30a103ed5c6940c961
Author: Mengyuan Shen <mengyuan.shen@outlook.com>
Date: 2026-02-27 16:26:11 +1100
Commit message:

 tags consistency for noRd and internal
Package: cellNexus
Commit: 9869643dc921c53834e40949aa7291237f83e98c
Author: Mengyuan Shen <mengyuan.shen@outlook.com>
Date: 2026-02-27 16:02:24 +1100
Commit message:

 remove , refactor directly in
Package: cellNexus
Commit: cabee9a4c55691c8f7f76bb4acfefcc8606ce36f
Author: Mengyuan Shen <mengyuan.shen@outlook.com>
Date: 2026-02-27 15:17:07 +1100
Commit message:

 rename read_parquet to avoid package function conflict
Package: cellNexus
Commit: 801cb2d958988be6acbea67ec0ffe209d1b14653
Author: Mengyuan Shen <mengyuan.shen@outlook.com>
Date: 2026-02-27 14:57:59 +1100
Commit message:

 update readability section
Package: cellNexus
Commit: 73382a4f15715992ae74891bce7a97c608978a29
Author: Mengyuan Shen <mengyuan.shen@outlook.com>
Date: 2026-02-27 14:39:16 +1100
Commit message:

 update syntax, no cat
Package: cellNexus
Commit: c0e100cc37ed012598af775d9e4fead529d9e9c1
Author: Mengyuan Shen <mengyuan.shen@outlook.com>
Date: 2026-02-27 14:35:03 +1100
Commit message:

 package unit test coverage to 71%
Package: cellNexus
Commit: 962b6fb90614b4d5f5dabd0722b7d7ae07350d45
Author: Mengyuan Shen <129487421+myushen@users.noreply.github.com>
Date: 2026-02-27 10:44:51 +1100
Commit message:

 Merge pull request #87 from myushen/cell_communication

Cell communication
Package: cellNexus
Commit: b9d5b9d315f200e0a482d48409cc3ce3801fbf9f
Author: myushen <mengyuan.shen@outlook.com>
Date: 2026-02-27 10:27:54 +1100
Commit message:

 fix check warning
Package: cellNexus
Commit: 6adfb028ced454e008c2b1b4c9de1c6c6ad060df
Author: Mengyuan Shen <mengyuan.shen@outlook.com>
Date: 2026-02-26 17:48:13 +1100
Commit message:

 out consistency..
Package: cellNexus
Commit: 476915fd7cf6573abb6729a3be5bbee492033bfc
Author: Mengyuan Shen <mengyuan.shen@outlook.com>
Date: 2026-02-26 17:47:53 +1100
Commit message:

 man pages have runnable examples
Package: cellNexus
Commit: fee86ecee63f78580cdd55eee927e0e62e538ae7
Author: Mengyuan Shen <mengyuan.shen@outlook.com>
Date: 2026-02-26 16:55:49 +1100
Commit message:

 vignette uses biocstyle, and has a table of contents
Package: cellNexus
Commit: af082515ff73668db5b3aacb7e3637ef72fd2e43
Author: Mengyuan Shen <mengyuan.shen@outlook.com>
Date: 2026-02-26 16:42:21 +1100
Commit message:

 update NEWS and CITATION
Package: cellNexus
Commit: 36efc050b5bfd9d624c4793ea07821f90630e270
Author: Mengyuan Shen <mengyuan.shen@outlook.com>
Date: 2026-02-26 16:36:01 +1100
Commit message:

 Add NEWS.md
Package: cellNexus
Commit: 16c4768b093e3fa40ab37a62d5d2951c34e1b00a
Author: myushen <mengyuan.shen@outlook.com>
Date: 2026-02-26 16:11:17 +1100
Commit message:

 enable sct in get_SCE
Package: cellNexus
Commit: 28dd294e1620421403e7a2449869d09dc3c961e8
Author: myushen <mengyuan.shen@outlook.com>
Date: 2026-02-26 16:08:48 +1100
Commit message:

 update documentation and sct assay
Package: cellNexus
Commit: 6a38c4dd3596b4a3359fdcf2cc122b1d7b3c20ea
Author: myushen <mengyuan.shen@outlook.com>
Date: 2026-02-26 14:53:49 +1100
Commit message:

 remove import_SCE(). its in cellnexuscloud package
Package: cellNexus
Commit: a9706297b37d285f9e77cfb45eebe058c2958244
Author: myushen <mengyuan.shen@outlook.com>
Date: 2026-02-26 14:35:51 +1100
Commit message:

 calling internal data using data(...)
Package: cellNexus
Commit: ce07f1f96de61c036fc5d295d0c2daa200c0c770
Author: myushen <mengyuan.shen@outlook.com>
Date: 2026-02-25 17:08:04 +1100
Commit message:

 dont use assertthat, update readme
Package: cellNexus
Commit: 91e5dcf3fcdc8f12c93d856016fc20cbd3e9b828
Author: myushen <mengyuan.shen@outlook.com>
Date: 2026-02-25 16:51:17 +1100
Commit message:

 update author list
Package: cellNexus
Commit: fd21a0295efb8f9f08a611314d9afb0a52c6c96f
Author: myushen <mengyuan.shen@outlook.com>
Date: 2026-02-24 17:10:17 +1100
Commit message:

 address: LazyData,Depends, Imports, Suggests, Enhances fields
Package: cellNexus
Commit: 22f8ef509abc3c1503692d22d00b32b4bc9946d4
Author: myushen <mengyuan.shen@outlook.com>
Date: 2026-02-24 13:04:20 +1100
Commit message:

 avoid check warning
Package: cellNexus
Commit: 2a5b4ed2aa5ba640395e015ded0f8f9be5e2c170
Author: myushen <mengyuan.shen@outlook.com>
Date: 2026-02-24 11:22:38 +1100
Commit message:

 Merge branch 'master' of https://github.com/myushen/cellNexus
pull from remote
Package: cellNexus
Commit: ec43a7449f2fe61610ba5634ab9ef5c1ae1ee53a
Author: myushen <mengyuan.shen@outlook.com>
Date: 2026-02-24 11:18:57 +1100
Commit message:

 loads dplyr internally when calling cellNexus
Package: cellNexus
Commit: 240e1a0df1912f093ac6a82172f74a7113263aa6
Author: myushen <mengyuan.shen@outlook.com>
Date: 2026-02-24 11:13:17 +1100
Commit message:

 better split. cellnexus_metadata only contains curated columns. census_metadata contains CELLxGENE columns. metacell_metadata has all metacell related columns.
Package: cellNexus
Commit: bc5a05316f56e4ee37497162164fe87d85fd8cc1
Author: Jared Andrews <jared.andrews07@gmail.com>
Date: 2026-02-22 18:59:23 -0600
Commit message:

 Update manifest.json
Package: cellNexus
Commit: 9f6a192f8a978ac498abc2a6f2ac48fce0604ce5
Author: Jared Andrews <jared.andrews07@gmail.com>
Date: 2026-02-22 18:44:05 -0600
Commit message:

 app ui updates
Package: cellNexus
Commit: 4b253e6f344f443ac2f1ff99211786c462f8bdb3
Author: Jared Andrews <jared.andrews07@gmail.com>
Date: 2026-02-22 17:42:45 -0600
Commit message:

 Update manifest.json
Package: cellNexus
Commit: f904fe9fcc47cfc5434f94380906f8f0fd6e3256
Author: Jared Andrews <jared.andrews07@gmail.com>
Date: 2026-02-22 17:39:45 -0600
Commit message:

 allow app return as list for deployment
Package: cellNexus
Commit: e612b827888b3ff5136f64a1b7bc2ca2b6d74d8c
Author: Jared Andrews <jared.andrews07@gmail.com>
Date: 2026-02-22 17:18:51 -0600
Commit message:

 Update manifest.json
Package: cellNexus
Commit: 620e2f76db33a4d2d46fc8e4ca74244e3950062c
Author: Jared Andrews <jared.andrews07@gmail.com>
Date: 2026-02-22 17:11:55 -0600
Commit message:

 fix a few `check` notes
Package: cellNexus
Commit: 77de57769e567380a93baa5c67281d60283a910c
Author: Jared Andrews <jared.andrews07@gmail.com>
Date: 2026-02-22 14:08:53 -0600
Commit message:

 Update manifest.json
Package: cellNexus
Commit: 17b7182b5de950242d61dc97c2b9ec2c1e9bf991
Author: Jared Andrews <jared.andrews07@gmail.com>
Date: 2026-02-22 14:06:03 -0600
Commit message:

 cleaner data loading for app deployment
Package: cellNexus
Commit: a69586051dcd05232dcd8739374d7212f8476e18
Author: Jared Andrews <jared.andrews07@gmail.com>
Date: 2026-02-22 12:42:54 -0600
Commit message:

 Update manifest.json
Package: cellNexus
Commit: 9e7cfe3f38c4845b89fb8e13a89720ef202602ad
Author: Jared Andrews <jared.andrews07@gmail.com>
Date: 2026-02-22 12:27:38 -0600
Commit message:

 more proper data storage
Package: cellNexus
Commit: 6d7deee7a7f5393b5c2022f43c86f7bae8c50e7d
Author: Jared Andrews <jared.andrews07@gmail.com>
Date: 2026-02-22 11:51:37 -0600
Commit message:

 Update manifest.json
Package: cellNexus
Commit: 49941b02e9aff5b15f6e1f630c72f550523f6156
Author: Jared Andrews <jared.andrews07@gmail.com>
Date: 2026-02-22 04:36:29 -0600
Commit message:

 Update manifest.json
Package: cellNexus
Commit: 621dfbde078945038380690f7ebd90aff3b3bcac
Author: Jared Andrews <jared.andrews07@gmail.com>
Date: 2026-02-22 04:27:29 -0600
Commit message:

 Update manifest.json
Package: cellNexus
Commit: 0ac3aed35edcaaac79eb165270f834adbf34b7a3
Author: Jared Andrews <jared.andrews07@gmail.com>
Date: 2026-02-22 04:23:46 -0600
Commit message:

 app manifest for publishing
Package: cellNexus
Commit: ac024d59d11a683ac2f3d161b5e0d8af7e5ca86f
Author: Jared Andrews <jared.andrews07@gmail.com>
Date: 2026-02-22 04:14:49 -0600
Commit message:

 parallelize downloads
Package: cellNexus
Commit: 6ff3fc65381d0a9072940d0b45ac3caddee23d89
Author: Jared Andrews <jared.andrews07@gmail.com>
Date: 2026-02-22 03:38:17 -0600
Commit message:

 add python query block
Package: cellNexus
Commit: 0379ad5a3a3ae75e8e05c290661663c2e85dc29b
Author: Jared Andrews <jared.andrews07@gmail.com>
Date: 2026-02-22 02:57:23 -0600
Commit message:

 Create app.r
Package: cellNexus
Commit: b5346a6c5d4002b4d0a354e33100948b1e46bc62
Author: Jared Andrews <jared.andrews07@gmail.com>
Date: 2026-02-20 23:37:18 -0600
Commit message:

 Merge branch 'MangiolaLaboratory:master' into app_updates
Package: cellNexus
Commit: df7da2a24c6149dac10c08ee8c71476a84e277bf
Author: Stefano Mangiola <mangiolastefano@gmail.com>
Date: 2026-02-20 10:29:49 +0100
Commit message:

 Merge pull request #84 from MangiolaLaboratory/website

Change image alignment in index.md from center to left for better lay…
Package: cellNexus
Commit: fa24d57b4429bf32a1336e7bbfaf827115f5a1e7
Author: Stefano Mangiola <mangiolastefano@gmail.com>
Date: 2026-02-20 10:28:55 +0100
Commit message:

 Change image alignment in index.md from center to left for better layout consistency
Package: cellNexus
Commit: 2ed14cf15a01067f06cc0395fb30e03906ab7078
Author: Stefano Mangiola <mangiolastefano@gmail.com>
Date: 2026-02-20 09:44:54 +0100
Commit message:

 Merge pull request #83 from MangiolaLaboratory/website

Update image styling in index.md for improved responsiveness
Package: cellNexus
Commit: e494caa4642ae12392f27ed3fa822838bdff98ff
Author: Stefano Mangiola <mangiolastefano@gmail.com>
Date: 2026-02-20 09:28:57 +0100
Commit message:

 Update image styling in index.md for improved responsiveness
Package: cellNexus
Commit: 9f76b860cf984618452841a9daa5ed2a3e6cf60c
Author: Stefano Mangiola <mangiolastefano@gmail.com>
Date: 2026-02-19 18:56:07 +0100
Commit message:

 Merge pull request #82 from MangiolaLaboratory/website

Update image path in index.md for documentation consistency
Package: cellNexus
Commit: a89c259064ceb138f80de30898c6653de6c27154
Author: Stefano Mangiola <mangiolastefano@gmail.com>
Date: 2026-02-19 18:55:35 +0100
Commit message:

 Update image path in index.md for documentation consistency
Package: cellNexus
Commit: 4d25a9ea816ac1ae35accf9ffa04f85e6d28d0b3
Author: Stefano Mangiola <mangiolastefano@gmail.com>
Date: 2026-02-19 16:19:45 +0100
Commit message:

 Merge pull request #81 from MangiolaLaboratory/website

Add git configuration step for pkgdown deployment
Package: cellNexus
Commit: dab33dd5c5cb0aad15331f52313190ba3a6d6798
Author: Stefano Mangiola <mangiolastefano@gmail.com>
Date: 2026-02-19 15:25:55 +0100
Commit message:

 Add git configuration step for pkgdown deployment

- Added a step to set the git user name and email for the GitHub Actions bot, ensuring proper attribution during the deployment of the pkgdown site.
Package: cellNexus
Commit: 920f9cbf8df6362517c99cdbc5dc23aa4c4b8bc6
Author: Stefano Mangiola <mangiolastefano@gmail.com>
Date: 2026-02-19 13:05:19 +0100
Commit message:

 Merge pull request #80 from MangiolaLaboratory/website

Add installation step in pkgdown workflow
Package: cellNexus
Commit: 6fb64a9d4aa480a758ecdf1f9dca2f5176651a89
Author: Stefano Mangiola <mangiolastefano@gmail.com>
Date: 2026-02-19 13:04:42 +0100
Commit message:

 Add installation step in pkgdown workflow

- Introduced a new step to install the package before building and deploying the pkgdown site, ensuring that the latest changes are reflected in the documentation.
Package: cellNexus
Commit: f7a46824f50fa2da5fbf3aee0598ddd9542d18ec
Author: Stefano Mangiola <mangiolastefano@gmail.com>
Date: 2026-02-19 10:29:22 +0100
Commit message:

 Merge pull request #79 from MangiolaLaboratory/website

Add pkgdown configuration and documentation files
Package: cellNexus
Commit: c3030e48c78a81b1655f5fa92dbd699cf8f66eb7
Author: Stefano Mangiola <mangiolastefano@gmail.com>
Date: 2026-02-18 22:09:15 +0100
Commit message:

 Add pkgdown configuration and documentation files

- Create _pkgdown.yml for site configuration and navigation.
- Add index.md as the main landing page for the documentation.
- Introduce vignettes for "Metadata Explore" and "Gene Expression Explore" to guide users through data exploration.
- Include additional HTML and CSS for custom styling in pkgdown.
- Update DESCRIPTION to include the new documentation URL.
- Add favicon and web app manifest files for improved site branding.
Package: cellNexus
Commit: 37894e6eadf0e47f572e1754ea7a457b3eea1861
Author: Mengyuan Shen <129487421+myushen@users.noreply.github.com>
Date: 2026-02-09 09:55:51 +1100
Commit message:

 Merge branch 'MangiolaLaboratory:master' into master
Package: cellNexus
Commit: 8e0c07c5fb93d7bb95d981904f3f0c45e2d4d958
Author: myushen <mengyuan.shen@outlook.com>
Date: 2026-02-06 17:48:55 +1100
Commit message:

 get_cell_communication_strength wrapper, version bump
Package: cellNexus
Commit: dc751b84ae3d7e97a545f7aa6fe4a0b5c4d7ee5a
Author: myushen <mengyuan.shen@outlook.com>
Date: 2026-02-05 10:36:35 +1100
Commit message:

 1. pull 0.99.8 from devel.
2. solve conflicts. design progress bar on "Reading files...".
3. version bump to 0.99.9

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

# Conflicts:
#	DESCRIPTION
#	R/counts.R
#	vignettes/cellNexus.Rmd
Package: cellNexus
Commit: ee0d9c7b68bee0a12065d0a231c7b87383a79e6e
Author: Mengyuan Shen <129487421+myushen@users.noreply.github.com>
Date: 2026-01-27 13:42:35 +1100
Commit message:

 Merge pull request #57 from MangiolaLaboratory/copilot/fix-56

Implement left_join version of parquet files to reduce download size
Package: cellNexus
Commit: baba4e232c477f52999b8ba6cca3ea42dc89dc56
Author: myushen <mengyuan.shen@outlook.com>
Date: 2026-01-27 11:57:36 +1100
Commit message:

 bioccheck test locally, version bump
Package: cellNexus
Commit: 1c6087106f3a3798e908ca9603a813e90278110a
Author: myushen <mengyuan.shen@outlook.com>
Date: 2026-01-23 17:15:23 +1100
Commit message:

 pull master, solve conflicts

Merge branch 'master' of https://github.com/myushen/cellNexus into HEAD

# Conflicts:
#	DESCRIPTION
#	R/metadata.R
#	dev/5_unify_and_update_sce_metadata.R
#	man/get_metadata_url.Rd
Package: cellNexus
Commit: 073bae061e797b8df60c1ad50d11fe48c761b5a9
Author: myushen <mengyuan.shen@outlook.com>
Date: 2026-01-20 14:10:34 +1100
Commit message:

 update dev
Package: cellNexus
Commit: 70b66ac0fce72e1e0b639d63f0e07f3a6347572f
Author: Mengyuan Shen <129487421+myushen@users.noreply.github.com>
Date: 2026-01-13 11:24:33 +1100
Commit message:

 Merge pull request #77 from myushen/master

Speed up vignette builds to avoid bioconductor timeouts
Package: cellNexus
Commit: e766102620a3c3e204cc19ebc985288699eac5a4
Author: Mengyuan Shen <129487421+myushen@users.noreply.github.com>
Date: 2025-10-09 14:40:14 +1100
Commit message:

 Merge branch 'master' into copilot/fix-56
Package: cellNexus
Commit: f491d9f49db2ae213927591adfe59655b55b93c1
Author: Mengyuan Shen <mengyuan.shen@outlook.com>
Date: 2025-09-24 14:52:19 +1000
Commit message:

 progress bar works for querying multiple assays
Package: cellNexus
Commit: ff77ea9011b3a8d42591b35357da747e325cfff6
Author: Mengyuan Shen <129487421+myushen@users.noreply.github.com>
Date: 2025-09-19 14:30:51 +1000
Commit message:

 Merge pull request #62 from myushen/join_metadata

unit test
Package: cellNexus
Commit: eb629f9e6e87b9322fc6c2c6e3af5151726256e5
Author: Mengyuan Shen <mengyuan.shen@outlook.com>
Date: 2025-09-19 14:28:01 +1000
Commit message:

 use_split_files return one file. unit test
Package: cellNexus
Commit: e5e171dac2357ce41cf27ec6c68d8aae6475c949
Author: Mengyuan Shen <129487421+myushen@users.noreply.github.com>
Date: 2025-09-19 11:34:25 +1000
Commit message:

 Merge pull request #61 from myushen/join_metadata

Join metadata
Package: cellNexus
Commit: 2af752eacc593ede34fcc4c95add9daf4ec941a2
Author: myushen <mengyuan.shen@outlook.com>
Date: 2025-09-19 10:57:26 +1000
Commit message:

 Merge branch 'join_metadata' of https://github.com/myushen/cellNexus into join_metadata
Package: cellNexus
Commit: 02796582a2b8980ebea35826e14d087da0a3af02
Author: myushen <mengyuan.shen@outlook.com>
Date: 2025-09-19 10:46:10 +1000
Commit message:

 dev
Package: cellNexus
Commit: 0bcb1415c6ea8c67bdbd617e3a80310cc8a1c779
Author: Mengyuan Shen <mengyuan.shen@outlook.com>
Date: 2025-09-19 10:44:27 +1000
Commit message:

 split sample annotation doesnt help much, thus combine sample and cell. join_metacell, join_census function remain
Package: cellNexus
Commit: 8ba8db1e149d9b3ee7d174fcc21303cb04173ca9
Author: Mengyuan Shen <mengyuan.shen@outlook.com>
Date: 2025-09-18 13:49:43 +1000
Commit message:

 fix locating directory path
Package: cellNexus
Commit: 933aa4b27db220f0338c8e0f0751479f7188ed0c
Author: Mengyuan Shen <mengyuan.shen@outlook.com>
Date: 2025-09-17 16:34:11 +1000
Commit message:

 add progress bar for reading files
Package: cellNexus
Commit: f59c04c5799c063b6b8a85e86616204c079a3f11
Author: Mengyuan Shen <129487421+myushen@users.noreply.github.com>
Date: 2025-09-15 17:02:12 +1000
Commit message:

 Merge pull request #59 from myushen/join_metadata

Join metadata
Package: cellNexus
Commit: 9bb9b9573ec0fdd30f4acff9abd34ad799d6af7a
Author: Mengyuan Shen <mengyuan.shen@outlook.com>
Date: 2025-09-15 17:00:59 +1000
Commit message:

 fix
Package: cellNexus
Commit: 12430b7afddd08dd5a8aa6840b798926a9d2da29
Author: Mengyuan Shen <mengyuan.shen@outlook.com>
Date: 2025-09-15 15:59:53 +1000
Commit message:

 fix unit test
Package: cellNexus
Commit: 404bc744b5a810ceec6eee0e08a55f0d5a6d2f1b
Author: Mengyuan Shen <mengyuan.shen@outlook.com>
Date: 2025-09-15 13:59:39 +1000
Commit message:

 get_metadata handles split files when use_split_files=TRUE.

Implementation of join_metacell_table, join_census_table, keep_quality_cells functions
Package: cellNexus
Commit: f71fe1db3c71b5e3a985ded215af54caa28d9a75
Author: Mengyuan Shen <129487421+myushen@users.noreply.github.com>
Date: 2025-09-12 18:42:46 +1000
Commit message:

 Merge branch 'copilot/fix-56' into join_metadata
Package: cellNexus
Commit: d97065cf89b4657cf73098e3ab7c1328744efb5d
Author: Mengyuan Shen <129487421+myushen@users.noreply.github.com>
Date: 2025-09-12 18:25:02 +1000
Commit message:

 Merge branch 'master' into copilot/fix-56
Package: cellNexus
Commit: 71b6c9c8f3ff069d00c5e49a60f330e776be6ed6
Author: Mengyuan Shen <mengyuan.shen@outlook.com>
Date: 2025-09-12 18:09:18 +1000
Commit message:

 fix and unit tests. `keep_quality_cells()` to filter out low quality cells quickly
Package: cellNexus
Commit: 710a478eebf89ba5c19a8d896cab99b52b6ee78e
Author: Mengyuan Shen <mengyuan.shen@outlook.com>
Date: 2025-09-12 16:32:26 +1000
Commit message:

 use_split_files arguments to join splitted cellnexus cell and sample metadata.

split census and metacell metadata out from the main. call to join when necessary.
Package: cellNexus
Commit: 7d8ca23258a7d8d64dc911267b8a1dc167109bae
Author: Mengyuan Shen <mengyuan.shen@outlook.com>
Date: 2025-09-12 11:43:53 +1000
Commit message:

 split and join sample and cellnexus_cell metadata work
Package: cellNexus
Commit: dc705e70357cab990db5d979c04a29d6477fbfe2
Author: myushen <mengyuan.shen@outlook.com>
Date: 2025-09-02 15:42:09 +1000
Commit message:

 helper function for good quality cells
Package: cellNexus
Commit: fd09dfae4f428f29458fbbefffec1d58474d7f87
Author: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Date: 2025-08-29 23:12:02 +0000
Commit message:

 Improve robustness of split metadata joining and add comprehensive tests

Co-authored-by: stemangiola <7232890+stemangiola@users.noreply.github.com>
Package: cellNexus
Commit: 9b8379af060503d2bcc7e08eee5a443b8320acfe
Author: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Date: 2025-08-29 23:09:27 +0000
Commit message:

 Implement left_join functionality for split metadata files

Co-authored-by: stemangiola <7232890+stemangiola@users.noreply.github.com>
Package: cellNexus
Commit: f8263304a5582dad60e630117e3602c314dd37fe
Author: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com>
Date: 2025-08-29 23:00:56 +0000
Commit message:

 Initial plan
Package: CSOA
Commit: fe3c38cb539374005aab2110b9597a03d1b2207b
Author: andrei-stoica26 <andreistoica@foxmail.com>
Date: 2026-03-19 10:00:13 +0800
Commit message:

 Bumped version
Package: CSOA
Commit: 6feeacfec4c85cf670ee51726913824d62ab3fd4
Author: andrei-stoica26 <andreistoica@foxmail.com>
Date: 2026-03-19 09:59:31 +0800
Commit message:

 Removed wesBinaryGradient
Package: cicero
Commit: 2cc70b941c97b890327d761ede0c238e54e4c2c0
Author: Hannah Pliner <hpliner@gmail.com>
Date: 2026-03-18 22:35:53 +0100
Commit message:

 update deprecations
Package: MsDataHub
Commit: 1d997f090ffd167f1f255de5ac283f38a6cff498
Author: Laurent Gatto <laurent.gatto@uclouvain.be>
Date: 2026-03-18 21:03:02 +0100
Commit message:

 Merge pull request #13 from rformassspectrometry/jomain

docs: add descriptions of new data sets to vignette
Package: MsDataHub
Commit: f028d65bb112711bf003f3512ac15775cf36dfd9
Author: Johannes Rainer <johannes.rainer@gmail.com>
Date: 2026-03-18 07:59:28 +0100
Commit message:

 docs: add descriptions of new data sets to vignette

- Add description for the newly added data sets to the vignette (issue #12).
Package: wiggleplotr
Commit: ce7c8daf78df4d218ef0101acfc8c63aab5fbce6
Author: Kaur Alasoo <kauralasoo@gmail.com>
Date: 2026-03-18 21:13:26 +0200
Commit message:

 Merge branch 'devel' of git.bioconductor.org:packages/wiggleplotr
Package: wiggleplotr
Commit: 5fe9770c17da9c0efd58cc5c275340865b94f8a4
Author: Kaur Alasoo <kauralasoo@gmail.com>
Date: 2026-03-18 21:02:54 +0200
Commit message:

 Merge pull request #27 from kauralasoo/parquet_coverage

Add support for parquet coverage files and fix deprecated dplyr syntax
Package: wiggleplotr
Commit: ede9fec086f9639ea80c5309f3bb68d4f0efb9ce
Author: Kaur Alasoo <kauralasoo@gmail.com>
Date: 2026-02-10 09:57:51 +0200
Commit message:

 Replace deprecated dplyr and ggplot2 syntax.
Package: wiggleplotr
Commit: 63840336a9fe0fe6f391df71588169cf18bb3fac
Author: Kaur Alasoo <kauralasoo@gmail.com>
Date: 2025-12-30 15:10:20 +0200
Commit message:

 Sort parquet file after reading it in
Package: wiggleplotr
Commit: b5f497038c539a2ae8121b3034627eae302e3dbc
Author: Kaur Alasoo <kauralasoo@gmail.com>
Date: 2025-11-06 23:41:22 +0200
Commit message:

 Read specific region directly from the parquet file
Package: wiggleplotr
Commit: e86c12a1a731a061316984f21630d833a4e1ba2c
Author: Kaur Alasoo <kauralasoo@gmail.com>
Date: 2025-11-04 17:27:47 +0200
Commit message:

 Read RNA-seq coverage from Parquet files instead of BigWig files
Package: cicero
Commit: 3a9e8f64cd4d4690dd4fd49829ea92ae837ad908
Author: Hannah Pliner <hpliner@gmail.com>
Date: 2026-03-18 18:41:29 +0100
Commit message:

 version
Package: cicero
Commit: 9d04c3753b88ce64b2fe4968a54ed35d2ae129ea
Author: Hannah Pliner <hpliner@gmail.com>
Date: 2026-03-18 18:33:59 +0100
Commit message:

 version bump
Package: cicero
Commit: 7e7360fe97449d0678fbf7863c835385239e8e79
Author: Hannah Pliner <hpliner@gmail.com>
Date: 2026-03-18 18:25:45 +0100
Commit message:

 version bump
Package: cicero
Commit: da5bca78c156f33780811c44c30c64a3a036ddc5
Author: Hannah Pliner <hpliner@gmail.com>
Date: 2026-03-18 18:22:43 +0100
Commit message:

 Merge remote-tracking branch 'origin/master'
Package: cicero
Commit: 2523a6422f1485869f9c397d276421f90ccee706
Author: Hannah Pliner <hpliner@gmail.com>
Date: 2026-03-18 18:06:40 +0100
Commit message:

 workaround for monocle deprecation error
Package: cicero
Commit: 07f8731b2d2029ab774621b768b20259238ede4d
Author: Hannah A Pliner <hpliner@gmail.com>
Date: 2024-09-03 03:07:35 +0200
Commit message:

 Update runCicero.R
Package: cicero
Commit: 26b56abfc45f9722a2797d40ec8de3fd036bbbde
Author: Hannah A Pliner <hpliner@gmail.com>
Date: 2024-09-03 03:00:20 +0200
Commit message:

 Merge pull request #96 from Puriney/patch-1

Update runCicero.R
Package: cicero
Commit: 8ef1ce7fe8901f1280f2921d180b738db4e0f9ea
Author: Hannah Pliner <hpliner@gmail.com>
Date: 2024-09-02 20:03:12 -0400
Commit message:

 Merge remote-tracking branch 'origin/master'
Package: cicero
Commit: fedf1c47fb04f57ab25ff56c210ac45fba037674
Author: Hannah Pliner <hpliner@gmail.com>
Date: 2024-09-02 20:02:59 -0400
Commit message:

 Merge remote-tracking branch 'bioc/master'
Package: cicero
Commit: 93474c1f84c958b26ccbe6d1f7a5fe8472566bed
Author: Yun YAN <Puriney@users.noreply.github.com>
Date: 2024-02-06 12:03:45 -0600
Commit message:

 Update runCicero.R
Package: cicero
Commit: 10720b05f39b648fb023357bb5054c3ccb970b6c
Author: Hannah A Pliner <hpliner@gmail.com>
Date: 2023-05-04 19:26:02 +0200
Commit message:

 Update check-standard.yaml
Package: cicero
Commit: b1cd65ec78ef9f049e3ce7718c0c6a3d367f77da
Author: Hannah Pliner <hpliner@gmail.com>
Date: 2023-02-27 19:39:39 +0100
Commit message:

 Update data objects
Package: cicero
Commit: f5f6799208836ef2c3964fcc1722c0119e80405e
Author: Hannah Pliner <hpliner@gmail.com>
Date: 2023-02-26 00:23:02 +0100
Commit message:

 Merge branch 'master' of github.com:cole-trapnell-lab/cicero-release
Package: cicero
Commit: 46db306eec3a8aa1bbfde5ec9e088c94f9c20791
Author: Hannah Pliner <hpliner@gmail.com>
Date: 2023-02-26 00:22:54 +0100
Commit message:

 update workflow
Package: cicero
Commit: ed32a7a82925b3be3cf299f04a5fd4eab9dbdc27
Author: Hannah A Pliner <hpliner@gmail.com>
Date: 2023-02-26 00:08:01 +0100
Commit message:

 Update README.md
Package: MSnbase
Commit: f6bac75e651931d922e037b39fdb0ac2fb62c074
Author: Laurent Gatto <lgatto@protonmail.ch>
Date: 2026-03-18 18:05:17 +0100
Commit message:

 bump version
Package: MSnbase
Commit: 7f1fc6ee433cff7ce85a260b20c25cb7215ff33a
Author: Laurent Gatto <lgatto@protonmail.ch>
Date: 2026-03-18 17:00:41 +0100
Commit message:

 more fix tests and warnings
Package: MSnbase
Commit: 0301b6b3bc549e7a4d12f8fe4a239ddac6a53f60
Author: Laurent Gatto <lgatto@protonmail.ch>
Date: 2026-03-18 13:31:39 +0100
Commit message:

 more fix tests and warnings
Package: MSnbase
Commit: 29137c4a3b1f5dfba7950dff77d75f9bb1dd1861
Author: Laurent Gatto <lgatto@protonmail.ch>
Date: 2026-03-18 13:05:53 +0100
Commit message:

 more fix tests and warnings
Package: MSnbase
Commit: 51d2420a00429d9b7beb6905df674dede77314e4
Author: Laurent Gatto <lgatto@protonmail.ch>
Date: 2026-03-18 13:05:31 +0100
Commit message:

 more fix tests and warnings
Package: MSnbase
Commit: 48cd6f8ce5ad50d192b37d5d947fbdd1f6e7e1cd
Author: Laurent Gatto <lgatto@protonmail.ch>
Date: 2026-03-18 13:00:10 +0100
Commit message:

 fix tests and warnings
Package: MSnbase
Commit: 507473b9bbbc60097f6905d8e414aa9ea396534c
Author: Laurent Gatto <lgatto@protonmail.ch>
Date: 2026-03-17 22:12:41 +0100
Commit message:

 use r/bioc devel
Package: scRNAseqApp
Commit: 3f56d699d88ab28c56ad64eedc64f8360182a6e0
Author: Jianhong Ou <jianhong.ou@gmail.com>
Date: 2026-03-18 12:51:46 -0400
Commit message:

 add search link for species.
Package: PolySTest
Commit: 9185a149f34d2e01e2b245d5bbb5e705af0d953e
Author: veitveit <veits@bmb.sdu.dk>
Date: 2026-03-18 17:33:06 +0100
Commit message:

 temporary version for bioconductor
Package: PolySTest
Commit: 4c9d5bf475c59fd923c237ee7ea5bb117fa7966b
Author: veitveit <veits@bmb.sdu.dk>
Date: 2026-03-18 17:32:44 +0100
Commit message:

 temporary version for bioconductor
Package: PolySTest
Commit: 582ba729dc574040627c8cc60d6d8876f032cfea
Author: veitveit <veits@bmb.sdu.dk>
Date: 2026-03-17 08:02:19 +0100
Commit message:

 more fixes
Package: PolySTest
Commit: b8f289d5e25664158036a23a23b5d961baaeb88c
Author: veitveit <veits@bmb.sdu.dk>
Date: 2026-03-17 07:30:44 +0100
Commit message:

 small fix of shiny app
Package: pathlinkR
Commit: 5adccf7adb74fb4fd39f71b592a1d302dcb16f5c
Author: Travis Blimkie <travis.m.blimkie@gmail.com>
Date: 2026-03-18 09:12:24 -0700
Commit message:

 Added argument for better font size control in plotFoldChange
Package: mzR
Commit: 22865a4d05ffc3d8d896add3c660fba08cfd93d4
Author: Laurent Gatto <lgatto@protonmail.ch>
Date: 2026-03-18 17:12:52 +0100
Commit message:

 fix isseu #315
Package: mzR
Commit: bc55bd303fef201a5f95029d1f3d0f6d6381e23e
Author: Laurent Gatto <laurent.gatto@uclouvain.be>
Date: 2026-03-18 17:05:15 +0100
Commit message:

 Merge pull request #317 from jorainer/jomain

Remove dependency from msdata and small bug fix in mzML import
Package: mzR
Commit: eac9debc41ad2f2f5e7293dd0c78105bad44f5a1
Author: Johannes Rainer <johannes.rainer@gmail.com>
Date: 2026-03-13 07:54:33 +0100
Commit message:

 Use BioC devel
Package: mzR
Commit: d679664f522c8aeebe60512ab3b720fd420eeedc
Author: Johannes Rainer <johannes.rainer@gmail.com>
Date: 2026-03-12 15:55:01 +0100
Commit message:

 tests: fix unit tests removing references to msdata
Package: mzR
Commit: 4fc19cb7526e28913ca610ad531a6bbef1d569ee
Author: Johannes Rainer <johannes.rainer@gmail.com>
Date: 2026-03-12 15:47:00 +0100
Commit message:

 refactor: load test files from MsDataHub

- Load the test files from *MsDataHub* and removing the dependency
  from *msdata*.
Package: mzR
Commit: 8c096294323cf849d4cdb4c03397d3fdd13b7497
Author: Johannes Rainer <johannes.rainer@gmail.com>
Date: 2026-02-26 14:22:29 +0100
Commit message:

 fix RcppExports
Package: mzR
Commit: 49c7fc6f225c06ec9b35f70abc41f473f0f7c7fa
Author: Johannes Rainer <johannes.rainer@gmail.com>
Date: 2026-02-26 13:44:04 +0100
Commit message:

 fix: catch potential error in spectrum id parsing
Package: mzR
Commit: fa8dd67c1d9580d53077186d9d6aaf8d6eb04f26
Author: Johannes Rainer <johannes.rainer@gmail.com>
Date: 2026-02-26 13:25:49 +0100
Commit message:

 Merge remote-tracking branch 'bioconductor/devel' into jomain
Package: mzR
Commit: 83ef5dd55222b69c8f4e483c113b5b2c8095241a
Author: Johannes Rainer <johannes.rainer@gmail.com>
Date: 2026-02-10 14:22:39 +0100
Commit message:

 First fixes for replacement msdata -> MsDataHub
Package: Voyager
Commit: fa06d54ae0aa86041eb9805d7c903e62216999c1
Author: Lambda Moses <dlu2@caltech.edu>
Date: 2026-03-18 12:11:17 -0400
Commit message:

 Forgot that biscale is not imported but suggested
Package: MsBackendMassbank
Commit: b93ed941478757a4a4c5dbe946d44196a9ae5e59
Author: Johannes Rainer <5506112+jorainer@users.noreply.github.com>
Date: 2026-03-18 15:57:48 +0100
Commit message:

 Merge pull request #61 from rformassspectrometry/jomain

refactor: used rbindlistWithRownames to combine data
Package: MsBackendMassbank
Commit: 2740db80786c0bbcbb0ba4218abbd727f8d1a220
Author: Johannes Rainer <johannes.rainer@gmail.com>
Date: 2026-03-18 15:39:59 +0100
Commit message:

 refactor: used rbindlistWithRownames to combine data
Package: trackViewer
Commit: f069bceca0fa73b83c9006fadf060f026867c8f0
Author: Jianhong Ou <jianhong.ou@gmail.com>
Date: 2026-03-18 10:21:14 -0400
Commit message:

 Fix the mis-match y-axis for dandelion.plot when max score is smaller than 1.
Package: trackViewer
Commit: 6c1f5eabc07d4429c35d4de05c9c92806407be66
Author: Jianhong Ou <jianhong.ou@gmail.com>
Date: 2026-03-17 16:17:37 -0400
Commit message:

 fix a typo.
Package: sfi
Commit: e0897f47b43af099b43c082b707f37253133c9b4
Author: yufree <yufree@live.cn>
Date: 2026-03-18 09:43:00 -0400
Commit message:

 bump version to 0.99.5
Package: MetaboAnnotatoR
Commit: 806e76bc7ec3fa3a1dd24cdc859c83caa6d522f3
Author: Gomes Da Graca <ggomesda@ic.ac.uk>
Date: 2026-03-18 13:35:33 +0000
Commit message:

 vignette updated after fixing the library data calls
Package: MetaboAnnotatoR
Commit: 7b42738d70ffc162399044d43fe3e69dbad4f41f
Author: Gomes Da Graca <ggomesda@ic.ac.uk>
Date: 2026-03-18 13:34:43 +0000
Commit message:

 tests updated
Package: MetaboAnnotatoR
Commit: fa8f760b8a2a707fac4cbead53110adc41ad902f
Author: Gomes Da Graca <ggomesda@ic.ac.uk>
Date: 2026-03-18 13:32:56 +0000
Commit message:

 examples fixed
Package: MetaboAnnotatoR
Commit: a6060d1fcfbf8f17afdc8453f7f4cf0901ba9967
Author: Gomes Da Graca <ggomesda@ic.ac.uk>
Date: 2026-03-18 13:31:57 +0000
Commit message:

 usage fixed
Package: MetaboAnnotatoR
Commit: 0d2208b3321813189519cfacf341eb1817e0ab34
Author: Gomes Da Graca <ggomesda@ic.ac.uk>
Date: 2026-03-18 13:30:32 +0000
Commit message:

 more global variables added
Package: MetaboAnnotatoR
Commit: 989dcf1461f3a420016d77a698337a0dfbbbe887
Author: Gomes Da Graca <ggomesda@ic.ac.uk>
Date: 2026-03-18 13:26:06 +0000
Commit message:

 fixed examples
Package: MetaboAnnotatoR
Commit: e16a265687881f9899b0da2e95a7113f8d49ef95
Author: Gomes Da Graca <ggomesda@ic.ac.uk>
Date: 2026-03-18 13:25:34 +0000
Commit message:

 fixed examples
Package: MetaboAnnotatoR
Commit: cbd6ac3506875df4efdff29a74667b5d518363d2
Author: Gomes Da Graca <ggomesda@ic.ac.uk>
Date: 2026-03-17 22:44:21 +0000
Commit message:

 documentation fixed
Package: MetaboAnnotatoR
Commit: df96e3712c1ddc9c77fb7c9e5a36ec2bb3d239ba
Author: Gomes Da Graca <ggomesda@ic.ac.uk>
Date: 2026-03-17 22:33:57 +0000
Commit message:

 documentation updated
Package: MetaboAnnotatoR
Commit: 9591233bab555548517d2ff04fa7b3aaf0c58833
Author: Gomes Da Graca <ggomesda@ic.ac.uk>
Date: 2026-03-17 22:31:28 +0000
Commit message:

 tabs removed
Package: MetaboAnnotatoR
Commit: 0330bfe26e0e7d0f8d338867b401486cd18a1fc4
Author: Gomes Da Graca <ggomesda@ic.ac.uk>
Date: 2026-03-17 22:29:16 +0000
Commit message:

 library data call corrected to avoid calling data() inside the function
Package: MetaboAnnotatoR
Commit: 97c5f2670da816de0c20b4640557aeb759a4d349
Author: Gomes Da Graca <ggomesda@ic.ac.uk>
Date: 2026-03-17 14:02:46 +0000
Commit message:

 small addition
Package: MetaboAnnotatoR
Commit: 28b06bac8ac042eee5004c5252cd1af4dcdbaadd
Author: Gomes Da Graca <ggomesda@ic.ac.uk>
Date: 2026-03-17 12:59:33 +0000
Commit message:

 default libraries loading fixed after lazy data set to false
Package: MetaboAnnotatoR
Commit: 32cbc4b84bcf90388cfb200f5029dad71caaf1b4
Author: Gomes Da Graca <ggomesda@ic.ac.uk>
Date: 2026-03-17 09:46:33 +0000
Commit message:

 default libraries loading fixed after lazy data set to false
Package: MetaboAnnotatoR
Commit: acf3de783f96dd4150762341133beacb0cbc6d20
Author: Gomes Da Graca <ggomesda@ic.ac.uk>
Date: 2026-03-15 17:34:29 +0000
Commit message:

 tabs removed
Package: MetaboAnnotatoR
Commit: edfa21d62dab3b9d85ff73984f9cb15bb750eec3
Author: Gomes Da Graca <ggomesda@ic.ac.uk>
Date: 2026-03-15 17:30:44 +0000
Commit message:

 Lazy data is now false
Package: MetaboAnnotatoR
Commit: c0ca4ae195fd1ad4217911388a4fba96a4eb0650
Author: Gomes Da Graca <ggomesda@ic.ac.uk>
Date: 2026-03-15 14:58:34 +0000
Commit message:

 correction in the example
Package: MetaboAnnotatoR
Commit: 3186e9c785a792cac4abc131eb9919d438ee6603
Author: Gomes Da Graca <ggomesda@ic.ac.uk>
Date: 2026-03-15 14:23:51 +0000
Commit message:

 format corrections after check
Package: MetaboAnnotatoR
Commit: 90c0879e46b82662e6f64c61a38179dbc66b5c04
Author: Gomes Da Graca <ggomesda@ic.ac.uk>
Date: 2026-03-10 14:39:52 +0000
Commit message:

 new extdata location and description
Package: MetaboAnnotatoR
Commit: 90f455fb27b65a1a549de8457de9414844e3a5fe
Author: Gomes Da Graca <ggomesda@ic.ac.uk>
Date: 2026-03-10 14:38:20 +0000
Commit message:

 extdata paths updated
Package: MetaboAnnotatoR
Commit: 17861fd2ab76c50e65bd9acebe5b2b2054230a1d
Author: Gomes Da Graca <ggomesda@ic.ac.uk>
Date: 2026-03-10 14:36:42 +0000
Commit message:

 extdata path updated
Package: MetaboAnnotatoR
Commit: a86837944c3f470e179482e3d581f8485ecb91d5
Author: Gomes Da Graca <ggomesda@ic.ac.uk>
Date: 2026-03-10 14:35:34 +0000
Commit message:

 documentation part corrected
Package: MetaboAnnotatoR
Commit: 0bed83022ecb26007ccb52ed25383ae1b8d0c0fd
Author: Gomes Da Graca <ggomesda@ic.ac.uk>
Date: 2026-03-10 14:34:21 +0000
Commit message:

 files moved to extdata
Package: MetaboAnnotatoR
Commit: ed15a3426c037e27988ccec98eadc0ad64ccc79f
Author: Gomes Da Graca <ggomesda@ic.ac.uk>
Date: 2026-03-10 14:33:00 +0000
Commit message:

 corrections after testing package
Package: MetaboAnnotatoR
Commit: 3b106b35b71a659edd62a6c15a0fcc5c7151eb1b
Author: Gomes Da Graca <ggomesda@ic.ac.uk>
Date: 2026-03-10 11:32:16 +0000
Commit message:

 documentation corrected
Package: MetaboAnnotatoR
Commit: 3ef11f7cca18df765f805211edeaa50b9dda66d9
Author: Gomes Da Graca <ggomesda@ic.ac.uk>
Date: 2026-03-10 11:02:23 +0000
Commit message:

 addition to documentation
Package: MetaboAnnotatoR
Commit: 3c8d76345d7eb5a313c5fefea7237aebbca99707
Author: Gomes Da Graca <ggomesda@ic.ac.uk>
Date: 2026-03-10 10:44:41 +0000
Commit message:

 typo in examples corrected
Package: MetaboAnnotatoR
Commit: da35a581b39170fef5a606cf8ad1b57104817ca8
Author: Goncalo Graca <45899755+gggraca@users.noreply.github.com>
Date: 2026-03-10 09:44:53 +0000
Commit message:

 Update DESCRIPTION

New version bump after merging from Biocfixes
Package: MetaboAnnotatoR
Commit: f766fa6046b04f18b48d76cde8044cc1fcbf9c26
Author: Goncalo Graca <45899755+gggraca@users.noreply.github.com>
Date: 2026-03-10 09:43:36 +0000
Commit message:

 Merge pull request #11 from gggraca/biocfixes

Biocfixes
Package: MetaboAnnotatoR
Commit: 9fdc46bec27ffab7bb0c1475ea4eeb6ee39d4206
Author: Gomes Da Graca <ggomesda@ic.ac.uk>
Date: 2026-03-09 21:35:40 +0000
Commit message:

 tests updated
Package: MetaboAnnotatoR
Commit: aba7dae7bdff23927a389f6a5810bf828a620171
Author: Gomes Da Graca <ggomesda@ic.ac.uk>
Date: 2026-03-09 21:34:48 +0000
Commit message:

 documentation updated
Package: MetaboAnnotatoR
Commit: c11d4b8416f515605b458d777c820eba5676d71c
Author: Gomes Da Graca <ggomesda@ic.ac.uk>
Date: 2026-03-09 21:33:36 +0000
Commit message:

 documentation updated
Package: MetaboAnnotatoR
Commit: 35ecabe55cdd04db3af3f7764b9e8d6342aaf900
Author: Gomes Da Graca <ggomesda@ic.ac.uk>
Date: 2026-03-09 21:32:13 +0000
Commit message:

 documentation updated
Package: MetaboAnnotatoR
Commit: 98ce60de8437f5d6887dfd41101a17a65553e22a
Author: Gomes Da Graca <ggomesda@ic.ac.uk>
Date: 2026-03-09 21:30:52 +0000
Commit message:

 documentation and examples updated
Package: MetaboAnnotatoR
Commit: 4f783894b0ae60d166faf0213bd8915995350067
Author: Gomes Da Graca <ggomesda@ic.ac.uk>
Date: 2026-03-09 21:30:16 +0000
Commit message:

 documentation and examples updated
Package: MetaboAnnotatoR
Commit: 5e9ed869cd958500a37dde63fe72df47958c34b3
Author: Gomes Da Graca <ggomesda@ic.ac.uk>
Date: 2026-03-09 21:29:30 +0000
Commit message:

 documentation and examples updated
Package: MetaboAnnotatoR
Commit: addca795f52ac4ac1aa66353bbec6d9c9845b9ee
Author: Gomes Da Graca <ggomesda@ic.ac.uk>
Date: 2026-03-09 21:28:45 +0000
Commit message:

 documentation and examples updated
Package: MetaboAnnotatoR
Commit: 02e22b05e4d4a49bc73edb240072edd087607d31
Author: Gomes Da Graca <ggomesda@ic.ac.uk>
Date: 2026-03-09 21:27:56 +0000
Commit message:

 documentation and examples updated
Package: MetaboAnnotatoR
Commit: 3e47f89aa2893a77cec11793721a29050c1ee9bf
Author: Gomes Da Graca <ggomesda@ic.ac.uk>
Date: 2026-03-09 21:27:08 +0000
Commit message:

 documentation updated
Package: MetaboAnnotatoR
Commit: 4ab3864059cfdae32d36af954a2199f3b626a15e
Author: Gomes Da Graca <ggomesda@ic.ac.uk>
Date: 2026-03-09 21:25:02 +0000
Commit message:

 documentation and examples updated
Package: MetaboAnnotatoR
Commit: 586935407b9f06c3e91989b74e8cc6063b11e075
Author: Gomes Da Graca <ggomesda@ic.ac.uk>
Date: 2026-03-06 17:45:05 +0000
Commit message:

 vignette updated after function changes
Package: MetaboAnnotatoR
Commit: 25046c0b4aee5506980dcac2ee4329aa5235ba77
Author: Gomes Da Graca <ggomesda@ic.ac.uk>
Date: 2026-03-06 17:43:09 +0000
Commit message:

 implicit data directories removed and replaced by user-defined
Package: MetaboAnnotatoR
Commit: f871b350d6187f9fc4fee648899a8c10b4c84fbc
Author: Gomes Da Graca <ggomesda@ic.ac.uk>
Date: 2026-03-06 17:41:48 +0000
Commit message:

 documentation updates
Package: MetaboAnnotatoR
Commit: 4c3f45e75583b9b41be9ff4ec1fefbe2d3c17374
Author: Gomes Da Graca <ggomesda@ic.ac.uk>
Date: 2026-03-05 21:46:06 +0000
Commit message:

 importFrom added for csv functions
Package: MetaboAnnotatoR
Commit: 05879475892e959f12d28bb9eb829243b2a8a475
Author: Gomes Da Graca <ggomesda@ic.ac.uk>
Date: 2026-03-05 21:34:35 +0000
Commit message:

 corrections to the plot candidate functions
Package: MetaboAnnotatoR
Commit: 6c7e50bdc5f94c0aaa0d579ab30f7e98a4606b7f
Author: Gomes Da Graca <ggomesda@ic.ac.uk>
Date: 2026-03-05 21:19:22 +0000
Commit message:

 documentation updated
Package: MetaboAnnotatoR
Commit: 9b0d7e2cc8e3ba98e8e7d4046344149ca2fb4d26
Author: Gomes Da Graca <ggomesda@ic.ac.uk>
Date: 2026-03-05 21:18:03 +0000
Commit message:

 new documented functions
Package: MetaboAnnotatoR
Commit: 79636b6b37934cde457dead7e8fee7b52709d4c8
Author: Gomes Da Graca <ggomesda@ic.ac.uk>
Date: 2026-03-05 21:16:06 +0000
Commit message:

 new exported function
Package: MetaboAnnotatoR
Commit: a1b0ac45a4db592fbcebf75875bf1612638eb05d
Author: Gomes Da Graca <ggomesda@ic.ac.uk>
Date: 2026-03-05 21:13:36 +0000
Commit message:

 function plotResultSpec moved
Package: MetaboAnnotatoR
Commit: e5eb40a9ed9b2c6daecb3950800565c0b507c3e2
Author: Gomes Da Graca <ggomesda@ic.ac.uk>
Date: 2026-03-05 21:11:29 +0000
Commit message:

 new exported function added
Package: MetaboAnnotatoR
Commit: c8f7967323f0d26d2f7f6b030ea26b974dbed257
Author: Gomes Da Graca <ggomesda@ic.ac.uk>
Date: 2026-03-05 20:26:47 +0000
Commit message:

 functions, related tests and documentation removed
Package: MetaboAnnotatoR
Commit: 76fda41737c7cd81b12cfbf085152031164a405f
Author: Gomes Da Graca <ggomesda@ic.ac.uk>
Date: 2026-03-05 20:21:01 +0000
Commit message:

 vignette updated
Package: MetaboAnnotatoR
Commit: feb1c6c52d9697ed295561b5ece76e70ba0dd957
Author: Gomes Da Graca <ggomesda@ic.ac.uk>
Date: 2026-03-05 20:20:10 +0000
Commit message:

 new plotting function added
Package: MetaboAnnotatoR
Commit: e2b7fc34284cbd31df6f0f3f4210c226b45232ba
Author: Gomes Da Graca <ggomesda@ic.ac.uk>
Date: 2026-03-05 15:43:30 +0000
Commit message:

 vignette updated after changes in main annotation functions
Package: MetaboAnnotatoR
Commit: cbef473fb139c4e217f14038f6555d21c491877f
Author: Gomes Da Graca <ggomesda@ic.ac.uk>
Date: 2026-03-05 15:03:16 +0000
Commit message:

 removed line that produced NA rankedResult when results was NULL
Package: MetaboAnnotatoR
Commit: 67cda578477761522934d9a73cfaa5a4f9f22c74
Author: Gomes Da Graca <ggomesda@ic.ac.uk>
Date: 2026-03-05 15:00:37 +0000
Commit message:

 changes to improve RC annotations results plotting
Package: MetaboAnnotatoR
Commit: 93176bff5388572c08aa047a022581cc451e18a4
Author: Gomes Da Graca <ggomesda@ic.ac.uk>
Date: 2026-03-05 09:25:41 +0000
Commit message:

 fixed plotting for AIF
Package: MetaboAnnotatoR
Commit: 3f345a3b1d8a02a4bc9b0c3ff7f1d3bcb2071dfe
Author: Gomes Da Graca <ggomesda@ic.ac.uk>
Date: 2026-03-04 16:13:31 +0000
Commit message:

 new function to save the results
Package: MetaboAnnotatoR
Commit: df17bd8e590c86be08bf8f14fe4c6abe78ad1b28
Author: Gomes Da Graca <ggomesda@ic.ac.uk>
Date: 2026-03-02 10:37:22 +0000
Commit message:

 small changes in the example
Package: MetaboAnnotatoR
Commit: 04d09fb0793d7bc8ff3890990691c37a01e14563
Author: Gomes Da Graca <ggomesda@ic.ac.uk>
Date: 2026-02-27 17:23:03 +0000
Commit message:

 test removed as function was removed
Package: MetaboAnnotatoR
Commit: c6c8832dd6032b5061e493061df2bf63995c3a60
Author: Gomes Da Graca <ggomesda@ic.ac.uk>
Date: 2026-02-27 17:21:24 +0000
Commit message:

 test updated to the new outputs of annotateRC
Package: MetaboAnnotatoR
Commit: 40651c7540ccdae60081f2536879f03dadc707fb
Author: Gomes Da Graca <ggomesda@ic.ac.uk>
Date: 2026-02-27 17:19:10 +0000
Commit message:

 .mzML extension added to sample name
Package: MetaboAnnotatoR
Commit: 18db8195f618a96ac8f2aee1b13e8dbc2b37b08c
Author: Gomes Da Graca <ggomesda@ic.ac.uk>
Date: 2026-02-27 17:18:25 +0000
Commit message:

 file redundant
Package: MetaboAnnotatoR
Commit: db8827fe1b865d0e8022eafe611f9fccb389dded
Author: Gomes Da Graca <ggomesda@ic.ac.uk>
Date: 2026-02-27 17:17:38 +0000
Commit message:

 outputs lists only, no files
Package: MetaboAnnotatoR
Commit: 7f91625a1a59b2b9925ee03d5b63a665e8ddffca
Author: Gomes Da Graca <ggomesda@ic.ac.uk>
Date: 2026-02-26 17:03:12 +0000
Commit message:

 adaptations to store object in workspace only
Package: MetaboAnnotatoR
Commit: ff21e3e4ee567cee11f405f0d6636638de7e9310
Author: Gomes Da Graca <ggomesda@ic.ac.uk>
Date: 2026-02-26 15:10:09 +0000
Commit message:

 all saved outputs removed
Package: MetaboAnnotatoR
Commit: aad5e04e07cd5a04f22295376df97e044681843c
Author: Gomes Da Graca <ggomesda@ic.ac.uk>
Date: 2026-02-26 10:44:51 +0000
Commit message:

 more objects added to the results list
Package: MetaboAnnotatoR
Commit: 5c53b900450d7df0b49cb235372fc574c4e5a99b
Author: Gomes Da Graca <ggomesda@ic.ac.uk>
Date: 2026-02-26 10:12:52 +0000
Commit message:

 save data suppressed
Package: sfi
Commit: c89743232bec08ba1f3e950190023fd0c43ff813
Author: yufree <yufree@live.cn>
Date: 2026-03-18 09:22:59 -0400
Commit message:

 Trigger build
Package: sfi
Commit: 5d3736fab47c6f3d948eabba1f0a72dae087aaf2
Author: yufree <yufree@live.cn>
Date: 2026-03-18 09:17:45 -0400
Commit message:

 Trigger build
Package: sfi
Commit: 942aa73f431650aab5afab39cbd4987ee56a3033
Author: yufree <yufree@live.cn>
Date: 2026-03-18 09:16:45 -0400
Commit message:

 update new function name according to review
Package: asuri
Commit: 47bc30e857a1c7de11cfa4ec04c6178ab316210f
Author: aberral <aberralgonzalez@gmail.com>
Date: 2026-03-18 12:42:05 +0100
Commit message:

 Minor fixes
Package: BamScale
Commit: f74eb1a5cb24e9560aee33c9839dbc4115f8b99c
Author: Chirag Parsania <chirag.parsania@gmail.com>
Date: 2026-03-18 22:38:21 +1100
Commit message:

 Increment version number to 0.99.6
Package: beadarray
Commit: c7ea9708ca17c975bd505ca3657a365acb7e6895
Author: markdunning <mark.dunning@gmail.com>
Date: 2026-03-18 10:53:50 +0000
Commit message:

 Reinstate BeadDataPackR to list of dependancies
Package: GSVA
Commit: 2f9c1a646fde1bb4b97b3e3c12d7c68080d5a976
Author: Robert Castelo <robert.castelo@upf.edu>
Date: 2026-03-18 11:49:40 +0100
Commit message:

 Bump version
Package: GSVA
Commit: 1206b3ad1ce38cddcc01898d268b61ee19cb8b1f
Author: Robert Castelo <robert.castelo@upf.edu>
Date: 2026-03-18 11:49:16 +0100
Commit message:

 Fixing versions >= 2.0 wrongly reported in the NEWS file, as noted in issue #261
Package: beadarray
Commit: 011450a34d53d375efe505a329fd949a8d583e80
Author: markdunning <mark.dunning@gmail.com>
Date: 2026-03-18 09:59:40 +0000
Commit message:

 Update email and versions.

Remove source file R that isn't actually referenced anywhere
Package: beadarray
Commit: 3b5574f92f5d8f937782f0289fab87364b5082c9
Author: markdunning <mark.dunning@gmail.com>
Date: 2026-03-18 09:52:40 +0000
Commit message:

 Try to remove offending broken dependancies
Package: queeems
Commit: 8200e3ea6638edce38c81d6f4beaa91659627a15
Author: thsadiq <hassan.t.sadiq@gmail.com>
Date: 2026-03-18 10:43:16 +0200
Commit message:

 Addressed Bioc Build Warnings
Package: queeems
Commit: 52091bb5ba54b1e8c5a3d8b695f18e57259b00df
Author: thsadiq <hassan.t.sadiq@gmail.com>
Date: 2026-03-18 10:27:06 +0200
Commit message:

 Addressed Bioc Build Warnings
Package: BamScale
Commit: 741ddc1a4b7de5b8a2b6e4f969045d1e99c1480f
Author: Chirag Parsania <chirag.parsania@gmail.com>
Date: 2026-03-18 14:50:56 +1100
Commit message:

 Increment version number to 0.99.5
Package: BamScale
Commit: b82209656c055bed4030cf58e8d9c4f80e4c1013
Author: Chirag Parsania <chirag.parsania@gmail.com>
Date: 2026-03-18 14:48:08 +1100
Commit message:

 README correction
Package: BamScale
Commit: 2faa484d50fbe96127427df5e3015e9538250fe0
Author: Chirag Parsania <chirag.parsania@gmail.com>
Date: 2026-03-18 14:47:47 +1100
Commit message:

 improve benchmark
Package: BamScale
Commit: a08b6a300eec58e7c0eeffc0cbde57aff7f8ada8
Author: Chirag Parsania <chirag.parsania@gmail.com>
Date: 2026-03-18 14:33:00 +1100
Commit message:

 Merge branch 'perf/compact-read-columns'
Package: BamScale
Commit: 3032787aa160c7fdea41e46fd1edad027a88f0d6
Author: Chirag Parsania <chirag.parsania@gmail.com>
Date: 2026-03-18 11:34:15 +1100
Commit message:

 Optimize bam_read with compact internal string columns
Package: carnation
Commit: fa3b19951576877f84354ce091944448ba7624ad
Author: Apratim Mitra <16709900+mitraak@users.noreply.github.com>
Date: 2026-03-17 23:22:08 -0400
Commit message:

 Merge pull request #25 from NICHD-BSPC/v0.99.9

V0.99.9

- add scatter plot features
  - table can be filtered by significance
  - genes can be selected in the plot and shown in the table
  - genes can be selected in the table and added to 'Gene scratchpad'
- allow users to add pattern analysis results to carnation object using the 'Load data' -> 'New' UI
- add support for edgeR & limma
- show currently loaded dataset on 'Load data' page
- update contributors
Package: carnation
Commit: 627832fe287b768b264f1d4f453ad1c51080642a
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2026-03-17 23:11:54 -0400
Commit message:

 version bump
Package: carnation
Commit: 4419067f0da427c4b647b8c14cd7f585b78244c0
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2026-03-17 23:03:21 -0400
Commit message:

 pin R < 4.6 for bioc
Package: carnation
Commit: f1165d0f20bfde4674570db3490af7d7cf1e380c
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2026-03-17 23:03:08 -0400
Commit message:

 minor formatting
Package: carnation
Commit: fc3342da801aecbfc36eaa227dd9feb859904dc5
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2026-03-17 22:39:14 -0400
Commit message:

 updt scatter plt test w new params
Package: carnation
Commit: d33cad9ab5a2fbb4b734117170f024e62f7ac34b
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2026-03-17 22:38:55 -0400
Commit message:

 use reactive to hold scatter plt src
Package: carnation
Commit: ecb3a0f58be0a57d8bf6477a08ac64d4fc52c653
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2026-03-17 22:25:06 -0400
Commit message:

 updt imports, NAMESPACE
Package: carnation
Commit: f10cbda97b6652d6826888e2b8d150f138e59199
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2026-03-17 21:43:12 -0400
Commit message:

 change github actions github install branch
Package: carnation
Commit: 93a1bfaecadd5de2a1c07659429c0b205a967ae0
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2026-03-17 21:42:43 -0400
Commit message:

 add biocmanager install, conda install note
Package: carnation
Commit: 5957e1c7f8cadbfb26195a4850f9a6f3969373b0
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2026-03-17 21:42:14 -0400
Commit message:

 add bioc badges, devel page
Package: carnation
Commit: b96618aba22275b5dc01c5c0cb18045b88568b1a
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2026-03-17 16:54:45 -0400
Commit message:

 add DESeq2 column names
Package: carnation
Commit: f33543a090e79baf75378439a156408d8228f215
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2026-03-17 16:54:37 -0400
Commit message:

 tweak button label
Package: carnation
Commit: 1471e2874626d5ab5e0e20177e21af8947427b77
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2026-03-09 23:12:20 -0400
Commit message:

 add plotly imports to NAMESPACE
Package: carnation
Commit: 92becfc8dc3bba175e80a7f50b463a26844232e4
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2026-03-09 23:12:07 -0400
Commit message:

 add tbl & plt selection fr scatter
Package: carnation
Commit: c7d276d4ee21a505e1304906880469553c2a9500
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2026-03-09 23:11:31 -0400
Commit message:

 minor ws
Package: carnation
Commit: bf2cbaf0570310ed5604a5a94deaa06005cf5842
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2026-03-09 23:10:47 -0400
Commit message:

 set default selection type to box
Package: carnation
Commit: 14482babeb1b386b214ff8c0e331efeca15c9536
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2026-03-07 00:31:57 -0500
Commit message:

 add plotly imports
Package: carnation
Commit: ed5987abf3a9489c6602ed60e3cead93c7f5d642
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2026-03-07 00:31:32 -0500
Commit message:

 add src arg to scatter plotly plt
Package: carnation
Commit: 20c734657becb482ef65d93743c04ac551faf2eb
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2026-03-06 21:25:59 -0500
Commit message:

 renderdt reacts to scatter_dt
Package: carnation
Commit: c49bafbdde799436785d17719592ab19194a3ef5
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2026-03-06 17:21:01 -0500
Commit message:

 inc scatter plt legend char size
Package: carnation
Commit: f14b57fdcc708656ca9a47bf17a33ac99d720a28
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2026-03-06 17:20:50 -0500
Commit message:

 updt scatter plt docs
Package: carnation
Commit: d11ff5d39fe4fcacdf558b14786e0793f840856c
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2026-03-06 17:17:40 -0500
Commit message:

 updt plt w gene scratchpad
Package: carnation
Commit: 12bb3797847f1b43c73ad5e214a1851b7aba148e
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2026-03-06 17:16:45 -0500
Commit message:

 integrate tbl sel w gene scratchpad & global reset genes
Package: carnation
Commit: 0746a310211404443e0d1c235be406eb63f1c47d
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2026-03-06 17:16:08 -0500
Commit message:

 add scatter tbl selection
Package: carnation
Commit: 63e9518d549f204174977c2d7e97dd341fcd61c8
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2026-03-06 16:16:00 -0500
Commit message:

 add scatter tbl filters
Package: carnation
Commit: 6da9ff6daa99589428dedfc18235c45711d79108
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2026-03-06 13:47:36 -0500
Commit message:

 mv scatter tbl to observer
Package: carnation
Commit: 2541798f3ea17e874dab72d32f15acc3905535c3
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2026-03-06 13:43:31 -0500
Commit message:

 add sig column to scatter tbl
Package: carnation
Commit: 141e44dce3761787e2ed0d79021339b8f6b4d8da
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2026-03-06 13:29:13 -0500
Commit message:

 make legend entries larger
Package: carnation
Commit: 0a046495cf40c3c638e6e74ebf373ce100733065
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2026-03-06 13:29:01 -0500
Commit message:

 make scattergl by default
Package: carnation
Commit: 3fb3b9e99b7fd990c3a8c51c9a294eaadaeb2936
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2026-03-06 13:28:14 -0500
Commit message:

 split static/interactive plt outputs; switch frm renderUI to cond panel
Package: carnation
Commit: 7f9f487058d4bda8053bf0aa1cb244e4f0915e5f
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2026-03-06 13:27:55 -0500
Commit message:

 always show tbl
Package: carnation
Commit: d7eda219b525707783045741686fb4b77dbc8c9d
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2026-03-05 10:28:42 -0500
Commit message:

 fix typo
Package: carnation
Commit: 4ef27f10fd9e75143b32f1ec372bf83212afdf04
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2026-03-05 09:46:41 -0500
Commit message:

 updt NAMESPACE
Package: carnation
Commit: 762b76ffd44ba332aee5896c0a171fe123dcb226
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2026-03-05 09:44:35 -0500
Commit message:

 keep orphan dds obj
Package: carnation
Commit: 3455dc20dc35dbd6afd724668244a2970aec86f2
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2026-03-05 09:43:45 -0500
Commit message:

 add degpatterns obj validator
Package: carnation
Commit: 0791b87652a785b0635ccdd3b772a116efa4099b
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2026-03-05 09:40:56 -0500
Commit message:

 add degpatterns obj via ui
Package: carnation
Commit: 1e9e7532d2da2632cad1dee1d5c33b7cc900fc28
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2026-03-05 09:40:09 -0500
Commit message:

 rm comment
Package: carnation
Commit: 1d2d905ac9c7e0b74dca9bb9392c5454cedb733d
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2026-03-05 09:39:43 -0500
Commit message:

 add comment
Package: carnation
Commit: cc549a686c68808bfb0323c1548a842569a31131
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2026-03-05 09:39:05 -0500
Commit message:

 add/fix logic fr checking pre-existing paths
Package: carnation
Commit: 4b55ea9d50c5b0e321e7a4c37159267b01dea91d
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2026-03-05 09:38:37 -0500
Commit message:

 rm design slot before saving
Package: carnation
Commit: cfd99b36587584c18f44fa2c6d3e4b87160f3b6d
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2026-03-05 09:28:36 -0500
Commit message:

 fix typo
Package: carnation
Commit: 9419c95af6fccfde21a30f786339b214d00deebf
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2026-03-05 09:04:38 -0500
Commit message:

 mv loaded data card
Package: carnation
Commit: 3f7ae4d6fa1f8c637c1ea116cd6008d23695674c
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2026-03-03 16:38:40 -0500
Commit message:

 add bioconductor shields
Package: carnation
Commit: 167f0763483f896f027452e5c354183f7fc54665
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2026-03-02 20:42:51 -0500
Commit message:

 pin R < 4.3.0
Package: carnation
Commit: a25bda49a49c7742756d8e306c0a9649ae4cb288
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2026-03-02 20:32:07 -0500
Commit message:

 add support for edgeR & limma
Package: carnation
Commit: ddaeda6a46dfe1f4b38b7f50dd6842e4de424c98
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2026-03-02 20:22:29 -0500
Commit message:

 add styling for card
Package: carnation
Commit: 9fb6fc47f15a94e2bbfa9ca23e0ec7328022b6d2
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2026-03-02 16:34:34 -0500
Commit message:

 handle parent path of saved RDS being present in data areas
Package: carnation
Commit: db1d34bac719b9fb95bda1c0cb9563af61351cc2
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2026-03-02 14:18:52 -0500
Commit message:

 rm server stuff frm README
Package: carnation
Commit: d94f525888933179b96d507d2bcb123f10b92a80
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2026-03-02 14:15:18 -0500
Commit message:

 check for design slot before assignment
Package: carnation
Commit: bd0aea76f245ee9c55046164f4fa19ec633a7a82
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2026-03-02 14:12:24 -0500
Commit message:

 show currently loaded project name
Package: carnation
Commit: b187603f6958bf81df7f0f10cc51904cf0306f8d
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2026-03-02 13:06:03 -0500
Commit message:

 tweak function help
Package: carnation
Commit: c4fb249081acbd5628bc71a9e64bd1651d9f0ae4
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2026-03-02 11:09:30 -0500
Commit message:

 updt DESCRIPTION
Package: carnation
Commit: 20839a2d7ba82e574aa2ec1634c2678a533093fd
Author: Apratim Mitra <apratim.mitra@nih.gov>
Date: 2026-03-02 10:27:31 -0500
Commit message:

 updt contributors
Package: BUSpaRse
Commit: 23d0d0be1dbed95d3548c20a43cb12b4263f7417
Author: Lambda Moses <dlu2@caltech.edu>
Date: 2026-03-17 23:20:53 -0400
Commit message:

 Merge branch 'RELEASE_3_22' into devel
Package: BUSpaRse
Commit: 444ab852abbfa0eafcbe38768e4eb3878e6357ca
Author: Lambda Moses <dlu2@caltech.edu>
Date: 2026-03-17 23:20:31 -0400
Commit message:

 Old archives not working on the Ensembl website
Package: Rsubread
Commit: a2681547daa8a40bbc01e79e3418d097942e9126
Author: Yang Liao (Monash University) <yliao@m3v109.massive.org.au>
Date: 2026-03-18 10:02:05 +1100
Commit message:

 imporved manual
Package: clusterExperiment
Commit: 3a17003f4816b796ac601d33fc6d2f52cc843a82
Author: Elizabeth Purdom <epurdom@stat.berkeley.edu>
Date: 2026-03-17 15:43:28 -0700
Commit message:

 rerun documentation
Package: clusterExperiment
Commit: b82e4051fa49bf267b5077ed0d1632716cfdd7b3
Author: Elizabeth Purdom <epurdom@stat.berkeley.edu>
Date: 2026-03-17 15:42:20 -0700
Commit message:

 Merge branch 'claude/suspicious-antonelli'
Package: clusterExperiment
Commit: 9128cc1f1d45a5bf1d118c4e56c24f610e9bec06
Author: Elizabeth Purdom <epurdom@stat.berkeley.edu>
Date: 2026-03-17 15:42:01 -0700
Commit message:

 fix missing documentation
Package: clusterExperiment
Commit: 56d9563aecada310803f19ce9e1c38a38ddbdc75
Author: Elizabeth Purdom <epurdom@stat.berkeley.edu>
Date: 2026-03-17 15:41:19 -0700
Commit message:

 fix Rd \link{} targets missing package anchors

Add package prefixes to \link{} targets (e.g. \link[limma]{topTable}) to resolve R CMD CHECK NOTEs across clusterContrasts, getFeatures, mergeClusters, plotDendrogram, plotClustersTable, clusterSingle, makeReducedDims, and subset.

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
Package: clusterExperiment
Commit: 1fa6a8faa06afcadb97744ac0cdd4fe1df4c26d9
Author: Elizabeth Purdom <epurdom@stat.berkeley.edu>
Date: 2026-03-17 15:31:03 -0700
Commit message:

 bump up version
Package: clusterExperiment
Commit: c85eec8a8138d5672abac2d962e1c539f0a81c6c
Author: Elizabeth Purdom <epurdom@stat.berkeley.edu>
Date: 2026-03-17 15:30:48 -0700
Commit message:

 update documentation and fix tests
Package: clusterExperiment
Commit: f1a104d432f409dc9706e9aaa147c56435b54c8a
Author: Elizabeth Purdom <epurdom@stat.berkeley.edu>
Date: 2026-03-17 15:10:57 -0700
Commit message:

 Merge branch 'claude/suspicious-antonelli'
Package: clusterExperiment
Commit: b6048acf6fc399bd651e8dc4318598688a034ea2
Author: Elizabeth Purdom <epurdom@stat.berkeley.edu>
Date: 2026-03-17 14:51:36 -0700
Commit message:

 fix Rd documentation: replace \\itemize with \\describe where items use label/description format

Fixes 'Lost braces in \\itemize; meant \\describe?' warnings from R CMD CHECK across 19 R source files and one .Rd file.

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
Package: Rsubread
Commit: f4fb96e2a5f7e4eabc291c033c5d6eefea2278a1
Author: Yang Liao (Monash University) <yliao@m3v109.massive.org.au>
Date: 2026-03-18 08:34:57 +1100
Commit message:

 updated manual page of simReads
Package: Rsubread
Commit: 075787f019f92363d272de08f5e45ee7c54737e6
Author: Yang Liao (Monash University) <yliao@m3v109.massive.org.au>
Date: 2026-03-18 08:16:27 +1100
Commit message:

 Bumpped version number.
Package: MSnbase
Commit: 5aeafcbc637fc16aac321f0f2a7aca4a3aff3540
Author: Laurent Gatto <lgatto@protonmail.ch>
Date: 2026-03-17 22:05:03 +0100
Commit message:

 fix version
Package: MSnbase
Commit: c8637c930c8b120ea2f2b441933dacd60b1e573e
Author: Laurent Gatto <lgatto@protonmail.ch>
Date: 2026-03-17 22:03:58 +0100
Commit message:

 remove deps
Package: omicsViewer
Commit: 38cdd2aa8ae9a67ebeb82a3be32adab3d114b320
Author: Chen Meng <mengchen18@gmail.com>
Date: 2026-03-17 20:43:29 +0100
Commit message:

 fix: add remotes package to Dockerfile dependencies

devtools::install_github() requires the remotes package which was missing

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
Package: imageTCGAutils
Commit: 8c58e93c6e8302da41e9a6725ad7c7d56301a0a3
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2026-03-17 15:19:42 -0400
Commit message:

 version bump 0.99.19
Package: imageTCGAutils
Commit: bbac80aadf77e0f8d938c1487b6c71e50b88d3bc
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2026-03-17 15:17:03 -0400
Commit message:

 add NEWS.md file
Package: imageTCGAutils
Commit: 54e615253240575a4b76a68823bc325efd0a3f52
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2026-03-17 15:15:20 -0400
Commit message:

 stay within 80 char width
Package: imageTCGAutils
Commit: bbb5380fc899c67b70dbdadefeaaa98e5448efa3
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2026-03-17 15:08:53 -0400
Commit message:

 clarify relationship with imageFeatureTCGA
Package: imageTCGAutils
Commit: 1cdff095bca1f1f424e59a25ea129828387ffbb2
Author: LiNk-NY <marcel.ramos@sph.cuny.edu>
Date: 2026-03-17 15:08:37 -0400
Commit message:

 fix typo in title
Package: omicsViewer
Commit: 54b64f92cc2abf643226db1107bbd9f7aa86a0fd
Author: Chen Meng <mengchen18@gmail.com>
Date: 2026-03-17 20:17:04 +0100
Commit message:

 fix: correct meta_scatter_module documentation warnings

- Add @param id, remove stale @param input/output/session (old callModule API)
- Remove misplaced code example from @param reactive_status (caused lost braces note)
- Regenerate Rd with roxygen2
- Bump version to 1.15.3

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
Package: cosmosR
Commit: ffb736106059c3e84892bc81a292aa87ef204594
Author: Aurelien Dugourd <dugourd@ebi.ac.uk>
Date: 2026-03-17 16:51:31 +0000
Commit message:

 chore: transfer maintainer role from Attila Gabor to Aurélien Dugourd

Update Authors@R in DESCRIPTION to reflect the approved maintainer
change per Bioconductor core team request.

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
Package: plyranges
Commit: 90094094da5109e7c4551128fc69e0dacfa7f84c
Author: Mike Love <mikelove@users.noreply.github.com>
Date: 2026-03-17 11:53:08 -0400
Commit message:

 version bump and news
Package: kissDE
Commit: bd573b4186a4668a6f3eec1d1efcc84976567269
Author: Aurélie Siberchicot <aurelie.siberchicot@univ-lyon1.fr>
Date: 2026-03-17 15:21:31 +0100
Commit message:

 Clean up the README file
Package: kissDE
Commit: c1280c419572df1c5566fa439ad2557a019e8bc8
Author: Aurélie Siberchicot <aurelie.siberchicot@univ-lyon1.fr>
Date: 2026-03-17 15:20:44 +0100
Commit message:

 Update version number
Package: kissDE
Commit: 78bb5c1f6e6313e1a34de276dfb6b13a5ce685b1
Author: Aurélie Siberchicot <aurelie.siberchicot@univ-lyon1.fr>
Date: 2026-03-17 15:20:30 +0100
Commit message:

 Correct a field in DESCRIPTION
Package: flowSpecs
Commit: 5bcbe700272a8ed50f27bf576eb0acc89384530e
Author: Jakob Theorell <jakob.theorell@ki.se>
Date: 2026-03-17 11:14:05 +0100
Commit message:

 Bug fixes
Package: ExploreModelMatrix
Commit: d22b2d9cd2bf9e2deb2fbd900421fbea697b8d17
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2026-03-16 17:50:43 +0100
Commit message:

 version bump, 1.23.1
Package: ExploreModelMatrix
Commit: 27652e013f629658f6b6b95638893f4be0cfeffa
Author: Federico Marini <marinif@uni-mainz.de>
Date: 2026-03-16 17:50:31 +0100
Commit message:

 fixing icon names to avoid message of (possibly dismissed?) fa icons
Package: IntEREst
Commit: 0bcab3ff70c9e30675e9f4e1382335f12fe6f741
Author: gacatag <ali.oghabian@helsinki.fi>
Date: 2026-03-17 09:54:42 +0200
Commit message:

 Removing parameters baed on defunct fucntions/params in the source packages
Package: FlowSOM
Commit: b2d43e01f25ba49809672864b9ee1ab8c4ba7de9
Author: SofieVG <sofie.vangassen@gmail.com>
Date: 2026-03-17 10:41:52 +0100
Commit message:

 Removed #include  from the C script, as this is not supported anymore, and I don't think we actually still used it.
 </pre>
    </div>
  
    

      Package: atacInferCnv

      Commit: c68116d75a0cef1fbde190e54c7a73e21fb234f5

      Author:  Konstantin Okonechnikov <k.okonechnikov@gmail.com> 

      Date: 2026-03-17 09:48:54 +0100

      Commit message:


	  
		
 Bioconductor submission fixes
 

    

  
    

      Package: atacInferCnv

      Commit: 6de546aa06d119076abede9f20cc18627174ea4c

      Author:  Konstantin Okonechnikov <k.okonechnikov@gmail.com> 

      Date: 2026-03-17 08:13:34 +0100

      Commit message:


	  
		
 Bioconductor submission fix runAtacInferCnv
 

    

  
    

      Package: DOTSeq

      Commit: b906ad56955ea91d3b8335c68d95369b4fbd74fc

      Author:  lcscs12345 <lcscs12345@gmail.com> 

      Date: 2026-03-17 15:14:35 +0800

      Commit message:


	  
		
 fix id_mapping check
 

    

  
    

      Package: scoup

      Commit: cc2e0757de802ece32830ba5ba0c06f0d3f5bda6

      Author:  thsadiq <hassan.t.sadiq@gmail.com> 

      Date: 2026-03-17 07:05:45 +0200

      Commit message:


	  
		
 Updated citation
 

    

  
    

      Package: Rsubread

      Commit: b5a6885b11b5e35f7c170973638fd9f3c8a7329b

      Author:  Yang Liao (Monash University) <yliao@m3v109.massive.org.au> 

      Date: 2026-03-17 15:04:55 +1100

      Commit message:


	  
		
 added the strandSpecific option to simReads()
 

    

  
    

      Package: igblastr

      Commit: d8e780657c658379ea6cfe039583d05541f606a6

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

      Date: 2026-03-16 20:13:53 -0700

      Commit message:


	  
		
 Small update to README.md
 

    

  
    

      Package: igblastr

      Commit: 15bba547fbafb9951815112a2dff1ba0402b7df7

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

      Date: 2026-03-16 19:59:00 -0700

      Commit message:


	  
		
 Relax dep on GenomeInfoDb (>= 1.47.2)
 

    

  
    

      Package: CSOA

      Commit: 57fac962a0202970065eb829ed3e297f452c9aac

      Author:  andrei-stoica26 <andreistoica@foxmail.com> 

      Date: 2026-03-17 09:36:10 +0800

      Commit message:


	  
		
 Bumped version
 

    

  
    

      Package: CSOA

      Commit: ff99e7d2666ba92451df21e503f707ef91272ff5

      Author:  andrei-stoica26 <andreistoica@foxmail.com> 

      Date: 2026-03-17 09:35:26 +0800

      Commit message:


	  
		
 Minor edits
 

    

  
    

      Package: Rsubread

      Commit: b7c6160bf692578d9626a8306a69f8c8e97bf7f6

      Author:  Yang Liao (Monash University) <yliao@m3e108.massive.org.au> 

      Date: 2026-03-17 09:36:15 +1100

      Commit message:


	  
		
 added some debug outputs
 

    

  
    

      Package: BamScale

      Commit: b24c2b768ce629243e2191660b308aac7195017c

      Author:  Chirag Parsania <chirag.parsania@gmail.com> 

      Date: 2026-03-17 07:49:34 +1100

      Commit message:


	  
		
 performance improvement
 

    

  
    

      Package: BamScale

      Commit: ce957db983dd263bfcd30ec20568fee8e85e3b1d

      Author:  Chirag Parsania <chirag.parsania@gmail.com> 

      Date: 2026-03-17 07:48:49 +1100

      Commit message:


	  
		
 Increment version number to 0.99.4
 

    

  
    

      Package: igblastr

      Commit: 43eab5dcb042185acf073fc729c001051c052955

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

      Date: 2026-03-16 13:51:19 -0700

      Commit message:


	  
		
 Add low-level utilities read_auxdata() and write_auxdata().

Also the 'auxiliary_data' argument of igblastn() can now be a data.frame
in addition to the path to a file containing auxiliary data (.aux file).
 

    

  
    

      Package: AnVILPublish

      Commit: 38c02f5d52ef40e2e7d9b6593a3718ad109afff0

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

      Date: 2026-03-16 16:08:57 -0400

      Commit message:


	  
		
 version bump 1.21.1
 

    

  
    

      Package: AnVILPublish

      Commit: 0b739f1e7b1611c8eb0b904f6084f43f4e27a6c7

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

      Date: 2026-03-16 16:08:55 -0400

      Commit message:


	  
		
 bump RoxygenNote version
 

    

  
    

      Package: AnVILPublish

      Commit: ec93f5660337bc1df6fa189aa7c4100f4031af17

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

      Date: 2026-03-16 16:08:41 -0400

      Commit message:


	  
		
 export create_workspace function
 

    

  
    

      Package: ChIPpeakAnno

      Commit: bce96ffcce846486e2625d63268d2edd9c5690db

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

      Date: 2026-03-16 15:46:26 -0400

      Commit message:


	  
		
 fix the issue for biomaRt in vignettes.
 

    

  
    

      Package: spammR

      Commit: 233efe8a8b53a6c67f75baafae20cec03e3bfc0c

      Author:  Sara JC Gosline <sara.gosline@pnnl.gov> 

      Date: 2026-03-16 12:40:04 -0700

      Commit message:


	  
		
 updated dependences
 

    

  
    

      Package: spammR

      Commit: be5b39a01be03937e72e15e3c6a770b359b08cfc

      Author:  Sara JC Gosline <sara.gosline@pnnl.gov> 

      Date: 2026-03-11 05:38:18 -0700

      Commit message:


	  
		
 added software to biocviews
 

    

  
    

      Package: Rarr

      Commit: 5ad898410c678e206f29ea6078ab741bf614f502

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-03-16 15:57:16 +0100

      Commit message:


	  
		
 Bump version
 

    

  
    

      Package: Rarr

      Commit: ea6042c7d3feebd51d297367473e78434f948449

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-03-16 15:56:57 +0100

      Commit message:


	  
		
 Mention DelayedArray breaking change in NEWS
 

    

  
    

      Package: Rarr

      Commit: 391d1cace6d02cb4014070c1b2eb1726b74d86c5

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-03-16 15:55:00 +0100

      Commit message:


	  
		
 Remove methods dependency
 

    

  
    

      Package: Rarr

      Commit: 60c4e9f3faf77809c47924bdc235c96fe84b3bb7

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-03-16 16:15:05 +0100

      Commit message:


	  
		
 Export deprecation function stubs
 

    

  
    

      Package: Rarr

      Commit: 7610fcf1ac8d497f5c1e10722dc881b13431b1a2

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-03-16 14:59:09 +0100

      Commit message:


	  
		
 Use a slightly smoother deprecation process
 

    

  
    

      Package: Rarr

      Commit: 431d7b5782fdc4798c5fe9810d24a901dc2c0ad2

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-03-16 10:52:28 +0100

      Commit message:


	  
		
 Relax BiocCheck check
 

    

  
    

      Package: Rarr

      Commit: 0f0de5462d0fd80fd8efc832c0974e8359d98d41

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-03-16 10:51:53 +0100

      Commit message:


	  
		
 Add more benchmarks
 

    

  
    

      Package: Rarr

      Commit: f4ceaa70d267975badda49e15507f478efcb591e

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-03-16 10:32:07 +0100

      Commit message:


	  
		
 Remove all DelayedArray content

Move to the separate ZarrArray package
 

    

  
    

      Package: Rarr

      Commit: 80530bb49f99dae5567e40051743f02266c53d2a

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-03-15 18:21:00 +0100

      Commit message:


	  
		
 Remove unused dims computation in CLI wrapper 

    

  
    

      Package: Rarr

      Commit: 6a2d5409e815e89b9117b8972403c25aef0310c1

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-03-12 15:24:53 +0100

      Commit message:


	  
		
 Make is_signed an actual bool
 

    

  
    

      Package: Rarr

      Commit: f8f44a40f06d156b8b8c81702d6cc2bc8906e3e1

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-03-12 15:20:02 +0100

      Commit message:


	  
		
 Add stdbool header
 

    

  
    

      Package: BiocBuildReporter

      Commit: 2a578e473b1f3a12fb4a088b1d6dadf681bbdb12

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

      Date: 2026-03-16 13:03:48 -0400

      Commit message:


	  
		
 Version bump and small change

 - PR from package review
 

    

  
    

      Package: BiocBuildReporter

      Commit: 68b1d73551cb410a8e81b163e10c7196d784e59f

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

      Date: 2026-03-16 13:02:49 -0400

      Commit message:


	  
		
 Merge pull request #4 from Bisaloo/bioc-review

Small fixes related to Bioc review 

    

  
    

      Package: BiocBuildReporter

      Commit: 716bc46fc2e8e9bb8deed80bb1682cadf5c80227

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-03-16 17:56:53 +0100

      Commit message:


	  
		
 Add BiocStyle to Suggests
 

    

  
    

      Package: BiocBuildReporter

      Commit: ebe94bc721535c3555e1b4a415b1d92500f9aaaa

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-03-16 17:52:58 +0100

      Commit message:


	  
		
 Fix package installation instructions
 

    

  
    

      Package: BiocBuildReporter

      Commit: c9499db171d48cb76b479d01e8aa4008e84a65dd

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-03-05 19:57:42 +0100

      Commit message:


	  
		
 Fix long roxygen line
 

    

  
    

      Package: BiocBuildReporter

      Commit: 50938d3a8f3a59aeb0e6f7b37a701131db80ba6a

      Author:  Hugo Gruson <git@hugogruson.fr> 

      Date: 2026-03-05 17:36:47 +0100

      Commit message:


	  
		
 Add LICENSE.md to .Rbuildignore
 

    

  
    

      Package: VariantToolsData

      Commit: 43d49251730419601b4896783bd76b8c1f3b843e

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

      Date: 2026-03-16 12:28:40 -0400

      Commit message:


	  
		
 undeprecate
 

    

  
    

      Package: VariantTools

      Commit: faec495e76a27f029a845be1c3e3633da5fa245a

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

      Date: 2026-03-16 12:28:02 -0400

      Commit message:


	  
		
 undeprecate
 

    

  
    

      Package: LACHESIS

      Commit: 1828e01714b46df107d402b8581518db1702c5ba

      Author:  VerenaK90 <ve.koerber@web.de> 

      Date: 2026-03-16 15:46:52 +0000

      Commit message:


	  
		
 Deleted Untitled.ipynb
 

    

  
    

      Package: LACHESIS

      Commit: 0237fe4e84fadbb7f42ce174388330d2626c4423

      Author:  Verena Körber <47210805+VerenaK90@users.noreply.github.com> 

      Date: 2026-03-16 15:45:45 +0000

      Commit message:


	  
		
 Merge pull request #129 from VerenaK90/temp_vignette_update

Vignette Update 

    

  
    

      Package: LACHESIS

      Commit: b0d357a034ca31c55b0b1df96963d8453c54f509

      Author:  MaximiliaEggle <maximilia.eggle@dkfz-heidelberg.de> 

      Date: 2026-03-16 11:05:30 +0100

      Commit message:


	  
		
 Changes requested by Verenas review
 

    

  
    

      Package: LACHESIS

      Commit: 02002fb1c068ab768053c9496c4e95f8f631bd12

      Author:  MaximiliaEggle <maximilia.eggle@dkfz-heidelberg.de> 

      Date: 2026-03-13 16:27:14 +0100

      Commit message:


	  
		
 stylR package
 

    

  
    

      Package: LACHESIS

      Commit: bd3f4a0700a4f45047c25111521a0eef12658467

      Author:  MaximiliaEggle <maximilia.eggle@dkfz-heidelberg.de> 

      Date: 2026-03-13 16:23:21 +0100

      Commit message:


	  
		
 Update vignette
 

    

  
    

      Package: LACHESIS

      Commit: 5b0ada8d02b70f545ead60ff2f1ee534b7a00d72

      Author:  MaximiliaEggle <maximilia.eggle@dkfz-heidelberg.de> 

      Date: 2026-03-13 16:20:52 +0100

      Commit message:


	  
		
 plotSurvival re-add confidence interval, adapt style to match DiseaseTraj and classifyLach, add x axis label
 

    

  
    

      Package: LACHESIS

      Commit: 19f45305e541d8e86e57424d877e060c92152339

      Author:  MaximiliaEggle <maximilia.eggle@dkfz-heidelberg.de> 

      Date: 2026-03-13 16:18:18 +0100

      Commit message:


	  
		
 Add sage as vcf source
 

    

  
    

      Package: LACHESIS

      Commit: b2ddfa5cd37f6fcef4d13b58b5e28a368de14114

      Author:  MaximiliaEggle <maximilia.eggle@dkfz-heidelberg.de> 

      Date: 2026-03-12 14:03:06 +0100

      Commit message:


	  
		
 Merge pull request #126 from VerenaK90/temp_plotClinicalCorrelations

Separate plotting functions, additional plots for classifyLACHESIS and plotDiseaseTrajectories 

    

  
    

      Package: LACHESIS

      Commit: f9a3b072beb2d11fb01b64d01b23f7f8ec367462

      Author:  MaximiliaEggle <maximilia.eggle@dkfz-heidelberg.de> 

      Date: 2026-03-12 10:59:47 +0100

      Commit message:


	  
		
 Changes according to Anands review
 

    

  
    

      Package: LACHESIS

      Commit: e92ab078604638e21da17a77ef26aec602f1733f

      Author:  VerenaK90 <ve.koerber@web.de> 

      Date: 2026-03-02 13:24:31 +0000

      Commit message:


	  
		
 Updated documentation
 

    

  
    

      Package: LACHESIS

      Commit: d5d74373073da7782cccf47f7c99b735ed1ca0a7

      Author:  VerenaK90 <ve.koerber@web.de> 

      Date: 2026-03-02 13:12:50 +0000

      Commit message:


	  
		
 Reformatted lines in readVCF
 

    

  
    

      Package: LACHESIS

      Commit: aa13dbdf736832b9b334d152f87385b25083ca41

      Author:  VerenaK90 <ve.koerber@web.de> 

      Date: 2026-03-02 11:29:05 +0000

      Commit message:


	  
		
 added adjustcolor to imports
 

    

  
  


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