beadarray
Quality assessment and low-level analysis for Illumina BeadArray data
Bioconductor version: 3.23 · Package version: 2.62.2
Other Bioconductor versions
devel is the development version; release is the current stable one.
3.24 (devel), 3.23 (release)
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.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("beadarray")Details
| Maintainer | Mark Dunning <m.dunning@imperial.ac.uk> |
| Author | Mark Dunning, Mike Smith, Jonathan Cairns, Andy Lynch, Matt Ritchie |
| License | MIT + file LICENSE |
| Source branch | RELEASE_3_23 |
| Build report | Bioconductor build system, r-universe |
| biocViews | Microarray, OneChannel, Preprocessing, QualityControl, Software |
| Package Short Url | https://bioconductor.org/packages/beadarray/ |
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 2.62.2, https://bioconductor.org/packages/beadarray.
Generated from the package metadata; it may differ from the package's own citation.
Documentation
- Analysis of Bead-level Data using beadarray
- Analysis of bead-summary data
- Image Analysis with beadarray
- beadarray
Download
Follow the installation instructions to use this package in your R session.
| Source package | beadarray_2.62.2.tar.gz |
| Windows binary (x86_64) | beadarray_2.62.2.zip |
| macOS binary (arm64) | beadarray_2.62.2.tgz |
| macOS binary (x86_64) | beadarray_2.62.2.tgz |
Dependencies
Depends: R (>= 3.5.0), BiocGenerics (>= 0.3.2), Biobase (>= 2.17.8), hexbin
Imports: limma, AnnotationDbi, stats4, reshape2, GenomicRanges, IRanges, methods, ggplot2, BeadDataPackR
Suggests: lumi, vsn, affy, hwriter, beadarrayExampleData, illuminaHumanv3.db, gridExtra, BiocStyle, TxDb.Hsapiens.UCSC.hg19.knownGene, ggbio, knitr
Reverse dependencies
Depends On Me (1): beadarrayExampleData
Imports Me (4): arrayQualityMetrics, BeadArrayUseCases, blima, epigenomix
Suggests Me (3): blimaTestingData, lumi, maGUI