gespeR

DOI: 10.18129/B9.bioc.gespeR    

This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see gespeR.

Gene-Specific Phenotype EstimatoR

Bioconductor version: 3.9

Estimates gene-specific phenotypes from off-target confounded RNAi screens. The phenotype of each siRNA is modeled based on on-targeted and off-targeted genes, using a regularized linear regression model.

Author: Fabian Schmich

Maintainer: Fabian Schmich <fabian.schmich at bsse.ethz.ch>

Installation

To install this package, start R (version "3.6") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("gespeR")

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("gespeR")

 

PDF	R Script	An R package for deconvoluting off-target confounded RNAi screens
PDF		Reference Manual

Details

biocViews	CellBasedAssays, GeneTarget, ImmunoOncology, Preprocessing, Regression, Software, Visualization
Version	1.16.0
In Bioconductor since	BioC 3.1 (R-3.2) (4.5 years)
License	GPL-3
Depends	methods, graphics, ggplot2, R (>= 2.10)
Imports	Matrix, glmnet, cellHTS2, Biobase, biomaRt, doParallel, parallel, foreach, reshape2, dplyr
LinkingTo
Suggests	knitr
SystemRequirements
Enhances
URL	http://www.cbg.ethz.ch/software/gespeR
Depends On Me
Imports Me	eiR
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	gespeR_1.16.0.tar.gz
Windows Binary	gespeR_1.16.0.zip
Mac OS X 10.11 (El Capitan)	gespeR_1.16.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/gespeR
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/gespeR
Package Short Url	https://bioconductor.org/packages/gespeR/
Package Downloads Report	Download Stats