stageR
This is the released version of stageR; for the devel version, see stageR.
stageR: stage-wise analysis of high throughput gene expression data in R
Bioconductor version: Release (3.23)
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("stageR")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") 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 |
Details
| biocViews | Software, StatisticalMethod |
| Version | 1.34.0 |
| In Bioconductor since | BioC 3.6 (R-3.4) (9 years) |
| License | GNU General Public License version 3 |
| Depends | R (>= 3.4), SummarizedExperiment |
| Imports | methods, stats |
| System Requirements | |
| URL |
See More
| Suggests | knitr, rmarkdown, BiocStyle, methods, Biobase, edgeR, limma, DEXSeq, testthat |
| Linking To | |
| Enhances | |
| Depends On Me | rnaseqDTU |
| Imports Me | |
| Suggests Me | MethReg, muscat, satuRn |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | stageR_1.34.0.tar.gz |
| Windows Binary (x86_64) | stageR_1.34.0.zip |
| macOS Binary (big-sur-x86_64) | stageR_1.34.0.tgz |
| macOS Binary (sonoma-arm64) | stageR_1.34.0.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 3.23 | Source Archive |