Entering edit mode
6.9 years ago
chetana
▴
60
Hi everyone,
I'm relatively new to RNA-Seq data analysis. I was wondering if there are any software or tools out there to get the network analysis for expression data (which uses FPKM as the input). I've heard about WGCNA but I do wanna try other approaches if there are any. Thanks in advance.
Could you be more specfic about what you mean by "network analysis"?
Like a co-expression gene analysis that represents the output in the form of network or clusters.
Co- expression analysis is not the only way to create a network. You only need to find a set of genes with something in common...for example a list of differentially expressed genes.
Use DESEQ2 to calculate differential expression between samples....then get the list of genes that are differentially expressed ......then put that list into gprofiler for GSEA and STRINGDB for protein protein interaction mapping. Co-expression analyisis is a bit more involved.
Dont forget to upvote :)
Check out Miru: https://kajeka.com/miru/miru-about/
It can be extensively used for RNAseq network analysis for deciphering co-expression of genes involved..
Hi. The link isn't working. Is this actual still? Or what? Thnx
The name has changed to Graphia...its free and you can find it here: https://graphia.app/