API for lianos/multiGSEA
A unified interface to a plethora of gene set enrichment analysis methods
| Global functions | |
|---|---|
| .GeneSetDb | Man page |
| .GeneSetDb.GeneSetCollection | Source code |
| .GeneSetDb.data.frame | Source code |
| .GeneSetDb.list | Source code |
| .GeneSetDb.list.of.GeneSetCollections | Source code |
| .MultiGSEAResult | Man page |
| .get_kegg_pathway_db | Source code |
| .gsd.row.index | Source code |
| .gsdlist_conforms_to_gsd | Source code |
| .looks0centered | Source code |
| .onLoad | Source code |
| .rename_rows.bioc | Source code |
| .rename_rows.df | Source code |
| .replace | Source code |
| .target_column_idxs | Source code |
| .validate.inputs.full.design | Source code |
| .validate.inputs.logFC.only | Source code |
| .validate.inputs.preranked | Source code |
| .validateCollectionMetadata | Source code |
| .validateContrastVector | Source code |
| .validateDesign | Source code |
| .xformGdbForGSVA | Source code |
| GeneSetDb | Man page Source code |
| GeneSetDb-class | Man page |
| GeneSetDb.default | Source code |
| MultiGSEAResult | Man page |
| MultiGSEAResult-class | Man page |
| [,GeneSetDb,ANY,ANY,ANY-method | Man page |
| `fdata<-.DGEList` | Source code |
| `fdata<-.SummarizedExperiment` | Source code |
| `fdata<-.eSet` | Source code |
| `fdata<-` | Source code |
| `pdata<-.DGEList` | Source code |
| `pdata<-.EList` | Source code |
| `pdata<-.SummarizedExperiment` | Source code |
| `pdata<-.eSet` | Source code |
| `pdata<-` | Source code |
| addCollectionMetadata | Man page Source code |
| addGeneSetMetadata | Man page Source code |
| all.equal.GeneSetDb | Man page Source code |
| annotateGeneSetMembership | Man page Source code |
| append,GeneSetDb,ANY-method | Man page |
| approx.target.from.transformed | Source code |
| as.data.frame | Man page |
| as.data.frame.GeneSetDb | Man page Source code |
| as.list | Man page |
| as.list.GeneSetDb | Man page Source code |
| as_matrix | Source code |
| calculateIndividualLogFC | Man page Source code |
| check.dt | Source code |
| check.gsea.methods | Source code |
| collectionMetadata | Man page |
| combine,GeneSetDb,GeneSetDb-method | Man page |
| combine,MultiGSEAResult,MultiGSEAResult-method | Man page |
| conform | Man page |
| conform,GeneSetDb-method | Man page |
| conversion | Man page |
| corplot | Man page Source code |
| csplit | Source code |
| disp.estimated | Source code |
| do.camera | Source code |
| do.cameraPR | Source code |
| do.fgsea | Man page Source code |
| do.fry | Source code |
| do.geneSetTest | Source code |
| do.goseq | Man page Source code |
| do.logFC | Source code |
| do.ora | Source code |
| do.roast | Source code |
| do.romer | Source code |
| do.scoreSingleSamples.eigenWeightedMean | Source code |
| do.scoreSingleSamples.ewzscore | Source code |
| do.scoreSingleSamples.gsd | Source code |
| do.scoreSingleSamples.gsva | Source code |
| do.scoreSingleSamples.mean | Source code |
| do.scoreSingleSamples.zscore | Source code |
| do.svdGeneSetTest | Source code |
| downgradeObject | Source code |
| eigenWeightedMean | Man page Source code |
| encode_gskey | Man page Source code |
| exampleDgeResult | Man page Source code |
| exampleExpressionSet | Man page Source code |
| exampleGeneSetDF | Man page Source code |
| exampleGeneSetDb | Man page Source code |
| exampleGeneSets | Man page Source code |
| exampleMultiGSEAResult | Man page Source code |
| extract.genes | Source code |
| extract_preranked_stats | Source code |
| failWith | Man page Source code |
| fdata | Source code |
| fdata.DGEList | Source code |
| fdata.SummarizedExperiment | Source code |
| fdata.default | Source code |
| fdata.eSet | Source code |
| featureIdMap | Man page |
| featureIdType | Man page |
| featureIdType<- | Man page |
| featureIds | Man page |
| featureIds,GeneSetDb-method | Man page |
| featureIds,MultiGSEAResult-method | Man page |
| geneSet | Man page |
| geneSet,GeneSetDb-method | Man page |
| geneSet,MultiGSEAResult-method | Man page |
| geneSetCollectionURLfunction | Man page |
| geneSetCollectionURLfunction<- | Man page |
| geneSetDb | Man page Source code |
| geneSetSummaryByGenes | Man page |
| geneSetSummaryByGenes,GeneSetDb-method | Man page |
| geneSetSummaryByGenes,MultiGSEAResult-method | Man page |
| geneSetURL | Man page |
| geneSets | Man page |
| geneSets,GeneSetDb-method | Man page |
| geneSetsStats | Man page Source code |
| generate.preranked.stats | Source code |
| getGOslimGeneSetDb | Man page Source code |
| getHousekeepingGeneSetDb | Man page Source code |
| getKeggGeneSetDb | Man page Source code |
| getMSigGeneSetDb | Man page Source code |
| getPantherGOSLIM | Source code |
| getPantherGeneSetDb | Man page Source code |
| getPantherPathways | Source code |
| getReactomeGeneSetDb | Man page Source code |
| goseq | Man page Source code |
| gsdScore | Man page Source code |
| hasGeneSet | Man page Source code |
| hasGeneSetCollection | Man page Source code |
| incidenceMatrix | Man page Source code |
| init.gsd.db.from.list.of.lists | Source code |
| init.gsd.table.from.db | Source code |
| invalidMethods | Source code |
| iplot | Man page Source code |
| iplot.boxplot.plotly | Source code |
| iplot.density.plotly | Source code |
| iplot.gsea.plot | Source code |
| is.active | Man page Source code |
| is.conformed | Man page Source code |
| is.logFC.like | Source code |
| is.single.list.of.feature.vectors | Source code |
| isSingleCharacter | Source code |
| isSingleInteger | Source code |
| isSingleLogical | Source code |
| isSingleNumeric | Source code |
| load_id_xref | Man page Source code |
| logFC | Man page Source code |
| melt.gs.scores | Source code |
| mg.run | Source code |
| mg_add_points | Source code |
| mgheatmap | Man page Source code |
| mgheatmap2 | Man page Source code |
| mgres.camera | Source code |
| mgres.fgsea | Source code |
| mgres.fry | Source code |
| mgres.geneSetTest | Source code |
| mgres.goseq | Source code |
| mgres.logFC | Source code |
| mgres.ora | Source code |
| mgres.roast | Source code |
| mgres.romer | Source code |
| mgres.svdGeneSetTest | Source code |
| msg | Man page Source code |
| multiGSEA | Man page Source code |
| multiGSEA_methods | Man page Source code |
| na.check | Source code |
| ora | Man page Source code |
| org | Man page |
| org<- | Man page |
| p.matrix | Man page Source code |
| panel.cor | Source code |
| panel.hist | Source code |
| panel.spoints | Source code |
| pcWeightedMean | Man page Source code |
| pdata | Source code |
| pdata.DGEList | Source code |
| pdata.EList | Source code |
| pdata.SummarizedExperiment | Source code |
| pdata.default | Source code |
| pdata.eSet | Source code |
| plot_ora_bias | Man page Source code |
| qiagen.url.fn | Source code |
| readGeneSymbols | Source code |
| remap_identifiers | Man page Source code |
| rename.feature.columns | Source code |
| rename_rows | Man page Source code |
| rename_rows.DGEList | Source code |
| rename_rows.EList | Source code |
| rename_rows.SummarizedExperiment | Source code |
| rename_rows.default | Source code |
| rename_rows.eSet | Source code |
| resolve.species | Source code |
| result | Man page Source code |
| result.MultiGSEAResult | Man page Source code |
| resultNames | Man page Source code |
| results | Man page Source code |
| scale_rows | Man page Source code |
| scale_rows.Matrix | Source code |
| scale_rows.default | Source code |
| scale_rows.matrix | Source code |
| scale_rows.sparseMatrix | Source code |
| scoreSingleSamples | Man page Source code |
| species_info | Man page Source code |
| split_gskey | Man page Source code |
| ssGSEA.normalize | Man page Source code |
| subset.GeneSetDb | Man page Source code |
| subsetByFeatures | Man page |
| summarized | Man page |
| tabulateResults | Man page Source code |
| unconform | Man page |
| unconform,GeneSetDb-method | Man page |
| validate.DGEList | Source code |
| validate.X | Source code |
| validate.XwithWeights | Source code |
| validate.gene.sets.input | Source code |
| validate.inputs.goseq | Source code |
| validate.inputs.ora | Source code |
| validate.x.fry | Source code |
| validate.x.romer | Source code |
| validate.xmeta | Source code |
| validateInputs | Man page Source code |
| volcano.source.type | Source code |
| volcanoPlot | Man page Source code |
| volcanoStatsTable | Man page Source code |
| zScore | Man page Source code |
| ztransformPvalues | Man page Source code |
