MAGeCKFlute
This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see MAGeCKFlute.
Integrative analysis pipeline for pooled CRISPR functional genetic screens
Bioconductor version: 3.9
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("MAGeCKFlute")):
Installation
To install this package, start R (version "3.6") 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")| MAGeCKFlute.Rmd | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | BatchEffect, CRISPR, FunctionalGenomics, GeneSetEnrichment, ImmunoOncology, Normalization, Pathways, QualityControl, Software, Visualization |
| Version | 1.4.3 |
| In Bioconductor since | BioC 3.7 (R-3.5) (6 years) |
| License | GPL (>=3) |
| Depends | R (>= 3.5), ggplot2, stats, grDevices, utils, gridExtra |
| Imports | ggExtra, ggsci, ggrepel, clusterProfiler, png, data.table, pheatmap, sva, DOSE, biomaRt, grid, pathview |
| System Requirements | |
| URL |
See More
| Suggests | knitr, rmarkdown, BiocStyle, org.Mm.eg.db |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | MAGeCKFlute_1.4.3.tar.gz |
| Windows Binary | MAGeCKFlute_1.4.3.zip |
| Mac OS X 10.11 (El Capitan) | MAGeCKFlute_1.4.3.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/MAGeCKFlute |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/MAGeCKFlute |
| Bioc Package Browser | https://code.bioconductor.org/browse/MAGeCKFlute/ |
| Package Short Url | https://bioconductor.org/packages/MAGeCKFlute/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.9 | Source Archive |