recipe bioconductor-desubs

DEsubs: an R package for flexible identification of differentially expressed subpathways using RNA-seq expression experiments

Homepage:

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

License:

GPL-3

Recipe:

/bioconductor-desubs/meta.yaml

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

Versions:

1.24.0-0,  1.20.0-0,  1.18.0-0,  1.14.0-0,  1.12.0-0,  1.10.0-1,  1.8.1-1,  1.8.1-0

Depends:

• bioconductor-deseq2 >=1.38.0,<1.39.0

• bioconductor-ebseq >=1.38.0,<1.39.0

• bioconductor-edger >=3.40.0,<3.41.0

• bioconductor-graph >=1.76.0,<1.77.0

• bioconductor-limma >=3.54.0,<3.55.0

• bioconductor-rbgl >=1.74.0,<1.75.0

• r-base >=4.2,<4.3.0a0

• r-circlize

• r-ggplot2

• r-igraph

• r-jsonlite

• r-locfit

• r-matrix

• r-nbpseq

• r-pheatmap

Required By:

Installation

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

conda install bioconductor-desubs

and update with:

conda update bioconductor-desubs

or use the docker container:

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

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

Download stats

Link to this page

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