typo
 

 typo (ops)
 

 Merge pull request #7 from vjcitn/vjc

This fixes one dead link and provides more operational details in an appendix 

 finish new text, test
 

 version bump 0.99.67
 

 version bump 0.99.22
 

 rename CONCH in importCONCH
 

 release version
 

 release version
 

 add installation in vignette
 

 Migrate pr_check.yml to ci.yml (#6)

* Add ci.yml reusable-workflow wrapper

* Remove pr_check.yml (replaced by ci.yml) 

 remove Software in biocViews
 

 Make Nicolas maintainer again and add returns entry for time_weights
 

 Replace set.seed with withr::with_seed to satisfy bioconductor requirements
 

 Fix haplotype inference bug and add helper module
 

 add datasets available date
 

 Add UnsupportedPlatforms
 

 NEWS 1.0.0 release version
 

 add Installation in vignette
 

 add HistoImagePlot name in vignette
 

 Some R code cleanup, fixed some unit tests
 

 Fixed several potential bugs
 

 refactor: add tests for non simpleError in retry()
 

 Merge pull request #146 from rformassspectrometry/jomain

refactor: add parameters warningsAsErrors and verbose to retry() 

 refactor: add parameters warningsAsErrors and verbose to retry()
 

 Correct some misprints
 

 Merge pull request #15 from lbbe-software/master

Merge 

 Merge pull request #13 from lbbe-software/devel

Devel 

 Merge pull request #11 from lbbe-software/devel

Update the R-CMD-check workflow 

 Merge pull request #9 from lbbe-software/devel

Update the R-CMD-check workflow 

 Merge pull request #7 from lbbe-software/devel

Devel 

 Merge pull request #5 from lbbe-software/devel

Devel 

 include sessionInfo in DIA-NN vignette
 

 update NEWS
 

 update vignettes
 

 add packages for vignettes to suggest
 

 improve style collect-plot-results.R and calculateNormFactors.R
 

 nobars is moved to reformulas, however it is still included in lme4 for legacy. This gives one warning per session. However, when formally importing nobars from reformulas we get a warning in the build process and do not pas R CMD check.
 

 fix note w.r.t. no visible binding for global variables in pipes (plotVolcano) and no visible binding for  global functions
 

 add createPairwiseContrasts function to msqrob-utils.R
 

 fix calcNormFactors documentation
 

 update msqrob.R remove argument w from .create_model, remove ::: call for .vcovUnscaled, properly use constructed vcovUnscaled in case of missing parameters
 

 add importFrom stats median to calculateNormFactors + roxygenize
 

 calculateNormFactors: add to collate field + add roxygen documentation / update R version for devel
 

 Fix160 fgsea implementation (#161)

* Added new DAPsmatrix dataset and implemented fgsea in the FEA() method

* Updated NEWS.md

* Update FEA data input parameter name, added new FEA dataset for fgsea results, added new test for fgsea

* Fix on versioning, added DAPsmatrix in datalist, fixes in spacing and descriptions

---------

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

 Bioconductor Review changes 0.99.11
 

 Bioconductor Review changes 0.99.11
 

 Bioconductor Review changes 0.99.11
 

 Bioconductor Review changes 0.99.11
 

 estimateLC.R salivaEPIC
 

 change & to &&
 

 Remove :::
 

 remove heterogeneity plot as it completely fails on large data and is a source of failures when knitting
 

 further memory efficiency improvements
 

 Bump version
 

 Skip transpose codec for arrays of dimension 1
 

 Chore/39/replace rols dependency (#40)

* remove deprecated stato classes

these were deprecated several releases ago and are no longer used

* remove rols

replace with internal implementation

* fix for when ontology is zero length

* add .onload

sets ontology online option to true/false and detects correct state when loading the package

* add ontology method for model_seq

returns ontology for all models as well as the model sequence itself as a nested list

* fix typo in documentation

* rename ontology_set_online()

shortened to ontology_online()

* update vignette...

...to reflect changes to ontology interface

* Update README.rst

* import jsonlite

* fix .onload

defer the message to .onattach as per guidance

* import URLencode

* add documentation...

...for ontology(M) where M is a model sequence

* fix terms documentation for ontology_list

* remove stato generics

* fix tests for ontology_online

* import httr2

* fix BiocCheck warnings

- Use of "Error" in error message
- Use of class(m)[1]== in iterators
- Use of paste0 in stop()
- Escape curly brackets in roxygen blocks

* update news and version bump 

 Update C++ standard to C++17

Co-authored-by: Michael Stadler <stadler.michael@gmail.com>
Co-authored-by: Charlotte Soneson <charlottesoneson@gmail.com>
 

 Replace calcNormFactors with normLibSizes

Co-authored-by: Michael Stadler <stadler.michael@gmail.com>
Co-authored-by: Charlotte Soneson <charlottesoneson@gmail.com>
 

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

 Re-wrte plotting via ggplot2
 

 Fix issues with paste0
 

 Version bump
 

 feat: resume for BulkPipeline
 

 tweak
 

 edgeR 4.9.7
- voomLmFit() now supports offset.prior
 

 bumping version
 

 fix tests based on recent error
 

 update docs
 

 update docs
 

 Version bump. Added funding agency and author ORCID
 

 Added parameter input checks
 

 Merge pull request #27 from NICHD-BSPC/v0.99.10

V0.99.10

- add edgeR/limma support
- allow addition of degPatterns/pattern analysis results via UI
- improve object validation
- add helper functions to edit carnation default settings
- misc bug fixes 

 repin R to 4.6
 

 rm non ascii character
 

 updt Rd
 

 switch to examplesIf
 

 add comment
 

 repl sapply w apply
 

 rm redundant 'warning' string in message
 

 updt DESCRIPTION
 

 updt NEWS
 

 updt aut email
 

 add tests fr config funcs
 

 add funcs to init, set, merge local config
 

 add func to get local config yaml
 

 materialize a new obj
 

 factor out sanitize code to validation funcs
 

 correctly impute gene names into NA symbols
 

 only convert rownames that need conv
 

 check for supported cols fr new res upload
 

 check supported cols using internal func
 

 updt README formatting
 

 updt text to reflect supported tools
 

 if no obj added, show notif
 

 updt incoming obj sanitization
 

 cleanup README
 

 fix scatterplot showlegend bug
 

 more vignette updates
 

 Fix vignette Sweave LaTeX markup
 

 Fixed some unit tests, clean up some C code
 

 get version correctly aligned with bioc
 

 adding package refs and version info
 

 removing stray browser call
 

 Added unit tests on KCDF estimation
 

 bug fix: deprecated package msdata replaced by MsDataHub in example
 

 refactor to SummarizedExperiment
 

 Added ORCID
 

 Replaced @ accessor
 

 Typo
 

 Removed (switched to SummarizedExperiment)
 

 Added explanation on igraph for Seurat
 

 Made igraph as suggest, not working on R 4.6 yet
 

 Adopted SummarizedExperiment class
 

 Updated reference
 

 Version bump to 0.99.6
 

 Update vignette:
- Added Installation section (including instructions for BiocManager)
- Added section "Motivation for Bioconductor Integration"
 

 Added missing dependencies
 

 Replace :: with explicit imports with @importFrom
 

 Add chunk names
 

 Last version compatible with R 4.4
 

 Update README.md 

 Update README.md 

 R code cleanup
 

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

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

 edgeR 4.9.6
- cpm() and rpkm() now support prior offsets.
 

 Merge pull request #15 from rformassspectrometry/jomain

refactor: import retry() from MsCoreUtils 

 Update retry pattern
 

 refactor: import retry() from MsCoreUtils

- Remove `retry()` function and import it from *MsCoreUtils*.
- Use a stringent pattern to retry downloading; this might cause failures until
  we get a complete list of connection-specific errors.
 

 fix commits
 

 Reduce the need for loops and extra function calls (#33) 

 more seq_along and paste corrections
 

 Remove unnecessary paste0() and vapply()
 

 Avoid paste0() within file.path()
 

 update README and fix some tests
 

 switch from Rarr to ZarrArray
 

 bump version
 

 Added flexdashboard to list of requirements to overcome WARNING
 

 Add DensityPlot functionality to DO.UMAP
 

 disabled pkg update on windows
 

 clean up badges
 

 Bump version
 

 Merge remote-tracking branch 'origin/devel' into devel
sync pull request #77
 

 Merge pull request #77 from waldronlab/funding/add-fnd-authors-r-23616418917 

 igblastr 1.1.26

Add the following built-in germline dbs:

o _OGRDB.mouse.CAST_EiJ.IGH+IGK+IGL.202603

  Contains sequences from OGRDB germline sets:
    - `CAST/EiJ IGH` version 2
    - `CAST/EiJ IGKV` version 1
    - `CAST/EiJ IGLV` version 2
    - `IGKJ (all strains)` version 1
    - `IGLJ (all strains)` version 1

o _OGRDB.mouse.LEWES_EiJ.IGH+IGK+IGL.202603

  Contains sequences from OGRDB germline sets:
    - `LEWES/EiJ IGH` version 2
    - `LEWES/EiJ IGKV` version 1
    - `LEWES/EiJ IGLV` version 1
    - `IGKJ (all strains)` version 1
    - `IGLJ (all strains)` version 1

o _OGRDB.mouse.MSM_MsJ.IGH+IGK+IGL.202603

  Contains sequences from OGRDB germline sets:
    - `MSM/MsJ IGH` version 1
    - `MSM/MsJ IGKV` version 1
    - `MSM/MsJ IGLV` version 2
    - `IGKJ (all strains)` version 1
    - `IGLJ (all strains)` version 1

Also rename the following built-in germline dbs:

o _OGRDB.mouse.NOD_ShiLtJ.IGH+IGK+IGL.202501 (original name)
  --> _OGRDB.mouse.NOD_ShiLtJ.IGH+IGK+IGL.202205 (new name)

o _OGRDB.mouse.PWD_PhJ.IGH+IGK+IGL.202501 (original name)
  --> _OGRDB.mouse.PWD_PhJ.IGH+IGK+IGL.202410 (new name)

The new names better reflect the release date of the OGRDB germline sets
that they contain. The two original germline dbs were kept for backward
compatibility but the user gets a warning when they use them. The warning
suggests to use the new names instead and to remove the original dbs.
 

 Updated some unit tests
 

 bump version
 

 Update ggplot2 deprecated aes_string() usage.
 

 Replace mefa:::rep.data.frame with base row replication in tpptrSplineAUCs()
 

 Remove unused broom dependency from DESCRIPTION
 

 Update documentation after changes to function parameters
 

 Enrichment figure + updated vignette.
 

 Expand network image and link options
 

 Use modern bibentry and c.person in CITATION
 

 Bumped version
 

 Test version update and bugfix
 

 fix the package anchors for all Rd
 

 feat: integrate NLopt optimization library and expand SAINTexpress functionality with new C++ backends and documentation.
 

 Changes in file structure for warnings
 

 seems very clean now
 

 midway in repairing how S7 generics are coded, to eliminate doc warnings
 

 Explicit suppression of plots to speed up execution.

This is more understandable than only generating plots when a graphics device
is active, as this depends on the current state of the R session.
 

 Don't suppress plots by default in the pipeline functions.

This avoids surprising differences when prototyping something in an interactive
sesssion and then running it in a non-interactive script.

Also divert existing plots to a null device in the tests.
 

 upd doc rd
 

 rm ex to avoid err: could not find function ".scaleMatRcpp"
 

 refac s4, added es cliff, upd docstr and fct signature f clarity
 

 Update NEWS.Rd for release
 

 Deprecated mfa functions
 

 Replace deprecated scuttle functions with scrapper
 

 Bump actions/checkout from 5 to 6 (#184)

Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
 

 Added explicit option to skip figures for faster pipeline execution.

This cuts a few minutes off the overall CHECK time.
 

 small tweak to internal utility validate_redit_imgt_file()
 

 Avoid unnecessary deprecation warnings for internal normalizeCounts usage.
 

 Get ready to update the documentation website
 

 Added unit tests for splitComponent sf and sfc method
 

 Don't use == in unit tests #86
 

 installation modifications
 

 Version bump in devel
 

 Expanded vignette to briefly discuss software design choices
 

 chore(DESCRIPTION): bump version
 

 fix(query): return htslib_version() as a string instead of void
 

 feat(protein-turnover): Select fractions based on light isotope label type (#125) 

 fix(fractions): Speed up efficiency of fraction selection (#126) 

 feat(protein turnover): Add functionality to add heavy isotope label type to Spectronaut converter (#122)

Useful for protein turnover 

 Refactor assignment syntax in clean_DIANN.R 

 Feature diann anomaly (#119)

Co-authored-by: coderabbitai[bot] <136622811+coderabbitai[bot]@users.noreply.github.com> 

 Added a qc-filtered and normalized subset of the Visium 10X human cerebellum data available in the TENxVisiumData package
 

 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