recipe r-deconstructsigs

Takes sample information in the form of the fraction of mutations in each of 96 trinucleotide contexts and identifies the weighted combination of published signatures that, when summed, most closely reconstructs the mutational profile.

Homepage:

https://github.com/raerose01/deconstructSigs

License:

GPL3 / GPL (>= 2)

Recipe:

/r-deconstructsigs/meta.yaml

package r-deconstructsigs

(downloads) docker_r-deconstructsigs

versions:
1.9.0-3,  1.9.0-2,  1.9.0-1,  1.9.0-0,  1.8.0.1-4,  1.8.0.1-3,  1.8.0.1-2,  1.8.0.1-1,  1.8.0.1-0, 

1.9.0-3,  1.9.0-2,  1.9.0-1,  1.9.0-0,  1.8.0.1-4,  1.8.0.1-3,  1.8.0.1-2,  1.8.0.1-1,  1.8.0.1-0,  1.8.0-2,  1.8.0-0

depends bioconductor-bsgenome:

depends bioconductor-bsgenome.hsapiens.ucsc.hg19:

depends bioconductor-genomeinfodb:

depends r-base:

>=4.3,<4.4.0a0

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 r-deconstructsigs

and update with::

   mamba update r-deconstructsigs

To create a new environment, run:

mamba create --name myenvname r-deconstructsigs

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-deconstructsigs:<tag>

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

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Link to this page

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