gCrisprTools
This package is for version 3.17 of Bioconductor; for the stable, up-to-date release version, see gCrisprTools.
Suite of Functions for Pooled Crispr Screen QC and Analysis
Bioconductor version: 3.17
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("gCrisprTools")):
Installation
To install this package, start R (version "4.3") and enter:
if (!require("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")| Contrast_Comparisons_gCrisprTools | HTML | R Script |
| Example_Workflow_gCrisprTools | HTML | R Script |
| gCrisprTools_Vignette | HTML | R Script |
| Reference Manual | ||
| 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 | 2.6.0 |
| 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 |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | gCrisprTools_2.6.0.tar.gz |
| Windows Binary | gCrisprTools_2.6.0.zip |
| macOS Binary (x86_64) | gCrisprTools_2.6.0.tgz |
| macOS Binary (arm64) | gCrisprTools_2.6.0.tgz |
| 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 |
| Old Source Packages for BioC 3.17 | Source Archive |