Files in robertdouglasmorrison/DuffyTools
Duffy Lab Utility Tools

DESCRIPTION
Makefile
NAMESPACE
R/AA3mers.R R/DESeqTools.R R/DuffyTools_Envir.R R/Levenshtein.R R/ROC_Tools.R R/aliasTools.R R/annotationTable.R R/as.GeneID.R R/as.TRUEorFALSE.R R/as.percent.R R/as.rankPercentile.R R/baseDepthTable.R R/binaryTable.R R/blastTools.R R/cellCodeTools.R R/cellTypeTools.R R/cgFraction.R R/checkDuffyPackages.R R/checkPackages.R R/chromatogramTools.R R/clustal.R R/codonTools.R R/colorTools.R R/combineDuplicateGenes.R R/consensusRank.R R/convertHypertext.R R/curveFitTools.R R/deSignatureCompare.R R/diffExpressRankOrder.R R/distTools.R R/edgeRtools.R R/elapsedProcTime.R R/enrichment.R R/envTools.R R/erfc.R R/exportTargetToGFF.R R/expressionCluster.R R/expressionDifference.R R/expressionFileSetToMatrix.R R/expressionHeatmap.R R/expressionMatrixToDElist.R R/expressionMatrixToMvalue.R R/fastFindInterval.R R/fastSP2GP.R R/fastSeqID2Species.R R/fastaTools.R R/fastqTools.R R/fileSemaphore.R R/fileTools.R R/fingerprintTools.R R/forestPlotTools.R R/gaussian.R R/gene2OrigID.R R/gene2Product.R R/geneSetDensity.R R/geneSetEnrichment.R R/geneSetHits.R R/geneSetTools.R R/getFileLineCount.R R/getSamplePairIDs.R R/graphicsTools.R R/groupTools.R R/heatMapColors.R R/heatmap.R R/humanIDterms.R R/igblastTools.R R/infoContent.R R/josTools.R R/levenshtein.R R/lifeCycleTools.R R/linearRegressionTools.R R/localityPlot.R R/lymphocyteTools.R R/mafft.R R/mapsetTools.R R/markerGenes.R R/mathTools.R R/mergeTables.R R/metaRank.R R/metaResults.R R/multicoreTools.R R/normalizeTools.R R/objectSize.R R/oneDtable.R R/optionsTable.R R/orthologTools.R R/parasitemiaTools.R R/pcaTools.R R/peptideTools.R R/phredScoreTools.R R/phyloTreeTools.R R/pipe.GeneSetDensity.R R/pipe.GeneSetEnrichment.R R/pipe.MetaGeneSets.R R/pipe.QuSage.R R/pipe.RadarPlots.R R/plotTranscripts.R R/pvalueTools.R R/radial.plot.R R/rankProduct.R R/readALNfile.R R/readNEXUSfile.R R/reduceMatrixToModules.R R/repeatFraction.R R/samTools.R R/sampleTools.R R/scoreMarkerGenes.R R/shortGeneName.R R/significantGenes.R R/size_n_color.R R/snpTools.R R/spawnRcmd.R R/speciesTools.R R/splineTools.R R/stringTools.R R/table2html.R R/targetTools.R R/test.DuffyTools.R R/timeHourTools.R R/tmTools.R R/transcriptBlend.R R/transcriptDeconvolution.R R/validateMaps.R R/vargeneTools.R R/vennTools.R R/violinPlot.R R/vsaTools.R R/x11Tools.R
data/.DS_Store
data/Ag.Blood.GeneModules.rda
data/Ag.GO.BiologicalProcess.rda
data/Ag.GO.CellularComponent.rda
data/Ag.GO.MolecularFunction.rda
data/Ag.GSEA.rda
data/Ag.GeneProduct.rda
data/Ag.KEGG.Pathways.rda
data/Ag.MapSet.rda
data/Ag.MetabolicPathways.rda
data/Ag.PBMC.GeneModules.rda
data/Anan.AliasTable.rda
data/Anan.BTM.AntibodyResponses.rda
data/Anan.Blood.GeneModules.rda
data/Anan.CellCODE.ImmuneCell.TagData.rda
data/Anan.CellTypes.rda
data/Anan.GO.BiologicalProcess.rda
data/Anan.GO.CellularComponent.rda
data/Anan.GO.MolecularFunction.rda
data/Anan.GOslim.BiologicalProcess.rda
data/Anan.GOslim.CellularComponent.rda
data/Anan.GOslim.MolecularFunction.rda
data/Anan.GeneCellTypes.rda
data/Anan.HGNC.GeneFamily.rda
data/Anan.HumanImmuneSubsets.rda
data/Anan.ImmuneCell.TargetMatrix.rda
data/Anan.KEGG.Pathways.rda
data/Anan.MapSet.rda
data/Anan.MetabolicPathways.rda
data/Anan.MouseImmuneCell.TargetMatrix.rda
data/Anan.MouseImmuneSubsets.rda
data/Anan.PBMC.GeneModules.rda
data/Anan.Reactome.rda
data/Anan.WikiPathways.rda
data/BCG.MapSet.rda
data/Bbrevis.MapSet.rda
data/CodonMap.rda
data/Dr.BTM.AntibodyResponses.rda
data/Dr.Blood.GeneModules.rda
data/Dr.CellCODE.ImmuneCell.TagData.rda
data/Dr.CellTypes.rda
data/Dr.GO.BiologicalProcess.rda
data/Dr.GO.CellularComponent.rda
data/Dr.GO.MolecularFunction.rda
data/Dr.GOslim.BiologicalProcess.rda
data/Dr.GOslim.CellularComponent.rda
data/Dr.GOslim.MolecularFunction.rda
data/Dr.GeneCellTypes.rda
data/Dr.HGNC.GeneFamily.rda
data/Dr.HumanImmuneSubsets.rda
data/Dr.ImmuneCell.TargetMatrix.rda
data/Dr.KEGG.Pathways.rda
data/Dr.MapSet.rda
data/Dr.MetabolicPathways.rda
data/Dr.MouseImmuneCell.TargetMatrix.rda
data/Dr.MouseImmuneSubsets.rda
data/Dr.PBMC.GeneModules.rda
data/Dr.Reactome.rda
data/Dr.WikiPathways.rda
data/Drerio.AliasTable.rda
data/Eco.MapSet.rda
data/GNB.MapSet.rda
data/GeneCellTypes.rda
data/GeneSetCellTypes.rda
data/GeneSetLifeCycle.rda
data/GrammDol.MapSet.rda
data/Hs.AA3merFreqMap.rda
data/Hs.AliasTable.rda
data/Hs.BTM.AntibodyResponses.rda
data/Hs.Blood.GeneModules.rda
data/Hs.CellCODE.ImmuneCell.TagData.rda
data/Hs.CellTypes.rda
data/Hs.GO.BiologicalProcess.rda
data/Hs.GO.CellularComponent.rda
data/Hs.GO.MolecularFunction.rda
data/Hs.GOslim.BiologicalProcess.rda
data/Hs.GOslim.CellularComponent.rda
data/Hs.GOslim.MolecularFunction.rda
data/Hs.GSEA.rda
data/Hs.GeneCellTypes.rda
data/Hs.GeneProduct.rda
data/Hs.HGNC.GeneFamily.rda
data/Hs.HumanImmuneSubsets.rda
data/Hs.HumanLymphocyteSubsets.rda
data/Hs.ImmuneCell.MarkerGenes.rda
data/Hs.ImmuneCell.TargetMatrix.rda
data/Hs.KEGG.Pathways.rda
data/Hs.Lymphocyte.TargetMatrix.rda
data/Hs.MapSet.rda
data/Hs.MetabolicPathways.rda
data/Hs.MouseImmuneCell.TargetMatrix.rda
data/Hs.MouseImmuneSubsets.rda
data/Hs.PBMC.GeneModules.rda
data/Hs.Reactome.rda
data/Hs.WikiPathways.rda
data/Hs_hg19.MapSet.rda
data/ImmuneCell.MarkerGenes.rda
data/ImmuneCell.TargetMatrix.rda
data/JOS.MapSet.rda
data/LifeCycle.GeneSetStageCalls.rda
data/LifeCycle.GeneStageCalls.rda
data/LifeCycleData_RNAseq.rda
data/LifeCycleData_YoungWinzeler.rda
data/MTb.AliasTable.rda
data/MTb.GO.BiologicalProcess.rda
data/MTb.GO.CellularComponent.rda
data/MTb.GO.MolecularFunction.rda
data/MTb.GOslim.BiologicalProcess.rda
data/MTb.GOslim.CellularComponent.rda
data/MTb.GOslim.MolecularFunction.rda
data/MTb.GeneProduct.rda
data/MTb.HGNC.GeneFamily.rda
data/MTb.ISB.Corems.rda
data/MTb.KEGG.Pathways.rda
data/MTb.MapSet.rda
data/MTb.MetabolicPathways.rda
data/MTb.Reactome.rda
data/MTb.SNP_Table.rda
data/MTb.TFOE.Regulons.rda
data/MTb.Tuberculist.FunctionalGroups.rda
data/MTb.Tuberculist.GO.Ontology.rda
data/MTb.WikiPathways.rda
data/MTbS.MapSet.rda
data/Mabsc.GO.BiologicalProcess.rda
data/Mabsc.GO.CellularComponent.rda
data/Mabsc.GO.MolecularFunction.rda
data/Mabsc.GOslim.BiologicalProcess.rda
data/Mabsc.GOslim.CellularComponent.rda
data/Mabsc.GOslim.MolecularFunction.rda
data/Mabsc.HGNC.GeneFamily.rda
data/Mabsc.ISB.Corems.rda
data/Mabsc.KEGG.Pathways.rda
data/Mabsc.MapSet.rda
data/Mabsc.MetabolicPathways.rda
data/Mabsc.Reactome.rda
data/Mabsc.TFOE.Regulons.rda
data/Mabsc.Tuberculist.FunctionalGroups.rda
data/Mabsc.Tuberculist.GO.Ontology.rda
data/Mabsc.WikiPathways.rda
data/MacFas.AliasTable.rda
data/MacFas.BTM.AntibodyResponses.rda
data/MacFas.Blood.GeneModules.rda
data/MacFas.CellCODE.ImmuneCell.TagData.rda
data/MacFas.CellTypes.rda
data/MacFas.GO.BiologicalProcess.rda
data/MacFas.GO.CellularComponent.rda
data/MacFas.GO.MolecularFunction.rda
data/MacFas.GOslim.BiologicalProcess.rda
data/MacFas.GOslim.CellularComponent.rda
data/MacFas.GOslim.MolecularFunction.rda
data/MacFas.GSEA.rda
data/MacFas.GeneCellTypes.rda
data/MacFas.GeneProduct.rda
data/MacFas.HGNC.GeneFamily.rda
data/MacFas.HumanImmuneSubsets.rda
data/MacFas.HumanLymphocyteSubsets.rda
data/MacFas.ImmuneCell.TargetMatrix.rda
data/MacFas.KEGG.Pathways.rda
data/MacFas.Lymphocyte.TargetMatrix.rda
data/MacFas.MapSet.rda
data/MacFas.MetabolicPathways.rda
data/MacFas.MouseImmuneCell.TargetMatrix.rda
data/MacFas.MouseImmuneSubsets.rda
data/MacFas.PBMC.GeneModules.rda
data/MacFas.Reactome.rda
data/MacFas.WikiPathways.rda
data/MacMu.AliasTable.rda
data/MacMu.BTM.AntibodyResponses.rda
data/MacMu.Blood.GeneModules.rda
data/MacMu.CellCODE.ImmuneCell.TagData.rda
data/MacMu.CellTypes.rda
data/MacMu.GO.BiologicalProcess.rda
data/MacMu.GO.CellularComponent.rda
data/MacMu.GO.MolecularFunction.rda
data/MacMu.GOslim.BiologicalProcess.rda
data/MacMu.GOslim.CellularComponent.rda
data/MacMu.GOslim.MolecularFunction.rda
data/MacMu.GSEA.rda
data/MacMu.GeneCellTypes.rda
data/MacMu.GeneProduct.rda
data/MacMu.HGNC.GeneFamily.rda
data/MacMu.HumanImmuneSubsets.rda
data/MacMu.HumanLymphocyteSubsets.rda
data/MacMu.ImmuneCell.TargetMatrix.rda
data/MacMu.KEGG.Pathways.rda
data/MacMu.Lymphocyte.TargetMatrix.rda
data/MacMu.MapSet.rda
data/MacMu.MetabolicPathways.rda
data/MacMu.MouseImmuneCell.TargetMatrix.rda
data/MacMu.MouseImmuneSubsets.rda
data/MacMu.PBMC.GeneModules.rda
data/MacMu.Reactome.rda
data/MacMu.WikiPathways.rda
data/Mavium.MapSet.rda
data/Mchel.GO.BiologicalProcess.rda
data/Mchel.GO.CellularComponent.rda
data/Mchel.GO.MolecularFunction.rda
data/Mchel.GOslim.BiologicalProcess.rda
data/Mchel.GOslim.CellularComponent.rda
data/Mchel.GOslim.MolecularFunction.rda
data/Mchel.HGNC.GeneFamily.rda
data/Mchel.ISB.Corems.rda
data/Mchel.KEGG.Pathways.rda
data/Mchel.MapSet.rda
data/Mchel.MetabolicPathways.rda
data/Mchel.Reactome.rda
data/Mchel.TFOE.Regulons.rda
data/Mchel.Tuberculist.FunctionalGroups.rda
data/Mchel.Tuberculist.GO.Ontology.rda
data/Mchel.WikiPathways.rda
data/MeltingTempScript.rda
data/Mmu.KEGG.Pathways.rda
data/Mmus.AliasTable.rda
data/Mmus.BTM.AntibodyResponses.rda
data/Mmus.Blood.GeneModules.rda
data/Mmus.CellCODE.ImmuneCell.TagData.rda
data/Mmus.CellTypes.rda
data/Mmus.GO.BiologicalProcess.rda
data/Mmus.GO.CellularComponent.rda
data/Mmus.GO.MolecularFunction.rda
data/Mmus.GOslim.BiologicalProcess.rda
data/Mmus.GOslim.CellularComponent.rda
data/Mmus.GOslim.MolecularFunction.rda
data/Mmus.GSEA.rda
data/Mmus.GeneCellTypes.rda
data/Mmus.GeneProduct.rda
data/Mmus.HGNC.GeneFamily.rda
data/Mmus.HumanImmuneSubsets.rda
data/Mmus.HumanLymphocyteSubsets.rda
data/Mmus.ImmuneCell.MarkerGenes.rda
data/Mmus.ImmuneCell.TargetMatrix.rda
data/Mmus.KEGG.Pathways.rda
data/Mmus.Lymphocyte.TargetMatrix.rda
data/Mmus.MapSet.rda
data/Mmus.MetabolicPathways.rda
data/Mmus.MouseImmuneCell.TargetMatrix.rda
data/Mmus.MouseImmuneSubsets.rda
data/Mmus.PBMC.GeneModules.rda
data/Mmus.Reactome.rda
data/Mmus.WikiPathways.rda
data/Msmeg.AliasTable.rda
data/Msmeg.GO.BiologicalProcess.rda
data/Msmeg.GO.CellularComponent.rda
data/Msmeg.GO.MolecularFunction.rda
data/Msmeg.GOslim.BiologicalProcess.rda
data/Msmeg.GOslim.CellularComponent.rda
data/Msmeg.GOslim.MolecularFunction.rda
data/Msmeg.HGNC.GeneFamily.rda
data/Msmeg.ISB.Corems.rda
data/Msmeg.KEGG.Pathways.rda
data/Msmeg.MapSet.rda
data/Msmeg.MetabolicPathways.rda
data/Msmeg.Reactome.rda
data/Msmeg.TFOE.Regulons.rda
data/Msmeg.Tuberculist.FunctionalGroups.rda
data/Msmeg.Tuberculist.GO.Ontology.rda
data/Msmeg.WikiPathways.rda
data/OrthologTable.rda
data/PAM70MS.rda
data/Pb.AliasTable.rda
data/Pb.Blood.GeneModules.rda
data/Pb.CellCODE.LifeCycle.TagData.rda
data/Pb.GO.BiologicalProcess.rda
data/Pb.GO.CellularComponent.rda
data/Pb.GO.MolecularFunction.rda
data/Pb.GOslim.BiologicalProcess.rda
data/Pb.GOslim.CellularComponent.rda
data/Pb.GOslim.MolecularFunction.rda
data/Pb.GSEA.rda
data/Pb.GeneLifeCycle.rda
data/Pb.GeneProduct.rda
data/Pb.HGNC.GeneFamily.rda
data/Pb.HumanImmuneSubsets.rda
data/Pb.KEGG.Pathways.rda
data/Pb.LifeCycleStage.rda
data/Pb.MPMP.Pathways.rda
data/Pb.MapSet.rda
data/Pb.MetabolicPathways.rda
data/Pb.MouseImmuneSubsets.rda
data/Pb.PBMC.GeneModules.rda
data/Pb.ParasiteLifeCycle.rda
data/Pb.Reactome.rda
data/Pb.WikiPathways.rda
data/Pch.AliasTable.rda
data/Pch.Blood.GeneModules.rda
data/Pch.CellCODE.LifeCycle.TagData.rda
data/Pch.GO.BiologicalProcess.rda
data/Pch.GO.CellularComponent.rda
data/Pch.GO.MolecularFunction.rda
data/Pch.GOslim.BiologicalProcess.rda
data/Pch.GOslim.CellularComponent.rda
data/Pch.GOslim.MolecularFunction.rda
data/Pch.GSEA.rda
data/Pch.GeneLifeCycle.rda
data/Pch.GeneProduct.rda
data/Pch.HGNC.GeneFamily.rda
data/Pch.HumanImmuneSubsets.rda
data/Pch.KEGG.Pathways.rda
data/Pch.LifeCycleStage.rda
data/Pch.MPMP.Pathways.rda
data/Pch.MapSet.rda
data/Pch.MetabolicPathways.rda
data/Pch.MouseImmuneSubsets.rda
data/Pch.PBMC.GeneModules.rda
data/Pch.ParasiteLifeCycle.rda
data/Pch.Reactome.rda
data/Pch.WikiPathways.rda
data/Pco.Blood.GeneModules.rda
data/Pco.GO.BiologicalProcess.rda
data/Pco.GO.CellularComponent.rda
data/Pco.GO.MolecularFunction.rda
data/Pco.GOslim.BiologicalProcess.rda
data/Pco.GOslim.CellularComponent.rda
data/Pco.GOslim.MolecularFunction.rda
data/Pco.GSEA.rda
data/Pco.GeneProduct.rda
data/Pco.HGNC.GeneFamily.rda
data/Pco.HumanImmuneSubsets.rda
data/Pco.KEGG.Pathways.rda
data/Pco.LifeCycleStage.rda
data/Pco.MPMP.Pathways.rda
data/Pco.MapSet.rda
data/Pco.MetabolicPathways.rda
data/Pco.MouseImmuneSubsets.rda
data/Pco.PBMC.GeneModules.rda
data/Pco.Reactome.rda
data/Pco.WikiPathways.rda
data/PcoAH.Blood.GeneModules.rda
data/PcoAH.CellCODE.LifeCycle.TagData.rda
data/PcoAH.GO.BiologicalProcess.rda
data/PcoAH.GO.CellularComponent.rda
data/PcoAH.GO.MolecularFunction.rda
data/PcoAH.GOslim.BiologicalProcess.rda
data/PcoAH.GOslim.CellularComponent.rda
data/PcoAH.GOslim.MolecularFunction.rda
data/PcoAH.GSEA.rda
data/PcoAH.GeneLifeCycle.rda
data/PcoAH.GeneProduct.rda
data/PcoAH.HGNC.GeneFamily.rda
data/PcoAH.HumanImmuneSubsets.rda
data/PcoAH.KEGG.Pathways.rda
data/PcoAH.LifeCycleStage.rda
data/PcoAH.MPMP.Pathways.rda
data/PcoAH.MapSet.rda
data/PcoAH.MetabolicPathways.rda
data/PcoAH.MouseImmuneSubsets.rda
data/PcoAH.PBMC.GeneModules.rda
data/PcoAH.ParasiteLifeCycle.rda
data/PcoAH.Reactome.rda
data/PcoAH.WikiPathways.rda
data/Pcy.Blood.GeneModules.rda
data/Pcy.GO.BiologicalProcess.rda
data/Pcy.GO.CellularComponent.rda
data/Pcy.GO.MolecularFunction.rda
data/Pcy.GOslim.BiologicalProcess.rda
data/Pcy.GOslim.CellularComponent.rda
data/Pcy.GOslim.MolecularFunction.rda
data/Pcy.GSEA.rda
data/Pcy.GeneProduct.rda
data/Pcy.HGNC.GeneFamily.rda
data/Pcy.HumanImmuneSubsets.rda
data/Pcy.KEGG.Pathways.rda
data/Pcy.LifeCycleStage.rda
data/Pcy.MPMP.Pathways.rda
data/Pcy.MapSet.rda
data/Pcy.MetabolicPathways.rda
data/Pcy.MouseImmuneSubsets.rda
data/Pcy.PBMC.GeneModules.rda
data/Pcy.Reactome.rda
data/Pcy.WikiPathways.rda
data/Pf.AA3merFreqMap.rda
data/Pf.AliasTable.rda
data/Pf.Blood.GeneModules.rda
data/Pf.CellCODE.LifeCycle.TagData.rda
data/Pf.GO.BiologicalProcess.rda
data/Pf.GO.CellularComponent.rda
data/Pf.GO.MolecularFunction.rda
data/Pf.GOslim.BiologicalProcess.rda
data/Pf.GOslim.CellularComponent.rda
data/Pf.GOslim.MolecularFunction.rda
data/Pf.GSEA.rda
data/Pf.GeneLifeCycle.rda
data/Pf.GeneProduct.rda
data/Pf.HGNC.GeneFamily.rda
data/Pf.HumanImmuneSubsets.rda
data/Pf.KEGG.Pathways.rda
data/Pf.LifeCycleStage.rda
data/Pf.MPMP.Pathways.rda
data/Pf.MapSet.rda
data/Pf.MartiClusters.rda
data/Pf.MetabolicPathways.rda
data/Pf.MouseImmuneSubsets.rda
data/Pf.OrthologTable.rda
data/Pf.PBMC.GeneModules.rda
data/Pf.ParasiteLifeCycle.rda
data/Pf.PfEMP1.Groups.rda
data/Pf.Reactome.rda
data/Pf.SNP_Table.rda
data/Pf.WikiPathways.rda
data/Pf.ncRNA.geneMap.rda
data/PfDD2.MapSet.rda
data/PfHB3.MapSet.rda
data/PfIGH.MapSet.rda
data/PfIT.MapSet.rda
data/Pk.GeneLifeCycle.rda
data/PkH.AliasTable.rda
data/PkH.Blood.GeneModules.rda
data/PkH.GO.BiologicalProcess.rda
data/PkH.GO.CellularComponent.rda
data/PkH.GO.MolecularFunction.rda
data/PkH.GOslim.BiologicalProcess.rda
data/PkH.GOslim.CellularComponent.rda
data/PkH.GOslim.MolecularFunction.rda
data/PkH.GSEA.rda
data/PkH.GeneProduct.rda
data/PkH.HGNC.GeneFamily.rda
data/PkH.HumanImmuneSubsets.rda
data/PkH.KEGG.Pathways.rda
data/PkH.LifeCycleStage.rda
data/PkH.MPMP.Pathways.rda
data/PkH.MapSet.rda
data/PkH.MetabolicPathways.rda
data/PkH.MouseImmuneSubsets.rda
data/PkH.PBMC.GeneModules.rda
data/PkH.Reactome.rda
data/PkH.WikiPathways.rda
data/Pmalar.MapSet.rda
data/Povale.MapSet.rda
data/Pv.AA3merFreqMap.rda
data/Pv.AliasTable.rda
data/Pv.Blood.GeneModules.rda
data/Pv.CellCODE.LifeCycle.TagData.rda
data/Pv.GO.BiologicalProcess.rda
data/Pv.GO.CellularComponent.rda
data/Pv.GO.MolecularFunction.rda
data/Pv.GOslim.BiologicalProcess.rda
data/Pv.GOslim.CellularComponent.rda
data/Pv.GOslim.MolecularFunction.rda
data/Pv.GSEA.rda
data/Pv.GeneLifeCycle.rda
data/Pv.GeneProduct.rda
data/Pv.HGNC.GeneFamily.rda
data/Pv.HumanImmuneSubsets.rda
data/Pv.KEGG.Pathways.rda
data/Pv.LifeCycleStage.rda
data/Pv.MPMP.Pathways.rda
data/Pv.MapSet.rda
data/Pv.MetabolicPathways.rda
data/Pv.MouseImmuneSubsets.rda
data/Pv.PBMC.GeneModules.rda
data/Pv.ParasiteLifeCycle.rda
data/Pv.Reactome.rda
data/Pv.SNP_Table.rda
data/Pv.WikiPathways.rda
data/Pvvv.Blood.GeneModules.rda
data/Pvvv.GO.BiologicalProcess.rda
data/Pvvv.GO.CellularComponent.rda
data/Pvvv.GO.MolecularFunction.rda
data/Pvvv.GOslim.BiologicalProcess.rda
data/Pvvv.GOslim.CellularComponent.rda
data/Pvvv.GOslim.MolecularFunction.rda
data/Pvvv.GSEA.rda
data/Pvvv.GeneProduct.rda
data/Pvvv.HGNC.GeneFamily.rda
data/Pvvv.HumanImmuneSubsets.rda
data/Pvvv.KEGG.Pathways.rda
data/Pvvv.LifeCycleStage.rda
data/Pvvv.MPMP.Pathways.rda
data/Pvvv.MapSet.rda
data/Pvvv.MetabolicPathways.rda
data/Pvvv.MouseImmuneSubsets.rda
data/Pvvv.PBMC.GeneModules.rda
data/Pvvv.Reactome.rda
data/Pvvv.WikiPathways.rda
data/Py.Blood.GeneModules.rda
data/Py.GO.BiologicalProcess.rda
data/Py.GO.CellularComponent.rda
data/Py.GO.MolecularFunction.rda
data/Py.GOslim.BiologicalProcess.rda
data/Py.GOslim.CellularComponent.rda
data/Py.GOslim.MolecularFunction.rda
data/Py.GSEA.rda
data/Py.GeneProduct.rda
data/Py.HGNC.GeneFamily.rda
data/Py.HumanImmuneSubsets.rda
data/Py.KEGG.Pathways.rda
data/Py.LifeCycleStage.rda
data/Py.MPMP.Pathways.rda
data/Py.MapSet.rda
data/Py.MetabolicPathways.rda
data/Py.MouseImmuneSubsets.rda
data/Py.PBMC.GeneModules.rda
data/Py.Reactome.rda
data/Py.WikiPathways.rda
data/Py17X.AliasTable.rda
data/Py17X.Blood.GeneModules.rda
data/Py17X.CellCODE.LifeCycle.TagData.rda
data/Py17X.GO.BiologicalProcess.rda
data/Py17X.GO.CellularComponent.rda
data/Py17X.GO.MolecularFunction.rda
data/Py17X.GOslim.BiologicalProcess.rda
data/Py17X.GOslim.CellularComponent.rda
data/Py17X.GOslim.MolecularFunction.rda
data/Py17X.GSEA.rda
data/Py17X.GeneLifeCycle.rda
data/Py17X.GeneProduct.rda
data/Py17X.HGNC.GeneFamily.rda
data/Py17X.HumanImmuneSubsets.rda
data/Py17X.KEGG.Pathways.rda
data/Py17X.KappeModules.rda
data/Py17X.LifeCycleStage.rda
data/Py17X.MPMP.Pathways.rda
data/Py17X.MapSet.rda
data/Py17X.MetabolicPathways.rda
data/Py17X.MouseImmuneSubsets.rda
data/Py17X.PBMC.GeneModules.rda
data/Py17X.ParasiteLifeCycle.rda
data/Py17X.Reactome.rda
data/Py17X.WikiPathways.rda
data/Pym.AliasTable.rda
data/Pym.Blood.GeneModules.rda
data/Pym.GO.BiologicalProcess.rda
data/Pym.GO.CellularComponent.rda
data/Pym.GO.MolecularFunction.rda
data/Pym.GOslim.BiologicalProcess.rda
data/Pym.GOslim.CellularComponent.rda
data/Pym.GOslim.MolecularFunction.rda
data/Pym.GSEA.rda
data/Pym.GeneProduct.rda
data/Pym.HGNC.GeneFamily.rda
data/Pym.HumanImmuneSubsets.rda
data/Pym.KEGG.Pathways.rda
data/Pym.LifeCycleStage.rda
data/Pym.MPMP.Pathways.rda
data/Pym.MapSet.rda
data/Pym.MetabolicPathways.rda
data/Pym.MouseImmuneSubsets.rda
data/Pym.PBMC.GeneModules.rda
data/Pym.Reactome.rda
data/Pym.WikiPathways.rda
data/Rnor.AliasTable.rda
data/Rnor.MapSet.rda
data/Sty.MapSet.rda
data/Styph.AliasTable.rda
data/Styph.MapSet.rda
data/Tb.MapSet.rda
data/Tb.by.Hs.detectable.WB.rda
data/Tbr.MapSet.rda
data/Tbr427.MapSet.rda
data/TimeHourDatasets.rda
data/VSA.CassetteConstructs.rda
data/VSA.DomainConstructs.rda
data/VSA.MapSet.rda
data/VSA_3D7.MapSet.rda
data/VSA_3D7_noATS.MapSet.rda
data/VSA_DD2.MapSet.rda
data/VSA_DD2_noATS.MapSet.rda
data/VSA_HB3.MapSet.rda
data/VSA_HB3_noATS.MapSet.rda
data/VSA_IGH.MapSet.rda
data/VSA_IGH_noATS.MapSet.rda
data/VSA_IT4.MapSet.rda
data/VSA_IT4_noATS.MapSet.rda
data/VSA_PFCLIN.MapSet.rda
data/VSA_PFCLIN_noATS.MapSet.rda
data/VSA_RAJ116.MapSet.rda
data/VSA_RAJ116_noATS.MapSet.rda
data/VSA_REICH.MapSet.rda
data/VSA_REICH_noATS.MapSet.rda
data/VSA_noATS.MapSet.rda
data/VarGenes.MapSet.rda
data/josDomainMap.rda
data/pCSM312.MapSet.rda
data/pMP399.MapSet.rda
data/pYUB854.MapSet.rda
data/testFastq.txt.rda
data/var2csaDomainConstructs.rda
data/vargeneDomainMap.rda
data/vsaDomainMap.rda
data/vsaGeneMap.rda
man/.DS_Store
man/AAtoCodonOptimizedDNA.Rd man/BScountToPctParasitemia.Rd man/DESeq.DiffExpress.Rd man/DKMshift.Rd man/DNAtoAA.Rd man/DuffyTools.Rd man/MapSets.Rd man/SAM.DiffExpress.Rd man/SAM.diffExpressRankOrder.Rd man/Species.Rd man/Targets.Rd man/addMapSet.Rd man/addTarget.Rd man/alias2Gene.Rd man/allowCompressedFileName.Rd man/annotationTable.Rd man/as.Fasta.Rd man/as.TRUEorFALSE.Rd man/as.percent.Rd man/as.rankPercentile.Rd man/averageLineWithErrorBars.Rd man/baseDepthTable.Rd man/blastTools.Rd man/calcRP.Rd man/calcTM.Rd man/cgFraction.Rd man/checkDuffyPackages.Rd man/clipFastqFile.Rd man/colorBySpecies.Rd man/consensusRank.Rd man/convertGenomicBasesToCodingAA.Rd man/convertHypertext.Rd man/diffExpressRankOrder.Rd man/duffyRMA.Rd man/elapsedProcTime.Rd man/enrichment.Rd man/env.sub.Rd man/exportCurrentMapSet.Rd man/exportTargets.Rd man/expressionCluster.Rd man/expressionFileSetToMatrix.Rd man/expressionHeatmap.Rd man/expressionMatrixToDElist.Rd man/expressionMatrixToMvalue.Rd man/fastSeqID2Species.Rd man/fastSeqPos2GenePos.Rd man/fastqPatternSearch.Rd man/fastqToFasta.Rd man/file.cleanSpecialCharactersFromFileName.Rd man/gatherGeneSets.Rd man/gaussian.Rd man/gene2Alias.Rd man/gene2Product.Rd man/geneSetAnalysis.Rd man/geneSetEnrichment.Rd man/getCodonMap.Rd man/getCurrentGeneMap.Rd man/getCurrentSpecies.Rd man/getCurrentTarget.Rd man/getDensityKernelMode.Rd man/getFastaSeqFromFilePath.Rd man/getFileLineCount.Rd man/getGlobalMetrics.Rd man/getHumanIDterms.Rd man/getSamplePairIDs.Rd man/getSpeciesFromSeqID.Rd man/getVargeneDomainMap.Rd man/globalNormalize.Rd man/importMapSet.Rd man/levenshtein.Rd man/loadFasta.Rd man/localityPlot.Rd man/logmean.Rd man/mergeTables.Rd man/metaRanks.Rd man/metaResults.Rd man/movingAverage.Rd man/multicore.samplePairs.Rd man/multicore.setup.Rd man/myReverseComplement.Rd man/normal.Rd man/oneDtable.Rd man/openCompressedFile.Rd man/optionsTable.Rd man/ortholog.Rd man/phredScoreStringToInt.Rd man/pipe.GeneSetAnalysis.Rd man/pipe.GeneSetEnrichment.Rd man/plotMetaResults.Rd man/plotTranscripts.Rd man/rankEquivIntensity.Rd man/rankProductDiffExpress.Rd man/readALNfile.Rd man/readFastqFile.Rd man/setCurrentSpecies.Rd man/setCurrentTarget.Rd man/shortGeneName.Rd man/significantGenes.Rd man/spawnRcmd.Rd man/sqrtmean.Rd man/table2html.Rd man/tempFolder.Rd man/tukey.mean.Rd man/validateMapSet.Rd man/vsaTo3D7.Rd
src/fastLevenshtein.c
src/fastLevenshtein.o
src/fastLevenshtein.so
robertdouglasmorrison/DuffyTools documentation built on Jan. 11, 2019, 5:38 p.m.