anRichment is missing

Question

[michael.flower.14]

I'd like to try and use anRichment for WGCNA annotation. Unfortunately the site to download the install files seems to be down. Does anyone have the installation files?

https://horvath.genetics.ucla.edu/html/CoexpressionNetwork/GeneAnnotation/Tutorials/anRichment-Tutorial1.pdf

source("https://horvath.genetics.ucla.edu/html/CoexpressionNetwork/GeneAnnotation/installAnRichment.R"); installAnRichment();

[ATpoint]

WGCNA documentation hosted at UCLA is down for some days, multiple people have made posts on this. That's the danger when developers host code and documentation at sources that are not official repositories such as CRAN or GitHub. Nothing you can do about it other than trying to reach the developer via email.

[Tatyana]

The problem is back, Horwath's lab web is down again. Is it possible to get anRichment istallation file somewhere? (The greater problem is that this package is necessary to install other packages, for example, Omicsfold that I need).

[GenoMax]

See this link for the WGCNA documentation and code from Peter Langfelder : https://bioinformatics.stackexchange.com/questions/21885/where-to-access-the-wgcna-tutorial-documents-horvath-lab-site-down/21886#21886

ATPoint had found this.

[Tatyana]

Unfortunately, there are only tutorials and codes for tutorials for WGCNA, not installation files for any their packages... :(

[GenoMax]

Consider emailing Dr. Horvath about this. Until enough people make him aware of this issue WGCNA "problem" is unlikely to get fixed.

Answer 1

[Karissa]

Also having issues even installing anRichment. Running on an M2 mac and wondering if that is an issue. I hope the developers come up with a solution soon for putting their full tutorials and resources on CRAN/Bioc/github.

In the meantime, this paper may have a solution for perfomring enrichment on modules: https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-021-04554-1

Since the GO package included with WGCNA (anRichment [22]) does not provide support for many genomes (including plant genomes), we have added the package topGO [15] to perform this analysis. Using topGO, we tested overrepresentation of GO terms using a Kolmogorov–Smirnov test for GO enrichment of DEG genes.