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mageckTest Specifications

Process Details

  • Name: mageckTest
  • Process UUID: NDH9cXxQXKQApiVicPGBZhpdGgwyvs
  • Process Group: Crispr

Overview

This process performs statistical analysis of CRISPR screen data using MAGeCK (Model-based Analysis of Genome-wide CRISPR/Cas9 Knockout). It compares treatment and control conditions to identify genes whose knockout significantly affects cell fitness, generating comprehensive reports with statistical significance testing.

This process is implemented in Bash, which invokes MAGeCK for statistical analysis and R scripts for report generation using tidyr, ggplot2, and rmarkdown packages.

Key Functionality

  • Statistical Testing: Performs robust ranking aggregation and statistical testing to identify significantly enriched or depleted genes between treatment and control conditions
  • PDF Report Generation: Creates comprehensive PDF reports with visualizations and statistical summaries of the CRISPR screen results
  • HTML Report Creation: Generates interactive HTML reports using R markdown for detailed analysis review and sharing

Input/Output Specification

Inputs

Required Inputs

  • Count File

    • Description: MAGeCK count table containing sgRNA read counts across samples
    • Format: txt

  • Sample Labels

    • Description: Comma-separated treatment and control sample labels for comparison
    • Format: text

  • Test Prefix

    • Description: Prefix name for output files and analysis identification
    • Format: text

Outputs

  • HTML Report

    • Description: Interactive HTML report with detailed statistical analysis and visualizations
    • Format: html

  • Results Table

    • Description: Statistical test results including gene rankings, p-values, and significance scores
    • Format: txt

  • PDF Report

    • Description: Comprehensive PDF report with plots and statistical summaries of the CRISPR screen analysis
    • Format: pdf

References & Resources

  • Tool Documentation: Contact the team for details on MAGeCK statistical analysis implementation
  • Related Papers: Li, W., et al. (2014). MAGeCK enables robust identification of essential genes from genome-scale CRISPR/Cas9 knockout screens. Genome Biology, 15(12), 554. https://doi.org/10.1186/s13059-014-0554-4