oligo

Preprocessing tools for oligonucleotide arrays.

Bioconductor version: Release (2.12)

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 and Rafael Irizarry. Contributors: Ben Bolstad, Vincent Carey, Wolfgang Huber, Harris Jaffee, Jim MacDonald, Matt Settles

Maintainer: Benilton Carvalho <beniltoncarvalho at gmail.com>

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

PDF R Script oligo - Primer
PDF   Reference Manual
Text   NEWS

Details

biocViews Bioinformatics, DataImport, DifferentialExpression, ExonArray, GeneExpression, Microarray, OneChannel, Preprocessing, SNP, Software, TwoChannel
Version 1.24.2
In Bioconductor since BioC 2.0 (R-2.5)
License LGPL (>= 2)
Depends R (>= 2.15.0), BiocGenerics(>= 0.3.2), oligoClasses(>= 1.19.43), Biobase(>= 2.17.8)
Imports affyio(>= 1.25.0), affxparser(>= 1.29.11), Biostrings(>= 2.25.12), BiocGenerics(>= 0.3.2), DBI (>= 0.2-5), ff, graphics, methods, preprocessCore(>= 1.19.0), splines, stats, stats4, utils, zlibbioc
Suggests hapmap100kxba, pd.mapping50k.xba240, pd.huex.1.0.st.v2, pd.hg18.60mer.expr, pd.hugene.1.0.st.v1, maqcExpression4plex, genefilter, limma, RColorBrewer, oligoData, RUnit
System Requirements
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.aragene.1.0.st, pd.aragene.1.1.st, pd.atdschip.tiling, pd.ath1.121501, pd.barley1, pd.bovgene.1.0.st, pd.bovgene.1.1.st, pd.bovine, pd.bsubtilis, pd.cangene.1.0.st, pd.cangene.1.1.st, pd.canine, pd.canine.2, pd.celegans, pd.charm.hg18.example, pd.chicken, pd.citrus, pd.cotton, pd.cyngene.1.0.st, pd.cyngene.1.1.st, pd.cyrgene.1.0.st, pd.cyrgene.1.1.st, pd.cytogenetics.array, pd.drosgenome1, pd.drosophila.2, pd.e.coli.2, pd.ecoli, pd.ecoli.asv2, pd.equgene.1.0.st, pd.equgene.1.1.st, pd.feinberg.hg18.me.hx1, pd.feinberg.mm8.me.hx1, pd.felgene.1.0.st, pd.felgene.1.1.st, 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.hg18.60mer.expr, 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.hugene.2.0.st, pd.hugene.2.1.st, 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.mirna.2.0, pd.mirna.3.0, pd.mirna.3.1, pd.moe430a, pd.moe430b, pd.moex.1.0.st.v1, pd.mogene.1.0.st.v1, pd.mogene.1.1.st.v1, pd.mogene.2.0.st, pd.mogene.2.1.st, pd.mouse430.2, pd.mouse430a.2, pd.mu11ksuba, pd.mu11ksubb, pd.ovigene.1.0.st, pd.ovigene.1.1.st, pd.pae.g1a, pd.plasmodium.anopheles, pd.poplar, pd.porcine, pd.porgene.1.0.st, pd.porgene.1.1.st, pd.rae230a, pd.rae230b, pd.raex.1.0.st.v1, pd.ragene.1.0.st.v1, pd.ragene.1.1.st.v1, pd.ragene.2.0.st, pd.ragene.2.1.st, pd.rat230.2, pd.rcngene.1.1.st, pd.rg.u34a, pd.rg.u34b, pd.rg.u34c, pd.rhegene.1.0.st, pd.rhegene.1.1.st, pd.rhesus, pd.rice, pd.rjpgene.1.1.st, pd.rn.u34, pd.s.aureus, pd.soybean, pd.soygene.1.1.st, 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.zebgene.1.0.st, pd.zebgene.1.1.st, pd.zebrafish, pdInfoBuilder, SCAN.UPC, waveTiling
Imports Me charm, cn.farms, frma, ITALICS
Suggests Me BiocGenerics, fastseg, frmaTools, hapmap100khind, hapmap100kxba, hapmap500knsp, hapmap500ksty, hapmapsnp5, hapmapsnp6, maqcExpression4plex

Package Downloads

Package Source oligo_1.24.2.tar.gz
Windows Binary oligo_1.24.2.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard) oligo_1.24.2.tgz
Package Downloads Report Download Stats

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