Generate RNA-seq data from regulatory networks

add_sign_to_network | Add random signs to network edges |

add_weight_to_network | Add random weights to network edges |

as.CONFUSION | Coerce a matrix into "CONFUSION" object |

as.data.frame.CONFUSION | Coerce "CONFUSION" object into a data.frame |

create_network | Create a network object. |

create_network_from_adjacency | Create a network object from adjacency matrix |

fdr | Determine which associations are significant |

gen_gamma_poisson | Generate sample from overdispered Poisson |

gen_gaussian | Generate sample from a Gaussian graphical model. |

gen_gaussian_list | Generate samples from a Gaussian graphical model. |

get_adj_matrix_from_network | Get adjacency matrix of a network |

get_confusion_matrix | Get confusion matrix for predicted classes. |

get_degree_change | Get the change in degree for each node between two networks. |

get_degree_distribution | Get the degree distribution for a network. |

get_pathway_list | Get a list of pathways in the network |

get_reference_count_means | Obtain empirical distribution of mean RNA-seq counts |

get_sigma_from_precision_list | Compute covariance matrices from a list of precision matrices |

get_summary_for_node | Get summary for a node in the network. |

isSymmetric.shrinkage | Test if a shrinkage object is symmetric. |

normalize_cpls_scores | Normalize the cPLS scores |

plot.CONFUSION | Plots confusion matrix |

plot_network | Plot function for network class |

plot.network | Plot function for network class |

plot_network_diff | Plotting to compare two networks |

print.CONFUSION | Print function for objects of class "CONFUSION" |

random_precision_from_network_list | Generate partial correlations for a list of networks. |

remove_connections_to_node | Remove node from the network |

remove_node_from_clique | Remove node from a clique in the network |

remove_node_from_hub | Remove node from a hub in the network |

remove_node_from_module | Remove node from a module in the network |

remove_small_components_from_module | Removes small components within a network module. |

rewire_connections_to_node | Rewire node in the network. |

run_corr | Wrapper for correlation co-expression |

run_cpls | Combined partial least squares with negative-binomial |

run_cpls_parallel | Combined partial least squares with negative-binomial |

run_example | Example of SeqNet package |

run_glasso | Wrapper for glasso method |

run_icorr | Wrapper for inverse covariance matrix |

run_pcor | Wrapper for partial correlations from corpcor |

run_wgcna | Wrapper for WGCNA method |

scores_to_adjacency_matrix | Infer adjacency matrix from scores |

set_low_rank_scores_to_zero | Set low ranking scores to zero. |

summarize_confusion | Provides summary measures for confusion matrix |

vector_to_matrix | Turn a vector into a matrix |

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