MAGeCKFlute

DOI: 10.18129/B9.bioc.MAGeCKFlute    

Integrative Analysis Pipeline for Pooled CRISPR Functional Genetic Screens

Bioconductor version: Release (3.15)

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.

Author: Binbin Wang, Wubing Zhang, Feizhen Wu, Wei Li & X. Shirley Liu

Maintainer: Wubing Zhang <Watson5bZhang at gmail.com>

Installation

To install this package, start R (version "4.2") and enter:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("MAGeCKFlute")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("MAGeCKFlute")

 

HTML	R Script	MAGeCKFlute.Rmd
HTML	R Script	MAGeCKFlute_enrichment.Rmd
PDF		Reference Manual
Text		NEWS

Details

biocViews	CRISPR, FunctionalGenomics, GeneSetEnrichment, GeneTarget, KEGG, Normalization, Pathways, PooledScreens, QualityControl, Software, Visualization
Version	2.0.0
In Bioconductor since	BioC 3.7 (R-3.5) (4.5 years)
License	GPL (>=3)
Depends	R (>= 4.1)
Imports	Biobase, gridExtra, ggplot2, ggrepel, grDevices, grid, reshape2, stats, utils, DOSE, clusterProfiler, pathview, enrichplot, msigdbr, depmap
LinkingTo
Suggests	biomaRt, BiocStyle, dendextend, graphics, knitr, pheatmap, png, scales, sva, BiocManager
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	MAGeCKFlute_2.0.0.tar.gz
Windows Binary	MAGeCKFlute_2.0.0.zip (64-bit only)
macOS Binary (x86_64)	MAGeCKFlute_2.0.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/MAGeCKFlute
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/MAGeCKFlute
Package Short Url	https://bioconductor.org/packages/MAGeCKFlute/
Package Downloads Report	Download Stats