Package: scMitoMut 1.9.0

Wenjie Sun

scMitoMut: Single-cell Mitochondrial Mutation Analysis Tool

This package is designed for calling lineage-informative 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 calling and visualization. Mutation calling is done using beta-binomial distribution.

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

scMitoMut_1.9.0.tar.gz
scMitoMut_1.9.0.zip(r-4.7)scMitoMut_1.9.0.zip(r-4.6)scMitoMut_1.9.0.zip(r-4.5)
scMitoMut_1.9.0.tgz(r-4.6-x86_64)scMitoMut_1.9.0.tgz(r-4.6-arm64)scMitoMut_1.9.0.tgz(r-4.5-x86_64)scMitoMut_1.9.0.tgz(r-4.5-arm64)
scMitoMut_1.9.0.tar.gz(r-4.7-arm64)scMitoMut_1.9.0.tar.gz(r-4.7-x86_64)scMitoMut_1.9.0.tar.gz(r-4.6-arm64)scMitoMut_1.9.0.tar.gz(r-4.6-x86_64)
scMitoMut_1.9.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
scMitoMut/json (API)
NEWS

# Install 'scMitoMut' in R:

install.packages('scMitoMut', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/wenjie1991/scmitomut/issues

Uses libs:

openblas– Optimized BLAS
c++– GNU Standard C++ Library v3

On BioConductor:scMitoMut-1.9.0(bioc 3.24)scMitoMut-1.7.0(bioc 3.23)

preprocessing sequencing singlecell openblas cpp

4.65 score 3 stars 8 scripts 244 downloads 18 exports 46 dependencies

Last updated from:b32b9b661e. Checks:1 NOTE, 13 OK. Indexed: yes.

Target	Result	Time
bioc-checks	NOTE	174
linux-devel-arm64	OK	177
linux-devel-x86_64	OK	197
source / vignettes	OK	245
linux-release-arm64	OK	187
linux-release-x86_64	OK	193
macos-release-arm64	OK	120
macos-release-x86_64	OK	330
macos-oldrel-arm64	OK	119
macos-oldrel-x86_64	OK	230
windows-devel	OK	158
windows-release	OK	197
windows-oldrel	OK	156
wasm-release	OK	129

Exports:export_af export_binary export_df export_dt export_pval filter_loc get_pval is.mtmutObj open_h5_file parse_mgatk parse_table plot_af_coverage plot_heatmap process_locus_bmbb rm_mtmutObj run_model_fit subset_cell subset_loc

Dependencies:biocmake bit bit64 cli clipr cpp11 crayon data.table dir.expiry farver filelock ggplot2 glue gtable hms isoband labeling lifecycle magrittr pheatmap pillar pkgconfig plyr prettyunits progress R6 RColorBrewer Rcpp RcppArmadillo readr rhdf5 rhdf5filters Rhdf5lib rlang S7 scales stringi stringr tibble tidyselect tzdb utf8 vctrs viridisLite vroom withr

scMitoMut demo: CRC dataset

Wenjie Sun

Rendered fromAnalysis_colon_cancer_dataset.Rmdusingknitr::rmarkdownon May 25 2026.

Last update: 2026-05-25
Started: 2023-07-27

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Export the mutation matrix	export_af export_binary export_df export_dt export_pval
Filter mutations	filter_loc
Print mtmutObj object	format.mtmutObj is.mtmutObj print.mtmutObj
Get p-value list for single locus	get_pval
Open H5 file	open_h5_file
Load mtGATK output	parse_mgatk
Load allele count table	parse_table
QC plot: 2D scatter plot for coverage ~ AF	plot_af_coverage
Heatmap plot	plot_heatmap
Fit tree models for one locus	process_locus_bmbb
Remove mtmutObj object	rm_mtmutObj
Fit binomial mixture model for every candidate locus	run_model_fit
scMitoMut	scMitoMut-package scMitoMut
Subset cell and loci	subset_cell subset_loc