Package Recipe 'bioconductor-gatom'

recipe bioconductor-gatom

Finding an Active Metabolic Module in Atom Transition Network

Homepage:: https://bioconductor.org/packages/3.20/bioc/html/gatom.html
License:: MIT + file LICENCE
Recipe:: /bioconductor-gatom/meta.yaml

This package implements a metabolic network analysis pipeline to identify an active metabolic module based on high throughput data. The pipeline takes as input transcriptional and/or metabolic data and finds a metabolic subnetwork (module) most regulated between the two conditions of interest. The package further provides functions for module post-processing, annotation and visualization.

package bioconductor-gatom¶

Versions:

1.8.4-0, 1.4.0-0

Depends:

on bioconductor-bionet >=1.70.0,<1.71.0
on r-base >=4.5,<4.6.0a0
on r-data.table
on r-ggally
on r-ggplot2
on r-htmltools
on r-htmlwidgets
on r-igraph
on r-intergraph
on r-mwcsr
on r-network
on r-plyr
on r-shinycyjs >=1.0.0
on r-sna
on r-xml

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-gatom

to add into an existing workspace instead, run:

pixi add bioconductor-gatom

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-gatom

Alternatively, to install into a new environment, run:

conda create -n envname bioconductor-gatom

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-gatom:<tag>

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