recipe bioconductor-drugvsdisease

Comparison of disease and drug profiles using Gene set Enrichment Analysis

Homepage:

https://bioconductor.org/packages/3.16/bioc/html/DrugVsDisease.html

License:

GPL-3

Recipe:

/bioconductor-drugvsdisease/meta.yaml

Links:

biotools: drugvsdisease, doi: 10.1038/nmeth.3252

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.

package bioconductor-drugvsdisease

Versions:

2.40.0-0,  2.36.0-0,  2.34.0-0,  2.32.0-1,  2.32.0-0,  2.30.0-0,  2.28.0-1,  2.26.0-1,  2.24.2-0, 

2.40.0-0,  2.36.0-0,  2.34.0-0,  2.32.0-1,  2.32.0-0,  2.30.0-0,  2.28.0-1,  2.26.0-1,  2.24.2-0,  2.22.0-0,  2.20.1-0

Depends:

• bioconductor-affy >=1.76.0,<1.77.0

• bioconductor-annotate >=1.76.0,<1.77.0

• bioconductor-arrayexpress >=1.57.0,<1.58.0

• bioconductor-biocgenerics >=0.44.0,<0.45.0

• bioconductor-biomart >=2.54.0,<2.55.0

• bioconductor-cmap2data >=1.34.0,<1.35.0

• bioconductor-drugvsdiseasedata >=1.34.0,<1.35.0

• bioconductor-geoquery >=2.66.0,<2.67.0

• bioconductor-hgu133a.db >=3.13.0,<3.14.0

• bioconductor-hgu133a2.db >=3.13.0,<3.14.0

• bioconductor-hgu133plus2.db >=3.13.0,<3.14.0

• bioconductor-limma >=3.54.0,<3.55.0

• bioconductor-qvalue >=2.30.0,<2.31.0

• r-base >=4.2,<4.3.0a0

• r-runit

• r-xtable

Required By:

Installation

With an activated Bioconda channel (see set-up-channels), install with:

conda install bioconductor-drugvsdisease

and update with:

conda update bioconductor-drugvsdisease

or use the docker container:

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

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

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