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greenelab / ADAGEpath

An R package (ADAGEpath) to perform signature analysis using methodology from the ADAGE manuscript
BSD 3-Clause "New" or "Revised" License
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Install instruction, gene set activity, and case study #18

Closed tj8901nm closed 7 years ago

tj8901nm commented 7 years ago

This is a relatively large PR including changes required to prepare a case study. It

  1. adds more instruction on installation
  2. adds functions to calculate gene set activity
  3. removes default model and compendium in many functions
  4. enables setting control phenotype
  5. tunes color schemes in gene-gene network
  6. removes restriction on KEGG pathway size as default
  7. adds a new function to find associated signatures for gene sets
  8. adds a new function to automatically remove redundant signatures