Package Recipe 'bioconductor-gsean'

recipe bioconductor-gsean

Gene Set Enrichment Analysis with Networks

Homepage:: https://bioconductor.org/packages/3.20/bioc/html/gsean.html
License:: Artistic-2.0
Recipe:: /bioconductor-gsean/meta.yaml

Biological molecules in a living organism seldom work individually. They usually interact each other in a cooperative way. Biological process is too complicated to understand without considering such interactions. Thus, network-based procedures can be seen as powerful methods for studying complex process. However, many methods are devised for analyzing individual genes. It is said that techniques based on biological networks such as gene co-expression are more precise ways to represent information than those using lists of genes only. This package is aimed to integrate the gene expression and biological network. A biological network is constructed from gene expression data and it is used for Gene Set Enrichment Analysis.

package bioconductor-gsean¶

Versions:

1.30.0-0, 1.26.0-0, 1.22.0-0, 1.20.2-0, 1.18.0-1, 1.18.0-0, 1.14.0-0, 1.12.0-0, 1.10.0-1,

1.30.0-0, 1.26.0-0, 1.22.0-0, 1.20.2-0, 1.18.0-1, 1.18.0-0, 1.14.0-0, 1.12.0-0, 1.10.0-1, 1.10.0-0, 1.8.0-0, 1.6.0-0, 1.4.0-1, 1.2.0-0

Depends:

on bioconductor-fgsea >=1.36.0,<1.37.0
on bioconductor-fgsea >=1.36.2,<1.37.0a0
on bioconductor-ppinfer >=1.36.0,<1.37.0
on bioconductor-ppinfer >=1.36.0,<1.37.0a0
on libblas >=3.9.0,<4.0a0
on libgcc >=14
on liblapack >=3.9.0,<4.0a0
on liblzma >=5.8.2,<6.0a0
on libzlib >=1.3.1,<2.0a0
on r-base >=4.5,<4.6.0a0

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-gsean

to add into an existing workspace instead, run:

pixi add bioconductor-gsean

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-gsean

Alternatively, to install into a new environment, run:

conda create -n envname bioconductor-gsean

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-gsean:<tag>

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