Package Recipe 'bioconductor-desubs'

recipe bioconductor-desubs

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

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

1.36.0-0, 1.32.0-0, 1.28.0-0, 1.26.0-0, 1.24.0-0, 1.20.0-0, 1.18.0-0, 1.14.0-0, 1.12.0-0,

1.36.0-0, 1.32.0-0, 1.28.0-0, 1.26.0-0, 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:

on bioconductor-deseq2 >=1.50.0,<1.51.0
on bioconductor-ebseq >=2.8.0,<2.9.0
on bioconductor-edger >=4.8.0,<4.9.0
on bioconductor-graph >=1.88.0,<1.89.0
on bioconductor-limma >=3.66.0,<3.67.0
on bioconductor-rbgl >=1.86.0,<1.87.0
on r-base >=4.5,<4.6.0a0
on r-circlize
on r-ggplot2
on r-igraph
on r-jsonlite
on r-locfit
on r-matrix
on r-nbpseq
on r-pheatmap

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-desubs

to add into an existing workspace instead, run:

pixi add bioconductor-desubs

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-desubs

Alternatively, to install into a new environment, run:

conda create -n envname bioconductor-desubs

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-desubs:<tag>

(see bioconductor-desubs/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-desubs/README.html)