Incorporate some pathway sets
adamsardar opened this issue · comments
Pathway sets are always very difficult to use in an enrichment study, as we are unsure as to whether any error is the result of an incorrect method or incorrect data.
Wikpathways are probably the best bet (easiest reuse policy)
The Ideker group has a nice dataset: DDOT (data driven biological ontologies). Providing the license is permissive, we could also include these.
The Broad institute has some sets that are likely under permissive license.
Reactome is under Creative Commons:
Clear answer is MSigDB - they can be downloaded as entrez IDs and loaded in using fgsea
https://www.frontiersin.org/articles/10.3389/fphar.2019.00445/full
BioPlanet is new and looks like it could be a nice balance between coverage, annotation and link-out services to other providers.