recipe bioconductor-transomics2cytoscape

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

Homepage:

https://bioconductor.org/packages/3.18/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

(downloads) docker_bioconductor-transomics2cytoscape

versions:

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 bioconductor-keggrest:

>=1.42.0,<1.43.0

depends bioconductor-rcy3:

>=2.22.0,<2.23.0

depends r-base:

>=4.3,<4.4.0a0

depends r-dplyr:

depends r-pbapply:

depends r-purrr:

depends r-tibble:

requirements:

Installation

You need a conda-compatible package manager (currently either micromamba, mamba, or conda) and the Bioconda channel already activated (see set-up-channels).

While any of above package managers is fine, it is currently recommended to use either micromamba or mamba (see here for installation instructions). We will show all commands using mamba below, but the arguments are the same for the two others.

Given that you already have a conda environment in which you want to have this package, install with:

   mamba install bioconductor-transomics2cytoscape

and update with::

   mamba update bioconductor-transomics2cytoscape

To create a new environment, run:

mamba create --name myenvname bioconductor-transomics2cytoscape

with myenvname being a reasonable name for the environment (see e.g. the mamba docs for details and further options).

Alternatively, use the docker container:

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

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

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Link to this page

Render an install-with-bioconda 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)