mitoClone2

DOI: 10.18129/B9.bioc.mitoClone2    

This package is for version 3.14 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: 3.14

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>

Installation

To install this package, start R (version "4.1") 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")

 

HTML	R Script	Computation of phylogenetic trees and clustering of mutations
HTML	R Script	Variant Calling
PDF		Reference Manual
Text		NEWS

Details

biocViews	Alignment, Annotation, DataImport, Genetics, SNP, SingleCell, Software
Version	1.0.0
In Bioconductor since	BioC 3.14 (R-4.1) (< 6 months)
License	GPL-3
Depends	R (>= 4.1.0)
Imports	reshape2, GenomicRanges, pheatmap, deepSNV, grDevices, graphics, stats, utils, S4Vectors, Rhtslib, parallel, methods, ggplot2
LinkingTo	Rhtslib(>= 1.13.1)
Suggests	knitr, rmarkdown, Biostrings, testthat
SystemRequirements	GNU make, PhISCS (optional)
Enhances
URL	https://github.com/benstory/mitoClone2
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	mitoClone2_1.0.0.tar.gz
Windows Binary	mitoClone2_1.0.0.zip
macOS 10.13 (High Sierra)	mitoClone2_1.0.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/mitoClone2
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/mitoClone2
Package Short Url	https://bioconductor.org/packages/mitoClone2/
Package Downloads Report	Download Stats