Package index

All functions

annotateProteinInfoFromIndra()

Annotate Protein Information from Indra

bootstrapTopicModels()

Bootstrap the topic decomposition to find each topic's robust top words

compareTopicModels()

Test whether including PPIs changes topic structure beyond random chance

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

.populateEntityInformationInDataFrame()

Populate Entity Information in Data Frame

.validateAnnotateProteinInfoFromIndraInput()

Validate Annotate Protein Info Input

exportNetworkToHTML()

Export network data with Cytoscape visualization

filterSubnetworkByContext()

Filter a subnetwork by contextual relevance

getSubnetworkFromIndra()

Get subnetwork from INDRA database

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.