- recipe bioconductor-cogena
co-expressed gene-set enrichment analysis
- Homepage:
https://bioconductor.org/packages/3.20/bioc/html/cogena.html
- License:
LGPL-3
- Recipe:
- 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:
1.44.0-0,1.40.0-0,1.36.0-0,1.34.0-0,1.32.0-0,1.28.0-0,1.26.0-0,1.24.0-1,1.24.0-0,1.44.0-0,1.40.0-0,1.36.0-0,1.34.0-0,1.32.0-0,1.28.0-0,1.26.0-0,1.24.0-1,1.24.0-0,1.22.0-0,1.20.0-0,1.18.0-1,1.16.0-0,1.14.0-0,1.12.0-0- Depends:
on bioconductor-biobase
>=2.70.0,<2.71.0on r-amap
on r-apcluster
on r-base
>=4.5,<4.6.0a0on r-biwt
on r-class
on r-cluster
on r-corrplot
on r-devtools
on r-doparallel
on r-dplyr
on r-fastcluster
on r-foreach
on r-ggplot2
on r-gplots
on r-kohonen
on r-mclust
on r-reshape2
on r-stringr
on r-tibble
on r-tidyr
- 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-cogena
to add into an existing workspace instead, run:
pixi add bioconductor-cogena
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-cogena
Alternatively, to install into a new environment, run:
conda create -n envname bioconductor-cogena
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-cogena:<tag>
(see bioconductor-cogena/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:
[](http://bioconda.github.io/recipes/bioconductor-cogena/README.html)
