Package: mitoClone2
Type: Package
Title: Clonal Population Identification in Single-Cell RNA-Seq Data
        using Mitochondrial and Somatic Mutations
LinkingTo: Rhtslib (>= 1.13.1)
Version: 1.16.0
Authors@R: c( person(given = "Benjamin", family = "Story", role = c("aut", "cre"), email = "story.benjamin@gmail.com"),
	   person(given = "Lars", family = "Velten", role = "aut"),
	   person(given = "Gregor", family = "Mönke", role = "aut") )
Description: This package primarily identifies variants in
        mitochondrial genomes from BAM alignment files. It filters
        these variants to remove RNA editing events then estimates
        their evolutionary relationship (i.e. their phylogenetic tree)
        and groups single cells into clones. It also visualizes the
        mutations and providing additional genomic context.
License: GPL-3
VignetteBuilder: knitr
Encoding: UTF-8
LazyData: false
biocViews: Annotation, DataImport, Genetics, SNP, Software, SingleCell,
        Alignment
Imports: reshape2, GenomicRanges, pheatmap, deepSNV, grDevices, Matrix,
        graphics, stats, utils, S4Vectors, Rhtslib, parallel, methods,
        ggplot2
Suggests: knitr, rmarkdown, Biostrings, testthat
RoxygenNote: 7.1.0
SystemRequirements: GNU make, PhISCS (optional)
Depends: R (>= 4.4.0)
NeedsCompilation: yes
URL: https://github.com/benstory/mitoClone2
Bugreports: https://github.com/benstory/mitoClone2/issues
Config/pak/sysreqs: make libbz2-dev libicu-dev liblzma-dev libpng-dev
        libxml2-dev libssl-dev xz-utils zlib1g-dev
Repository: https://bioc-release.r-universe.dev
Date/Publication: 2025-10-29 15:11:00 UTC
RemoteUrl: https://github.com/bioc/mitoClone2
RemoteRef: RELEASE_3_22
RemoteSha: 43b5799afaa8158911677ed0c2efd41a90deb69a
Packaged: 2026-02-02 09:59:05 UTC; root
Author: Benjamin Story [aut, cre],
  Lars Velten [aut],
  Gregor Mönke [aut]
Maintainer: Benjamin Story <story.benjamin@gmail.com>
Built: R 4.5.2; x86_64-w64-mingw32; 2026-02-02 10:01:38 UTC; windows
Archs: x64
