gscreend

This package is for version 3.20 of Bioconductor; for the stable, up-to-date release version, see gscreend.

Analysis of pooled genetic screens

Bioconductor version: 3.20

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")
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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews CRISPR, PooledScreens, Software, StatisticalMethod

Version 1.20.0

In Bioconductor since BioC 3.10 (R-3.6) (5.5 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

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_1.20.0.tar.gz

Windows Binary (x86_64) gscreend_1.20.0.zip (64-bit only)

macOS Binary (x86_64) gscreend_1.20.0.tgz

macOS Binary (arm64) gscreend_1.20.0.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/

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