Selective Locally Linear Inference of Cellular Expression Relationships

assign_branches | Detect branches in the trajectory and assign cells to... |

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... |

width_k | Helper function for k selection |

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