To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("gespeR")

In most cases, you don't need to download the package archive at all.

gespeR

This package is for version 3.1 of Bioconductor; for the stable, up-to-date release version, see gespeR.

Gene-Specific Phenotype EstimatoR

Bioconductor version: 3.1

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>

Citation (from within R, enter citation("gespeR")):

Installation

To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("gespeR")

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, Preprocessing, Regression, Software, Visualization
Version 1.0.0
In Bioconductor since BioC 3.1 (R-3.2) (1 year)
License GPL-3
Depends methods, graphics, ggplot2, R (>= 2.10)
Imports Matrix, glmnet, cellHTS2, Biobase, biomaRt, doParallel, parallel, foreach, reshape2
LinkingTo
Suggests knitr
SystemRequirements
Enhances
URL http://www.cbg.ethz.ch/software/gespeR
Depends On Me
Imports Me
Suggests Me
Build Report

Package Archives

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

Package Source gespeR_1.0.0.tar.gz
Windows Binary gespeR_1.0.0.zip
Mac OS X 10.6 (Snow Leopard) gespeR_1.0.0.tgz
Mac OS X 10.9 (Mavericks) gespeR_1.0.0.tgz
Subversion source (username/password: readonly)
Git source https://github.com/Bioconductor-mirror/gespeR/tree/release-3.1
Package Short Url http://bioconductor.org/packages/gespeR/
Package Downloads Report Download Stats

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