API for BIONF/PhyloProfile
PhyloProfile
| Global functions | |
|---|---|
| addDimRedTaxaColors | Man page Source code |
| addFeatureColors | Man page Source code |
| addRankDivisionPlot | Man page Source code |
| calcPresSpec | Man page Source code |
| checkColorPalette | Man page Source code |
| checkInputValidity | Man page Source code |
| checkNewick | Man page Source code |
| checkOmaID | Man page Source code |
| checkOverlapDomains | Man page Source code |
| clusterDataDend | Man page Source code |
| compareMedianTaxonGroups | Man page Source code |
| compareTaxonGroups | Man page Source code |
| createArchiPlot | Man page Source code |
| createDimRedPlotData | Man page Source code |
| createGeneAgePlot | Man page |
| createLongMatrix | Man page Source code |
| createPercentageDistributionData | Man page Source code |
| createProfileFromOma | Man page Source code |
| createUnrootedTree | Man page Source code |
| createVarDistPlot | Man page Source code |
| createVariableDistributionData | Man page Source code |
| createVariableDistributionDataSubset | Man page Source code |
| dataCustomizedPlot | Man page Source code |
| dataFeatureTaxGroup | Man page Source code |
| dataMainPlot | Man page Source code |
| dataVarDistTaxGroup | Man page Source code |
| dimReduction | Man page Source code |
| distributionTest | Man page Source code |
| estimateGeneAge | Man page Source code |
| fallbackUmap | Man page Source code |
| fastaParser | Man page Source code |
| featureDistTaxPlot | Man page Source code |
| filterProfileData | Man page Source code |
| filteredProfile | Man page |
| finalProcessedProfile | Man page |
| fromInputToProfile | Man page Source code |
| fullProcessedProfile | Man page |
| geneAgePlotDf | Man page Source code |
| generateSinglePlot | Man page Source code |
| getAllDomainsOma | Man page Source code |
| getAllFastaOma | Man page Source code |
| getCommonAncestor | Man page Source code |
| getCoreGene | Man page Source code |
| getDataClustering | Man page Source code |
| getDataForOneOma | Man page Source code |
| getDendrogram | Man page Source code |
| getDistanceMatrix | Man page Source code |
| getDomainFolder | Man page Source code |
| getFastaFromFasInput | Man page Source code |
| getFastaFromFile | Man page Source code |
| getFastaFromFolder | Man page Source code |
| getIDsRank | Man page Source code |
| getInputTaxaID | Man page Source code |
| getInputTaxaName | Man page Source code |
| getNameList | Man page Source code |
| getOmaDataForOneOrtholog | Man page Source code |
| getOmaDomainFromURL | Man page Source code |
| getOmaMembers | Man page Source code |
| getQualColForVector | Man page Source code |
| getSelectedFastaOma | Man page Source code |
| getSelectedTaxonNames | Man page Source code |
| getTaxHierarchy | Man page Source code |
| getTaxonomyInfo | Man page Source code |
| getTaxonomyMatrix | Man page Source code |
| getTaxonomyRanks | Man page Source code |
| gridArrangeSharedLegend | Man page Source code |
| groupLabelDimRedData | Man page Source code |
| heatmapPlotting | Man page Source code |
| heatmapPlottingFast | Man page Source code |
| highlightProfilePlot | Man page Source code |
| id2name | Man page Source code |
| idList | Man page |
| joinPlotMergeLegends | Man page Source code |
| linearizeArchitecture | Man page Source code |
| mainLongRaw | Man page |
| mainTaxonomyRank | Man page Source code |
| modifyFeatureName | Man page Source code |
| pairDomainPlotting | Man page Source code |
| parseDomainInput | Man page Source code |
| parseInfoProfile | Man page Source code |
| performUmap | Man page Source code |
| plotDimRed | Man page Source code |
| plotDimRed3D | Man page Source code |
| ppTaxonomyMatrix | Man page |
| ppTree | Man page |
| prepareDimRedData | Man page Source code |
| processNcbiTaxonomy | Man page Source code |
| processOrthoID | Man page Source code |
| profileWithTaxonomy | Man page |
| qualitativeColours | Man page Source code |
| rankIndexing | Man page |
| rankList | Man page |
| reduceProfile | Man page Source code |
| resolveOverlapFeatures | Man page Source code |
| runPhyloProfile | Man page Source code |
| singleDomainPlotting | Man page Source code |
| sortDomains | Man page Source code |
| sortDomainsByList | Man page Source code |
| sortInputTaxa | Man page Source code |
| sortTaxaFromTree | Man page Source code |
| taxa2dist | Man page Source code |
| taxonNamesReduced | Man page |
| taxonomyMatrix | Man page |
| taxonomyTableCreator | Man page Source code |
| varDistTaxPlot | Man page Source code |
| wideToLong | Man page Source code |
| xmlParser | Man page Source code |
