recipe bioconductor-somaticsignatures

Somatic Signatures

Homepage:

https://bioconductor.org/packages/3.17/bioc/html/SomaticSignatures.html

License:

MIT + file LICENSE

Recipe:

/bioconductor-somaticsignatures/meta.yaml

Links:

biotools: somaticsignatures

The SomaticSignatures package identifies mutational signatures of single nucleotide variants (SNVs). It provides a infrastructure related to the methodology described in Nik-Zainal (2012, Cell), with flexibility in the matrix decomposition algorithms.

package bioconductor-somaticsignatures

versions:

2.36.0-0,  2.34.0-0,  2.30.0-0,  2.28.0-0,  2.26.0-1,  2.26.0-0,  2.24.0-0,  2.22.0-0,  2.20.0-1, 

2.36.0-0,  2.34.0-0,  2.30.0-0,  2.28.0-0,  2.26.0-1,  2.26.0-0,  2.24.0-0,  2.22.0-0,  2.20.0-1,  2.18.0-0,  2.16.0-0,  2.14.0-0,  2.12.1-0

depends bioconductor-biobase:

>=2.60.0,<2.61.0

depends bioconductor-biostrings:

>=2.68.0,<2.69.0

depends bioconductor-genomeinfodb:

>=1.36.0,<1.37.0

depends bioconductor-genomicranges:

>=1.52.0,<1.53.0

depends bioconductor-ggbio:

>=1.48.0,<1.49.0

depends bioconductor-iranges:

>=2.34.0,<2.35.0

depends bioconductor-pcamethods:

>=1.92.0,<1.93.0

depends bioconductor-s4vectors:

>=0.38.0,<0.39.0

depends bioconductor-variantannotation:

>=1.46.0,<1.47.0

depends r-base:

>=4.3,<4.4.0a0

depends r-ggplot2:

depends r-nmf:

depends r-proxy:

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-somaticsignatures

and update with::

   mamba update bioconductor-somaticsignatures

To create a new environment, run:

mamba create --name myenvname bioconductor-somaticsignatures

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-somaticsignatures:<tag>

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

Download stats

Link to this page

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