Introduction | Performing a gene set analysis | Gene set uncertainty analysis | Custom analyses | Further investigation options
Package: GiANT 1.3.4
GiANT: Gene Set Uncertainty in Enrichment Analysis
Toolbox for various enrichment analysis methods and quantification of uncertainty of gene sets, Schmid et al. (2016) <doi:10.1093/bioinformatics/btw030>.
Authors:
GiANT_1.3.4.tar.gz
GiANT_1.3.4.zip(r-4.7-any)GiANT_1.3.4.zip(r-4.6-any)GiANT_1.3.4.zip(r-4.5-any)
GiANT_1.3.4.tgz(r-4.6-any)GiANT_1.3.4.tgz(r-4.5-any)
GiANT_1.3.4.tar.gz(r-4.7-any)GiANT_1.3.4.tar.gz(r-4.6-any)
GiANT_1.3.4.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
GiANT/json (API)
| # Install 'GiANT' in R: |
| install.packages('GiANT', repos = c('https://hkestler.r-universe.dev', 'https://cloud.r-project.org')) |
Datasets:
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
Last updated from:aaed8ec41a. Checks:9 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel-x86_64 | OK | 155 | ||
| source / vignettes | OK | 163 | ||
| linux-release-x86_64 | OK | 162 | ||
| macos-release-arm64 | OK | 92 | ||
| macos-oldrel-arm64 | OK | 94 | ||
| windows-devel | OK | 99 | ||
| windows-release | OK | 104 | ||
| windows-oldrel | OK | 133 | ||
| wasm-release | OK | 147 |
Exports:analysis.averageCorrelationanalysis.averageTStatisticanalysis.customOverrepresentationanalysis.globalAncovaanalysis.globalTestanalysis.gseaanalysis.overrepresentationcreateSummaryTableevaluateGeneSetUncertaintyfilterGeneSetsgeneSetAnalysisglobal.ancovaglobal.overrepresentationglobal.testgls.corgls.foldChangegls.moderateTStatisticgls.nBinomTestgls.regressiongls.tStatisticgsAnalysisgss.enrichmentScoregss.fisherExactTestgss.gszgss.maxmeangss.meangss.mediangss.sumgss.wilcoxonRankTestmergeProbesForGenesparseGmtplotOverrepresentationpreprocessGssignificance.permutationsignificance.restandardizationsignificance.samplingtransformation.abstransformation.adjusttransformation.adjustAndBinarizetransformation.binarizetransformation.localFdrtransformation.ranktransformation.square
Dependencies:
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Enrichment analysis | GiANT |
| Example data | countdata |
| Create an overview table for an analysis | createSummaryTable |
| Quantify gene set uncertainty | evaluateGeneSetUncertainty |
| Filtering of gene sets | filterGeneSets |
| Main interface for enrichment analyses. | geneSetAnalysis |
| Gene-level statistics | gls gls.cor gls.foldChange gls.moderateTStatistic gls.nBinomTest gls.regression gls.tStatistic |
| Gene set statistics | gss gss.enrichmentScore gss.fisherExactTest gss.gsz gss.maxmean gss.mean gss.median gss.sum gss.wilcoxonRankTest |
| Global analyses | global global.ancova global.overrepresentation global.test |
| Gene set analysis. | gsAnalysis |
| Null distribution histogram and statistic of the input set for enrichment analyses. | hist.gsaResult |
| Example data to label samples in countdata (rows) in two classes 0 and 1 | labels |
| Merge multiple probes for one gene | mergeProbesForGenes |
| Venn Euler Diagramm | parseGmt |
| Example data for pathways to to gene set enrichtment analyses | pathways |
| Plots the results of an uncertainty analysis. | plot.uncertaintyResult |
| Plot overlap of gene sets and core set | plotOverrepresentation |
| Predefined enrichment analyses | analysis.averageCorrelation analysis.averageTStatistic analysis.customOverrepresentation analysis.globalAncova analysis.globalTest analysis.gsea analysis.overrepresentation predefinedAnalyses |
| Eliminate unknown genes from gene sets | preprocessGeneSets preprocessGs |
| Significance assessment | significance significance.permutation significance.restandardization significance.sampling |
| Summarize gene set analysis results | summary.gsaResult |
| Transformations | transformation transformation.abs transformation.adjust transformation.adjustAndBinarize transformation.binarize transformation.localFdr transformation.rank transformation.square |
