les
This is the released version of les; for the devel version, see les.
Identifying Differential Effects in Tiling Microarray Data
DOI: 10.18129/B9.bioc.les
Bioconductor version: Release (3.23)
The 'les' package estimates Loci of Enhanced Significance (LES) in tiling microarray data. These are regions of regulation such as found in differential transcription, CHiP-chip, or DNA modification analysis. The package provides a universal framework suitable for identifying differential effects in tiling microarray data sets, and is independent of the underlying statistics at the level of single probes.
Author: Julian Gehring, Clemens Kreutz, Jens Timmer
Maintainer: Julian Gehring <jg-bioc at gmx.com>
citation("les")):
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("les")
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("les")| Introduction to the les package: Identifying Differential Effects in Tiling Microarray Data with the Loci of Enhanced Significance Framework | R Script | |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | ChIPchip, DNAMethylation, DifferentialExpression, Microarray, Software, Transcription |
| Version | 1.62.0 |
| In Bioconductor since | BioC 2.7 (R-2.12) (16 years) |
| License | GPL-3 |
| Depends | R (>= 2.13.2), methods, graphics, fdrtool |
| Imports | boot, gplots, RColorBrewer |
| System Requirements | |
| URL |
See More
| Suggests | Biobase, limma |
| Linking To | |
| Enhances | parallel |
| Depends On Me | |
| Imports Me | GSRI |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | les_1.62.0.tar.gz |
| Windows Binary (x86_64) | les_1.62.0.zip |
| macOS Binary (big-sur-x86_64) | les_1.62.0.tgz |
| macOS Binary (sonoma-arm64) | les_1.62.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/les |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/les |
| Bioc Package Browser | https://code.bioconductor.org/browse/les/ |
| Package Short Url | https://bioconductor.org/packages/les/ |
| Package Downloads Report | Download Stats |