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GiANT (version 1.3.4)

Gene Set Uncertainty in Enrichment Analysis

Description

Toolbox for various enrichment analysis methods and quantification of uncertainty of gene sets, Schmid et al. (2016) .

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Version

Install

install.packages('GiANT')

Monthly Downloads

195

Version

1.3.4

License

Artistic-2.0

Maintainer

Hans Kestler

Last Published

September 5th, 2024

Functions in GiANT (1.3.4)

plotOverrepresentation

Plot overlap of gene sets and core set
plot

Plots the results of an uncertainty analysis.
mergeProbesForGenes

Merge multiple probes for one gene
preprocessGeneSets

Eliminate unknown genes from gene sets
parse GMT files

Venn Euler Diagramm
predefinedAnalyses

Predefined enrichment analyses
Transformations

Transformations
summary.gsaResult

Summarize gene set analysis results
pathways

Example data for pathways to to gene set enrichtment analyses
SignificanceAssessment

Significance assessment
labels

Example data to label samples in countdata (rows) in two classes 0 and 1
hist

Null distribution histogram and statistic of the input set for enrichment analyses.
GiANT-package

Enrichment analysis
createSummaryTable

Create an overview table for an analysis
gsAnalysis

Gene set analysis.
GeneSetStatistics

Gene set statistics
GlobalAnalysis

Global analyses
evaluateGeneSetUncertainty

Quantify gene set uncertainty
Filter gene sets

Filtering of gene sets
Gene set analysis

Main interface for enrichment analyses.
GeneLevelStatistics

Gene-level statistics
countdata

Example data