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To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("beadarray")
In most cases, you don't need to download the package archive at all.
beadarray
Quality assessment and low-level analysis for Illumina BeadArray data
Bioconductor version: 3.0
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 <Mark.Dunning at cruk.cam.ac.uk>
Citation (from within R,
enter citation("beadarray")):
Installation
To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("beadarray")
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("beadarray")
| R Script | beadarray.pdf | |
| R Script | beadlevel.pdf | |
| R Script | beadsummary.pdf | |
| R Script | ImageProcessing.pdf | |
| Reference Manual | ||
| Text | NEWS |
Details
| biocViews | Microarray, OneChannel, Preprocessing, QualityControl, Software |
| Version | 2.16.0 |
| In Bioconductor since | BioC 1.8 (R-2.3) |
| License | GPL-2 |
| Depends | R (>= 2.13.0), BiocGenerics(>= 0.3.2), Biobase(>= 2.17.8), methods, ggplot2 |
| Imports | BeadDataPackR, limma, AnnotationDbi, stats4, reshape2, GenomicRanges, IRanges, illuminaio |
| LinkingTo | |
| Suggests | lumi, vsn, affy, hwriter, beadarrayExampleData, illuminaHumanv3.db, gridExtra, BiocStyle, TxDb.Hsapiens.UCSC.hg19.knownGene, ggbio, Nozzle.R1, knitr |
| SystemRequirements | |
| Enhances | |
| URL | |
| Depends On Me | beadarrayExampleData |
| Imports Me | arrayQualityMetrics, BeadArrayUseCases, blima, epigenomix |
| Suggests Me | beadarraySNP, blimaTestingData, lumi |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Package Source | beadarray_2.16.0.tar.gz |
| Windows Binary | beadarray_2.16.0.zip (32- & 64-bit) |
| Mac OS X 10.6 (Snow Leopard) | beadarray_2.16.0.tgz |
| Mac OS X 10.9 (Mavericks) | beadarray_2.16.0.tgz |
| Browse/checkout source | (username/password: readonly) |
| Package Downloads Report | Download Stats |
Common Bioconductor workflows include:
- Oligonucleotide Arrays
- High-throughput Sequencing
- Counting Reads for Differential Expression (parathyroideSE vignette)
- Annotation
- Annotating Variants
- Annotating Ranges
- Flow Cytometry and other assays
- Candidate Binding Sites for Known Transcription Factors
- Cloud-enabled cis-eQTL search and annotation
- RNA-Seq workflow: gene-level exploratory analysis and differential expression
- Changing genomic coordinate systems with rtracklayer::liftOver
- Mass spectrometry and proteomics data analysis
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