.validateAnnotateProteinInfoFromIndraInput
                        Validate Annotate Protein Info Input
annotateProteinInfoFromIndra
                        Annotate Protein Information from Indra
backend_capabilities    What a backend supports
bootstrapTopicModels    Bootstrap the topic decomposition to find each
                        topic's robust top words
compareTopicModels      Test whether including PPIs changes topic
                        structure beyond random chance
convert_ids             Ground entities in a backend's namespaces
cytoscapeNetwork        Render a Cytoscape network visualisation
cytoscapeNetworkOutput
                        Shiny output binding for cytoscapeNetwork
decomposeSubnetworkByTopic
                        Decompose a subnetwork into topic-specific
                        subnetworks via joint NMF
decomposeSubnetworkIntoHierarchicalTopics
                        Recursively decompose a subnetwork into a
                        hierarchy of topic subnetworks
deleteEdgeFromNetwork   Delete an edge from a network edges data frame
exportNetworkToHTML     Export network data with Cytoscape
                        visualization
filter_by_curation      Remove evidence curated as incorrect
filterSubnetworkByContext
                        Filter a subnetwork by contextual relevance
get_curations           Get the curations of edges from a backend
get_entity_properties   Add a backend's properties of each entity
get_evidence            Get the evidence behind network edges
get_network             Get a network from a backend
getSubnetworkFromIndra
                        Get subnetwork from INDRA database
indra_backend           Create an INDRA backend
indra_evidence_sources
                        Evidence sources of INDRA
load_network            Load a network saved with save_network()
merge_networks          Combine networks from several queries or
                        backends
network_queries         Questions you can ask of a network backend
NetworkBackend-class    Network backend classes
NetworkQuery-class      Network query classes
prepare_entities        Prepare an entity table from MSstats results
previewNetworkInBrowser
                        Preview network in browser
print.topicHierarchy    Print a topic hierarchy as an indented tree
renderCytoscapeNetwork
                        Render a Cytoscape network in a Shiny
                        application. This function is used to render a
                        Cytoscape network visualization within a Shiny
                        application.
save_network            Save a network to a file
select_entities         Flag the entities to query
subnetwork_query        How are my selected entities connected to each
                        other?
validate_network        Validate a network against the edge and node
                        contract
