MAGeCKFlute

DOI: 10.18129/B9.bioc.MAGeCKFlute    

This is the development version of MAGeCKFlute; for the stable release version, see MAGeCKFlute.

Integrative analysis pipeline for pooled CRISPR functional genetic screens

Bioconductor version: Development (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>

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

Installation

To install this package, start R and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("MAGeCKFlute", version = "devel")

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 CRISPR, FunctionalGenomics, GeneSetEnrichment, MultipleComparison, Normalization, Pathways, PooledScreens, QualityControl, Software, Visualization, Workflow
Version 1.1.8
License GPL (>=3)
Depends R (>= 3.5), ggplot2, stats, grDevices, utils, pathview, gridExtra
Imports ggExtra, ggsci, ggrepel, clusterProfiler, png, data.table, pheatmap, RColorBrewer, sva, GOstats, Category, DOSE, biomaRt, grid
LinkingTo
Suggests knitr, rmarkdown, BiocStyle, org.Mm.eg.db, testthat
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
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Build Report  

Package Archives

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

Source Package MAGeCKFlute_1.1.8.tar.gz
Windows Binary MAGeCKFlute_1.1.8.zip
Mac OS X 10.11 (El Capitan) MAGeCKFlute_1.1.8.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/
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