scMitoMut
This is the development version of scMitoMut; for the stable release version, see scMitoMut.
Single-cell Mitochondrial Mutation Analysis Tool
Bioconductor version: Development (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("scMitoMut")):
Installation
To install this package, start R (version "4.4") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
# The following initializes usage of Bioc devel
BiocManager::install(version='devel')
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 | ||
| NEWS | Text |
Details
| biocViews | Preprocessing, Sequencing, SingleCell, Software |
| Version | 1.1.1 |
| 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 |
| System Requirements | |
| URL | http://github.com/wenjie1991/scMitoMut |
| Bug Reports | https://github.com/wenjie1991/scMitoMut/issues |
See More
| 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_1.1.1.tar.gz |
| Windows Binary | scMitoMut_1.1.1.zip |
| macOS Binary (x86_64) | scMitoMut_1.1.1.tgz |
| macOS Binary (arm64) | scMitoMut_1.1.1.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 |