Package: Rediscover
Type: Package
Title: Identify Mutually Exclusive Mutations
Version: 0.3.3
Authors@R: c(
    person(given = "Juan A.",
           family = "Ferrer-Bonsoms",
           role = c("aut", "cre"),
           email = "jafhernandez@tecnun.es"),
    person(given = "Laura",
           family = "Jareno",
           role = "aut"),
    person(given = "Angel",
           family = "Rubio",
           role = "aut"))
Maintainer: Juan A. Ferrer-Bonsoms <jafhernandez@tecnun.es>
Description: An optimized method for identifying mutually exclusive
        genomic events.  Its main contribution is a statistical
        analysis based on the Poisson-Binomial distribution that takes
        into account that some samples are more mutated than others.
        See [Canisius, Sander, John WM Martens, and Lodewyk FA Wessels.
        (2016) "A novel independence test for somatic alterations in
        cancer shows that biology drives mutual exclusivity but chance
        explains most co-occurrence." Genome biology 17.1 : 1-17.
        <doi:10.1186/s13059-016-1114-x>]. The mutations matrices are
        sparse matrices. The method developed takes advantage of the
        advantages of this type of matrix to save time and computing
        resources.
Depends: R (>= 4.0), Matrix, PoissonBinomial, ShiftConvolvePoibin,
        utils, matrixStats
Imports: maftools, data.table, parallel, RColorBrewer, methods
Suggests: knitr, rmarkdown, RUnit, BiocStyle, dplyr, kableExtra,
        magick, qvalue, testthat (>= 3.0.0)
License: Artistic-2.0
LazyData: true
RoxygenNote: 7.2.3
Encoding: UTF-8
biocViews: mutex
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2026-06-17 08:39:51 UTC; root
Config/testthat/edition: 3
Author: Juan A. Ferrer-Bonsoms [aut, cre], Laura Jareno [aut], Angel
        Rubio [aut]
Config/pak/sysreqs: libfftw3-dev libbz2-dev liblzma-dev xz-utils
        zlib1g-dev
Repository: https://jferrer-b.r-universe.dev
Date/Publication: 2025-12-19 17:10:09 UTC
RemoteUrl: https://github.com/cran/Rediscover
RemoteRef: HEAD
RemoteSha: c2ccd683b42cfd0199b888925a4761460070f315