recipe bioconductor-rtnsurvival

Survival analysis using transcriptional networks inferred by the RTN package

Homepage

https://bioconductor.org/packages/3.12/bioc/html/RTNsurvival.html

License

Artistic-2.0

Recipe

/bioconductor-rtnsurvival/meta.yaml

RTNsurvival is a tool for integrating regulons generated by the RTN package with survival information. For a given regulon, the 2-tailed GSEA approach computes a differential Enrichment Score (dES) for each individual sample, and the dES distribution of all samples is then used to assess the survival statistics for the cohort. There are two main survival analysis workflows: a Cox Proportional Hazards approach used to model regulons as predictors of survival time, and a Kaplan-Meier analysis assessing the stratification of a cohort based on the regulon activity. All plots can be fine-tuned to the user's specifications.

package bioconductor-rtnsurvival

Versions

1.14.0-0,  1.12.0-0,  1.10.0-0,  1.8.1-0,  1.6.0-0

Depends

• bioconductor-rtn >=2.14.0,<2.15.0

• bioconductor-rtnduals >=1.14.0,<1.15.0

• r-base >=4.0,<4.1.0a0

• r-data.table

• r-dunn.test

• r-egg

• r-ggplot2

• r-pheatmap

• r-rcolorbrewer

• r-scales

• r-survival

Required By

Installation

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

conda install bioconductor-rtnsurvival

and update with:

conda update bioconductor-rtnsurvival

or use the docker container:

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

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

Link to this page

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