recipe bioconductor-smite

Significance-based Modules Integrating the Transcriptome and Epigenome

Homepage

https://bioconductor.org/packages/3.13/bioc/html/SMITE.html

License

GPL (>=2)

Recipe

/bioconductor-smite/meta.yaml

Links

biotools: smite, doi: 10.1186/s12859-017-1477-3

This package builds on the Epimods framework which facilitates finding weighted subnetworks ("modules") on Illumina Infinium 27k arrays using the SpinGlass algorithm, as implemented in the iGraph package. We have created a class of gene centric annotations associated with p-values and effect sizes and scores from any researchers prior statistical results to find functional modules.

package bioconductor-smite

Versions

1.20.0-0,  1.18.0-1,  1.18.0-0,  1.16.0-0,  1.14.0-1,  1.12.0-1,  1.10.0-0,  1.8.0-0,  1.6.0-0

Depends

• bioconductor-annotationdbi >=1.54.0,<1.55.0

• bioconductor-biobase >=2.52.0,<2.53.0

• bioconductor-bionet >=1.52.0,<1.53.0

• bioconductor-genelendatabase >=1.28.0,<1.29.0

• bioconductor-genomicranges >=1.44.0,<1.45.0

• bioconductor-goseq >=1.44.0,<1.45.0

• bioconductor-iranges >=2.26.0,<2.27.0

• bioconductor-keggrest >=1.32.0,<1.33.0

• bioconductor-org.hs.eg.db >=3.13.0,<3.14.0

• bioconductor-reactome.db >=1.76.0,<1.77.0

• bioconductor-s4vectors >=0.30.0,<0.31.0

• r-base >=4.1,<4.2.0a0

• r-ggplot2

• r-hmisc

• r-igraph

• r-plyr

• r-scales

Required By

Installation

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

conda install bioconductor-smite

and update with:

conda update bioconductor-smite

or use the docker container:

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

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

Link to this page

Render an 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-smite/README.html)