.complexHeatmapDotPlot
                        Generate dot plot from input matrix with
                        ComplexHeatmap
.ggCellViolin           Produce single violin plot with data frame
                        passed from upstream
.ggScatter              Produce single scatter plot with data frame
                        passed from upstream
.ggplotLigerTheme       Generic ggplot theme setting for rliger package
.plotHeatmap            General heatmap plotting with prepared matrix
                        and data.frames
H5Apply                 Apply function to chunks of H5 data in
                        ligerDataset object
alignFactors            Align factor loadings to get final integration
as.liger.dgCMatrix      Converting other classes of data to a liger
                        object
as.ligerDataset.ligerDataset
                        Converting other classes of data to a
                        ligerDataset object
bmmc                    liger object of bone marrow subsample data with
                        RNA and ATAC modality
calcARI                 Calculate adjusted Rand index (ARI) by
                        comparing two cluster labeling variables
calcAgreement           Calculate agreement metric after integration
calcAlignment           Calculate alignment metric after integration
calcDatasetSpecificity
                        Calculate a dataset-specificity score for each
                        factor
calcNMI                 Calculate Normalized Mutual Information (NMI)
                        by comparing two cluster labeling variables
calcPurity              Calculate purity by comparing two cluster
                        labeling variables
ccGeneHuman             Cell cycle gene set for human
centroidAlign           *[Experimental]* Align factor loading by
                        centroid alignment (beta)
closeAllH5              Close all links (to HDF5 files) of a liger
                        object
commandDiff             Check difference of two liger command
convertOldLiger         Convert old liger object to latest version
coordinate              Access ligerSpatialDataset coordinate data
createH5LigerDataset    Create on-disk ligerDataset Object
createLiger             Create liger object
createLigerDataset      Create in-memory ligerDataset object
deg.marker              Data frame for example marker DEG test result
deg.pw                  Data frame for example pairwise DEG test result
downsample              Downsample datasets
exportInteractTrack     Export predicted gene-pair interaction
factorGSEA              Test all factors for enrichment in a gene set
getFactorMarkers        Find shared and dataset-specific markers
getProportionMito       Calculate proportion mitochondrial contribution
importPBMC              Import prepared dataset publically available
imputeKNN               Impute the peak counts from gene expression
                        data referring to an ATAC dataset after
                        integration
is.newLiger             Check if given liger object if under new
                        implementation
isH5Liger               Check if a liger or ligerDataset object is made
                        of HDF5 file
liger-class             liger class
ligerATACDataset-class
                        Subclass of ligerDataset for ATAC modality
ligerCommand-class      ligerCommand object: Record the input and time
                        of a LIGER function call
ligerDataset-class      ligerDataset class
ligerMethDataset-class
                        Subclass of ligerDataset for Methylation
                        modality
ligerRNADataset-class   Subclass of ligerDataset for RNA modality
ligerSpatialDataset-class
                        Subclass of ligerDataset for Spatial modality
ligerToSeurat           Convert between liger and Seurat object
linkGenesAndPeaks       Linking genes to putative regulatory elements
louvainCluster-deprecated
                        *[Superseded]* Louvain algorithm for community
                        detection
makeFeatureMatrix       Fast calculation of feature count matrix
makeInteractTrack-deprecated
                        *[Deprecated]* Export predicted gene-pair
                        interaction
makeRiverplot-deprecated
                        *[Deprecated]* Generate a river (Sankey) plot
mapCellMeta             Create new variable from categories in cellMeta
mergeH5                 Merge hdf5 files
mergeSparseAll          Merge matrices while keeping the union of rows
modalOf                 Return preset modality of a ligerDataset object
                        or that of all datasets in a liger object
normalize               *[Deprecated]* Normalize raw counts data
online_iNMF-deprecated
                        *[Deprecated]* Perform online iNMF on scaled
                        datasets
optimizeALS-deprecated
                        *[Deprecated]* Perform iNMF on scaled datasets
optimizeNewData         Perform factorization for new data
optimizeNewK            Perform factorization for new value of k
optimizeNewLambda       Perform factorization for new lambda value
optimizeSubset          Perform factorization for subset of data
pbmc                    liger object of PBMC subsample data with
                        Control and Stimulated datasets
pbmcPlot                liger object of PBMC subsample data with
                        plotting information available
plot.factorGSEA         GSEA plot for specific gene set and factor
                        using factorGSEA results
plotBarcodeRank         Create barcode-rank plot for each dataset
plotCellViolin          Generate violin/box plot(s) using liger object
plotClusterFactorDot    Make dot plot of factor loading in cell groups
plotClusterGeneDot      Make dot plot of gene expression in cell groups
plotClusterGeneViolin   Create violin plot for multiple genes grouped
                        by clusters
plotDensityDimRed       Create density plot basing on specified
                        coordinates
plotDimRed              Generate scatter plot(s) using liger object
plotEnhancedVolcano     Create volcano plot with EnhancedVolcano
plotGODot               Visualize GO enrichment test result in dot plot
plotGeneHeatmap         Plot Heatmap of Gene Expression or Factor
                        Loading
plotGeneLoadings        Visualize factor expression and gene loading
plotGeneViolin          Visualize gene expression or cell metadata with
                        violin plot
plotGroupClusterDimRed
                        Comprehensive group splited cluster plot on
                        dimension reduction with proportion
plotMarkerHeatmap       Create heatmap for showing top marker
                        expression in conditions
plotPairwiseDEGHeatmap
                        Create heatmap for pairwise DEG analysis result
plotProportion          Visualize proportion across two categorical
                        variables
plotProportionBox       Box plot of cluster proportion in each dataset,
                        grouped by condition
plotSankey              Make Riverplot/Sankey diagram that shows label
                        mapping across datasets
plotSpatial2D           Visualize a spatial dataset
plotVarFeatures         Plot the variance vs mean of feature expression
plotVolcano             Create volcano plot for Wilcoxon test result
print.factorGSEA        Show information about factorGSEA object
quantileAlignSNF        *[Superseded]* Quantile align (normalize)
                        factor loadings
quantileNorm            Quantile Align (Normalize) Factor Loadings
quantile_norm-deprecated
                        *[Superseded]* Quantile align (normalize)
                        factor loading
rawPeak                 Access ligerATACDataset peak data
read10X                 Load in data from 10X
read10XFiles            Read 10X cellranger files (matrix, barcodes and
                        features) into R session
read10XH5               Read 10X HDF5 file
readH5AD                Read matrix from H5AD file
readLiger               Read liger object from RDS file
readSubset              *[Superseded]* See 'downsample'
removeMissing           Remove missing cells or features from liger
                        object
restoreH5Liger          Restore links (to HDF5 files) for reloaded
                        liger/ligerDataset object
retrieveCellFeature     Retrieve a single matrix of cells from a slot
reverseMethData         Create "scaled data" for DNA methylation
                        datasets
runCINMF                Perform consensus iNMF on scaled datasets
runCluster              SNN Graph Based Community Detection
runGOEnrich             Run Gene Ontology enrichment analysis on
                        differentially expressed genes.
runGSEA                 Analyze biological interpretations of metagene
runGeneralQC            General QC for liger object
runINMF                 Perform iNMF on scaled datasets
runIntegration          Integrate scaled datasets with iNMF or variant
                        methods
runOnlineINMF           Perform online iNMF on scaled datasets
runPairwiseDEG          Find DEG between groups
runTSNE                 Perform t-SNE dimensionality reduction
runUINMF                Perform Mosaic iNMF (UINMF) on scaled datasets
                        with unshared features
runUMAP                 Perform UMAP Dimensionality Reduction
scaleNotCenter          Scale genes by root-mean-square across cells
selectBatchHVG          *[Experimental]* Batch-aware highly variable
                        gene selection
selectGenes             Select a subset of informative genes
selectGenesVST          Select variable genes from one dataset with
                        Seurat VST method
sub-liger               Subset liger with brackets
sub-ligerDataset        Subset ligerDataset object
sub-sub-liger           Get cell metadata variable
subsetLiger             Subset liger object
subsetLigerDataset      Subset ligerDataset object
suggestK                *[Experimental]* Suggest optimal K value for
                        the factorization
summary.factorGSEA      Show significant results from factorGSEA
updateLigerObject       Update old liger object to up-to-date structure
writeH5                 Write in-memory data into H5 file
writeH5AD               Write liger object to H5AD files
