calcARI                 Calculate adjusted Rand index
calcAgreement           Calculate agreement metric
calcAlignment           Calculate alignment metric
calcAlignmentPerCluster
                        Calculate alignment for each cluster
calcDatasetSpecificity
                        Calculate a dataset-specificity score for each
                        factor
calcGeneVars            Calculate variance of gene expression across
                        cells in an online fashion
calcPurity              Calculate purity
convertOldLiger         Convert older liger object into most current
                        version (based on class definition)
createLiger             Create a liger object.
getFactorMarkers        Find shared and dataset-specific markers
getGeneValues           Get gene expression values from list of
                        expression matrices.
getProportionMito       Calculate proportion mitochondrial contribution
imputeKNN               Impute the query cell expression matrix
liger-class             The LIGER Class
ligerToSeurat           Create a Seurat object containing the data from
                        a liger object
linkGenesAndPeaks       Linking genes to putative regulatory elements
louvainCluster          Louvain algorithm for community detection
makeFeatureMatrix       Fast calculation of feature count matrix
makeInteractTrack       Export predicted gene-pair interaction
makeRiverplot           Generate a river (Sankey) plot
mergeH5                 Merge hdf5 files
nnzeroGroups            nnzeroGroups
nonneg                  Perform thresholding on dense matrix
normalize               Normalize raw datasets to column sums
online_iNMF             Perform online iNMF on scaled datasets
optimizeALS             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
plotByDatasetAndCluster
                        Plot t-SNE coordinates of cells across datasets
plotClusterFactors      Plot heatmap of cluster/factor correspondence
plotClusterProportions
                        Plot cluster proportions by dataset
plotFactors             Plot scatter plots of unaligned and aligned
                        factor loadings
plotFeature             Plot specific feature on t-SNE coordinates
plotGene                Plot gene expression on dimensional reduction
                        (t-SNE) coordinates
plotGeneLoadings        Generate t-SNE plots and gene loading plots
plotGeneViolin          Plot violin plots for gene expression
plotGenes               Plot expression of multiple genes
plotWordClouds          Generate word clouds and t-SNE plots
quantileAlignSNF        Quantile align (normalize) factor loadings
quantile_norm           Quantile align (normalize) factor loadings
rank_matrix             rank_matrix
read10X                 Read 10X alignment data (including V3)
readSubset              Sample data for plotting
removeMissingObs        Remove cells/genes with no expression across
                        any genes/cells
reorganizeLiger         Construct a liger object organized by another
                        feature
restoreOnlineLiger      Restore links (to hdf5 files) for reloaded
                        online Liger object
runGSEA                 Analyze biological interpretations of metagene
runTSNE                 Perform t-SNE dimensionality reduction
runUMAP                 Perform UMAP dimensionality reduction
runWilcoxon             Perform Wilcoxon rank-sum test
scaleNotCenter          Scale genes by root-mean-square across cells
selectGenes             Select a subset of informative genes
seuratToLiger           Create liger object from one or more Seurat
                        objects
show                    show method for liger
subsetLiger             Construct a liger object with a specified
                        subset
suggestK                Visually suggest appropiate k value
suggestLambda           Visually suggest appropriate lambda value
sumGroups               sumGroups
