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Suite of Functions for Pooled Crispr Screen QC and Analysis

Bioconductor version: Release (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>

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


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

if (!require("BiocManager", quietly = TRUE))


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:

Contrast_Comparisons_gCrisprTools HTML R Script
Example_Workflow_gCrisprTools HTML R Script
gCrisprTools_Vignette HTML R Script
Reference Manual PDF


biocViews BiomedicalInformatics, CRISPR, CellBiology, DifferentialExpression, ExperimentalDesign, FunctionalGenomics, GeneSetEnrichment, Genetics, ImmunoOncology, MultipleComparison, Normalization, Pharmacogenetics, Pharmacogenomics, PooledScreens, Preprocessing, QualityControl, RNASeq, Regression, Software, SystemsBiology, Visualization
Version 2.10.0
In Bioconductor since BioC 3.4 (R-3.3) (8 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
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Suggests edgeR, knitr, AnnotationDbi,,, BiocGenerics, markdown, RUnit, sparrow, msigdbr, fgsea
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Follow Installation instructions to use this package in your R session.

Source Package gCrisprTools_2.10.0.tar.gz
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macOS Binary (x86_64) gCrisprTools_2.10.0.tgz
macOS Binary (arm64) gCrisprTools_2.10.0.tgz
Source Repository git clone
Source Repository (Developer Access) git clone
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