This is the released version of oligo; for the devel version, seeoligo .
Bioconductor version: Release (3.20)
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
Citation (from within R, enter citation("oligo")):
To install this package, start R (version "4.4") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("oligo")
For older versions of R, please refer to the appropriate Bioconductor release .
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("oligo")
oligo User's Guide
PDF
Reference Manual
PDF
NEWS
Text
biocViews
DataImport , DifferentialExpression , ExonArray , GeneExpression , Microarray , OneChannel , Preprocessing , SNP , Software , TwoChannel
Version
1.70.0
In Bioconductor since
BioC 2.0 (R-2.5) (17.5 years)
License
LGPL (>= 2)
Depends
R (>= 3.2.0), BiocGenerics (>= 0.13.11), oligoClasses (>= 1.29.6), Biobase (>= 2.27.3), Biostrings (>= 2.35.12)
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
System Requirements
URL
https://github.com/benilton/oligo
See More
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 , ACME , RCurl
Linking To
preprocessCore
Enhances
doMC , doMPI
Depends On Me
ITALICS , pdInfoBuilder , puma , SCAN.UPC , 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.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.clariom.d.human , pd.clariom.s.human , pd.clariom.s.human.ht , pd.clariom.s.mouse , pd.clariom.s.mouse.ht , pd.clariom.s.rat , pd.clariom.s.rat.ht , 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 , pd.atdschip.tiling , pumadata , maEndToEnd
Imports Me
ArrayExpress , cn.farms , frma , ITALICS , mimager
Suggests Me
fastseg , frmaTools , hapmap100khind , hapmap100kxba , hapmap500knsp , hapmap500ksty , hapmapsnp5 , hapmapsnp6 , maqcExpression4plex , aroma.affymetrix , maGUI , RCPA
Links To Me
Build Report
Build Report
Follow Installation instructions to use this package in your R session.