Package Recipe 'bioconductor-rtnsurvival'

recipe bioconductor-rtnsurvival

Survival analysis using transcriptional networks inferred by the RTN package

Homepage:: https://bioconductor.org/packages/3.20/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:

1.34.0-0, 1.30.0-0, 1.26.0-0, 1.24.0-0, 1.22.0-0, 1.18.0-0, 1.16.0-0, 1.14.1-0, 1.14.0-0,

1.34.0-0, 1.30.0-0, 1.26.0-0, 1.24.0-0, 1.22.0-0, 1.18.0-0, 1.16.0-0, 1.14.1-0, 1.14.0-0, 1.12.0-0, 1.10.0-0, 1.8.1-0, 1.6.0-0

Depends:

on bioconductor-rtn >=2.34.0,<2.35.0
on bioconductor-rtnduals >=1.34.0,<1.35.0
on r-base >=4.5,<4.6.0a0
on r-data.table
on r-dunn.test
on r-egg
on r-ggplot2
on r-pheatmap
on r-rcolorbrewer
on r-scales
on r-survival

Additional platforms:

Installation¶

You need a conda-compatible package manager (currently either pixi, conda, or micromamba) and the Bioconda channel already activated (see Usage). Below, we show how to install with either pixi or conda (for micromamba and mamba, commands are essentially the same as with conda).

Pixi¶

With pixi installed and the Bioconda channel set up (see Usage), to install globally, run:

pixi global install bioconductor-rtnsurvival

to add into an existing workspace instead, run:

pixi add bioconductor-rtnsurvival

In the latter case, make sure to first add bioconda and conda-forge to the channels considered by the workspace:

pixi workspace channel add conda-forge
pixi workspace channel add bioconda

Conda¶

With conda installed and the Bioconda channel set up (see Usage), to install into an existing and activated environment, run:

conda install bioconductor-rtnsurvival

Alternatively, to install into a new environment, run:

conda create -n envname bioconductor-rtnsurvival

with envname being the name of the desired environment.

Container¶

Alternatively, every Bioconda package is available as a container image for usage with your preferred container runtime. For e.g. docker, run:

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

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

Integrated deployment¶

Finally, note that many scientific workflow management systems directly integrate both conda and container based software deployment. Thus, workflow steps can be often directly annotated to use the package, leading to automatic deployment by the respective workflow management system, thereby improving reproducibility and transparency. Check the documentation of your workflow management system to find out about the integration.

Download stats¶

Link to this page¶

Render an badge with the following MarkDown:

[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/bioconductor-rtnsurvival/README.html)