Package: SparseSignatures
Version: 2.20.0
Date: 2025-09-23
Title: SparseSignatures
Authors@R: c(
    person("Daniele", "Ramazzotti", role=c("aut"),email="daniele.ramazzotti@unimib.it",
                comment = c(ORCID = "0000-0002-6087-2666")),
    person("Avantika", "Lal", role=c("aut")),
    person("Keli", "Liu", role=c("ctb")),
    person("Luca", "De Sano", role=c("cre","aut"), email="luca.desano@gmail.com",
                comment = c(ORCID = "0000-0002-9618-3774")),
    person("Robert", "Tibshirani", role=c("ctb")),
    person("Arend", "Sidow", role=c("aut")))
Depends: R (>= 4.1.0), NMF
Imports: nnlasso, nnls, parallel, data.table, Biostrings,
        GenomicRanges, IRanges, BSgenome, GenomeInfoDb, ggplot2,
        gridExtra, reshape2, RhpcBLASctl
Suggests: BiocGenerics, BSgenome.Hsapiens.1000genomes.hs37d5,
        BiocStyle, testthat, knitr,
Name: An R package for the extraction of sparse mutational signatures
        from whole genome sequencing data
Description: Point mutations occurring in a genome can be divided into
        96 categories based on the base being mutated, the base it is
        mutated into and its two flanking bases. Therefore, for any
        patient, it is possible to represent all the point mutations
        occurring in that patient's tumor as a vector of length 96,
        where each element represents the count of mutations for a
        given category in the patient. A mutational signature
        represents the pattern of mutations produced by a mutagen or
        mutagenic process inside the cell. Each signature can also be
        represented by a vector of length 96, where each element
        represents the probability that this particular mutagenic
        process generates a mutation of the 96 above mentioned
        categories. In this R package, we provide a set of functions to
        extract and visualize the mutational signatures that best
        explain the mutation counts of a large number of patients.
Encoding: UTF-8
License: file LICENSE
URL: https://github.com/danro9685/SparseSignatures
BugReports: https://github.com/danro9685/SparseSignatures
biocViews: BiomedicalInformatics, SomaticMutation
RoxygenNote: 7.3.2
VignetteBuilder: knitr
Config/pak/sysreqs: make libbz2-dev libicu-dev liblzma-dev libxml2-dev
        libssl-dev xz-utils zlib1g-dev
Repository: https://bioc-release.r-universe.dev
Date/Publication: 2025-10-29 14:44:43 UTC
RemoteUrl: https://github.com/bioc/SparseSignatures
RemoteRef: RELEASE_3_22
RemoteSha: 9b8de11ec2e68df62d97a83ca20a5986848e8b0a
NeedsCompilation: no
Packaged: 2026-03-01 09:37:45 UTC; root
Author: Daniele Ramazzotti [aut] (ORCID:
    <https://orcid.org/0000-0002-6087-2666>),
  Avantika Lal [aut],
  Keli Liu [ctb],
  Luca De Sano [cre, aut] (ORCID:
    <https://orcid.org/0000-0002-9618-3774>),
  Robert Tibshirani [ctb],
  Arend Sidow [aut]
Maintainer: Luca De Sano <luca.desano@gmail.com>
Built: R 4.5.2; ; 2026-03-01 09:40:43 UTC; windows
