API for robertdouglasmorrison/DuffyTools
Duffy Lab Utility Tools

Global functions
AA3merFreq	Source code
AAtoCodonOptimizedDNA	Man page
AnnotationTable	Man page
BScountPerML	Man page
BScountToPctParasitemia	Man page
CGIparse	Source code
DESeq.DiffExpress	Man page Source code
DKMshift	Man page
DNAVtoAAV	Man page Source code
DNAtoAA	Man page Source code
DNAtoBestPeptide	Man page
DNAtoFrameShiftingPeptides	Man page
DuffyTools	Man page
DuffyTools-package	Man page
EdgeR.DiffExpress	Man page Source code
ExonMap	Man page
FileLineCount	Man page
GeneMap	Man page
HTMLheader	Source code
HTMLincludeFile	Source code
HTMLincludeText	Source code
HTMLtable	Source code
HTMLtableRow	Source code
LimmaVoom.DiffExpress	Source code
MapSets	Man page
OptionsTable	Man page
PEXEL.search	Source code
RankProduct.DiffExpress	Man page
RrnaMap	Man page
SAM.DiffExpress	Man page Man page Source code
SAM.diffExpressRankOrder	Man page
SeqMap	Man page
Species	Man page
Targets	Man page
`.onAttach`	Source code
`.onLoad`	Source code
`.onUnload`	Source code
`AAtoCodonOptimizedDNA`	Source code
`ALNtoFasta`	Source code
`BScountPerML`	Source code
`BScountToPctParasitemia`	Source code
`CellTypeSetup`	Source code
`DKMshift`	Source code
`DNAtoBestPeptide`	Source code
`DNAtoCleanChromatogramDNA`	Source code
`DNAtoFrameShiftingPeptides`	Source code
`DuffyTools.defaults`	Source code
`LifeCycleSetup`	Source code
`MAD.outliers`	Source code
`SPVtoPctSPV`	Source code
`addAltGeneIdentifierColumn`	Source code
`addExcelLinksToTable`	Source code
`addExtraPathwayLinks`	Source code
`addGeneSymbolsToAliasTable`	Source code
`addHumanIDterms`	Source code
`addMapSet`	Source code
`addNameIDterms`	Source code
`addSpeciesToHtmlTitle`	Source code
`addTarget`	Source code
`adjustColorSet`	Source code
`adjustColor`	Source code
`adjustLifeCycleStageFileSet`	Source code
`adjustLifeCycleStageMatrix`	Source code
`alias2Gene`	Source code
`aliasGREP`	Source code
`alignedSeqDist`	Source code
`allOrthologs`	Source code
`allowCompressedFileName`	Source code
`appendMetaResultGroupValues`	Source code
`as.Fasta.data.frame`	Source code
`as.Fasta`	Source code
`as.GeneID`	Source code
`as.GeneUniverse`	Source code
`as.PvalueText`	Source code
`as.TRUEorFALSE`	Source code
`as.percent`	Source code
`as.rankPercentile`	Source code
`as.text.Fasta`	Source code
`bam2fastq`	Source code
`baseCallOnePeak`	Source code
`baseCallProfile`	Source code
`baseCallVerify`	Source code
`baseDepthTableSqueeze`	Source code
`baseDepthTableSubset`	Source code
`baseDepthTableToVector`	Source code
`baseDepthTable`	Source code
`baseDepthVectorToTable`	Source code
`baseDepthVector`	Source code
`bestLifeCycleStageTimeCall`	Source code
`bestTimeHour`	Source code
`biserial.cor.test`	Source code
`blastMatchPercentage`	Source code
`build.testFastq`	Source code
`buildAA3merFreqMap`	Source code
`buildCellCODEtagDataFromMatrix`	Source code
`buildCellTypeVectorSpace`	Source code
`buildCodonFreqMap`	Source code
`buildExtendedCodonMap`	Source code
`buildLifeCycleVectorSpace`	Source code
`buildTranscriptDeconvolutionTargetMatrix`	Source code
`calcCellCODE.SPVs`	Source code
`calcCellTypeProfileFromFile`	Source code
`calcCellTypeProfile`	Source code
`calcChromatogramPeakConfidence`	Source code
`calcExcessFoldOverMFCDTT`	Source code
`calcGeneSetDensity`	Source code
`calcLifeCycleStageFromFile`	Source code
`calcLifeCycleStage`	Source code
`calcMarkerGenesScore`	Source code
`calcTM`	Source code
`calcTimeScore`	Source code
`calculateCodonScores`	Source code
`calculateStandardCurveABCD`	Source code
`callBlast`	Source code
`callBlastn`	Source code
`callBlastp`	Source code
`callBlastx`	Source code
`callIgBlast`	Source code
`callTBlastn`	Source code
`catch.system`	Source code
`cellTypeEnrichment`	Source code
`cellTypeExpression`	Source code
`cellTypeGeneHeatmap`	Source code
`cellTypeHeatmap`	Source code
`cellTypePies`	Source code
`cgFraction`	Source code
`checkDuffyPackages`	Source code
`checkGroupNames`	Source code
`checkSNPtable`	Source code
`checkSampleNames`	Source code
`checkX11`	Source code
`chooseReadingFrame`	Source code
`chromatogramAssembly`	Source code
`chromatogramFromTable`	Source code
`chromatogramSequences`	Source code
`chromatogramToTable`	Source code
`cleanChromatogramDNA`	Source code
`cleanGeneSetModuleNames`	Source code
`cleanGeneSetName`	Source code
`clipBases`	Source code
`clipFastq`	Source code
`clipLongString`	Source code
`clipMinIntensity`	Source code
`closestDistMatch`	Source code
`clustal`	Source code
`codon.defaults`	Source code
`colorBySpecies`	Source code
`combineDuplicateGenes`	Source code
`combineRadarPlotResults`	Source code
`compareMarkerGenesScores`	Source code
`comparePlotFinish`	Source code
`comparePlotSetup`	Source code
`compareSignatures`	Source code
`compareTranscriptProportions`	Source code
`consensusRank`	Source code
`constructChromatogramBaseMatrix`	Source code
`convertAApositionToGenomicDNAposition`	Source code
`convertGenomicBasesToCodingAA`	Source code
`convertGenomicDNApositionToAAposition`	Source code
`convertGenomicDNAtoCodingDNA`	Source code
`correlationHeatmap`	Source code
`createMarkerGenes`	Source code
`cropBases`	Source code
`cropChromatogramByConfidence`	Source code
`cropChromatogramLowSignalTail`	Source code
`cropFastq`	Source code
`cv`	Source code
`deSignatureCompare`	Source code
`deconvoluteChromatogram`	Source code
`defaultCellTypeReference`	Source code
`defaultGeneSets`	Source code
`densityMetrics`	Source code
`diffExpressDistanceRankOrder`	Source code
`diffExpressMetaResultOrder`	Source code
`diffExpressRankOrder`	Source code
`diffExpressRankRankOrder`	Source code
`diffIgBlastProfiles`	Source code
`distToMatrix`	Source code
`do.TranscriptBlend.GenSA`	Source code
`do.TranscriptBlend.SteepDescent`	Source code
`domainCassetteDescriptor`	Source code
`domainCassetteEnrichment`	Source code
`drawCellTypeProfileDensityLine`	Source code
`drawCellTypeProfileIntensityLine`	Source code
`drawStageDensityLine`	Source code
`drawStageIntensityLine`	Source code
`dropAntiSenseGenes`	Source code
`duffyMagnitudeNormalize`	Source code
`duffyRMA.bgSubtract`	Source code
`duffyRMA.qn`	Source code
`duffyRMA`	Source code
`elapsedProcTime`	Source code
`emptyBaseDepthTable`	Source code
`emptyBaseDepthVector`	Source code
`enrichment`	Source code
`eosinophilExpressionComparison`	Source code
`eosinophilExpression`	Source code
`erfc`	Source code
`evaluateGeneSets`	Source code
`exportCurrentMapSet`	Source code
`exportTargetToGFF`	Source code
`exportTargets`	Source code
`expressionCluster`	Source code
`expressionDifference`	Source code
`expressionDist`	Source code
`expressionFileSetToMatrix`	Source code
`expressionHeatmap2`	Source code
`expressionHeatmap`	Source code
`expressionMatrixToDEfiles`	Source code
`expressionMatrixToDElist`	Source code
`expressionMatrixToFileSet`	Source code
`expressionMatrixToMvalue`	Source code
`extractChromatogramConsensusSequence`	Source code
`extractGeneSymbolFromProduct`	Source code
`fastADist`	Source code
`fastFindInterval`	Source code
`fastLeven.C`	Source code
`fastMafft`	Source code
`fastSP2GP`	Source code
`fastSP2GPcleanup`	Source code
`fastSP2GPready`	Source code
`fastSP2GPsetup`	Source code
`fastSeqID2Species`	Source code
`fastqCompressFile`	Source code
`fastqCompressFolder`	Source code
`fastqDemultiplex`	Source code
`fastqMerge`	Source code
`fastqPatternSearch`	Source code
`fastqReader`	Source code
`fastqToChunks`	Source code
`fastqToFasta`	Source code
`fastqToOverlapReadlets`	Source code
`fastqToPairedFiles`	Source code
`fastqToPeptides`	Source code
`fastqWriter`	Source code
`file.cleanSpecialCharactersFromFileName`	Source code
`file.combine`	Source code
`file.delete`	Source code
`file.find`	Source code
`file.lock`	Source code
`file.readable`	Source code
`file.unlock`	Source code
`fileSet.CellCODE.Proportions`	Source code
`fileSet.GeneSetDensity`	Source code
`fileSet.PCAplot`	Source code
`fileSet.TranscriptDeconvolution`	Source code
`fileSet.syntheticTranscriptome`	Source code
`findAndLoadMapSet`	Source code
`findBestIMGTgeneData`	Source code
`findVar2csaDomains`	Source code
`findVsaCassettes`	Source code
`findVsaDomains`	Source code
`fingerprintDistance`	Source code
`fit.transcriptBlend`	Source code
`fitCellTypeProfileFromFileSet`	Source code
`fitCellTypeProfileFromFile`	Source code
`fitCellTypeProfileFromMatrix`	Source code
`fitCellTypeProfile`	Source code
`fixChromatogramNcalls`	Source code
`force.jitter.ChromatogramFit.sequences`	Source code
`format4html`	Source code
`forward.4pl`	Source code
`gatherAllSignatures`	Source code
`gatherDensitySignature`	Source code
`gatherGeneSets`	Source code
`gatherGeneSignature`	Source code
`gatherQusageSignature`	Source code
`genSA.Chromatogram.residual`	Source code
`gene2Alias`	Source code
`gene2CellType`	Source code
`gene2Fasta`	Source code
`gene2OrigID`	Source code
`gene2ProductAllSpecies`	Source code
`gene2Product`	Source code
`geneProteinValidation`	Source code
`geneSetBestMatch`	Source code
`geneSetCellType`	Source code
`geneSetDensity`	Source code
`geneSetFitDataFrame`	Source code
`geneSetGrep`	Source code
`geneSetHitsToPie`	Source code
`geneSetHits`	Source code
`geneSetOverlap`	Source code
`geneSetsDensityPlot`	Source code
`getAA3merFreqMap`	Source code
`getAllSpeciesFilePrefixes`	Source code
`getAllSpecies`	Source code
`getAllTargets`	Source code
`getAndSetTarget`	Source code
`getAnnotationTrue`	Source code
`getAnnotationValue`	Source code
`getBestIMGTgeneData`	Source code
`getCellCODEtagData`	Source code
`getCellTypeColors`	Source code
`getCellTypeGeneAssociation`	Source code
`getCellTypeGeneSetAssociation`	Source code
`getCellTypeMatrix`	Source code
`getCellTypeReference`	Source code
`getCellTypeTopGenes`	Source code
`getChromatogramSequenceConfidence`	Source code
`getCodonMap`	Source code
`getCurrentCdsMap`	Source code
`getCurrentExonMap`	Source code
`getCurrentGeneMap`	Source code
`getCurrentMapSet`	Source code
`getCurrentRrnaMap`	Source code
`getCurrentSeqMap`	Source code
`getCurrentSpeciesFilePrefix`	Source code
`getCurrentSpecies`	Source code
`getCurrentTargetFilePrefix`	Source code
`getCurrentTargetSpecies`	Source code
`getCurrentTarget`	Source code
`getDensityKernelMode`	Source code
`getFastaSeqFromFilePath`	Source code
`getFileLineCount`	Source code
`getFingerprintSubstitutionMatrix`	Source code
`getGeneInfoContent`	Source code
`getGlobalMetrics`	Source code
`getHumanIDterms`	Source code
`getIMGTdata`	Source code
`getIgBlastProfiles`	Source code
`getJOSdomainMap`	Source code
`getJOSgeneMap`	Source code
`getLifeCycleMatrix`	Source code
`getLymphocyteGeneMap`	Source code
`getLymphocyteRegions`	Source code
`getMaxPhredScore`	Source code
`getOptionTrue`	Source code
`getOptionValue`	Source code
`getOtherSpeciesFilePrefix`	Source code
`getPlotDeviceType`	Source code
`getSamplePairIDs`	Source code
`getSpeciesFromSeqID`	Source code
`getSpeciesText`	Source code
`getTimeHourConsensusBestHour`	Source code
`getTimeHourGeneFCDTT`	Source code
`getTimeHourGeneMFCDTT`	Source code
`getTimeHourGenes`	Source code
`getTranscriptDeconvolutionTargetMatrix`	Source code
`getVSAdomainMap`	Source code
`getVSAgeneMap`	Source code
`getVar2csaDomainMap`	Source code
`getVargeneDomainMap`	Source code
`getVargeneDomains`	Source code
`globalNormalize`	Source code
`heatMapLegend`	Source code
`htmlTitle`	Source code
`igblastGroupName`	Source code
`igblastJnames`	Source code
`igblastVnames`	Source code
`importMapSet`	Source code
`importTargets`	Source code
`inspectChromatogramPair`	Source code
`intToPhred`	Source code
`inverse.4pl`	Source code
`is.Fasta`	Source code
`is.Rstudio`	Source code
`jitter.density`	Source code
`josCassettes`	Source code
`josDomainCassette`	Source code
`josGeneProduct`	Source code
`kaplanMeier`	Source code
`lmSlopeDifference`	Source code
`loadABiChromatogram`	Source code
`loadAliasTable`	Source code
`loadBinaryTable`	Source code
`loadCellTypeMatrix`	Source code
`loadChromatogram`	Source code
`loadCuratedChromatogram`	Source code
`loadFasta`	Source code
`loadInfoContent`	Source code
`loadKnownSNPtable`	Source code
`loadMapSet`	Source code
`loadMultipleChromatograms`	Source code
`loadTimeHourData`	Source code
`localityPlot`	Source code
`lowComplexityPeptides`	Source code
`lowReadCountAdjustment`	Source code
`mafft`	Source code
`makeAllDensityPlots`	Source code
`makeBinaryTable`	Source code
`makeBlastDB`	Source code
`makeFingerprintSubstitutionMatrix`	Source code
`makeMAplot`	Source code
`makeScatterplot`	Source code
`makeSmallGeneProductDF`	Source code
`makeVolcanoPlot`	Source code
`mapset.defaults`	Source code
`markerGeneOverlap`	Source code
`matrix.CellCODE.Proportions`	Source code
`matrix.GeneSetBubblePlots`	Source code
`matrix.GeneSetDensity`	Source code
`matrix.OneBubblePlot`	Source code
`matrix.OneRadarPlot`	Source code
`matrix.PCAplot.family`	Source code
`matrix.PCAplot`	Source code
`matrix.RadarPlots`	Source code
`matrix.TranscriptDeconvolution`	Source code
`measureCodonFreq`	Source code
`measureDensityDifferences`	Source code
`measureDominantCodons`	Source code
`measureMotifConfidence`	Source code
`medianChromatogramPeakSeparation`	Source code
`merge.baseDepthTables`	Source code
`mergeIntegerTables`	Source code
`mergeTables`	Source code
`mergeTranscriptProportions`	Source code
`metaResultsToHTML`	Source code
`modelBlendChromatogram`	Source code
`modelFitChromatogram`	Source code
`modelFitOneCodon`	Source code
`motifCodonChromatogram`	Source code
`motifCodonConfidence`	Source code
`motifSubsetChromatogram`	Source code
`multicore.by`	Source code
`multicore.currentCoreCount`	Source code
`multicore.lapply`	Source code
`multicore.samplePairs`	Source code
`multicore.seqID.order`	Source code
`multicore.setup`	Source code
`multicore.tapply`	Source code
`multicore.totalCoreCount`	Source code
`objectSize`	Source code
`oldPhredScoreStringToInt`	Source code
`openCompressedFile`	Source code
`openPlot`	Source code
`orig2GeneID`	Source code
`originalSamplePairID`	Source code
`orthologSet`	Source code
`orthologTransform`	Source code
`ortholog`	Source code
`p.valid`	Source code
`pctParasitemiaToBScount`	Source code
`pdbAtomicDistance`	Source code
`pdbResidueDistance`	Source code
`peakpickChromatogram`	Source code
`peakpickTraceM`	Source code
`peptide.Evalue`	Source code
`peptide2BestProtein`	Source code
`peptides2Proteome`	Source code
`phredScoreStringToInt`	Source code
`piValueRankOrder`	Source code
`piValue`	Source code
`pipe.GSEA`	Source code
`pipe.GeneSetBubblePlots`	Source code
`pipe.GeneSetDensity`	Source code
`pipe.GeneSetEnrichment`	Source code
`pipe.MetaGeneSets`	Source code
`pipe.OneBubblePlot`	Source code
`pipe.OneRadarPlot`	Source code
`pipe.PlotCellSortGatingGenes`	Source code
`pipe.QuSage`	Source code
`pipe.RadarPlots`	Source code
`pipe.ScoreMarkerGenes`	Source code
`pipe.ShowMarkerGenes`	Source code
`plotALN`	Source code
`plotCellTypeClusters`	Source code
`plotCellTypeDistanceTree`	Source code
`plotCellTypeForest`	Source code
`plotCellTypeProfileFromFileSet`	Source code
`plotCellTypeProfileFromMatrix`	Source code
`plotCellTypeProfileIntensity`	Source code
`plotCellTypeProfileUnitVectors`	Source code
`plotCellTypeProfiles`	Source code
`plotCellTypeVolcano`	Source code
`plotChromatogram`	Source code
`plotCodonFitInputs`	Source code
`plotCodonFitResults`	Source code
`plotFoldChange`	Source code
`plotFullChromatogramAsPDF`	Source code
`plotIgBlastDiffProfile`	Source code
`plotIgBlastOverlayProfile`	Source code
`plotIgBlastProfile`	Source code
`plotInfoContent`	Source code
`plotLifeCycleStageFromFileSet`	Source code
`plotLifeCycleStageFromMatrix`	Source code
`plotLifeCycleStageIntensity`	Source code
`plotLifeCycleStageUnitVectors`	Source code
`plotLifeCycleStages`	Source code
`plotMFCDTTdistribution`	Source code
`plotMetaResults`	Source code
`plotMultipleChromatograms`	Source code
`plotPhyloTree`	Source code
`plotRatiosTwoFiles`	Source code
`plotRatios`	Source code
`plotSNP_Pvalue`	Source code
`plotTimeHourCurveOneGene`	Source code
`plotTimeHourCurvesFromFileSet`	Source code
`plotTimeHourCurvesFromMatrix`	Source code
`plotTranscriptProportions`	Source code
`plotTranscripts`	Source code
`prepChromatogramPair`	Source code
`printPlot`	Source code
`profileIgBlastCoverage`	Source code
`proteomeDiffAbundance`	Source code
`radarPlot`	Source code
`rankEquivIntensity`	Source code
`readAnnotationTable`	Source code
`readBlastOutput`	Source code
`readDEgroupsData`	Source code
`readFasta`	Source code
`readFastq`	Source code
`readIgBlastOutput`	Source code
`readOptionsTable`	Source code
`readPDB`	Source code
`recombineLifeCycleStageIntensity`	Source code
`remove.testFile`	Source code
`removeTempFolder`	Source code
`renumberALN`	Source code
`repeatFraction`	Source code
`reshapeCellTypeMatrix`	Source code
`revCompChromatogram`	Source code
`revCompPeakPosition`	Source code
`revCompTraceMatrix`	Source code
`sampleDensityPlot`	Source code
`scoreMarkerGenes`	Source code
`sd.pop`	Source code
`selectBestChromatogramReference`	Source code
`selectBestChromatogramSequence`	Source code
`selectSignatureFiles`	Source code
`setChromatogramBestAAframe`	Source code
`setCurrentSpecies`	Source code
`setCurrentTarget`	Source code
`showMarkerGenes`	Source code
`significantGenes`	Source code
`solexaCharScoreToSolexaIntScore`	Source code
`solexaCharScoresToPhredScores`	Source code
`solexaScore2phredScore`	Source code
`solexaToPhred`	Source code
`sparse.t.test`	Source code
`spawnRcmd`	Source code
`standardizeChromatogram`	Source code
`subsetChromatogramByRange`	Source code
`subsetChromatogramBySequence`	Source code
`subsetChromatogram`	Source code
`subtractChromatogram`	Source code
`sum.baseDepthTableSubset`	Source code
`sum.baseDepthTable`	Source code
`summarizeALN`	Source code
`surveyBestTimeHour`	Source code
`symmetricOrthologPairs`	Source code
`syntheticChromatogram`	Source code
`syntheticTraceMatrix`	Source code
`syntheticTraceVector`	Source code
`table2html`	Source code
`target.defaults`	Source code
`tempFolder`	Source code
`test.DuffyTools`	Source code
`test.as.percent`	Source code
`test.codonTools`	Source code
`test.mapsetTools`	Source code
`test.readFastq`	Source code
`test.speciesTools`	Source code
`test.writeFastq`	Source code
`transcriptBlend`	Source code
`translateChromatogramSeqConfidence`	Source code
`translateChromatogramSequence`	Source code
`trimGeneSetNameLink`	Source code
`two.means.difference`	Source code
`updateMapSetGeneProductTerms`	Source code
`validateAllProteins`	Source code
`vargeneProfile`	Source code
`vennOverlap.data.frames`	Source code
`vennOverlap`	Source code
`verifyLifeCycleSetup`	Source code
`violinPlot`	Source code
`violinplot.default`	Source code
`violinplot.formula`	Source code
`violinplot`	Source code
`vlnbxp`	Source code
`vlnplt`	Source code
`voteSmoothConfidenceMatrix`	Source code
`vsaCassettes`	Source code
`vsaDomainCassette`	Source code
`vsaGeneProduct`	Source code
`vsaTo3D7`	Source code
`vsaToOrig3D7`	Source code
`whichAnnotationTrue`	Source code
`writeALN`	Source code
`writeCellTypeClusterExtras`	Source code
`writeCuratedChromatogram`	Source code
`writeFasta`	Source code
`writeFastq`	Source code
`writeLongFasta`	Source code
`xyzDist`	Source code
`z.score`	Source code
abline.segment	Source code
addConfidenceLines	Source code
addMapSet	Man page
addOrigIDterms	Source code
addTarget	Man page
alias2Gene	Man page
aliasGREP	Man page
allowCompressedFileName	Man page
as.AA3mers	Source code
as.Fasta	Man page
as.TRUEorFALSE	Man page
as.link	Source code
as.percent	Man page
as.rankPercentile	Man page
averageLineWithErrorBars	Man page Source code
baseDepthTable	Man page
baseDepthTableSubset	Man page
baseDepthTableToVector	Man page
baseDepthVector	Man page
baseDepthVectorToTable	Man page
bestAAreadingFrame	Source code
bestMatchingFingerprint	Source code
br	Source code
calcRP	Man page Source code
calcRandomGeneSetPvalues	Source code
calcTM	Man page
callBlast	Man page
callBlastn	Man page
callBlastp	Man page
cgFraction	Man page
checkDuffyPackages	Man page
checkIntraGeneOverlaps	Source code
clipFastq	Man page
codonUsageFrequency	Source code
colorBySpecies	Man page
comments	Source code
compareOneSignature	Source code
consensusRank	Man page
convertAApositionToGenomicDNAposition	Man page
convertGenomicBasesToCodingAA	Man page
convertGenomicDNAtoCodingDNA	Man page
convertHypertext	Man page Source code
diffExpressDistanceRankOrder	Man page
diffExpressRankOrder	Man page
do.GSEA	Source code
do.QuSage	Source code
duffy.ROC	Source code
duffyMagnitudeNormalize	Man page
duffyRMA	Man page
duffyRMA.bgSubtract	Man page
duffyRMA.qn	Man page
elapsedProcTime	Man page
emptyBaseDepthTable	Man page
emptyBaseDepthVector	Man page
enrichment	Man page
enrichment.Nway	Man page Source code
enrichment2html	Source code
env.sub	Man page Source code
errorBar	Source code
exportCurrentMapSet	Man page
exportTargets	Man page
expressionCluster	Man page
expressionFileSetToMatrix	Man page
expressionHeatmap	Man page
expressionMatrixToDElist	Man page
expressionMatrixToFileSet	Man page
expressionMatrixToMvalue	Man page
extractBlastXMLdetails	Source code
extractOneXMLiterationSet	Source code
factorBaseLocations	Man page
fastAAreadingFrame	Source code
fastSeqID2Species	Man page
fastSeqPos2GenePos	Man page
fastqPatternSearch	Man page
fastqToFasta	Man page
file.cleanSpecialCharactersFromFileName	Man page
fit.gaussian	Man page Man page Source code Source code
fit.gumbel	Man page Source code Source code
fit.lorentzian	Man page Source code Source code
fit.normal	Man page Source code
fit.pulse	Source code
fit.sine	Source code
fit.triangleWave	Source code
forestPlot	Source code
gatherGeneSets	Man page
gaussian	Man page Man page Source code Source code
gene2Alias	Man page
gene2Product	Man page
gene2ProductAllSpecies	Man page
geneSetAnalysis	Man page
geneSetDensity	Man page
geneSetEnrichment	Man page Source code
geneSetMetaEnrichment	Source code
getAllSpecies	Man page
getAllSpeciesFilePrefixes	Man page
getAllTargets	Man page
getAnnotationTrue	Man page
getAnnotationValue	Man page
getCodonMap	Man page
getCurrentExonMap	Man page
getCurrentGeneMap	Man page
getCurrentRrnaMap	Man page
getCurrentSeqMap	Man page
getCurrentSpecies	Man page
getCurrentSpeciesFilePrefix	Man page
getCurrentTarget	Man page
getCurrentTargetFilePrefix	Man page
getCurrentTargetSpecies	Man page
getDensityKernelMode	Man page
getFDRoneGeneSet	Source code
getFastaSeqFromFilePath	Man page
getFileLineCount	Man page
getGlobalMetrics	Man page
getHumanIDterms	Man page
getOptionTrue	Man page
getOptionValue	Man page
getOtherSpeciesFilePrefix	Man page
getSamplePairIDs	Man page
getSpeciesFromSeqID	Man page
getSpeciesText	Man page
getVSAdomainMap	Man page
getVSAgeneMap	Man page
getVargeneDomainMap	Man page
globalNormalize	Man page
gumbel	Man page Source code Source code
heatMapColors	Source code Source code
hexDecode	Source code
hydropathyScore	Source code
importMapSet	Man page
importTargets	Man page
indentPrint	Source code
levenshtein	Man page Source code
levenshteinDistanceMatrix	Man page Source code
lf	Source code
linkto	Source code
loadFasta	Man page
localityPlot	Man page
logMeanPlusSD	Man page Source code
logMedianPlusSD	Man page Source code
logmean	Man page Source code
lorentzian	Man page Source code Source code
mailto	Source code
makeGenePlotLinks	Source code
makeInfoContentTable	Source code
merge.baseDepthTables	Man page
mergeIntegerTables	Man page
mergeTables	Man page
metaEnrichment2html	Source code
metaRank.data.frames	Man page Source code
metaRank2html	Man page Source code
metaRanks	Man page Source code
metaResults	Man page Source code
metaResultsToHTML	Man page
molecularWeight	Source code
movingAverage	Man page Source code
multicore.by	Man page
multicore.currentCoreCount	Man page
multicore.lapply	Man page Man page
multicore.samplePairs	Man page Man page
multicore.setup	Man page Man page
multicore.tapply	Man page Man page
multicore.totalCoreCount	Man page
myReverse	Man page Source code
myReverseComplement	Man page Source code
normal	Man page Source code
oneDtable	Man page Source code
openCompressedFile	Man page
originalSamplePairID	Man page
ortholog	Man page
orthologSet	Man page
p.combine	Source code
p.combine.fisher	Source code
p.combine.stouffer	Source code
padStringWidth	Source code
pctParasitemiaToBScount	Man page
peptide.mergeOverlaps	Source code
peptideChopper	Source code
peptideRedundancySniffer	Source code
peptideTable	Source code
peptideTableSet	Source code
peptideViewer	Source code
phredScoreStringToInt	Man page
pipe.GeneSetAnalysis	Man page
pipe.GeneSetEnrichment	Man page
plotMetaResults	Man page
plotRatios	Man page
plotTranscripts	Man page
pulse	Source code
quickFileLineCountLookup	Man page Source code
quickFileLineCountRecord	Man page Source code
rankEquivIntensity	Man page
rankProduct	Man page Source code
rankProductDiffExpress	Man page Source code
readALN	Man page Source code
readAnnotationTable	Man page
readBlastOutput	Man page
readFastq	Man page
readNEXUS	Man page Source code
readOptionsTable	Man page
reduceMatrixToModules	Source code
removeTempFolder	Man page
scanText	Source code
setCurrentSpecies	Man page
setCurrentTarget	Man page
shortGeneName	Man page Source code
significantGenes	Man page
simulate.enrichment.Nway	Source code
sine	Source code
spawnRcmd	Man page
spline.line	Source code
sqrtmean	Man page Source code
sub.baseDepthTable	Man page
sub.baseDepthTableSubset	Man page
table.nosort	Source code
table2html	Man page
tag	Source code
tempFolder	Man page
triangleWave	Source code
tukey.biweight	Man page Source code
tukey.logmean	Man page Source code
tukey.mean	Man page Source code
unitIntervalMA	Man page Source code
untag	Source code
validateMapSet	Man page Source code
vsaGeneProduct	Man page
vsaTo3D7	Man page
webPNG	Source code
whichAnnotationTrue	Man page
wrap.text	Source code
writeALN	Man page
writeAsWebPage	Source code
writeFasta	Man page
writeFastq	Man page
writeLongFasta	Man page
writeRequestInfo	Source code