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. |