ceRNA_interactions      ceRNA interactions
check_and_convert_expression_data
                        Checks if expression data is in matrix or
                        ExpressionSet format and converts the latter to
                        a standard matrix. Alternatively, a big.matrix
                        descriptor object can be supplied to make use
                        of shared memory between parallelized workers
                        through the bigmemory package.
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 model
fn_get_shared_miRNAs    Identify miRNAs for which both genes have miRNA
                        binding sites aka miRNA response elements in
                        the competing endogeneous RNA hypothesis
gene_expr               Gene expression test data set
genes_pairwise_combinations
                        Compute all pairwise interactions for a number
                        of genes as indices
mir_expr                miRNA expression test data set
mir_interactions        miRNA / gene interactions
mircode_ensg            mircode predicted miRNA gene interactions
mircode_symbol          mircode predicted miRNA gene interactions
precomputed_cov_matrices
                        covariance matrices under the null hypothesis
                        that sensitivity correlation is zero
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 matrices
sponge                  Compute competing endogeneous RNA interactions
                        using Sparse Partial correlations ON Gene
                        Expression (SPONGE)
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 without regression, single or
                        pooled miRNAs, are compared.
sponge_subsampling      Sponge subsampling
targetscan_ensg         targetscan predicted miRNA gene interactions
targetscan_symbol       targetscan predicted miRNA gene interactions
