oligo
This package is for version 2.11 of Bioconductor;
for the stable, up-to-date release version, see
oligo.
Preprocessing tools for oligonucleotide arrays.
Bioconductor version: 2.11
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 <Benilton.Carvalho at cancer.org.uk>
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
biocViews
Bioinformatics,
DataImport,
DifferentialExpression,
ExonArray,
GeneExpression,
Microarray,
OneChannel,
Preprocessing,
SNP,
Software,
TwoChannel
Version
1.22.0
In Bioconductor since
BioC 2.0 (R-2.5) (9 years)
License
LGPL (>= 2)
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
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,
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pd.aragene.1.0.st,
pd.aragene.1.1.st,
pd.atdschip.tiling,
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pd.felgene.1.0.st,
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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,
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pd.mapping250k.sty,
pd.mapping50k.hind240,
pd.mapping50k.xba240,
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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.moe430a,
pd.moe430b,
pd.moex.1.0.st.v1,
pd.mogene.1.0.st.v1,
pd.mogene.1.1.st.v1,
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pd.rat230.2,
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pd.zebgene.1.0.st,
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