plgem
This is the development version of plgem; for the stable release version, see plgem.
Detect differential expression in microarray and proteomics datasets with the Power Law Global Error Model (PLGEM)
Bioconductor version: Development (3.24)
The Power Law Global Error Model (PLGEM) has been shown to faithfully model the variance-versus-mean dependence that exists in a variety of genome-wide datasets, including microarray and proteomics data. The use of PLGEM has been shown to improve the detection of differentially expressed genes or proteins in these datasets.
Author: Mattia Pelizzola <mattia.pelizzola at gmail.com> and Norman Pavelka <normanpavelka at gmail.com>
Maintainer: Norman Pavelka <normanpavelka at gmail.com>
citation("plgem")):
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("plgem")
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("plgem")| An introduction to PLGEM | R Script | |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | DifferentialExpression, GeneExpression, ImmunoOncology, MassSpectrometry, Microarray, Proteomics, Software |
| Version | 1.85.0 |
| In Bioconductor since | BioC 1.6 (R-2.1) or earlier (> 21 years) |
| License | GPL-2 |
| Depends | R (>= 2.10) |
| Imports | utils, Biobase(>= 2.5.5), MASS, methods |
| System Requirements | |
| URL | http://www.genopolis.it |
See More
| Suggests | |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | INSPEcT |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | plgem_1.85.0.tar.gz |
| Windows Binary (x86_64) | plgem_1.85.0.zip |
| macOS Binary (big-sur-x86_64) | plgem_1.85.0.tgz |
| macOS Binary (sonoma-arm64) | plgem_1.85.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/plgem |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/plgem |
| Bioc Package Browser | https://code.bioconductor.org/browse/plgem/ |
| Package Short Url | https://bioconductor.org/packages/plgem/ |
| Package Downloads Report | Download Stats |