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

Global functions
.get.mbSetObj Source code
.load.microbiomeanalyst.lib Source code
.plotQualityProfileLoop Source code
.read.microbiomeanalyst.lib Man page Source code
.readDataTable Man page Source code
.set.mbSetObj Source code
AddErrMsg Man page Source code
ApplyAbundanceFilter Man page Source code
ApplyVarianceFilter Man page Source code
CalculateHyperScore Man page Source code
ClearFactorStrings Source code
ClearRCommandHistory Source code
ClearStrings Source code
ComputeColorGradient Source code Source code
ComputeColorGradientCorr Source code
ComputeGoods Source code
CoreMicrobeAnalysis Man page Source code
CreateALPHDIVdoc Source code
CreateAnalNullMsg Source code
CreateBETADIVdoc Source code
CreateCOREdoc Source code
CreateCORRdoc Source code
CreateEnrichInputDoc Source code
CreateEnrichIntr Source code
CreateEnrichORAdoc Source code
CreateEnrichOverview Source code
CreateEnrichProcessDoc Source code
CreateFUNCPREDdoc Source code
CreateFUNCPROFdoc Source code
CreateFooter Source code
CreateHCdoc Source code
CreateHEATTREEdoc Source code
CreateHeader Source code
CreateIOdoc Source code
CreateIntr Source code
CreateLEFSEdoc Source code
CreateMDPRnwReport Man page Source code
CreateMETAGENOSEQdoc Source code
CreateNORMdoc Source code
CreatePCAdoc Source code
CreatePHYLOGENETICTREEdoc Source code
CreatePPDAnalDoc Source code
CreatePPDIntr Source code
CreatePPDOverview Source code
CreatePPDResultDoc Source code
CreatePPDRnwReport Source code
CreatePhyloseqObj Man page Source code
CreateRAREFCTIONCURVEdoc Source code
CreateRFdoc Source code
CreateRNASEQdoc Source code
CreateSDPRnwReport Man page Source code
CreateTaxaEnrichRnwReport Source code
CreateUNIVARdoc Source code
CreateVISEXPLRdoc Source code
CrossReferencing Man page Source code
FeatureCorrelation Man page Source code
GenerateTemplates Man page Source code
GetAovRes Source code
GetBashFullPath Source code
GetBetaDiversityStats Source code
GetColorGradient Source code
GetColorSchema Man page Source code
GetCorrNetName Source code
GetCurrentImg Source code
GetDataForPie Man page Source code
GetDiscreteInx Source code
GetExtendRange Source code
GetFinalNameMap Man page Source code
GetGeneListStat Man page Source code
GetGroupNames Source code
GetHTMLMetSet Source code
GetHighTaxaLvlNm Source code
GetHtMetaCpInfo Source code
GetLowerTaxaLvlNm Source code
GetMDI Source code
GetMapTable Man page Source code
GetMetaInfo Source code
GetMetaTaxaInfo Source code
GetMsetEvidence Source code
GetMsetMembers Source code
GetMsetNames Source code
GetMsetPval Source code
GetMsetReferences Source code
GetNameMapCol Source code
GetNumbericalInx Source code
GetORA.colorBar Source code
GetORA.mat Source code
GetORA.rowNames Source code
GetORATable Man page Source code
GetPieTaxaAbund Source code
GetPieTaxaNames Source code
GetRCommandHistory Source code
GetRFConf.Table Man page Source code
GetRFConfColNames Source code
GetRFConfMat Source code
GetRFConfRowNames Source code
GetRFOOB Source code
GetRFSigColNames Source code
GetRFSigMat Source code
GetRFSigRowNames Source code
GetRandomNumbers Source code
GetResColNames Source code
GetResMat Source code
GetResRowNames Source code
GetSamplNames Source code
GetSampleGrpInfo Source code
GetSampleGrpNo Source code
GetSampleNamesaftNorm Source code
GetSeriesColors Source code
GetShortNames Source code
GetSigTable Source code
GetSigTable.Corr Man page Source code
GetSigTable.LEFSE Man page Source code
GetSigTable.METAGENOSEQ Man page Source code
GetSigTable.RNASeq Man page Source code
GetSigTable.UNIVAR Man page Source code
GetStressNMDS Source code
GetTaxaFeatSize Source code
GetTaxaNames Source code
GetTseaCol Source code
GetTseaRowNames Source code
GetTtestRes Source code
Init.mbSetObj Man page Source code
Init16SAnalMode Source code
InitPieColors Source code
InitShotAnalMode Source code
IsPoorReplicate Source code
IsTreeUploaded Source code
KendallCorrFunc Source code
LoadKEGGKO_lib Source code
MakeRankedCountTables Source code
MapKO2KEGGEdges Source code
Match.Pattern Man page Source code
PCoA3D.Anal Man page Source code
PCoA3DAnal.16SRef Man page Source code
PearsonCorrFunc Source code
Perform16FunAnot Man page Source code
PerformAlphaDiversityComp Man page Source code
PerformCategoryComp Man page Source code
PerformExprFilter Source code
PerformKOEnrichAnalysis_KO01100 Man page Source code
PerformKOEnrichAnalysis_List Source code
PerformKOEnrichAnalysis_Table Man page Source code
PerformKOProjection Man page Source code
PerformKOmapping Man page Source code
PerformLayOut Source code
PerformLefseAnal Man page Source code
PerformMetagenomeSeqAnal Man page Source code
PerformNetworkCorrelation Man page Source code
PerformNormalization Man page Source code
PerformRNAseqDE Man page Source code
PerformRarefaction Man page Source code
PerformRefDataMapping Man page Source code
PerformUnivarTest Man page Source code
PlotAlphaBoxData Man page Source code
PlotAlphaData Man page Source code
PlotBetaDiversity Man page Source code
PlotBoxData Man page Source code
PlotBoxDataCorr Source code
PlotCorr Man page Source code
PlotCorrHeatMap Man page Source code
PlotDataPieFromPie Man page Source code
PlotEnrichNet.Overview Man page Source code
PlotFunAnotSummary Man page Source code
PlotFunctionStack Man page Source code
PlotGroupDataHeattree Source code
PlotGroupPieGraph Man page Source code
PlotHeatmap Man page Source code
PlotImpVar Man page Source code
PlotImpVarLEfSe Man page Source code
PlotLEfSeSummary Man page Source code
PlotLibSizeView Man page Source code
PlotOverallPieGraph Man page Source code
PlotOverviewDataHeattree Source code
PlotPhylogeneticTree Man page Source code
PlotPiechart Man page Source code
PlotRF.Classify Man page Source code
PlotRF.VIP Man page Source code
PlotRNASeqDotPlot Man page Source code
PlotRNAseqVolcano Man page Source code
PlotRareCurve Man page Source code
PlotRarefactionCurve Man page Source code
PlotSampleDataHeattree Source code
PlotSamplePieGraph Man page Source code
PlotSampleTaxaAundanceBar Man page Source code
PlotSelectedSample Man page Source code
PlotTaxaAbundanceArea Man page Source code
PlotTaxaAbundanceBarSamGrp Man page Source code
PlotTaxaAundanceBar Man page Source code
PlotTreeGraph Man page Source code
PlotUsrRefPCoA3DScore Man page Source code
PrepareBoxPlot Source code
PrepareCorrExpValues Source code
PrepareDownloadData Source code
PrepareEnrichNet Man page Source code
PrepareHeatTreePlot Man page Source code
PrepareHeatTreePlotAbR Source code
PrepareHeatTreePlotDataParse_cmf Man page Source code
PrepareHeatTreePlotDataParse_cmf_diff_table Man page Source code
PrepareHeatTreePlotDataParse_cmf_plot Man page Source code
PrepareMergedData Man page Source code
PrepareNetworkExp Source code
PreparePCA4Shotgun Man page Source code
PreparePDFReport Man page Source code
PrepareQueryJson Man page Source code
RF.Anal Man page Source code
Read16SAbundData Man page Source code
Read16SBiomData Man page Source code
Read16STabData Man page Source code
Read16STaxaTable Man page Source code
ReadMothurData Man page Source code
ReadSampleTable Man page Source code
ReadShotgunBiomData Man page Source code
ReadShotgunTabData Man page Source code
ReadTreeFile Man page Source code
RecordRCommand Source code
RemoveDuplicates Source code
RunFastSpar Man page Source code
RunFastSpar_mem Source code
SanityCheckData Man page Source code
Save2KEGGJSON Source code
SaveCurrentSession Source code
SavePiechartImg Man page Source code
SetCurrentMetaData Source code
SetCurrentSelectedTaxLevel Source code
SetModuleType Man page Source code
SetMsetLib Man page Source code
Setup.MapData Man page Source code
ShowMemoryUse Source code
SparccToNet Source code
SpearmanCorrFunc Source code
SpeciesMappingExact Source code
UpdateListInput Man page Source code
UpdatePieData Man page Source code
UpdateSampleItems Man page Source code
UtilMakeCountTables Source code
UtilMakePhyloseqObjs Source code
ValidateFeatureName Source code
abundances Source code
assignTax Source code
cleanMem Source code
clr_transform Source code
color_scale Source code
condenseOTUs Man page Source code
constructPhyloTree Source code
constructSeqTab Source code
convertIgraph2JSONExp Source code
core Source code
core_heatmap Source code
core_members Source code
doKO2NameMapping Source code
doKOFiltering Source code
edgeRnorm Source code
fast_tax_glom Source code
fast_tax_glom_first Source code
fast_tax_glom_mem Source code
fastpR Source code
generate_breaks Source code
getIdx Source code
getOTUTable Source code
ggrare2 Source code
gm_mean Source code Source code
isEmptyMatrix Source code
kaijuMap Source code
kaijuTaxa Source code
load_MASS Source code
load_ape Source code
load_biocparallel Source code
load_biomformat Source code
load_cairo Source code
load_datatable Source code
load_deseq Source code
load_edgeR Source code
load_genefilter Source code
load_ggfortify Source code
load_ggplot Source code
load_ggrepel Source code
load_globaltest Source code
load_gplots Source code
load_grid Source code
load_gridExtra Source code
load_igraph Source code
load_metacoder Source code
load_metagenomeseq Source code
load_pheatmap Source code
load_phyloseq Source code
load_ppcor Source code
load_randomforest Source code
load_rcolorbrewer Source code
load_reshape Source code
load_rjsonio Source code
load_splitstackshape Source code
load_stringr Source code
load_tax4fun Source code
load_vegan Source code
load_viridis Source code
load_xtable Source code
overlap_ratio Source code
parse_taxonomy_silva_128 Source code
phyloseq_to_edgeR Source code
plot_core Source code
prevalence Source code
prevalence_nsamples Source code
processRawSeq Source code
rescale2NewRange Source code
rmHostCon Source code
scale_colours Source code
scale_vec_colours Source code
seqSanityCheck Source code
setParameters Source code
simpleCap Source code
template.match Source code
xia-lab/MicrobiomeAnalystR documentation built on Oct. 17, 2019, 9:05 a.m.