recipe bioconductor-transomics2cytoscape

A tool set for 3D Trans-Omic network visualization with Cytoscape

Homepage

https://bioconductor.org/packages/3.14/bioc/html/transomics2cytoscape.html

License

Artistic-2.0

Recipe

/bioconductor-transomics2cytoscape/meta.yaml

transomics2cytoscape generates a file for 3D transomics visualization by providing input that specifies the IDs of multiple KEGG pathway layers, their corresponding Z-axis heights, and an input that represents the edges between the pathway layers. The edges are used, for example, to describe the relationships between kinase on a pathway and enzyme on another pathway. This package automates creation of a transomics network as shown in the figure in Yugi.2014 (https://doi.org/10.1016/j.celrep.2014.07.021) using Cytoscape automation (https://doi.org/10.1186/s13059-019-1758-4).

package bioconductor-transomics2cytoscape

Versions

1.4.0-0,  1.2.1-0,  1.0.0-1,  1.0.0-0

Depends

• bioconductor-keggrest >=1.34.0,<1.35.0

• bioconductor-rcy3 >=2.14.0,<2.15.0

• r-base >=4.1,<4.2.0a0

• r-dplyr

Required By

Installation

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

conda install bioconductor-transomics2cytoscape

and update with:

conda update bioconductor-transomics2cytoscape

or use the docker container:

docker pull quay.io/biocontainers/bioconductor-transomics2cytoscape:<tag>

(see bioconductor-transomics2cytoscape/tags for valid values for <tag>)

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-transomics2cytoscape/README.html)