CoRe

CoRe identifies core fitness genes from genome-wide pooled CRISPR-Cas9 knock-out screens to determine genes invariantly required for cellular viability and to support cancer dependency and therapeutic target safety analyses.

Key Features:

• Implementation: R package that analyzes genome-wide pooled CRISPR-Cas9 knock-out screen data.
• Core-fitness identification: Detects genes invariantly crucial for cellular viability across tissues, conditions, and genomic contexts.
• Joint analysis across screens: Implements novel methods to perform joint analyses across multiple CRISPR-Cas9 screens to increase reliability of core-fitness calls.
• Scale and accuracy: Designed for genome-wide pooled screens enabling large-scale, high-accuracy detection of cancer dependencies.
• Benchmarking and evaluation: Benchmarked against state-of-the-art tools and widely used reference gene sets, reporting improved reliability of identified core-fitness genes.

Scientific Applications:

• Cancer dependency mapping: Systematic exploration of cancer cell dependencies and essential genes required for cell survival across contexts.
• Therapeutic target validation: Informing safety profiling and prioritization of potential therapeutic targets by identifying universally essential genes.
• Genetic disease research: Investigating mechanisms underlying tissue-specific genetic diseases by identifying invariant essential genes.

Methodology:

Implements novel joint-analysis methods for integrating multiple genome-wide pooled CRISPR-Cas9 knock-out screens and includes benchmarking against state-of-the-art tools and reference gene sets.