+ 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
 

 Add files via upload 

 Remove optional from depth-ratio metrics documentation 

 Update test-collapseEvents.R 

 Update UPDhmm.Rmd 

 Update test-calculateEvents.R
 

 Update processChromosome.R
 

 Update blocksVcf.R
 

 Update calculateEvents.Rd
 

 Merge branch 'dev' of https://github.com/saraamenasantamaria/UPDhmm into dev
 

 Update collapseEvents.R
 

 Update collapseEvents.Rd
 

 Modify vignette
 

 Update NAMESPACE
 

 Update UPDhmm.Rmd
 

 Update collapseEvents.Rd
 

 Update identifyRecurrentRegions.R
 

 Update markRecurrentRegions.R
 

 Update NAMESPACE
 

 Update identifyRecurrentRegions.Rd
 

 Update processChromosome.R
 

 Update test-calculateEvents.R
 

 Update calculateEvents.Rd
 

 Update blocksVcf.Rd
 

 Update test-collapseEvents.R
 

 Update calculateEvents.R
 

 Update test-collapseEvents.R
 

 Update collapseEvents.R
 

 Update collapseEvents.Rd
 

 Update test-collapseEvents.R
 

 Update calculateEvents.Rd
 

 Update collapseEvents.R
 

 Update calculateEvents.R 

 Update applyViterbi.R
 

 Update calculateEvents.R
 

 Update vcfCheck.R
 

 Apply suggestion from @Copilot

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

 Update vcfCheck.R
 

 Update processChromosome.R
 

 Update applyViterbi.R
 

 Update vcfCheck.R
 

 update
 

 update
 

 update documentation
 

 Update UPDhmm.Rmd
 

 Update test-processChromosome.R
 

 Update vcfCheck.R
 

 Update processChromosome.Rd
 

 Create blocksVcfNew.Rd
 

 Delete asDfVcf.Rd
 

 Delete addRatioDepth.Rd
 

 Update DESCRIPTION
 

 Update UPDhmm.Rmd
 

 Update test-calculateEvents.R
 

 Update blocksVcfNew.r
 

 Update test-calculateEvents.R
 

 Update test-applyViterbi.R
 

 Update processChromosome.R
 

 Update applyViterbi.R
 

 Delete test-asDfVcf.R
 

 Create test-blocksVcfNew.R
 

 Update test-processChromosome.R
 

 Update processChromosome.R
 

 Update calculateEvents.R
 

 Delete asDfVcf.R
 

 Create blocksVcfNew.r
 

 Update test-processChromosome.R
 

 Update test-blocksVcf.R
 

 Update test-applyViterbi.R
 

 Update asDfVcf.R
 

 Update vcfCheck.R
 

 Update calculateEvents.R
 

 Update UPDhmm.Rmd
 

 Update UPDhmm.Rmd
 

 Update UPDhmm.Rmd
 

 Delete test-addOr.R
 

 Update calculateEvents.R
 

 Update calculateEvents.R
 

 data.table has been changed to data.frame

data.table has been changed to data.frame
 

 Update vcfCheck.R
 

 Update applyViterbi.R

The variable names have been updated.
 

 Update processChromosome.R

The calculation of Mendelian errors per block and read depth/coverage ratios per individual has been added. Thanks to the precomputation of coded genotypes (geno_coded) and chromosome-level totals (total_sum and total_valid), these calculations are performed efficiently in a vectorized way, counting Mendelian-inconsistent genotypes and computing “inside/outside” ratios per block without iterating over each variant individually, which optimizes the pipeline performance. 

 Update blocksVcf.R

The blocksVcf function has been optimized through vectorization to efficiently identify blocks of contiguous variants with the same state. The function works with data.table and, in addition to summarizing the start and end positions of each block, the number of variants, and the coded genotypes (geno_coded), it can optionally calculate the sum of quality values for each variant within the block and the count of variants with valid values, ignoring NAs, providing additional information useful for downstream analyses. 

 Update applyViterbi.R

The genotypes argument and genotype encoding have been removed from this function, since numeric genotypes (geno_coded) are precomputed in vcfCheck. 

 Delete R/addRatioDepth.R

This function is removed to optimize ratio calculations in the existing functions. 

 Add maintainer ORCID iD to DESCRIPTION

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

 Fix SVD dimnames: preserve row/colnames on rotation matrix

SVD (unlike prcomp) does not carry over dimnames from the input matrix.
This caused NULL rownames in nb_pca_rotation, breaking nb_transfer's
row-indexed assignment, and NULL colnames causing dimnames errors when
subsetting by PC index.

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

 Remove duplicate utility functions from zzz.R

netboostPackagePath(), netboostTmpPath(), and netboostMCUPGMAPath()
were defined identically in both tools.R and zzz.R. Keep only the
definitions in tools.R which is loaded first by R's collation order.

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

 Remove redundant prcomp() call in nb_moduleEigengenes()

Derive PCA scores (V) and rotation (U/d) directly from the
already-computed SVD instead of calling prcomp() which internally
performs a second full SVD on the same data.

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

 Anchor regex patterns in nb_summary() module renumbering

Add ^ anchor to all grepl/gsub patterns matching module names like
"ME3_" so they don't inadvertently match "ME30_" or "ME31_".

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

 corrected some typo and CXX standard
 

 Bumb version after merging upstream and adding new citation
 

 Merge pull request #820 from sneumann/fix/addXcms2025

Add xcms (2025) citation 

 docs: add new xcms reference to the vignette
 

 Add xcms (2025) citation
 

 Update group_by syntax in Simulation.R for dplyr compatibility 

 Add reference to new paper
 

 Use txdbmaker (#119)

* import makeTxDbFromGFF from txdbmaker
* bump version to 2.6.1
* bump bioconductor version
 

 bump
 

 Updated version number and maintainer from Jessica Anderson (formerly McClintock) to Evan Johnson
 

 Updated News with Yaoan's proper surname, Leng
 

 Merge branch 'devel' of https://github.com/jessmcc22/BatchQC into devel
 

 Added a package manpage with a stub NAMESPACE.

As the Bioc build system doesn't like it when you don't have a NAMESPACE.
 

 New description Bioconductor

Merge remote-tracking branch 'upstream/devel'

# Conflicts:
#	DESCRIPTION
 

 Fixed bug in removemargins
 

 Fixed problem with time_unit parameter in PlotPeacoQC
 

 Merge branch 'master' of https://github.com/saeyslab/PeacoQC
 

 remove flowworkspace dependency
 

 Fleshed out vignette preamble to avoid warnings.

Also got rid of redirection for the time being, to cajole the BioC build system
into completing the build.
 

 Upate dataset to be compliant with recent versions of MagellanNTK/Prostar2
 

 fix: replace defunct summarise_each with across, remove ::: calls

- Replace dplyr::summarise_each(funs(...)) with summarise(across(...))
  as summarise_each was removed in recent dplyr versions
- Remove cosmosR::: self-namespace calls for keep_controllable_neighbours
  and keep_observable_neighbours
- Add utils::globalVariables() for NSE variables (., HMDB_mapper_vec, target)
- Bump version to 1.19.1

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

 Upate dataset to be compliant with recent versions of MagellanNTK/Prostar2
 

 Improve documentation and use camelCase
 

 feat: add beta_values function

- Move the `beta_values()` function from the *xcms* package to here.
 

 Merge pull request #20 from billila/master

add Makevars file 

 bump version for devel
 

 Merge pull request #88 from gagneurlab/merge-devel

Merge devel 

 Bug fix: update UCSC / AnnotationHub RefSeq track handling
 

 Replace dplyr::as_tibble with as.data.frame for Hits objects + add diagnostics

- Replace dplyr::as_tibble(hits) with as.data.frame(hits) for S4 Hits objects
  to fix potential S4Vectors compatibility issue in newer Bioconductor
- Add diagnostic output in vignette to show RT class/structure after rtDetect
- Add NULL check in vignette before using RT$SKA3 to prevent crash and
  provide informative error message
- Bump version to 1.17.4
 

 Merge branch 'devel'
 

 updating vignettes around aggregation
 

 Add "internal data" to IMGT germline dbs

install_IMGT_germline_db() now computes and adds "internal data" to
the installed db (only when 'tcr.db=FALSE' at the moment). Not documented
yet. Also needs some extensive testing.

This new feature relies on compute_imgt_intdata(), a low-level utility
to compute IgBLAST internal data for a set of germline V gene allele
gapped sequences.
 

 Merge branch 'release' into devel
 

 Fix safe_deparse bug on small random effects
 

 Merge branch 'release' into misc 

 only log to hundredths of a second
 

 ignore Rproj
 

 Update preprocess_mgx_mtx -> preprocess_dna_mtx
 

 Update maaslin_plot_results.Rd 

 Update maaslin3_manual.Rmd

Updated replotting section to include the coef and heat map replotting parameters. 

 Update LICENSE 

 Update README.md 

 Merge pull request #34 from biobakery/devel

Fixed multiple random effects 

 Merge pull request #32 from biobakery/devel

Removed line break in "Prevalence associations possibly..." 

 Merge pull request #29 from biobakery/devel

Updated N_not_zero calculation 

 Merge pull request #27 from biobakery/devel

Fixed bug when running group comparisons after model misfit 

 Merge pull request #24 from biobakery/devel

Added small_random_effects and associated warnings 

 Merge pull request #21 from biobakery/devel

Update DESCRIPTION 

 Merge pull request #19 from biobakery/devel

Update version 

 Merge pull request #16 from biobakery/devel

Changed assay_type to assay.type 

 Merge pull request #14 from biobakery/devel

Allow assay_type 

 Merge pull request #12 from biobakery/devel

Devel 

 Merge pull request #10 from biobakery/devel

Fix metadata bug 

 Merge pull request #8 from biobakery/devel

Bioconductor submission updates 

 Merge pull request #61 from drighelli/new_light_fix

SpaceTrooper utilities vignette, README fixing 

 Bump version to 1.3.2
 

 fixed typos
 

 Fixed typo in README
 

 updated logo placement
 

 update image resolution
 

 Tweak pkgdown navbar and logo settings
 

 changed summarise to reframe
 

 simplified unit test
 

 chore: Address second review comments
 

 fixed plyranges import
 

 docs fixed for warnings
 

 Author info updated
 

 Details extended
 

 Orcids added
 

 removed prints
 

 Update vignette for MSstatsQC-ML
 

 Bump version
 

 Try force-installing some packages in GHA
 

 Bug fix - bump to v1.3.2
 

 Update README.md 

 Fix documentation and examples
 

 fixed seurat deprecation error
 

 Bumped-up version and updated NEWS.md
 

 Bugfix: solve inconsistencies in conversions to/from SCE (#132)

* Improved readability of the 'genes' plot from cleanPlots()

* Improved genes' plot

The genes plot that is part of the `cleanPlots()` now uses
log-scale and shows the top 20 genes with `reppel`

* Improved handling of cells' IDs and genes' names in SCE conversions

* Fixed broken link to vignette in README.md

* Improved warnings in conversion from SCE

Improved retrieval of cells/genes names from SCE data

Fixed raw matrix checks at construction/conversion

Fixed reg tests

* Updated NEWS.md 

 Restored backward compatibility in `mitochondrialPercentagePlot()`
 

 minor, message omitted
 

 Merge pull request #47 from rformassspectrometry/jomain

Use MsDataHub instead of msdata 

 bump version
 

 drop dependency on msdata

- Use *MsDataHub* instead of *msdata*
 

 addressed Bioc reviewer comments
 

 Replace msdata with MsDataHub

- Load test and example files from *MsDataHub* and drop dependency on
  the *msdata* package (issue #24).
 

 refactor: replace msdata with MsDataHub

- Load example data from *MsDataHub* and remove dependencie on *msdata*.
 

 bumps version
 

 changes Fetchdata call to allow compatibility with latest SeuratObject version
 

 version bump
 

 move functions supporting enrichmentSets to utils
 

 move functions supporting enrichmentSets to utils
 

 tests for plotEnrich and update documentation
 

 add tests for enrichmentSets functions
 

 re-update description file with current dependencies after troubleshooting
 

 reverting description file for troubleshooting
 

 change to R v4.4.0 requirement
 

 styler formatting and add Rsamtools to imports
 

 updates to change project name
 

 bioc reviews allow rc strand
 

 suggest Rsamtools to resolve windows install issues
 

 only use the BiocStyle output style
 

 reformat code for Bioconductor review
 

 add required packages for enrichmentSets
 

 update logo
 

 lazy data true added
 

 update to dev version
 

 update version
 

 use layer instead of slot
 

 update to bruker support email 

 remove deprecated message, bump version
 

 Bump version
 

 Make allowed values for H5type explicit in docs
 

 Allow passing both a H5type ID or name in H5type

This improves consistency across h5createDataset() and h5createAttribute() since the  former was only working with name and the latter only with IDs
 

 Run match.arg() on encoding early
 

 Add test for #68
 

 Make withr dependency explicit
 

 Add more tests for [ and [<- methods
 

 ci: drop installation of msdata
 

 Merge pull request #129 from rformassspectrometry/jomain

Replace msdata with MsDataHub 

 Merge pull request #188 from gdrplatform/GDR-2332

Gdr 2332 

 refactor: update as per review
 

 ci: trigger build
 

 refactor: update
 

 test: add unit tests
 

 refactor: fix todos
 

 version bump 2.23.4
 

 version bump 2.23.3
 

 tryCatch on utils::download.file and provide reason when error occurs
 

 update RoxygenNote version
 

 version bump
 

 Normalization biocView added
 

 Merge branch 'master' of https://github.com/eralpdogu/MSstatsQC
 

 Update README.md

Added definitions of machine learning tools 

 References updated
 

 bumping version plus deprecation error fix
 

 update version number
 

 Add NEWS
 

 Bump version and add NEWS
 

 fix gene name issue (e.g., - to .) in PlotSpatialExpression
 

 Bug fix
 

 Add header file as well.