How to perform Weighted gene co-expression network analysis (WGCNA) without coding?

#wgcna #nocoding #bioinformatics
In this video i have performed Weighted gene co-expression network analysis (WGCNA) analysis without coding using online idep web-based tool.

How to analyze public RNA-seq datasets using iDEP tool

[Nature-ki]

This is really amazing and easy explanation. I will do this type of analysis in near future. and refer to your video

[sreeram]

sir tutorial nicely explained but please explain the theory bit more in detail

[mdsymunrabby]

How do I get the Design file of the specific gene ID?

[sakibsarkerii]

Sir, I have been following your videos from last one year. I have learned a lot of things from your videos. Sir, can u make a video about how to apply WGCNA in microarray dataset using R? Please sir, I will be very grateful if you make a video on this topic. I have been trying to perform WGCNA in GSE62232 but I am failing.

[Paachi]

Sir, where s ur institute, want to come and learn especially R, python, WGCNA, Deseq2, Roc, PCA .Practical ly i want to learn, m doing phd in bioinformatics without nothing, Can u pls help me .

[tanusreedatta]

Hello brother, is it only for Arabidopsis or I can use other plant ids?

[taramin]

Thanks for sharing this video you kinda saved me
I still have question, what is the edge threshold
thank

[prashanthjavali]

Hi sir this is very usefull video, My question is if i have microarray data specially expression profiling by array and i want to perform WGNCA analysis can i able to performe with idep server ? If yes kindly help me on this

[nikhilchand]

I am performing iDEP with gene ids of wheat.
But on loading data in iDEP it shows disconnected from the server. Please provide any suggestion to resolve the problem.

[taramin]

one more question 🙋 which step can I set the p.value to 0.05? THANK YOU^^

[RjAtifAyub]

If sample size is less then 15 then what we should do?

[sanjuktaghosh]

Hi Dr Asif. You said atleast 15 samples. So, is it total 15 samples taking all groups or each group should have 15 samples? Also do you have a video where you have prepared the gene count file from RNA-Seq sample data?

[sreeram]

design file is the metadata file know sir

[nikhilchand]

Good afternoon sir
I am using list of wheat gene ids with TraesCS4D02G203800 but iDEP showing error I'd not recognised.
What I have to do sir?

[subhankarraha]

Dear sir, i want to verify some genes of my interest are co-expressed or not via this iDEP tool. Is it possible, is their any need of special R coding


If I want to check specific genes are responsible for specific hormonal pathway. can I do it via this iDEP tool? ( If the RNA SEQ data is not available in iDEV itself)


Thank you in advanced