recipe bioconductor-smite

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.

Homepage

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

License

GPL (>=2)

Recipe

/bioconductor-smite/meta.yaml

Links

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

package bioconductor-smite

(downloads) docker_bioconductor-smite

Versions

1.10.0-0, 1.8.0-0, 1.6.0-0

Depends bioconductor-annotationdbi

>=1.44.0,<1.45.0

Depends bioconductor-biobase

>=2.42.0,<2.43.0

Depends bioconductor-bionet

>=1.42.0,<1.43.0

Depends bioconductor-genelendatabase

>=1.18.0,<1.19.0

Depends bioconductor-genomicranges

>=1.34.0,<1.35.0

Depends bioconductor-goseq

>=1.34.0,<1.35.0

Depends bioconductor-iranges

>=2.16.0,<2.17.0

Depends bioconductor-kegg.db

>=3.2.0,<3.3.0

Depends bioconductor-org.hs.eg.db

>=3.7.0,<3.8.0

Depends bioconductor-reactome.db

>=1.66.0,<1.67.0

Depends bioconductor-s4vectors

>=0.20.0,<0.21.0

Depends r-base

>=3.5.1,<3.5.2.0a0

Depends r-ggplot2

Depends r-hmisc

Depends r-igraph

Depends r-plyr

Depends r-scales

Requirements

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>)