include clusterProfiler ecosystem

epigen / 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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Closed sreichl closed 5 months ago

sreichl commented 1 year ago

https://yulab-smu.top/biomedical-knowledge-mining-book/
for ORA/GSEA: clusterProfiler
to visualize the results: enrichplot
The clusterProfiler 4.0 paper, Wu et al., 2021, to get a first overview: https://www.sciencedirect.com/science/article/pii/S2666675821000667
an excellent book written by Guangchuang Yu, the developer. Explains in detail how to run the packages and visualize the results. https://yulab-smu.top/biomedical-knowledge-mining-book/

sreichl commented 5 months ago

we cover most of the functionality already and it is a very fragmented ecosystem.