# Rank Constrained Similarity Learning for single cell RNA sequencing data

## Documentation for package ‘RCSL’ version 1.18.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

ann | Cell type annotations of 'yan' datasets by Yan et al.
BDSM | Calculate the bolock-diagnal matrix B min_B>=0, B*1=1, F'*F=I ||B - A||_1 + r*||B||^2 + 2*lambda*trace(F'*L*F)
EProjSimplexdiag | Solve the problem: min 1/2*x'*L*x-x'*d s.t. x>=0, 1'x=1
EstClusters | Estimate the optimal number of clusters C for clustering
EucDist | Solve the problem: ||A-B||^2 = ||A||^2 + ||B||^2 - 2*A'*B
GenesFilter | Perform the step of gene filtering to normalizaed gene expression data
getLineage | Infer the development lineage based on the clustering results from RCSL and the pseudotime
NeigRepresent | Calculate the neighbor representation of cells to the low-dimensional gene expression matrix
PlotMST | Plot the visualization of constructed Minimum Spanning Tree based on the clustering results of RCSL
PlotPseudoTime | Infer the pseudo-temporal ordering between the cell types using the distance from a cell type to the predefined starting cell type.
PlotTrajectory | Infer the developmental trajectories based on the clustering results from RCSL
RCSL | Perform the RCSL program
SimS | Calculate the initial similarity matrix
TrajectoryAnalysis | Trajectory analysis
yan | A public scRNA-seq dataset by Yan et al.