Main CLI

These are the workhorse programs of BPReveal. Each one accepts a single argument, which is the name of a JSON file. For example,

trainSoloModel trainingConfig.json

• interpretFlat
  • BNF
  • Parameter Notes
  • Output Specification
  • Additional Information
  • History
  • API
  • main()
  • Schema
• interpretPisa
  • BNF
  • Parameter Notes
  • Output Specification
  • HISTORY
  • API
  • main()
  • Schema
• makePredictions
  • BNF
  • Parameter Notes
  • Output Specification
  • API
  • getReader()
  • getWriter()
  • main()
  • Schema
• motifScan
  • Configuration Json
  • Quantile json
  • Output Specification
  • API
  • main()
  • Schema
• motifSeqletCutoffs
  • BNF
  • Parameter Notes
  • Output Specification
  • API
  • main()
  • Schema
• prepareBed
  • BNF
  • Parameter Notes
  • Additional information
  • History
  • API
  • loadRegionsByChrom()
  • loadRegionsByBed()
  • loadRegionsByRegex()
  • loadRegions()
  • removeOverlaps()
  • filterByMaxCounts()
  • filterByMinCounts()
  • validateRegions()
  • rewriteOldBigwigsFormat()
  • prepareBeds()
  • Schema
• prepareTrainingData
  • BNF
  • Parameter Notes
  • Output specification
  • Additional information
  • History
  • API
  • revcompSeq()
  • getSequences()
  • getHead()
  • writeH5()
  • Schema
• trainCombinedModel
  • BNF
  • Parameter Notes
  • HISTORY
  • API
  • main()
  • Schema
• trainSoloModel
  • BNF
  • Parameter Notes
  • Additional information
  • API
  • main()
  • Schema
• trainTransformationModel
  • BNF
  • Parameter Notes
  • History
  • API
  • main()
  • Schema