scMitoMut
This package is for version 3.19 of Bioconductor; for the stable, up-to-date release version, see scMitoMut.
Single-cell Mitochondrial Mutation Analysis Tool
Bioconductor version: 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 gmail.com>
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 | ||
| NEWS | Text |
Details
| 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 |
| 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_1.0.0.tar.gz |
| Windows Binary (x86_64) | scMitoMut_1.0.0.zip |
| macOS Binary (x86_64) | scMitoMut_1.0.0.tgz |
| macOS Binary (arm64) | scMitoMut_1.0.0.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 |