scMitoMut

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

Single-cell Mitochondrial Mutation Analysis Tool

Bioconductor version: Release (3.20)

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] , 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 "4.4") 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	1.2.0
In Bioconductor since	BioC 3.19 (R-4.4) (0.5 years)
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
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
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report	Build Report

Package Archives

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

Source Package	scMitoMut_1.2.0.tar.gz
Windows Binary (x86_64)	scMitoMut_1.2.0.zip
macOS Binary (x86_64)	scMitoMut_1.2.0.tgz
macOS Binary (arm64)	scMitoMut_1.2.0.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/
Package Downloads Report	Download Stats