Man pages for SPONGE
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 |
