gCrisprTools

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

All versions

3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13, 3.12, 3.11, 3.10, 3.9, 3.8, 3.7, 3.6, 3.5, 3.4

Suite of Functions for Pooled Crispr Screen QC and Analysis

Bioconductor version: Development (3.24)

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")):

Russell Bainer, Dariusz Ratman, Steve Lianoglou, Peter Haverty. gCrisprTools: Suite of Functions for Pooled Crispr Screen QC and Analysis. doi:10.18129/B9.bioc.gCrisprTools, R package version 2.19.0, https://bioconductor.org/packages/gCrisprTools.

Generated from the package metadata; it may differ from the package's own citation.

Installation

To install this package, start R (version "4.6") and enter:

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

## The following initializes the development version of Bioconductor
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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	BiomedicalInformatics, CRISPR, CellBiology, DifferentialExpression, ExperimentalDesign, FunctionalGenomics, GeneSetEnrichment, Genetics, ImmunoOncology, MultipleComparison, Normalization, Pharmacogenetics, Pharmacogenomics, PooledScreens, Preprocessing, QualityControl, RNASeq, Regression, Software, SystemsBiology, Visualization
Version	2.19.0
In Bioconductor since	BioC 3.4 (R-3.3) (10 years)
License	Artistic-2.0
Depends	R (>= 4.1)
Imports	Biobase, limma, ggplot2, SummarizedExperiment, grid, rmarkdown, grDevices, graphics, methods, ComplexHeatmap, stats, utils, parallel, MatrixGenerics, methods
System Requirements
URL

Suggests	edgeR, knitr, AnnotationDbi, org.Mm.eg.db, org.Hs.eg.db, BiocGenerics, markdown, RUnit, sparrow, msigdbr, fgsea
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report	Build Report, r-universe

Package Archives

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

Source Package	gCrisprTools_2.19.0.tar.gz
Windows Binary (x86_64)	gCrisprTools_2.19.0.zip (64-bit only)
macOS Binary (big-sur-x86_64)	gCrisprTools_2.19.0.tgz
macOS Binary (sonoma-arm64)	gCrisprTools_2.19.0.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