affy
Methods for Affymetrix Oligonucleotide Arrays
Bioconductor version: 3.23 · Package version: 1.90.0
The package contains functions for exploratory oligonucleotide array analysis. The dependence on tkWidgets only concerns few convenience functions. 'affy' is fully functional without it.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("affy")Details
| Maintainer | Robert D. Shear <rshear@ds.dfci.harvard.edu> |
| Author | Rafael A. Irizarry <rafa@ds.dfci.harvard.edu>, Laurent Gautier <lgautier@gmail.com>, Benjamin Milo Bolstad <bmb@bmbolstad.com>, and Crispin Miller <cmiller@picr.man.ac.uk> with contributions from Magnus Astrand <Magnus.Astrand@astrazeneca.com>, Leslie M. Cope <cope@mts.jhu.edu>, Robert Gentleman, Jeff Gentry, Conrad Halling <challing@agilixcorp.com>, Wolfgang Huber, James MacDonald <jmacdon@u.washington.edu>, Benjamin I. P. Rubinstein, Christopher Workman <workman@cbs.dtu.dk>, John Zhang |
| License | LGPL (>= 2.0) |
| URL | https://bioconductor.org/packages/affy |
| Bug Reports | https://github.com/rafalab/affy/issues |
| Downloads rank | 9806 |
| Source branch | RELEASE_3_23 |
| biocViews | Microarray, OneChannel, Preprocessing, Software |
Documentation
Download
Follow the installation instructions to use this package in your R session.
| Source package | affy_1.90.0.tar.gz |
| Windows binary (x86_64) | affy_1.90.0.zip |
| macOS binary (arm64) | affy_1.90.0.tgz |
| macOS binary (x86_64) | affy_1.90.0.tgz |
Dependencies
Depends: R (>= 2.8.0), BiocGenerics (>= 0.1.12), Biobase (>= 2.5.5)
Imports: affyio (>= 1.13.3), BiocManager, graphics, grDevices, methods, preprocessCore, stats, utils
LinkingTo: preprocessCore
Suggests: tkWidgets (>= 1.19.0), affydata, widgetTools, hgu95av2cdf
Reverse dependencies
Depends On Me (33): affyContam, affydata, affyPLM, AffyRNADegradation, AgiMicroRna, ALLMLL, altcdfenvs, AmpAffyExample, arrayMvout, bronchialIL13, ChimpHumanBrainData, CLL, Cormotif, curatedBladderData, DrugVsDisease, ecoliLeucine, ExiMiR, frmaTools, gcrma, maPredictDSC, MAQCsubset, maskBAD, mvoutData, panp, prebs, PREDAsampledata, qpcrNorm, RPA, SCAN.UPC, SpikeIn, SpikeInSubset, webbioc, XhybCasneuf
Imports Me (33): affycoretools, affyILM, affylmGUI, arrayQualityMetrics, bapred, bnem, CAFE, ChIPXpress, Cormotif, DeSousa2013, Doscheda, ffpe, frma, gcrma, GEOsubmission, HTqPCR, iCheck, lumi, makecdfenv, mimager, MSnbase, PECA, plier, puma, pvac, rat2302frmavecs, rCGH, Rnits, signatureSearchData, STATegRa, tilingArray, TurboNorm, vsn
Suggests Me (27): AnnotationForge, aroma.affymetrix, ArrayExpress, arrays, ath1121501frmavecs, autonomics, beadarray, BiocGenerics, Biostrings, BufferedMatrixMethods, categoryCompare, ecolitk, estrogen, factDesign, ffpeExampleData, GeneRegionScan, hexbin, Hiiragi2013, isatabr, limma, made4, maGUI, piano, PREDA, qcmetrics, siggenes, TCGAbiolinks