Skip to contents

Changelog

Source: NEWS.md

MutSeqR 0.99.2 (2025-09-15)

Preparing for Bioconductor release. This change removes bmd_toxicR from the package. ToxicR dependency is not supported by Bioconductor. See ToxicR_archive branch for bmd_toxicr function. Modifies signature_fitting() to use SigProfilerMatrixGenerator python dependency rather than R dependency.

MutSeqR 0.99.1 (2025-08-13)

Preparing for Bioconductor release. This change adds MutSeqRData to suggests, and alters how the examples are run (now depends on the ExperimentHub accessions).

MutSeqR 0.99.0 (2025-06-19)

Initial public version.

Major changes

  • Added filter_mut() to workflow: germline identification via vaf_cutoff, region filtering, and depth correction now occur here instead of the import functions.
  • calculate_mut_freq() is renamed to calculate_mf().
  • calculate_mf() no longer requires depth; users may:
    1. calculate depth from mutation data,
    2. supply a separate depth table, or
    3. omit depth entirely (only mutation counts returned).
  • correct_depth option moved to calculate_mf().
  • plot_spectra(), plot_trinucleotide(), and spectra_comparison() now use mf_data instead of raw mutations.
  • Output options added: VCF, FASTA, SigProfiler-compatible format, Excel workbook.
  • Example dataset (~44MB) added.

New features

Other

  • Removed custom_regions parameter; replaced by generalized regions argument.
  • Public release 🎉
  • See the vignette for details.