mitoClone2
Clonal Population Identification in Single-Cell RNA-Seq Data using Mitochondrial and Somatic Mutations
Bioconductor version: 3.24 · Package version: 1.19.0
Other Bioconductor versions
devel is the development version; release is the current stable one.
3.24 (devel), 3.23 (release)
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.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("mitoClone2")Details
| Maintainer | Benjamin Story <story.benjamin@gmail.com> |
| Author | Benjamin Story [aut, cre], Lars Velten [aut], Gregor Mönke [aut] |
| License | GPL-3 |
| URL | https://github.com/benstory/mitoClone2 |
| System Requirements | GNU make, PhISCS (optional) |
| Source branch | devel |
| Build report | Bioconductor build system, r-universe |
| biocViews | Alignment, Annotation, DataImport, Genetics, SNP, SingleCell, Software |
| Package Short Url | https://bioconductor.org/packages/mitoClone2/ |
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 1.19.0, https://bioconductor.org/packages/mitoClone2.
Generated from the package metadata; it may differ from the package's own citation.
Documentation
Download
Follow the installation instructions to use this package in your R session.
| Source package | mitoClone2_1.19.0.tar.gz |
| Windows binary (x86_64) | mitoClone2_1.19.0.zip |
| macOS binary (arm64) | mitoClone2_1.19.0.tgz |
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