R: Analysis of Biological Count Data, Especially from Single-Cell RNA-Seq

# Analysis of Biological Count Data, Especially from Single-Cell RNA-Seq

## Documentation for package ‘countland’ version 0.1.2

- DESCRIPTION file
- Package NEWS

## Help Pages

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 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