CaRpools

CaRpools provides comprehensive analysis and workflow management as an R package for pooled CRISPR/Cas9 next-generation sequencing (NGS) screens, enabling exploratory data analysis, normalization, statistical analysis, visualization, and standardized reporting.

Key Features:

• Complete Workflow Integration: Integrates end-to-end processing of pooled CRISPR/Cas9 screen data from input handling to result interpretation for NGS-derived datasets.
• Exploratory Data Analysis Tools: Supplies functions for investigating guide- and gene-level patterns and distributions within pooled screening data.
• Screening Documentation Support: Provides facilities to capture and record experimental screening metadata and parameters for reproducibility of pooled screens.
• Standardized Analysis Reports: Generates consistent reports summarizing normalization, statistical outcomes, and visualization results for CRISPR/Cas9 screens.

Scientific Applications:

• Gene function discovery: Analysis of pooled CRISPR/Cas9 screens to identify genes affecting phenotypes observed in NGS readouts.
• Genetic interaction identification: Detection of interactions between perturbations in pooled screens using statistical analysis of guide-level data.
• Cellular pathway exploration: Prioritization of pathway components and modules by aggregating guide- and gene-level screen results.

Methodology:

Processing of pooled CRISPR/Cas9 NGS data including normalization, statistical analysis, and visualization.