Package: ACME
Exports: do.aGFF.calc, findRegions, read.resultsGFF, findClosestGene, write.sgr, getRefflat
ExportMethods: show, print, plot
ExportClasses: aGFF, aGFFCalc

Package: AnnBuilder
Exports: ABPkgBuilder, athPkgBuilder, chrLocPkgBuilder, cMapPathBuilder, GOPkgBuilder, homoPkgBuilder, KEGGPkgBuilder, SPPkgBuilder, yeastPkgBuilder, writeSourceUrlConfig, readSourceUrlConfig, downloadSourceData, makeSrcInfo, map2LL, getSrcUrl, queryGEO, parseData, loadFromUrl, readData, createEmptyDPkg, parser, EG, GEO, UG, KEGG, GP, IPI, YEAST, GO, PFAM, srcUrl, baseFile, getFileExt, pfamBuilder, resolveMaps, getSrcUrl
ExportClasses: EG, GEO, UG, GO, KEGG, GP, IPI, YEAST, PFAM, pubRepo

Package: BSgenome
Exports: available.genomes, getSeq, buildDataFiles
ExportMethods: initialize, names, show, length, [[, $, seqnames, mseqnames, unload
ExportClasses: BSgenome

Package: BioMVCClass
ExportMethods: ordering, grLayout, rNames, ordering<-, grLayout<-, rNames<-, incidMat, gTestStat, gsTestStat, expData, descr, incidMat<-, gTestStat<-, gsTestStat<-, expData<-, descr<-
ExportClasses: graphModel, exprModel, graphView, heatmapView, GSE, gseModel

Package: Biobase
Exports: Aggregate, addVigs2WinMenu, as.data.frame.ExpressionSet, assayDataNew, assayDataValidMembers, assayDataElementNames, assayDataElement, assayDataElementReplace, assayDataElement<-, biocReposList, cache, copyEnv, copySubstitute, getObjectSlots, createPackage, df2pD, dumpPackTxt, esApply, getPkgVigs, isUnique, l2e, listLen, matchpt, multiassign, note, openPDF, openVignette, package.version, reverseSplit, rowMax, rowMedians, rowMin, rowQ, read.exprSet, read.phenoData, read.pD, readExpressionSet, read.AnnotatedDataFrame, read.MIAME, selectSome, strbreak, testBioCConnection, lcSuffix, lcPrefix, lcPrefixC, updateOldESet, updateObjectFromSlots, userQuery
ExportMethods: [, [[, $, abstract, addVarMetadataEntry, aggenv, aggfun, annotatedDataFrameFrom, annotation, coerce, combine, content, contents, convertVarLabels, description, dims, eList, experimentData, expinfo, exprs, exprs2excel, featureNames, featureData, featureData<-, geneNames, getExpData, getUnits, getVarMetadata, hybridizations, initfun, iter, length, locked, makeDataPackage, normControls, notes, otherInfo, pData, phenoData, preproc, sampleNames, samples, se.exprs, split, storageMode, update2MIAME, varLabels, varMetadata, reporterInfo, annotation<-, description<-, eList<-, experimentData<-, exprs<-, featureNames<-, geneNames<-, notes<-, preproc<-, pData<-, phenoData<-, sampleNames<-, varLabels<-, varMetadata<-, assayData<-, reporterInfo<-, se.exprs<-, storageMode<-, write.exprs, as.data.frame.exprSet, dim, dimLabels, assayData, reporterNames, pubMedIds, pubMedIds<-, isVersioned, isCurrent, classVersion, classVersion<-, updateObject, updateObjectTo, initialize, show, Compare
ExportClasses: aggregator, container, eSet, phenoData, MIAME, characterORMIAME, annotatedDataset, AssayData, data.frameOrNULL, exprMatrix, exprSet, AnnotatedDataFrame, Versions, VersionsNull, Versioned, VersionedBiobase, ExpressionSet, MultiSet, SnpSet, ScalarCharacter

Package: Biostrings
Exports: readFASTA, writeFASTA, gregexpr2, IUPAC_CODE_MAP, AMINO_ACID_CODE, GENETIC_CODE, DNA_ALPHABET, RNA_ALPHABET, AA_ALPHABET, letter, BString, DNAString, RNAString, AAString, views, adjacentViews, matchDNAPattern, alignScore
ExportMethods: initialize, length, [, [[, show, ==, !=, as.character, toString, nchar, toComplex, as.complex, as.matrix, as.list, start, end, alphabet, subBString, substr, substring, subject, first, last, width, desc, BStringViews, writeFASTA, reverse, complement, reverseComplement, alphabetFrequency, matchPattern, countPattern, mismatch, matchProbePair, mask, needwunsQS
ExportClasses: BString, DNAString, RNAString, AAString, BStringViews

Package: Category
Exports: .doHyperGTest, applyByCategory, cateGOry, chrBandInciMat, findAMstats, geneGoHyperGeoTest, geneKeggHyperGeoTest, getPathNames, makeChrBandGraph, makeChrBandInciMat, makeEBcontr, MAPAmat, probes2MAP, probes2Path, ttperm
ExportMethods: hyperGTest, universeBuilder, categoryToEntrezBuilder, categoryName, makeValidParams, chrGraph, pvalues, geneCounts, universeCounts, universeMappedCount, geneMappedCount, annotation, geneIds, geneIds<-, geneIdsByCategory, geneIdUniverse, condGeneIdUniverse, testName, pvalueCutoff, pvalueCutoff<-, testDirection, testDirection<-, description, universeGeneIds, ontology, ontology<-, conditional, conditional<-, isConditional, oddsRatios, expectedCounts, htmlReport, sigCategories, initialize, show, summary
ExportClasses: HyperGParams, GOHyperGParams, KEGGHyperGParams, PFAMHyperGParams, ChrMapHyperGParams, HyperGResultBase, HyperGResult, ChrMapHyperGResult

Package: CoCiteStats
Exports: actorAdjTable, gene.geneslist.sig, gene.geneslist.statistic, gene.gene.statistic, paperLen, twowayTable, twTStats

Package: DynDoc
Exports: baseVigDesc, editVignetteCode, getPkgVigList, getVigInfo, getVigInfoNames, getVignette, getVignetteCode, getVignetteHeader, hasVigHeaderField, tangleToR, tangleToRFinish, tangleToRRuncode, tangleToRSetup, .transformNames, transformVigInfoLine
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
Exports: Image, is.Image, stopIfNotImage, read.image, choose.image, TrueColor, Grayscale, morphKern, hist.Image, image.Image, print.Image, propagate
ExportMethods: copy, display, animate, write.image, header, assert, combine, tile, show, [, channel, features, features<-, colorMode, colorMode<-, fileName, fileName<-, compression, compression<-, resolution, resolution<-, sampleFilter, sampleFilter<-, imageData, imageData<-, blur, gblur, contrast, denoise, despeckle, edge, enhance, equalize, cgamma, mediansmooth, noise, resize, rotate, resample, segment, sharpen, umask, thresh, athresh, cthresh, affinet, modulate, negate, normalize, normalize2, fill, flip, flop, erode, dilate, opening, closing, distmap, watershed, getObjects, paintObjects, matchObjects, stackObjects, rmObjects, propagate
ExportClasses: Image

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: GGtools
Exports: HMworkflow, thinHM2rac, exclMono, thinHM2meta, df2snpMeta, make_racExSet, countRare, getRare, genesym, snpID, getpsid, oneFit, genoStrings, extract_p, plot_mlp, fastAGM, fastHET, plot_EvG, snps3PrimeTo, snps5PrimeTo, snpsNear, Strains2rac, wrapSNPmetaWh, INBREDSworkflow, addAnno, tx_rsnum, getSNPindices
ExportMethods: snps, snpNames, racAssays, snpScreen, show, rarebase, SNPalleles, exprs, initialize, coerce
ExportClasses: racExSet, genesym, snpScreenResult, snpMeta, snpMetaWhole, oGtypeExSet

Package: GOstats
Exports: combGOGraph, compCorrGraph, compGdist, enumPairs, .getWHEC, GOGraph, GOLeaves, idx2dimnames, isTriad, makeGOGraph, notConn, oneGOGraph, reduce2Degreek, shortestPath, simLL, simLP, simUI, triadCensus, hyperGtable, hyperG2Affy, GOHyperG, probeSetSummary, termGraphs, inducedTermGraph, plotGOTermGraph, selectedGenes
ExportMethods: hyperGTest, getGoGraph, pvalues, isConditional, description, oddsRatios, expectedCounts, htmlReport, goDag, geneCounts, universeCounts, geneIds, geneIdUniverse, condGeneIdUniverse, universeMappedCount, geneMappedCount, annotation, testName, summary
ExportClasses: GOHyperGResult

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

Package: GeneR
Exports: .seqSize, nSeq, .paramFromIndex, as.segSet, or.segSet, Xor.segSet, not.segSet, and.segSet, plot.segSet, as.data.frame.segSet, as.matrix.segSet, as.globalSeg, or.globalSeg, Xor.globalSeg, not.globalSeg, and.globalSeg, size.globalSeg, Length.globalSeg, Max.globalSeg, Min.globalSeg, as.matrix.globalSeg, plot.globalSeg, range.globalSeg, plot.profile, and.default, or.default, Xor.default, not.default, size.default, Min.default, Max.default, Length.default, insertSeq, strComp, strCompoSeq, placeString, revComp, getSeq, exactWord, dnaToRna, rnaToDna, assemble, concat, compoSeq, appendSeq, bankDensityProfile, densityProfile, freeSeq, freeAllSeq, sizeSeq, sliceSegment, seqSkew, GCcontent, setStrand, getStrand, setBegSeq, getBegSeq, setSeqSize, getSeqSize, getEndSeq, setAccn, getAccn, setParam, getParam, RtoA, AtoT, TtoA, RtoT, TtoR, AtoR, indexFasta, indexGbk, indexEmbl, makeIndex, deleteCR, posMaskedSeqFile, posMaskedSeq, upperSeq, lowerSeq, getOrfs, maxOrf, strTranslate, translate, showTable, readEmblLocation, readGbkLocation, readSeq, sizeSeqEmbl, sizeSeqGbk, sizeSeqFasta, fastaDescription, readFasta, readGbk, readEmbl, randomSeq, shuffleSeq, strReadEmbl, strReadGbk, strReadFasta, or, Xor, and, not, size, Min, Max, Length, .minimalSeg, relist, relistage, xorRecouvr, seqSrs, seqNcbi, writeEmblLine, writeEmblComment, writeEmblSeq, writeFasta, strWriteFasta, mask, unionSeg, bankSummary, readEmblDescript, .transf.limites, Match

Package: GeneticsBase
Exports: LD, LDband, LDdist, alleleCount, alleleLevels, alleles, alleleSummary, binsearch, callCodes, callCodes<-, carrier, convert, decodeCallCodes, description, description<-, desMarkers, diseq.inner, diseq.ci, dominant, ci.balance, errorMetrics, errorMetrics<-, extractAlleles, founderGeneSet, geneSet, genotypeFileFormats, genotypeLevels, genotypes, genotypeSummary, gregorius, haplo.score.w, haplo.score.slide.w, haplo.em.w, haplo.scan.w, head, HWE, HWE.chisq, HWE.exact, heterozygote, homozygote, html, html.GeneticsBaseSummary, html.markerSummary, html.LD, latex, latex.GeneticsBaseSummary, latex.markerSummary, latex.LD, LDView, left, makeMarkerInfo, makeTransTable, makeTransTableList, markerFileFormats, markerInfo, markerInfo<-, markerNames, markerSummary, missingCodes, missingCodes<-, nallele, nmarker, nobs, notes, notes<-, ped2geneSet, PGtables, phase, phase<-, phenotypeFileFormats, ploidy, ploidy<-, power.casectrl, print.GeneticsBaseSummary, print.markerSummary, read.fbat.phe, read.pbat.phe, read.phe, readGenes, readGenes.fbat.ped, readGenes.hapmap.ped, readGenes.pbat.ped, readGenes.ped, readGenes.perlegen, readGenes.pfizer, read.pfizer.Listing, read.pfizer.Pivot, recessive, right, sampleInfo, sampleInfo<-, studyInfo, studyInfo<-, summary.LD, tail, transTables, transTables<-, txt, txt.default
ExportMethods: head, html, latex, left, plot, right, show, tail, LD, LDband, LDdist, [, [[, alleleCount, alleleLevels, alleles, callCodes, callCodes<-, carrier, description, description<-, dominant, errorMetrics, errorMetrics<-, genotypeLevels, genotypes, head, heterozygote, homozygote, HWE, markerInfo, markerInfo<-, markerNames, missingCodes, missingCodes<-, nallele, nmarker, nobs, notes, notes<-, phase, phase<-, ploidy, ploidy<-, plot, recessive, sampleInfo, sampleInfo<-, show, studyInfo, studyInfo<-, tail, transTables, transTables<-
ExportClasses: LD, LDband, LDdist, geneSet

Package: GeneticsDesign
Exports: gregorius, power.casectrl, GPC, GPC.default

Package: GeneticsPed
Exports: Pedigree, as.Pedigree, is.Pedigree, generatePedigree, check, checkId, codeUnit, extend, family, family<-, generation, generation<-, geneContribution, isFounder, nIndividual, removeIndividual, summary.Pedigree, geneFlowT, geneFlowTinv, gameteFlowM, kinship, mendelianSamplingD, inbreeding, inverseAdditive, relationshipAdditive, gpi

Package: GlobalAncova
Exports: GAGO, GlobalAncova.decomp, pair.compare, Plot.sequential, Plot.all
ExportMethods: GlobalAncova, GlobalAncova.closed, Plot.genes, Plot.subjects

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

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, search.compounds.by.name, search.glycans.by.name, search.compounds.by.composition, search.glycans.by.composition, search.glycans.by.mass, search.compounds.by.mass, search.compounds.by.subcomp, search.glycans.by.kcam, bget

Package: MVCClass
ExportMethods: callFun, shortName, preprocessFun, from, childUpdateDataMessage, parentUpdateDataMessage, childName, type, mData, dataName, handleMessage, modelData, modelName, linkData, virtualData, updateModel, provideInfo, modelVar, model, viewList, controller, parentMVC, childMVCList, win, winNum, plotDevice, plotPar, drArea, dfRows, xvar, yvar, clist, motionEvent, clickEvent, identifyView, updateView, redrawView, xval, yval, callFun<-, shortName<-, preprocessFun<-, from<-, childUpdateDataMessage<-, parentUpdateDataMessage<-, childName<-, type<-, mData<-, dataName<-, modelVar<-, modelData<-, modelName<-, linkData<-, virtualData<-, model<-, viewList<-, controller<-, parentMVC<-, childMVCList<-, win<-, winNum<-, plotDevice<-, plotPar<-, drArea<-, dfRows<-, xvar<-, yvar<-, clist<-, xval<-, yval<-
ExportClasses: gEventFun, gAddDataMessage, gAddViewMessage, gUpdateDataMessage, gUpdateViewMessage, gAddChildMessage, gSendParentMessage, gSendChildMessage, gMessage, gModifyMessage, gAddMessage, gUpdateMessage, dfModel, gModel, MVC, singleModelMVC, linkedModelMVC, plotView, sPlotView, spreadView, genView, gAskAncestorMessage, qqPlotView

Package: MassSpecWavelet
Exports: cwt, getLocalMaximumCWT, getRidge, getRidgeLength, identifyMajorPeaks, localMaximum, peakDetectionCWT, plotLocalMax, plotPeak, plotRidgeList, tuneInPeakInfo

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

Package: MergeMaid
Exports: mergeExprs
ExportMethods: exprs, geneNames, names, notes, phenoData, length, show, summary, geneStudy, coeff, stdcoeff, zscore, pairwise.cors, maxcors, integrative.cors, modelOutcome, intCor, plot, hist, intcorDens, intersection, exprs<-, geneNames<-, names<-, notes<-, phenoData<-, geneStudy<-, coeff<-, stdcoeff<-, zscore<-
ExportClasses: mergeExpressionSet, mergeCor, mergeCoeff

Package: Mfuzz
Exports: acore, cselection, cselection, fill.NA, filter.NA, filter.std, filter.std, kmeans2, kmeans2.plot, mfuzz, mfuzz.plot, mfuzz.plot2, mfuzzColorBar, overlap, overlap.plot, partcoef, randomise, standardise, standardise2, top.count

Package: PGSEA
Exports: .rwb
ExportClasses: smc

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

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, doSnpinfo, doGeneinfo
ExportMethods: show, geneDetails, popDetails, submitters, toolInfo, allGeneMeta
ExportClasses: SNPperMeta, SNPperGeneMeta, fromSNPper

Package: RWebServices
Exports: createMap, generateDataMap, generateDataTest, generateFunctionMap, regAddonCvt, regAddonCvt2, regTestCvt, printLookup, checkJava2R, reflectObj, checkPkgVersion, cvtCharacterFromJava, cvtCharacterToJava, matchCharacterToJava, cvtIntegerFromJava, cvtIntegerToJava, matchIntegerToJava, cvtLogicalFromJava, cvtLogicalToJava, matchLogicalToJava, cvtNumericFromJava, cvtNumericToJava, matchNumericToJava, cvtRawFromJava, cvtRawToJava, matchRawToJava, cvtComplexFromJava, cvtComplexToJava, matchComplexToJava, cvtVectorFromJava, cvtVectorToJava, matchVectorToJava, cvtListFromJava, cvtListToJava, matchListToJava, cvtArrayFromJava, cvtArrayToJava, matchArrayToJava, cvtMatrixFromJava, cvtMatrixToJava, matchMatrixToJava, cvtFactorFromJava, cvtFactorToJava, matchFactorToJava, cvtDataFrameFromJava, cvtDataFrameToJava, matchDataFrameToJava, cvtEnvFromJava, cvtEnvToJava, matchEnvToJava, cvtUnknownFromJava, cvtUnknownToJava, matchUnknownToJava, cvtCharacterToJava2, matchCharacterToJava2, cvtIntegerToJava2, matchIntegerToJava2, cvtLogicalToJava2, matchLogicalToJava2, cvtNumericToJava2, matchNumericToJava2, cvtRawToJava2, matchRawToJava2, cvtComplexFromJava2, cvtComplexToJava2, matchComplexToJava2, cvtListToJava2, matchListToJava2, cvtFactorFromJava2, cvtFactorToJava2, matchFactorToJava2, cvtDataFrameFromJava2, cvtDataFrameToJava2, matchDataFrameToJava2, cvtCharArrayFromJava2, cvtCharArrayToJava2, matchCharArrayToJava2, cvtIntegerArrayFromJava2, cvtIntegerArrayToJava2, matchIntegerArrayToJava2, cvtNumericArrayFromJava2, cvtNumericArrayToJava2, matchNumericArrayToJava2, cvtLogicalArrayFromJava2, cvtLogicalArrayToJava2, matchLogicalArrayToJava2, cvtRawArrayFromJava2, cvtRawArrayToJava2, matchRawArrayToJava2, cvtComplexArrayFromJava2, cvtComplexArrayToJava2, matchComplexArrayToJava2, cvtCharMatrixFromJava2, cvtCharMatrixToJava2, matchCharMatrixToJava2, cvtIntegerMatrixFromJava2, cvtIntegerMatrixToJava2, matchIntegerMatrixToJava2, cvtNumericMatrixFromJava2, cvtNumericMatrixToJava2, matchNumericMatrixToJava2, cvtLogicalMatrixFromJava2, cvtLogicalMatrixToJava2, matchLogicalMatrixToJava2, cvtRawMatrixFromJava2, cvtRawMatrixToJava2, matchRawMatrixToJava2, cvtComplexMatrixFromJava2, cvtComplexMatrixToJava2, matchComplexMatrixToJava2, cvtEnvFromJava2, cvtEnvToJava2, matchEnvToJava2, unpackAntScript, sinkSetup, sinkRetrieve
ExportMethods: typeInfo2Java, show
ExportClasses: SinkOutput, RJavaSignature, RJavaPkgFunctions, RawMatrix, CharMatrix, LogicalMatrix, IntegerMatrix, NumericMatrix, ComplexMatrix, RawArray, CharArray, LogicalArray, IntegerArray, NumericArray, ComplexArray

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, dbAppendTable

Package: Resourcerer
Exports: resourcerer2BioC, getResourcerer

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

Package: Ringo
Exports: autocor, chipAlongChrom, corPlot, computeRunningMedians, sliding.median, sliding.quantile, findPeaksOnSmoothed, peakByThreshold, newPeak, relatePeaks, preprocess, nimblegenNorm, readNimblegen, as.data.frame.peakList

Package: Rredland
Exports: openRedlWorld, readRDF, restoreBDB, cleanXSDT, getArcsWith, getObjectProperties, getDatatypeProperties, getOWLClasses, getPropertyRange, getOWLProperties, getPropertiesWithDomain, getClassElements, getClassGraph, getOWLSubclasses, nodeFromURIString, world
ExportMethods: ref, freeRedl, getStatus, setStatus, makeRedlURI, show, size, coerce, world
ExportClasses: redlWorld, redlModel, redlURI, redlNode

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: SAGx
Exports: clin2mim, cluster.q, estimatep0, fetchSignal, firstpass, fom, fp.fn, Fstat, gap, GSEA.mean.t, JT.test, list.experiments, list.intersection.p, mat2TeX, myclus, normalise, one.probeset.per.gene, outlier, p0.mom, pava, pava.fdr, R2BASE, R2mim, rank.genes, rank.trend, rsd.test, samrocN, samrocNboot, union.of.pways, Xprep, Xprep.resid
ExportMethods: show, plot
ExportClasses: samroc.result

Package: SNPchip
Exports: showSummary, centromere, chromosomeSize, unsplitS4
ExportMethods: getSnpAnnotation, alleleA, alleleB, chromosome, chromosomeAnnotation, chromosomeAnnotation<-, coerce, copyNumber, dbSnpId, enzyme, fData, fData<-, fragmentLength, initialize, plotSnp, position, show, smoothSnp, summary
ExportClasses: AnnotatedSnpSet, AnnotatedSnpCallSet, AnnotatedSnpCopyNumberSet

Package: ScISI
Exports: JaccardCoef, ScISI2html, calcGraphStats, checkComplex, checkSGN, compBijection, compareComplex, createGODataFrame, createGOMatrix, createMipsDataFrame, createMipsMatrix, createYeastDataObj, edgeProp, findSubComp, getAPMSData, getGOInfo, getLocOrfs, getMipsInfo, graphSumStats, list2Matrix, maximizeSimilarity, meanDeg, mergeBGMat, recCompSize, rmByEvi, runAlignment, runCompareComplex, sumStats, unWantedComp, xtraGONodes
ExportMethods: ID, Desc, getURL
ExportClasses: yeastData

Package: TypeInfo
Exports: IndependentTypeSpecification, SimultaneousTypeSpecification, ReturnTypeSpecification, TypedSignature, StrictIsTypeTest, InheritsTypeTest, checkArgs, checkReturnValue, typeInfo, typeInfo<-, paramNames, hasParameterType, hasReturnType
ExportMethods: initialize, coerce, checkArgs, showTypeInfo
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Package: adSplit
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Package: affycomp
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Package: affycoretools
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Package: annaffy
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Package: annotate
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Package: arrayQuality
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Package: beadarray
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ExportClasses: ExpressionSetIllumina, BeadLevelList

Package: beadarraySNP
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Package: bgx
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Package: bioDist
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Package: biocViews
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ExportMethods: coerce, show, htmlDoc, htmlValue, htmlFilename
ExportClasses: Htmlized, PackageDetail, pdAuthorMaintainerInfo, pdVignetteInfo, pdDownloadInfo, pdDetailsInfo, pdDescriptionInfo, pdVigsAndDownloads, RepositoryDetail, rdPackageTable, BiocView, bvTitle, bvPackageTable, bvSubViews, bvParentViews

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

Package: cellHTS
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Package: cghMCR
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ExportClasses: cghMCR

Package: codelink
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ExportMethods: [, show
ExportClasses: Codelink

Package: copa
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Package: cosmo
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ExportMethods: plot, summary, print, show
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Package: cosmoGUI
Exports: constraintBuilder

Package: ctc
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Package: edd
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Package: fbat
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Package: flowCore
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ExportClasses: flowFrame, flowSet, filter, rectangleGate, polygonGate, polytopeGate, ellipsoidGate, sampleFilter, multiFilter, filterResult, randomFilterResult, logicalFilterResult, multipleFilterResult, setOperationFilter, norm2Filter, kmeansFilter, transform, transformMap, transformList, transformFilter

Package: flowViz
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Package: gaggle
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Package: gcrma
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Package: genefilter
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ExportMethods: genefinder, show, plot, [, sens, spec, area, pAUC, AUC, rowpAUCs, nsFilter
ExportClasses: rowROC

Package: geneplotter
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Package: globaltest
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Package: gpls
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Package: graph
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Package: hexbin
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Package: hypergraph
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Package: iSNetwork
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ExportMethods: initialize, updateModel, updateView, clickEvent, motionEvent, handleMessage, identifyView, provideInfo

Package: iSPlot
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Package: idiogram
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ExportClasses: cytoband

Package: impute
Exports: impute.knn

Package: limma
ExportMethods: show
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Package: makecdfenv
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ExportClasses: Cdf

Package: marray
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Package: multtest
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Package: oligo
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ExportClasses: FeatureSet, ExpressionFeatureSet, SnpFeatureSet, TilingFeatureSet, SnpQSet, SnpCopyNumberSet, SnpCallSet, oligoSnpSet, ExonFeatureSet, PDInfo, DBPDInfo, SNPPDInfo, AffySNPPDInfo, platformDesign

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: pcaMethods
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Package: pdInfoBuilder
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ExportClasses: PkgSeed, PDInfoPkgSeed, AffySNPPDInfoPkgSeed

Package: pdmclass
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Package: pkgDepTools
Exports: getInstallOrder, makeDepGraph

Package: prada
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Package: quantsmooth
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Package: rama
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Package: rbsurv
Exports: rbsurv

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, rect.box.idx
ExportMethods: print, show, summary, plot, fluors, addParameter, checkvars, coerce, dim.FCS, equals, fixvars
ExportClasses: FCS, FCSmetadata, FCSsummary, FCSgate

Package: seqLogo
Exports: seqLogo, makePWM
ExportMethods: plot, summary, print, show
ExportClasses: pwm

Package: siggenes
Exports: args.ebam, args.finda0, args.sam, ebam, ebam2excel, ebam2html, filterALL, find.a0, fudge2, help.ebam, help.finda0, help.sam, link.genes, link.siggenes, list.siggenes, pi0.est, plotArguments, sam, sam2excel, sam2html, sam.plot2, sam.dstat, sam.wilc, sam.snp, d.stat, cat.stat, wilc.stat, z.ebam, cat.ebam, wilc.ebam, z.find, denspr, na.handling
ExportMethods: show, print, plot, summary, identify
ExportClasses: SAM, EBAM, FindA0, sumSAM, sumEBAM

Package: simpleaffy
ExportMethods: [, avbg, calculated.from, calls, fc, get.array.subset, getQCParams, group, maxbg, means, members, minbg, pData, percent.present, plot, qc, qcProbes, ratios, sfs, spikeInProbes, target, tt
ExportClasses: PairComp, QCStats

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

Package: splots
Exports: plotScreen

Package: tilingArray
Exports: normalizeByReference, segment, costMatrix, findSegments, sampleStep, readCel2eSet, posMin, otherStrand, plotAlongChrom, plotAlongChromLegend, plotSegmentationHeatmap, plotSegmentationDots, plotFeatures, comparisonPlot, plotPenLL, qcPlots, PMindex, BGindex, segChrom, 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: topGO
Exports: GOplot, showSigOfNodes, getPvalues, groupGOTerms, annFUN.hgu, annFUN.gene2GO, annFUN.GO2genes, reverseArch, getGraphRoot, buildGOgraph.topology, inducedGraph, buildLevels, getNoOfLevels, mapGenes2GOgraph, .sigAllMethods, .getFromNode, .genesInNode, .countsInNode, .writeToNodes
ExportMethods: initialize, description, ontology, allGenes, feasible, graph, geneSelectionFun, description<-, ontology<-, feasible<-, graph<-, geneSelectionFun<-, print, show, updateGenes, genes, numGenes, geneScore, sigGenes, numSigGenes, usedGO, attrInTerm, genesInTerm, scoresInTerm, countGenesInTerm, termStat, updateTerm<-, allMembers, Name, members, testStatistic, Name<-, allMembers<-, members<-, numMembers, numAllMembers, runTest, sigMembers<-, sigAllMembers, numSigAll, sigMembers, numSigMembers, contTable, allScore, membersScore, score<-, rankMembers, getSigGroups, genTable, GenTable, elim, cutOff, elim<-, cutOff<-, updateGroup, Weights<-, Weights, sigRatio<-, getSigRatio, score, testName, testClass, score<-, testName<-, testClass<-, printGenes, penalise, alternative, testStatPar, printGraph, GOFisherTest, GOKSTest, GOtTest, expressionMatrix, phenotype
ExportClasses: topGOdata, topGOresult, groupStats, classicCount, classicScore, elimCount, elimScore, weightCount, weightScore

Package: vsn
Exports: vsn, vsnh, vsnPlotPar, getIntensityMatrix, normalize.AffyBatch.vsn, vsnMatrix, vsn2trsf, sagmbAssess, sagmbSimulateData, plotVsnLogLik
ExportMethods: vsn2, justvsn, meanSdPlot, predict, logLik, show, exprs, nrow, ncol, dim
ExportClasses: vsn, vsnInput

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

Package: xcms
Exports: etg, medianFilter, retexp, specNoise, specPeaks, SSgauss, xcmsRaw, xcmsSet
ExportMethods: cdfpaths, cdfpaths<-, diffreport, fillPeaks, findMZBoxes, findPeaks.centWave, findPeaks.matchedFilter, findPeaks, getEIC, getPeaks, getScan, getSpec, group, groupidx, groupidx<-, groupnames, groups, groups<-, groupval, mzrange, peaks, peaks<-, plotChrom, plotPeaks, plotRaw, plotrt, plotScan, plotSpec, plotSurf, plotTIC, profinfo, profinfo<-, profMedFilt, profMethod, profMethod<-, profMz, profRange, profStep, profStep<-, rawEIC, retcor, revMz, rtrange, sampclass, sampclass<-, sampnames, sampnames<-, show, sortMz
ExportClasses: xcmsEIC, xcmsRaw, xcmsSet