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)
  • Feeding custom prior into bean run

Model description

• BEAN model description
  • Variant and guide-level phenotypes
  • Learning editing rate from reporter
  • Sorting screen model (bean run ... sorting)
  • Inference
  • Adjusting editing rates by accessibility with --scale-by-acc
  • Over-dispersed multinomial count data modeling

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
  • bean build-prior
    • Build custom prior for batch integration
    • Full parameters

Screen data structure

• CRISPR Reporter Screen analysis with BEAN
  • Data Structure
  • Changing column names
  • Subsetting & addition
    • Subsetting & selection
  • Getting edit rates from allele counts

Indices and tables

• Index

• Module Index

• Search Page