wrapped_curl_perform() returns an actual HTTP status code
 

 version bump
 

 ucscSchema() no longer returns an invisible value
 

 udpate news
 

 bump cache
 

 fixing
 

 fix CVParam
 

 updates_for_bioc_review3
 

 updates_for_bioc_review1
 

 updates_bioc_review
 

 updates_bioc1
 

 updated_Tutorial_Oct
 

 updated_readme
 

 updated_oct8
 

 Readme updated
 

 Update based on Bioconductor review
 

 updated examples
 

 example improved
 

 examples updated
 

 Updated contributor email, mutiple fixes suggested by BiocCheck::BiocCheck()
 

 Merge branch 'master' into devel
 

 Update check-bioc.yml cache v4 

 update vignette and README
 

 Update links
 

 Merge pull request #5 from khoroshevskyi/master

Updated bedbase ids and docs 

 Fixed missing files and incorrect links
 

 Clarify about mouse gaps
 

 Update readme, AH107305
 

 Bump version
 

 Import tail
 

 Use evaluation from S4Arrays to capture subsetting indices
 

 Add cache-version to fix macOS cache collision
 

 Remove unnecessary steps and update actions
 

 Remove unused amd64 workflow
 

 Remove outdated workflow
 

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

 Use %notin% operator
 

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

 handled corner case where network is empty in reduce_solution_network
 

 built new doc
 

 added double threshold function
 

 corrected the reduce_solution_network function
 

 Update README.md 

 Update README.md 

 Update README.md 

 reduce img size
 

 reduced pathlength
 

 install suggested dependencies
 

 bioc check update to Release 3.19
 

 Update README.md 

 trying to fix reshape2 dependency
 

 added some support functions
 

 added moon support functions
 

 fixed example of moon
 

 updated omnipath part of PKN
 

 translate decouplrnival output
 

 Merge branch 'master' into devel
 

 update combineBCR

#546 #557

combineBCR now passes multiple options for clustering, edit distance calculations, alignment using clonalCluster.

This process also ensures CTstrict is properly formatted into `Heavy_Light` to function downstream
 

 Fixing issue with Light Chains

#557 allow passing of IGL, IGK or Light to get respectve light chains. Updated doucmentation accordingly
 

 Update README.md 

 initial implementation

#546 Allowing for hamming and other distances in efficient way through retooling of buildNetwork() in immApex
 

 Merge pull request #555 from BorchLab/percentKmer-semicolon

Fix semicolon issue 

 Fix single-chain combineExpression

#550
 

 update vignette articles
 

 docs rebuild
 

 Bump version: 3.19.3 → 3.19.4
 

 adjusted handle preserving `req_perform1` to updated signature in `httr2` v1.2.2 (Dec 2025)
 

 fixed internal method name clash: renamed `copy_attrs` → `copy_all_attrs` in `tbl_attrs`
 

 protect against calling `httr2::url_parse` on non-url strings
 

 bump version of h5py to one with compiled binaries for macOS-arm64
 

 Merge pull request #140 from salix-d/fix-.set_colorby

Fix .set colorby 

 Fix to .set_colorby

the single & was preventing the use of a character vector since it wouldn't stop even if the length was greater than 1 

 doc: fix example
 

 version bump
 

 doc: document gsetX input parameter
 

 add ignore biocCheck
 

 change minimum R version to 4.3.3
 

 add file
 

 remove logo folder (asked by BioC)
 

 igblastr 1.1.5: Some immprovements to igdata_info()

Also add read_igblastn_AIRR_output() and read_igblastn_fmt7_output().
 

 Remove large data files from vignettes
 

 Merge upstream/devel, keeping GitHub main version
 

 fixing version number for bioconductor submission criterion
 

 correct version number
 

 fix bugs from demo.rmd
 

 Graph/Docs: consolidate fixes and docs updates; remove .github/instructions from tracking; add demo assets and vignettes
 

 remove rproj file
 

 //
 

 .
 

 test citation
 

 ..
 

 update information
 

 edit description file
 

 update citation
 

 ////
 

 re-conf
 

 。
 

 SparseArray 1.11.9: Protect against the "OpenMP/fork deadlock"

See https://stackoverflow.com/questions/49049388 for details about
the "OpenMP/fork deadlock" problem.

The solution implemented in this commit is to call omp_pause_resource()
when returning from a .Call() that executes OMP-parallelized code.
See R/thread-control.R for the details.
 

 Merge pull request #109 from EHSRB-BSRSE-Bioinformatics/bioc_review_fix

add citation 

 Merge pull request #108 from EHSRB-BSRSE-Bioinformatics/bioc_review_fix

Address bioconductor review 

 update file extensions
 

 fix filter mut test since snv in germ mnv changes
 

 vectorise plot_radar
 

 vectorise spectra comparison
 

 vectorise cluster spectra
 

 vectorise find_bs_genome
 

 vectorise rename_columns and move to import_helper file
 

 vectorise sidak
 

 vectorise lollipop plot and add subtype resolution parameter
 

 remove looping in cleveland plot - use facets
 

 load library yulab.utils in Rmd. Add human BSgenome to imports pkdown
 

 install = TRUE for pkgdown build call
 

 add yulab.utils to cmd check imports
 

 add pkgdown to the list of extra packages for pkgdown action
 

 try just adding the suggested  packages in extra-packages like in the CMD check workflow
 

 Remove GenVisR dependency.
 

 install biocmanager devel from github for pkgdown action
 

 specify R devel version for pkgdown action
 

 Add interpretation to the Rmds
 

 Change pkgdown action dependency build
 

 fix pkgdown articles
 

 add notice
 

 style with styler
 

 rm donttest from sigfitting example. Fix bug in reversecomp ex.
 

 version bump 1.7.4
 

 slots are internal and should not be documented
 

 use docType class and rename Rd to TENxParquet-class
 

 add both examples in TENxGeoJSON
 

 add nucleus_segmentations example file
 

 add boundary argument to constructor function and class
 

 keep rows that have in_cell == TRUE
 

 .add_map_to_sce clean up
 

 update docs and remove mappingPattern
 

 add source URL link for mouse brain data
 

 remove mapping references in TENxVisium
 

 add mapping slot and mappingPattern argument to TENxVisium and TENxVisiumHD
 

 add comment to segmented_outs example
 

 import only select colnames in TENxSpatialParquet import
 

 minor updates to TENxSpatialParquet examples
 

 add mappings parquet file to extdata
 

 add TENxParquet virtual class and TENxMappingParquet derivative
 

 eventPointerBAM detection function
 

 updated vignette
 

 upgrade to R4.5 fixes a ggcyto and ggplot error
 

 does calling the library(ggcyto) fix R-CMD-check error for windows-latest only?
 

 shortened/clean up some more of vignette code; to update the consensus gating next

to update vignette to include using cd3-
split into two subsections
 

 modified bc no need to return anything. the default would be auto applied already
 

 Merge pull request #7 from leejasme/test_PR

Test PR 

 Move input checks to an internal function to handle it all

But need a return list for which args to set back to defaults?
 

 select the first if multiple rows satisfy the criteria.

for regular case, the new anchor should be the min and
for flipped, the new anchor should be the max (the row orders are in descending)
 

 Update README.md (#5)

 

 replaced ifelse with dplyr::case_when
 

 remove dependency of magrittr pipe (vignette to be updated)
 

 convert pipes to native pipes. next to test
 

 working on changing magrittr to native pipes
 

 version bump in devel
 

 - possibility to add coloured ellipses to MDS plots (linked to dot colour)
- bumped version to 0.99.5
 

 moved GHA to Bioconductor 3.23
 

 Removed hotfix in GSEA() and updated new version in DESCRIPTION AND NEWS.md (#156)

Co-authored-by: Alessia Campo <acampo@kb-bioinfo01.cancer.dk> 

 Document new data types for writing
 

 Allow writing higher bits and unsigned data types
 

 Document partial support for VLen-UTF8
 

 Fix in the calculations of the strandedness() function, and its corresponding unit tests
 

 bump version
 

 Trigger build
 

 update R version to R-devel
 

 add chunk labels to RunningWorkflow.Rmd
 

 remove minor comment
 

 Update affiliation and email in Introduction.Rmd yaml front matter
 

 fix and simplify R-CMD-check-bioc workflow
 

 txdbmaker 1.7.3: Various deprecations

Deprecate functions supportedUCSCFeatureDbTracks() and
supportedUCSCFeatureDbTables(). Use list_UCSC_tracks() from package
UCSC.utils instead.

Also deprecate the 'track', 'url', and 'goldenPath.url' arguments
of functions makeFeatureDbFromUCSC() and UCSCFeatureDbTableSchema().
 

 added URL and BugReports to docs
 

 use examplesIf
 

 update RoxygenNote
 

 change Services.Rd docType from data to methods
 

 version bump 1.23.2
 

 merged conflict fixed

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

# Conflicts:
#	DESCRIPTION
#	NEWS.md
 

 fix bugs caused by plyranges update
 

 update desc (#772)

Signed-off-by: Daena Rys <rysdaena8@gmail.com>
Co-authored-by: Tuomas Borman <60338854+TuomasBorman@users.noreply.github.com>
Co-authored-by: Muluh <127390183+Daenarys8@users.noreply.github.com>
Co-authored-by: Maija <203342482+mm-hak@users.noreply.github.com>
Co-authored-by: Hindrek Teder <hindrek.teder@gmail.com>
Co-authored-by: Tuomas Borman <tvborm@utu.fi> 

 GenomicRanges 1.63.1: Suggests UCSC.utils instead of rtracklayer

Use UCSC.utils::fetch_UCSC_track_data() instead of rtracklayer::getTable()
in makeGRangesFromDataFrame()'s examples. This allows us to replace
rtracklayer with UCSC.utils in Suggests.
 

 :memo: docs: add vegan 2.7-1 requirement for rCLR and rAitchison (#758)

Co-authored-by: Tuomas Borman <60338854+TuomasBorman@users.noreply.github.com> 

 update mia_logo (#784)

Co-authored-by: Muluh <127390183+Daenarys8@users.noreply.github.com> 

 Fix on verbosity
 

 Mention empty chunk reading improvement
 

 Do not assign on reading empty chunk
 

 Drop now unused outbuffer_size arg from zstd C code
 

 Do not precompute decompressed buffer size
 

 v2.1.3
 

 v2.0.2
 

 handle regulon without idxATAC
 

 v2.0.1
 

 remove some pkgs in Imports to Suggests
 

 update docs
 

 optimize getMotifMatrix
 

 Bumped version, updated NEWS.
 

 Enable use of arbitrary quantiles as effect size summaries.
 

 Extend runPca to support PCA on a subset of features.

... while still reporting the rotation matrix for all features.
 

 Updated versions of some libscran libraries.
 

 Consolidates internal data creation

Moves the creation and saving of internal data objects to a single script.

In the old way, only one of the two dataframes will get saved as internal data, which is a long running bug.
 

 Update ensembl look-up to v25
 

 Updates HPA data to version 25

Updates the download list and example data to reflect the
Human Protein Atlas (HPA) data version 25.
This ensures the package uses the latest available data.
Removes and recreates binary data files to reflect version changes.
 

 version bump
 

 Bump version
 

 Fix R CMD check NOTE about bashisms
 

 Added utility to determine the expected/actual version of igraph.
 

 Rolled out download instructions to a separate script for convenience.
 

 fix timeout 2
 

 bump up verion
 

 version 1.1.1
 

 update documentation with examples transparent background
 

 replace hex sticker in README and documentation
 

 update NEWS with hex sticker logo
 

 update NEWS and version bump
 

 Bump version
 

 Run autoreconf
 

 Remove bundled bzip

System bzip is required by R itself
 

 Remove outdated worklow
 

 Set up rhub workflow
 

 Remove LICENSE file and Bump the version
 

 Correcting the license format
 

 Updated news
 

 igblastr 1.1.4: Add utilities to update IgBLAST auxiliary and internal data

NCBI occasionally updates some of the files in the 'internal_data/'
and 'optional_file/' directories between IgBLAST releases, and it is
recommended to use the new files. They make the new files available
at https://ftp.ncbi.nih.gov/blast/executables/igblast/release/patch/

The user can now install these new files by calling update_live_igdata().
See '?update_live_igdata' for more information.
 

 new datasets for avoiding api calls
 

 Remove outdated README note
 

 Use toString() where relevant
 

 Mark regex as fixed
 

 Import back utils::tail
 

 Support numcodecs lz4
 

 Fix lazy eval issue
 

 Group all codec steps together
 

 Add read_c_order benchmark test
 

 Fix encode/decode naming for transpose codec
 

 Use _ instead of - in codec name
 

 Run devtools::document()
 

 Split codecs in files depending on their type
 

 Move all codec related steps in .compress_and_write_chunk
 

 Increment version number to 0.99.6
 

 styler on gitignore
 

 R style changes
 

 vignette updates
 

 vignette updates
 

 version bump 1.13.2
 

 version bump 1.13.1
 

 add chunk labels to vignette
 

 new bump added
 

 version bump, 1.1.2
 

 Modify multi-group statistic
 

 clarify threshold
 

 Merge pull request #10 from imbeimainz/dea_limma_wip

DeeDeeExperiment update 

 re-rendering manpages
 

 Lea's name reported correctly in all vignettes