mitoClone2
This is the released version of mitoClone2; for the devel version, see mitoClone2.
All Bioconductor versions of mitoClone2
3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14
Clonal Population Identification in Single-Cell RNA-Seq Data using Mitochondrial and Somatic Mutations
Bioconductor version: 3.23 · Package version: 1.18.0
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"):
Benjamin Story, Lars Velten, Gregor Mönke. mitoClone2: Clonal Population Identification in Single-Cell RNA-Seq Data using Mitochondrial and Somatic Mutations. doi:10.18129/B9.bioc.mitoClone2, R package version 1.18.0, https://bioconductor.org/packages/mitoClone2.
Generated from the package metadata; it may differ from the package's own citation.
Installation
To install this package, start R (version "4.6") 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.
Details
| Version | 1.18.0 |
| License | GPL-3 |
| URL | https://github.com/benstory/mitoClone2 |
| System Requirements | GNU make, PhISCS (optional) |
| Last updated | 2026-04-28 |
| In Bioconductor since | BioC 3.14 (R-4.1) (4 years) |
| Downloads rank | 1687 of 2,418 |
| Source branch | RELEASE_3_23 |
| Build report | Bioconductor build system, r-universe |
| biocViews | Alignment, Annotation, DataImport, Genetics, SNP, SingleCell, Software |
| Package Short Url | https://bioconductor.org/packages/mitoClone2/ |
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 |
Download
Follow the installation instructions to use this package in your R session.
| Source package | mitoClone2_1.18.0.tar.gz |
| Windows binary (x86_64) | mitoClone2_1.18.0.zip |
| macOS binary (arm64) | mitoClone2_1.18.0.tgz |
| macOS binary (x86_64) | mitoClone2_1.18.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/mitoClone2 |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/mitoClone2 |
| Package Downloads Report | Download Stats |
Dependencies
Depends: R (>= 4.4.0)
Imports: reshape2, GenomicRanges, pheatmap, deepSNV, grDevices, Matrix, graphics, stats, utils, S4Vectors, Rhtslib, parallel, methods, ggplot2
LinkingTo: Rhtslib (>= 1.13.1)
Suggests: knitr, rmarkdown, Biostrings, testthat