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

Bioconductor version: Release (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))


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


To view documentation for the version of this package installed in your system, start R and enter:

Computation of phylogenetic trees and clustering of mutations HTML R Script
Variant Calling HTML R Script
Reference Manual PDF


biocViews Alignment, Annotation, DataImport, Genetics, SNP, SingleCell, Software
Version 1.10.0
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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Follow Installation instructions to use this package in your R session.

Source Package mitoClone2_1.10.0.tar.gz
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macOS Binary (x86_64) mitoClone2_1.10.0.tgz
macOS Binary (arm64) mitoClone2_1.10.0.tgz
Source Repository git clone
Source Repository (Developer Access) git clone
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