regular maintenance
 

 Addressed warning messages
 

 README edits
 

 Fix vignettebuilder again

Wasn't careful when merging.
 

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

 remove needless caption
 

 SMaller file size!
 

 output: github_document only seems to work in Rmd (??)
 

 Not needed
 

 Update after quarto
 

 New pre-built vignette for GitHub landing page
 

 FIxed some links
 

 Merge pull request #18 from wolfganghuber/devel

Some wording improvements 

 Merge pull request #17 from wolfganghuber/devel

Updates to the lemur package vignette, mostly cosmetic 

 many cosmetic changes
 

 add help function addCellBorders, addCellLinks and addBackgroundImage.
 

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

 Trying latest bioc github workflow
 

 manpage updated
 

 Adapt smoppix to newer packages
 

 add remove_gaps()
 

 Minor wording fixes.
 

 Bump version
 

 version bump 0.99.45
 

 check for NULL when running BiocPkgDash() with no inputs
 

 fixed compiler error regarding CHARACTER_POINTER
 

 fix indentation NOTE
 

 version bump 0.99.43
 

 added offset of -1 in cellCounts range of matched CIGAR
 

 add to Description field in DESCRIPTION
 

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

 ci: add more missing tex deps
 

 fix: uninitialized variable warning
 

 chore: gitignore build artifacts
 

 fix: drop legacy allocator hint arg
 

 add yaml to Imports
 

 regular maintenance
 

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

 Bug fix for multiple entries in condition_key
 

 CI 

 fix: correct syntax in vignette code chunks
 

 fix: stack imbalance
 

 Merge pull request #189 from gdrplatform/GDR-3286

Gdr 3286 

 fix: added prefixes in zzz.R
 

 refactor: use assignInNamespace for explicit package variable initialization
 

 fix: resolve stack imbalance in sprintf by decoupling env identifier calls
 

 docs: fix vignette index entry and add missing chunk labels
 

 Merge pull request #45 from snaketron/fix_build_check

Minor adjustments to let checks pass (at least errors and warnings) 

 Merge branch 'main' into fix_get_joint_graph 

 merge code bugfixes in graph.R
 

 - try older cran version of blaster (1.0.6)
 

 - added non-cran package as remotes
 

 - adapted deduplication for potential directed graphs by using key-based sorting
 

 - fixed two critical bugs in get_joint_graph:
1.) When clustering two repertoires with two chains, CDR3b edges between-repertoire got deleted due to typo in helper function get_ix()
2.) Duplicated edges removal with which_multiple removed also the CDR3b edge of double edges between-repertoire clones

- added test-multi-chain-clustering to testthat
 

 merged bumped version
 

 merge, improved model
 

 Merge pull request #43 from snaketron/devel

fix group model, bump ersion, add another vignette, simplify models 

 bump version to 1.1.5 for Bioconductor devel
 

 Finalize version change for bump on devel for Bioc builder
 

 docs rebuild
 

 Bump version: 3.99.36 → 3.99.37
 

 Bump version: 3.99.35 → 3.99.36
 

 really removed all `seed =` stuff
 

 docs rebuild
 

 Bump version: 3.99.33 → 3.99.34
 

 updated `NEWS`: `v3.99.34`
 

 Merge branch 'devel' of https://github.com/saezlab/MetaProViz into devel
 

 Bump version: 3.99.32 → 3.99.33
 

 typo
 

 added enrichment example to cluster_pk
 

 enable plotting threshold seperately of similarity threshold
 

 NA handling for correlation
 

 new font for plotting
 

 changed examples
 

 exported cluter_pk and viz_graph
 

 Bump version: 3.99.31 → 3.99.32
 

 moved cluster_pk function to RefacorPriorKnowledge.R and removed cluster_pk folder
 

 more testing
 

 outsourced parameter check
 

 Remove local log/result folders from repo
 

 created VizGraph.R and re-wrote cluster_pk() to match MetaProViz styling
 

 debug graph coloring and naming
 

 added plotting test script
 

 created helper plotting function
 

 bump version
 

 use limma instead of perform_lm in injection lm plots
 

 improve examples to reduce check runtime
 

 man page improvement
 

 git clone update
 

 bump to 1.29.10, updated EHID of MSA.Mask
 

 ENH: Check upstream API version (Bioconductor/Contributions#3986)
 

 DOC: Transposed words (Bioconductor/Contributions#3986)
 

 Fixed example
 

 Version change for Bioc
 

 Fixed treeplot as it was updated in its enrichplot package
 

 Update datasets
 

 bump v1.25.1 -> .2
 

 update
 

 Revert "Refactor spectrum processing to support Bioconductor Spectra objects …" (#14)

This reverts commit 794d1a108fcd5f3594182302eff97ead40dce319. 

 Merge pull request #12 from chain-buds/dev

20250917-bioc-submission-debug 

 Merge pull request #180 from gdrplatform/GDR-3282

Gdr 3282 

 bump version
 

 Merge branch 'main' of github.com:gdrplatform/gDRutils
 

 bug fix: make RcppML optional with NMF fallback
 

 update pkg ver
 

 minor edits to slightly improve performance
 

 use vars in facet_wrap
 

 add note about eps value selection in vignette
 

 rename functions to Bioconductor lowerCamelCase
 

 version bump devel
 

 Shortened hg38_chr18 to first 1,000,000 bp
 

 Make make_meth_rse print number of matching meth sites per file
 

 build: update the version script to add a 2000 base offset 

 LungCancerBamFiles() now returns the concordant_uniq BAMs that are compatible with the current P53 annotation
 

 Resolve align issue for upset
 

 Fix plyranges-related check failures; bump version

Co-authored-by: Cursor <cursoragent@cursor.com>
 

 Fix version history
 

 version bump 0.99.40
 

 add conditional in vignette used when generating README.md
 

 wip generate README.md from README.Rmd
 

 update examples with examplesIf
 

 use markdown with Roxygen2
 

 oops, delete big file mistakenly added in previous commit
 

 fixed another NULL ptr bug
 

 added more memory for CBCL mode as well
 

 fixed a bug in reporting corrected UMU (UB:Z:)
 

 Merge pull request #12 from andrewmccluskey-uog/revisions

Revisions 

 BiocCheck fixes
 

 Update NEWS, remove print
 

 enable changing of mapping result bulk name
 

 remove unnecessary messages
 

 log2able mapping
 

 further adjust distance metrics
 

 further adjust distance metrics
 

 further adjust distance metrics
 

 fix duplicated *-1
 

 fix colors in scale being assigned instead of parameterised
 

 additional metrics
 

 Multitrajectory binning
 

 0.99.2
 

 .
 

 version bump
 

 Resolve merge conflicts in misc.R
 

 updated version info related to xgboost bug
 

 avoid RCurl and use grepl for URL ID
 

 v3.12.1 bug fixes to meansTest and spectrumRepresentation
 

 Merge pull request #72 from EBRogers/patch-1

Refactor spectrumRepresentation assignment logic to fix #65 

 Add na.rm parameter to meansTest method

Added na.rm parameter to meansTest method for handling NA values at feature summarization. 

 bug(process-spectra): rename 'bi' to 'bilateral' in the smoothing function to fix the bug where the bilateral filter could not be used due to the 'bi' naming
 

 Skip test if any ensembl subdomain is unreachable
 

 Resolve merge conflicts in misc.R and DESCRIPTION
 

 Update DESCRIPTION
 

 Update README.md 

 Update DESCRIPTION 

 fixed the select issue
 

 fix: vignette listing of Add.GeneList
 

 0.99.1
 

 Merge pull request #22 from jonocarroll/fix_subset

Fix subset 

 add GroupedDataFrame class, dispatching for slicing and methods, plus tests
 

 use .s4_subset when grouped
 

 align to .rs.describeObject
 

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

 Fixed spelling and grammar
 

 igblastr 1.1.12

o Add argument 'verbose' to functions install_IMGT_germline_db(),
  install_IMGT_c_region_db(), and augment_germline_db_[VDJ]().

o Add reset_germline_dbs() and reset_c_region_dbs(). See corresponding
  man pages for the details.

o Last but not least: Internal helper create_region_db() now drops
  alleles with identical names **and** identical sequences.
  IMPORTANT NOTES:
  - This change can affect the content of the cached dbs created by
    install_IMGT_germline_db() or install_IMGT_c_region_db(), especially
    in the 'tcr.db=TRUE' case, so it is recommended to reinstall them.
  - This change also affects the content of built-in C-region db
    _IMGT.mouse.IGH.202509 (now it should contain 55 alleles instead of
    56). So list_c_region_dbs(), use_c_region_db(), and load_c_region_db()
    will issue a warning telling the user to reset their C-region dbs
    with reset_c_region_dbs().
 

 Handle the matrix vs dgCMatrix case via method dispatch
 

 Generate a fleshed-out package manpage, added links to DESCRIPTION.
 

 ci: add minimal read persmissions for rworkflows workflow 

 build: update renv and dependencies 

 docs: add a joss submission badge 

 version bump
 

 version bump
 

 added quick diagnostic
 

 version bump
 

 explicit logical labels to fix xgb weird behavior
 

 fix for xgboost>3.1, removed support for <2
 

 slight doc modif #138
 

 version bump
 

 Re-knit README.Rmd
 

 switch github aciton for readme to render instead of knit to deal w yaml
 

 fix citation
 

 fix format issue in pkgdown article
 

 Merge pull request #110 from EHSRB-BSRSE-Bioinformatics/devel

Changes made to make MutSeqR compatible with Bioconductor. 

 rm genoeinfodb from namespace
 

 Merge branch 'main' into devel 

 make plyranges::mutate fix (rm it) for ecngsdb fix
 

 Clean up README by removing unnecessary lines

Removed output and encoding specifications from README. 

 Re-knit README.Rmd
 

 fix workflow add knitr package
 

 change citation to manual for now
 

 stop eval of README chunks
 

 I removed MutSeqR from the suggests for now as it cannot be installed without devel version
 

 Remove GenVisR from suggests
 

 Replace devtools with BiocManager for package install 

 Merge branch 'main' of https://github.com/EHSRB-BSRSE-Bioinformatics/duplex-sequencing
 

 trigger workflow
 

 trigger workflow
 

 don't run other code chunks
 

 tweak notice
 

 update rmd
 

 Update proast.min.R from PROAST build
 

 increase default block size
 

 Add nb_consensus and nb_consensus_transfer for multi-dataset consensus network analysis

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

 + features, capabilities
 

 + features, capabilities
 

 + better long-read processing
 

 Merge pull request #40 from BBCG/convprob

+ evaluate probability of conventional base

If a base has at least one modifications, and neither the probability of any of modifications nor the probability of the conventional base reach the `min.prob`, this base will be masked in this particular read and not counted neither as modified nor as conventional.

Surprisingly, generateCytosineReport beats modkit on it's field: for epialleleR in oligo tests, the beta of modified bases is higher and the beta of non-modified is lower.

```
generateCytosineReport(
  bam="~/work/data/bam/promethion/oligo-test/5mC_rep1.bam",
  report.file="~/work/data/bam/promethion/oligo-test/epialleleR/5mC_rep1.cx.tsv",
  threshold.reads=FALSE, filter.reads=FALSE, cytosine.context="CX", report.context="CX",
  min.mapq=0, min.baseq=0, min.prob=round(256*0.66796875), nthreads=4,
  highest.prob=FALSE
)
generateCytosineReport(
  bam="~/work/data/bam/promethion/oligo-test/5mC_rep2.bam",
  report.file="~/work/data/bam/promethion/oligo-test/epialleleR/5mC_rep2.cx.tsv",
  threshold.reads=FALSE, filter.reads=FALSE, cytosine.context="CX", report.context="CX",
  min.mapq=0, min.baseq=0, min.prob=round(256*0.67578125), nthreads=4,
  highest.prob=FALSE
)

rep1.epi <- fread("~/work/data/bam/promethion/oligo-test/epialleleR/5mC_rep1.cx.tsv")
rep1.epi[, `:=` (cov=meth+unmeth, beta=meth/(meth+unmeth))]
rep1.mod <- fread("~/work/data/bam/promethion/oligo-test/modkit/5mC_rep1.cx.bedMethyl",
                  col.names=c("rname", "V2", "pos", "V4", "cov", "strand", "V7", "V8", "V9",
                              "V10", "beta", "meth", "V13", "V14", "V15", "V16", "V17", "V18"))
rep1 <- merge.data.table(
  rep1.epi[, .(rname, pos, strand, context, meth.epi=meth, cov.epi=cov, beta.epi=meth/cov)],
  rep1.mod[, .(rname, pos, strand, meth.mod=meth, cov.mod=cov, beta.mod=meth/cov)],
  by=c("rname", "pos", "strand"), all=TRUE
)[order(rname, pos, strand)]
rep1[context=="CG"][meth.mod>2000, table(beta.epi>beta.mod)]
rep1[context=="CG"][meth.mod<2000, table(beta.epi<beta.mod)]
``` 

 + evaluate probability of conventional base
 

 upd readme
 

 +nfiltered in VCF report
 

 upd docs
 

 filter by min.context.sites, new default
 

 accout for 0
 

 filtering by context bases, cleaner flow
 

 filtering by context bases, more examples
 

 +longread, +targets
 

 ++docs
 

 + long-read seq aln
 

 + targets
 

 typo
 

 + read intervals
 

 + read intervals
 

 + read intervals
 

 + read intervals in paired-end
 

 + read intervals
 

 postfixed typos
 

 + filterReads
 

 + filterReads
 

 + filterReads
 

 + filterReads
 

 fix for incorrect number of cigar elements
 

 filterReads in bedReport
 

 filterReads in bedReport
 

 Update NEWS.md 

 Update UPDhmm.Rmd - fix indentation 

 Modify documentation
 

 Enhance identifyRecurrentRegions to use overlap-based hierarchical clustering

Previously, identifyRecurrentRegions defined recurrent regions by directly
merging overlapping intervals and counting the number of unique samples
supporting each merged region. This approach treated any overlap equally and
could group together events with minimal shared genomic span.

This update introduces an overlap-aware, agglomerative hierarchical clustering
strategy to define recurrent regions more precisely. Events are now grouped
based on the degree of overlap similarity rather than simple overlap presence.

Changes include:

1. **Function update**:

Replaced direct interval reduction (reduce()) with chromosome-wise
agglomerative hierarchical clustering.

Defined pairwise distances between events as
1 - (overlap_width / max(event_widths)), assigning a maximum distance
to non-overlapping pairs.

Added max_dist parameter to control clustering stringency when cutting
the dendrogram.

Added linkage parameter to specify the hierarchical clustering method
(default: "complete").

Collapsed valid clusters into recurrent regions spanning all contributing
events.

Preserved original events per cluster as supporting_events.

2. **Documentation update**:

Expanded function description to reflect the clustering-based definition
of recurrence.

Added documentation for max_dist and linkage parameters.

Updated @details to describe the distance metric and clustering workflow.

3. **Test update**:

Updated existing tests to reflect the new clustering-based definition of
recurrence.
 

 Update collapseEvents.Rd
 

 Enhance markRecurrentRegions to consider minimum overlap fraction

Previously, markRecurrentRegions annotated a region as recurrent
if it overlapped any recurrent region, regardless of the fraction
of overlap.

This update introduces a `min_overlap` parameter (default 0.7),
so that a region is only marked as recurrent if at least a
specified fraction of its length overlaps a recurrent region.

Changes include:
1. **Function update**:
   - Added `min_overlap` parameter.
   - Calculated overlap fraction using `IRanges::width()` and `GenomicRanges::pintersect()`.
   - Only annotate regions exceeding the threshold.

2. **Documentation update**:
   - Added `min_overlap` parameter description.
   - Updated `@details` to explain the new rule for recurrent annotation.
   - Adjusted examples to reflect the new behavior.

3. **Test update**:
   - Modified existing test cases to validate `min_overlap` functionality.
   - Ensures that regions partially overlapping below the threshold are not marked as recurrent.
 

 Update collapseEvents.R

- Replaced total_size computation from sum of individual event sizes to the actual genomic span (region_max - region_min).
- Calculated the proportion of the region covered (prop_covered) using merged IRanges to avoid double-counting overlapping events.
 

 Update R/blocksVcf.R

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

 Update DESCRIPTION
 

 Update test-processChromosome.R
 

 Update test-calculateEvents.R
 

 Update test-applyViterbi.R
 

 Update collapseEvents.R
 

 Update blocksVcf.R
 

 Update blocksVcf.Rd
 

 Update blocksVcf.R
 

 Update test-processChromosome.R
 

 Update test-blocksVcf.R