siggenes
This is the released version of siggenes; for the devel version, see siggenes.
Multiple Testing using SAM and Efron's Empirical Bayes Approaches
Bioconductor version: Release (3.23)
Identification of differentially expressed genes and estimation of the False Discovery Rate (FDR) using both the Significance Analysis of Microarrays (SAM) and the Empirical Bayes Analyses of Microarrays (EBAM).
Author: Holger Schwender
Maintainer: Holger Schwender <holger.schw at gmx.de>
citation("siggenes")):
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("siggenes")
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("siggenes")| identify.sam.html | HTML | |
| plot.ebam.html | HTML | |
| plot.finda0.html | HTML | |
| plot.sam.html | HTML | |
| print.ebam.html | HTML | |
| print.finda0.html | HTML | |
| print.sam.html | HTML | |
| siggenes Manual | R Script | |
| siggenesRnews.pdf | ||
| summary.ebam.html | HTML | |
| summary.sam.html | HTML | |
| Reference Manual |
Details
| biocViews | DifferentialExpression, ExonArray, GeneExpression, Microarray, MultipleComparison, SNP, Software |
| Version | 1.86.0 |
| In Bioconductor since | BioC 1.6 (R-2.1) or earlier (> 21 years) |
| License | LGPL (>= 2) |
| Depends | Biobase, multtest, splines, methods |
| Imports | stats4, grDevices, graphics, stats, scrime (>= 1.2.5) |
| System Requirements | |
| URL |
See More
| Suggests | affy, annotate, genefilter, KernSmooth |
| Linking To | |
| Enhances | |
| Depends On Me | KCsmart |
| Imports Me | asuri, minfi, trio, XDE, DeSousa2013, NPFD |
| Suggests Me | logicFS |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | siggenes_1.86.0.tar.gz |
| Windows Binary (x86_64) | siggenes_1.86.0.zip |
| macOS Binary (big-sur-x86_64) | siggenes_1.86.0.tgz |
| macOS Binary (sonoma-arm64) | siggenes_1.86.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/siggenes |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/siggenes |
| Bioc Package Browser | https://code.bioconductor.org/browse/siggenes/ |
| Package Short Url | https://bioconductor.org/packages/siggenes/ |
| Package Downloads Report | Download Stats |