API for xia-lab/MicrobiomeAnalystR
MicrobiomeAnalystR - A comprehensive R package for statistical, visual, and functional analysis of the microbiome.
| Global functions | |
|---|---|
| .checkSampleConsistencyMeta | Source code |
| .compute.mummichogRTSigPvals | Source code |
| .compute.mummichogSigPvals | Source code |
| .do.anova | Source code |
| .do.ttests | Source code |
| .get.mbSetObj | Source code |
| .getDynLoadPath | Source code |
| .init.Permutations | Source code |
| .init.RT.Permutations | Source code |
| .load.scripts.on.demand | Source code |
| .perform.computing | Source code |
| .perform.mummichogRTPermutations | Source code |
| .perform.my.maaslin | Source code |
| .perform_edger | Source code |
| .permanova_pairwise | Source code |
| .prepare.batch | Source code |
| .prepare.deseq | Source code |
| .prepare.global | Source code |
| .prepare.maaslin2 | Source code |
| .prepare_rnaseq | Source code |
| .read.microbiomeanalyst.lib.rds | Man page Source code |
| .readDataTable | Man page |
| .replace.by.lod | Source code |
| .save.deseq.res | Source code |
| .save.global.res | Source code |
| .save.maaslin.res | Source code |
| .search.compoundLib | Source code |
| .set.mbSetObj | Source code |
| .setup.library | Source code |
| .to.numeric.mat | Source code |
| AddErrMsg | Man page Source code |
| AddFeatureToReport | Source code |
| ApplyAbundanceFilter | Man page Source code |
| ApplyAbundanceFilterMeta | Man page Source code |
| ApplyMetaboFilter | Man page Source code |
| ApplyVarianceFilter | Man page Source code |
| ApplyVarianceFilterMeta | Man page Source code |
| AutoNorm | Source code |
| AutoScale | Source code |
| CalculateHyperScore | Man page Source code |
| CheckMetaDataIntegrity | Man page Source code |
| CheckRawDataAlreadyNormalized | Source code |
| CleanData | Man page Source code |
| CleanTaxaNames | Source code |
| ClearFactorStrings | Source code |
| ClearRCommandHistory | Source code |
| ClearStrings | Source code |
| CompareMet | Source code |
| CompareMic | Source code |
| CompareSummaryStats | Man page Source code |
| Compound_function_mzlist | Source code |
| ComputeColorGradient | Source code |
| ComputeColorGradientCorr | Source code |
| ComputeEncasing | Source code |
| ComputeGoods | Source code |
| ComputeMummichogRTPermPvals | Source code |
| Convert2Dictionary | Source code |
| CoreMicrobeAnalysis | Man page Source code |
| CreateFakeFile | Source code |
| CreateFooter | Man page |
| CreateMDPRnwReport | Man page |
| CreateMMPFakeFile | Source code |
| CreatePhyloseqObj | Man page Source code |
| CreatePhyloseqObjMeta | Man page Source code |
| CreateRHistAppendix | Man page |
| CreateSDPRnwReport | Man page |
| CreateStaticHeatmap | Source code |
| CrossReferencing | Man page Source code |
| D2K | Source code |
| DeepCleanTaxaNames | Source code |
| FeatureCorrelation | Man page |
| GenerateTemplates | Man page |
| GetAllDataNames | Source code |
| GetBashFullPath | Source code |
| GetBetaDiversityStats | Source code |
| GetColorSchema | Man page Source code |
| GetColorSchemaFromFactor | Source code |
| GetCurrentImg | Source code |
| GetCurrentMsg | Source code |
| GetDataForPie | Man page Source code |
| GetDatasetNamesString | Source code |
| GetDiscreteInx | Source code |
| GetErrMsg | Man page Source code |
| GetExtendRange | Source code Source code |
| GetFeatureNum | Source code |
| GetFilesToBeSaved | Source code |
| GetFinalNameMap | Man page Source code |
| GetGeneListStat | Man page Source code |
| GetGroupNamesMeta | Source code |
| GetHTMLMetSet | Source code |
| GetHighTaxaLvlNm | Source code |
| GetHtGroupItems | Source code |
| GetHtMetaCpInfo | Source code |
| GetInitLib | Source code |
| GetKeggProjectionType | Source code |
| GetLibscale | Source code |
| GetLowerTaxaLvlNm | Source code |
| GetMapTable | Man page |
| GetMetaByCol | Source code |
| GetMetaCol | Source code |
| GetMetaColLength | Source code |
| GetMetaDataCol | Source code |
| GetMetaDataGroups | Source code Source code |
| GetMetaDataStatus | Source code |
| GetMetaDatasets | Source code |
| GetMetaGeneIDType | Source code |
| GetMetaInfo | Source code |
| GetMetaInfoMeta | Source code |
| GetMetaResultColNames | Source code |
| GetMetaResultGeneIDLinks | Source code |
| GetMetaResultGeneIDs | Source code |
| GetMetaResultGeneSymbols | Source code |
| GetMetaResultMatrix | Source code |
| GetMetaResultPathSymbols | Source code |
| GetMetaSigGeneCount | Source code |
| GetMetaStat | Source code |
| GetMetaStatNames | Source code |
| GetMetaSummary | Source code |
| GetMetaTaxaInfo | Source code |
| GetMetaTypes | Source code |
| GetMetaboResColNames | Source code |
| GetMetaboResRowNames | Source code |
| GetMetadataMsg | Source code |
| GetMsetEvidence | Source code |
| GetMsetMembers | Source code |
| GetMsetNames | Source code |
| GetMsetPval | Source code |
| GetMsetReferences | Source code |
| GetNameMapCol | Source code |
| GetNumOfLists | Source code |
| GetNumbericalInx | Source code |
| GetORA.colorBar | Source code |
| GetORA.mat | Source code |
| GetORA.rowNames | Source code |
| GetORATable | Man page Source code |
| GetOS | Source code |
| GetOmicsDataDims | Source code |
| GetOrigSmplGroupNamesPerMeta | Source code |
| GetOrigSmplGroupNamesPerMetaInd | Source code |
| GetOrigSmplNms | Source code |
| GetOrigSmplNmsInd | Source code |
| GetPieTaxaAbund | Source code |
| GetPieTaxaNames | Source code |
| GetRCommandHistory | Source code |
| GetRFConf.Table | Man page |
| GetRandomNumbers | Source code |
| GetRawClassNms | Source code |
| GetRawFileNms | Source code |
| GetResColNames | Source code |
| GetResColNamesMeta | Source code |
| GetResMat | Source code |
| GetResMatrix | Source code |
| GetResMetabo | Source code |
| GetResMetric | Source code |
| GetResRowNames | Source code Source code |
| GetSamplNames | Source code |
| GetSampleGroups | Source code |
| GetSampleGrpInfo | Source code |
| GetSampleGrpNo | Source code |
| GetSampleInfo | Source code |
| GetSampleNamesaftNorm | Source code |
| GetSampleNumber | Source code |
| GetSanityVec | Source code |
| GetSeriesColors | Source code |
| GetShortNames | Source code |
| GetSigGeneCount | Source code |
| GetSigTable | Source code |
| GetSigTable.Corr | Man page |
| GetSigTable.LEFSE | Man page |
| GetSigTable.METAGENOSEQ | Man page |
| GetSigTable.RNASeq | Man page |
| GetSigTable.UNIVAR | Man page |
| GetStressNMDS | Source code |
| GetSummaryData | Source code |
| GetTaxaFeatSize | Source code |
| GetTaxaNames | Source code |
| GetTseaCol | Source code |
| GetTseaRowNames | Source code |
| GetUniqueMetaNames | Source code |
| IncludeDataset | Source code |
| Init.DataMeta | Man page Source code |
| Init.mbSetObj | Man page Source code |
| InitPieColors | Source code |
| IsPoorReplicate | Source code |
| IsTreeUploaded | Source code |
| LoadKEGGKO_lib | Source code |
| LogNorm | Source code |
| MapKO2KEGGEdges | Source code |
| Match.Pattern | Man page |
| MergeDatasets | Man page Source code |
| MessageOutput | Source code |
| MiRKAT | Source code |
| MiRKAT_continuous | Source code |
| PCoA3D.Anal | Man page Source code |
| PCoA3DAnal.16SRef | Man page Source code |
| Perform16FunAnot | Source code |
| Perform16FunAnot_mem | Man page Source code |
| PerformAlphaDiversityComp | Man page Source code |
| PerformAlphaGLM | Source code |
| PerformBatchCorrection | Man page Source code |
| PerformBetaDiversity | Man page Source code |
| PerformCategoryComp | Man page Source code |
| PerformDEAnalyse | Man page Source code |
| PerformDataMerging | Source code |
| PerformFastUnivTests | Source code |
| PerformKOEnrichAnalysis_KO01100 | Man page Source code |
| PerformKOEnrichAnalysis_List | Source code |
| PerformKOProjection | Man page Source code |
| PerformKOmapping | Man page Source code |
| PerformLayOut | Source code |
| PerformLefseAnal | Man page Source code |
| PerformMantelTest | Source code |
| PerformMetaEffectSize | Man page Source code |
| PerformMetaboNormalization | Man page Source code |
| PerformMetagenomeSeqAnal | Man page Source code |
| PerformNetworkCorrelation | Man page Source code |
| PerformNormalization | Man page Source code |
| PerformNormalizationMeta | Man page Source code |
| PerformPairDEAnalyse | Source code |
| PerformPartialCorr | Man page Source code |
| PerformRNAseqDE | Man page Source code |
| PerformRarefaction | Man page Source code |
| PerformRefDataMapping | Man page Source code |
| PerformSeqCheck | Source code |
| PerformSeqImport | Source code |
| PerformSeqProcessing | Source code |
| PerformUnivTests | Source code |
| PerformUnivarTest | Man page Source code |
| PlotAlphaBoxData | Man page Source code |
| PlotAlphaData | Man page Source code |
| PlotAlphaGLM | Source code |
| PlotBetaSummary | Man page |
| PlotBoxData | Man page Source code |
| PlotBoxDataCorr | Man page Source code |
| PlotBoxMultiData | Source code |
| PlotBoxMultiMetabo | Source code |
| PlotCorr | Man page |
| PlotCovariateMap | Source code |
| PlotCovariateMapMas | Source code |
| PlotDataOverview | Source code |
| PlotDataPieFromPie | Man page Source code |
| PlotDataProfile | Source code |
| PlotDensityView | 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 |
| PlotMetaDensity | Man page Source code |
| PlotMetaPCA | Man page Source code |
| PlotOverallPieGraph | Man page Source code |
| PlotOverviewDataHeattree | Source code |
| PlotPCAView | Man page Source code |
| PlotPhylogeneticTree | Man page Source code |
| PlotPiechart | Man page Source code |
| PlotRF.Classify | Man page Source code |
| PlotRF.VIP | 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 |
| PlotSelectedFeature | 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 |
| PlotlyCompManht | Source code |
| PlotlyTaxaAbundance | Source code |
| PostProcessMaaslin | 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 |
| PreparePCA4Shotgun | Man page Source code |
| PreparePDFReport | Man page |
| PrepareQueryJson | Man page Source code |
| RF.Anal | Man page Source code |
| Read16SAbundData | Man page Source code |
| Read16SAbundDataMeta | Man page Source code |
| Read16SBiomData | Man page Source code |
| Read16STabData | Man page Source code |
| Read16STaxaTable | Man page Source code |
| Read16STaxaTableMeta | Man page Source code |
| ReadDataForMetaInfo | Source code |
| ReadMetabolicTable | Man page Source code |
| ReadMothurData | Man page Source code |
| ReadPeakList | Source code |
| ReadRawMeta | Source code |
| ReadSampleTable | Man page Source code |
| ReadSampleTableMeta | Man page Source code |
| ReadSampleTableMetaInd | Man page Source code |
| ReadShotgunBiomData | Man page Source code |
| ReadShotgunTabData | Man page Source code |
| ReadTreeFile | Man page Source code |
| RecordRCommand | Source code |
| RemoveData | Source code |
| RemoveDuplicates | Source code |
| RemoveSelectedMeta | Source code |
| RemoveSelectedMetaInd | Source code |
| ReplaceMissingByLoD | Source code |
| RunFastSpar | Man page |
| SanityCheckData | Man page Source code |
| SanityCheckDataMeta | Man page Source code |
| SanityCheckMetData | Man page Source code |
| SanityCheckSampleData | Man page Source code |
| SanityCheckSampleDataMeta | Man page Source code |
| Save2KEGGJSON | Source code |
| SavePiechartImg | Man page Source code |
| SelectData | Source code |
| SelectRefData | Source code |
| Set.Config | Source code |
| SetCurrentData | Source code Source code |
| SetCurrentMetaData | Source code Source code |
| SetCurrentSelectedTaxLevel | Source code |
| SetDataTypeOfMeta | Man page Source code |
| SetGroupItems | Source code |
| SetMetaAttributes | Man page Source code |
| SetMetaTypes | Source code |
| SetModuleType | Man page Source code |
| SetParam | Source code |
| SetSelMetaData | Source code |
| SetTaxonSetLib | Man page Source code |
| Setup.MapData | Man page Source code |
| SetupMetaStats | Source code |
| ShowMemoryUse | Source code |
| SparccToNet | Source code |
| SpeciesMappingExact | Source code |
| SquareRootNorm | Source code |
| Tax4Fun | Source code |
| UnzipUploadedFile | Source code |
| UpdateConfItems | Man page Source code |
| UpdateListInput | Man page Source code |
| UpdateMetaColName | Source code |
| UpdateMetaColNameInd | Source code |
| UpdateMetaData | Source code |
| UpdateMetaLevels | Source code |
| UpdateMetaLevelsInd | Source code |
| UpdateMetaOrder | Source code |
| UpdateMetaOrderInd | Source code |
| UpdateMetaType | Source code |
| UpdatePieData | Man page Source code |
| UpdateSampleBasedOnLoading | Source code |
| UpdateSampleGroups | Source code |
| UpdateSampleGroupsInd | Source code |
| UpdateSampleItems | Man page Source code |
| UtilMakeCountTables | Source code |
| UtilMakePhyloseqObjs | Source code |
| ValidateFeatureName | Source code |
| abn_est | Source code |
| abundances | Source code |
| assert_equal_class | Source code |
| assert_equal_type | Source code |
| assert_length_1_or_n | Source code |
| blastTableReducer | Source code |
| calcKRVstat | Source code |
| calcRsquared | Source code |
| calculate_Reads | Source code |
| case_when | Man page Source code |
| checkParing | Source code |
| check_length_1_or_n | Source code |
| checkfac | Source code |
| cleanMem | Source code |
| clr_transform | Source code |
| color_scale | Source code |
| composeParamFun | Source code |
| condenseOTUs | Man page Source code |
| core | Source code |
| core_heatmap | Source code |
| core_members | Source code |
| create.adducts | Source code |
| doKOFiltering | Source code |
| edgeRnorm | Source code |
| exportOTUtaxaInfo | Source code |
| exportSampleNMs | Source code |
| exportSampleTrackTable | Source code |
| fast.write | Source code |
| fast_tax_glom | Source code |
| fast_tax_glom_first | Source code |
| fast_tax_glom_mem | Source code |
| filtKOmap | Source code |
| generateColorArr | Source code |
| generateColorGradient | Source code |
| generatePCAscatter | Source code |
| generateResFigures | Source code |
| generate_breaks | Source code |
| get.fun.lib.path | Source code |
| getIdx | Source code |
| getLambda_davies | Source code |
| getQ | Source code |
| getindivP_davies | Source code |
| gg2list_new | Source code |
| gg_color_hue | Source code |
| gg_color_hue_scatter | Source code |
| ggplotly_modified | Source code |
| ggrare2 | Source code |
| glm_qqplot | Source code |
| gm_mean | Source code |
| importTax4FunReferenceData | Source code |
| inconsistent_lengths_message | Source code |
| isEmptyMatrix | Source code |
| libSizeQuickView | 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_ggfortify | Source code |
| load_ggplot | Source code |
| load_ggraph | 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_iheatmapr | Source code |
| load_metacoder | Source code |
| load_metagenomeseq | Source code |
| load_pheatmap | Source code |
| load_phyloseq | Source code |
| load_ppcor | Source code |
| load_qs | Source code |
| load_randomforest | Source code |
| load_rcolorbrewer | Source code |
| load_reshape | Source code |
| load_splitstackshape | Source code |
| load_stringr | Source code |
| load_tax4fun | Source code |
| load_vegan | Source code |
| load_viridis | Source code |
| load_visNetwork | Source code |
| load_xtable | Source code |
| makeFunctionalPrediction | Source code |
| make_ecpdlist | Source code |
| my.16sfun.anot | Source code |
| my.corr.net | Source code |
| my.fast.spar | Source code |
| my.json.scatter | Source code |
| my.json.scatter.pair | Source code |
| my.pcoa.3d | Source code |
| my.reduce.dimension | Source code |
| my.secom.anal | Source code |
| my.sparcc.net | Source code |
| myFastList | Source code |
| mz_tolerance | Source code |
| overlap_ratio | Source code |
| parse_taxonomy_silva_128 | Source code |
| performPeakEnrich | Source code |
| plotSeqDiagnotics | Source code |
| plot_core | Source code |
| prevalence | Source code |
| prevalence_nsamples | Source code |
| print_glm_stats | Source code |
| qc.boxplot2 | Source code |
| qc.pcaplot2 | Source code |
| readDataQs | Source code |
| readDataset | Source code |
| readSet | Source code |
| read_seq_len | Source code |
| recordEnrTable | Source code |
| rescale2NewRange | Source code |
| residuals_plot | Source code |
| rgba_to_hex_opacity | Source code |
| rowcolFt | Source code |
| rowcoltt | Source code |
| runRefBlast | Source code |
| s_diff_est | Source code |
| saveDataQs | Source code |
| saveSet | Source code |
| scale_colours | Source code |
| scale_mat | Source code |
| scale_range | Source code |
| scale_rows | Source code |
| scale_vec_colours | Source code |
| setIncludeMeta | Source code |
| simpleCap | Source code |
| sparse_dist | Source code |
| sparse_linear | Source code |
| subsetPhyloseqByDataset | Source code |
| summaryRes | Source code |
| sweaveBash4exec | Source code |
| sweaveBash4execPro | Source code |
| sweaveRScript4exec | Source code |
| tr | Source code |
| unitAutoScale | Source code |
| validate_fastq | Source code |
