Package: adSplit
Exports: adSplit, diana2means, drawRandomPS, randomDiana2means, makeLID2PROBESenv

Package: affycomp
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Package: affycoretools
Exports: limma2annaffy, foldFilt, vennSelect, vennCounts2, plotma, probes2table, affystart, plotDeg, plotHist, plotPCA, convert.back, hyperG2annaffy

Package: annaffy
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Package: AnnBuilder
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Package: annotate
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ExportClasses: chromLocation, FramedHTMLPage, GOTerms, homoData, HTMLPage, pubMedAbst

Package: Biobase
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Package: biocViews
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ExportMethods: coerce, show, htmlDoc, htmlValue, htmlFilename
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Package: bioDist
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Package: biomaRt
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ExportClasses: martTable, Mart

Package: Biostrings
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ExportClasses: BString, DNAString, RNAString, BStringViews

Package: bridge
Exports: bridge.2samples, bridge.3samples

Package: Category
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Package: cellHTS
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Package: cghMCR
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Package: CoCiteStats
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Package: codelink
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ExportMethods: [, show
ExportClasses: Codelink

Package: copa
Exports: copa, plotCopa, copaPerm, tableCopa, scatterPlotCopa

Package: ctc
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Package: DynDoc
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ExportMethods: chunk<-, chunk, chunkList, chunkName, chunks, codeChunk, codeChunks, evalChunk, evalEnv, getAllCodeChunks, getChunk, getDepends, getKeywords, getOptions, getRequires, getSuggests, indexEntry, numChunks, numOptions, path, pdfPath, setChunk<-, show, summary, SweaveOptions, vigPackage, vigPkgVersion
ExportClasses: chunkList, codeChunk, DynDoc, SweaveOptions, Vignette, vignetteCode

Package: EBImage
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ExportMethods: write.image, display, channels, toGray, toRGB, toRed, toGreen, toBlue, getRed, getGreen, getBlue, normalize, minMax, as.integer, as.double, as.array, summary, [, show, correctType, isCorrectType
ExportClasses: array, Image2D, Image3D

Package: edd
Exports: eddDistList, T3, U01, N01, LN01, B82, CS1, B28, centerScale, dmixnorm, edd, eddObsolete, flatQQNorm, flatQQNormY, fq.matrows, latEDtable, makeCandmat.raw, makeCandmat.theor, maxKSp, mkt, plotED, pmixnorm, qmixnorm, rmixnorm, rmixnorm.alt
ExportMethods: CDFname, genName, latexTag, Mad, med, parms, plotlim, qfName, qfun, stub, tag, testVec
ExportClasses: eddDist

Package: externalVector
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ExportClasses: noneIndex, allIndex, externalAllocator, externalResource, externalStorage, externalVector, externalVectorWithStorage, gcAllocator, indirectExternalMatrix, indirectExternalVector, matrixIndex, NAIndex, nativeStorageMethods, nativeStorageMethodsList, positiveIndex, simpleStorage, sliceIndex, vectorIndex

Package: gcrma
Exports: average.for.PAV, base.profiles, base.profiles.mm, base.profiles.nc, bg.adjust.affinities, bg.adjust.constant, bg.adjust.fullmodel, bg.adjust.gcrma, bg.adjust.mm, bg.adjust.optical, bg.parameters.ns, check.probes, compute.affinities, compute.affinities.local, compute.affinity.coef, fast.bkg, gcrma, gcrma.bg.transformation, gcrma.bg.transformation.fast, gcrma.engine, gcrma.engine2, getCDF, getProbePackage, just.gcrma, justGCRMA, left.sigma, mem.bkg, PAV, plotBaseProfiles

Package: genefilter
Exports: Anova, allNA, anyNA, coxfilter, cv, eSetFilter, fastT, ttest, shorth, rowttests, colttests, rowFtests, colFtests, rowSds, rowpAUCs, filterfun, findLargest, gapFilter, genefilter, genescale, getFilterNames, getFuncDesc, getRdAsText, isESet, kOverA, maxA, pOverA, parseArgs, parseDesc, setESetArgs, showESet
ExportMethods: genefinder

Package: GeneMeta
Exports: CountPlot, dstar, f.Q, IDRplot, multExpFDR, mu.tau2, sigmad, tau2.DL, var.tau2, zScoreFDR, zScorePermuted, zScores
ExportMethods: getdF

Package: geneplotter
Exports: alongChrom, cColor, cPlot, cScale, dChip.colors, greenred.colors, GetColor, plotChr, plotExpressionGraph, make.chromOrd, savepng, savepdf, saveeps, savetiff, smoothScatter, densCols, histStack, openHtmlPage, closeHtmlPage, multiecdf, multidensity
ExportMethods: Makesense, imageMap
ExportClasses: file, connection

Package: GeneR
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Package: GenomeBase
Exports: buildDataFiles
ExportMethods: initialize, show, $, unload
ExportClasses: BStringGenome

Package: GEOquery
Exports: parseGEO, parseGSM, parseGSE, parseGDS, parseGPL, getGEO, GDS2MA, GDS2eSet, getGEOfile
ExportMethods: Meta, Columns, GPLList, GSMList, Table, dataTable, Accession, show
ExportClasses: GDS, GEODataTable, GEOData, GSE, GPL, GSM, GDS

Package: GlobalAncova
ExportMethods: GlobalAncova, GlobalAncova.closed, Plot.genes, Plot.subjects

Package: globaltest
Exports: globaltest, permutations, sampling, geneplot, sampleplot, regressionplot, checkerboard, gt.multtest, mlogit
ExportMethods: [, show, result, p.value, length, names, names<-, sort, hist, z.score, scale, plot, combine, fit, summary, residuals, fitted.values, coefficients
ExportClasses: gt.result, gt.barplot, mlogit

Package: GOstats
Exports: combGOGraph, compCorrGraph, compGdist, dropECode, enumPairs, getEvidence, getGOChildren, getGOOntology, getGOParents, getGOTerm, getOntology, .getWHEC, GOGraph, GOLeaves, hasGOannote, idx2dimnames, isTriad, makeGOGraph, notConn, oneGOGraph, reduce2Degreek, shortestPath, simLL, simLP, simUI, triadCensus, hyperGtable, hyperG2Affy

Package: gpls
Exports: gpls, glpls1a, glpls1a.cv.error, glpls1a.train.test.error, glpls1a.mlogit, glpls1a.logit.all, glpls1a.mlogit.cv.error

Package: graph
Exports: boundary, buildRepDepGraph, hashtable, calcProb, calcSumProb, duplicatedEdges, graph2SparseM, listEdges, randomEGraph, randomGraph, randomNodeGraph, ugraph, validGraph, eWV, pathWeights, .dropEdges, aveNumEdges, sparseM2Graph, gxlTreeNEL, ftM2adjM, ftM2graphNEL, .ftM2other, int2ftM, ftM2int, aM2bpG, mostEdges, numNoEdges
ExportMethods: DFS, Dist, acc, addEdge, addNode, adj, asGraphProperty, bNode, clearNode, clusteringCoefficient, combineNodes, complement, connComp, degree, dumpGXL, eNode, edgeID, edgeL, edgeMatrix, edgeNames, edgeOrder, edgeWeights, edgemode, edgemode<-, edges, fromEdges, fromEdges<-, toEdges<-, nodes<-, fromGXL, getNodes, hash, idstring, inEdges, initialize, intersection, intersection2, intersection3, isAdjacent, isConnected, isDirected, join, label, nodeID, nodeType, nodes, numNodes, numEdges, property, property<-, removeEdge, removeNode, show, subGraph, threshold, toEdges, toGXL, union, validateGXL, coerce, toDotR, attrDefaults, attrDefaults<-, edgeDataDefaults, edgeDataDefaults<-, nodeDataDefaults, nodeDataDefaults<-, edgeData, edgeData<-, nodeData, nodeData<-, attrDataItem, attrDataItem<-, removeAttrDataItem<-
ExportClasses: gNode, gEdge, simpleEdge, hashtable, generalGraph, distGraph, clusterGraph, graphH, graph, graphNEL, file, connection, propertyHolder, graphAM, attrData

Package: hexbin
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ExportMethods: erode, hsmooth, plot, summary, show, coerce
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Package: hypergraph
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ExportClasses: Hypergraph, Hyperedge, DirectedHyperedge

Package: Icens
Exports: Bisect, BVcliques, BVclmat, BVmacprod, BVsupport, EM, EMICM, EMICMmac, Intersection, ISDM, Maclist, Macmat, MLEintvl, PGM, Plotboxes, PMGA, rescaleP, Subset, VEM, VEMICMmac

Package: idiogram
Exports: .usedChromExprs, .rwb
ExportClasses: cytoband

Package: impute
Exports: impute.knn

Package: iSPlot
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ExportMethods: initialize, updateModel, redrawView, updateView, clickEvent, motionEvent, handleMessage

Package: KEGGSOAP
Exports: color.pathway.by.objects, get.best.best.neighbors.by.gene, getBestNeighbors, get.best.neighbors.by.gene, get.compounds.by.pathway, get.enzymes.by.pathway, get.genes.by.motifs, get.genes.by.organism, get.genes.by.pathway, get.motifs.by.gene, get.paralogs.by.gene, get.pathways.by.compounds, get.pathways.by.enzymes, get.pathways.by.genes, get.pathways.by.reactions, get.reactions.by.pathway, list.databases, list.organisms, list.pathways, mark.pathway.by.objects

Package: makecdfenv
Exports: getInfoInFile, make.cdf.env, make.cdf.package, pmormm, read.cdffile
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ExportClasses: Cdf

Package: MeasurementError.cor
Exports: cor.me.vector, cor.me.matrix

Package: Mfuzz
Exports: acore, cselection, cselection, fill.NA, filter.NA, filter.std, filter.std, kmeans2, kmeans2.plot, mfuzz, mfuzz.plot, overlap, overlap.plot, partcoef, randomise, standardise, standardise2, top.count

Package: MVCClass
ExportMethods: callFun, shortName, preprocessFun, from, childUpdateDataMessage, parentUpdateDataMessage, childName, type, mData, dataName, handleMessage, modelData, modelName, linkData, virtualData, updateModel, model, viewList, controller, parentMVC, childMVCList, win, winNum, plotDevice, plotPar, drArea, dfRows, xvar, yvar, clist, ordering, motionEvent, clickEvent, updateView, redrawView, grLayout, callFun<-, shortName<-, preprocessFun<-, from<-, childUpdateDataMessage<-, parentUpdateDataMessage<-, childName<-, type<-, mData<-, dataName<-, modelData<-, modelName<-, linkData<-, virtualData<-, model<-, viewList<-, controller<-, parentMVC<-, childMVCList<-, win<-, winNum<-, plotDevice<-, plotPar<-, drArea<-, dfRows<-, xvar<-, yvar<-, clist<-, ordering<-, grLayout<-
ExportClasses: gEventFun, gAddDataMessage, gAddViewMessage, gUpdateDataMessage, gUpdateViewMessage, gAddChildMessage, gSendParentMessage, gSendChildMessage, gMessage, gAddMessage, gUpdateMessage, graphModel, exprModel, dfModel, gModel, MVC, plotView, sPlotView, spreadView, graphView, heatmapView, genView

Package: pamr
Exports: pamr.adaptthresh, pamr.batchadjust, pamr.confusion, pamr.cv, pamr.fdr, pamr.from.excel, pamr.decorrelate, pamr.geneplot, pamr.knnimpute, pamr.knnimpute.old, pamr.listgenes, pamr.makeclasses, pamr.menu, pamr.cube.root, pamr.indeterminate, pamr.pairscore, pamr.plotcen, pamr.plotcvprob, pamr.plotcv, pamr.plotfdr, pamr.predictmany, pamr.predict, pamr.score.to.class1, pamr.score.to.class2, pamr.surv.to.class2, pamr.confusion.survival, pamr.plotsurvival, pamr.plotstrata, pamr.pvalue.survival, pamr.to.excel, pamr.train, print.pamrtrained, print.pamrcved, pamr.test.errors.surv.compute, pamr.xl.compute.offset, pamr.xl.error.trace, pamr.xl.get.offset, pamr.xl.derive.adjusted.prior, pamr.xl.get.default.training.parameters, pamr.xl.get.uniform.prior, pamr.xl.get.sample.prior, pamr.xl.get.class.names, pamr.xl.get.class.labels, pamr.xl.get.number.of.classes, pamr.xl.process.data, pamr.xl.compute.cv.confusion, pamr.xl.compute.confusion, pamr.xl.is.a.subset, pamr.xl.listgenes.compute, pamr.xl.plot.test.probs.compute, pamr.xl.plot.training.error.compute, pamr.xl.plotcen.compute, pamr.xl.plotcv.compute, pamr.xl.plotcvprob.compute, pamr.xl.predict.test.class, pamr.xl.predict.test.class.only, pamr.xl.predict.test.probs, pamr.xl.test.data.impute, pamr.xl.test.errors.surv.compute, pamr.xl.test.errors.compute, pamr.xl.transform.class.labels, pamr.xl.transform.data, pamr.xl.transform.test.data, pamr.xl.plotsurvival, pamr.xl.plotsurvival.test, pamr.xl.predict.test.surv.class, pamr.xl.plotsurvival.strata, pamr.xl.test.get.soft.classes, pamr.xl.get.threshold.range, pamr.xl.get.soft.class.labels

Package: pathRender
Exports: rendercMAPPathway

Package: pdmclass
Exports: pdmClass, pdmGenes, pdmClass.cv, predict.pls, predict.svd

Package: prada
Exports: analysePlate, as.all, barploterrbar, combineFrames, csApply, ddCt, eListWrite, fitNorm2, getPradaPar, plotNorm2, devDims, plotPlate, readCytoSet, readFCS, readSDM, removeCensored, setPradaPars, thresholds, threePanelPlot, devRes, .drawCircle, .drawPie, vpLocation, touchFCS, combineGates
ExportMethods: colnames, colnames<-, description, description<-, exprs, exprs<-, initialize, length, [, [[, [[<-, pData, phenoData, phenoData<-, show, plot, gate, applyGate, drawGate, gate<-, names, names<-, as.gateSet, nrow, ncol, appendGates
ExportClasses: cytoFrame, cytoSet, gate, gateSet, ddCtSet

Package: PROcess
Exports: bslnoff, isPeak, pk2bmkr, getMzs, lnn, quality, sigma, getPeaks, noise, read.files, specZoom, intg, peaks, rmBaseline, renorm, binning, gelmap, aveSpec, align, getPeaks2, avesd, is.multiple

Package: rama
Exports: arrange.row, est.shift, fit.model, is.row.na, ls.effect, mat.mean, ratio.plot, weight.plot

Package: RBGL
Exports: articulationPoints, astarSearch, aver.wavefront, bandwidth, bellman.ford.sp, betweenness.centrality.clustering, biConnComp, brandes.betweenness.centrality, circle.layout, connectedComp, cuthill.mckee.ordering, dag.sp, dijkstra.sp, edgeConnectivity, edmunds.karp.max.flow, extractPath, floyd.warshall.all.pairs.sp, fruchtermanReingoldForceDirectedLayout, gursoyAtunLayout, highlyConnSG, init.incremental.components, incremental.components, is.triangulated, ith.wavefront, isomorphism, johnson.all.pairs.sp, kamada.kawai.spring.layout, kCores, kCliques, kingOrdering, maxClique, maxWavefront, minCut, minDegreeOrdering, mstree.kruskal, prim.minST, gprofile, push.relabel.max.flow, randomGraphLayout, rms.wavefront, same.component, separates, sequential.vertex.coloring, sloan.ordering, sp.between, sp.between.old, sp.between.scalar, strongComp, transitive.closure, tsort
ExportMethods: bfs, dfs

Package: Rdbi
Exports: dbAppendTable, dbClearResult, dbColumnInfo, dbConnect, dbConnectionInfo, dbDisconnect, dbGetQuery, dbGetResult, dbListTables, dbReadTable, dbReconnect, dbResultInfo, dbSendQuery, dbWriteTable, double.quote, expand.asis, .Last.lib, list.to.csv, list.to.key.pair.string, printListPairs, single.quote, strip.line.feeds

Package: RdbiPgSQL
Exports: make.db.names, PgSQL, psql, rpgsql.cast.values, rpgsql.cast.values.1042, rpgsql.cast.values.1043, rpgsql.cast.values.1082, rpgsql.cast.values.1083, rpgsql.cast.values.25, rpgsql.cast.values.default, rpgsql.data.type, rpgsql.data.type.dates, rpgsql.data.type.default, rpgsql.data.type.times, rpgsql.format.values, rpgsql.format.values.dates, rpgsql.format.values.default, rpgsql.format.values.times

Package: Resourcerer
Exports: resourcerer2BioC, getResourcerer

Package: rflowcyt
Exports: ContourScatterPlot, standard, boxplot.FCS, plotdensity.FCS, plotECDF.FCS, plotvar.FCS, parallel.coordinates, parallelCoordinates, ImageParCoord, read.FCS, read.series.FCS, convertS3toS4, make.grid, make.density, pairs.CSP, legend.CSP, metaData, percentile.FCS, PercentPos.FCS, ProbBin.FCS, breakpoints.ProbBin, createGate, emp.f, extractGateHistory, extractGatedData, fcs.type.facscan256, get.h, get.num.modes, get.p, pkci2.flowcytest, summary.ProbBin.FCS, runflowcytests, plot2sets.FCS, plotQA.FCS, MODE, icreateGate, showgate.FCS, JointImageParCoord, plot.ProbBin.FCS, KS.flowcytest, WLR.flowcytest, ROC.FCS
ExportMethods: print, show, summary, plot, fluors, addParameter, checkvars, coerce, dim.FCS, equals, fixvars
ExportClasses: FCS, FCSmetadata, FCSsummary, FCSgate

Package: Rgraphviz
Exports: agopen, agwrite, agread, graphvizVersion, buildNodeList, buildEdgeList, removedEdges, getDefaultAttrs, getNodeNames, getNodeLabels, checkAttrs, layoutGraph, makeNodeAttrs, pieGlyph, drawAgNode, drawTxtLabel
ExportMethods: lines, plot, AgNode, AgNode<-, getNodeXY, agraph, edgemode, laidout, layoutType, boundBox, AgEdge, AgEdge<-, getNodeXY, botLeft, upRight, shape, style, color, fillcolor, getNodeCenter, getNodeHeight, getNodeRW, getNodeLW, name, txtLabel, arrowsize, arrowhead, arrowtail, splines, sp, ep, head, tail, numSplines, getSpline, cPoints, pointList, bezierPoints, bLines, getX, getY, getPoints, labelText, labelColor, labelLoc, labelJust, labelWidth, labelFontsize, show, edgeNames, edgeL, toDot, imageMap, from, to
ExportClasses: Ragraph, boundingBox, AgNode, AgEdge, BezierCurve, xyPoint, AgTextLabel, pNode, pEdge

Package: ROC
Exports: AUC, AUCi, dxrule.sca, pAUC, pAUCi, ROC, rocdemo.sca, trapezint
ExportMethods: plot
ExportClasses: rocc

Package: RSNPper
Exports: .SNPperBaseURL, dot, geneInfo, geneLayout, geneSNPs, ginfoHandler, ginrangeHandler, glayHandler, itemsInRange, nsnpHandler, outPaste, sinrangeHandler, SNPinfo, snpinfoHandler, useSNPper, useSNPper2

Package: Ruuid
Exports: getuuid
ExportMethods: show, as.character, ==, !=, uuid
ExportClasses: Ruuid, uuidt

Package: SAGElyzer
Exports: butsInTBox, calNormFact, chunkKNN, closeConn, con4Unix, con4Win, doTag2UG, doUG2Tag, executeQuery, findNeighborTags, findNG4Tag, GEOSAGEWidget, getBinding, getColNames, getColSQL, getColumnNames, getDBArgs, getDMProc, getFileNames, getGEOSAGE, getKNN, getKNNProc, getLibCounts, getLibInfo, getLibNNum, getMapFileName, getNormFactor, getSAGEKNN, getSAGESQL, getSampleId, getSLyzerArgs, getTableNames, getTag, getTargetRow, getTasks, getTaskTips, getTotalRNum, getUniqTags, getUnixDBArgs, getWinDBArgs, KNNArgsWidget, linkTag2UG, makeConnection, mapFile2Tag, mapLib2File, mapSAGE2UG, mapSAGEWidget, mergeSAGE, mergeSAGEWidget, modSLyzerArgs, noChunkKNN, procSAGE, query4Unix, queryInfoDB, querySAGE, remapTagNUG, runSLyzer, SAGE4Unix, SAGEFromGEO, SAGELyzer, SAGEMapper, SAGEWidget, setKNNArgs, setSLyzerArgs, showDBError, tableExists, writeSAGE2DB, writeSAGE4Unix, writeSAGE4Win, writeSAGECounts, writeSAGEKNN, writeSLyzerArgs

Package: sizepower
Exports: sampleSize.randomized, sampleSize.matched, power.randomized, power.matched, power.multi

Package: stam
Exports: stam.net, stam.cv, stam.fit, stam.predict, stam.evaluate, stam.writeHTML, stam.graph.plot, stam.rgb.colors
ExportMethods: getGOterm, getGOchildren, getGOparents, writeHTML, print, initialize
ExportClasses: stamNode, stamINode, stamLeaf, stamNet, stamFit, stamCV, stamPrediction, stamEval

Package: tilingArray
Exports: normalizeByReference, segment, costMatrix, findSegments, sampleStep, readCel2eSet, posMin, otherStrand, plotAlongChrom, comparisonPlot, residuals.breakpointsPretend, breakpoints.breakpointsPretend
ExportMethods: plot, show, confint, logLik
ExportClasses: segmentation

Package: tkWidgets
Exports: DPExplorer, args2XML, argsWidget, dataViewer, dbArgsWidget, eExplorer, fileBrowser, fileWizard, find.type, guess.header, guess.sep, importPhenoData, importWizard, listSelect, objViewer, objectBrowser, pExplorer, pickItems, tkMIAME, tkSampleNames, tkphenoData, vExplorer, viewVignette, WLValue<-, WName, WRButtons, values.Widget, WValue, WValue<-, WbuttonFun, WbuttonText, WcanEdit, WfromText, WpostFun, WpreFun, WtoText, WwList, WwList<-, print.Widget, WLValue, WEnd, appendSepDir, getWvalues, hasChar, stdType, objNameToList, getPkgContents, getFileContents, pickFiles, pickObjs, print.pWidget, hasPrefix, hasSuffix, hasChar, formatArg
ExportClasses: colInfo

Package: vsn
Exports: vsn, vsnh, vsnPlotPar, getIntensityMatrix, normalize.AffyBatch.vsn, sagmbAssess, sagmbSimulateData, meanSdPlot, nchoosek

Package: widgetInvoke
Exports: createWF, widgetInvoke, fun2wFun, writeWIxml, readWIxml, testWIfun
ExportMethods: argDefault, argLocation, argName, argRequired, argType, argWidgetType, funName, funArgList, nItems, itemNames, defaultValue, returnType
ExportClasses: wFun, funArg, SimpleW

Package: widgetTools
Exports: button, checkButton, dropdownList, entryBox, env<-, funs, funs<-, label, listBox, makeViewer, oneVScrList, pWidgets, getListOption, pWidgets<-, postFun, postFuns<-, preFun, preFuns<-, radioButton, textBox, tooltip, widget, writeList, writeText, vName, vName<-, wEnv, wEnv<-, wFuns, wFuns<-, wHeight, wHeight<-, wName, wName<-, wNotify, wNotify<-, wPostFun, wPostFun<-, wPreFun, wPreFun<-, wTitle, wTitle<-, wType, wType<-, wValue, wValue<-, wView, wView<-, safeFileOpen, widgetView, getListValue, getTextValue, getEntryValue
ExportClasses: basicPW, widget, widgetView