Add cell segmentation for gene expression plot.
 

 Deprecated
  requsted on bioc-devel
 

 vignette updates
 

 fix: resolve undeclared BSgenome import warning from BiocCheck

R/motif_proximity.R called BSgenome::getSeq() but BSgenome was not
declared in DESCRIPTION, which triggered the R CMD check warning about
an undeclared '::' import. Since getSeq is a Biostrings generic (already
imported) and BSgenome only supplies the method, switch the call to
Biostrings::getSeq(), matching how match_bkg.R already extracts
sequences from a BSgenome. Also add BSgenome to Suggests so the
genome-sampling code paths guarded by requireNamespace() can be
installed and exercised in the check environment.

While here, fix a quiet/quietly typo in two requireNamespace() example
blocks (sequence_complexity and utils-sequence) and their generated Rd.
 

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

 Fix DO.MultiDGE now implements glmGamPoi test after subsetting for each cell type
 

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

 bugfix
 

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

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

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

 fix bug in function DO.MultiDGE
 

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

 Addition of glmGamPoi to DO.MultiDGE analysis in pseudoBulk approaches -> additional arguments method_pb and design_fit_glm
 

 fixed multiple accumulation of read counts
 

 modified getline to fgets for windows
 

 changed the default soft-clipping enabling: enable when junction is disabled.
 

 done visium hd read mapping
 

 Bump version
 

 chore: bump version to 0.99.3 (#79) 

 fix(check): resolve R CMD check TIMEOUT and BiocCheck NOTEs (#77)

* Fix indentation: convert 2-space to 4-space per Bioconductor style guide

Applies styler::style_dir() with scope=indention, indent_by=4
across all R/ source files and vignettes/

* style: fix function argument alignment to use 4-space indentation

Replace paren-aligned continuation lines with 4-space indents in
R/buildQset.R, calculateEnrichment.R, classes.R, combineQsets.R,
makeDMRs.R, makeQset.R, mixQsets.R, plotting.R, qseaCNV.R,
qseaExtra.R, and utilityFunctions.R to satisfy BiocCheck indentation note

* refactor: fix 4-space indentation in glue strings and function signatures

Fix BiocCheck NOTE "Consider multiples of 4 spaces for line indents"
by removing leading whitespace from continuation lines inside glue::glue()
strings and aligning function parameter lists to 4-space indent.

Files changed: R/PCA.R, R/alterQset.R, R/makeDMRs.R, R/makeQset.R,
R/plotting.R

* refactor(makeDMRs,plotting): fix remaining non-4-space indents in string literals

Remove leading whitespace from continuation lines inside warning()/glue()
strings and restore correct } else { alignment in makeDMRs.R.
Clears the final 3 lines flagged by BiocCheck indentation NOTE.

* style: fix 2-space to 4-space indentation in sampleQC and utils

* style: fix over-indented continuation lines in asValidGranges

* style: reapply indentation after main rebase

* Fix plotly PNG device error on headless build servers

- Skip plotly::ggplotly() during non-interactive builds in pca.Rmd
  (plotly internally opens a PNG device which fails without X11)
- Add dev = pdf to knitr::opts_chunk() in all 5 vignettes
  to prevent the default PNG device being used on headless servers

* style: add missing chunk labels to all vignettes

* fix(vignettes): use pdf device in pca vignette chunks

Switch the knitr chunk device in  from PNG to PDF
to avoid graphics device issues in headless build environments.

* docs: update NEWS.md and regenerate man pages for v0.99.3

- Add v0.99.3 NEWS.md entry summarizing style and vignette fixes
- Regenerate man/ documentation to reflect any updated roxygen2 tags

* style: normalize R and vignette indentation to 4 spaces for BiocCheck

* style: remove trailing whitespace-only indent lines flagged by BiocCheck

* style(R/qseaCNV.R): wrap lines > 80 chars to satisfy BiocCheck note

* style(R/buildQset.R): wrap lines > 80 chars to satisfy BiocCheck note

* style(R/PCA.R): wrap lines > 80 chars to satisfy BiocCheck note

* style(R/qseaExtra.R): wrap lines > 80 chars to satisfy BiocCheck note

* style(R/makeDMRs.R): wrap lines > 80 chars to satisfy BiocCheck note

* style(R/analyseDMRs.R): wrap lines > 80 chars to satisfy BiocCheck note

* style(R/alterQset.R): wrap lines > 80 chars to satisfy BiocCheck note

* style(R/calculateEnrichment.R): wrap lines > 80 chars to satisfy BiocCheck note

* style(R/dplyrVerbs.R): wrap lines > 80 chars to satisfy BiocCheck note

* style(R/genome.R): wrap lines > 80 chars to satisfy BiocCheck note

* style(R/makeQset.R): wrap lines > 80 chars to satisfy BiocCheck note

* style(R/mixQsets.R): wrap lines > 80 chars to satisfy BiocCheck note

* style(R/classes.R): wrap lines > 80 chars to satisfy BiocCheck note

* style(R/combineQsets.R): wrap lines > 80 chars to satisfy BiocCheck note

* style(R/plotting.R): wrap lines > 80 chars to satisfy BiocCheck note

* style(R/sampleQC.R): wrap lines > 80 chars to satisfy BiocCheck note

* style(R/utilityFunctions.R): wrap lines > 80 chars to satisfy BiocCheck note

* style(R/utils.R): wrap lines > 80 chars to satisfy BiocCheck note

* style(R/utilityFunctions.R): wrap lines > 80 chars to satisfy BiocCheck note

* style(R/alterQset.R): wrap lines > 80 chars to satisfy BiocCheck note

* style(R/analyseDMRs.R): wrap lines > 80 chars to satisfy BiocCheck note

* style(R/calculateEnrichment.R): wrap lines > 80 chars to satisfy BiocCheck note

* style(R/combineQsets.R): wrap lines > 80 chars to satisfy BiocCheck note

* style(R/dplyrVerbs.R): wrap lines > 80 chars to satisfy BiocCheck note

* style(R/mixQsets.R): wrap lines > 80 chars to satisfy BiocCheck note

* style: wrap lines longer than 80 characters

* fix: restore vignette YAML front matter

* fix: restore roxygen metadata to 7.3.3

* style: wrap reported R source lines

* style: wrap reported vignette lines

* style: wrap remaining core source findings

* style: wrap remaining helper source findings

* style: wrap remaining vignette findings

* style(r): wrap long lines in helper sources

* style(r): normalize wrapping in plotting helpers

* docs(vignettes): reflow examples and prose

* docs(man): regenerate man files with roxygen

* style: add final line to .Rbuildignore

* refactor(r): remove paste from condition signals

* docs: guard poolSamples example with dontrun

* style: move roxygen version to the same position as in main (it was moved accidentally during debuggin)

* docs: update NEWS with all the changes made in style/wrap-lines-from-format-notes

* fix(check): resolve TIMEOUT, qsea import NOTE, and global-var NOTE

- Fix skip_long_checks() to use getOption() instead of options();
  the old call returned a named list so the guard never fired and
  slow BAM-processing tests always ran, exceeding the 15-min limit.
- Add options(skip_long_checks = TRUE) in tests/testthat.R so
  R CMD check skips long-running tests.
- Add @import qsea via R/mesa-package.R and regenerate NAMESPACE to
  resolve 'Package in Depends field not imported from' NOTE.
- Replace all qsea::: and janitor::: calls with public-API equivalents
  (qsea::getParameters()[["BSgenome"]], slot assignment @, tileGenome)
  to resolve 'Unexported objects imported by :::' NOTE.
- Declare five data-object names in utils::globalVariables() to
  resolve 'no visible binding for global variable' NOTE.

* fix(qseaCNV): correct makeGenomeWindows to use fixed-width tiles + rebase

tileGenome(..., cut.last.tile.in.chrom=FALSE) distributes tiles evenly
across chromosomes, producing wrong window widths and boundaries that
break the hmmCopyGC/hmmCopyMap overlap check in addHMMcopyCNV.
Replace with a direct reimplementation using GRanges/IRanges/Seqinfo
public APIs: fixed-width tiles, last partial window dropped — identical
to the original qsea:::makeGenomeWindows behaviour.

Also rebases fix/rcmd-check-notes onto style/wrap-lines-from-format-notes
and regenerates man/ with devtools::document().

* test: reset global mesa options before state-sensitive assertions

Calling devtools::test() in a dirty interactive session carries over
options like mesa_parallel, mesa_TxDb, mesa_genome, and mesa_annoDb,
causing expect_error(annotateWindows()) and expect_false(getMesaParallel())
to fail. Explicitly reset to NULL/FALSE at the start of the relevant
test blocks so tests are robust to session-state pollution.

* test: cache qsea fixtures and gate slowest blocks to fit 15-min budget

Add tests/testthat/helper-fixtures.R with a memoised cachedExampleQset()
so repeated qsea::getExampleQseaSet() builds in test-editQset.R and
test-DMRs.R reuse a single simulation per (repl, depth). Gate the
heaviest blocks (test-DMRs.R "Calculating DMRs", test-exampleQset.R
"Testing general functionality", test-pca.R "UMAPs") behind
skip_long_checks() so R CMD check stays under the Bioconductor 15-min
tests budget while devtools::test() still runs everything locally.

* docs: update man files' documentation

* docs(NEWS): add PR #77 links to all entries from this branch

* docs(NEWS): add missing addHMMcopyCNV makeGenomeWindows bug fix entry

* style: wrap lines > 80 chars in mixQsets.R, utils.R, plotting.R, qseaExtra.R, sampleQC.R

* docs(PCA,buildQset): replace getExampleQseaSet() in examples with exampleTumourNormal

* docs(buildQset): wrap addNormalisation examples in \donttest{}

exampleTumourNormal is filtered to CpG_density >= 5 and has no
low-density background windows; getExampleQseaSet() is retained
for these examples but hidden from R CMD check timing.

* docs: documented man/addNormalisation.Rd and man/getDimRed.Rd

* docs: mesa version updated to 0.99.2.9000

* docs: mesa version updated to 0.99.2.9000

* docs(NEWS): condense PR #77 entries; use ragg_png vignette device

Tighten the 0.99.2.9000 NEWS section: fold the three BiocCheck NOTE
resolutions into one bullet and trim wording, and drop the duplicate
### FIXED block that repeated the same #77 fixes under the old 0.99.0
heading.

Switch all vignette chunks to dev = "ragg_png" and add ragg to Suggests,
matching the NEWS entry.

* docs(ENCODEbadRegions): unwrap @source URL to fix pkgdown build and stay under 80 chars

* docs(ENCODEbadRegions): regenerate Rd to match unwrapped @source URL

Regenerate man/ENCODEbadRegions.Rd from the roxygen source so the
\source{} block no longer wraps the URL in a \url{} tag. pkgdown's
Rd parser fails on a \url{} tag that spans a line break, which aborted
build_reference() (and the pkgdown deploy) on this topic. The plain
wrapped URL parses cleanly and keeps every line under 80 characters.

* fix(qseaCNV): correct window-start seq() call in addHMMcopyCNV

The makeGenomeWindows reimplementation passed each chromosome length
positionally to seq() (matching 'from') while also supplying from = 1L,
which errors with "formal argument 'from' matched by multiple actual
arguments" and broke addHMMcopyCNV(). Use an explicit closure so the
chromosome end maps to 'to'.

* fix(sampleQC): guard BSgenome check against length-0 comparison

After dropping qsea:::getGenome(), addHyperStableFraction() compared the
BSgenome parameter directly, which throws "argument is of length zero"
when that parameter is NULL. Use identical() for a safe, intentional
error path.

* fix(mixSamples): report missing sample names instead of stopifnot

Replacing qsea:::checkSamples() with stopifnot() produced an unhelpful
"... is not TRUE" error. Compute the missing names with setdiff() and
stop() naming them.

* fix(mixThreeQsetSamples): report missing sample names instead of stopifnot

Same fix as mixSamples(): replace the generic stopifnot() with a
setdiff()-based check that names the missing sample(s).

* docs(utils): mark remove_almost_empty_cols internal, drop stale Rd

remove_almost_empty_cols() is an unexported, internally-used-only helper,
but its roxygen block (lacking @noRd) generated a help page. Add @noRd so
no man page is produced and remove the orphaned Rd. Also corrects the
@details text, which still claimed the removal message came from an
internal janitor helper after the code switched to a plain message().

* docs(NEWS.md): remove irrelevant change

---------

Co-authored-by: fperezmartinez <felipe.perezmartinez@manchester.ac.uk> 

 style: standardize 4-space indentation and fix vignette build issues per Bioconductor style guide (#75)

* Fix indentation: convert 2-space to 4-space per Bioconductor style guide

Applies styler::style_dir() with scope=indention, indent_by=4
across all R/ source files and vignettes/

* style: fix function argument alignment to use 4-space indentation

Replace paren-aligned continuation lines with 4-space indents in
R/buildQset.R, calculateEnrichment.R, classes.R, combineQsets.R,
makeDMRs.R, makeQset.R, mixQsets.R, plotting.R, qseaCNV.R,
qseaExtra.R, and utilityFunctions.R to satisfy BiocCheck indentation note

* refactor: fix 4-space indentation in glue strings and function signatures

Fix BiocCheck NOTE "Consider multiples of 4 spaces for line indents"
by removing leading whitespace from continuation lines inside glue::glue()
strings and aligning function parameter lists to 4-space indent.

Files changed: R/PCA.R, R/alterQset.R, R/makeDMRs.R, R/makeQset.R,
R/plotting.R

* refactor(makeDMRs,plotting): fix remaining non-4-space indents in string literals

Remove leading whitespace from continuation lines inside warning()/glue()
strings and restore correct } else { alignment in makeDMRs.R.
Clears the final 3 lines flagged by BiocCheck indentation NOTE.

* style: fix 2-space to 4-space indentation in sampleQC and utils

* style: fix over-indented continuation lines in asValidGranges

* style: reapply indentation after main rebase

* Fix plotly PNG device error on headless build servers

- Skip plotly::ggplotly() during non-interactive builds in pca.Rmd
  (plotly internally opens a PNG device which fails without X11)
- Add dev = pdf to knitr::opts_chunk() in all 5 vignettes
  to prevent the default PNG device being used on headless servers

* style: add missing chunk labels to all vignettes

* fix(vignettes): use pdf device in pca vignette chunks

Switch the knitr chunk device in  from PNG to PDF
to avoid graphics device issues in headless build environments.

* docs: update NEWS.md and regenerate man pages for v0.99.3

- Add v0.99.3 NEWS.md entry summarizing style and vignette fixes
- Regenerate man/ documentation to reflect any updated roxygen2 tags

* style: normalize R and vignette indentation to 4 spaces for BiocCheck

* style: remove trailing whitespace-only indent lines flagged by BiocCheck

* docs: update man/ files

* fix(vignettes): switch figure device from pdf to ragg_png

Replaces dev = "pdf" with dev = "ragg_png" in all five vignette setup
chunks. The pdf device produced poor-quality embedded figures in HTML
vignette output. ragg_png renders high-quality PNG without requiring
Cairo or X11, resolving the headless build server issue cleanly.

Adds ragg to Suggests in DESCRIPTION.

* docs: mesa version updated to 0.99.2.9000

* docs: mesa version updated to 0.99.2.9000

* docs(NEWS.md): switch figure device from pdf to png, as it was like that on 0.99.2

---------

Co-authored-by: fperezmartinez <felipe.perezmartinez@manchester.ac.uk> 

 Replace mzR with RaMS for mzML reading

mzR pulls in netCDF/HDF5 system libraries and requires Rcpp
compilation, which makes installation slow and often fails on
fresh/CI/Docker environments. RaMS is a pure-R mzML reader with only
lightweight CRAN dependencies, so it installs in seconds.

getmzml() output is unchanged: a data.frame with mz, intensity, and rt
(seconds) columns. RaMS reports retention time in minutes, so it is
converted to seconds. Verified byte-for-byte identical output against
mzR on a 9.8M-row file.

Bump version to 1.1.0 (Bioc devel).

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>
 

 Merge branch 'RELEASE_3_23' into devel
 

 fix typo
 

 fix hvg selection
 

 +scater
 

 track changes v1.2.0-.1
 

 bug fix: overwrite of 'th'
 

 order deps alphabetically
 

 scrapper: seq-crc
 

 scrapper updates: Visium HD (binned) workflow
 

 scrapper updates: seq-deconvolution chapter
 

 wording
 

 scrapper updates: seq-intermediate-processing chapter
 

 scrapper: ind-clu
 

 scrapper: ind-norm
 

 formatting
 

 auto-update gitignore
 

 scrapper: img-ccc
 

 scrapper revision: img-qc
 

 scrapper revision: img-workflow-cos/xen
 

 scrapper updates: seq-QC chapter
 

 scrapper revision: crs-workflow-xenvis
 

 install beachmat.hdf5
 

 remove manual installation of dependency packages (SPE, AUCell)
 

 remove manual installation of dependency packages (SPE, AUCell)
 

 # update DESCRIPTION
 

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

 refactor(ucsc): centralize RestUri calls with rtracklayer user agent

All UCSC REST API calls now identify as "rtracklayer" via a shared
wrapper, consistent with rtracklayerGET/POST.

Refs lawremi/restfulr#4
 

 Merge branch 'main' into devel 

 Merge pull request #67 from pnnl/view-fix

updated biocviews to fix dependency issue and use BiocFileCache 

 updated examples to use BiocFileCache

I hope this will make the build more reliable
 

 Merge pull request #66 from pnnl/z-test-update

Z test update 

 tried to fix hg pages
 

 updated examples to use BiocFileCache

I hope this will make the build more reliable
 

 Update both readme files
 

 update version number
 

 Finish adding plotting methods to the LRT vignette
 

 Split into three separate vignettes for simulation, rate estimation and likelihood ratio testing
 

 Add LRT vignette
 

 Fix return variable name in LRT function 

 Fix geneId assignment in betaTblIdx 

 Refactor runEMH1FkLRT to use h0Beta values 

 Bugfix for mainExpectationMaximizationFkH0 

 add likelihood ratio test functions for fk

Add likelihood ratio test for fk

- Add one-line call in likelihoodRatioTest() to run fk LRT
- Implement fk LRT pipeline (computeFkLRT, computeFkLRTParams, runEMH0FkLRT, runEMH1FkLRT) adapted from beta LRT
- Reuse constructBetaLRTTable() to build fk LRT output 

 updated
 

 bump version
 

 updated help pages and bumped ersion
 

 version bump 1.1.2
 

 bump version
 

 allow additional attributes in SquaregffBy
 

 Bump version
 

 Specify types in benchmarks
 

 Add test for writing NA warning
 

 Remove debug escape hatch
 

 Error on unsupported codec
 

 Merge pull request #17 from KlausVigo/devel

Devel 

 further typos...
 

 fix sf on row subset
 

 fixed more tests...
 

 fixed wrong param name
 

 removed sanity check based on old scrna pipeline
 

 fixed typo
 

 handle se inputs to agg
 

 more updates for scrapper...
 

 first shot at moving to scrapper...
 

 Merge pull request #60 from gdrplatform/GDR-3420

GDR-3420: add custom annotation support to import_data 

 chore: bump version to 1.11.3
 

 Merge pull request #197 from gdrplatform/GDR-3420

GDR-3420: allow custom annotations in merge_data 

 docs: regenerate man pages
 

 feat: allow custom annotations in merge_data and cleanup_metadata

Add optional cell_line_annotation and drug_annotation parameters to
merge_data() and cleanup_metadata(). When provided, these bypass the
automatic package-based lookup (gDRinternal/gDRtestData), enabling
open-source users to supply their own annotation CSVs.
 

 fix: use backtick formatting instead of \pkg{} in vignette

The raw \pkg{ggplot2} LaTeX macro is valid in roxygen/Rd files but
undefined in the vignette's LaTeX preamble, causing an 'Undefined
control sequence' error that broke the Bioconductor vignette build.
Replace it with the plain inline-code form used elsewhere for package
names.
 

 Merge pull request #79 from gdrplatform/GDR-3417

GDR-3417: add workshop drug annotations 

 docs: remove Dimensions column from DepMap dataset table
 

 fix: correct version to 1.11.4 and simplify NEWS entry
 

 chore: bump version to 1.11.4
 

 igblastr 1.3.9

Replace arguments 'with.intdata' and 'with.auxdata' with 'intdata'
and 'auxdata' in function install_custom_germline_db().

The new arguments can be NULL, or "auto", or a data.frame containing
custom annotations (internal or auxiliary data}, or the path to a file
containing custom annotations.

Setting 'intdata' or 'auxdata' to "auto" achieves the same as setting
the old 'with.intdata' or 'with.auxdata' arguments to TRUE, that is,
it tells install_custom_germline_db() to compute and add the annotations
to the new germline db.

Alternatively, the user can now supply their own custom annotations
by passing a data.frame -- or the path to a file containing annotations --
to 'intdata' or 'auxdata'.

See '?install_custom_germline_db' for more information.
 

 Update
 

 Merge pull request #9 from sa-lee/claude/bioc-build-failure-0rdfv7

ci: test against Bioconductor devel (3.24) to catch build failures 

 fix(vignette): build TxDb from local GTF via useHub=FALSE

The Bioconductor 3.24 (devel) build fails when re-building the vignette at
the tximeta-run chunk:

  Quitting from fluentGenomics.Rmd:189-194 [tximeta-run]
  Error: error in evaluating the argument 'x' in selecting a method for
  function 'bfcadd': object 'bfc' not found
   1. tximeta::tximeta(coldata, dropInfReps = TRUE)
   2.  getTxDb(txomeInfo, useHub = useHub, skipFtp = skipFtp)
   3.   checkViaAHub(txomeInfo, srcName, ensSrc, dbType)
   4.    BiocFileCache::bfcadd(bfc, ...)

This is an upstream regression in tximeta 1.31.2: its internal
checkViaAHub() references an unbound variable 'bfc' on the AnnotationHub
code path (the default useHub = TRUE). Older tximeta (Bioc 3.22) is
unaffected, which is why this only shows up on devel.

Pass useHub = FALSE so tximeta builds the TxDb directly from the local GTF
already registered by makeLinkedTxome in the setup chunk, avoiding the
broken checkViaAHub path. This is also more robust for the build machines
since it does not depend on AnnotationHub.
 

 fix sequence search API
 

 version bump 1.1.1
 

 use local file df in cloud_compare.R
 

 add transfer script --dry-run
 

 Merge branch 'devel' of https://github.com/BorchLab/scRepertoire into devel
Getting hex sticker fixed
 

 update documentation
 

 Fixing warnings
 

 Update data files
 

 Update DaparToolshedData
 

 Calling DNAMultipleAlignment from MultipleAlignment not Biostrings
 

 Update DaparToolshedData
 

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

 Merge branch 'main' into devel 

 Minor changes
 

 Update DaparToolshedData
 

 Untrack file DaparToolshedData.Rproj
 

 Merge pull request #16 from KlausVigo/master

Add citation 

 Merge pull request #15 from KlausVigo/master

remove ignored files 

 Bioconductor 0.99.29 nlme fit, CpG bacthing, Methylation scale, these changes were made to improve performance
 

 illustrate use of percent_mutation() in the vignette
 

 update bioc version
 

 update bioc version
 

 adding functions to vignette and bump version to 0.99.5
 

 Adding user functions to load data and validate h5
 

 Merge branch 'devel' into update_clampdata_readers 

 Update vignette to use new CLAMPData reader functions
 

 uploaded summary for results in get_started
 

 Address Bioconductor revision 1
 

 fixed missing )
 

 Bump version
 

 Fix comment in source code

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

 Fix typos in help page of saveHDF5GSVA() and loadHDF5GSVA()

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

 Update unit tests for serialization, update example for saveHDF5GSVA() / loadHDF5GSVA
 

 Removed unnecessary parameter from the internal .pull_param() helper function
 

 version bump
 

 Merge pull request #388 from rformassspectrometry/jomain

docs: better explain parallel processing 

 bump version
 

 import write.phylip from MultipleAlignment and fix example for saveAlignments.
 

 doc: remove column with no info
 

 chore: as per review
 

 doc: add prism data
 

 doc: update data description
 

 chore: update data description
 

 feat: add motif_proximity() for enrichment near genomic anchors

motif_proximity() and plot_motif_proximity() test whether a motif's hits
are spatially enriched near a set of anchor coordinates, genome-wide. It
is the distance-based sibling of motif_peaks(): binomial (default),
anchor-randomisation permutation, and KS nulls; hit- and anchor-counting
modes; strand-aware directional (upstream/downstream) testing; and either
precomputed hits or internal scanning of an XStringSet or BSgenome.

motif_peaks() gains a seq.strand argument that orients local mode by
feature strand, so mirror-image peaks across strands combine, and its
examples now document the windowed genome-coordinate recipe.

Also fix two stale motif_peaks(sequences, motif=) calls (the
implant_motifs example and the SequenceSearches vignette) left over from
the CentriMo rewrite, and add a proximity-enrichment section to that
vignette.
 

 update example to generate calls
 

 Adaptations for BioC 3.24; version number bumped to 1.45.1
 

 feat: add no.overlaps option to motif_coocc()

Forward scan_sequences2()'s no.overlaps / no.overlaps.by to the
internal-scan path. Because motif_coocc()'s Fisher test is on
per-sequence presence/absence, collapsing overlaps never removes the
last hit from a sequence, so the p-/q-values are unchanged; the option
only affects the descriptive spatial columns under max.distance, where
it stops tandem/overlapping matches of one motif being counted as
separate instances. Dedup stays within each motif (relying on
scan_sequences2()'s no.overlaps.by.motif = FALSE) so between-motif
overlaps, i.e. heterodimer footprints, are preserved. Default FALSE,
matching scan_sequences2()/enrich_motifs2(); ignored with a warning on
the precomputed-hits path. Adds roxygen, NEWS note, and tests.
 

 # added MultipleAlignment
 

 Bioconductor 0.99.28 SVA matrix plot out of range
 

 feat: geom_motif/geom_logo layers and motif_tree2 tip logos

Add ggplot2 layers that embed sequence logos into arbitrary ggplot
constructions, reusing the view_motifs() logo renderer:

- geom_motif()/annotate_motif() take universalmotif objects (honouring
  use.type); geom_logo()/annotate_logo() take bare row-named numeric
  matrices. annotate_*() place one logo at fixed coordinates; geom_*()
  position from aesthetics (bounding box, or x/y anchor with
  width/height) and can draw a different motif per group via a named
  list plus a `motif` selector aesthetic. Built on shared ggproto
  objects GeomMotif/StatMotif/StatLogo; letter colours are resolved
  internally so the layers never touch the plot's fill scale.

- motif_tree2() now draws aligned tip logos by default (tiplogo = TRUE,
  aligned via view_motifs2()), the motifs serve as tip labels. Its
  default layout changes to "rectangular"; tip logos are drawn only on
  rectangular/slanted layouts (others warn and skip) and not for dist
  input. New args: tiplogo, tiplogo.align, tiplogo.width,
  tiplogo.height, tiplogo.offset.

Also fix a pre-existing renderer bug shared with view_motifs()/
view_logo(): with a small min.height, letters shorter than their
per-letter y.spacer allotment were scaled by a negative height and
flipped below the baseline. The spacer is now capped at half the
letter height.

Replace the cowplot side-by-side tree+motifs vignette section with a
motif_tree2() example, and document the ggtree >= 3.13 requirement for
tip labels (ggtree's empty() calls the removed ggplot2:::is.waive()
under ggplot2 4.0). Adds tests and NEWS entries.
 

 fix test, update news and description
 

 Fix DOI, update Date, reword Description field

- Correct DOI from 10.2174/1389202924666230517115655 to
  10.2174/0113892029264990231013112156 (was returning 404)
- Update Date to 2026-06-07
- Reword Description to not start with package name (R CMD check NOTE)

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
 

 Fixed bug in addSpecificityProxyScore
 

 Merge pull request #169 from jorainer/jomain

fix: address all SQL injection security issues 

 define updateObject() methods for MultipleAlignment derivatives
 

 major fix in Unload.gdsn()
 

 Bioconductor 0.99.25 Correcting PARAM = empty to NULL
 

 import DNAMultipleAlignment from MultipleAlignment.
 

 small tweak to README.md
 

 Optimize permutation testing: 2.3x faster, identical results

- Replace per-feature prefiltering loops with vectorized colMeans/apply
- Replace aov() per feature with vectorized one-way ANOVA F-statistic
- Replace adonis2 with direct PERMANOVA F formula (avoids formula parsing
  and PCoA machinery overhead; called 21x per permutation)
- Exploit diagonal structure of M: replace O(p^3) eigen() decomposition
  with O(p) diag() extraction in calculate_mahalanobis_dist_robust
- Aggregate ensemble using diagonal vectors instead of full p x p matrices
- Hoist combn() out of gradient descent iteration loop
- Reuse dist_observed instead of recomputing distance matrix post-run
- Suppress spurious NaN warnings from log2 on CLR-transformed data

Parity verified: p-values identical, all other outputs within machine
epsilon (max_diff < 2e-14). Benchmarked at n=100, p=300, n_perms=100.

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
 

 fix: security issue in fetchTablesFromEnsembl
 

 Fix manual install
 

 Add files via upload 

 Add files via upload 

 Delete NAMESPACE 

 Delete vignettes/PostChicago_v17.Rmd 

 Delete R directory 

 Add files via upload 

 Add files via upload 

 Add files via upload 

 Delete NAMESPACE 

 Delete vignettes directory 

 Delete R directory 

 Add files via upload 

 Delete man directory 

 Delete R/utils_v9.R 

 Add files via upload 

 Add files via upload 

 Add files via upload 

 Delete NAMESPACE 

 Delete man directory 

 Delete R/PostChicagoTidyNestedRemoved_v18.R 

 Add files via upload 

 Add files via upload 

 Delete inst/extdata directory 

 Add files via upload 

 Add files via upload 

 Add files via upload 

 Delete DESCRIPTION 

 Bioconductor 0.99.24 R-Makefile changed adding Cross-reactive detection
 

 Fix vignette
 

 Remove INSTALL file (content already in vignette)
 

 added DBPZ_Core_CHUNK_READS for controling subread/subjunc batch size
 

 Biostrings 2.81.3: MultipleAlignment objects now have their own package

MultipleAlignment objects and associated functionality are now implemented
and documented in the new MultipleAlignment package.
 

 fix: declare htmltools in Suggests to resolve R CMD check warning

htmltools was used via :: in app-launcher.R but not listed in
DESCRIPTION, causing an undeclared dependency warning in R CMD check.
Added it to Suggests since it is only needed by the Shiny app feature.
 

 version bump to 1.29.3
 

 add 'as.matrix' argument to percent_mutation()
 

 Version bump to exclude rproj
 

 ^xMerge branch 'master' into devel
 

 fix commented out tests regarding new seeds
 

 remove unnecessary requirement
 

 DESeq2 lfcShrink option (#151)

* added shrinkage option and extra free args to downstream methods (#53)
* changed default edgeR norm to TMMwsp
* fix warning import on 2 lines
* move NEWS to inst/
* code style & typo fixes
* add r-universe GitHub action
* NEWS and v1.27.2 bump
---------

Co-authored-by: plger <pl.germain@gmail.com> 

 update news and bump version
 

 add text.height parameter in axis.params
 

 released new bioconductor version and updated news
 

 igblastr 1.3.7: Add percent_mutation()

The function computes the percent mutation in the V, D, J segments of
a set of BCR or TCR sequences, at the nucleotide or amino acid levels.
See '?percent_mutation' for more information.
 

 refactor: export MsBackendHdf5Peaks class
 

 Update installation guide in README
 

 add dark mode switch
 

 Bump version from 1.23.0 to 1.23.1 

 feat(metabolomics): Add new MZMinetoMSstatsFormat converter (#132) 

 fix(maxquant): Filter out decoys with decoy column (#133) 

 fix(anomaly scores): Standardize column names for the Run name (#134) 

 fix(fragpipe): Fix PTM tooltip w.r.t. column name (#214) 

 feat(spectronaut): Add annotation and run order uploads for large spectronaut uploads (#212) 

 Fix #185: thread censoredInt correctly and remove spurious unique() in exported script (#210) 

 fix(loadpage): switched file reads to data.table::fread (#208) 

 fix(statistical-page): Add horizontal scrollbar for p-value tables (#205) 

 Merge pull request #386 from rformassspectrometry/jomain

Support dataStorageBasePath for MsBackendHdf5Peaks 

 ci: update GHA
 

 Merge branch 'main' into jomain
 

 tests: adapt MsBackend testing suite
 

 version bump
 

 Merge pull request #98 from gdrplatform/GDR-3418

Gdr 3418 

 ci: post test-result commit status from external_check job
 

 ci: rename workflow to CI
 

 fix: use install = TRUE in pkgdown to load package for examples
 

 Update NEWS and bump version
 

 Ignore AI directories
 

 Remove mfa dependency
 

 Remove deprecated MFA simulation
 

 Updated version to match version from bioconductor release.
 

 Updated the package version and dependencies.
 

 Updated the code. Reduced the minimum number of centers needed for bluster k-means from 5000 to 3000 centers.
 

 Updated code to run on the neighbourhood composition matrix.
 

 Updated method description.
 

 Replaced dimRed with dimRed_init specific to initial clustering. Reduced the minimum number of centers used in bluster k-means from 5000 to 3000.
 

 maintenance
 

 gemma_call document headers
 

 Move phyloseq from Imports to Suggests; bump to 0.99.10

phyloseq was listed as a hard dependency but is never called by any MeLSI
function — the only references were vestigial importFrom declarations in
zzz.R/NAMESPACE added to suppress R CMD check notes. On HPC systems this
forced a full igraph compile (10+ min) and created GLIBCXX mismatch issues.
Moving to Suggests makes it optional: users who already have phyloseq keep
full integration via the vignette; users who don't are no longer forced to
install it.

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
 

 version bump
 

 Update version
 

 Merge pull request #77 from gdrplatform/GDR-3410

[GDR-3410] Add public data from DepMap Portal 

 chore: as per review
 

 chore: update with main branch
 

 doc: add public data from DepMap Portal
 

 chore: add public data from DepMap Portal
 

 version bump
 

 rename logo to fix warning