beadarray
This is the released version of beadarray; for the devel version, see beadarray.
Quality assessment and low-level analysis for Illumina BeadArray data
Bioconductor version: Release (3.23)
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.dunning at imperial.ac.uk>
citation("beadarray")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") 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")| Analysis of Bead-level Data using beadarray | HTML | R Script |
| Analysis of bead-summary data | HTML | R Script |
| Image Analysis with beadarray | HTML | R Script |
| Introduction to beadarray | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | Microarray, OneChannel, Preprocessing, QualityControl, Software |
| Version | 2.62.1 |
| In Bioconductor since | BioC 1.8 (R-2.3) (20.5 years) |
| License | MIT + file LICENSE |
| Depends | R (>= 3.5.0), BiocGenerics(>= 0.3.2), Biobase(>= 2.17.8), hexbin |
| Imports | limma, AnnotationDbi, stats4, reshape2, GenomicRanges, IRanges, methods, ggplot2, BeadDataPackR |
| System Requirements | |
| URL |
See More
| Suggests | lumi, vsn, affy, hwriter, beadarrayExampleData, illuminaHumanv3.db, gridExtra, BiocStyle, TxDb.Hsapiens.UCSC.hg19.knownGene, ggbio, knitr |
| Linking To | |
| Enhances | |
| Depends On Me | beadarrayExampleData |
| Imports Me | arrayQualityMetrics, blima, epigenomix, BeadArrayUseCases |
| 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_2.62.1.tar.gz |
| Windows Binary (x86_64) | beadarray_2.62.1.zip (64-bit only) |
| macOS Binary (big-sur-x86_64) | beadarray_2.62.1.tgz |
| macOS Binary (sonoma-arm64) | beadarray_2.62.1.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 |
| Old Source Packages for BioC 3.23 | Source Archive |