Subcommands

• bean count
  • bean count[-samples]: Count (reporter) screen data
  • Input file format
  • Output file format
  • Full parameters
• bean count-samples
  • bean count[-samples]: Count (reporter) screen data
  • Input file format
  • Output file format
  • Full parameters
• bean profile
  • bean profile: Profile editing patterns
  • Output
  • Full parameters
• bean qc
  • bean qc: QC of reporter screen data
  • Output
  • Full parameters
• bean filter
  • filter: Filtering (and optionally translating) alleles
  • Output
  • Translating alleles
  • Full parameters
• bean get-splice-sites
  • Getting splice sites
  • Parameters
• bean run
  • bean run: Quantify variant effects
  • Usage example
  • Input
  • Output
  • Full parameters
• bean create-screen
  • bean create-screen: Create ReporterScreen object from flat files
  • Full parameters
• bean build-prior
  • Build custom prior for batch integration
  • Full parameters