MAGeCKFlute

DOI: 10.18129/B9.bioc.MAGeCKFlute    

Integrative analysis pipeline for pooled CRISPR functional genetic screens

Bioconductor version: Release (3.10)

MAGeCKFlute is designed for analyzing CRISPR screenings. It takes gene summary file returned by MAGeCK, as input, and surports quality control, normalization, and screen hit identification in the CRISPR screen. Furthermore, for identified hits, customized functional enrichment analysis will be done on biological pathways, protein complex and other molecular customized signatures.

Author: Wubing Zhang, Feizhen Wu, Binbin Wang

Maintainer: Wubing Zhang<Watson5bZhang at gmail.com>

Citation (from within R, enter citation("MAGeCKFlute")):

Installation

To install this package, start R (version "3.6") and enter:

if (!requireNamespace("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 BatchEffect, CRISPR, FunctionalGenomics, GeneSetEnrichment, GeneTarget, KEGG, Normalization, Pathways, PooledScreens, QualityControl, Software, Visualization
Version 1.6.3
In Bioconductor since BioC 3.7 (R-3.5) (2 years)
License GPL (>=3)
Depends R (>= 3.5)
Imports clusterProfiler, DOSE, enrichplot, gridExtra, pathview, biomaRt, sva, ggsci, ggplot2, ggrepel, ggpubr, data.table, pheatmap, png, grDevices, grid, stats, utils, dendextend, scales, Biobase, GO.db
LinkingTo
Suggests knitr, testthat
SystemRequirements
Enhances
URL
Depends On Me
Imports Me SpidermiR
Suggests Me
Links To Me
Build Report  

Package Archives

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

Source Package MAGeCKFlute_1.6.3.tar.gz
Windows Binary MAGeCKFlute_1.6.3.zip
Mac OS X 10.11 (El Capitan) MAGeCKFlute_1.6.3.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
Old Source Packages for BioC 3.10 Source Archive

Documentation »

Bioconductor

R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations: