Advanced Gene Set Enrichment Analysis


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Documentation for package ‘SetRank’ version 1.1.0

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buildSetCollection Create a gene set collection
createCytoscapeVizMap Create a Cytoscape visual style for one or more SetRank networks.
createIDConverter Create a function to convert gene or protein IDs
createPathwayTable Creates a table of all significant pathways in different conditions.
cytoscapeExport Prepare networks for visualization in Cytoscape
exportGeneNets Create gene interaction networks for all significant gene sets.
exportMultipleResults Export multiple SetRank networks and accompanying tables.
exportSingleResult Export a SetRank network and accompanying tables.
fixGraphML Fix the igraph graphML export
generateContinuousMapping Generates a continuous VizMap property mapping.
generatePMapping Generates a visual property mapping for p-value attributes
membershipTable Create a gene set membership table.
propertyFunctions Attribute handlers for generating the VizMap XML
setRankAnalysis Advanced gene set enrichment analysis.
styleXML VizMap XML template