Rank Constrained Similarity Learning for single cell RNA sequencing data

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Documentation for package ‘RCSL’ version 1.16.0

• 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.