Vignette and READ.ME

[jleechung]

• include vignette - sections include:
  • proActiv workflow
  • identifying alternate promoter usage with DEXSeq
  • visualization of:
    • alternate promoter usage
    • promoter categories (proportion, by position)
    • tSNE
• update READ.ME - sections include:
  • quick start
  • creating promoter annotation
  • estimating promoter activity
• further reduce promoter annotation
  • store promoter id as integer
• add mm10 and mm9 promoter annotations
• modify proActiv to accept condition argument
  • allows summarization of results by condition