beadarray

DOI: 10.18129/B9.bioc.beadarray  

Quality assessment and low-level analysis for Illumina BeadArray data

Bioconductor version: Release (3.16)

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 "4.2") 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")

 

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 2.48.0
In Bioconductor since BioC 1.8 (R-2.3) (17 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_2.48.0.tar.gz
Windows Binary beadarray_2.48.0.zip (64-bit only)
macOS Binary (x86_64) beadarray_2.48.0.tgz
macOS Binary (arm64) beadarray_2.48.0.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

Documentation »

Bioconductor

R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations: