Alternatives to cytoscape for integrative analysis of Rna-seq data
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3.1 years ago

Hello everyone, I have multiple files of DEGs and I want to integrate these data and visuvalize them but I don't know how to do that, I tried to Install cytoscape but it keeps asking for Java script when it is already present, Can someone suggest me any other application and methods through which I can integrate my data.

rna-seq enrichment • 1.7k views
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3.1 years ago
Ridha ▴ 130

Hey ashwing, So, if I understand you correctly, you have multiple gene lists of interests and would like to meta-analyze them to find pathways unique and common between your gene lists? If yes,

I would suggest metascape and Network Analyst. I find them very helpful for analyzing multiple gene lists. In both of them, you will find an option for multiple gene lists. Also, they are user-friendly; you can easily learn how to use them. Check out their tutotrials in the websites.

Another option is to use clusterProfiler package in R. Good luck!

P.S. copy and paste your error in google and hopefully you will find a solution for the problem with cytoscape. I remember encountring such a problem when firstly downloaded it.

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Hey ridha, thanks for your comment, I was able to download cytoscape again and it worked, I have the gene name list of DEGs in excel, do you know I can start integrating them into cytoscape.

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I am not sure how familiar you are with cytoscape, but in cytoscape there are many apps/plug-ins that you can downlaod to perform the analysis you want. Are you looking for pathway enrichment analysis? Then I suggest you download the ClueGO app and clusterpedia. For CleuGO, you need permission from the authors of this app. You will have to request a license key from the authors (check their website) and will get a code for actviating it (for me I think it took around 1 or 2 days) Once you have these apps, you can just copy paste your gene lists and perform your analysis. I would recommend reading the tutorials provided by the developers.

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