Files in xia-lab/MicrobiomeAnalystR
MicrobiomeAnalystR - A comprehensive R package for statistical, visual, and functional analysis of the microbiome.
.DS_Store
.Rbuildignore
.gitignore
DESCRIPTION
MicrobiomeAnalystR.Rproj
NAMESPACE
R/general_anal.R
R/general_graphics.R
R/general_io.R
R/general_load_libs.R
R/general_misc.R
R/general_multivar.R
R/general_proc.R
R/general_reporter.R
R/mdp_io.R
R/mdp_utils.R
R/meta_methods.R
R/meta_proc.R
R/meta_qc.R
R/mmp_utils.R
R/multifac_metadata.R
R/plotly_utils.R
R/seq_proc.R
R/tsea_utils.R
R/utils_16s2fun.R
R/utils_corrnet.R
R/utils_dimreduction.R
R/utils_fastspar.R
R/utils_maaslin.R
R/utils_meta.R
R/utils_mirkat.R
R/utils_pcoa3d.R
R/utils_peak2fun.R
R/utils_ppd.R
R/utils_scatter3d.R
R/utils_scatter_json.R
R/utils_sdp.R
R/utils_secom.R
R/utils_sparcc.R
README.Rmd
README.md
docs/microbiomeanalystr_logo.png
man/AddErrMsg.Rd
man/ApplyAbundanceFilter.Rd
man/ApplyAbundanceFilterMeta.Rd
man/ApplyMetaboFilter.Rd
man/ApplyVarianceFilter.Rd
man/ApplyVarianceFilterMeta.Rd
man/CalculateHyperScore.Rd
man/CheckMetaDataIntegrity.Rd
man/CleanData.Rd
man/CompareSummaryStats.Rd
man/CoreMicrobeAnalysis.Rd
man/CreateFooter.Rd
man/CreateMDPRnwReport.Rd
man/CreatePhyloseqObj.Rd
man/CreatePhyloseqObjMeta.Rd
man/CreateRHistAppendix.Rd
man/CreateSDPRnwReport.Rd
man/CrossReferencing.Rd
man/FeatureCorrelation.Rd
man/GenerateTemplates.Rd
man/GetColorSchema.Rd
man/GetDataForPie.Rd
man/GetErrMsg.Rd
man/GetFinalNameMap.Rd
man/GetGeneListStat.Rd
man/GetMapTable.Rd
man/GetORATable.Rd
man/GetRFConf.Table.Rd
man/GetSigTable.Corr.Rd
man/GetSigTable.LEFSE.Rd
man/GetSigTable.METAGENOSEQ.Rd
man/GetSigTable.RNASeq.Rd
man/GetSigTable.UNIVAR.Rd
man/Init.DataMeta.Rd
man/Init.mbSetObj.Rd
man/Match.Pattern.Rd
man/MergeDatasets.Rd
man/PCoA3D.Anal.Rd
man/PCoA3DAnal.16SRef.Rd
man/Perform16FunAnot_mem.Rd
man/PerformAlphaDiversityComp.Rd
man/PerformBatchCorrection.Rd
man/PerformBetaDiversity.Rd
man/PerformCategoryComp.Rd
man/PerformDEAnalyse.Rd
man/PerformKOEnrichAnalysis_KO01100.Rd
man/PerformKOProjection.Rd
man/PerformKOmapping.Rd
man/PerformLefseAnal.Rd
man/PerformMetaEffectSize.Rd
man/PerformMetaboNormalization.Rd
man/PerformMetagenomeSeqAnal.Rd
man/PerformNetworkCorrelation.Rd
man/PerformNormalization.Rd
man/PerformNormalizationMeta.Rd
man/PerformPartialCorr.Rd
man/PerformRNAseqDE.Rd
man/PerformRarefaction.Rd
man/PerformRefDataMapping.Rd
man/PerformUnivarTest.Rd
man/PlotAlphaBoxData.Rd
man/PlotAlphaData.Rd
man/PlotBetaSummary.Rd
man/PlotBoxData.Rd
man/PlotBoxDataCorr.Rd
man/PlotCorr.Rd
man/PlotDataPieFromPie.Rd
man/PlotEnrichNet.Overview.Rd
man/PlotFunAnotSummary.Rd
man/PlotFunctionStack.Rd
man/PlotGroupPieGraph.Rd
man/PlotHeatmap.Rd
man/PlotImpVar.Rd
man/PlotImpVarLEfSe.Rd
man/PlotLEfSeSummary.Rd
man/PlotLibSizeView.Rd
man/PlotMetaDensity.Rd
man/PlotMetaPCA.Rd
man/PlotOverallPieGraph.Rd
man/PlotPCAView.Rd
man/PlotPhylogeneticTree.Rd
man/PlotPiechart.Rd
man/PlotRF.Classify.Rd
man/PlotRF.VIP.Rd
man/PlotRareCurve.Rd
man/PlotRarefactionCurve.Rd
man/PlotSamplePieGraph.Rd
man/PlotSampleTaxaAundanceBar.Rd
man/PlotSelectedSample.Rd
man/PlotTaxaAbundanceArea.Rd
man/PlotTaxaAbundanceBarSamGrp.Rd
man/PlotTaxaAundanceBar.Rd
man/PlotTreeGraph.Rd
man/PlotUsrRefPCoA3DScore.Rd
man/PrepareEnrichNet.Rd
man/PrepareHeatTreePlot.Rd
man/PrepareHeatTreePlotDataParse_cmf.Rd
man/PrepareHeatTreePlotDataParse_cmf_diff_table.Rd
man/PrepareHeatTreePlotDataParse_cmf_plot.Rd
man/PrepareMergedData.Rd
man/PreparePCA4Shotgun.Rd
man/PreparePDFReport.Rd
man/PrepareQueryJson.Rd
man/RF.Anal.Rd
man/Read16SAbundData.Rd
man/Read16SAbundDataMeta.Rd
man/Read16SBiomData.Rd
man/Read16STabData.Rd
man/Read16STaxaTable.Rd
man/Read16STaxaTableMeta.Rd
man/ReadMetabolicTable.Rd
man/ReadMothurData.Rd
man/ReadSampleTable.Rd
man/ReadSampleTableMeta.Rd
man/ReadSampleTableMetaInd.Rd
man/ReadShotgunBiomData.Rd
man/ReadShotgunTabData.Rd
man/ReadTreeFile.Rd
man/RunFastSpar.Rd
man/SanityCheckData.Rd
man/SanityCheckDataMeta.Rd
man/SanityCheckMetData.Rd
man/SanityCheckSampleData.Rd
man/SanityCheckSampleDataMeta.Rd
man/SavePiechartImg.Rd
man/SetDataTypeOfMeta.Rd
man/SetMetaAttributes.Rd
man/SetModuleType.Rd
man/SetTaxonSetLib.Rd
man/Setup.MapData.Rd
man/UpdateConfItems.Rd
man/UpdateListInput.Rd
man/UpdatePieData.Rd
man/UpdateSampleItems.Rd
man/case_when.Rd
man/condenseOTUs.Rd
man/dot-read.microbiomeanalyst.lib.rds.Rd
man/dot-readDataTable.Rd
src/Makevars
src/Makevars.win
src/decorana.f
src/init.c
src/rowttests.c
src/util.c
src/util.h
vignettes/Introduction_to_MicrobiomeAnalystR.Rmd
vignettes/Marker_Data_Profiling.Rmd
vignettes/MicrobiomeAnalystR_dada2_processing_raw_data.Rmd
vignettes/Projection_with_Public_Data.Rmd
vignettes/Shotgun_Data_Profiling.Rmd
vignettes/Taxon_Set_Enrichment_Analysis.Rmd
