GiANT: Gene Set Uncertainty in Enrichment Analysis

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Toolbox for various enrichment analysis methods and quantification of uncertainty of gene sets.

Author
Florian Schmid, Christoph Müssel, Johann M. Kraus, Hans A. Kestler
Date of publication
2015-12-29 07:53:08
Maintainer
Hans Kestler <hans.kestler@uni-ulm.de>
License
Artistic-2.0
Version
1.2

View on CRAN

Man pages

createSummaryTable
Create an overview table for an analysis
evaluateGeneSetUncertainty
Quantify gene set uncertainty
filterGenesets
Filtering of gene sets
geneSetAnalysis
Main interface for enrichment analyses.
GiANT-package
Enrichment analysis
globalAnalysis
Global analyses
gls
Gene-level statistics
gsAnalysis
Gene set analysis.
gss
Gene set statistics
hist
Null distribution histogram and statistic of the input set...
mergeProbesForGenes
Merge multiple probes for one gene
parseGmt
Venn Euler Diagramm
plot
Plots the results of an uncertainty analysis.
plotOverrepresentation
Plot overlap of gene sets and core set
predefinedAnalyses
Predefined enrichment analyses
preprocessGeneSets
Eliminate unknown genes from gene sets
significance
Significance assessment
summary
Summarize gene set analysis results
transformation
Transformations

Files in this package

GiANT
GiANT/inst
GiANT/inst/doc
GiANT/inst/doc/giant_package_vignette.Snw
GiANT/inst/doc/giant_package_vignette.pdf
GiANT/inst/doc/giant_package_vignette.R
GiANT/NAMESPACE
GiANT/R
GiANT/R/utils.R
GiANT/R/transformations.R
GiANT/R/combineDuplicates.R
GiANT/R/preprocessGeneSets.R
GiANT/R/analysis.R
GiANT/R/hist.R
GiANT/R/enrProcedure.R
GiANT/R/plotOverrepresentation.R
GiANT/R/parseGmt.R
GiANT/R/evaluateGeneSetUncertainty.R
GiANT/R/summary.gsaResult.R
GiANT/R/geneSetAnalysis.R
GiANT/R/gss.R
GiANT/R/global.R
GiANT/R/significance.R
GiANT/R/gls.R
GiANT/vignettes
GiANT/vignettes/giant_bibliography.bib
GiANT/vignettes/vignette_randomGeneSetValues.pdf
GiANT/vignettes/giant_package_vignette.Snw
GiANT/vignettes/modules.pdf
GiANT/MD5
GiANT/build
GiANT/build/vignette.rds
GiANT/DESCRIPTION
GiANT/man
GiANT/man/parseGmt.Rd
GiANT/man/evaluateGeneSetUncertainty.Rd
GiANT/man/gsAnalysis.Rd
GiANT/man/filterGenesets.Rd
GiANT/man/predefinedAnalyses.Rd
GiANT/man/preprocessGeneSets.Rd
GiANT/man/significance.Rd
GiANT/man/plotOverrepresentation.Rd
GiANT/man/mergeProbesForGenes.Rd
GiANT/man/geneSetAnalysis.Rd
GiANT/man/createSummaryTable.Rd
GiANT/man/hist.Rd
GiANT/man/gls.Rd
GiANT/man/globalAnalysis.Rd
GiANT/man/plot.Rd
GiANT/man/gss.Rd
GiANT/man/GiANT-package.Rd
GiANT/man/summary.Rd
GiANT/man/transformation.Rd