gespeR

Gene-Specific Phenotype EstimatoR

Bioconductor version: Release (3.17)

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 (version "4.3") and enter:

if (!require("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")

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

Details

biocViews	CellBasedAssays, GeneTarget, ImmunoOncology, Preprocessing, Regression, Software, Visualization
Version	1.31.0
In Bioconductor since	BioC 3.1 (R-3.2) (8.5 years)
License	GPL-3
Depends	methods, graphics, ggplot2, R (>= 2.10)
Imports	Matrix, glmnet, cellHTS2, Biobase, biomaRt, doParallel, parallel, foreach, reshape2, dplyr
Linking To
Suggests	knitr
System Requirements
Enhances
URL	http://www.cbg.ethz.ch/software/gespeR

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Package Archives

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

Source Package	gespeR_1.31.0.tar.gz
Windows Binary	gespeR_1.32.0.zip
macOS Binary (x86_64)
macOS Binary (arm64)	gespeR_1.31.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/gespeR
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/gespeR
Bioc Package Browser	https://code.bioconductor.org/browse/gespeR/
Package Short Url	https://bioconductor.org/packages/gespeR/
Package Downloads Report	Download Stats