gscreend

DOI: 10.18129/B9.bioc.gscreend    

Analysis of pooled genetic screens

Bioconductor version: Release (3.15)

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 "4.2") 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")

 

HTML	R Script	Example_simulated
PDF		Reference Manual
Text		NEWS

Details

biocViews	CRISPR, PooledScreens, Software, StatisticalMethod
Version	1.10.0
In Bioconductor since	BioC 3.10 (R-3.6) (3 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
Links To Me
Build Report

Package Archives

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

Source Package	gscreend_1.10.0.tar.gz
Windows Binary	gscreend_1.10.0.zip
macOS Binary (x86_64)	gscreend_1.10.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/gscreend
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/gscreend
Package Short Url	https://bioconductor.org/packages/gscreend/
Package Downloads Report	Download Stats