beadarray

This is the development version of beadarray; for the stable release version, see beadarray.

All versions

3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13, 3.12, 3.11, 3.10, 3.9, 3.8, 3.7, 3.6, 3.5, 3.4, 3.3, 3.2, 3.1, 3.0, 2.14, 2.13, 2.12, 2.11, 2.10, 2.9, 2.8, 2.7, 2.6, 2.5

Quality assessment and low-level analysis for Illumina BeadArray data

Bioconductor version: Development (3.24)

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.dunning at imperial.ac.uk>

Citation (from within R, enter citation("beadarray")):

Mark Dunning, Mike Smith, Jonathan Cairns, Andy Lynch, Matt Ritchie. beadarray: Quality assessment and low-level analysis for Illumina BeadArray data. doi:10.18129/B9.bioc.beadarray, R package version 2.63.4, https://bioconductor.org/packages/beadarray.

Generated from the package metadata; it may differ from the package's own citation.

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("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")

Introduction to beadarray	HTML	R Script
Analysis of Bead-level Data using beadarray	HTML	R Script
Analysis of bead-summary data	HTML	R Script
Image Analysis with beadarray	HTML	R Script
Reference Manual	PDF
NEWS	Text
LICENSE	Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	Microarray, OneChannel, Preprocessing, QualityControl, Software
Version	2.63.4
In Bioconductor since	BioC 1.8 (R-2.3) (20.5 years)
License	MIT + file LICENSE
Depends	R (>= 3.5.0), BiocGenerics (>= 0.3.2), Biobase (>= 2.17.8), hexbin
Imports	limma, AnnotationDbi, stats4, reshape2, GenomicRanges, IRanges, methods, ggplot2, BeadDataPackR
System Requirements
URL

Suggests	lumi, vsn, affy, hwriter, beadarrayExampleData, illuminaHumanv3.db, gridExtra, BiocStyle, TxDb.Hsapiens.UCSC.hg19.knownGene, ggbio, knitr
Linking To
Enhances
Depends On Me	beadarrayExampleData
Imports Me	arrayQualityMetrics, BeadArrayUseCases, blima, epigenomix
Suggests Me	blimaTestingData, lumi, maGUI
Links To Me
Build Report	Build Report, r-universe

Package Archives

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

Source Package	beadarray_2.63.4.tar.gz
Windows Binary (x86_64)	beadarray_2.63.4.zip (64-bit only)
macOS Binary (big-sur-x86_64)	beadarray_2.63.4.tgz
macOS Binary (sonoma-arm64)	beadarray_2.63.4.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