beadarray

DOI: 10.18129/B9.bioc.beadarray    

This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see beadarray.

Quality assessment and low-level analysis for Illumina BeadArray data

Bioconductor version: 3.9

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>

Installation

To install this package, start R (version "3.6") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

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")

 

PDF	R Script	beadarray.pdf
PDF	R Script	beadlevel.pdf
PDF	R Script	beadsummary.pdf
PDF	R Script	ImageProcessing.pdf
PDF		Reference Manual
Text		NEWS
Text		LICENSE

Details

biocViews	Microarray, OneChannel, Preprocessing, QualityControl, Software
Version	2.34.0
In Bioconductor since	BioC 1.8 (R-2.3) (13.5 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
LinkingTo
Suggests	lumi, vsn, affy, hwriter, beadarrayExampleData, illuminaHumanv3.db, gridExtra, BiocStyle, TxDb.Hsapiens.UCSC.hg19.knownGene, ggbio, Nozzle.R1, knitr
SystemRequirements
Enhances
URL
Depends On Me	beadarrayExampleData
Imports Me	arrayQualityMetrics, BeadArrayUseCases, blima, epigenomix
Suggests Me	beadarraySNP, blimaTestingData, lumi
Links To Me
Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	beadarray_2.34.0.tar.gz
Windows Binary	beadarray_2.34.0.zip (32- & 64-bit)
Mac OS X 10.11 (El Capitan)	beadarray_2.34.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/beadarray
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/beadarray
Package Short Url	https://bioconductor.org/packages/beadarray/
Package Downloads Report	Download Stats