Center                  Recapitulate Seurat centering scaled and
                        transformed data
Cluster                 Perform spectral clustering on dot products.
CountIndex              Internal function for calculating count index.
Dot                     Calculate pairwise dot products of counts
                        between all cells.
Embed                   Perform spectral embedding on dot products.
IMA                     run integer matrix approximation
IMA_Compute_Init_Scaled
                        rescale if max val is above upper bound
IMA_Update_Factor       Update factor matrix - see SUSTain code
IMA_init                function to initialize U, V, and Lambda
IMA_params              Parameter class for IMA
Log                     Recapitulate Seurat log transformation
Normalize               Recapitulate Seurat normalization
PlotEigengap            Plots eigenvalues to investigate the optimal
                        number of clusters
PlotEmbedding           Plot cells using spectral embedding of dot
                        products.
PlotGeneCounts          Generate a strip plot for counts across
                        selected genes
PlotIMA                 Plot cells using integer matrix approximation
PlotIMAElbow            Plot the difference between the observed and
                        reconstructed count matrix using integer matrix
                        approximation and a series of total features.
PlotMarker              Plot cell using spectral embedding and display
                        counts in a given gene.
PlotSharedCounts        Plot cells using matrix of counts summed by
                        clusters of genes.
PrintGeneNumber         Restore count matrix to original state
RankMarkerGenes         Rank the top marker genes for each cluster from
                        spectral clustering.
RemoveEmpty             Internal function to remove empty columns and
                        rows
RescaleVariance         Recapitulate Seurat scaling to unit variance
RestoreCounts           Restore count matrix to original state
RunIMA                  Perform integer matrix approximation on count
                        matrix.
ScikitManifoldSpectralEmbedding
                        Recapitulate scikit.manifold.spectral_embedding
                        from python.
ScoreCells              Calculate several scores for counts across
                        cells
ScoreGenes              Calculate several scores for count-based gene
                        expression.
SharedCounts            Combine groups of genes with similar counts by
                        clustering and summing.
Subsample               Subsample cells to a standard number of counts
                        by randomly sampling observations without
                        replacement.
SubsampleCol            Internal function for subsampling a column from
                        a sparse matrix.
SubsetCells             Subsets cells using a vector of cell indices
SubsetGenes             Subsets genes using a vector of gene indices
countland               Initialize a countland object from a dgCMatrix
countland-class         An S4 class to represent a countland object
listCols                Split dgCMatrix into column vectors.
