MAGeCKFlute

DOI: 10.18129/B9.bioc.MAGeCKFlute    

Integrative analysis pipeline for pooled CRISPR functional genetic screens

Bioconductor version: Release (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 (version "3.5") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("MAGeCKFlute", version = "3.8")

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 1.2.2
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_1.2.2.tar.gz
Windows Binary MAGeCKFlute_1.2.2.zip
Mac OS X 10.11 (El Capitan) MAGeCKFlute_1.2.2.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
Old Source Packages for BioC 3.8 Source Archive

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