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: 1.15.4
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
git_url: https://git.bioconductor.org/packages/mitoClone2
git_branch: devel
git_last_commit: 57551ab
git_last_commit_date: 2025-10-22
Repository: Bioconductor 3.22
Date/Publication: 2025-10-23
Packaged: 2025-10-23 22:52:14 UTC; biocbuild
Author: Benjamin Story [aut, cre],
  Lars Velten [aut],
  Gregor Mönke [aut]
Maintainer: Benjamin Story <story.benjamin@gmail.com>
Built: R 4.6.0; x86_64-w64-mingw32; 2025-10-29 21:08:41 UTC; windows
Archs: x64
