# Selective Locally Linear Inference of Cellular Expression Relationships

## Documentation for package ‘SLICER’ version 0.2.0

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

## 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