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FGNet (version 3.6.2)

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

3.6.2

License

GPL (>= 2)

Maintainer

Sara Aibar

Last Published

February 15th, 2017

Functions in FGNet (3.6.2)

format_results

Format FEA results from external tools.
keywordsTerm

Select keyword term
fea_david

FEA - DAVID
plotGoAncestors

Plot GO term ancestors
fea2incidMat

Transforms FEA output into incidence matrices.
analyzeNetwork

Analyze Functional Network
FGNet-package

Functional gene networks derived from biological enrichment analyses
getTerms

Get terms in the metagroups/clusters.
format_david

Format DAVID output
FGNet_report

FGNet report
clustersDistance

Plots distances between metagroups.
organisms

FGNet data
readGeneTermSets

Read gene-term sets
functionalNetwork

Creates and plots the functional gene network.
FGNet_GUI

FGNet graphical user interface
fea_gtLinker

FEA - Gene-Term Linker
fea_topGO

FEA - topGO
fea_gage

FEA - GAGE
plotKegg

Plot KEGG pathway