Files in xia-lab/MetaboAnalystR3.0
An R Package for Comprehensive Analysis of Metabolomics Data
DESCRIPTION
LICENSE
MetaboAnalystR3.0.Rproj
NAMESPACE
R/All_generic_utils.R
R/biomarker_utils.R
R/data_trimming.R
R/dependencies_function_imported.R
R/enrich_graphics.R
R/enrich_integ.R
R/enrich_mset.R
R/enrich_name_match.R
R/enrich_path_graphics.R
R/enrich_path_stats.R
R/enrich_stats.R
R/gene_fun_utils.R
R/general_anot_utils.R
R/general_data_utils.R
R/general_load_libs.R
R/general_misc_utils.R
R/general_norm_utils.R
R/general_proc_utils.R
R/generic_c_utils.R
R/meta_data_utils.R
R/meta_methods.R
R/networks_data.R
R/networks_enrich.R
R/networks_view.R
R/others_batch_check.R
R/others_lipomics.R
R/parameters_db.R
R/parameters_optimization.R
R/peak_utils.R
R/peaks_to_function.R
R/power_utils.R
R/preproc_utils.R
R/project_sharing_utils.R
R/share_projects.R
R/spectra_utils.R
R/stats_chemometrics.R
R/stats_classification.R
R/stats_clustering.R
R/stats_correlations.R
R/stats_opls.R
R/stats_plot3d.R
R/stats_sigfeatures.R
R/stats_spls.R
R/stats_univariates.R
R/sweave_report_biomarker.R
R/sweave_report_enrichment.R
R/sweave_report_integmex.R
R/sweave_report_meta_analysis.R
R/sweave_report_mummichog.R
R/sweave_report_network.R
R/sweave_report_pathway.R
R/sweave_report_power.R
R/sweave_report_stats.R
R/sweave_report_time.R
R/sweave_reporter.R
R/time_asca_heatmap2.R
R/time_mb.R
R/time_pca_anova2.R
README.md
docs/MetaboAnalystR_3.0.0_manual.pdf
docs/MetaboAnalystRlogo.png
docs/log_v3.0.png
inst/CITATION
inst/database/sqlite/GeneID_25Species_JE/.DS_Store
inst/database/sqlite/GeneID_25Species_JE/ath_genes.sqlite
inst/database/sqlite/GeneID_25Species_JE/bsu_genes.sqlite
inst/database/sqlite/GeneID_25Species_JE/bta_genes.sqlite
inst/database/sqlite/GeneID_25Species_JE/cel_genes.sqlite
inst/database/sqlite/GeneID_25Species_JE/cjo_genes.sqlite
inst/database/sqlite/GeneID_25Species_JE/dme_genes.sqlite
inst/database/sqlite/GeneID_25Species_JE/dre_genes.sqlite
inst/database/sqlite/GeneID_25Species_JE/eco_genes.sqlite
inst/database/sqlite/GeneID_25Species_JE/gga_genes.sqlite
inst/database/sqlite/GeneID_25Species_JE/hsa_genes.sqlite
inst/database/sqlite/GeneID_25Species_JE/mlo_genes.sqlite
inst/database/sqlite/GeneID_25Species_JE/mmu_genes.sqlite
inst/database/sqlite/GeneID_25Species_JE/mtb_genes.sqlite
inst/database/sqlite/GeneID_25Species_JE/osa_genes.sqlite
inst/database/sqlite/GeneID_25Species_JE/pae_genes.sqlite
inst/database/sqlite/GeneID_25Species_JE/pfa_genes.sqlite
inst/database/sqlite/GeneID_25Species_JE/ppu_genes.sqlite
inst/database/sqlite/GeneID_25Species_JE/rno_genes.sqlite
inst/database/sqlite/GeneID_25Species_JE/sau_genes.sqlite
inst/database/sqlite/GeneID_25Species_JE/sce_genes.sqlite
inst/database/sqlite/GeneID_25Species_JE/smm_genes.sqlite
inst/database/sqlite/GeneID_25Species_JE/ssc_genes.sqlite
inst/database/sqlite/GeneID_25Species_JE/syf_genes.sqlite
inst/database/sqlite/GeneID_25Species_JE/tbr_genes.sqlite
inst/database/sqlite/GeneID_25Species_JE/tma_genes.sqlite
inst/lists/ions.csv
inst/lists/neutraladdition.csv
inst/lists/neutralloss.csv
inst/rules/extended_adducts_neg.csv
inst/rules/extended_adducts_pos.csv
inst/rules/primary_adducts_neg.csv
inst/rules/primary_adducts_pos.csv
man/ANOVA.Anal.Rd
man/ANOVA2.Anal.Rd
man/ASCAfun.res.Rd
man/ASCAfun1.Rd
man/ASCAfun2.Rd
man/AddErrMsg.Rd
man/CVTest.LRmodel.Rd
man/C_imodwt_r.Rd
man/C_modwt_r.Rd
man/CalculateFeatureRanking.Rd
man/CalculateGlobalTestScore.Rd
man/CalculateHyperScore.Rd
man/CalculateImpVarCutoff.Rd
man/CalculateOraScore.Rd
man/CalculatePairwiseDiff.Rd
man/CalculateQeaScore.Rd
man/CalculateSSP.Rd
man/CheckMetaDataConsistency.Rd
man/CleanData.Rd
man/CleanDataMatrix.Rd
man/CleanNumber.Rd
man/ClearNegatives.Rd
man/ClearStrings.Rd
man/ClearUserDir.Rd
man/Compound_function_mzlist.Rd
man/ComputeAverageCurve.Rd
man/ComputeHighLow.Rd
man/Convert2Mummichog.Rd
man/CreateANOVAdoc.Rd
man/CreateAOV2doc.Rd
man/CreateASCAdoc.Rd
man/CreateAnalNullMsg.Rd
man/CreateBiomarkerInputDoc.Rd
man/CreateBiomarkerIntr.Rd
man/CreateBiomarkerOverview.Rd
man/CreateBiomarkerRatioOverview.Rd
man/CreateBiomarkerRnwReport.Rd
man/CreateCorrDoc.Rd
man/CreateEBAMdoc.Rd
man/CreateEnrichAnalDoc.Rd
man/CreateEnrichInputDoc.Rd
man/CreateEnrichIntr.Rd
man/CreateEnrichORAdoc.Rd
man/CreateEnrichOverview.Rd
man/CreateEnrichProcessDoc.Rd
man/CreateEnrichQEAdoc.Rd
man/CreateEnrichRnwReport.Rd
man/CreateEnrichSSPdoc.Rd
man/CreateFooter.Rd
man/CreateGSEAAnalTable.Rd
man/CreateGraph.Rd
man/CreateHCdoc.Rd
man/CreateHeatmap2doc.Rd
man/CreateIntegPathwayAnalysisRnwReport.Rd
man/CreateIntegratedPathwayAnalInputDoc.Rd
man/CreateIntegratedPathwayAnalIntr.Rd
man/CreateIntegratedPathwayDoc.Rd
man/CreateIntegratedPathwayGeneMapTable.Rd
man/CreateIntegratedPathwayNameMapTable.Rd
man/CreateIntegratedPathwayResultsTable.Rd
man/CreateKMdoc.Rd
man/CreateLadder.Rd
man/CreateLibFromKEGG.Rd
man/CreateMBdoc.Rd
man/CreateMappingResultTable.Rd
man/CreateMetaAnalTable.Rd
man/CreateMetaAnalysisDEdoc.Rd
man/CreateMetaAnalysisInputDoc.Rd
man/CreateMetaAnalysisIntr.Rd
man/CreateMetaAnalysisNORMdoc.Rd
man/CreateMetaAnalysisOutput.Rd
man/CreateMetaAnalysisOverview.Rd
man/CreateMetaAnalysisRnwReport.Rd
man/CreateMetaTable.Rd
man/CreateModelBiomarkersDoc.Rd
man/CreateMultiBiomarkersDoc.Rd
man/CreateMummichogAnalTable.Rd
man/CreateMummichogAnalysisDoc.Rd
man/CreateMummichogInputDoc.Rd
man/CreateMummichogIntro.Rd
man/CreateMummichogLibs.Rd
man/CreateMummichogOverview.Rd
man/CreateMummichogRnwReport.Rd
man/CreateNORMdoc.Rd
man/CreateNetworkExplorerDoc.Rd
man/CreateNetworkExplorerInputDoc.Rd
man/CreateNetworkExplorerIntr.Rd
man/CreateNetworkExplorerOverview.Rd
man/CreateNetworkExplorerRnwReport.Rd
man/CreateNetworkGeneMapTable.Rd
man/CreateNetworkNameMapTable.Rd
man/CreateOPLSDAdoc.Rd
man/CreatePCAdoc.Rd
man/CreatePLSdoc.Rd
man/CreatePathAnalDoc.Rd
man/CreatePathInputDoc.Rd
man/CreatePathIntr.Rd
man/CreatePathProcessDoc.Rd
man/CreatePathResultDoc.Rd
man/CreatePathRnwReport.Rd
man/CreatePowerAnalDoc.Rd
man/CreatePowerInputDoc.Rd
man/CreatePowerIntr.Rd
man/CreatePowerOverview.Rd
man/CreatePowerParametersDoc.Rd
man/CreatePowerRnwReport.Rd
man/CreateRFdoc.Rd
man/CreateRHistAppendix.Rd
man/CreateROCLabelsTable.Rd
man/CreateRatioTable.Rd
man/CreateSAMdoc.Rd
man/CreateSOMdoc.Rd
man/CreateSPLSDAdoc.Rd
man/CreateSVMdoc.Rd
man/CreateSemiTransColors.Rd
man/CreateStatIOdoc.Rd
man/CreateStatIntr.Rd
man/CreateStatRnwReport.Rd
man/CreateSummaryTable.Rd
man/CreateTimeSeriesAnalNullMsg.Rd
man/CreateTimeSeriesIOdoc.Rd
man/CreateTimeSeriesRnwReport.Rd
man/CreateUNIVdoc.Rd
man/CreateUnivROCTable.Rd
man/CreateUnivarBiomarkersDoc.Rd
man/CreateVennMetaTable.Rd
man/CreateiPCAdoc.Rd
man/CrossReferencing.Rd
man/Densitygrouping_slave.Rd
man/EBAM.Init.Rd
man/ExperimentsCluster_doe.Rd
man/ExtractMS2data.Rd
man/FC.Anal.paired.Rd
man/FC.Anal.unpaired.Rd
man/FeatureCorrelation.Rd
man/FilterVariable.Rd
man/FisherLSD.Rd
man/FormatPeakList.Rd
man/Get.ConcRef.Rd
man/Get.Leverage.Rd
man/Get.VIP.Rd
man/Get.asca.tss.Rd
man/Get.bwss.Rd
man/Get.pAUC.Rd
man/Get.pred.Rd
man/Get.rpart.summary.Rd
man/GetAbundanceLabel.Rd
man/GetAccuracyInfo.Rd
man/GetAllDataNames.Rd
man/GetAllKMClusterMembers.Rd
man/GetAllSOMClusterMembers.Rd
man/GetCIs.Rd
man/GetCMD.Rd
man/GetCandidateList.Rd
man/GetCircleInfo.Rd
man/GetCompoundDetails.Rd
man/GetConvertFullPath.Rd
man/GetExtendRange.Rd
man/GetFC.Rd
man/GetFeatureNumbers.Rd
man/GetFinalNameMap.Rd
man/GetFisherPvalue.Rd
man/GetHTMLMetSet.Rd
man/GetHTMLPathSet.Rd
man/GetImpFeatureMat.Rd
man/GetKEGGNodeInfo.Rd
man/GetKMClusterMembers.Rd
man/GetLassoFreqs.Rd
man/GetLimmaResTable.Rd
man/GetMapTable.Rd
man/GetMaxPCAComp.Rd
man/GetMeanROC.Rd
man/GetMetSetName.Rd
man/GetMetaResultMatrix.Rd
man/GetMetaSigHitsTable.Rd
man/GetMsetLibCheckMsg.Rd
man/GetMsetLibSearchResult.Rd
man/GetMsetNames.Rd
man/GetMummichogPathSetDetails.Rd
man/GetNetworkGeneMappingResultTable.Rd
man/GetNewSampleNames.Rd
man/GetORA.pathNames.Rd
man/GetORA.smpdbIDs.Rd
man/GetORATable.Rd
man/GetQEA.keggIDs.Rd
man/GetQEA.pathNames.Rd
man/GetQEATable.Rd
man/GetRCommandHistory.Rd
man/GetRFConf.Table.Rd
man/GetRFConfMat.Rd
man/GetRFOOB.Rd
man/GetRFSigMat.Rd
man/GetROC.coords.Rd
man/GetROCLassoFreq.Rd
man/GetROCTtestP.Rd
man/GetSOMClusterMembers.Rd
man/GetSSPTable.Rd
man/GetSVMSigMat.Rd
man/GetSampleSizeLadder.Rd
man/GetSelectedDataNames.Rd
man/GetSelectedDataNumber.Rd
man/GetSigTable.ASCA.Rd
man/GetSigTable.Anova.Rd
man/GetSigTable.Aov2.Rd
man/GetSigTable.Corr.Rd
man/GetSigTable.EBAM.Rd
man/GetSigTable.FC.Rd
man/GetSigTable.MB.Rd
man/GetSigTable.RF.Rd
man/GetSigTable.Rd
man/GetSigTable.SAM.Rd
man/GetSigTable.SVM.Rd
man/GetSigTable.TT.Rd
man/GetSigTable.Volcano.Rd
man/GetSuggestedSAMDelta.Rd
man/GetTTSigMat.Rd
man/GetTopInx.Rd
man/GetTrainTestSplitMat.Rd
man/GetTtestRes.Rd
man/GetUnivReport.Rd
man/GetVariableLabel.Rd
man/GetVennGeneNames.Rd
man/GetXYCluster.Rd
man/GroupPeakList.Rd
man/HMDBID2KEGGID.Rd
man/HMDBID2Name.Rd
man/ImportRawMSData.Rd
man/ImportRawMSDataList.Rd
man/ImputeVar.Rd
man/InitDataObjects.Rd
man/InitPowerAnal.Rd
man/InitStatAnalMode.Rd
man/InitTimeSeriesAnal.Rd
man/IsSmallSmplSize.Rd
man/IsSpectraProcessingOK.Rd
man/KEGGID2HMDBID.Rd
man/KEGGID2Name.Rd
man/KEGGPATHID2SMPDBIDs.Rd
man/Kmeans.Anal.Rd
man/LSD.test.Rd
man/LoadKEGGKO_lib.Rd
man/LoadKEGGLib.Rd
man/LoadSmpLib.Rd
man/LogNorm.Rd
man/MSspec.fillPeaks.Rd
man/MSspec.rtCorrection.Rd
man/MapCmpd2KEGGNodes.Rd
man/MapKO2KEGGEdges.Rd
man/Match.Pattern.Rd
man/MergeDatasets.Rd
man/MergeDuplicates.Rd
man/MetaboAnalystR.Rd
man/MetaboliteMappingExact.Rd
man/Noise_evaluate.Rd
man/Normalization.Rd
man/OPLSDA.Permut.Rd
man/OPLSR.Anal.Rd
man/PCA.Anal.Rd
man/PCA.Flip.Rd
man/PCA.GENES.Rd
man/PLSDA.CV.Rd
man/PLSDA.Permut.Rd
man/PLSR.Anal.Rd
man/PeakPicking_MatchedFilter_slave.Rd
man/PeakPicking_centWave_slave.Rd
man/PeakPicking_core.Rd
man/PeakPicking_prep.Rd
man/Perform.ASCA.Rd
man/Perform.ASCA.permute.Rd
man/Perform.Permut.Rd
man/Perform.UnivROC.Rd
man/Perform.permutation.Rd
man/PerformAdductMapping.Rd
man/PerformApproxMatch.Rd
man/PerformBatchCorrection.Rd
man/PerformCV.explore.Rd
man/PerformCV.test.Rd
man/PerformCurrencyMapping.Rd
man/PerformDataInspect.Rd
man/PerformDataTrimming.Rd
man/PerformDetailMatch.Rd
man/PerformEachDEAnal.Rd
man/PerformIndNormalization.Rd
man/PerformIntegCmpdMapping.Rd
man/PerformIntegGeneMapping.Rd
man/PerformIntegPathwayAnalysis.Rd
man/PerformKOEnrichAnalysis_KO01100.Rd
man/PerformKOEnrichAnalysis_List.Rd
man/PerformLimmaDE.Rd
man/PerformMSDataOutput.Rd
man/PerformMapping.Rd
man/PerformMetaMerge.Rd
man/PerformMultiMatch.Rd
man/PerformPSEA.Rd
man/PerformParamsOptimization.Rd
man/PerformPeakAlignment.Rd
man/PerformPeakAnnotation.Rd
man/PerformPeakFiling.Rd
man/PerformPeakGrouping.Rd
man/PerformPeakPicking.Rd
man/PerformPeakProfiling.Rd
man/PerformPowerProfiling.Rd
man/PerformPvalCombination.Rd
man/PerformVoteCounting.Rd
man/Plot.Permutation.Rd
man/Plot.sampletrend.Rd
man/PlotANOVA.Rd
man/PlotANOVA2.Rd
man/PlotASCA.Permutation.Rd
man/PlotASCAModel.Rd
man/PlotAccuracy.Rd
man/PlotAscaImpVar.Rd
man/PlotBoxPlot.Rd
man/PlotCmpdSummary.Rd
man/PlotCmpdView.Rd
man/PlotConcRange.Rd
man/PlotCorr.Rd
man/PlotCorrHeatMap.Rd
man/PlotDetailROC.Rd
man/PlotEBAM.Cmpd.Rd
man/PlotEIC.Rd
man/PlotEnrichNet.Overview.Rd
man/PlotFC.Rd
man/PlotHCTree.Rd
man/PlotHeatMap.Rd
man/PlotHeatMap2.Rd
man/PlotImpVar.Rd
man/PlotImpVars.Rd
man/PlotInmexGraph.Rd
man/PlotInmexPath.Rd
man/PlotIntegPaths.Rd
man/PlotInteraction.Rd
man/PlotKEGGPath.Rd
man/PlotKmeans.Rd
man/PlotLoadingCmpd.Rd
man/PlotMBTimeProfile.Rd
man/PlotMS.RT.Rd
man/PlotMS2Spectra.Rd
man/PlotMSEA.Overview.Rd
man/PlotMSPeaksPerm.Rd
man/PlotMetaVenn.Rd
man/PlotMetpaPath.Rd
man/PlotModelScree.Rd
man/PlotNormSummary.Rd
man/PlotOPLS.MDL.Rd
man/PlotOPLS.Permutation.Rd
man/PlotOPLS.Splot.Rd
man/PlotOPLS2DScore.Rd
man/PlotORA.Rd
man/PlotPCA.overview.Rd
man/PlotPCA2DScore.Rd
man/PlotPCA3DScore.Rd
man/PlotPCA3DScoreImg.Rd
man/PlotPCABiplot.Rd
man/PlotPCALoading.Rd
man/PlotPCAPairSummary.Rd
man/PlotPCAScree.Rd
man/PlotPLS.Classification.Rd
man/PlotPLS.Imp.Rd
man/PlotPLS.Permutation.Rd
man/PlotPLS2DScore.Rd
man/PlotPLS3DScore.Rd
man/PlotPLS3DScoreImg.Rd
man/PlotPLSLoading.Rd
man/PlotPLSPairSummary.Rd
man/PlotPathSummary.Rd
man/PlotPathwayMZHits.Rd
man/PlotPeaks2Paths.Rd
man/PlotPowerProfile.Rd
man/PlotPowerStat.Rd
man/PlotProbView.Rd
man/PlotQEA.MetSet.Rd
man/PlotQEA.Overview.Rd
man/PlotRF.Classify.Rd
man/PlotRF.Outlier.Rd
man/PlotRF.VIP.Rd
man/PlotROC.LRmodel.Rd
man/PlotROC.Rd
man/PlotROCTest.Rd
man/PlotRSVM.Classification.Rd
man/PlotRSVM.Cmpd.Rd
man/PlotSAM.Cmpd.Rd
man/PlotSAM.FDR.Rd
man/PlotSOM.Rd
man/PlotSPLS2DScore.Rd
man/PlotSPLS3DScore.Rd
man/PlotSPLS3DScoreImg.Rd
man/PlotSPLSDA.Classification.Rd
man/PlotSPLSLoading.Rd
man/PlotSPLSPairSummary.Rd
man/PlotSampleNormSummary.Rd
man/PlotSelectedFeature.Rd
man/PlotSigVar.Rd
man/PlotSubHeatMap.Rd
man/PlotTT.Rd
man/PlotTestAccuracy.Rd
man/PlotVolcano.Rd
man/Predict.class.Rd
man/PrepareIntegData.Rd
man/PrepareNetworkData.Rd
man/PreparePDFReport.Rd
man/PreparePermResult.Rd
man/PreparePrenormData.Rd
man/PrepareQueryJson.Rd
man/PrepareROCData.Rd
man/PrepareROCDetails.Rd
man/PrepareVennData.Rd
man/RF.Anal.Rd
man/ROCPredSamplesTable.Rd
man/RSVM.Anal.Rd
man/RSVM.Rd
man/RT.Adjust_Slave.Rd
man/RankFeatures.Rd
man/Read.BatchCSVdata.Rd
man/Read.MSspec.Rd
man/Read.PeakList.Rd
man/Read.PeakListData.Rd
man/Read.TextData.Rd
man/ReadIndData.Rd
man/ReadPairFile.Rd
man/RecordRCommand.Rd
man/RegisterData.Rd
man/RemoveCmpd.Rd
man/RemoveData.Rd
man/RemoveDuplicates.Rd
man/RemoveFile.Rd
man/RemoveFolder.Rd
man/RemoveGene.Rd
man/RemoveMissingPercent.Rd
man/ReplaceMin.Rd
man/RerenderMetPAGraph.Rd
man/SAM.Anal.Rd
man/SOM.Anal.Rd
man/SPLSR.Anal.Rd
man/SanityCheckData.Rd
man/SanityCheckIndData.Rd
man/SanityCheckMummichogData.Rd
man/SaveTransformedData.Rd
man/SearchByCompound.Rd
man/SearchByName.Rd
man/SearchMsetLibraries.Rd
man/SearchNetDB.Rd
man/SelectMultiData.Rd
man/SetAnalysisMode.Rd
man/SetAnnotationParam.Rd
man/SetCachexiaSetUsed.Rd
man/SetCandidate.Rd
man/SetClass.Rd
man/SetCurrentGroups.Rd
man/SetCurrentMsetLib.Rd
man/SetCustomData.Rd
man/SetDesignType.Rd
man/SetKEGG.PathLib.Rd
man/SetMetabolomeFilter.Rd
man/SetMummichogPval.Rd
man/SetMummichogPvalFromPercent.Rd
man/SetOrganism.Rd
man/SetPeakEnrichMethod.Rd
man/SetPeakFormat.Rd
man/SetPeakList.GroupValues.Rd
man/SetPeakParam.Rd
man/SetPlotParam.Rd
man/SetSMPDB.PathLib.Rd
man/Setup.AdductData.Rd
man/Setup.BiofluidType.Rd
man/Setup.ConcData.Rd
man/Setup.HMDBReferenceMetabolome.Rd
man/Setup.KEGGReferenceMetabolome.Rd
man/Setup.MapData.Rd
man/Setup.UserMsetLibData.Rd
man/SetupKEGGLinks.Rd
man/SetupMSdataMatrix.Rd
man/SetupSMPDBLinks.Rd
man/SlaveCluster_doe.Rd
man/Statistic_doe.Rd
man/SumNorm.Rd
man/Ttests.Anal.Rd
man/UnzipUploadedFile.Rd
man/UpdateData.Rd
man/UpdateEC_Rules.Rd
man/UpdateGraphSettings.Rd
man/UpdateInstrumentParameters.Rd
man/UpdateIntegPathwayAnalysis.Rd
man/UpdateOPLS.Splot.Rd
man/UpdatePCA.Loading.Rd
man/UpdatePLS.Loading.Rd
man/Volcano.Anal.Rd
man/XSet2MSet.Rd
man/add_trace.Rd
man/analyze.lipids.Rd
man/aof.Rd
man/aov.between.Rd
man/aov.repeated.Rd
man/aov.within.Rd
man/calcCV.Rd
man/calcGaussianS.Rd
man/calcPPS2.Rd
man/calcRCS_GSValues.Rd
man/calculateConcISO.Rd
man/calculateGPRT.Rd
man/calculatePPKs.Rd
man/calculateSet_doe.Rd
man/computeConc.Rd
man/creatPeakTable.Rd
man/createCVset.Rd
man/doCompoundMapping.Rd
man/doGeneIDMapping.Rd
man/doKEGG2NameMapping.Rd
man/doKOFiltering.Rd
man/dot-compute.mummichog.RT.fgsea.Rd
man/dot-compute.mummichog.fgsea.Rd
man/dot-emptyscan.remove.Rd
man/dot-init.Permutations.Rd
man/dot-init.RT.Permutations.Rd
man/dot-read.metaboanalyst.lib.Rd
man/dot-readDataTable.Rd
man/fgsea2.Rd
man/fillpathways.Rd
man/genLogisticRegMdl.Rd
man/getDataFromTextArea.Rd
man/heckbert.Rd
man/iPCA.Anal.Rd
man/isEmptyMatrix.Rd
man/kwtest.Rd
man/mSet2xcmsSet.Rd
man/make_cpdlib.Rd
man/make_cpdlist.Rd
man/make_ecpdlist.Rd
man/map.Rd
man/multi.stat.Rd
man/mz.trim_random.Rd
man/mz.trim_specific.Rd
man/optimize.xcms.doe.Rd
man/optimizxcms.doe.peakpicking.Rd
man/parseFisher.Rd
man/parseTukey.Rd
man/performMB.Rd
man/plot.MS_3D.Rd
man/plotProfile.Rd
man/rda2list.Rd
man/resultIncreased_doe.Rd
man/rt.trim_random.Rd
man/rt.trim_specific.Rd
man/sparse.mint.block_iteration.Rd
man/splsda.Rd
man/ssm_trim.Rd
man/template.match.Rd
man/updateRawSpectraParam.Rd
man/usr2png.Rd
news.md
src/Internal_utils_batch.c
src/Internal_utils_batch.h
src/decorana.f
src/init.c
src/mzROI.c
src/util.c
src/util.h
src/xcms_binners.c
src/xcms_binners.h
tests/testthat.R
tests/testthat/test-basic.R
tests/testthat/test-metaboanalystr-analytical.R
tests/testthat/test-metaboanalystr-pathway-enrichment.R
vignettes/Batch_effect_correction.Rmd
vignettes/Biomarker_Analysis.Rmd
vignettes/Enrichment_Analysis.Rmd
vignettes/Introduction_to_MetaboAnalystR.Rmd
vignettes/Joint_Pathway_Analysis.Rmd
vignettes/MS_Peaks_to_Pathways.Rmd
vignettes/Meta_Analysis.Rmd
vignettes/MetaboAnalystR_3_workflow_Towards_Optimized_Workflow_for_Global_Metabolomics.Rmd
vignettes/Network_Explorer_Module.Rmd
vignettes/Pathway_Analysis.Rmd
vignettes/Power_Analysis_Module.Rmd
vignettes/Statistical_Analysis_Module.Rmd
vignettes/Time_Series_or_Two_Factor_Design.Rmd
vignettes/vignette_figures/Example1_BC PCAdpi300.png
vignettes/vignette_figures/Example1_BC Trenddpi300.png
vignettes/vignette_figures/Example2_image_BC PCAdpi300.png
vignettes/vignette_figures/Example2_image_BC Trenddpi300.png
vignettes/vignette_figures/IBD_BC_pca_score2d_0_dpi72.png
vignettes/vignette_figures/IBD_BCfree_pca_score2d_0_dpi72.png
vignettes/vignette_figures/PCA.png
vignettes/vignette_figures/Peak_Intensity.png
vignettes/vignette_figures/TIC_trimmed.png
vignettes/vignette_figures/Tic_trimmed_IBD.png
vignettes/vignette_figures/bc.csv
vignettes/vignette_figures/data_inspect_TJ_ori.png
vignettes/vignette_figures/datainspect.png
vignettes/vignette_figures/fc_0_dpi72.png
vignettes/vignette_figures/metaboanalyst_input.csv
vignettes/vignette_figures/norm_0_dpi72.png
vignettes/vignette_figures/pca_score2d_0_dpi72.png
vignettes/vignette_figures/pca_score3d_0_dpi72.png
vignettes/vignette_figures/peaks_to_paths_dpi144.png
vignettes/vignette_figures/pls_cv_0_dpi72.png
vignettes/vignette_figures/pls_imp_0_dpi72.png
vignettes/vignette_figures/pls_score2d_0_dpi72.png
vignettes/vignette_figures/trimmed_TIC_2.png
vignettes/vignette_figures/tt_0_dpi72.png
