oligoClasses
DOI:
10.18129/B9.bioc.oligoClasses
Classes for high-throughput arrays supported by oligo and crlmm
Bioconductor version: Release (3.5)
This package contains class definitions, validity checks, and initialization methods for classes used by the oligo and crlmm packages.
Author: Benilton Carvalho and Robert Scharpf
Maintainer: Benilton Carvalho <beniltoncarvalho at gmail.com> and Robert Scharpf <rscharpf at jhsph.edu>
Citation (from within R,
enter citation("oligoClasses")):
Installation
To install this package, start R and enter:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("oligoClasses")
Documentation
Details
Version
1.38.0
In Bioconductor since
BioC 2.1 (R-2.6) (10 years)
License
GPL (>= 2)
Depends
R (>= 2.14)
Imports
BiocGenerics(>= 0.3.2),
Biobase(>= 2.17.8), methods, graphics,
IRanges(>= 2.5.17),
GenomicRanges(>= 1.23.7),
SummarizedExperiment,
Biostrings(>= 2.23.6),
affyio(>= 1.23.2),
ff,
foreach,
BiocInstaller, utils,
S4Vectors(>= 0.9.25),
RSQLite
LinkingTo
Suggests
hapmapsnp5,
hapmapsnp6,
pd.genomewidesnp.6,
pd.genomewidesnp.5,
pd.mapping50k.hind240,
pd.mapping50k.xba240,
pd.mapping250k.sty,
pd.mapping250k.nsp,
genomewidesnp6Crlmm(>= 1.0.7),
genomewidesnp5Crlmm(>= 1.0.6),
RUnit,
human370v1cCrlmm,
SNPchip,
VanillaICE,
crlmm
SystemRequirements
Depends On Me
cn.farms,
crlmm,
mBPCR,
oligo,
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.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,
puma,
waveTiling
Imports Me
affycoretools,
ArrayTV,
charm,
frma,
ITALICS,
mimager,
MinimumDistance,
pdInfoBuilder,
puma,
SNPchip,
VanillaICE
Package Archives
Follow
Installation instructions to use this
package in your R session.
Source Repository
git clone https://git.bioconductor.org/packages/oligoClasses