Man pages for xia-lab/MicrobiomeAnalystR
MicrobiomeAnalystR - A comprehensive R package for statistical, visual, and functional analysis of the microbiome.

AddErrMsgAdds an error message
ApplyAbundanceFilterFunction to filter uploaded data
ApplyVarianceFilterFunction to filter uploaded data
CalculateHyperScoreCalculate enrichment score.
condenseOTUsHelper Function that will take the OTU Table (as a...
CoreMicrobeAnalysisPerform core microbiome analysis
CreateMDPRnwReportFunction to create PDF report for MDP module
CreatePhyloseqObjFunction to recreate phyloseq object
CreateSDPRnwReportFunction to create PDF report for SDP module
CrossReferencingPerform cross referencing.
dot-readDataTableRead data table
dot-read.microbiomeanalyst.libRead RDS files from the internet
FeatureCorrelationMain function to calculate correlation of all other feature...
GenerateTemplatesFunction to generate templates
GetColorSchemaFunction to get color palette for graphics.
GetDataForPieUtility function to exract data for piechart.
GetFinalNameMapGetter to return final map
GetGeneListStatFunction to get gene list statistics
GetMapTableGetter function
GetORATableGetter function
GetRFConf.TableGetter function
GetSigTable.CorrGetter function
GetSigTable.LEFSEGetter function
GetSigTable.METAGENOSEQGetter function
GetSigTable.RNASeqGetter function
GetSigTable.UNIVARGetter function
Init.mbSetObjConstructs a mbSet object for storing data
Match.PatternMatch Patterns Function
PCoA3D.AnalMain function to perform PCoA analysis
PCoA3DAnal.16SRefFunction to create PCoA
Perform16FunAnotMain function to perform 16S functional annotation
PerformAlphaDiversityCompPerform alpha diversity
PerformCategoryCompFunction to perform categorical comparison.
PerformKOEnrichAnalysis_KO01100Function to prepare KO enrichment analysis.
PerformKOEnrichAnalysis_TablePerform KO Enrichment Analysis
PerformKOmappingFunction to perform KO mapping.
PerformKOProjectionFunction to perform KO projection
PerformLefseAnalMain function to perform LEfSe analysis
PerformMetagenomeSeqAnalMain function to perform metagenome seq analysis
PerformNetworkCorrelationFunction to call for correlation network
PerformNormalizationFunction to perform normalization
PerformRarefactionUtility function to perform rarefraction (used by...
PerformRefDataMappingFunction to perform reference data mapping.
PerformRNAseqDEMain function to perform RNAseq analysis
PerformUnivarTestMain function to perform classical univariate analysis.
PlotAlphaBoxDataFunction to create box plots for alpha diversity analysis
PlotAlphaDataFunction to plot alpha-diversity analysis.
PlotBetaDiversityFunction to plot beta diversity.
PlotBoxDataFunction to create box plots of important features
PlotCorrPlot Pattern Search
PlotCorrHeatMapFunction to create correlation heat map
PlotDataPieFromPieFunction to plot pie-chart data.
PlotEnrichNet.OverviewCreate network for enrichmnet overview
PlotFunAnotSummaryPlot functional annotation summary
PlotFunctionStackFunction to plot stacked bar chart of functional data.
PlotGroupPieGraphMain function to plot pie graphs of microbiome data.
PlotHeatmapMain function to plot heatmap.
PlotImpVarHelper function to plot variable importance (for RF and...
PlotImpVarLEfSePlot LEfSe summary
PlotLEfSeSummaryPlot LEfSe summary
PlotLibSizeViewFunction to plot library size
PlotOverallPieGraphMain function to plot pie graphs of microbiome data.
PlotPhylogeneticTreeFunction to prepare data for phylogenetic tree.
PlotPiechartFunction to create pie-chart plot.
PlotRareCurveFunction to plot rarefraction curves
PlotRarefactionCurveFunction to create rarefraction curves of microbiome data
PlotRF.ClassifyPlot Random Forest Classification
PlotRF.VIPPlot variable importance ranked by MeanDecreaseAccuracy
PlotRNASeqDotPlotPlot fold-change dot plot
PlotRNAseqVolcanoFunction to plot volacano analysis results from RNAseq...
PlotSamplePieGraphMain function to plot sample-wise pie graphs of microbiome...
PlotSampleTaxaAundanceBarFunction to create bar plots of selected taxa level.
PlotSelectedSampleFunction to create a summary of a sample using a piechart at...
PlotTaxaAbundanceAreaPlot functional annotation summary
PlotTaxaAbundanceBarSamGrpFunction to plot group-wise bar charts.
PlotTaxaAundanceBarFunction to plot bar charts for alpha diversity
PlotTreeGraphFunction to plot tree graphics for dendogram.
PlotUsrRefPCoA3DScoreFunction to plot 3D score plot.
PrepareEnrichNetFunction to prepare data for enrichment network.
PrepareHeatTreePlotFunction to plot heat tree
PrepareHeatTreePlotDataParse_cmfFunction to prepare heat tree data
PrepareHeatTreePlotDataParse_cmf_diff_tableFunction to prepare heat tree data
PrepareHeatTreePlotDataParse_cmf_plotFunction to prepare heat tree data
PrepareMergedDataFunction to merge user data with public data.
PreparePCA4ShotgunFunction to prepare shotgun data for PCA.
PreparePDFReportFunction to create PDF report
PrepareQueryJsonFunction to prepare query for JSON.
Read16SAbundDataMain function to read 16S data
Read16SBiomDataFunction to read 16S data in biom format
Read16STabDataFunction to read 16S data
Read16STaxaTableFunction to read 16S taxonomy table from txt format
ReadMothurDataFunction to read 16S data in mothur format
ReadSampleTableFunction to read in sample data
ReadShotgunBiomDataMain function to read in shotgun data
ReadShotgunTabDataMain function to read in shotgun data
ReadTreeFileFunction to read in tree files.
RF.AnalPerforms Random Forest Analysis
RunFastSparFunction to call FastSpar
SanityCheckDataMain function to sanity check on uploaded data
SavePiechartImgFunction to save pie-chart
SetModuleTypeFunction to set analysis type
SetMsetLibSet the microbe set library
Setup.MapDataFunction to set up data for TSEA
UpdateListInputFunction to filter list data based on a minimum count
UpdatePieDataFunction to update pie-chart data.
UpdateSampleItemsFunction to update samples
xia-lab/MicrobiomeAnalystR documentation built on Oct. 17, 2019, 9:05 a.m.