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FGNet (version 3.4.0)

Functional Gene Networks derived from biological enrichment analyses

Description

Build and visualize functional gene and term networks from clustering of enrichment analyses in multiple annotation spaces. The package includes a graphical user interface (GUI) and functions to perform the functional enrichment analysis through DAVID, GeneTerm Linker, gage (GSEA) and topGO.

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Version

Version

3.4.0

License

GPL (>= 2)

Maintainer

Sara Aibar

Last Published

February 15th, 2017

Functions in FGNet (3.4.0)

FGNet-package

Functional gene networks derived from biological enrichment analyses
format_david

Format DAVID output
getTerms

Get terms in the metagroups/clusters.
keywordsTerm

Select keyword term
organisms

FGNet data
fea2incidMat

Transforms FEA output into incidence matrices.
format_results

Format FEA results from external tools.
readGeneTermSets

Read gene-term sets
functionalNetwork

Creates and plots the functional gene network.
analyzeNetwork

Analyze Functional Network
clustersDistance

Plots distances between metagroups.
plotGoAncestors

Plot GO term ancestors
plotKegg

Plot KEGG pathway
FGNet_GUI

FGNet graphical user interface
FGNet_report

FGNet report