gCrisprTools

DOI: 10.18129/B9.bioc.gCrisprTools    

Suite of Functions for Pooled Crispr Screen QC and Analysis

Bioconductor version: Release (3.14)

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 "4.1") 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 Contrast_Comparisons_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 2.0.0
In Bioconductor since BioC 3.4 (R-3.3) (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
LinkingTo
Suggests edgeR, knitr, AnnotationDbi, org.Mm.eg.db, org.Hs.eg.db, BiocGenerics, markdown, RUnit, sparrow, msigdbr, fgsea
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_2.0.0.tar.gz
Windows Binary gCrisprTools_2.0.0.zip
macOS 10.13 (High Sierra) gCrisprTools_2.0.0.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
Old Source Packages for BioC 3.14 Source Archive

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