mitoClone2
This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see mitoClone2.
Clonal Population Identification in Single-Cell RNA-Seq Data using Mitochondrial and Somatic Mutations
Bioconductor version: 3.16
This package primarily identifies variants in mitochondrial genomes from BAM alignment files. It filters these variants to remove RNA editing events then estimates their evolutionary relationship (i.e. their phylogenetic tree) and groups single cells into clones. It also visualizes the mutations and providing additional genomic context.
Author: Benjamin Story [aut, cre], Lars Velten [aut], Gregor Mönke [aut]
Maintainer: Benjamin Story <story.benjamin at gmail.com>
citation("mitoClone2")):
Installation
To install this package, start R (version "4.2") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("mitoClone2")
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("mitoClone2")| Computation of phylogenetic trees and clustering of mutations | HTML | R Script |
| Variant Calling | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | Alignment, Annotation, DataImport, Genetics, SNP, SingleCell, Software |
| Version | 1.4.0 |
| In Bioconductor since | BioC 3.14 (R-4.1) (2.5 years) |
| License | GPL-3 |
| Depends | R (>= 4.1.0) |
| Imports | reshape2, GenomicRanges, pheatmap, deepSNV, grDevices, graphics, stats, utils, S4Vectors, Rhtslib, parallel, methods, ggplot2 |
| System Requirements | GNU make, PhISCS (optional) |
| URL | https://github.com/benstory/mitoClone2 |
See More
| Suggests | knitr, rmarkdown, Biostrings, testthat |
| Linking To | Rhtslib(>= 1.13.1) |
| 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 | mitoClone2_1.4.0.tar.gz |
| Windows Binary | mitoClone2_1.4.0.zip |
| macOS Binary (x86_64) | mitoClone2_1.4.0.tgz |
| macOS Binary (arm64) | mitoClone2_1.4.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/mitoClone2 |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/mitoClone2 |
| Bioc Package Browser | https://code.bioconductor.org/browse/mitoClone2/ |
| Package Short Url | https://bioconductor.org/packages/mitoClone2/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.16 | Source Archive |