fdrame
This is the development version of fdrame; for the stable release version, see fdrame.
FDR adjustments of Microarray Experiments (FDR-AME)
Bioconductor version: Development (3.24)
This package contains two main functions. The first is fdr.ma which takes normalized expression data array, experimental design and computes adjusted p-values It returns the fdr adjusted p-values and plots, according to the methods described in (Reiner, Yekutieli and Benjamini 2002). The second, is fdr.gui() which creates a simple graphic user interface to access fdr.ma
Author: Yoav Benjamini, Effi Kenigsberg, Anat Reiner, Daniel Yekutieli
Maintainer: Effi Kenigsberg <effiken.fdrame at gmail.com>
citation("fdrame")):
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")
## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")
BiocManager::install("fdrame")
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("fdrame")| Annotation Overview | |
| Reference Manual |
Details
| biocViews | DifferentialExpression, Microarray, MultipleComparison, Software |
| Version | 1.85.0 |
| In Bioconductor since | BioC 1.7 (R-2.2) (21 years) |
| License | GPL (>= 2) |
| Depends | |
| Imports | tcltk, graphics, grDevices, stats, utils |
| System Requirements | |
| URL |
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| Suggests | |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | fdrame_1.85.0.tar.gz |
| Windows Binary (x86_64) | fdrame_1.85.0.zip (64-bit only) |
| macOS Binary (big-sur-x86_64) | fdrame_1.85.0.tgz |
| macOS Binary (sonoma-arm64) | fdrame_1.85.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/fdrame |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/fdrame |
| Bioc Package Browser | https://code.bioconductor.org/browse/fdrame/ |
| Package Short Url | https://bioconductor.org/packages/fdrame/ |
| Package Downloads Report | Download Stats |