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 |
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