recipe bioconductor-plasmut

Stratifying mutations observed in cell-free DNA and white blood cells as germline, hematopoietic, or somatic

Homepage:

https://bioconductor.org/packages/3.18/bioc/html/plasmut.html

License:

Artistic-2.0

Recipe:

/bioconductor-plasmut/meta.yaml

A Bayesian method for quantifying the liklihood that a given plasma mutation arises from clonal hematopoesis or the underlying tumor. It requires sequencing data of the mutation in plasma and white blood cells with the number of distinct and mutant reads in both tissues. We implement a Monte Carlo importance sampling method to assess the likelihood that a mutation arises from the tumor relative to non-tumor origin.

package bioconductor-plasmut

(downloads) docker_bioconductor-plasmut

versions:

1.0.0-0

depends r-base:

>=4.3,<4.4.0a0

depends r-dplyr:

depends r-tibble:

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-plasmut

and update with::

   mamba update bioconductor-plasmut

To create a new environment, run:

mamba create --name myenvname bioconductor-plasmut

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-plasmut:<tag>

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

Download stats

Link to this page

Render an install-with-bioconda badge with the following MarkDown:

[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/bioconductor-plasmut/README.html)