I'm looking for a tool/webserver/galaxy-workflow that can do the following steps:
1) Take a bunch of SNPs in the form of RS IDs
2) Map the SNPs to nearby genes, based on some tunable criteria (distance)
3) Perform GSEA on these genes to find enriched pathways/sets
It would be extra nice if this tool was up to date with recent genome builds etc, minimizing the need to liftover and so on.
Any suggestions?
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written
by
Purpleone
2 answers
How about i-GSEA4GWAS (http://gsea4gwas.psych.ac.cn/)?
Here is one: SNP Set Enrichment Analysis (SSEA), which contains a user-friendly interface and is freely available at http://cbcl.ics.uci.edu/SSEA. A second is VSEA (variable set enrichment analysis) and its use is described here for coronary heart disease.
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