recipe bioconductor-scmitomut

Single-cell Mitochondrial Mutation Analysis Tool

Homepage:

https://bioconductor.org/packages/3.20/bioc/html/scMitoMut.html

License:

Artistic-2.0

Recipe:

/bioconductor-scmitomut/meta.yaml

This package is designed for calling lineage-informative mitochondrial mutations using single-cell sequencing data, such as scRNASeq and scATACSeq (preferably the latter due to RNA editing issues). It includes functions for mutation calling and visualization. Mutation calling is done using beta-binomial distribution.

package bioconductor-scmitomut

versions:

1.2.0-0

depends bioconductor-rhdf5:

>=2.50.0,<2.51.0

depends bioconductor-rhdf5:

>=2.50.0,<2.51.0a0

depends bioconductor-zlibbioc:

>=1.52.0,<1.53.0

depends bioconductor-zlibbioc:

>=1.52.0,<1.53.0a0

depends libblas:

>=3.9.0,<4.0a0

depends libgcc:

>=13

depends liblapack:

>=3.9.0,<4.0a0

depends libstdcxx:

>=13

depends r-base:

>=4.4,<4.5.0a0

depends r-data.table:

depends r-ggplot2:

depends r-magrittr:

depends r-pheatmap:

depends r-plyr:

depends r-rcolorbrewer:

depends r-rcpp:

depends r-rcpparmadillo:

depends r-readr:

depends r-stringr:

requirements:

additional platforms:

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-scmitomut

and update with::

   mamba update bioconductor-scmitomut

To create a new environment, run:

mamba create --name myenvname bioconductor-scmitomut

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-scmitomut:<tag>

(see `bioconductor-scmitomut/tags`_ for valid values for ``<tag>``)

Download stats

Link to this page

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