gscreend

DOI: 10.18129/B9.bioc.gscreend    

Analysis of pooled genetic screens

Bioconductor version: Release (3.10)

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 "3.6") and enter:

if (!requireNamespace("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")

 

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Details

biocViews CRISPR, PooledScreens, Software, StatisticalMethod
Version 1.0.0
In Bioconductor since BioC 3.10 (R-3.6) (< 6 months)
License GPL-3
Depends R (>= 3.6)
Imports SummarizedExperiment, nloptr, fGarch, methods, BiocParallel, graphics
LinkingTo
Suggests knitr, testthat
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_1.0.0.tar.gz
Windows Binary gscreend_1.0.0.zip
Mac OS X 10.11 (El Capitan) gscreend_1.0.0.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/
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