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oligoClasses

This is thereleased version of oligoClasses; for the devel version, seeoligoClasses.

Classes for high-throughput arrays supported by oligo and crlmm

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DOI: 10.18129/B9.bioc.oligoClasses


Bioconductor version: Release (3.22)

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, entercitation("oligoClasses")):

Installation

To install this package, start R (version "4.5") and enter:

if (!require("BiocManager", quietly = TRUE))    install.packages("BiocManager")BiocManager::install("oligoClasses")

For older versions of R, please refer to the appropriateBioconductor release.

Documentation

Reference ManualPDF
NEWSText

Need some help? Ask on the Bioconductor Support site!

Details

biocViewsInfrastructure,Software
Version1.72.0
In Bioconductor sinceBioC 2.1 (R-2.6) (18 years)
LicenseGPL (>= 2)
DependsR (>= 2.14)
ImportsBiocGenerics(>= 0.27.1),Biobase(>= 2.17.8), methods, graphics,IRanges(>= 2.5.17),GenomicRanges(>= 1.23.7),SummarizedExperiment,Biostrings(>= 2.23.6),affyio(>= 1.23.2),foreach,BiocManager, utils,S4Vectors(>= 0.9.25),RSQLite,DBI,ff
System Requirements
URL
See More
Suggestshapmapsnp5,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,VanillaICE,crlmm
Linking To
EnhancesdoMC,doMPI,doSNOW,doParallel,doRedis
Depends On Mecn.farms,crlmm,mBPCR,oligo,puma,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,maEndToEnd
Imports Meaffycoretools,frma,ITALICS,mimager,MinimumDistance,pdInfoBuilder,puma,VanillaICE
Suggests Mehapmapsnp6,aroma.affymetrix,scrime
Links To Me
Build ReportBuild Report

Package Archives

FollowInstallation instructions to use this package in your R session.

Source PackageoligoClasses_1.72.0.tar.gz
Windows Binary (x86_64) oligoClasses_1.72.0.zip (64-bit only)
macOS Binary (x86_64)oligoClasses_1.72.0.tgz
macOS Binary (arm64)oligoClasses_1.72.0.tgz
Source Repositorygit clone https://git.bioconductor.org/packages/oligoClasses
Source Repository (Developer Access)git clone git@git.bioconductor.org:packages/oligoClasses
Bioc Package Browserhttps://code.bioconductor.org/browse/oligoClasses/
Package Short Urlhttps://bioconductor.org/packages/oligoClasses/
Package Downloads ReportDownload Stats

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