Package: plasmut
Type: Package
Title: Stratifying mutations observed in cell-free DNA and white blood
        cells as germline, hematopoietic, or somatic
Version: 1.11.0
Authors@R: 
  c(person(given = "Adith",
           family = "Arun",
           role = c("aut", "cre"),
           email = "adith.3.arun@gmail.com"),
    person(given = "Robert",
           family = "Scharpf",
           role = "aut"))
Description: A Bayesian method for quantifying the liklihood that a
        given plasma mutation arises from clonal hematopoesis or the
        underlying tumor. It requires sequencing data of the mutation
        in plasma and white blood cells with the number of distinct and
        mutant reads in both tissues. We implement a Monte Carlo
        importance sampling method to assess the likelihood that a
        mutation arises from the tumor relative to non-tumor origin.
License: Artistic-2.0
Encoding: UTF-8
biocViews: Bayesian, SomaticMutation, GermlineMutation, Sequencing
RoxygenNote: 7.2.3
Imports: tibble, stats, dplyr
Depends: R (>= 4.3.0)
Suggests: knitr, rmarkdown, tidyverse, ggrepel, magrittr, qpdf,
        BiocStyle, biocViews, testthat (>= 3.0.0)
VignetteBuilder: knitr
Config/testthat/edition: 3
Repository: https://bioc.r-universe.dev
Date/Publication: 2026-04-28 13:01:40 UTC
RemoteUrl: https://github.com/bioc/plasmut
RemoteRef: HEAD
RemoteSha: 7b0b25f1fc6489c1b91f39a42f0d7de3c00606ae
NeedsCompilation: no
Packaged: 2026-07-10 06:02:51 UTC; root
Author: Adith Arun [aut, cre],
  Robert Scharpf [aut]
Maintainer: Adith Arun <adith.3.arun@gmail.com>