recipe bioconductor-yapsa

This package provides functions and routines useful in the analysis of somatic signatures (cf. L. Alexandrov et al., Nature 2013). In particular, functions to perform a signature analysis with known signatures (LCD = linear combination decomposition) and a signature analysis on stratified mutational catalogue (SMC = stratify mutational catalogue) are provided.

Homepage

https://bioconductor.org/packages/3.9/bioc/html/YAPSA.html

License

GPL-3

Recipe

/bioconductor-yapsa/meta.yaml

Links

biotools: yapsa, doi: 10.1038/nmeth.3252

package bioconductor-yapsa

(downloads) docker_bioconductor-yapsa

Versions

1.8.0-0, 1.6.0-0, 1.4.0-0

Depends bioconductor-complexheatmap

>=1.20.0,<1.21.0

Depends bioconductor-genomeinfodb

>=1.18.0,<1.19.0

Depends bioconductor-genomicranges

>=1.34.0,<1.35.0

Depends bioconductor-gtrellis

>=1.14.0,<1.15.0

Depends bioconductor-keggrest

>=1.22.0,<1.23.0

Depends bioconductor-somaticsignatures

>=2.18.0,<2.19.0

Depends bioconductor-variantannotation

>=1.28.0,<1.29.0

Depends r-base

>=3.5.1,<3.5.2.0a0

Depends r-circlize

Depends r-corrplot

Depends r-dendextend

Depends r-getoptlong

Depends r-ggplot2

Depends r-gridextra

Depends r-lsei

Depends r-pmcmr

Depends r-reshape2

Requirements

Installation

With an activated Bioconda channel (see 2. Set up channels), install with:

conda install bioconductor-yapsa

and update with:

conda update bioconductor-yapsa

or use the docker container:

docker pull quay.io/biocontainers/bioconductor-yapsa:<tag>

(see bioconductor-yapsa/tags for valid values for <tag>)