beadarray
Quality assessment and low-level analysis for Illumina BeadArray data
Bioconductor version: Release (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 | R Script | |
| beadlevel.pdf | R Script | |
| beadsummary.pdf | R Script | |
| ImageProcessing.pdf | R Script | |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
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 |
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.
| 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/ |
| Package Downloads Report | Download Stats |