oligo
Preprocessing tools for oligonucleotide arrays.
Bioconductor version: 2.9
A package to analyze oligonucleotide arrays (expression/SNP/tiling/exon) at probe-level. It currently supports Affymetrix (CEL files) and NimbleGen arrays (XYS files).
Author: Benilton Carvalho <Benilton.Carvalho at cancer.org.uk>, Rafael A. Irizarry with contributions from Ben Bolstad, Vince Carey, Robert Gentleman, Wolfgang Huber
Maintainer: Benilton Carvalho <Benilton.Carvalho at cancer.org.uk>
To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("oligo")
To cite this package in a publication, start R and enter:
citation("oligo")
Documentation
Details
| biocViews |
Microarray, OneChannel, TwoChannel, Preprocessing, SNP, DifferentialExpression, ExonArray, GeneExpression, Bioinformatics, DataImport |
| Depends |
R (>= 2.13.0), oligoClasses(>= 1.13.9) |
| Imports |
affyio(>= 1.19.4), affxparser(>= 1.23.1), Biobase(>= 2.11.8), Biostrings, DBI (>= 0.2-5), ff, graphics, methods, preprocessCore(>= 1.13.5), splines, stats, utils, zlibbioc |
| Suggests |
hapmap100kxba, pd.mapping50k.xba240, pd.huex.1.0.st.v2, pd.hg18.60mer.expr, maqcExpression4plex, genefilter, limma, RColorBrewer, oligoData |
| System Requirements |
|
| License |
LGPL (>= 2) |
| URL |
|
| Depends On Me |
ITALICS, oligoData, pd.081229.hg18.promoter.medip.hx1, pd.2006.07.18.hg18.refseq.promoter, pd.2006.07.18.mm8.refseq.promoter, pd.2006.10.31.rn34.refseq.promoter, pd.ag, pd.ath1.121501, pd.barley1, pd.bovine, pd.bsubtilis, pd.canine, pd.canine.2, pd.celegans, pd.charm.hg18.example, pd.chicken, pd.citrus, pd.cotton, pd.cytogenetics.array, pd.drosgenome1, pd.drosophila.2, pd.e.coli.2, pd.ecoli, pd.ecoli.asv2, pd.feinberg.hg18.me.hx1, pd.feinberg.mm8.me.hx1, pd.genomewidesnp.5, pd.genomewidesnp.6, pd.hc.g110, pd.hg.focus, pd.hg.u133.plus.2, pd.hg.u133a, pd.hg.u133a.2, pd.hg.u133a.tag, pd.hg.u133b, pd.hg.u219, pd.hg.u95a, pd.hg.u95av2, pd.hg.u95b, pd.hg.u95c, pd.hg.u95d, pd.hg.u95e, pd.ht.hg.u133.plus.pm, pd.ht.hg.u133a, pd.ht.mg.430a, pd.hu6800, pd.huex.1.0.st.v2, pd.hugene.1.0.st.v1, pd.hugene.1.1.st.v1, pd.maize, pd.mapping250k.nsp, pd.mapping250k.sty, pd.mapping50k.hind240, pd.mapping50k.xba240, pd.medicago, pd.mg.u74a, pd.mg.u74av2, pd.mg.u74b, pd.mg.u74bv2, pd.mg.u74c, pd.mg.u74cv2, pd.mirna.1.0, pd.moe430a, pd.moe430b, pd.moex.1.0.st.v1, pd.mogene.1.0.st.v1, pd.mogene.1.1.st.v1, pd.mouse430.2, pd.mouse430a.2, pd.mu11ksuba, pd.mu11ksubb, pd.pae.g1a, pd.plasmodium.anopheles, pd.poplar, pd.porcine, pd.rae230a, pd.rae230b, pd.raex.1.0.st.v1, pd.ragene.1.0.st.v1, pd.ragene.1.1.st.v1, pd.rat230.2, pd.rg.u34a, pd.rg.u34b, pd.rg.u34c, pd.rhesus, pd.rice, pd.rn.u34, pd.s.aureus, pd.soybean, pd.sugar.cane, pd.tomato, pd.u133.x3p, pd.vitis.vinifera, pd.wheat, pd.x.laevis.2, pd.x.tropicalis, pd.xenopus.laevis, pd.yeast.2, pd.yg.s98, pd.zebrafish, pdInfoBuilder |
| Imports Me |
charm, cn.farms, frma, ITALICS |
| Suggests Me |
fastseg, frmaTools, hapmap100khind, hapmap100kxba, hapmap500knsp, hapmap500ksty, hapmapsnp5, hapmapsnp6, maqcExpression4plex |
| Version |
1.18.1 |
| Since |
Bioconductor 2.0 (R-2.5) |
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