Network Analysis for MS-based Proteomics Experiments

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Documentation for package ‘MSstatsBioNet’ version 1.5.2

• DESCRIPTION file
• User guides, package vignettes and other documentation
• Package NEWS
• Package README

Help Pages

.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
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
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.