beadarray

This package is for version 3.19 of Bioconductor; for the stable, up-to-date release version, see beadarray.

Quality assessment and low-level analysis for Illumina BeadArray data

Bioconductor version: 3.19

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 "4.4") 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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews Microarray, OneChannel, Preprocessing, QualityControl, Software

Version 2.54.0

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

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_2.54.0.tar.gz

Windows Binary (x86_64) beadarray_2.54.0.zip (64-bit only)

macOS Binary (x86_64) beadarray_2.54.0.tgz

macOS Binary (arm64) beadarray_2.54.0.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/

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