Files in robertdouglasmorrison/DuffyTools
Duffy Lab Utility Tools
DESCRIPTION
Makefile
NAMESPACE
R/AA3mers.R
R/DESeqTools.R
R/DuffyTools_Envir.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/chromatogramAssembly.R
R/chromatogramModeling.R
R/chromatogramMotifs.R
R/chromatogramPairTools.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/eosinophilTools.R
R/erfc.R
R/exportTargetToGFF.R
R/expressionCluster.R
R/expressionDifference.R
R/expressionFileSetToMatrix.R
R/expressionHeatmap.R
R/expressionMatrixToDEfiles.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/geneProteinValidation.R
R/geneSetDensity.R
R/geneSetEnrichment.R
R/geneSetTools.R
R/geneUniverse.R
R/getFileLineCount.R
R/getSamplePairIDs.R
R/graphicsTools.R
R/groupTools.R
R/heatMapColors.R
R/heatmap.R
R/humanIDterms.R
R/hydropathyScore.R
R/igblastTools.R
R/imgtTools.R
R/infoContent.R
R/jitter.density.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/pdbTools.R
R/peptideTools.R
R/pexelTools.R
R/phredScoreTools.R
R/phyloTreeTools.R
R/piValueTools.R
R/pipe.GeneSetBubblePlots.R
R/pipe.GeneSetDensity.R
R/pipe.GeneSetEnrichment.R
R/pipe.MarkerGenes.R
R/pipe.MetaGeneSets.R
R/pipe.QuSage.R
R/pipe.RadarPlots.R
R/plotDeviceTools.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/rstudioTools.R
R/samTools.R
R/sampleTools.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/standardCurve.4PL.Tools.R
R/statsTools.R
R/stringTools.R
R/survivalTools.R
R/systemTools.R
R/table2html.R
R/tableTools.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/13.Blood.CellTypes.GeneSetAssociation.rda
data/27.Blood.CellTypes.GeneSetAssociation.rda
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/Agris.13.Blood.CellTypes.AllGeneSets.rda
data/Agris.27.Blood.CellTypes.AllGeneSets.rda
data/Agris.BTM.AntibodyResponses.rda
data/Agris.Blood.GeneModules.rda
data/Agris.BloodGen3.GeneModules.rda
data/Agris.GO.BiologicalProcess.rda
data/Agris.GO.CellularComponent.rda
data/Agris.GO.MolecularFunction.rda
data/Agris.GOslim.BiologicalProcess.rda
data/Agris.GOslim.CellularComponent.rda
data/Agris.GOslim.MolecularFunction.rda
data/Agris.HGNC.GeneFamily.rda
data/Agris.KEGG.Pathways.rda
data/Agris.MapSet.rda
data/Agris.MetabolicPathways.rda
data/Agris.Mouse.Spleen.CellTypes.AllGeneSets.rda
data/Agris.PBMC.GeneModules.rda
data/Agris.Panther.Pathways.rda
data/Agris.Reactome.rda
data/Agris.STRING.rda
data/Agris.WikiPathways.rda
data/Anan.13.Blood.CellTypes.AllGeneSets.rda
data/Anan.13.Blood.CellTypes.GeneAssociation.rda
data/Anan.13.Blood.CellTypes.TargetMatrix.rda
data/Anan.13.Blood.CellTypes.TopGeneSets.rda
data/Anan.27.Blood.CellTypes.AllGeneSets.rda
data/Anan.27.Blood.CellTypes.GeneAssociation.rda
data/Anan.27.Blood.CellTypes.TargetMatrix.rda
data/Anan.27.Blood.CellTypes.TopGeneSets.rda
data/Anan.AliasTable.rda
data/Anan.BTM.AntibodyResponses.rda
data/Anan.Blood.GeneModules.rda
data/Anan.BloodGen3.GeneModules.rda
data/Anan.CellCODE.ImmuneCell.TagData.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.HGNC.GeneFamily.rda
data/Anan.ImmuneCell.MarkerGenes.rda
data/Anan.KEGG.Pathways.rda
data/Anan.MapSet.rda
data/Anan.MetabolicPathways.rda
data/Anan.Mouse.Spleen.CellTypes.AllGeneSets.rda
data/Anan.Mouse.Spleen.CellTypes.GeneAssociation.rda
data/Anan.Mouse.Spleen.CellTypes.TargetMatrix.rda
data/Anan.Mouse.Spleen.CellTypes.TopGeneSets.rda
data/Anan.PBMC.GeneModules.rda
data/Anan.Panther.Pathways.rda
data/Anan.Reactome.rda
data/Anan.STRING.rda
data/Anan.WikiPathways.rda
data/Asteph.MapSet.rda
data/BCG.GO.BiologicalProcess.rda
data/BCG.GO.CellularComponent.rda
data/BCG.GO.MolecularFunction.rda
data/BCG.GOslim.BiologicalProcess.rda
data/BCG.GOslim.CellularComponent.rda
data/BCG.GOslim.MolecularFunction.rda
data/BCG.HGNC.GeneFamily.rda
data/BCG.Hypoxia.AllGeneSets.rda
data/BCG.Hypoxia.GeneAssociation.rda
data/BCG.Hypoxia.TargetMatrix.rda
data/BCG.Hypoxia.TopGeneSets.rda
data/BCG.ISB.Corems.rda
data/BCG.KEGG.Pathways.rda
data/BCG.MapSet.rda
data/BCG.MetabolicPathways.rda
data/BCG.Reactome.rda
data/BCG.TB.Phenotypes.AllGeneSets.rda
data/BCG.TB.Phenotypes.GeneAssociation.rda
data/BCG.TB.Phenotypes.TargetMatrix.rda
data/BCG.TB.Phenotypes.TopGeneSets.rda
data/BCG.TFOE.Regulons.rda
data/BCG.Tuberculist.FunctionalGroups.rda
data/BCG.Tuberculist.GO.Ontology.rda
data/BCG.WikiPathways.rda
data/Bbrevis.MapSet.rda
data/CMV.MapSet.rda
data/CodonMap.rda
data/Dmel.MapSet.rda
data/Dr.13.Blood.CellTypes.AllGeneSets.rda
data/Dr.13.Blood.CellTypes.GeneAssociation.rda
data/Dr.13.Blood.CellTypes.TargetMatrix.rda
data/Dr.13.Blood.CellTypes.TopGeneSets.rda
data/Dr.27.Blood.CellTypes.AllGeneSets.rda
data/Dr.27.Blood.CellTypes.GeneAssociation.rda
data/Dr.27.Blood.CellTypes.TargetMatrix.rda
data/Dr.27.Blood.CellTypes.TopGeneSets.rda
data/Dr.AliasTable.rda
data/Dr.BTM.AntibodyResponses.rda
data/Dr.Blood.GeneModules.rda
data/Dr.BloodGen3.GeneModules.rda
data/Dr.CellCODE.ImmuneCell.TagData.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.HGNC.GeneFamily.rda
data/Dr.ImmuneCell.MarkerGenes.rda
data/Dr.KEGG.Pathways.rda
data/Dr.MapSet.rda
data/Dr.MetabolicPathways.rda
data/Dr.Mouse.Spleen.CellTypes.AllGeneSets.rda
data/Dr.Mouse.Spleen.CellTypes.GeneAssociation.rda
data/Dr.Mouse.Spleen.CellTypes.TargetMatrix.rda
data/Dr.Mouse.Spleen.CellTypes.TopGeneSets.rda
data/Dr.PBMC.GeneModules.rda
data/Dr.Panther.Pathways.rda
data/Dr.Reactome.rda
data/Dr.STRING.rda
data/Dr.WikiPathways.rda
data/Eco.MapSet.rda
data/GNB.MapSet.rda
data/GeneCellTypes.rda
data/GeneSetCellTypes.rda
data/GeneSetLifeCycle.rda
data/GrammDol.MapSet.rda
data/Gsurd.13.Blood.CellTypes.AllGeneSets.rda
data/Gsurd.13.Blood.CellTypes.GeneAssociation.rda
data/Gsurd.13.Blood.CellTypes.TargetMatrix.rda
data/Gsurd.13.Blood.CellTypes.TopGeneSets.rda
data/Gsurd.27.Blood.CellTypes.AllGeneSets.rda
data/Gsurd.27.Blood.CellTypes.GeneAssociation.rda
data/Gsurd.27.Blood.CellTypes.TargetMatrix.rda
data/Gsurd.27.Blood.CellTypes.TopGeneSets.rda
data/Gsurd.BTM.AntibodyResponses.rda
data/Gsurd.Blood.GeneModules.rda
data/Gsurd.BloodGen3.GeneModules.rda
data/Gsurd.GO.BiologicalProcess.rda
data/Gsurd.GO.CellularComponent.rda
data/Gsurd.GO.MolecularFunction.rda
data/Gsurd.GOslim.BiologicalProcess.rda
data/Gsurd.GOslim.CellularComponent.rda
data/Gsurd.GOslim.MolecularFunction.rda
data/Gsurd.HGNC.GeneFamily.rda
data/Gsurd.ImmuneCell.MarkerGenes.rda
data/Gsurd.KEGG.Pathways.rda
data/Gsurd.MapSet.rda
data/Gsurd.MetabolicPathways.rda
data/Gsurd.Mouse.Spleen.CellTypes.AllGeneSets.rda
data/Gsurd.Mouse.Spleen.CellTypes.GeneAssociation.rda
data/Gsurd.Mouse.Spleen.CellTypes.TargetMatrix.rda
data/Gsurd.Mouse.Spleen.CellTypes.TopGeneSets.rda
data/Gsurd.PBMC.GeneModules.rda
data/Gsurd.Panther.Pathways.rda
data/Gsurd.Reactome.rda
data/Gsurd.STRING.rda
data/Gsurd.WikiPathways.rda
data/Hs.13.Blood.CellTypes.AllGeneSets.rda
data/Hs.13.Blood.CellTypes.GeneAssociation.rda
data/Hs.13.Blood.CellTypes.TargetMatrix.rda
data/Hs.13.Blood.CellTypes.TopGeneSets.rda
data/Hs.27.Blood.CellTypes.AllGeneSets.rda
data/Hs.27.Blood.CellTypes.GeneAssociation.rda
data/Hs.27.Blood.CellTypes.MarkerGenes.rda
data/Hs.27.Blood.CellTypes.TargetMatrix.rda
data/Hs.27.Blood.CellTypes.TopGeneSets.rda
data/Hs.AA3merFreqMap.rda
data/Hs.AliasTable.rda
data/Hs.BTM.AntibodyResponses.rda
data/Hs.Barcode.SNPs.rda
data/Hs.Blood.GeneModules.rda
data/Hs.BloodGen3.GeneModules.rda
data/Hs.CellCODE.ImmuneCell.TagData.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.GeneProduct.rda
data/Hs.HGNC.GeneFamily.rda
data/Hs.HumanLymphocyteSubsets.rda
data/Hs.IMGT.VDJC.rda
data/Hs.ImmuneCell.MarkerGenes.rda
data/Hs.KEGG.Pathways.rda
data/Hs.MapSet.rda
data/Hs.MetabolicPathways.rda
data/Hs.Mouse.Spleen.CellTypes.AllGeneSets.rda
data/Hs.Mouse.Spleen.CellTypes.GeneAssociation.rda
data/Hs.Mouse.Spleen.CellTypes.TargetMatrix.rda
data/Hs.Mouse.Spleen.CellTypes.TopGeneSets.rda
data/Hs.PBMC.GeneModules.rda
data/Hs.Panther.Pathways.rda
data/Hs.Reactome.rda
data/Hs.STRING.rda
data/Hs.WikiPathways.rda
data/Hs_hg19.MapSet.rda
data/ImmuneCell.MarkerGenes.rda
data/JOS.MapSet.rda
data/KSHV.MapSet.rda
data/Kphaf.MapSet.rda
data/LifeCycle.GeneSetStageCalls.rda
data/LifeCycle.GeneStageCalls.rda
data/LifeCycleData_RNAseq.rda
data/LifeCycleData_YoungWinzeler.rda
data/MT_HN878.BTM.AntibodyResponses.rda
data/MT_HN878.Blood.GeneModules.rda
data/MT_HN878.BloodGen3.GeneModules.rda
data/MT_HN878.GO.BiologicalProcess.rda
data/MT_HN878.GO.CellularComponent.rda
data/MT_HN878.GO.MolecularFunction.rda
data/MT_HN878.GOslim.BiologicalProcess.rda
data/MT_HN878.GOslim.CellularComponent.rda
data/MT_HN878.GOslim.MolecularFunction.rda
data/MT_HN878.HGNC.GeneFamily.rda
data/MT_HN878.ISB.Corems.rda
data/MT_HN878.KEGG.Pathways.rda
data/MT_HN878.MetabolicPathways.rda
data/MT_HN878.Panther.Pathways.rda
data/MT_HN878.Reactome.rda
data/MT_HN878.STRING.rda
data/MT_HN878.TFOE.Regulons.rda
data/MT_HN878.Tuberculist.FunctionalGroups.rda
data/MT_HN878.Tuberculist.GO.Ontology.rda
data/MT_HN878.WikiPathways.rda
data/MTb.AliasTable.rda
data/MTb.BTM.AntibodyResponses.rda
data/MTb.Barcode.SNPs.rda
data/MTb.Blood.GeneModules.rda
data/MTb.BloodGen3.GeneModules.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.Hypoxia.AllGeneSets.rda
data/MTb.Hypoxia.GeneAssociation.rda
data/MTb.Hypoxia.TargetMatrix.rda
data/MTb.Hypoxia.TopGeneSets.rda
data/MTb.ISB.Corems.rda
data/MTb.KEGG.Pathways.rda
data/MTb.MapSet.rda
data/MTb.MetabolicPathways.rda
data/MTb.PBMC.GeneModules.rda
data/MTb.Panther.Pathways.rda
data/MTb.Reactome.rda
data/MTb.Regulons.rda
data/MTb.SNP_Table.rda
data/MTb.STRING.rda
data/MTb.TB.Phenotypes.AllGeneSets.rda
data/MTb.TB.Phenotypes.GeneAssociation.rda
data/MTb.TB.Phenotypes.TargetMatrix.rda
data/MTb.TB.Phenotypes.TopGeneSets.rda
data/MTb.TFOE.Regulons.rda
data/MTb.Tuberculist.FunctionalGroups.rda
data/MTb.Tuberculist.GO.Ontology.rda
data/MTb.WikiPathways.rda
data/MTb.iModulons.rda
data/MTbHN878.Hypoxia.AllGeneSets.rda
data/MTbHN878.Hypoxia.GeneAssociation.rda
data/MTbHN878.Hypoxia.TargetMatrix.rda
data/MTbHN878.Hypoxia.TopGeneSets.rda
data/MTbHN878.MapSet.rda
data/MTbHN878.TB.Phenotypes.AllGeneSets.rda
data/MTbHN878.TB.Phenotypes.GeneAssociation.rda
data/MTbHN878.TB.Phenotypes.TargetMatrix.rda
data/MTbHN878.TB.Phenotypes.TopGeneSets.rda
data/MTbS.MapSet.rda
data/Mabsc.BTM.AntibodyResponses.rda
data/Mabsc.Blood.GeneModules.rda
data/Mabsc.BloodGen3.GeneModules.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.Hypoxia.AllGeneSets.rda
data/Mabsc.Hypoxia.GeneAssociation.rda
data/Mabsc.Hypoxia.TargetMatrix.rda
data/Mabsc.Hypoxia.TopGeneSets.rda
data/Mabsc.ISB.Corems.rda
data/Mabsc.KEGG.Pathways.rda
data/Mabsc.MapSet.rda
data/Mabsc.MetabolicPathways.rda
data/Mabsc.Panther.Pathways.rda
data/Mabsc.Reactome.rda
data/Mabsc.STRING.rda
data/Mabsc.TB.Phenotypes.AllGeneSets.rda
data/Mabsc.TB.Phenotypes.GeneAssociation.rda
data/Mabsc.TB.Phenotypes.TargetMatrix.rda
data/Mabsc.TB.Phenotypes.TopGeneSets.rda
data/Mabsc.TFOE.Regulons.rda
data/Mabsc.Tuberculist.FunctionalGroups.rda
data/Mabsc.Tuberculist.GO.Ontology.rda
data/Mabsc.WikiPathways.rda
data/MacFas.13.Blood.CellTypes.AllGeneSets.rda
data/MacFas.13.Blood.CellTypes.GeneAssociation.rda
data/MacFas.13.Blood.CellTypes.TargetMatrix.rda
data/MacFas.13.Blood.CellTypes.TopGeneSets.rda
data/MacFas.27.Blood.CellTypes.AllGeneSets.rda
data/MacFas.27.Blood.CellTypes.GeneAssociation.rda
data/MacFas.27.Blood.CellTypes.TargetMatrix.rda
data/MacFas.27.Blood.CellTypes.TopGeneSets.rda
data/MacFas.AliasTable.rda
data/MacFas.BTM.AntibodyResponses.rda
data/MacFas.Blood.GeneModules.rda
data/MacFas.BloodGen3.GeneModules.rda
data/MacFas.CellCODE.ImmuneCell.TagData.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.GeneProduct.rda
data/MacFas.HGNC.GeneFamily.rda
data/MacFas.HumanLymphocyteSubsets.rda
data/MacFas.ImmuneCell.MarkerGenes.rda
data/MacFas.KEGG.Pathways.rda
data/MacFas.MapSet.rda
data/MacFas.MetabolicPathways.rda
data/MacFas.Mouse.Spleen.CellTypes.AllGeneSets.rda
data/MacFas.Mouse.Spleen.CellTypes.GeneAssociation.rda
data/MacFas.Mouse.Spleen.CellTypes.TargetMatrix.rda
data/MacFas.Mouse.Spleen.CellTypes.TopGeneSets.rda
data/MacFas.PBMC.GeneModules.rda
data/MacFas.Panther.Pathways.rda
data/MacFas.Reactome.rda
data/MacFas.STRING.rda
data/MacFas.WikiPathways.rda
data/MacMu.13.Blood.CellTypes.AllGeneSets.rda
data/MacMu.13.Blood.CellTypes.GeneAssociation.rda
data/MacMu.13.Blood.CellTypes.TargetMatrix.rda
data/MacMu.13.Blood.CellTypes.TopGeneSets.rda
data/MacMu.27.Blood.CellTypes.AllGeneSets.rda
data/MacMu.27.Blood.CellTypes.GeneAssociation.rda
data/MacMu.27.Blood.CellTypes.TargetMatrix.rda
data/MacMu.27.Blood.CellTypes.TopGeneSets.rda
data/MacMu.AliasTable.rda
data/MacMu.BTM.AntibodyResponses.rda
data/MacMu.Barcode.SNPs.rda
data/MacMu.Blood.GeneModules.rda
data/MacMu.BloodGen3.GeneModules.rda
data/MacMu.CellCODE.ImmuneCell.TagData.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.GeneProduct.rda
data/MacMu.HGNC.GeneFamily.rda
data/MacMu.HumanLymphocyteSubsets.rda
data/MacMu.ImmuneCell.MarkerGenes.rda
data/MacMu.KEGG.Pathways.rda
data/MacMu.MapSet.rda
data/MacMu.MetabolicPathways.rda
data/MacMu.Mouse.Spleen.CellTypes.AllGeneSets.rda
data/MacMu.Mouse.Spleen.CellTypes.GeneAssociation.rda
data/MacMu.Mouse.Spleen.CellTypes.TargetMatrix.rda
data/MacMu.Mouse.Spleen.CellTypes.TopGeneSets.rda
data/MacMu.PBMC.GeneModules.rda
data/MacMu.Panther.Pathways.rda
data/MacMu.Reactome.rda
data/MacMu.STRING.rda
data/MacMu.WikiPathways.rda
data/Mavium.BloodGen3.GeneModules.rda
data/Mavium.GO.BiologicalProcess.rda
data/Mavium.GO.CellularComponent.rda
data/Mavium.GO.MolecularFunction.rda
data/Mavium.GOslim.BiologicalProcess.rda
data/Mavium.GOslim.CellularComponent.rda
data/Mavium.GOslim.MolecularFunction.rda
data/Mavium.HGNC.GeneFamily.rda
data/Mavium.Hypoxia.AllGeneSets.rda
data/Mavium.ISB.Corems.rda
data/Mavium.KEGG.Pathways.rda
data/Mavium.MapSet.rda
data/Mavium.MetabolicPathways.rda
data/Mavium.Panther.Pathways.rda
data/Mavium.Reactome.rda
data/Mavium.STRING.rda
data/Mavium.TB.Phenotypes.AllGeneSets.rda
data/Mavium.TB.Phenotypes.GeneAssociation.rda
data/Mavium.TB.Phenotypes.TargetMatrix.rda
data/Mavium.TB.Phenotypes.TopGeneSets.rda
data/Mavium.TFOE.Regulons.rda
data/Mavium.Tuberculist.FunctionalGroups.rda
data/Mavium.Tuberculist.GO.Ontology.rda
data/Mavium.WikiPathways.rda
data/Mchel.BTM.AntibodyResponses.rda
data/Mchel.Blood.GeneModules.rda
data/Mchel.BloodGen3.GeneModules.rda
data/Mchel.GO.BiologicalProcess.rda
data/Mchel.GO.CellularComponent.rda
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data/Rnor.Mouse.Spleen.CellTypes.TargetMatrix.rda
data/Rnor.Mouse.Spleen.CellTypes.TopGeneSets.rda
data/Sty.MapSet.rda
data/Styph.AliasTable.rda
data/Styph.GO.BiologicalProcess.rda
data/Styph.GO.CellularComponent.rda
data/Styph.GO.MolecularFunction.rda
data/Styph.GOslim.BiologicalProcess.rda
data/Styph.GOslim.CellularComponent.rda
data/Styph.GOslim.MolecularFunction.rda
data/Styph.Hypoxia.AllGeneSets.rda
data/Styph.MapSet.rda
data/Styph.TB.Phenotypes.AllGeneSets.rda
data/TB.Phenotypes.GeneSetAssociation.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
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man/BScountToPctParasitemia.Rd
man/DESeq.DiffExpress.Rd
man/DKMshift.Rd
man/DNAtoAA.Rd
man/DuffyTools.Rd
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man/SAM.diffExpressRankOrder.Rd
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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
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man/expressionHeatmap.Rd
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man/fastSeqID2Species.Rd
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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
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man/getCurrentSpecies.Rd
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man/getFileLineCount.Rd
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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
