Package index • MSstatsBioNet

All functions

NetworkBackend-class IndraBackend-class: Network backend classes
NetworkQuery-class SubnetworkQuery-class: Network query classes
add_entity_values(): Copy the values of an entity table onto a network's nodes
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
.validateAnnotateProteinInfoFromIndraInput(): Validate Annotate Protein Info Input
exportNetworkToHTML(): Export network data with Cytoscape visualization
filterSubnetworkByContext(): Filter a subnetwork by contextual relevance
filter_by_curation(): Remove evidence curated as incorrect
filter_by_ptm_site(): Keep the edges that modify a PTM site in the network
getSubnetworkFromIndra(): Get subnetwork from INDRA database
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
indra_backend(): Create an INDRA backend
INDRA_DATABASE_SOURCES INDRA_TEXT_MINED_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
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