SetRank: Advanced Gene Set Enrichment Analysis

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

Author
Cedric Simillion
Date of publication
2016-05-11 12:06:23
Maintainer
Cedric Simillion <cedric.simillion@dkf.unibe.ch>
License
GPL-3
Version
1.1.0

View on CRAN

Man pages

buildSetCollection
Create a gene set collection
createCytoscapeVizMap
Create a Cytoscape visual style for one or more SetRank...
createIDConverter
Create a function to convert gene or protein IDs
createPathwayTable
Creates a table of all significant pathways in different...
cytoscapeExport
Prepare networks for visualization in Cytoscape
exportGeneNets
Create gene interaction networks for all significant gene...
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

Files in this package

SetRank
SetRank/inst
SetRank/inst/extdata
SetRank/inst/extdata/gene_net_style_template.xml
SetRank/inst/doc
SetRank/inst/doc/vignette.pdf
SetRank/inst/doc/vignette.ltx
SetRank/NAMESPACE
SetRank/R
SetRank/R/set_operators.R
SetRank/R/createCytoscapeVizMap.R
SetRank/R/analysis.R
SetRank/R/sysdata.rda
SetRank/R/buildSets.R
SetRank/R/gene_nets.R
SetRank/R/tables.R
SetRank/vignettes
SetRank/vignettes/p-value_correction.png
SetRank/vignettes/vignette.ltx
SetRank/MD5
SetRank/build
SetRank/build/vignette.rds
SetRank/DESCRIPTION
SetRank/man
SetRank/man/generatePMapping.Rd
SetRank/man/exportMultipleResults.Rd
SetRank/man/createIDConverter.Rd
SetRank/man/fixGraphML.Rd
SetRank/man/createPathwayTable.Rd
SetRank/man/cytoscapeExport.Rd
SetRank/man/styleXML.Rd
SetRank/man/createCytoscapeVizMap.Rd
SetRank/man/exportGeneNets.Rd
SetRank/man/setRankAnalysis.Rd
SetRank/man/generateContinuousMapping.Rd
SetRank/man/propertyFunctions.Rd
SetRank/man/buildSetCollection.Rd
SetRank/man/membershipTable.Rd
SetRank/man/exportSingleResult.Rd