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

deleteEdgeFromNetwork()

Delete an edge from a network edges data frame

.populateEntityInformationInDataFrame()

Populate Entity Information in Data Frame

.populateEntityInformationWithGilda()

Populate entity grounding columns via Gilda

.populateEntityInformationWithIndraCogex()

Populate entity grounding columns via INDRA cogex APIs

.populateKinaseInfoInDataFrame()

Populate Kinase Info in Data Frame

.populatePhophataseInfoInDataFrame()

Populate Phosphatase Info in Data Frame

.populateTranscriptionFactorInfoInDataFrame()

Populate Transcription Factor Info in Data Frame

.populateUniprotIdsInDataFrame()

Populate Uniprot IDs 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

renderCytoscapeNetwork()

Render a Cytoscape network in a Shiny application. This function is used to render a Cytoscape network visualization within a Shiny application.