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Single-cell Mitochondrial Mutation Analysis Tool

Bioconductor version: Release (3.19)

This package is designed for analyzing mitochondrial mutations using single-cell sequencing data, such as scRNASeq and scATACSeq (preferably the latter due to RNA editing issues). It includes functions for mutation filtering and visualization. In the future, the visualization tool will become an independent package. Mutation filtering is performed by fitting a statistical model to account for various sources of noise, including PCR error, sequencing error, mtDNA sampling and/or heteroplasmy dynamics. The model tests whether the observed allele frequency of a locus in a cell can be explained by the noise model. If not, we classify it as a mutation. The input for this analysis is the allele frequency. The noise model consists of three independent models: binomial, binomial-mixture, and beta-binomial models.

Author: Wenjie Sun [cre, aut] , Leila Perie [ctb]

Maintainer: Wenjie Sun <sunwjie at>

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


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:

CRC_dataset_demo HTML R Script
Reference Manual PDF


biocViews Preprocessing, Sequencing, SingleCell, Software
Version 1.0.0
In Bioconductor since BioC 3.19 (R-4.4) (< 6 months)
License Artistic-2.0
Depends R (>= 4.3.0)
Imports data.table, Rcpp, magrittr, plyr, stringr, utils, stats, methods, ggplot2, pheatmap, zlibbioc, RColorBrewer, rhdf5, readr, parallel, grDevices
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Suggests testthat (>= 3.0.0), BiocStyle, knitr, rmarkdown, VGAM, R.utils
Linking To Rcpp, RcppArmadillo
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Follow Installation instructions to use this package in your R session.

Source Package scMitoMut_1.0.0.tar.gz
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macOS Binary (x86_64) scMitoMut_1.0.0.tgz
macOS Binary (arm64) scMitoMut_1.0.0.tgz
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