add_modules_to_network
                        Internal function for adding a set of modules
                        to the network
add_random_module_to_network
                        Adds a random module of a given size to the
                        network
as_single_module        Collapses all modules in network into a single
                        module
check_adjacency_cpp     C++ implementation to check if a matrix is an
                        adjacency matrix
components_in_adjacency
                        C++ implementation to obtain connected
                        components in a graph.
connect_module_structure
                        Connect disconnected components in an adjacency
                        matrix
create_cytoscape_file   Create an edge table file for Cytoscape
create_empty_module     Create a module
create_empty_network    Create a network object.
create_module_from_adjacency_matrix
                        Create a module from an adjacency matrix
create_module_from_association_matrix
                        Create a module from an association matrix
create_modules_for_network
                        Randomly sample subsets of genes for each
                        module
create_network_from_adjacency_matrix
                        Create a network object from an adjacency
                        matrix
create_network_from_association_matrix
                        Create a network object from an association
                        matrix
create_network_from_modules
                        Create a network object.
dzinb                   The Zero-Inflated Negative Binomial
                        Distribution
ecdf_cpp                C++ implementation of empirical CDF
edges_from_adjacency_cpp
                        C++ implementation for obtaining an edge list
                        from adjacency matrix
est_params_from_reference
                        Estimate ZINB parameters from reference data
gen_gaussian            Generate observations from a Gaussian graphical
                        model.
gen_partial_correlations
                        Generate partial correlations for a list of
                        networks.
gen_rnaseq              Generate RNA-seq data from an underlying
                        network
gen_zinb                Generate ZINB counts from an underlying network
get_adjacency_matrix    Get adjacency matrix
get_adjacency_matrix.default
                        Get adjacency matrix
get_adjacency_matrix.matrix
                        Get adjacency matrix
get_adjacency_matrix.network
                        Get adjacency matrix
get_adjacency_matrix.network_module
                        Get adjacency matrix
get_association_matrix
                        Get association matrix
get_association_matrix.default
                        Get association matrix
get_association_matrix.matrix
                        Get association matrix
get_association_matrix.network
                        Get association matrix
get_association_matrix.network_module
                        Get association matrix
get_degree_distribution
                        Get the degree distribution for a network.
get_edge_weights_from_module
                        Get edge weights.
get_layout_for_modules
                        Internal function used to create coordinates
                        based on a set of modules
get_network_characteristics
                        Characteristics of the network topology
get_network_modules     Get a list of modules from the network
get_node_names          Get node names
get_node_names.default
                        Get node names
get_node_names.matrix   Get node names
get_node_names.network
                        Get node names
get_node_names.network_module
                        Get node names
get_sigma               Get the covariance matrix
get_sigma.default       Get the covariance matrix
get_sigma.matrix        Get the covariance matrix
get_sigma.network       Get the covariance matrix
get_sigma.network_module
                        Get the covariance matrix
get_summary_for_node    Get summary for a node in the network.
heatmap_network         Plot heatmap representation of a network
is_symmetric_cpp        C++ implementation to check if a matrix is
                        symmetric
is_weighted             Check if an object is weighted
is_weighted.default     Check if an object is weighted
is_weighted.matrix      Check if an object is weighted
is_weighted.network     Check if an object is weighted
is_weighted.network_module
                        Check if an object is weighted
perturb_network         Perturbs the connections in a network
plot.network            Plot function for 'network' object
plot.network_module     Plot function for 'network_module' object.
plot.network_plot       Plot function for 'network_plot' class
plot_gene_pair          Scatter plot of two gene expressions
plot_modules            Visualize a network and its modules
plot_network            Visualize a network
plot_network_diff       Plot the difference between two networks
plot_network_sim        Plot the similarity between two networks
print.network           Print function for 'network' object.
print.network_module    Print function for 'network_module' object.
print.network_plot      Print function for 'network_plot' class
pzinb                   The Zero-Inflated Negative Binomial
                        Distribution
qzinb                   The Zero-Inflated Negative Binomial
                        Distribution
random_module           Create a random module
random_module_structure
                        Create a random network structure for a module
random_network          Create a network object.
reference               RNA-seq reference dataset
remove_connections      Remove connections in a network
remove_connections.default
                        Remove connections in a network
remove_connections.matrix
                        Remove connections in a network
remove_connections.network
                        Remove connections in a network
remove_connections.network_module
                        Remove connections in a network
remove_connections_to_node
                        Remove connections to a node
remove_connections_to_node.default
                        Remove connections to a node
remove_connections_to_node.matrix
                        Remove connections to a node
remove_connections_to_node.network
                        Remove connections to a node
remove_connections_to_node.network_module
                        Remove connections to a node
remove_weights          Removes the weights of all connections
remove_weights.default
                        Removes the weights of all connections
remove_weights.matrix   Removes the weights of all connections
remove_weights.network
                        Removes the weights of all connections
remove_weights.network_module
                        Removes the weights of all connections
replace_module_in_network
                        Internal function for replacing a module in the
                        network
rewire_connections      Rewire connections
rewire_connections.default
                        Rewire connections
rewire_connections.matrix
                        Rewire connections
rewire_connections.network
                        Rewire connections
rewire_connections.network_module
                        Rewire connections
rewire_connections_to_node
                        Rewire connections to a node
rewire_connections_to_node.default
                        Rewire connections to a node
rewire_connections_to_node.matrix
                        Rewire connections to a node
rewire_connections_to_node.network
                        Rewire connections to a node
rewire_connections_to_node.network_module
                        Rewire connections to a node
ring_lattice_cpp        C++ implementation for creating a ring lattice
rzinb                   The Zero-Inflated Negative Binomial
                        Distribution
sample_link_nodes       Sample link nodes for new module
sample_module_nodes     Sample nodes for new module
sample_reference_data   Sample genes from reference dataset
set_module_edges        Internal function used to set the edges in a
                        module
set_module_name         Set the name for a module
set_module_weights      Internal function to set the connection weights
                        for a module
set_node_names          Set the node names in a network
update_module_with_random_weights
                        Generate small-world network structure for
                        module
