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-4.5)GiANT_1.3.4.zip(r-4.4)GiANT_1.3.4.zip(r-4.3)
GiANT_1.3.4.tgz(r-4.4-any)GiANT_1.3.4.tgz(r-4.3-any)
GiANT_1.3.4.tar.gz(r-4.5-noble)GiANT_1.3.4.tar.gz(r-4.4-noble)
GiANT_1.3.4.tgz(r-4.4-emscripten)GiANT_1.3.4.tgz(r-4.3-emscripten)
GiANT.pdf |GiANT.html✨
GiANT/json (API)
| # Install 'GiANT' in R: |
| install.packages('GiANT', repos = c('https://hkestler.r-universe.dev', 'https://cloud.r-project.org')) |
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
Last updated 3 months agofrom:aaed8ec41a. Checks:OK: 7. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Nov 01 2024 |
| R-4.5-win | OK | Nov 01 2024 |
| R-4.5-linux | OK | Nov 01 2024 |
| R-4.4-win | OK | Nov 01 2024 |
| R-4.4-mac | OK | Nov 01 2024 |
| R-4.3-win | OK | Nov 01 2024 |
| R-4.3-mac | OK | Nov 01 2024 |
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 |
