Sparse Partial Correlations On Gene Expression

ceRNA_interactions | ceRNA interactions |

check_and_convert_expression_data | Checks if expression data is in matrix or ExpressionSet... |

fn_elasticnet | Computes an elastic net model |

fn_gene_miRNA_F_test | Perform F test for gene-miRNA elastic net model |

fn_get_model_coef | Extract the model coefficients from an elastic net model |

fn_get_rss | Compute the residual sum of squares error for an elastic net... |

fn_get_shared_miRNAs | Identify miRNAs for which both genes have miRNA binding sites... |

gene_expr | Gene expression test data set |

genes_pairwise_combinations | Compute all pairwise interactions for a number of genes as... |

mircode_ensg | mircode predicted miRNA gene interactions |

mircode_symbol | mircode predicted miRNA gene interactions |

mir_expr | miRNA expression test data set |

mir_interactions | miRNA / gene interactions |

precomputed_cov_matrices | covariance matrices under the null hypothesis that... |

precomputed_null_model | A null model for testing purposes |

sample_zero_mscor_cov | Sampling zero multiple miRNA sensitivity covariance matrices |

sample_zero_mscor_data | Sample mscor coefficients from pre-computed covariance... |

sponge | Compute competing endogeneous RNA interactions using Sparse... |

sponge_build_null_model | Build null model for p-value computation |

sponge_compute_p_values | Compute p-values for SPONGE interactions |

sponge_edge_centralities | Computes edge centralities |

sponge_gene_miRNA_interaction_filter | Determine miRNA-gene interactions to be considered in SPONGE |

sponge_network | Prepare a sponge network for plotting |

sponge_node_centralities | Computes various node centralities |

sponge_plot_network | Plot a sponge network |

sponge_plot_network_centralities | plot node network centralities |

sponge_plot_simulation_results | Plot simulation results for different null models |

sponge_run_benchmark | run sponge benchmark where various settings, i.e. with or... |

sponge_subsampling | Sponge subsampling |

targetscan_ensg | targetscan predicted miRNA gene interactions |

targetscan_symbol | targetscan predicted miRNA gene interactions |

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