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gCrisprTools

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

Suite of Functions for Pooled Crispr Screen QC and Analysis


Bioconductor version: Development (3.19)

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. Version 2.0 extends these applications to include a variety of tools for contextualizing and integrating signals across many experiments, incorporates extended signal enrichment methodologies via the "sparrow" package, and streamlines many formal requirements to aid in interpretablity.

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

Maintainer: Russell Bainer <russ.bainer at gmail.com>

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

Installation

To install this package, start R (version "4.4") and enter:


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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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")
Contrast_Comparisons_gCrisprTools HTML R Script
Example_Workflow_gCrisprTools HTML R Script
gCrisprTools_Vignette HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews BiomedicalInformatics, CRISPR, CellBiology, DifferentialExpression, ExperimentalDesign, FunctionalGenomics, GeneSetEnrichment, Genetics, ImmunoOncology, MultipleComparison, Normalization, Pharmacogenetics, Pharmacogenomics, PooledScreens, Preprocessing, QualityControl, RNASeq, Regression, Software, SystemsBiology, Visualization
Version 2.9.0
In Bioconductor since BioC 3.4 (R-3.3) (7.5 years)
License Artistic-2.0
Depends R (>= 4.1)
Imports Biobase, limma, RobustRankAggreg, ggplot2, SummarizedExperiment, grid, rmarkdown, grDevices, graphics, methods, ComplexHeatmap, stats, utils, parallel
System Requirements
URL
See More
Suggests edgeR, knitr, AnnotationDbi, org.Mm.eg.db, org.Hs.eg.db, BiocGenerics, markdown, RUnit, sparrow, msigdbr, fgsea
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Package Archives

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

Source Package gCrisprTools_2.9.0.tar.gz
Windows Binary gCrisprTools_2.9.0.zip
macOS Binary (x86_64) gCrisprTools_2.9.0.tgz
macOS Binary (arm64)
Source Repository git clone https://git.bioconductor.org/packages/gCrisprTools
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/gCrisprTools
Bioc Package Browser https://code.bioconductor.org/browse/gCrisprTools/
Package Short Url https://bioconductor.org/packages/gCrisprTools/
Package Downloads Report Download Stats