| Center | Recapitulate Seurat centering scaled and transformed data |
| Cluster | Perform spectral clustering on dot products. |
| CountIndex | Internal function for calculating count index. |
| countland | Initialize a countland object from a dgCMatrix |
| countland-class | An S4 class to represent a countland object |
| 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_init | function to initialize U, V, and Lambda |
| IMA_params | Parameter class for IMA |
| IMA_Update_Factor | Update factor matrix - see SUSTain code |
| listCols | Split dgCMatrix into column vectors. |
| Log | Recapitulate Seurat log transformation |
| Normalize | Recapitulate Seurat normalization |
| PlotEigengap | Plots eigenvalues to investigate the optimal number of... |
| 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... |
| PlotMarker | Plot cell using spectral embedding and display counts in a... |
| PlotSharedCounts | Plot cells using matrix of counts summed by clusters of... |
| PrintGeneNumber | Restore count matrix to original state |
| RankMarkerGenes | Rank the top marker genes for each cluster from spectral... |
| 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... |
| Subsample | Subsample cells to a standard number of counts by randomly... |
| SubsampleCol | Internal function for subsampling a column from a sparse... |
| SubsetCells | Subsets cells using a vector of cell indices |
| SubsetGenes | Subsets genes using a vector of gene indices |
