beadarray
This is the development version of beadarray; for the stable release version, see beadarray.
Quality assessment and low-level analysis for Illumina BeadArray data
Bioconductor version: Development (3.20)
The package is able to read bead-level data (raw TIFFs and text files) output by BeadScan as well as bead-summary data from BeadStudio. Methods for quality assessment and low-level analysis are provided.
Author: Mark Dunning, Mike Smith, Jonathan Cairns, Andy Lynch, Matt Ritchie
Maintainer: Mark Dunning <m.j.dunning at sheffield.ac.uk>
citation("beadarray")
):
Installation
To install this package, start R (version "4.4") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
# The following initializes usage of Bioc devel
BiocManager::install(version='devel')
BiocManager::install("beadarray")
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("beadarray")
beadarray.pdf | R Script | |
beadlevel.pdf | R Script | |
beadsummary.pdf | R Script | |
ImageProcessing.pdf | R Script | |
Reference Manual | ||
NEWS | Text | |
LICENSE | Text |
Details
biocViews | Microarray, OneChannel, Preprocessing, QualityControl, Software |
Version | 2.55.0 |
In Bioconductor since | BioC 1.8 (R-2.3) (18.5 years) |
License | MIT + file LICENSE |
Depends | R (>= 2.13.0), BiocGenerics(>= 0.3.2), Biobase(>= 2.17.8), hexbin |
Imports | BeadDataPackR, limma, AnnotationDbi, stats4, reshape2, GenomicRanges, IRanges, illuminaio, methods, ggplot2 |
System Requirements | |
URL |
See More
Suggests | lumi, vsn, affy, hwriter, beadarrayExampleData, illuminaHumanv3.db, gridExtra, BiocStyle, TxDb.Hsapiens.UCSC.hg19.knownGene, ggbio, Nozzle.R1, knitr |
Linking To | |
Enhances | |
Depends On Me | beadarrayExampleData |
Imports Me | arrayQualityMetrics, blima, epigenomix, BeadArrayUseCases, RobLoxBioC |
Suggests Me | lumi, blimaTestingData, maGUI |
Links To Me | |
Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
Source Package | beadarray_2.55.0.tar.gz |
Windows Binary | beadarray_2.55.0.zip (64-bit only) |
macOS Binary (x86_64) | beadarray_2.55.0.tgz |
macOS Binary (arm64) | beadarray_2.55.0.tgz |
Source Repository | git clone https://git.bioconductor.org/packages/beadarray |
Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/beadarray |
Bioc Package Browser | https://code.bioconductor.org/browse/beadarray/ |
Package Short Url | https://bioconductor.org/packages/beadarray/ |
Package Downloads Report | Download Stats |