AddSickleJrMetadata     Add metadata to an object of class SickleJr
BuildKNNGraphLaplacians
                        Build KNN graphs and generate their graph
                        Laplacians
BuildSNNGraphLaplacians
                        Build SNN graphs and generate their graph
                        Laplacians
CalculateUMAPSickleJr   Calculate the UMAP for an object of class
                        SickleJr
ClusterSickleJr         Cluster the \mathbf{H} matrix
CreateSickleJr          Create an object of class SickleJr
DetermineClusters       Perform clustering diagnostics
DetermineDFromIRLBA     Create elbow plots of the singular values
                        derived from IRLBA to determine D for large
                        datasets
GenerateWmatricesandHmatrix
                        Initialize the \mathbf{W} matrices in each
                        modality and the shared \mathbf{H} matrix
MinibatchDiagnosticPlot
                        Plot a diagnostic plot for the mini-batch
                        algorithm
NormalizeCountMatrices
                        Normalize the count matrices and set whether to
                        use the Poisson KL divergence or the Frobenius
                        norm
PlotLossvsLatentFactors
                        Create plots to help determine the number of
                        latent factors
PlotSickleJrUMAP        Generate UMAP plots for an object of class
                        SickleJr
RunjrSiCKLSNMF          Run jrSiCKLSNMF on an object of class SickleJr
SetLambdasandRowReg     Set lambda values and type of row
                        regularization for an object of class SickleJr
SetWandHfromWHinitials
                        Set \mathbf{W} matrices and \mathbf{H} matrix
                        from pre-calculated values
SickleJr-class          The SickleJr class
SimData                 A simulated dataset for use with jrSiCKLSNMF
SimSickleJrSmall        A small SickleJr object containing a subset of
                        data from the SimData data object. Contains the
                        completed analysis from the 'Getting Started'
                        vignette for a small subset of 10 cells with
                        150 genes and 700 peaks. The clusters derived
                        from this dataset are not accurate; this
                        dataset is intended for use with code examples.
jrSiCKLSNMF             Run jrSiCKLSNMF outside of a SickleJr object
