CoExpNets is based on the excellent and widely used WGNCA package, but incorporates a refinement we detail in the following paper https://bmcsystbiol.biomedcentral.com/articles/10.1186/s12918-017-0420-6. It provides ways to create, access and exploit networks based on basic WGCNA features and ideas but we extend them a little bit and make it accessible through a Web interface.
An interesting part of this is that we make available a series of packages like CoExpROSMAP https://github.com/juanbot/CoExpROSMAP and CoExpGTEx https://github.com/juanbot/CoExpGTEx with already created networks you can use and exploit through the main package, CoExpNets.
Simply do this
devtools::install_github('juanbot/CoExpNets')And that will be all. More help to come soon. In the meantime, you can access the tutorials in the package.
The development of this suite of packages is leaded by Juan A. Botía. Co-expression network creation is leaded by Juan A. Botía and Mina Ryten from the Ryten Lab but many people contributed in some way including Jana Vandrovcova, Mar Matarin, Paola Forabosco, Conceisao Bettencourt, Seb Guelfi, Sonia García-Ruiz.
Sonia García-Ruíz is deploying all these co-expression networks at this Web page from the Ryten Lab
https://snca.atica.um.es/coexp/Run/Catalog/
which is currently under construction.
If you want to check examples of collaborations in which we used CoExpNets for annotation of genes, their function, cell type and main co-expressed genes, check the following PUBMED references
- https://www.ncbi.nlm.nih.gov/pubmed/30328509
- https://www.ncbi.nlm.nih.gov/pubmed/29365066
- https://www.ncbi.nlm.nih.gov/pubmed/29127725
- https://www.ncbi.nlm.nih.gov/pubmed/28899015
- https://www.ncbi.nlm.nih.gov/pubmed/28575651
- https://www.ncbi.nlm.nih.gov/pubmed/26912063
- https://www.ncbi.nlm.nih.gov/pubmed/26707700
And if we use the resource please cite us, with the GitHub URL and also this paper