Welcome to bean documentation!

bean improves CRISPR pooled screen analysis by 1) unconfounding variable per-guide editing outcome by considering genotypic outcome from reporter sequence and 2) through accurate modeling of screen procedure.

Workflows

• Workflow tutorials
  • Variant sorting screen tutorial
  • Tiling sorting screen tutorial
  • Variant survival screen tutorial
  • Tiling survival screen tutorial
  • Sorting screen tutorial without reporter edits
  • Visualize result (variant screens)

API references

• Input file format
  • sgRNA_info_table.csv
  • sample_list.csv
• 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

Screen data structure

• ReporterScreen
  • Data wrangling examples
    • ReporterScreen API tutorial
      • Subsetting & addition
        • Subsetting & selection
        • LFC calculation & Addition
      • Getting edit rates from allele counts
        • Calculating LFC
        • Allele translation
        • Writing

Indices and tables

• Index

• Module Index

• Search Page