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This is the development version of mitoClone2; for the stable release version, see mitoClone2.

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

Bioconductor version: Development (3.19)

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")):


To install this package, start R (version "4.4") and enter:

if (!require("BiocManager", quietly = TRUE))

# The following initializes usage of Bioc devel


For older versions of R, please refer to the appropriate Bioconductor release.


Reference Manual PDF


biocViews Alignment, Annotation, DataImport, Genetics, SNP, SingleCell, Software
Version 1.9.1
In Bioconductor since BioC 3.14 (R-4.1) (2.5 years)
License GPL-3
Depends R (>= 4.1.0)
Imports reshape2, GenomicRanges, pheatmap, deepSNV, grDevices, graphics, stats, utils, S4Vectors, Rhtslib, parallel, methods, ggplot2
System Requirements GNU make, PhISCS (optional)
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Suggests knitr, rmarkdown, Biostrings, testthat
Linking To Rhtslib(>= 1.13.1)
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