Package Recipe 'bioconductor-transomics2cytoscape'

recipe bioconductor-transomics2cytoscape

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

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

1.20.0-0, 1.16.0-0, 1.12.0-0, 1.10.0-0, 1.8.0-0, 1.4.0-0, 1.2.1-0, 1.0.0-1, 1.0.0-0

Depends:

on bioconductor-keggrest >=1.50.0,<1.51.0
on bioconductor-rcy3 >=2.30.0,<2.31.0
on r-base >=4.5,<4.6.0a0
on r-dplyr
on r-pbapply
on r-purrr
on r-tibble

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-transomics2cytoscape

to add into an existing workspace instead, run:

pixi add bioconductor-transomics2cytoscape

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-transomics2cytoscape

Alternatively, to install into a new environment, run:

conda create -n envname bioconductor-transomics2cytoscape

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-transomics2cytoscape:<tag>

(see bioconductor-transomics2cytoscape/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-transomics2cytoscape/README.html)