MAGeCKFlute

DOI: 10.18129/B9.bioc.MAGeCKFlute    

This package is for version 3.8 of Bioconductor; for the stable, up-to-date release version, see MAGeCKFlute.

Integrative analysis pipeline for pooled CRISPR functional genetic screens

Bioconductor version: 3.8

MAGeCKFlute is designed to surporting downstream analysis, utilizing the gene summary data provided through MAGeCK or MAGeCK-VISPR. Quality control, normalization, and screen hit identification for CRISPR screen data are performed in pipeline. Identified hits within the pipeline are categorized based on experimental design, and are subsequently interpreted by functional enrichment analysis.

Author: Wubing Zhang, Feizhen Wu, Binbin Wang

Maintainer: Wubing Zhang<Watson5bZhang at gmail.com>

Installation

To install this package, start R (version "3.5") 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
PDF		Reference Manual
Text		NEWS

Details

biocViews	BatchEffect, CRISPR, FunctionalGenomics, GeneSetEnrichment, ImmunoOncology, Normalization, Pathways, QualityControl, Software, Visualization
Version	1.2.3
In Bioconductor since	BioC 3.7 (R-3.5) (1 year)
License	GPL (>=3)
Depends	R (>= 3.5), ggplot2, stats, grDevices, utils, pathview, gridExtra
Imports	ggExtra, ggsci, ggrepel, clusterProfiler, png, data.table, pheatmap, sva, DOSE, biomaRt, grid, bladderbatch
LinkingTo
Suggests	knitr, rmarkdown, BiocStyle, org.Mm.eg.db
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_1.2.3.tar.gz
Windows Binary	MAGeCKFlute_1.2.3.zip
Mac OS X 10.11 (El Capitan)	MAGeCKFlute_1.2.3.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	http://bioconductor.org/packages/MAGeCKFlute/
Package Downloads Report	Download Stats