gscreend
This package is for version 3.10 of Bioconductor; for the stable, up-to-date release version, see gscreend.
Analysis of pooled genetic screens
Bioconductor version: 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("gscreend")):
Installation
To install this package, start R (version "3.6") 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 | ||
| NEWS | Text |
Details
| biocViews | CRISPR, PooledScreens, Software, StatisticalMethod |
| Version | 1.0.0 |
| 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 |
See More
| Suggests | knitr, testthat |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | 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 |
| Bioc Package Browser | https://code.bioconductor.org/browse/gscreend/ |
| Package Short Url | https://bioconductor.org/packages/gscreend/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.10 | Source Archive |