Man pages for xia-lab/MicrobiomeAnalystR
MicrobiomeAnalystR - A comprehensive R package for statistical, visual, and functional analysis of the microbiome.
| AddErrMsg | Adds an error message |
| ApplyAbundanceFilter | Function to filter uploaded data |
| ApplyAbundanceFilterMeta | Function to filter uploaded data in meta-analysis module |
| ApplyMetaboFilter | Function to filter uploaded metabolomic data |
| ApplyVarianceFilter | Function to filter uploaded data |
| ApplyVarianceFilterMeta | Function to filter uploaded data |
| CalculateHyperScore | Calculate enrichment score. |
| case_when | https://github.com/s-fleck/lest/tree/master/R |
| CheckMetaDataIntegrity | Check if data are ready for meta-analysis |
| CleanData | Perform data cleaning |
| CompareSummaryStats | Perform alpha diversity meta-analysis |
| condenseOTUs | Helper Function that will take the OTU Table (as a... |
| CoreMicrobeAnalysis | Perform core microbiome analysis |
| CreateFooter | Create report of analyses (Met Enrichment) |
| CreateMDPRnwReport | Function to create PDF report for MDP module |
| CreatePhyloseqObj | Function to recreate phyloseq object |
| CreatePhyloseqObjMeta | Function to recreate phyloseq object in meta-analysis module |
| CreateRHistAppendix | Create report of analyses |
| CreateSDPRnwReport | Function to create PDF report for SDP module |
| CrossReferencing | Perform cross referencing. |
| dot-readDataTable | Read data table |
| dot-read.microbiomeanalyst.lib.rds | Read RDS files from the internet |
| FeatureCorrelation | Main function to calculate correlation of all other feature... |
| GenerateTemplates | Function to generate templates |
| GetColorSchema | Function to get color palette for graphics. |
| GetDataForPie | Utility function to exract data for piechart. |
| GetErrMsg | Gets the error message |
| GetFinalNameMap | Getter to return final map |
| GetGeneListStat | Function to get gene list statistics |
| GetMapTable | Getter function |
| GetORATable | Getter function |
| GetRFConf.Table | Getter function |
| GetSigTable.Corr | Getter function |
| GetSigTable.LEFSE | Getter function |
| GetSigTable.METAGENOSEQ | Getter function |
| GetSigTable.RNASeq | Getter function |
| GetSigTable.UNIVAR | Getter function |
| Init.DataMeta | Init resources & global settings & variables. |
| Init.mbSetObj | Constructs a mbSet object for storing data |
| Match.Pattern | Match Patterns Function |
| MergeDatasets | Merge two or more datasets into merged phyloseq object |
| PCoA3D.Anal | Main function to perform PCoA analysis |
| PCoA3DAnal.16SRef | Function to create PCoA |
| Perform16FunAnot_mem | Main function to perform 16S functional annotation |
| PerformAlphaDiversityComp | Perform alpha diversity |
| PerformBatchCorrection | Perform batch correction of meta-analysis datasets |
| PerformBetaDiversity | Function to plot beta diversity. |
| PerformCategoryComp | Function to perform categorical comparison. |
| PerformDEAnalyse | Perform differential analysis |
| PerformKOEnrichAnalysis_KO01100 | Function to prepare KO enrichment analysis. |
| PerformKOmapping | Function to perform KO mapping. |
| PerformKOProjection | Function to perform KO projection |
| PerformLefseAnal | Main function to perform LEfSe analysis |
| PerformMetaboNormalization | Function to perform normalization on metabolomics data |
| PerformMetaEffectSize | Perform differential abundance analysis on individual dataset... |
| PerformMetagenomeSeqAnal | Main function to perform metagenome seq analysis |
| PerformNetworkCorrelation | Function to call for correlation network |
| PerformNormalization | Function to perform normalization |
| PerformNormalizationMeta | Function to perform normalization |
| PerformPartialCorr | Perform Partial Correlation Analysis |
| PerformRarefaction | Utility function to perform rarefraction (used by... |
| PerformRefDataMapping | Function to perform reference data mapping. |
| PerformRNAseqDE | Main function to perform RNAseq analysis |
| PerformUnivarTest | Main function to perform classical univariate analysis. |
| PlotAlphaBoxData | Function to create box plots for alpha diversity analysis |
| PlotAlphaData | Function to plot alpha-diversity analysis. |
| PlotBetaSummary | Perform beta diversity meta-analysis |
| PlotBoxData | Function to create box plots of important features |
| PlotBoxDataCorr | Function to create box plots of important features |
| PlotCorr | Plot Pattern Search |
| PlotDataPieFromPie | Function to plot pie-chart data. |
| PlotEnrichNet.Overview | Create network for enrichmnet overview |
| PlotFunAnotSummary | Plot functional annotation summary |
| PlotFunctionStack | Function to plot stacked bar chart of functional data. |
| PlotGroupPieGraph | Main function to plot pie graphs of microbiome data. |
| PlotHeatmap | Main function to plot heatmap. |
| PlotImpVar | Helper function to plot variable importance (for RF and... |
| PlotImpVarLEfSe | Plot LEfSe summary |
| PlotLEfSeSummary | Plot LEfSe summary |
| PlotLibSizeView | Function to plot library size |
| PlotMetaDensity | Plot density plot of datasets in meta-analysis module |
| PlotMetaPCA | Plot PCA plot for meta-analysis samples |
| PlotOverallPieGraph | Main function to plot pie graphs of microbiome data. |
| PlotPCAView | Plot PCA plot for multi-omics samples |
| PlotPhylogeneticTree | Function to prepare data for phylogenetic tree. |
| PlotPiechart | Function to create pie-chart plot. |
| PlotRareCurve | Function to plot rarefraction curves |
| PlotRarefactionCurve | Function to create rarefraction curves of microbiome data |
| PlotRF.Classify | Plot Random Forest Classification |
| PlotRF.VIP | Plot variable importance ranked by MeanDecreaseAccuracy |
| PlotSamplePieGraph | Main function to plot sample-wise pie graphs of microbiome... |
| PlotSampleTaxaAundanceBar | Function to create bar plots of selected taxa level. |
| PlotSelectedSample | Function to create a summary of a sample using a piechart at... |
| PlotTaxaAbundanceArea | Plot functional annotation summary |
| PlotTaxaAbundanceBarSamGrp | Function to plot group-wise bar charts. |
| PlotTaxaAundanceBar | Function to plot bar charts for alpha diversity |
| PlotTreeGraph | Function to plot tree graphics for dendogram. |
| PlotUsrRefPCoA3DScore | Function to plot 3D score plot. |
| PrepareEnrichNet | Function to prepare data for enrichment network. |
| PrepareHeatTreePlot | Function to plot heat tree |
| PrepareHeatTreePlotDataParse_cmf | Function to prepare heat tree data |
| PrepareHeatTreePlotDataParse_cmf_diff_table | Function to prepare heat tree data |
| PrepareHeatTreePlotDataParse_cmf_plot | Function to prepare heat tree data |
| PrepareMergedData | Function to merge user data with public data. |
| PreparePCA4Shotgun | Function to prepare shotgun data for PCA. |
| PreparePDFReport | Function to create PDF report |
| PrepareQueryJson | Function to prepare query for JSON. |
| Read16SAbundData | Main function to read 16S data |
| Read16SAbundDataMeta | Function to read 16S Abundance data in meta-analysis module |
| Read16SBiomData | Function to read 16S data in biom format |
| Read16STabData | Function to read 16S data |
| Read16STaxaTable | Function to read 16S taxonomy table from txt format |
| Read16STaxaTableMeta | Function to read 16S taxonomy table from txt format in... |
| ReadMetabolicTable | Main function to read metabolomics table |
| ReadMothurData | Function to read 16S data in mothur format |
| ReadSampleTable | Function to read in sample data |
| ReadSampleTableMeta | Function to read in sample data in meta-analysis module... |
| ReadSampleTableMetaInd | Function to read in sample data in meta-analysis module |
| ReadShotgunBiomData | Main function to read in shotgun data |
| ReadShotgunTabData | Main function to read in shotgun data |
| ReadTreeFile | Function to read in tree files. |
| RF.Anal | Performs Random Forest Analysis |
| RunFastSpar | Function to call FastSpar |
| SanityCheckData | Main function to sanity check on uploaded microbiome data |
| SanityCheckDataMeta | Individual sanity check on selected datase in meta-analysis... |
| SanityCheckMetData | Function to sanity check on uploaded metabolomics data |
| SanityCheckSampleData | SanityCheckSampleData |
| SanityCheckSampleDataMeta | SanityCheckSampleData |
| SavePiechartImg | Function to save pie-chart |
| SetDataTypeOfMeta | SetDataTypeOfMeta |
| SetMetaAttributes | SetMetaAttributes' |
| SetModuleType | Function to set analysis type |
| SetTaxonSetLib | Set the microbe set library |
| Setup.MapData | Function to set up data for TSEA |
| UpdateConfItems | Function to update confounders used for partial correlation |
| UpdateListInput | Function to filter list data based on a minimum count |
| UpdatePieData | Function to update pie-chart data. |
| UpdateSampleItems | Function to update samples |
