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mSigSpectra 0.1.3

• Changes requested in the CRAN review of 0.1.2:
  • License field is now GPL-3 and the redundant LICENSE file has been removed.
  • Acronyms (VCF, SBS, DBS, ID, PDF) are spelled out in DESCRIPTION and software names are single-quoted.
  • Added \value sections to the documentation of check_and_remove_discarded_variants(), is_catalog(), and subset_catalog(), and to all internal helper documentation.
  • quick_check_vcf() no longer uses print() to format the multiple-ALT warning.

mSigSpectra 0.1.2

• Initial CRAN submission.
• Provides a four-step pipeline for building mutational-spectrum catalogs from VCF files: read_vcf(), split_vcf(), annotate_sbs_or_dbs_vcf() / annotate_id_vcf(), and vcf_to_sbs_catalog() / vcf_to_dbs_catalog() / vcf_to_id_catalog().
• Supports SBS, DBS, and indel (ID) catalogs for GRCh37, GRCh38, and GRCm38 reference genomes or any BSgenome genome. Adds transcript-strand annotation where transcript-ranges info is available.
• Ships example Strelka and Mutect VCFs in inst/extdata/ and a vignette demonstrating the full pipeline.

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
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