recipe bioconductor-desubs

DEsubs is a network-based systems biology package that extracts disease-perturbed subpathways within a pathway network as recorded by RNA-seq experiments. It contains an extensive and customizable framework covering a broad range of operation modes at all stages of the subpathway analysis, enabling a case-specific approach. The operation modes refer to the pathway network construction and processing, the subpathway extraction, visualization and enrichment analysis with regard to various biological and pharmacological features. Its capabilities render it a tool-guide for both the modeler and experimentalist for the identification of more robust systems-level biomarkers for complex diseases.






package bioconductor-desubs

(downloads) docker_bioconductor-desubs


1.8.1-1, 1.8.1-0

Depends bioconductor-deseq


Depends bioconductor-deseq2


Depends bioconductor-ebseq


Depends bioconductor-edger


Depends bioconductor-graph


Depends bioconductor-limma


Depends bioconductor-rbgl


Depends r-base


Depends r-circlize

Depends r-ggplot2

Depends r-igraph

Depends r-jsonlite

Depends r-locfit

Depends r-matrix

Depends r-nbpseq

Depends r-pheatmap



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

conda install bioconductor-desubs

and update with:

conda update bioconductor-desubs

or use the docker container:

docker pull<tag>

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