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beadarray

Quality assessment and low-level analysis for Illumina BeadArray data


Bioconductor version: Release (3.18)

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

Installation

To install this package, start R (version "4.3") and enter:


if (!require("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")
beadarray.pdf PDF R Script
beadlevel.pdf PDF R Script
beadsummary.pdf PDF R Script
ImageProcessing.pdf PDF R Script
Reference Manual PDF
NEWS Text
LICENSE Text

Details

biocViews Microarray, OneChannel, Preprocessing, QualityControl, Software
Version 2.52.0
In Bioconductor since BioC 1.8 (R-2.3) (18 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, BeadArrayUseCases, blima, epigenomix
Suggests Me beadarraySNP, blimaTestingData, lumi
Links To Me
Build Report Build Report

Package Archives

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

Source Package beadarray_2.52.0.tar.gz
Windows Binary beadarray_2.52.0.zip (64-bit only)
macOS Binary (x86_64) beadarray_2.52.0.tgz
macOS Binary (arm64) beadarray_2.52.0.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