v2.13.5 rescale_ref() fix
 

 Moving from scuttle/scran use in the single-cell vignette to scrapper/bluster to fix deprecation warnings. Reduced timing in the spatCor() example by adding a subset of filtered and normalized spatial human cerebellum data to the package
 

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

 Import txdbmaker
 

 bump version
 

 Updated required versions of all libraries to their latest versions.
 

 Add .github to .Rbuildignore
 

 Add GitHub Actions CI workflow using waldronlab reusable workflow

- Implements the centralized  workflow.
- Adopts the MultiAssayExperiment triggering strategy (pull requests and
  specific path pushes) to save CI resources on this large data package.
- Adds necessary permissions for pkgdown deployment.

Co-authored-by: Gemini Code Assist <gemini@google.com>
 

 Merge legacy inst/NEWS content into top-level NEWS.md

- Moved the original package description from `inst/NEWS` into `NEWS.md`
  under an initial 1.0.0 release heading.
- Updated 2.43.1 release notes to better reflect recent commits.

Co-authored-by: Gemini Code Assist <gemini@google.com>
 

 Modernize package: update maintainer, format metadata, and adopt LFS

- Updated package maintainer to Levi Waldron and transitioned from legacy
  `Author`/`Maintainer` fields to standard `Authors@R` in DESCRIPTION.
- Formatted DESCRIPTION dependencies and biocViews to strictly use one
  item per line for readability.
- Cleaned up invalid biocViews terms to align with current ExperimentData
  standards.
- Bumped R version dependency to >= 4.0.0 and package version to 2.43.1.
- Converted vignette from legacy Sweave (.Rnw) to RMarkdown (.Rmd).
- Replaced unnecessary `affy` dependency with `Biobase` in Suggests and
  vignette code.
- Added a proper `CITATION` file for the 2018 Genome Biology paper
  (PMID: 30253799) using `bibentry()`.
- Initialized Git LFS to track all `.rda` and `.RData` files in `data/`
  to adhere to large file handling best practices.
- Removed deprecated `zzz.R` warning.
- Generated `NEWS.md` detailing the transition.

Co-authored-by: Gemini Code Assist <gemini@google.com>
 

 Alias disambiguation improved.
 

 use Pest from MsDataHub
 

 Bump version: 0.99.11
 

 Deprecate scran functions
 

 cumulative line, aes
 

 rebuild man pages
 

 update news
 

 installation modifications
 

 installation modifications
 

 UnsupportedPlatforms
 

 ported fix typo to doc
 

 caps in Biocpkg
 

 updated doc, exported getExpectation
 

 ci: trigger build
 

 refactor: update logic for unit tests
 

 refactor: appease lintr
 

 refactor: appease lintr
 

 refactor: update
 

 refactor: update code
 

 refactor: logic
 

 refactor: update script
 

 refactor: add support for xlsx files for new envision format
 

 Workaround to correctly write all-zero sparse arrays.
 

 fix: support spectraData<- on Spectra of length 1
 

 Support calculation of per-group medians in aggregateAcrossCells().

Mostly provided for back-compatibility with scuttle's deprecated functions.
For performance reasons, it is disabled by default.
 

 Add input preparation helpers for counts and metadata
 

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

 Add ZarrArray to Suggests
 

 Fix lint
 

 Support NAs in |S type as well
 

 Run devtools::document()
 

 Add note about NA support in VLen-UTF8
 

 Add tests for NA roundtrip
 

 Support NAs when writing strings
 

 remove DSS as suggested package
 

 Joined support site, iterating version number to trigger re-check of package.
 

 Update to 0.99.3 -- remove Nicolas maintainer status
 

 add rBLAST in examples
 

 Updated manual files
 

 Updated notes
 

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

 version 2.21.3 (2026-04-09)
- Bug fix to replace deprecated `arma::is_finite` by `std::isfinite`
 

 Update src/utils.h

Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com> 

 has_blast check added everywhere
 

 Docs: adjusted convertAnnotation documentation
 

 ci: trigger build
 

 refactor: update unit tests
 

 chore: bump version and update NEWS.md
 

 fix MSnbase and import setNames
 

 Direct summarizeAssayByGroup to tatami.sums.by.group as an alternative.

For developers who don't want to depend on scrapper.
 

 Consolidate each row/column tatami utility into a single function.

We add a row= argument to specify what the user wants, instead of having to
call a separate function. All previous row/column variants are soft-deprecated.
 

 fixed r check
 

 tanglegram
 

 update collapse height, #409
 

 bug fixed and optimize daylight algorithm
 

 docs: modernize roxygen documentation and fix typos

- Fix 'aesthethics' typos in multiple R files

- Convert roxygen comments to markdown syntax for better readability

- Update DESCRIPTION version to 4.1.1.004

- Update NEWS.md

- Regenerate man pages
 

 Merge pull request #697 from davidcerny/modify-geom_rootedge

Add a `data` argument to `geom_rootedge()` 

 Merge pull request #695 from xiangpin/devel

fix bug of nodepie 

 update
 

 update docs
 

 Merge pull request #694 from xiangpin/from_theme

from_theme 

 Merge pull request #692 from xiangpin/outward_taxalink

fix issue of geom_taxalink because of outward argument 

 update print method
 

 fix issue of geom_taxalink because of outward argument
 

 cleanup code
 

 update bioc version
 

 update NEWS
 

 fix reviewers comment
 

 fix news.md reviewers comment
 

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

 more fixing
 

 Address reviewer comments: documentation, vignette, naming, examples
 

 Address reviewer comments: documentation, vignette, naming, examples
 

 Fix Imports
 

 remove LimROTS_DREAM.Rmd
 

 adding dream to Limma_boot and permutating
 

 Fix missing item in all_sig_pal and sbs_palette documentation and increment version number
 

 fix errors
 

 checksums update
 

 update maintainer 

 update to bruker support email 

 new line signature 

 Update main.yml 

 API solutions
 

 move closing brace to own line for sigboot documentation
 

 Avoid re-building vignettes when checking the code in the GHA workflow
 

 Bump version
 

 Swap endianness rather than using rev()
 

 Mention fill value changes
 

 Allow writing and reading NAs as fill value
 

 Add test for bug reported by hpages
 

 version bump
 

 Move multiport related code to serve-managed.R worker for docker only
 

 Merge branch 'multiport' into 'master'

Replace Apache/rApache with httpuv multi-port server

See merge request alserglab/pr/phantasus/phantasus!6 

 minor fixes
 

 Merge remote-tracking branch 'origin/master'
 

 fix JS tests
 

 Fix date tag
 

 Gitlab CI
 

 Fix links in README 

 Merge remote-tracking branch 'upstream/devel'
 

 fix saving to gct bug
 

 Merge conflict DESCRIPTION
 

 Upgrading GHA worflow to work with Node.js 24
 

 Second review: remove direct slot access, remove ggplot print, use seq_along/seq_len, add README.md for extdata
 

 Minor improvements to summarizeAssayByGroup because it's quite popular.

- Add support for C++ multi-threading when calling aggregate_across_cells.
- Bind to beachmat's executor for safe parallelization with unknown matrices.
- Remove 'median' from the default 'statistics=' to use the fast path.
- Wrap subsetting operations in DelayedArrays to avoid allocations.
 

 Removed mkl dependency for mac support and removed .bbsoptions for upcoming R universe build system
 

 block some CHR-dependent unit tests, fix some doc
 

 version bump
 

 updated argument descriptions
 

 Merge branch 'devel' into BIOC_DEVEL
 

 Merge branch 'devel'
 

 doc updates
 

 Merge branch 'master' of github.com:MarioniLab/miloR
 

 Bump version
 

 version bump
 

 fix: sample name handling in run_oarfish, flexiplex barcode list loading
 

 WIP: refactor find_barcode
 

 Merge branch 'RELEASE_3_22' into devel
 

 bump GHA BioC version
 

 Convert to AuthorsR
 

 Fix function name in vignette
 

 Update downsample logic for scuttle/tatami and fix tests (#129)

* move to non-exact comparison

* Updated downsampling C++ code to use new scuttle functions.

Also added some more checks to ensure we don't lose integer precision.

* Stripped out test comparisons to downsampleMatrix.

These tests no longer make sense because the downsampling is no longer done on
a per-event basis (i.e. single UMIs or reads in each count). Rather, the new
algorithm operates on the entire count at once, for greater efficiency.

This all means that UMI and read counts are no longer interchangeable, which
means that the results from downsampleReads/Matrix are no longer directly
comparable. This is okay - the test itself was highly contrived anyway as it
only works when every UMI has a single read.

* Bumped version and date, updated NEWS.

---------

Co-authored-by: LTLA <infinite.monkeys.with.keyboards@gmail.com> 

 Minor typo fix for the unknown matrix warning/error.
 

 Merge pull request #384 from rformassspectrometry/jomain

refactor: add parameter direction to shiftPeaks() 

 Merge pull request #145 from rformassspectrometry/jomain

feat: add function retry() 

 refactor: change parameter to only retry on pattern
 

 feat: add function retry()

- Add `retry()` that allows evaluating an expression repeatedly with a delay in
  between tries. This is used in various backend classes that need to download
  content from the internet to ensure functions don't break because of a
  temporary connection problem to the resource.
 

 readme
 

 Merge pull request #97 from myushen/atlas_versioning

Download Atlas ID versioning data frame 

 delete unused pre-made data.
version up
 

 metadata version bump, new atlas versioning for counts.
 

 Atlas version README
 

 Bump version to 0.99.6 to trigger BiocCheck
 

 Trigger rebuild
 

 Update README
 

 add package help page, update vignette with BiocStyle, update README, add SE example
 

 edgeR 4.9.5
- New function DGEListFromTximeta().
- Fixes and argument changes to DGEListFromTximport().
- catchSalmon() can now read compressed quant files.
- Fix document links to help pages in other packages.
- Fixes to normLibSizes() and calcNormFactors() when a prior offset matrix exists.
 

 Removing chromstaRData from examples and vignette
 

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

 bump version
 

 update email
 

 Bugfix in examples
 

 Code cleanup and added unit tests for parameter objects and gene sets
 

 prompt user before cloning
 

 add package doc with roxygen2
 

 include sessionInfo output in README.md
 

 update prose in README.md
 

 update get_caf chunk in vignette
 

 tests fixed, minor bugfix in selecting NAs
 

 transit blaster -> rBLAST, warning fixes, man fixes, dependencies
 

 fix step bugs
 

 bug fix get_pop_descriptor saves to cache location

- force arg added
 

 refactor(groupComparisonLiP): Use ptm_label_type and protein_label_type for groupComparisonPTM dependency (#47) 

 Fix example scope in impute_KNN_data and update version
 

 Ready for Bioconductor submission: all checks passed
 

 Improve efficiency
 

 fix label param in test
 

 fix documentation
 

 simplify helper code
 

 fix issue in self comparing
 

 fix return
 

 Adding correlate method
 

 remove failing GHA bioc-checks
 

 Remove BBSoptions
 

 Allow scoreMarkers to only return the indices of the top markers.

This avoids having to call the DFrame constructor for a bit of efficiency if
the user doesn't care about the effect sizes. If we do need a DFrame, we create
it directly in Rcpp to avoid calling the S4Vectors::DFrame constructor.
 

 update readme
 

 Remove ZarrArray for Suggests for now
 

 Remove unnecessary R headers from snappy copy
 

 anndata to suggests
 

 update version 0.99.30
 

 fix: avoid 1:
 

 fix: revision of roxygen documentation
 

 fix: default black_list as NULL
 

 rm: get_optimal_clustering function
 

 rm: global metrics of clustering agreement depending on aricode, NMI and ARI
 

 fix: void 1:...; use seq_len() or seq_along() and avoid sapply(); use
vapply().
 

 fix: lines length
 

 fix text
 

 add: benchmarking fig
 

 bump version
 

 depend on PTMods 0.99.4
 

 fix indentation
 

 docs: completed vignette with PTMods references
 

 Docs: add addCarbamidomethyl as a parameter in plotSpectraPTM
 

 docs: added clarifications on the use of addCarbamidomethyl = TRUE by default
 

 Bump version
 

 Reimport req_user_agent()
 

 Move non biomart utilities to dedicated pkgdown section
 

 change license
 

 Bump version
 

 Eliminado library(rsconnect) del codigo fuente y actualizacion de version
 

 version bump to trigger new build...
 

 HDF5Array 1.39.1: Internal util compute_max_string_size() is now in h5mread
 

 Refactor package state handling and clean reviewer-facing package metadata

- remove <<- usage from exporting, reporting, and visualization helpers
- keep explicit local state for manifests, report assets, enrichment outputs, and plot messages
- restore selective SummarizedExperiment replacement imports for rowData<- and colData<-
- clean DESCRIPTION metadata and dependency duplication
- tighten namespace imports and address BiocCheck style issues for vapply and seq_len/seq_along
- simplify pkgdown articles by dropping the redundant reference guide entry
 

 Address reviewer comments: documentation, vignette, naming, examples
 

 Throttle down to 2 cores to avoid CHECK errors.
 

 Bypass some warnings now that we've deprecated everything.
 

 Address reviewer comments: documentation, vignette, naming, examples
 

 fix versioning
 

 limpa 1.3.11
- dpc() now calls either dpcON() or dpcCN() depending on `model` argument.
- Original dpc() renamed to dpcLegacy().
- New arguments for EListFromLongFormatFile(), readDIANN() and readSpectronaut().
- readSpectronaut() now reads run information columns.
 

 Removed bayesbio dependency
 

 Cleaned out vignettes to reflect the historical nature of this package.
 

 remove interactiveDisplay
 

 version bump 0.99.15
 

 update get_caf example
 

 add build_vrs_index and setup_vrs_toolkit helpers
 

 unexport local calls
 

 Merge pull request #23 from rformassspectrometry/convertAnnotation

Feat: keep NAs in input vector for addModfications 

 Merge pull request #22 from rformassspectrometry/addModifications

Add getModificationsCounts and throw error when multiple modifications in add modfications 

 feat: add getModificationsCounts and throw error when multiple modifications on amino acid

getModificationsCounts gives a named numerical vector with all
modifications and their counts in given sequences.

addFixed and VariableModifications used to take the first instance of
given modifications on the same amino acid. Because this is not
supported, it is preferred to throw an error.
 

 ensure 'wb' mode for windows systems
 

 test with Csparsematrix for scuttle change
 

 fixed imports
 

 major refactoring of the interface, breaking main function in steps
 

 updated doc
 

 catch flbias
 

 Merge branch 'devel'
 

 Removed dependency from haplo.stats and corrected some flaws.
 

 bump version, update news
 

 Merge branch 'rformassspectrometry:master' into readqfeatures_verbose
 

 add verbose argument to .splitSE
 

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

 bump upg

:wq
:wQ
 

 Merge pull request #6 from BorchLab/roxygen

blank in data Rd 

 fix vignette
 

 first NEWS file
 

 add installation text in two places
 

 fix PlinkArray reference in README.md
 

 fix C warnings
 

 Update README badges to use dynamic Bioconductor shields
 

 Fix compatibility with R-devel and Bioconductor 3.22/3.23

- Fix test failure: ggplot2 4.0+ S7 objects return typeof "object" not "list"
- Replace deprecated element_line(size=) with element_line(linewidth=)
- Replace library(HybridMTest) with requireNamespace(); move to Suggests
- Migrate makeTxDbFromGRanges import from GenomicFeatures to txdbmaker
- Add txdbmaker, rlang, S4Vectors to Imports
- Fix undefined globals (Print, queryHits, download.file, aes vars)
- Add .Rbuildignore; update License field in DESCRIPTION
- Bump version to 1.9.5
 

 Update README.md
 

 GenomicFeatures 1.63.2: Move C code from GenomicRanges

The C code supporting transcriptLocs2refLocs() and transcriptWidths()
used to be in GenomicRanges and is now in GenomicFeatures.
 

 Bump the version
 

 add survival vignettes
 

 add assay.type to LimROTS_survival
 

 unit tests for LimROTS and survival
 

 data.exp to x
 

 remove log2 FC keep only corrected one
 

 Merge branch 'guideflandre-main'