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mitoClone2

This is the development version of mitoClone2; for the stable release version, see mitoClone2.

Clonal Population Identification in Single-Cell RNA-Seq Data using Mitochondrial and Somatic Mutations

Bioconductor version: Development (3.18)

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 (from within R, enter citation("mitoClone2")):

Installation

To install this package, start R (version "4.3") and enter: 

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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 PDF
NEWS Text

Details

biocViews Alignment, Annotation, DataImport, Genetics, SNP, SingleCell, Software
Version 1.7.0
In Bioconductor since BioC 3.14 (R-4.1) (2 years)
License GPL-3
Depends R (>= 4.1.0)
Imports reshape2, GenomicRanges, pheatmap, deepSNV, grDevices, graphics, stats, utils, S4Vectors, Rhtslib, parallel, methods, ggplot2
Linking To Rhtslib(>= 1.13.1)
Suggests knitr, rmarkdown, Biostrings, testthat
System Requirements GNU make, PhISCS (optional)
Enhances
URL https://github.com/benstory/mitoClone2
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Depends On Me
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Package Archives

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

Source Package mitoClone2_1.7.0.tar.gz
Windows Binary mitoClone2_1.7.0.zip
macOS Binary (x86_64)
macOS Binary (arm64)
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