recipe bioconductor-cogena

co-expressed gene-set enrichment analysis

Homepage:

https://bioconductor.org/packages/3.18/bioc/html/cogena.html

License:

LGPL-3

Recipe:

/bioconductor-cogena/meta.yaml

Links:

biotools: cogena, doi: 10.1186/s12864-016-2737-8

cogena is a workflow for co-expressed gene-set enrichment analysis. It aims to discovery smaller scale, but highly correlated cellular events that may be of great biological relevance. A novel pipeline for drug discovery and drug repositioning based on the cogena workflow is proposed. Particularly, candidate drugs can be predicted based on the gene expression of disease-related data, or other similar drugs can be identified based on the gene expression of drug-related data. Moreover, the drug mode of action can be disclosed by the associated pathway analysis. In summary, cogena is a flexible workflow for various gene set enrichment analysis for co-expressed genes, with a focus on pathway/GO analysis and drug repositioning.

package bioconductor-cogena

versions:

1.36.0-0,  1.34.0-0,  1.32.0-0,  1.28.0-0,  1.26.0-0,  1.24.0-1,  1.24.0-0,  1.22.0-0,  1.20.0-0, 

1.36.0-0,  1.34.0-0,  1.32.0-0,  1.28.0-0,  1.26.0-0,  1.24.0-1,  1.24.0-0,  1.22.0-0,  1.20.0-0,  1.18.0-1,  1.16.0-0,  1.14.0-0,  1.12.0-0

depends bioconductor-biobase:

>=2.62.0,<2.63.0

depends r-amap:

depends r-apcluster:

depends r-base:

>=4.3,<4.4.0a0

depends r-biwt:

depends r-class:

depends r-cluster:

depends r-corrplot:

depends r-devtools:

depends r-doparallel:

depends r-dplyr:

depends r-fastcluster:

depends r-foreach:

depends r-ggplot2:

depends r-gplots:

depends r-kohonen:

depends r-mclust:

depends r-reshape2:

depends r-stringr:

depends r-tibble:

depends r-tidyr:

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-cogena

and update with::

   mamba update bioconductor-cogena

To create a new environment, run:

mamba create --name myenvname bioconductor-cogena

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-cogena:<tag>

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

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