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SCREE: a comprehensive pipeline for single-cell multi-modal CRISPR screen data processing and analysis.

Hailin Wei1,2, Tong Han1,2, Taiwen Li3,4

  • 1Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of Ministry of Education, Department of Orthopedics, Tongji Hospital, School of Life Science and Technology, Tongji University, 200092, China.

Briefings in Bioinformatics
|March 31, 2023
PubMed
Summary
This summary is machine-generated.

SCREE is a new bioinformatics pipeline for analyzing single-cell CRISPR screens. It supports RNA, ATAC, and multimodal data, offering comprehensive analysis from alignment to functional insights.

Keywords:
analyses pipelinegene regulatory circuitsperturbation efficiencysingle-cell CRISPR screens

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Area of Science:

  • * Genomics and Systems Biology
  • * Bioinformatics and Computational Biology

Background:

  • * Single-cell CRISPR screens are crucial for dissecting gene regulatory networks.
  • * Advances allow multimodal profiling (gene expression, chromatin accessibility, protein levels).
  • * Existing analysis tools lack comprehensive functionality for diverse single-cell CRISPR screen data.

Purpose of the Study:

  • * To introduce Single-cell CRISPR screens data analysEs and perturbation modEling (SCREE), a versatile pipeline.
  • * To address the limitations of current methods in analyzing complex single-cell CRISPR screen data.
  • * To provide a unified platform for various data types and analytical needs.

Main Methods:

  • * Developed SCREE, a comprehensive bioinformatics pipeline.
  • * Integrated modules for read alignment, sgRNA assignment, and quality control.
  • * Incorporated clustering, visualization, and perturbation analysis functionalities.
  • * Enabled modeling of perturbation efficiency and gene regulatory scores.
  • * Supported RNA, ATAC, and multimodal single-cell CRISPR screen data.

Main Results:

  • * SCREE facilitates robust analysis of diverse single-cell CRISPR screen data types.
  • * The pipeline offers end-to-end analysis, from raw reads to functional interpretation.
  • * SCREE supports multimodal data integration for deeper biological insights.
  • * Demonstrated utility in evaluating perturbation enrichment and modeling efficiency.

Conclusions:

  • * SCREE provides a flexible and comprehensive solution for single-cell CRISPR screen data analysis.
  • * The pipeline enhances the investigation of gene regulatory circuits using multimodal single-cell data.
  • * SCREE empowers researchers with advanced tools for perturbation modeling and functional genomics.