Diffusion scores on biological networks

checks | Sanity checks for input |

connect_undirected_graph | Function to connect a non connected graph |

convertSparse | S4 sparse matrix to arma::sp_mat |

default_graph_param | Generate data.frame with default vertex attributes |

diffuse | Diffuse scores on a network |

diffuse_mc | Compute the heatrank using permutations |

diffuse_raw | Diffuse scores on a network |

diffuStats | diffuStats: an R package to compute and benchmark diffusion... |

generate_graph | Generate a random graph |

generate_input | Generate a random input for graph diffusion |

graph_toy | Toy graph to play with diffusion |

is_kernel | Check if a matrix is a valid kernel |

kernels | Compute graph kernels |

largest_cc | Largest connected component |

named.list | Create a named list |

ParallelHeatrank | Compute heatrank in parallel |

perf | Compare diffusions to a target score on a grid of parameters |

perf_eval | Compute performance of diffusion scores on a single case |

scores2colours | Translate values into colours |

scores2shapes | Translate values into shapes |

serialHeatrank | Compute heatrank for a single case |

sparsify2 | Sparsify arma::mat into arma::sp_mat |

to_list | Convert input to list format |

to_x_from_list | Convert list format to desired format |

which_format | In which format is the input? |

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