Files in BIONF/PhyloProfile

PhyloProfile

.github/issue_template.md .github/pull_request_template.md CONTRIBUTING.md LICENSE.md R/analyzeDistribution.R R/clusterProfile.R R/compareTaxaGroups.R R/createColorScheme.R R/createDomainPlot.R R/createProfilePlot.R R/createTaxonomyMatrix.R R/data.R R/estimateGeneAge.R R/getFastaSeqs.R R/getOmaBrowser.R R/identifyCoreGene.R R/parseDomainInput.R R/parseMainInput.R R/parsePhyloProfile.R R/parsePhylotree.R R/runPhyloprofile.R R/umapClustering.R README.md inst/PhyloProfile/R/analyzeDistribution.R inst/PhyloProfile/R/clusterProfile.R inst/PhyloProfile/R/createArchitecturePlot.R inst/PhyloProfile/R/createDetailedPlot.R inst/PhyloProfile/R/createProfilePlot.R inst/PhyloProfile/R/downloadFilteredCustomized.R inst/PhyloProfile/R/downloadFilteredMain.R inst/PhyloProfile/R/downloadPlotSettings.R inst/PhyloProfile/R/estimateGeneAge.R inst/PhyloProfile/R/exportNcbiTax.R inst/PhyloProfile/R/functions.R inst/PhyloProfile/R/getFastaDemo.R inst/PhyloProfile/R/groupComparison.R inst/PhyloProfile/R/identifyCoreGene.R inst/PhyloProfile/R/importNcbiTax.R inst/PhyloProfile/R/resetTaxData.R inst/PhyloProfile/R/selectTaxonRank.R inst/PhyloProfile/R/updateNcbiTax.R inst/PhyloProfile/global.R inst/PhyloProfile/server.R inst/PhyloProfile/ui.R man/addDimRedTaxaColors.Rd man/addFeatureColors.Rd man/addRankDivisionPlot.Rd man/calcPresSpec.Rd man/checkColorPalette.Rd man/checkInputValidity.Rd man/checkNewick.Rd man/checkOmaID.Rd man/checkOverlapDomains.Rd man/clusterDataDend.Rd man/compareMedianTaxonGroups.Rd man/compareTaxonGroups.Rd man/createArchiPlot.Rd man/createDimRedPlotData.Rd man/createGeneAgePlot.Rd man/createLongMatrix.Rd man/createPercentageDistributionData.Rd man/createProfileFromOma.Rd man/createUnrootedTree.Rd man/createVarDistPlot.Rd man/createVariableDistributionData.Rd man/createVariableDistributionDataSubset.Rd man/dataCustomizedPlot.Rd man/dataFeatureTaxGroup.Rd man/dataMainPlot.Rd man/dataVarDistTaxGroup.Rd man/dimReduction.Rd man/distributionTest.Rd man/estimateGeneAge.Rd man/fallbackUmap.Rd man/fastaParser.Rd man/featureDistTaxPlot.Rd man/filterProfileData.Rd man/filteredProfile.Rd man/finalProcessedProfile.Rd man/fromInputToProfile.Rd man/fullProcessedProfile.Rd man/geneAgePlotDf.Rd man/generateSinglePlot.Rd man/getAllDomainsOma.Rd man/getAllFastaOma.Rd man/getCommonAncestor.Rd man/getCoreGene.Rd man/getDataClustering.Rd man/getDataForOneOma.Rd man/getDendrogram.Rd man/getDistanceMatrix.Rd man/getDomainFolder.Rd man/getFastaFromFasInput.Rd man/getFastaFromFile.Rd man/getFastaFromFolder.Rd man/getIDsRank.Rd man/getInputTaxaID.Rd man/getInputTaxaName.Rd man/getNameList.Rd man/getOmaDataForOneOrtholog.Rd man/getOmaDomainFromURL.Rd man/getOmaMembers.Rd man/getQualColForVector.Rd man/getSelectedFastaOma.Rd man/getSelectedTaxonNames.Rd man/getTaxHierarchy.Rd man/getTaxonomyInfo.Rd man/getTaxonomyMatrix.Rd man/getTaxonomyRanks.Rd man/gridArrangeSharedLegend.Rd man/groupLabelDimRedData.Rd man/heatmapPlotting.Rd man/heatmapPlottingFast.Rd man/highlightProfilePlot.Rd man/id2name.Rd man/idList.Rd man/joinPlotMergeLegends.Rd man/linearizeArchitecture.Rd man/mainLongRaw.Rd man/mainTaxonomyRank.Rd man/modifyFeatureName.Rd man/pairDomainPlotting.Rd man/parseDomainInput.Rd man/parseInfoProfile.Rd man/performUmap.Rd man/plotDimRed.Rd man/plotDimRed3D.Rd man/ppTaxonomyMatrix.Rd man/ppTree.Rd man/prepareDimRedData.Rd man/processNcbiTaxonomy.Rd man/processOrthoID.Rd man/profileWithTaxonomy.Rd man/qualitativeColours.Rd man/rankIndexing.Rd man/rankList.Rd man/reduceProfile.Rd man/resolveOverlapFeatures.Rd man/runPhyloProfile.Rd man/singleDomainPlotting.Rd man/sortDomains.Rd man/sortDomainsByList.Rd man/sortInputTaxa.Rd man/sortTaxaFromTree.Rd man/taxa2dist.Rd man/taxonNamesReduced.Rd man/taxonomyMatrix.Rd man/taxonomyTableCreator.Rd man/varDistTaxPlot.Rd man/wideToLong.Rd man/xmlParser.Rd tests/testthat.R tests/testthat/testCreateDataProfilePlot.R tests/testthat/testCreateDistributionPlot.R tests/testthat/testCreateDomainPlot.R tests/testthat/testCreateTaxonomyMatrix.R tests/testthat/testEstimateGeneAge.R tests/testthat/testIdentifyCoreGene.R tests/testthat/testOMAparser.R tests/testthat/testParseDomainInput.R tests/testthat/testParseMainInput.R tests/testthat/testParsePhyloProfile.R vignettes/PhyloProfile-vignette.Rmd