gscreend

DOI: 10.18129/B9.bioc.gscreend  

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

Analysis of pooled genetic screens

Bioconductor version: Development (3.18)

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>

Installation

To install this package, start R (version "4.3") 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

PDF		Reference Manual

Details

biocViews	CRISPR, PooledScreens, Software, StatisticalMethod
Version	1.15.0
In Bioconductor since	BioC 3.10 (R-3.6) (3.5 years)
License	GPL-3
Depends	R (>= 3.6)
Imports	SummarizedExperiment, nloptr, fGarch, methods, BiocParallel, graphics
LinkingTo
Suggests	knitr, testthat, rmarkdown
SystemRequirements
Enhances
URL	https://github.com/imkeller/gscreend
BugReports	https://github.com/imkeller/gscreend/issues
Depends On Me
Imports Me
Suggests Me
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Build Report

Package Archives

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

Source Package
Windows Binary	gscreend_1.15.0.zip
macOS Binary (x86_64)	gscreend_1.15.0.tgz
macOS Binary (arm64)
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