Files in PhyloProfile

PhyloProfile

README.md

NAMESPACE

DESCRIPTION

LICENSE

R/getOmaBrowser.R R/analyzeDistribution.R R/data.R R/createProfilePlot.R R/createColorScheme.R R/createTaxonomyMatrix.R R/parsePhyloProfile.R R/clusterProfile.R R/parsePhylotree.R R/runPhyloprofile.R R/compareTaxaGroups.R R/parseMainInput.R R/createDomainPlot.R R/identifyCoreGene.R R/getFastaSeqs.R R/parseDomainInput.R R/estimateGeneAge.R

inst/NEWS.Rd

inst/CITATION

inst/doc/PhyloProfile-vignette.Rmd

inst/doc/PhyloProfile-vignette.html

inst/doc/PhyloProfile-vignette.R

inst/extdata/test.main.fasta

inst/extdata/test.main.wide

inst/extdata/test.main.long

inst/extdata/test.main.xml

inst/extdata/domainFiles/101621at6656.domains

inst/extdata/data/idList.txt

inst/extdata/data/preProcessedTaxonomy.txt

inst/extdata/data/rankList.txt

inst/extdata/fastaFiles/concatenatedFile.fa

inst/extdata/fastaFiles/RAT@[e-mail]

inst/PhyloProfile/ui.R inst/PhyloProfile/global.R

inst/PhyloProfile/help.html

inst/PhyloProfile/server.R inst/PhyloProfile/R/updateNcbiTax.R inst/PhyloProfile/R/analyzeDistribution.R inst/PhyloProfile/R/selectTaxonRank.R inst/PhyloProfile/R/createProfilePlot.R inst/PhyloProfile/R/clusterProfile.R inst/PhyloProfile/R/downloadFilteredCustomized.R inst/PhyloProfile/R/functions.R inst/PhyloProfile/R/createDetailedPlot.R inst/PhyloProfile/R/downloadFilteredMain.R inst/PhyloProfile/R/identifyCoreGene.R inst/PhyloProfile/R/getFastaDemo.R inst/PhyloProfile/R/groupComparison.R inst/PhyloProfile/R/resetTaxData.R inst/PhyloProfile/R/createArchitecturePlot.R inst/PhyloProfile/R/estimateGeneAge.R

inst/PhyloProfile/data/newTaxa.txt

inst/PhyloProfile/scripts/hmmscanParser.py

inst/PhyloProfile/scripts/pfamscanParser.py

inst/PhyloProfile/scripts/convert_oma_standalone_orthoxml.py

build/vignette.rds

tests/testthat.R tests/testthat/testParseMainInput.R tests/testthat/testEstimateGeneAge.R

tests/testthat/mainOrthoxmlTest.xml

tests/testthat/taxonomyMatrixTest.txt

tests/testthat/testCreateDataProfilePlot.R tests/testthat/testParseDomainInput.R tests/testthat/testIdentifyCoreGene.R

tests/testthat/mainWideTest.txt

tests/testthat/testParsePhyloProfile.R tests/testthat/testCreateDomainPlot.R

tests/testthat/mainFastaTest.txt

tests/testthat/testCreateTaxonomyMatrix.R tests/testthat/testCreateDistributionPlot.R

tests/testthat/taxonNamesTest.txt

tests/testthat/idListTest.txt

tests/testthat/rankListTest.txt

tests/testthat/testOMAparser.R

tests/testthat/domains/101621at6656.domains

vignettes/PhyloProfile-vignette.Rmd

vignettes/posterSub.png

data/idList.RData

data/ppTree.RData

data/filteredProfile.RData

data/profileWithTaxonomy.RData

data/mainLongRaw.RData

data/finalProcessedProfile.RData

data/rankList.RData

data/taxonomyMatrix.RData

data/ppTaxonomyMatrix.RData

data/superTaxonProfile.RData

data/taxonNamesReduced.RData

data/fullProcessedProfile.RData

man/dataCustomizedPlot.Rd man/varDistTaxPlot.Rd man/getDataClustering.Rd man/getCoreGene.Rd man/profileWithTaxonomy.Rd man/highlightProfilePlot.Rd man/rankList.Rd man/dataVarDistTaxGroup.Rd man/geneAgePlotDf.Rd man/createVariableDistributionDataSubset.Rd man/createPercentageDistributionData.Rd man/getInputTaxaName.Rd man/parseDomainInput.Rd man/clusterDataDend.Rd man/wideToLong.Rd man/parseInfoProfile.Rd man/checkOmaID.Rd man/getIDsRank.Rd man/mainTaxonomyRank.Rd man/getTaxonomyRanks.Rd man/getQualColForVector.Rd man/getSelectedTaxonNames.Rd man/ppTaxonomyMatrix.Rd man/getCommonAncestor.Rd man/calcPresSpec.Rd man/estimateGeneAge.Rd man/heatmapPlotting.Rd man/filteredProfile.Rd man/reduceProfile.Rd man/createProfileFromOma.Rd man/pairDomainPlotting.Rd man/getOmaDomainFromURL.Rd man/sortInputTaxa.Rd man/getAllFastaOma.Rd man/getDomainFolder.Rd man/getDendrogram.Rd man/rankIndexing.Rd man/gridArrangeSharedLegend.Rd man/getFastaFromFolder.Rd man/filterProfileData.Rd man/compareTaxonGroups.Rd man/createLongMatrix.Rd man/finalProcessedProfile.Rd man/getSelectedFastaOma.Rd man/singleDomainPlotting.Rd man/processNcbiTaxonomy.Rd man/compareMedianTaxonGroups.Rd man/distributionTest.Rd man/createGeneAgePlot.Rd man/getFastaFromFasInput.Rd man/qualitativeColours.Rd man/createVariableDistributionData.Rd man/createRootedTree.Rd man/getOmaMembers.Rd man/sortTaxaFromTree.Rd man/mainLongRaw.Rd man/getInputTaxaID.Rd man/getDataForOneOma.Rd man/taxa2dist.Rd man/sortDomains.Rd man/taxonomyTableCreator.Rd man/taxonomyMatrix.Rd man/getAllDomainsOma.Rd man/createArchiPlot.Rd man/getNameList.Rd man/fullProcessedProfile.Rd man/checkInputValidity.Rd man/getTaxonomyMatrix.Rd man/ppTree.Rd man/generateSinglePlot.Rd man/featureDistTaxPlot.Rd man/getFastaFromFile.Rd man/taxonNamesReduced.Rd man/fastaParser.Rd man/fromInputToProfile.Rd man/superTaxonProfile.Rd man/checkNewick.Rd man/dataFeatureTaxGroup.Rd man/getTaxonomyInfo.Rd man/createVarDistPlot.Rd man/runPhyloProfile.Rd man/idList.Rd man/getOmaDataForOneOrtholog.Rd man/xmlParser.Rd man/getDistanceMatrix.Rd man/dataMainPlot.Rd

PhyloProfile documentation built on March 27, 2021, 6:01 p.m.