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'
 

 Docs: bump version and add NEWS entry
 

 docs: wrong documentation corrected
 

 Feat: add Boekweg datasets
 

 Merge pull request #15 from rformassspectrometry/tmtms3

Tmtms3 

 Merge branch 'main' into tmtms3 

 merge
 

 add tmtms3 data
 

 working on #97
 

 version bump in devel
 

 KS
 

 Merge branch 'main' into devel
 

 Merge pull request #41 from guideflandre/PTModsDependency

Add PTMods dependencies 

 Build: bump cache version
 

 docs: revert to 1.15.2
 

 docs: trigger git build again
 

 build: trigger github activity
 

 Docs: include PTMods dependency in vignettes
 

 Docs: completed the vignette
 

 Feat: match closest fragment instead of common in label fragments to avoid longer object warning
 

 tests: corrected the failing tests
 

 Build: add PTMods dependency in .github workflow
 

 tests: improve tests from calculateFragments
 

 Merge branch 'rformassspectrometry:main' into PTModsDependency
 

 docs: correct NEWS
 

 style: plotSpectraPTM includes new PTMods dependencies and bold peptide
 

 Docs: modified example of error thrown when both positional and variable mods are present
 

 Doc: removed late NEWS addition
 

 style: remove unnecessary comments
 

 Optimise parseModifiedSequence based on PR remarks
 

 Update R/fragments-calculate.R

Co-authored-by: Sebastian Gibb <mail@sebastiangibb.de> 

 add NEWS info
 

 update selenocysteine and pyrrolysine masses
 

 remove old test commit
 

 add unimod import dependency
 

 Merge branch 'calculateFragments' of https://github.com/guideflandre/PSMatch into calculateFragments
 

 Merge branch 'calculateFragments' of https://github.com/guideflandre/PSMatch into calculateFragments
 

 Merge branch 'rformassspectrometry:main' into calculateFragments
 

 KS
 

 KS
 

 KS
 

 remove the expected warning string, throwing error on windows
 

 KS
 

 Allow tolerance in tests to accomodate the riscv64 architecture (#133) 

 KS
 

 KS
 

 remove BBSoptions
 

 update DESCRIPTION for new Bioc release
 

 Final cleanup: removed Date field
 

 Fix BiocCheck issues: runnable examples, Biostrings integration, remove global env assign
 

 Remove .Rproj from tracking; add to .gitignore
 

 ZarrArray 0.99.3: Drop underscore prefix from class names

S4 classes ZarrArraySeed, ZarrArray, ZarrMatrix, and ZarrRealizationSink
were originally defined in the Rarr package but were recently removed
from it, as planned. So, moving forward with the transition plan, we can
now drop the temporary underscore prefix from the corresponding classes
defined in the ZarrArray package, that is, from _ZarrArraySeed,
_ZarrArray, _ZarrMatrix, and _ZarrRealizationSink. Note that this prefix
was only a temporary hack to avoid class name conflicts.
 

 install magick in workflow
 

 Merge pull request #39 from guideflandre/citation

docs: changed to correct citation link 

 version bump 1.5.1
 

 update RoxygenNote
 

 chore(deps): update actions/upload-artifact action to v7 (#188)

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

 Update combineBCR.Rd
 

 v2.7.3
 

 Deprecated
unresponsive
 

 Deprecated
 unresponsive
 

 Deprecated
unresponsive
 

 Deprecated
unresponsive
 

 Merge pull request #573 from BorchLab/bioc-3.24-release

Bioc 3.24 release 

 Update pkgdown.yml

wesbite update
 

 update site
 

 syncing index and README
 

 Create immReferent.Rmd
 

 switch to devel default
 

 versioning
 

 Merge pull request #572 from BorchLab/bc-dev-branch

Bc dev branch 

 Update immLynx.Rmd
 

 updating the immGLIPH vignette
 

 add clonalBin function
 

 refining unit tests
 

 #536 Expanding alluvial funcitonality
 

 update getCirclize

More ooptions and add vizCirclise
 

 adding articles to rbuildignore
 

 Update index.md

update data link in pkgdwn site
 

 bugfix

Signed-off-by: xuz1 <xuz@niehs.nih.gov>
 

 Merge pull request #15 from BorchLab/timeout-testthat

Timeout testthat 

 Removed the umbrella roxygen block
 

 Deprecated
 

 moving towards devel default
 

 version bumping
 

 minor, message omitted
 

 syncing with Bioconductor
 

 Delete settings.local.json
 

 Merge pull request #27 from Qile0317/vec-input

Allow `Ibex_matrix()` to take in AA character vectors 

 make ibex matrix accept vectors
 

 fix verbosity
 

 minor NEWS formatting
 

 improve testing and update wordlist