oligo
This package is for version 3.2 of Bioconductor;
for the stable, up-to-date release version, see
oligo.
Preprocessing tools for oligonucleotide arrays
Bioconductor version: 3.2
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
Maintainer: Benilton Carvalho <benilton at unicamp.br>
Citation (from within R,
enter citation("oligo")):
Installation
To install this package, start R and enter:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("oligo")
Documentation
To view documentation for the version of this package installed
in your system, start R and enter:
browseVignettes("oligo")
Details
Version
1.34.2
In Bioconductor since
BioC 2.0 (R-2.5) (9 years)
License
LGPL (>= 2)
Imports
affyio(>= 1.35.0),
affxparser(>= 1.39.4),
DBI (>= 0.3.1),
ff, graphics, methods,
preprocessCore(>= 1.29.0),
RSQLite (>= 1.0.0), splines, stats, stats4, utils,
zlibbioc
Suggests
BSgenome.Hsapiens.UCSC.hg18,
hapmap100kxba,
pd.hg.u95av2,
pd.mapping50k.xba240,
pd.huex.1.0.st.v2,
pd.hg18.60mer.expr,
pd.hugene.1.0.st.v1,
maqcExpression4plex,
genefilter,
limma,
RColorBrewer,
oligoData,
BiocStyle,
knitr,
RUnit,
biomaRt,
AnnotationDbi,
GenomeGraphs,
RCurl,
ACME,
biomaRt,
AnnotationDbi,
GenomeGraphs,
RCurl
SystemRequirements
Depends On Me
ITALICS,
oligoData,
pd.081229.hg18.promoter.medip.hx1,
pd.2006年07月18日.hg18.refseq.promoter,
pd.2006年07月18日.mm8.refseq.promoter,
pd.2006年10月31日.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.chigene.1.0.st,
pd.chigene.1.1.st,
pd.chogene.2.0.st,
pd.chogene.2.1.st,
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.drogene.1.0.st,
pd.drogene.1.1.st,
pd.drosgenome1,
pd.drosophila.2,
pd.e.coli.2,
pd.ecoli,
pd.ecoli.asv2,
pd.elegene.1.0.st,
pd.elegene.1.1.st,
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.fingene.1.0.st,
pd.fingene.1.1.st,
pd.genomewidesnp.5,
pd.genomewidesnp.6,
pd.guigene.1.0.st,
pd.guigene.1.1.st,
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.hta.2.0,
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.margene.1.0.st,
pd.margene.1.1.st,
pd.medgene.1.0.st,
pd.medgene.1.1.st,
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.mirna.4.0,
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.mta.1.0,
pd.mu11ksuba,
pd.mu11ksubb,
pd.nugo.hs1a520180,
pd.nugo.mm1a520177,
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.rabgene.1.0.st,
pd.rabgene.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.1.0.st,
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.1.0.st,
pd.rjpgene.1.1.st,
pd.rn.u34,
pd.rta.1.0,
pd.rusgene.1.0.st,
pd.rusgene.1.1.st,
pd.s.aureus,
pd.soybean,
pd.soygene.1.0.st,
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,
puma,
pumadata,
SCAN.UPC,
waveTiling
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