scMitoMut
This is the development version of scMitoMut; for the stable release version, see scMitoMut.
Single-cell Mitochondrial Mutation Analysis Tool
Bioconductor version: Development (3.24)
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")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
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 | 1.9.0 |
| In Bioconductor since | BioC 3.19 (R-4.4) (2.5 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
Follow Installation instructions to use this package in your R session.
| Source Package | scMitoMut_1.9.0.tar.gz |
| Windows Binary (x86_64) | scMitoMut_1.9.0.zip |
| macOS Binary (big-sur-x86_64) | scMitoMut_1.9.0.tgz |
| macOS Binary (sonoma-arm64) | scMitoMut_1.9.0.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 |