scMitoMut
This is thereleased version of scMitoMut; for the devel version, seescMitoMut.
Single-cell Mitochondrial Mutation Analysis Tool
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: 0000-0002-3100-2346, Leila Perie [ctb]
Maintainer: Wenjie Sun <sunwjie at gmail.com>
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 appropriateBioconductor 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 | 1.6.0 |
| 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 |
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
FollowInstallation instructions to use this package in your R session.
| Source Package | scMitoMut_1.6.0.tar.gz |
| Windows Binary (x86_64) | scMitoMut_1.6.0.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/ |
| Package Downloads Report | Download Stats |