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Bioconductor - beadarray (development version)

beadarray

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

Quality assessment and low-level analysis for Illumina BeadArray data

Bioconductor version: Development (3.22)

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 "4.5") and enter:


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

# The following initializes usage of Bioc devel
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")
Details biocViews Microarray, OneChannel, Preprocessing, QualityControl, Software Version 2.59.0 In Bioconductor since BioC 1.8 (R-2.3) (19 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, 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.

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