Welcome to ScreenPro2’s documentation!

User Guide

• ScreenPro2
  • Introduction
  • Installation
  • Usage
  • Analysis Workflow
  • Supported CRISPR Screen Platforms
  • License
  • Citation
• Tutorials

Module Documentation

• CRISPR Screen Assays
  • GImaps
  • PooledScreens
    • PooledScreens.buildPhenotypeData()
    • PooledScreens.calculateDrugScreen()
    • PooledScreens.calculateDrugScreenDESeq()
    • PooledScreens.calculateFlowBasedScreen()
    • PooledScreens.copy()
    • PooledScreens.countNormalization()
    • PooledScreens.drawVolcano()
    • PooledScreens.filterLowCounts()
    • PooledScreens.getPhenotypeScores()
    • PooledScreens.listPhenotypeScores()
• NGS screen processing module
  • GuideCounter
    • GuideCounter.build_counts_anndata()
    • GuideCounter.get_counts_matrix()
    • GuideCounter.load_counts_matrix()
    • GuideCounter.load_library()
  • Cas9 CRISPR-Cas system (single or dual sgRNA libraries)
    • fastq_to_count_dual_guide()
    • fastq_to_count_single_guide()
    • map_to_library_dual_guide()
    • map_to_library_single_guide()
  • Cas12 CRISPR-Cas system (multiplexed crRNA libraries)
• Phenotype calculation modules
  • Phenotype score calculation
  • Phenotype statistics calculation
  • Combined score calculation
    • runPhenoScore()
  • Other related modules and functions
    • matrixStat()
    • multipleTestsCorrection()
    • calculateDelta()
    • compareByReplicates()
    • compareByTargetGroup()
    • generatePseudoGeneAnnData()
    • getBestTargetByTSS()
    • getPhenotypeData()
• Visualization modules
  • plotCountDistribution()
  • plotReplicateScatter()
  • label_as_black()
  • label_by_color()
  • label_resistance_hit()
  • label_sensitivity_hit()
  • volcano_plot()
  • DataDashboard
  • DrugScreenDashboard
    • DrugScreenDashboard.GammaVolcanoPlot()
    • DrugScreenDashboard.RhoGammaScatter()
    • DrugScreenDashboard.RhoVolcanoPlot()
• Data loading module
  • loadScreenProcessingData()
  • load_cas9_sgRNA_library()

Extended Notes

• History
  • 1.0.0
  • 0.4.0 - after (June 2024 - July 2024)
  • 0.2.11 - 0.3.5 (Apr 2024 - June 2024)
  • 0.2.7 - 0.2.10 (Mar 2024 - Apr 2024)
  • 0.2.5 – 0.2.6 (Dec 2023 - Feb 2024)
  • 0.2.1 - 0.2.4 (July 2023 - Nov 2023)
  • 0.2.0 (May 2022)
• References

Indices and tables

• Index

• Module Index

• Search Page