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cmap / cmapR

Tools for manipulating annotated data matrices
BSD 3-Clause "New" or "Revised" License
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Connectivity Score implementation #53

Closed enricoferrero closed 4 years ago

enricoferrero commented 4 years ago

Hi Ted,

Not really an issue per se, but I was wondering if you have any plans to extend the package to also compute the Connectivity Score as implemented by Subramanian et al., 2017?

Alternatively, are you aware of any other R package or code snippets that implement it?

Thank you, Enrico

tnat1031 commented 4 years ago

Hi @enricoferrero ,

Sorry for the delayed reply. We don't have immediate plans to implement the full set of connectivity scores (weighted enrichment, normalization, conversion to tau) in cmapR, particularly because the latter steps are quite involved and require access to precomputed background enrichment score distributions, which may not be generally possible.

We do however offer the full connectivity workflow as a set of docker containers: https://hub.docker.com/r/cmap/sig_introspect_tool/ - for computing pairwise connectivities within a dataset https://hub.docker.com/r/cmap/sig_gutcbackground_tool/ - for converting pairwise connectives into a background for computing tau https://hub.docker.com/r/cmap/sig_gutc_tool/ - for computing tau values

The GSEA-MSigDB R package implements the enrichment score (function GSEA.EnrichmentScore), which may be useful if that's something you'd like to compute.

Thanks a lot, Ted