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adamsardar / metaDEGth

metaDEGth: meta-analysis of Differentially Expressed Genes using parametric, empirically-derived P-value distributions
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Incorporate some pathway sets #7

Closed adamsardar closed 4 years ago

adamsardar commented 5 years ago

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.

adamsardar commented 5 years ago

Wikpathways are probably the best bet (easiest reuse policy)

adamsardar commented 5 years ago

The Ideker group has a nice dataset: DDOT (data driven biological ontologies). Providing the license is permissive, we could also include these.

adamsardar commented 5 years ago

The Broad institute has some sets that are likely under permissive license.

adamsardar commented 4 years ago

Reactome is under Creative Commons:

https://reactome.org/license

adamsardar commented 4 years ago

Clear answer is MSigDB - they can be downloaded as entrez IDs and loaded in using fgsea

adamsardar commented 4 years ago

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.