Simple explanation and usage of WGCNA package?

Question

[m.sadman.sakib]

Dear valued community members,

I am a novice biological science phd student started to delve into doing analysis independently. I came upon WGCNA package and would like to apply it to my data. Now, I have read about it in the tutorials and it is explained in great details there from Steve Horvath. But I am looking for some other simpler resources or comments from you or some example code chunks that could help me to make a pipeline for making the analysis. I have some basic questions, like,

1. What type of normalised data are used as input? Can DESeq2 normalized counts can be used as inputs? Or any other, like CPM/TPM/FPKM/RPKM?

2. When to do WGCNA? Say, I have differential expression results. Now, do I do WGCNA with all the genes and find modules and check whether differentially expressed genes are overlapping with certain gene modules? Or I do WGCNA first and focus entirely on the gene modules related to my phenotype of interest, and do not care about the differential expressions?

3. Overall interpretation of the results coming from the analysis and further usage of it.

I would really appreciate if you can give me some suggestions while you were doing WGCNA analysis yourself. Or redirect me to some online resources that is much more concise and can be understood easily for a bench scientist.

Thanks a lot in advance!

Answer 1

[Arup Ghosh]

Check the attached thread, Where to find WGCNA tutorials? .

[m.sadman.sakib]

Thank you very much, Arup!

[Kevin Blighe]

See also this answer by me: A: The RNA-Seq data input for WGCNA in terms of gene co-expression network construc

[m.sadman.sakib]

Thank you very much, Kevin!

[m.sadman.sakib]

@Kevin: Also, I wish there was a separate webpage where one can find all your detailed bioconductor answers! They are soooo valuable for newbies like myself!

[Kevin Blighe]

No repository or web-page - no. I can remember all answers that I have given, but not the URLs. I usually just search in a search engine, for example, blighe biostars tcga cnv

My footprint on Bioconductor is not as large as that on Biostars.

[m.sadman.sakib]

Sorry, I meant to say your Biostar answers! But thanks for the tip for searching your answers! I will do it like that in future!

Answer 2

[mflab]

Hello, it seems that the authors have changed affiliations/jobs and the current tutorials are uploaded here: https://www.dropbox.com/scl/fo/4vqfiysan6rlurfo2pbnk/h?rlkey=thqg8wlpdn4spu3ihjuc1kmlu&dl=0

I believe I found the link originally from a discussion in bioconductor from the authors, but the last update was from March 2024 and there was still no plans to upload their tutorials and all documentation to GitLab...