GO.human                GO - human
GO.mouse                GO - mouse
GO.voc                  Gene ontology vocabulary
assortativity           Calculating network assortativity
attr.human              Human GENCODE annotations (v22)
attr.mouse              Mouse GENCODE annotations (M7)
auc_multifunc           Calculating AUC for functional groups from
                        ranked lists
auprc                   Area under the precision recall curve
auroc_analytic          Area under the receiver operating
                        characteristic curve
biogrid                 BIOGRID v3.4.126
build_binary_network    Builds a binary network
build_coexp_GEOID       Builds a coexpression network given a GEO ID
build_coexp_expressionSet
                        Builds a coexpression network from an
                        expressionSet
build_coexp_network     Builds a coexpression network from an
                        expressionSet
build_semantic_similarity_network
                        Builds a semantic similarity network
build_weighted_network
                        Builds a weighted network
calculate_multifunc     Performing multifunctionality analysis
conv_smoother           Plot smoothed curve
example_annotations     Example of annotations
example_binary_network
                        Example of binary network
example_coexpression    Example of binary network
example_neighbor_voting
                        Example of binary network
extend_network          Builds an extended network from a binary
                        network
filter_network          Filter on matrix
filter_network_cols     Filter on columns
filter_network_rows     Filter on rows
filter_orthologs        Filter on orthologs
fmeasure                Fmeasure of precision-recall
genes                   Genes from BIOGRID v3.4.126
get_auc                 Calculates the area under a curve
get_biogrid             Downloading and filtering BIOGRID
get_counts              Get counts
get_density             Get density
get_expression_data_gemma
                        Obtain expression matrix from the GEMMA
                        database
get_expression_matrix_from_GEO
                        Obtain expression matrix from GEO database
get_phenocarta          Downloading and filtering Phenocarta
get_prc                 Build precision-recall curve
get_roc                 Build receiver operating characteristic curve
make_annotations        Creating gene annotations
make_gene_network       Creating gene-by-gene network
make_genelist           Creating list of all genes in the data set.
make_transparent        Make a color transparent (Taken from an answer
                        on StackOverflow by Nick Sabbe)
neighbor_voting         Evaluating Gene Function Prediction
node_degree             Calculate node degree
ortho                   Gene orthologs
pheno                   Phenocarta
plot_densities          Plot densities
plot_density_compare    Plot density comparisons
plot_distribution       Plot distribution histogram
plot_network_heatmap    Plot network heatmap
plot_prc                Plot precision recall curve
plot_roc                Plot receiver operating characteristic curve
plot_roc_overlay        Plot ROC overlay
plot_value_compare      Plot value comparisons
predictions             Performing Gene Function Prediction
repmat                  Rep function for matrices
run_GBA                 Performing 'Guilt by Association' Analysis
