recipe r-mobster

Model-based subclonal deconvolution from bulk sequencing.

Homepage:

https://github.com/caravagnalab/mobster

Documentation:

https://caravagnalab.github.io/mobster/

License:

GPL3 / GPL-3.0-or-later

Recipe:

/r-mobster/meta.yaml

MOBSTER is a package that implements a statistical model for tumour subclonal deconvolution which combines Dirichlet mixtures with distributions predicted by theoretical population genetics. The model implemented is a parametric (finite) mixture with multiple Beta components, and one Pareto power law tail. Beta components capture mutations that rise up in frequency by positive selection, and the Pareto tail models alleles resulting from neutral, intra-clone, evolutionary dynamics.

package r-mobster

versions:

0.1.1-0

depends r-base:

>=4.4,<4.5.0a0

depends r-cli:

depends r-clisymbols:

depends r-cowplot:

depends r-crayon:

depends r-dndscv:

depends r-dplyr:

depends r-easypar:

depends r-ggplot2:

depends r-ggpubr:

depends r-ggrepel:

depends r-ggthemes:

depends r-magrittr:

depends r-pio:

depends r-sads:

depends r-tidyr:

depends r-tidyverse:

depends r-vcfr:

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 r-mobster

and update with::

   mamba update r-mobster

To create a new environment, run:

mamba create --name myenvname r-mobster

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/r-mobster:<tag>

(see `r-mobster/tags`_ for valid values for ``<tag>``)

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