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epigen
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enrichment_analysis
A Snakemake workflow for performing genomic region set and gene set enrichment analyses using LOLA, GREAT, GSEApy, pycisTarget and RcisTarget.
https://epigen.github.io/enrichment_analysis/
MIT License
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PPI analysis using STRING R package
#12
Closed
sreichl
closed
2 months ago
sreichl
commented
1 year ago
code in macroStim project
apply to all provided gene sets (e.g., up regulated)
or go beyond and implement "network-based" enrichment analysis using e.g., OMNIPATH testing if genes are closer in the network than random chance / background gene set of expressed genes
sreichl
commented
2 months ago
STRING query only returns the graph without much context.
STRING graph visualization not useful for many genes
Interactive web analysis is more meaningful and useful.
Network approach interesting, but currently not required for any project.