scMitoMut

This is the released version of scMitoMut; for the devel version, see scMitoMut.

Single-cell Mitochondrial Mutation Analysis Tool

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DOI: 10.18129/B9.bioc.scMitoMut

Bioconductor version: Release (3.22)

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.

Author: Wenjie Sun [cre, aut] ORCID iD ORCID: 0000-0002-3100-2346 , Leila Perie [ctb]

Maintainer: Wenjie Sun <sunwjie at gmail.com>

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

Installation

To install this package, start R (version "4.5") and enter:


if (!require("BiocManager", quietly = TRUE))
 install.packages("BiocManager")
BiocManager::install("scMitoMut")

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

Documentation

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

browseVignettes("scMitoMut")

CRC_dataset_demo HTML R Script

Reference Manual PDF

NEWS Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews Preprocessing, Sequencing, SingleCell, Software

Version 1.6.0

In Bioconductor since BioC 3.19 (R-4.4) (1.5 years)

License Artistic-2.0

Depends R (>= 4.3.0)

Imports data.table, Rcpp, magrittr, plyr, stringr, utils, stats, methods, ggplot2, pheatmap, RColorBrewer, rhdf5, readr, parallel, grDevices

System Requirements

URL http://github.com/wenjie1991/scMitoMut

Bug Reports https://github.com/wenjie1991/scMitoMut/issues

Suggests testthat (>= 3.0.0), BiocStyle, knitr, rmarkdown, VGAM, R.utils

Linking To Rcpp, RcppArmadillo

Enhances

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Package Archives

Follow Installation instructions to use this package in your R session.

Source Package scMitoMut_1.6.0.tar.gz

Windows Binary (x86_64) scMitoMut_1.5.0.zip

macOS Binary (x86_64) scMitoMut_1.6.0.tgz

macOS Binary (arm64) scMitoMut_1.6.0.tgz

Source Repository git clone https://git.bioconductor.org/packages/scMitoMut

Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/scMitoMut

Bioc Package Browser https://code.bioconductor.org/browse/scMitoMut/

Package Short Url https://bioconductor.org/packages/scMitoMut/

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