Biobase

Biobase: Base functions for Bioconductor

Bioconductor version: 2.8

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

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

Maintainer: Biocore Team c/o BioC user list <bioconductor at stat.math.ethz.ch>

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

Details

biocViews Infrastructure, Bioinformatics
Depends R (>= 2.7.0), methods, utils
Imports
Suggests tools, tkWidgets, ALL
System Requirements
License Artistic-2.0
URL
Depends On Me a4Base, a4Core, ACME, affy, affycomp, affycompData, affyContam, affycoretools, affylmGUI, affyPLM, affyQCReport, Agi4x44PreProcess, AgiMicroRna, ALL, altcdfenvs, annaffy, AnnotationDbi, ArrayExpress, arrayMvout, ArrayTools, beadarray, beadarraySNP, bgx, BicARE, BiocCaseStudies, bioDist, BioMVCClass, BioNet, bladderbatch, Category, CCl4, cellHTS, cellHTS2, ceuhm3, CGHbase, CGHcall, CGHregions, charm, cheung2010, clippda, CLL, clusterStab, CMA, cn.farms, codelink, colonCA, convert, copa, crlmm, davidTiling, ddCt, DESeq, DFP, DLBCL, dressCheck, dualKS, dyebias, EBarrays, edd, eisa, encoDnaseI, ExiMiR, factDesign, fibroEset, flowClust, flowCore, frma, gaga, gaschYHS, GeneAnswers, GeneMeta, geneplotter, geneRecommender, GeneRegionScan, GeneSelectMMD, GeneSelector, GeneSpring, GeneTraffic, genoset, GEOquery, GGBase, GGdata, GGtools, golubEsets, goProfiles, GOstats, GSEABase, GSEAlm, GSVAdata, harbChIP, HELP, hmyriB36, hopach, HTqPCR, humanStemCell, idiogram, iterativeBMA, Iyer517, kidpack, leeBamViews, LMGene, lumi, lumiBarnes, lungExpression, LVSmiRNA, macat, maDB, MAQCsubset, MAQCsubsetAFX, MAQCsubsetILM, maSigPro, MergeMaid, methylumi, Mfuzz, MiChip, MLInterfaces, MSnbase, Mulcom, multtest, mvoutData, Neve2006, oligoClasses, oneChannelGUI, ontoTools, OrderedList, OTUbase, OutlierD, PAnnBuilder, panp, pcaMethods, pcot2, pdInfoBuilder, pdmclass, PGSEA, phenoTest, plgem, PLPE, prada, ProData, PROMISE, puma, pumadata, qpcrNorm, R453Plus1Toolbox, RbcBook1, rbsurv, reb, RefPlus, Resourcerer, rHVDM, Ringo, RMAGEML, Rmagpie, rMAT, RNAinteract, rnaSeqMap, RpsiXML, RTCA, RTools4TB, Rtreemix, safe, siggenes, simpleaffy, SNPchip, SpeCond, SpikeInSubset, spkTools, TDARACNE, tigre, tilingArray, topGO, tspair, vsn, webbioc, XDE, yeastCC
Imports Me ABarray, aCGH, adSplit, affy, affyQCReport, AgiMicroRna, annotate, AnnotationDbi, annotationTools, ArrayExpressHTS, arrayQualityMetrics, ArrayTools, attract, betr, biocViews, BioSeqClass, Category, CGHnormaliter, charm, ChromHeatMap, ConsensusClusterPlus, cycle, EBarrays, ecolitk, farms, flowCore, flowFlowJo, flowFP, flowMeans, flowStats, flowUtils, flowViz, frma, frmaTools, gcrma, genefilter, GeneMeta, geneplotter, geneRecommender, GeneRegionScan, GeneSelectMMD, GeneSpring, GeneTraffic, genomeIntervals, genoset, GEOsubmission, girafe, globaltest, GOstats, GSEABase, GSRI, GSVA, Harshlight, HEM, hopach, HTqPCR, iFlow, imageHTS, lapmix, LiquidAssociation, lumi, maanova, makecdfenv, makePlatformDesign, maSigPro, mBPCR, MCRestimate, metaArray, methylumi, MiChip, MiPP, multiscan, oligo, OrderedList, PAnnBuilder, panp, PCpheno, plateCore, plier, ppiStats, prada, PROMISE, puma, pvac, qpgraph, R453Plus1Toolbox, rflowcyt, Rmagpie, rMAT, Rtreemix, safe, SAGx, ShortRead, simpleaffy, SLGI, SNPchip, spkTools, splicegear, TEQC, tigre, timecourse, topGO, twilight, webbioc, XDE, xmapcore
Suggests Me annotate, betr, BiocCaseStudies, biocViews, breastCancerMAINZ, breastCancerNKI, breastCancerTRANSBIG, breastCancerUNT, breastCancerUPP, breastCancerVDX, BSgenome, Category, dyebiasexamples, estrogen, farms, genefilter, geneplotter, GlobalAncova, globaltest, hexbin, les, nem, pkgDepTools, ROC, survcomp, tkWidgets, vbmp, widgetTools, yeastExpData, yeastRNASeq
Version 2.12.2
Since Bioconductor 1.6 (R-2.1) or earlier

Package Downloads

Package Source Biobase_2.12.2.tar.gz
Windows Binary Biobase_2.12.2.zip (32- & 64-bit)
MacOS 10.5 (Leopard) binary Biobase_2.12.2.tgz
Package Downloads Report Download Stats

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