Package: scMitoMut
Title: Single-cell Mitochondrial Mutation Analysis Tool
Version: 1.0.0
Authors@R: c(
  person("Wenjie", "Sun", email = "sunwjie@gmail.com", role = c("cre", "aut"), comment=c(ORCID="0000-0002-3100-2346")),
  person("Leila", "Perie", email = "leila.perie@curie.fr", role = "ctb")
  )
Description: 
    This package is designed for analyzing mitochondrial mutations using
    single-cell sequencing data, such as scRNASeq and scATACSeq (preferably the
    latter due to RNA editing issues). It includes functions for mutation
    filtering and visualization. In the future, the visualization tool will
    become an independent package. Mutation filtering is performed by fitting a
    statistical model to account for various sources of noise, including PCR
    error, sequencing error, mtDNA sampling and/or heteroplasmy dynamics. The
    model tests whether the observed allele frequency of a locus in a cell can
    be explained by the noise model. If not, we classify it as a mutation. The
    input for this analysis is the allele frequency. The noise model consists
    of three independent models: binomial, binomial-mixture, and beta-binomial
    models.
License: Artistic-2.0
Encoding: UTF-8
Depends: R (>= 4.3.0)
Imports: data.table, Rcpp, magrittr, plyr, stringr, utils, stats,
        methods, ggplot2, pheatmap, zlibbioc, RColorBrewer, rhdf5,
        readr, parallel, grDevices
LinkingTo: Rcpp, RcppArmadillo
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.3.1
Suggests: testthat (>= 3.0.0), BiocStyle, knitr, rmarkdown, VGAM,
        R.utils
Config/testthat/edition: 3
BugReports: https://github.com/wenjie1991/scMitoMut/issues
URL: http://github.com/wenjie1991/scMitoMut
VignetteBuilder: knitr
NeedsCompilation: yes
biocViews: Preprocessing, Sequencing, SingleCell
git_url: https://git.bioconductor.org/packages/scMitoMut
git_branch: RELEASE_3_19
git_last_commit: d2dc2ef
git_last_commit_date: 2024-04-30
Repository: Bioconductor 3.19
Date/Publication: 2024-05-01
Packaged: 2024-05-02 01:45:04 UTC; biocbuild
Author: Wenjie Sun [cre, aut] (<https://orcid.org/0000-0002-3100-2346>),
  Leila Perie [ctb]
Maintainer: Wenjie Sun <sunwjie@gmail.com>
Built: R 4.4.0; x86_64-w64-mingw32; 2024-05-02 13:29:31 UTC; windows
Archs: x64
