stageR

This package is for version 3.8 of Bioconductor; for the stable, up-to-date release version, see stageR.

stageR: stage-wise analysis of high throughput gene expression data in R


Bioconductor version: 3.8

The stageR package allows automated stage-wise analysis of high-throughput gene expression data. The method is published in Genome Biology at https://genomebiology.biomedcentral.com/articles/10.1186/s13059-017-1277-0

Author: Koen Van den Berge and Lieven Clement

Maintainer: Koen Van den Berge <koen.vdberge at gmail.com>

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

Installation

To install this package, start R (version "3.5") and enter:


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

BiocManager::install("stageR")

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("stageR")
stageR: stage-wise analysis of high-throughput gene expression data in R HTML R Script
Reference Manual PDF

Details

biocViews Software, StatisticalMethod
Version 1.4.0
In Bioconductor since BioC 3.6 (R-3.4) (6.5 years)
License GNU General Public License version 3
Depends R (>= 3.4), SummarizedExperiment
Imports methods, stats
System Requirements
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Suggests knitr, rmarkdown, BiocStyle, methods, Biobase, edgeR, limma, DEXSeq, testthat
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Depends On Me rnaseqDTU
Imports Me
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Package Archives

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

Source Package stageR_1.4.0.tar.gz
Windows Binary stageR_1.4.0.zip
Mac OS X 10.11 (El Capitan) stageR_1.4.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/stageR
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/stageR
Bioc Package Browser https://code.bioconductor.org/browse/stageR/
Package Short Url https://bioconductor.org/packages/stageR/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.8 Source Archive