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crispr-screens-base-editing-analysis - Analyze base-editing screens for variant function

Analyzes base-editing screens, sgRNA designs, editing efficiency, bystander edits, indels, variant fitness, and ClinVar or COSMIC annotations.

Tags

Updated: 2026-10-16
CRISPR screeningbase editingvariant functionsgRNA designamplicon sequencingCRISPResso2variant annotation

Capabilities

Analyze base-editing screensDesign variant-scanning sgRNAsSelect editor chemistryCalculate editing windows

Typical Inputs

Amplicon sequencing datasgRNA libraryCDS sequence

Typical Outputs

Per-sgRNA editing quantificationBystander-edit measurementsIndel measurements

What this skill does

  • Analyze base-editing screens
  • Design variant-scanning sgRNAs
  • Select editor chemistry
  • Calculate editing windows
  • Quantify bystander edits
  • Filter sgRNA efficiency
  • Interpret indel byproducts
  • Score variant fitness
  • Annotate variants

Inputs

  • Amplicon sequencing data
  • sgRNA library
  • CDS sequence
  • Target amino-acid position
  • Target nucleotide base
  • Screen log-fold changes
  • Variant annotations

Outputs

  • Per-sgRNA editing quantification
  • Bystander-edit measurements
  • Indel measurements
  • Filtered sgRNA set
  • Predicted amino-acid changes
  • Variant fitness scores
  • Target-bystander attribution
  • ClinVar or COSMIC annotations

Requirements

  • CRISPResso2 2.2.14 or later
  • BE-Hive 1.0 or later
  • pandas 2.2 or later
  • Biopython 1.83 or later
  • NumPy 1.26 or later
  • SciPy 1.12 or later
  • scikit-learn 1.4 or later
  • Broad be-validation-pipeline 1.0 or later
  • Python environment

Source

  • Spec: SKILL.md

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