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gscreend

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

Analysis of pooled genetic screens


Bioconductor version: Development (3.19)

Package for the analysis of pooled genetic screens (e.g. CRISPR-KO). The analysis of such screens is based on the comparison of gRNA abundances before and after a cell proliferation phase. The gscreend packages takes gRNA counts as input and allows detection of genes whose knockout decreases or increases cell proliferation.

Author: Katharina Imkeller [cre, aut], Wolfgang Huber [aut]

Maintainer: Katharina Imkeller <k.imkeller at dkfz.de>

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

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("gscreend")

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("gscreend")
Example_simulated HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews CRISPR, PooledScreens, Software, StatisticalMethod
Version 1.17.3
In Bioconductor since BioC 3.10 (R-3.6) (4.5 years)
License GPL-3
Depends R (>= 3.6)
Imports SummarizedExperiment, nloptr, fGarch, methods, BiocParallel, graphics
System Requirements
URL https://github.com/imkeller/gscreend
Bug Reports https://github.com/imkeller/gscreend/issues
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Suggests knitr, testthat, rmarkdown, BiocStyle
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Package Archives

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

Source Package gscreend_1.17.3.tar.gz
Windows Binary gscreend_1.17.3.zip
macOS Binary (x86_64) gscreend_1.17.3.tgz
macOS Binary (arm64) gscreend_1.17.3.tgz
Source Repository git clone https://git.bioconductor.org/packages/gscreend
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/gscreend
Bioc Package Browser https://code.bioconductor.org/browse/gscreend/
Package Short Url https://bioconductor.org/packages/gscreend/
Package Downloads Report Download Stats