- recipe bioconductor-mitoclone2
Clonal Population Identification in Single-Cell RNA-Seq Data using Mitochondrial and Somatic Mutations
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.
- package bioconductor-mitoclone2¶
- depends bioconductor-deepsnv:
- depends bioconductor-genomicranges:
- depends bioconductor-rhtslib:
- depends bioconductor-s4vectors:
- depends libblas:
- depends libgcc-ng:
- depends liblapack:
- depends libstdcxx-ng:
- depends r-base:
- depends r-ggplot2:
- depends r-pheatmap:
- depends r-reshape2:
While any of above package managers is fine, it is currently recommended to use either micromamba or mamba (see here for installation instructions). We will show all commands using mamba below, but the arguments are the same for the two others.
Given that you already have a conda environment in which you want to have this package, install with:
mamba install bioconductor-mitoclone2 and update with:: mamba update bioconductor-mitoclone2
To create a new environment, run:
mamba create --name myenvname bioconductor-mitoclone2
myenvnamebeing a reasonable name for the environment (see e.g. the mamba docs for details and further options).
Alternatively, use the docker container:
docker pull quay.io/biocontainers/bioconductor-mitoclone2:<tag> (see `bioconductor-mitoclone2/tags`_ for valid values for ``<tag>``)