Changelog

Source: NEWS.md

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

• render_report() added for standardized summary reporting.

Other

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