gCrisprTools

DOI: 10.18129/B9.bioc.gCrisprTools    

This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see gCrisprTools.

Suite of Functions for Pooled Crispr Screen QC and Analysis

Bioconductor version: 3.9

Set of tools for evaluating pooled high-throughput screening experiments, typically employing CRISPR/Cas9 or shRNA expression cassettes. Contains methods for interrogating library and cassette behavior within an experiment, identifying differentially abundant cassettes, aggregating signals to identify candidate targets for empirical validation, hypothesis testing, and comprehensive reporting.

Author: Russell Bainer, Dariusz Ratman, Steve Lianoglou, Peter Haverty

Maintainer: Peter Haverty <haverty.peter at gene.com>

Installation

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

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("gCrisprTools")

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("gCrisprTools")

 

HTML	R Script	Example_Workflow_gCrisprTools
HTML	R Script	gCrisprTools_Vignette
PDF		Reference Manual
Text		NEWS

Details

biocViews	BiomedicalInformatics, CRISPR, CellBiology, DifferentialExpression, ExperimentalDesign, FunctionalGenomics, GeneSetEnrichment, Genetics, ImmunoOncology, MultipleComparison, Normalization, Pharmacogenetics, Pharmacogenomics, PooledScreens, Preprocessing, QualityControl, RNASeq, Regression, Software, SystemsBiology, Visualization
Version	1.12.0
In Bioconductor since	BioC 3.4 (R-3.3) (3 years)
License	Artistic-2.0
Depends	R (>= 3.3)
Imports	Biobase, limma, RobustRankAggreg, ggplot2, PANTHER.db, rmarkdown, grDevices, graphics, stats, utils, parallel
LinkingTo
Suggests	edgeR, knitr, grid, AnnotationDbi, org.Mm.eg.db, org.Hs.eg.db, RUnit, BiocGenerics
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	gCrisprTools_1.12.0.tar.gz
Windows Binary	gCrisprTools_1.12.0.zip
Mac OS X 10.11 (El Capitan)	gCrisprTools_1.12.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/gCrisprTools
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/gCrisprTools
Package Short Url	https://bioconductor.org/packages/gCrisprTools/
Package Downloads Report	Download Stats