recipe bioconductor-mitoclone2

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

Homepage:

https://bioconductor.org/packages/3.16/bioc/html/mitoClone2.html

License:

GPL-3

Recipe:

/bioconductor-mitoclone2/meta.yaml

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

Versions:

1.4.0-0,  1.0.0-2,  1.0.0-1,  1.0.0-0

Depends:

• bioconductor-deepsnv >=1.44.0,<1.45.0

• bioconductor-genomicranges >=1.50.0,<1.51.0

• bioconductor-rhtslib >=2.0.0,<2.1.0

• bioconductor-s4vectors >=0.36.0,<0.37.0

• libblas >=3.9.0,<4.0a0

• libgcc-ng >=12

• liblapack >=3.9.0,<4.0a0

• libstdcxx-ng >=12

• r-base >=4.2,<4.3.0a0

• r-ggplot2

• r-pheatmap

• r-reshape2

Required By:

Installation

With an activated Bioconda channel (see set-up-channels), install with:

conda install bioconductor-mitoclone2

and update with:

conda update bioconductor-mitoclone2

or use the docker container:

docker pull quay.io/biocontainers/bioconductor-mitoclone2:<tag>

(see bioconductor-mitoclone2/tags for valid values for <tag>)

Download stats

Link to this page

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