gespeR
This package is for version 3.7 of Bioconductor; for the stable, up-to-date release version, see gespeR.
Gene-Specific Phenotype EstimatoR
Bioconductor version: 3.7
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("gespeR")):
Installation
To install this package, start R (version "3.5") 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 | R Script | |
| Reference Manual |
Details
| biocViews | CellBasedAssays, GeneTarget, Preprocessing, Regression, Software, Visualization |
| Version | 1.12.0 |
| In Bioconductor since | BioC 3.1 (R-3.2) (9 years) |
| License | GPL-3 |
| Depends | methods, graphics, ggplot2, R (>= 2.10) |
| Imports | Matrix, glmnet, cellHTS2, Biobase, biomaRt, doParallel, parallel, foreach, reshape2, dplyr |
| System Requirements | |
| URL | http://www.cbg.ethz.ch/software/gespeR |
See More
| Suggests | knitr |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | eiR |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | gespeR_1.12.0.tar.gz |
| Windows Binary | gespeR_1.12.0.zip |
| Mac OS X 10.11 (El Capitan) | gespeR_1.12.0.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 |
| Old Source Packages for BioC 3.7 | Source Archive |