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type: software
title: 'MAGeCKFlute: Integrative Analysis Pipeline for Pooled CRISPR Functional Genetic
  Screens'
version: 2.9.0
doi: 10.32614/CRAN.package.MAGeCKFlute
abstract: CRISPR (clustered regularly interspaced short palindrome repeats) coupled
  with nuclease Cas9 (CRISPR/Cas9) screens represent a promising technology to systematically
  evaluate gene functions. Data analysis for CRISPR/Cas9 screens is a critical process
  that includes identifying screen hits and exploring biological functions for these
  hits in downstream analysis. We have previously developed two algorithms, MAGeCK
  and MAGeCK-VISPR, to analyze CRISPR/Cas9 screen data in various scenarios. These
  two algorithms allow users to perform quality control, read count generation and
  normalization, and calculate beta score to evaluate gene selection performance.
  In downstream analysis, the biological functional analysis is required for understanding
  biological functions of these identified genes with different screening purposes.
  Here, We developed MAGeCKFlute for supporting downstream analysis. MAGeCKFlute provides
  several strategies to remove potential biases within sgRNA-level read counts and
  gene-level beta scores. The downstream analysis with the package includes identifying
  essential, non-essential, and target-associated genes, and performing biological
  functional category analysis, pathway enrichment analysis and protein complex enrichment
  analysis of these genes. The package also visualizes genes in multiple ways to benefit
  users exploring screening data. Collectively, MAGeCKFlute enables accurate identification
  of essential, non-essential, and targeted genes, as well as their related biological
  functions. This vignette explains the use of the package and demonstrates typical
  workflows.
authors:
- family-names: Zhang
  given-names: Wubing
  email: Watson5bZhang@gmail.com
- family-names: Wang
  given-names: Binbin
- family-names: Wu
  given-names: Feizhen
- family-names: Liu
  given-names: Wei Li & X. Shirley
repository: https://bioc.r-universe.dev
commit: 056f3705c90bbcdcc8ddbe4f40f3d5842f2152d2
contact:
- family-names: Zhang
  given-names: Wubing
  email: Watson5bZhang@gmail.com