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SetRank (version 1.0.0)

Advanced Gene Set Enrichment Analysis

Description

Implements an algorithm to conduct advanced gene set enrichment analysis on the results of genomics experiments.

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Version

Install

install.packages('SetRank')

Monthly Downloads

20

Version

1.0.0

License

GPL-3

Maintainer

Cedric Simillion

Last Published

December 8th, 2015

Functions in SetRank (1.0.0)

fixGraphML

Fix the igraph graphML export
createIDConverter

Create a function to convert gene or protein IDs
createPathwayTable

Creates a table of all significant pathways in different conditions.
buildSetCollection

Create a gene set collection
exportGeneNets

Create gene interaction networks for all significant gene sets.
styleXML

VizMap XML template
setRankAnalysis

Advanced gene set enrichment analysis.
exportSingleResult

Export a SetRank network and accompanying tables.
propertyFunctions

Attribute handlers for generating the VizMap XML
generateContinuousMapping

Generates a continuous VizMap property mapping.
cytoscapeExport

Prepare networks for visualization in Cytoscape
generatePMapping

Generates a visual property mapping for p-value attributes
membershipTable

Create a gene set membership table.
createCytoscapeVizMap

Create a Cytoscape visual style for one or more SetRank networks.
exportMultipleResults

Export multiple SetRank networks and accompanying tables.