CASPR

CASPR analyzes single- and paired-guide RNA pooled CRISPRi and CRISPR-del screens to identify functional long non-coding RNAs (lncRNAs) that mediate cellular phenotypes.

Key Features:

• Versatility across modalities: Supports single-guide RNA (sgRNA) and paired-guide RNA designs for both CRISPRi and CRISPR-del pooled screens.
• End-to-end analysis: Performs processing from raw screen data through hit identification in a single computational pipeline.
• Consensus predictions: Integrates multiple algorithms to balance sensitivity and specificity in hit calling.
• Benchmarking performance: Evaluated against ground-truth sets of cancer-associated lncRNAs and demonstrates superior sensitivity for identifying functional lncRNAs.
• Parameter identification: Identifies predictive parameters for lncRNA hits, specifically expression levels and annotation quality of transcription start sites.

Scientific Applications:

• lncRNA functional discovery: Facilitates identification of lncRNAs with functional roles in cellular processes from pooled CRISPR screens.
• Cancer lncRNA characterization: Applied to discovery and validation of cancer-associated lncRNAs using benchmarked ground-truth sets.
• CRISPRi and CRISPR-del screen analysis: Enables analysis and comparison of CRISPRi and CRISPR-del modalities for interrogating annotated lncRNAs.

Methodology:

Generates consensus predictions by integrating multiple algorithms to improve accuracy in identifying true positive lncRNA hits.