Get Sigora working for all organisms and various gene signature repositories

[Witold Wolski]

(Lukas an you give feedback please?).

We want to have similar functionality like webgestalt.

• various organisms
• similar genesets as webgestalt i.e. GO::Bioprocess GO::CellularComponent.
• various ID types (not only uniprot).

Try to understand the code in fgcz.gsea.ora by running the vignette.

Create a new markdown where you use sigora api to make a ORA analysis using sigora.
Add a section to the markdown file how sigora works.

Add the markdown here:

https://github.com/protViz/fgcz.gsea.ora/tree/master/inst/rmarkdown_reports

• use annotationHUB to map to genesets and to map to ENTREZ ids. )(https://github.com/protViz/fgcz.gsea.ora/blob/master/inst/run_scripts/annotationHub.R)

• using Uniprot https://github.com/protViz/fgcz.gsea.ora/blob/master/R/make_ids_uniprot.R

• use MSIGDB r package to map ENTREZ ids to genesets from MSIG and get it running with sigora.

• sigora::idmap works only for human and mouse, is it really needed? Get the it running with PIG and DOG -> (WEW - example data).