Incorporate gene set enrichment analysis tool

IGS / gEAR

The gEAR Portal was created as a data archive and viewer for gene expression data including microarrays, bulk RNA-Seq, single-cell RNA-Seq and more.

https://umgear.org

GNU Affero General Public License v3.0

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Incorporate gene set enrichment analysis tool #268

Open jorvis opened 2 years ago

jorvis commented 2 years ago

Initial outline given by Rani attached. GSEA-gEAR.docx

DiffxPy is another tool to consider.

Also: EnrichR

adkinsrs commented 2 years ago

https://scanpy.readthedocs.io/en/stable/generated/scanpy.queries.enrich.html#scanpy.queries.enrich

Something worth looking into as well

carlocolantuoni commented 12 months ago

we can conceptualize these interactions with external gene list databases and related tools as happening in 2 directions: 1] we have a gene cart in nemo analytics and want to check the external data bases for enrichments in the gene cart 2] we know of a gene group defined in an external database and want to import it into nemo analytics as a gene cart