Package: MutationalPatterns
Type: Package
Title: Comprehensive genome-wide analysis of mutational processes
Description: Mutational processes leave characteristic footprints in
        genomic DNA. This package provides a comprehensive set of
        flexible functions that allows researchers to easily evaluate
        and visualize a multitude of mutational patterns in base
        substitution catalogues of e.g. healthy samples, tumour
        samples, or DNA-repair deficient cells. The package covers a
        wide range of patterns including: mutational signatures,
        transcriptional and replicative strand bias, lesion
        segregation, genomic distribution and association with genomic
        features, which are collectively meaningful for studying the
        activity of mutational processes. The package works with single
        nucleotide variants (SNVs), insertions and deletions (Indels),
        double base substitutions (DBSs) and larger multi base
        substitutions (MBSs). The package provides functionalities for
        both extracting mutational signatures de novo and determining
        the contribution of previously identified mutational signatures
        on a single sample level. MutationalPatterns integrates with
        common R genomic analysis workflows and allows easy association
        with (publicly available) annotation data.
Version: 3.21.1
Date: 2025-07-30
Authors@R: c(
    person("Freek", "Manders", email = "F.M.Manders@prinsesmaximacentrum.nl", role = c("aut"), 
    comment = c(ORCID = "0000-0001-6197-347X")),
    person("Francis", "Blokzijl", role = "aut",
    comment = c(ORCID = "0000-0002-8084-8444")),
    person("Roel", "Janssen", role = "aut",
    comment = c(ORCID = "0000-0003-4324-5350")),
    person("Jurrian", "de Kanter", role = "ctb",
    comment = c(ORCID = "0000-0001-5665-3711")),
    person("Rurika", "Oka", role = "ctb",
    comment = c(ORCID = "0000-0003-4107-7250")),
    person("Mark", "van Roosmalen", email = "vanBoxtelBioinformatics@prinsesmaximacentrum.nl", role = "cre"),
    person("Ruben", "van Boxtel", role = c("aut", "cph"),
    comment = c(ORCID = "0000-0003-1285-2836")),
    person("Edwin", "Cuppen", role = "aut",
    comment = c(ORCID = "0000-0002-0400-9542")))
License: MIT + file LICENSE
URL: https://doi.org/doi:10.1186/s12864-022-08357-3
Imports: stats, S4Vectors, BiocGenerics (>= 0.18.0), BSgenome (>=
        1.40.0), VariantAnnotation (>= 1.18.1), dplyr (>= 0.8.3),
        tibble(>= 2.1.3), purrr (>= 0.3.2), tidyr (>= 1.0.0), stringr
        (>= 1.4.0), magrittr (>= 1.5), ggplot2 (>= 2.1.0), pracma (>=
        1.8.8), IRanges (>= 2.6.0), Seqinfo, GenomeInfoDb (>= 1.45.9),
        Biostrings (>= 2.40.0), ggdendro (>= 0.1-20), cowplot (>=
        0.9.2), ggalluvial (>= 0.12.2), RColorBrewer, methods
Depends: R (>= 4.2.0), GenomicRanges (>= 1.24.0), NMF (>= 0.20.6)
Suggests: BSgenome.Hsapiens.UCSC.hg19 (>= 1.4.0), BiocStyle (>= 2.0.3),
        TxDb.Hsapiens.UCSC.hg19.knownGene (>= 3.2.2), biomaRt (>=
        2.28.0), gridExtra (>= 2.2.1), rtracklayer (>= 1.32.2), ccfindR
        (>= 1.6.0), GenomicFeatures, AnnotationDbi, testthat, knitr,
        rmarkdown
biocViews: Genetics, SomaticMutation
ZipData: NA
RoxygenNote: 7.3.2
Encoding: UTF-8
VignetteBuilder: knitr
Config/pak/sysreqs: make libbz2-dev libicu-dev liblzma-dev libpng-dev
        libxml2-dev libssl-dev xz-utils zlib1g-dev
Repository: https://bioc.r-universe.dev
Date/Publication: 2026-02-16 10:59:04 UTC
RemoteUrl: https://github.com/bioc/MutationalPatterns
RemoteRef: HEAD
RemoteSha: e9acc2833d699e3d00832cc4866b31e05505ba31
NeedsCompilation: no
Packaged: 2026-02-24 06:14:00 UTC; root
Author: Freek Manders [aut] (ORCID: <https://orcid.org/0000-0001-6197-347X>),
  Francis Blokzijl [aut] (ORCID: <https://orcid.org/0000-0002-8084-8444>),
  Roel Janssen [aut] (ORCID: <https://orcid.org/0000-0003-4324-5350>),
  Jurrian de Kanter [ctb] (ORCID:
    <https://orcid.org/0000-0001-5665-3711>),
  Rurika Oka [ctb] (ORCID: <https://orcid.org/0000-0003-4107-7250>),
  Mark van Roosmalen [cre],
  Ruben van Boxtel [aut, cph] (ORCID:
    <https://orcid.org/0000-0003-1285-2836>),
  Edwin Cuppen [aut] (ORCID: <https://orcid.org/0000-0002-0400-9542>)
Maintainer: Mark van Roosmalen <vanBoxtelBioinformatics@prinsesmaximacentrum.nl>
Built: R 4.6.0; ; 2026-02-24 06:17:27 UTC; windows
