recipe bioconductor-drugvsdisease

This package generates ranked lists of differential gene expression for either disease or drug profiles. Input data can be downloaded from Array Express or GEO, or from local CEL files. Ranked lists of differential expression and associated p-values are calculated using Limma. Enrichment scores (Subramanian et al. PNAS 2005) are calculated to a reference set of default drug or disease profiles, or a set of custom data supplied by the user. Network visualisation of significant scores are output in Cytoscape format.







biotools: drugvsdisease, doi: 10.1038/nmeth.3252

package bioconductor-drugvsdisease

(downloads) docker_bioconductor-drugvsdisease


2.24.2-0, 2.22.0-0, 2.20.1-0

Depends bioconductor-affy


Depends bioconductor-annotate


Depends bioconductor-arrayexpress


Depends bioconductor-biocgenerics


Depends bioconductor-biomart


Depends bioconductor-cmap2data


Depends bioconductor-drugvsdiseasedata


Depends bioconductor-geoquery


Depends bioconductor-hgu133a.db


Depends bioconductor-hgu133a2.db


Depends bioconductor-hgu133plus2.db


Depends bioconductor-limma


Depends bioconductor-qvalue


Depends r-base


Depends r-runit

Depends r-xtable



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

conda install bioconductor-drugvsdisease

and update with:

conda update bioconductor-drugvsdisease

or use the docker container:

docker pull<tag>

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