DOI: 10.18129/B9.bioc.mitoClone2  

This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see mitoClone2.

Clonal Population Identification in Single-Cell RNA-Seq Data using Mitochondrial and Somatic Mutations

Bioconductor version: 3.16

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.

Author: Benjamin Story [aut, cre], Lars Velten [aut], Gregor Mönke [aut]

Maintainer: Benjamin Story <story.benjamin at>

Citation (from within R, enter citation("mitoClone2")):


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HTML R Script Computation of phylogenetic trees and clustering of mutations
HTML R Script Variant Calling
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biocViews Alignment, Annotation, DataImport, Genetics, SNP, SingleCell, Software
Version 1.4.0
In Bioconductor since BioC 3.14 (R-4.1) (1.5 years)
License GPL-3
Depends R (>= 4.1.0)
Imports reshape2, GenomicRanges, pheatmap, deepSNV, grDevices, graphics, stats, utils, S4Vectors, Rhtslib, parallel, methods, ggplot2
LinkingTo Rhtslib(>= 1.13.1)
Suggests knitr, rmarkdown, Biostrings, testthat
SystemRequirements GNU make, PhISCS (optional)
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