recipe bioconductor-mitoclone2

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

Homepage:

https://bioconductor.org/packages/3.18/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:

1.8.1-0,  1.6.0-0,  1.4.0-1,  1.4.0-0,  1.0.0-2,  1.0.0-1,  1.0.0-0

depends bioconductor-deepsnv:

>=1.48.0,<1.49.0

depends bioconductor-deepsnv:

>=1.48.0,<1.49.0a0

depends bioconductor-genomicranges:

>=1.54.0,<1.55.0

depends bioconductor-genomicranges:

>=1.54.1,<1.55.0a0

depends bioconductor-rhtslib:

>=2.4.0,<2.5.0

depends bioconductor-rhtslib:

>=2.4.0,<2.5.0a0

depends bioconductor-s4vectors:

>=0.40.0,<0.41.0

depends bioconductor-s4vectors:

>=0.40.2,<0.41.0a0

depends libblas:

>=3.9.0,<4.0a0

depends libgcc-ng:

>=12

depends liblapack:

>=3.9.0,<4.0a0

depends libstdcxx-ng:

>=12

depends r-base:

>=4.3,<4.4.0a0

depends r-ggplot2:

depends r-pheatmap:

depends r-reshape2:

requirements:

Installation

You need a conda-compatible package manager (currently either micromamba, mamba, or conda) and the Bioconda channel already activated (see set-up-channels).

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

with myenvname being 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>``)

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