Biobase

Biobase: Base functions for Bioconductor

Bioconductor version: Release (2.14)

Functions that are needed by many other packages or which replace R functions.

Author: R. Gentleman, V. Carey, M. Morgan, S. Falcon

Maintainer: Bioconductor Package Maintainer <maintainer at bioconductor.org>

To install this package, start R and enter:

    source("http://bioconductor.org/biocLite.R")
    biocLite("Biobase")

To cite this package in a publication, start R and enter:

    citation("Biobase")

Documentation

PDF R Script An introduction to Biobase and ExpressionSets
PDF R Script Bioconductor Overview
PDF R Script esApply Introduction
PDF R Script Notes for eSet developers
PDF R Script Notes for writing introductory 'how to' documents
PDF R Script quick views of eSet instances
PDF   Reference Manual
Text   NEWS

Details

biocViews Infrastructure, Software
Version 2.24.0
In Bioconductor since BioC 1.6 (R-2.1) or earlier
License Artistic-2.0
Depends R (>= 2.10), BiocGenerics(>= 0.3.2), utils
Imports methods
Suggests tools, tkWidgets, ALL, RUnit, golubEsets
System Requirements
URL
Depends On Me a4Base, a4Core, ACME, affy, affycomp, affycompData, affyContam, affycoretools, affyPLM, affyQCReport, AGDEX, AgiMicroRna, ALL, altcdfenvs, annaffy, AnnotationDbi, AnnotationForge, antiProfilesData, ArrayExpress, arrayMvout, ArrayTools, BAGS, bcellViper, beadarray, beadarrayExampleData, beadarraySNP, bgx, BicARE, BiocCaseStudies, bioDist, BioMVCClass, BioNet, birta, bladderbatch, BrainStars, CAMERA, cancerclass, cancerdata, casper, Category, categoryCompare, CCl4, cellHTS, cellHTS2, ceu1kg, ceuhm3, CGHbase, CGHcall, CGHregions, charm, cheung2010, chimera, chroGPS, clippda, CLL, clusterStab, CMA, cn.farms, cn.mops, codelink, colonCA, convert, copa, CopyNumber450k, davidTiling, ddCt, DESeq, DEXSeq, DFP, DLBCL, dressCheck, dsQTL, DSS, dualKS, dyebias, EBarrays, EDASeq, eisa, encoDnaseI, epigenomix, epivizr, ExiMiR, fabia, fabiaData, factDesign, fastseg, fibroEset, flowBeads, flowClust, frma, gaga, gaschYHS, GeneAnswers, GeneExpressionSignature, GeneMeta, geneplotter, geneRecommender, GeneRegionScan, GeneSelectMMD, GeneSelector, geNetClassifier, genoset, GEOquery, GGdata, GOFunction, golubEsets, goProfiles, GOstats, GSEABase, GSEAlm, GSVAdata, GWASTools, hapFabia, harbChIP, HCsnip, HELP, Hiiragi2013, hmyriB36, hopach, HTqPCR, htSeqTools, HTSFilter, humanStemCell, HybridMTest, iBMQ, idiogram, inSilicoDb, inSilicoMerging, isobar, iterativeBMA, Iyer517, kidpack, leeBamViews, leukemiasEset, LMGene, lumi, lumiBarnes, lungExpression, macat, MAQCsubset, MAQCsubsetAFX, MAQCsubsetILM, maSigPro, massiR, MergeMaid, metagenomeSeq, methyAnalysis, methylumi, Mfuzz, MiChip, MIMOSA, MineICA, minfi, MiRaGE, miRNATarget, MLInterfaces, MLSeq, MmPalateMiRNA, MSnbase, Mulcom, multtest, mvoutData, Neve2006, NOISeq, nondetects, NormqPCR, nucleR, oligo, oneChannelGUI, OrderedList, OTUbase, OutlierD, PADOG, PAnnBuilder, panp, pcaMethods, pcot2, pdInfoBuilder, pdmclass, PGSEA, phenoTest, plgem, PLPE, plrs, prada, PREDA, PREDAsampledata, ProData, PROMISE, prot2D, puma, pumadata, qpcrNorm, R453Plus1Toolbox, RbcBook1, rbsurv, ReadqPCR, reb, RefPlus, Resourcerer, rHVDM, Ringo, Risa, Rmagpie, rMAT, RNAinteract, rnaSeqMap, Roleswitch, RpsiXML, rqubic, RTCA, RTopper, Rtreemix, safe, SCAN.UPC, SeqGSEA, sigaR, siggenes, simpleaffy, SpeCond, SPEM, SpikeInSubset, spkTools, splicegear, spliceSites, stepwiseCM, TDARACNE, tigre, tilingArray, topGO, tspair, tweeDEseqCountData, twilight, UNDO, VegaMC, viper, vsn, waveTiling, webbioc, xcms, XDE, yeastCC
Imports Me ABarray, aCGH, adSplit, affyILM, affyQCReport, AgiMicroRna, annmap, annotate, AnnotationDbi, AnnotationForge, annotationTools, ArrayExpressHTS, arrayQualityMetrics, ArrayTools, asmn, attract, betr, bigmemoryExtras, biocViews, BioSeqClass, biosvd, BiSeq, BrainStars, bsseq, CAFE, Category, ccTutorial, ceu1kgv, cgdv17, CGHnormaliter, charm, ChIPQC, ChIPXpress, ChromHeatMap, clipper, ConsensusClusterPlus, crlmm, cycle, DeSousa2013, easyRNASeq, EBarrays, ecolitk, ExiMiR, farms, ffpe, Fletcher2013a, flowCore, flowFlowJo, flowFP, flowMatch, flowMeans, flowQB, flowStats, flowType, flowUtils, flowViz, flowWorkspace, flowWorkspace, frma, frmaTools, gCMAP, gCMAPWeb, gcrma, genefilter, GeneMeta, geneRecommender, GeneRegionScan, GeneSelectMMD, genomeIntervals, GenomicFeatures, GEOsubmission, GGBase, ggbio, GGtools, girafe, globaltest, gmapR, GOFunction, GOstats, GSRI, GSVA, Gviz, Harshlight, HEM, hopach, HTqPCR, IdMappingAnalysis, imageHTS, KEGGdzPathwaysGEO, lapmix, LiquidAssociation, lumi, LVSmiRNA, maanova, MafDb.ALL.wgs.phase1.release.v3.20101123, MafDb.ALL.wgs.phase1.release.v3.20101123, MafDb.ESP6500SI.V2.SSA137.dbSNP138, MafDb.ESP6500SI.V2.SSA137.dbSNP138, makecdfenv, maSigPro, mBPCR, MCRestimate, MeSHDbi, metaArray, methyAnalysis, methylumi, MiChip, MIMOSA, MinimumDistance, MiPP, MMDiff, mmnet, MmPalateMiRNA, multiscan, mzR, ncdfFlow, npGSEA, nucleR, oligoClasses, openCyto, OrderedList, PADOG, PAnnBuilder, panp, pcaGoPromoter, PCpheno, piano, plateCore, plier, ppiStats, prada, PROMISE, puma, pvac, pvca, qcmetrics, QDNAseq, qpgraph, QUALIFIER, QuasR, qusage, randPack, ReadqPCR, ReportingTools, RforProteomics, RGalaxy, Rmagpie, rMAT, rols, rqubic, rSFFreader, Rtreemix, SAGx, ShortRead, SimBindProfiles, simpleaffy, SLGI, SNPchip, spade, spkTools, splicegear, synapter, TEQC, timecourse, topGO, TSSi, twilight, VanillaICE, VariantAnnotation, VariantFiltering, virtualArray, XDE, yri1kgv
Suggests Me annotate, betr, BiocCaseStudies, BiocCheck, BiocGenerics, biocViews, breastCancerMAINZ, breastCancerNKI, breastCancerTRANSBIG, breastCancerUNT, breastCancerUPP, breastCancerVDX, BSgenome, Category, ccTutorial, DART, DESeq2, dyebiasexamples, estrogen, farms, genefilter, genefu, GlobalAncova, globaltest, Heatplus, les, mammaPrintData, messina, nem, OSAT, pkgDepTools, rheumaticConditionWOLLBOLD, ROC, seventyGeneData, survcomp, TargetScore, tkWidgets, TypeInfo, vbmp, widgetTools, yeastExpData, yeastRNASeq

Package Downloads

Package Source Biobase_2.24.0.tar.gz
Windows Binary Biobase_2.24.0.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard) Biobase_2.24.0.tgz
Mac OS X 10.9 (Mavericks)
Package Downloads Report Download Stats

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