Selective Locally Linear Inference of Cellular Expression Relationships


[Up] [Top]

Documentation for package ‘SLICER’ version 0.2.0

Help Pages

assign_branches Detect branches in the trajectory and assign cells to branches
cell_order Sort cells according to their progress through a process
compute_geodesic_entropy Compute the geodesic entropy profile of a trajectory
conn_knn_graph Construct a k-nearest neighbor graph that is fully connected
detect_cell_types Identify clusters corresponding to putative cell types
find_extreme_cells Identify candidate start cells for the trajectory
graph_gene Plot trajectory colored by expression level of a gene
graph_process_distance Plot trajectory colored by process distance
process_distance Determine the position of each cell within the trajectory
select_genes Select genes to use in building a cell trajectory
select_k Select the number of nearest neighbors for LLE to use
traj This is a dataset containing a synthetic branching trajectory.
width_k Helper function for k selection