Simple explanation and usage of WGCNA package?
2
0
Entering edit mode
4.0 years ago

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!

wgcna RNA-Seq ChIP-Seq • 2.2k views
ADD COMMENT
2
Entering edit mode
4.0 years ago

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

ADD COMMENT
0
Entering edit mode

Thank you very much, Arup!

ADD REPLY
2
Entering edit mode
ADD REPLY
1
Entering edit mode

Thank you very much, Kevin!

ADD REPLY
0
Entering edit mode

@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!

ADD REPLY
0
Entering edit mode

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.

ADD REPLY
1
Entering edit mode

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!

ADD REPLY
0
Entering edit mode
6 weeks ago
mflab • 0

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...

ADD COMMENT

Login before adding your answer.

Traffic: 2160 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6