PitViper: a software for comparative meta-analysis and annotation of functional screening data.

Area of Science:

• Genomics
• Bioinformatics
• Molecular Biology

Background:

• Advancements in shRNA and CRISPR technologies enable functional genomics screening.
• CRISPR-based systems like CRISPRi and CRISPRa modulate gene expression and DNA accessibility.
• A need exists for integrated software to analyze diverse functional screening outputs.

Purpose of the Study:

• To develop PitViper, a flexible, interactive, open-source software for functional genomics screening data integration.
• To provide a cohesive framework for comprehensive analysis of screening data.
• To offer reliable results for various screened elements.

Main Methods:

• Developed PitViper, an end-to-end automated and reproducible bioinformatics pipeline.
• Integrated gold-standard methods for functional screening analysis.
• Performed sensitivity analyses using genome-wide CRISPRi screening data.

Main Results:

• PitViper successfully integrates diverse functional genomics screening outputs.
• Demonstrated PitViper's utility in identifying super-enhancer liabilities in a leukemia cell line via CRISPRi screening.
• Showcased the software's flexibility and interactivity for data analysis and reanalysis.

Conclusions:

• PitViper addresses the gap in integrated analysis tools for functional genomics screening.
• It provides a robust solution for researchers analyzing CRISPRi and other screening data.
• PitViper is a valuable resource for advancing functional genomics research.