build: rename codecov.yml to codecov.yaml 

 chore(deps): update actions/upload-artifact action to v6 (#178)

Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> 

 update vignette
 

 update of EventPointerBAM
 

 delete rproj
 

 update readme.
 

 sia to ia
 

 add geros funtions, clean up package
 

 correct suffixes for single tool analysis
 

 dynamic and condensed onput
 

 version with indiv file uploads
 

 making sia reactive
 

 update docu
 

 add diff dds slot
 

 ass highlights and spider
 

 reindent
 

 limpa 1.3.2
- Case study vignette with DIA-NN data
 

 igblastr 1.1.8: Add extract_codons() and translate_codons()

Also rename argument 'max_codons' of function translate_fwr4()
to 'max.codons'.
 

 Fix version number for Bioconductor devel
 

 Merge branch 'main' into feature/beta-smoother-tm-centering 

 updating readme
 

 update contributing.md
 

 complie demo data into R data
 

 Docs: fix roxygen issues and reorganize sources for Bioconductor submission
 

 version_bump to trigger bioc build
 

 Bumped version after reverting commits which broke graphical tests.
 

 Revert "Pushing snapshots to github to try and resolve R CMD build errors"

This reverts commit f16d4fec4f2eb12dc12c0ee502c1cd8aec430d94.
 

 Updated snapshots because of failing test on mac-os
 

 refactor: use Rf_ prefix for R API calls (#138)

 

 fix version (again)
 

 rm so,o
 

 version bump
 

 Merge pull request #6 from Vitek-Lab/feature-anomaly

Feature anomaly 

 fix filter_few_obs processing
 

 fix(summarizePSMs): Fix line that summarizes PSMs
 

 bug(Fragpipe): Fix converter to be backwards compatible to anomaly model changes
 

 Merge pull request #5 from Vitek-Lab/feature-spec-qval

fix spec bug 

 Apply moderation changes and bump version
 

 Update DESCRIPTION 

 tests: update tests
 

 introduce a netParseDate() function to abstract the libcurl dependency away from the udc logic
 

 network stuff used by utc should compile on windows now
 

 remove internet.[ch] as they are no longer needed
 

 feat: use NA as value instead of string 

 docs: remove non-default function arguments in prepareSignature
 

 docs: change the vignette installation instruction to Bioc
 

 dont bioc check
 

 try again
 

 try earlier
 

 new try fix gha
 

 try installing quarto
 

 putting in docs and error, resolves #95
 

 new version bump
 

 tempdir remode from examples
 

 Slightly scale the median to avoid issues with float imprecision in the tests.

Otherwise, we'd be checking for float equality for the observation with
distance equal to the median, and the outcome depends on the precision of the
calculation; this might result in slightly different results between our C++
and the R-based reference calculations in our test suite.
 

 Added relevant system headers for completeness.
 

 trackDb track file path is relative to the genome directory
 

 rewrite networking stack on top of libcurl (again)
 

 Fix DESCRIPTION and CITATION, bump to 0.99.8
 

 Updated the vendored tatami_stats.
 

 Try to install fansi from source
 

 Manually clear cache
 

 Fix documentation and loading of example data
 

 igblastr 1.1.7

Add utility functions translate_J_alleles(), J_allele_has_stop_codon(),
and translate_fwr4().

Rename auxdata column CDR3_stop to cdr3_end.
 

 Fix warning message
 

 Reoxygenate
 

 Remove LazyData from DESCRIPTION
 

 Print notification when falling back to an unknown matrix

- Provide options for turning this notice into a warning or error.
- Require a more recent assorthead to use the latest tatami_r.
 

 Consistent bedGraph terminology
 

 Updated installation instructions for official Bioconductor devel version
 

 Updated vignette
 

 Updated to 0.99.10
 

 Allowed filtering of non-zero thresholds; improved filtering sample number logic
 

 Suppressed redundant messaging; internal param change
 

 Added eBayes `trend` and `robust` options, changed the input data filtering to allow non-zero thresholding, added diagnostic plots option.
 

 Moved FDR filter functions to this file
 

 Added option for using simplied sample display names
 

 Updated to 0.99.10
 

 By default, FDR calcs now return the true BH-corrected FDR values.  A legacy option is provided to return to the method used in Southall et al 2013.
 

 Changed default max_overlaps to 10
 

 Document fill_value string fix in NEWS
 

 Add test for #94
 

 Replace dash in v3 codec names
 

 Add test for vlen-utf8 v3
 

 Version bump to 1.0.1
 

 fix a typo.
 

 new version bump added
 

 corrected examples
 

 examples fixed
 

 error in example fixed
 

 date updated
 

 Merge pull request #55 from drighelli/enhancements

# Changes in version 1.1.2

* adding volume instead of area for MERFISH.
* refactoring log2CountArea to log2DensitySignal
* added size and alpha arguments to plotCellsFovs
* added scaleBar argument to plotCellsFovs, plotCentroids, plotPolygons and plotZoomFovsMap
 

 Merge branch 'devel' into enhancements 

 fixing news versioning
 

 every check is ok
 

 enhancing documentation of computeQCScore about randomness and seed setting
 

 adding scale bar to plots
 

 fixing version in news file
 

 fixing epsilon for log2 ctrl tot ratio
 

 bumping version, adding notes on serious bug fixing
 

 modifying epsilon in spatialPerCellQC
 

 bug fixing coldata cell_id alignment with countmat cell_id
 

 updating to biocrelease
 

 Clarify installation instructions for SpaceTrooper

Updated installation instructions for SpaceTrooper package. 

 version bump
 

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

 Updating visuals of readme
 

 igblastr 1.1.6

Add function compute_auxdata() to compute the auxiliary data for a
set of germline J gene allele sequences.

Rename functions get_igblast_auxiliary_data() and
load_igblast_auxiliary_data() to get_auxdata_path() and load_auxdata(),
respectively. The old names can still be used but are deprecated.
 

 Merge pull request #213 from toby-clark4/p-fix

fixed 0 p-value inf values 

 build: update Rbuildignore to ignore more unnecessary files 

 chore(deps): update actions/checkout action (#175)

Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> 

 chore(deps): update actions/checkout digest to 8e8c483 (#173)

Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> 

 docs: fix writing errors uing vale 

 1. Remove .Rproj from version control 2. Update .gitignore, DESCRIPTION
3. Add extdata description
 

 restrict to feature in VisiumIO
 

 update RoxygenNote
 

 wrap text to 80 char width
 

 version bump 1.7.5
 

 version bump 1.31.4
 

 Update TCGAutils Quick Reference link and image 

 Update README.md 

 Update README.md 

 Update README.md

add note for STAR mapping parameter things 

 Update README.md 

 Update README.md

fixed typo 

 build conda environment from .yml file 

 Update README.md

fix typos in the conda installation section 

 Update NormalizationMethods.R 

 Update README.md 

 Update README.md

Fixed some typos. 

 Fix vignette, version bump 0.99.5
 

 Remove .Rproj, update docs, and bump version to 0.99.1
 

 Mention fixes in NEWS
 

 Fix long Rd line
 

 Replace aes_string() by aes()
 

 Fix vignette, version bump 0.99.4
 

 various package adjustments - version bump 0.99.3
 

 bug fix: plot cluster plots time point in correct order
 

 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