Multimodal Single-Cell Omics Dimensionality Reduction

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Documentation for package ‘jrSiCKLSNMF’ version 1.2.1

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

Help Pages

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
jrSiCKLSNMF	Run jrSiCKLSNMF outside of a SickleJr object
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	The SickleJr class
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.