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BaderLab / netDx

R package with netDx software and data for examples
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Move from EasyCyrest to r2cytoscape #29

Closed shraddhapai closed 7 years ago

shraddhapai commented 7 years ago

Automated net construction in Cytoscape currently occurs via a custom package we started developing called EasyCyRest.

We should probably move to "r2cytoscape", which has a lot of R functions for generic cyrest functionality. https://github.com/cytoscape/cytoscape-automation/tree/master/for-scripters/R/r2cytoscape

Functionality with cyrest:

  1. Generate integrated PSN (currently uses EasyCyrest to create JSON)
  2. Generate enrichment map with nodes colour-coded by top score in feature selection. Automatically generates EM and applies AutoAnnotate.
shraddhapai commented 7 years ago

Done in v1.0. Need to keep both packages for now because of unique functionality in each.