addDimRedTaxaColors     Add colors for taxa in dimension reduction plot
addFeatureColors        Add colors for each feature/domain
addRankDivisionPlot     Add taxonomy rank division lines to the heatmap
                        plot
calcPresSpec            Calculate percentage of present species in each
                        super taxon
checkColorPalette       Check if a color pallete has enough colors for
                        a list of items
checkInputValidity      Check the validity of the input phylogenetic
                        profile file
checkNewick             Check the validity of input newick tree
checkOmaID              Check the validity of input OMA IDs
checkOverlapDomains     Identify feature type(s) containing overlapped
                        domains/features
clusterDataDend         Create a hclust object from the distance matrix
compareMedianTaxonGroups
                        Compare the median values of a variable between
                        2 taxon groups
compareTaxonGroups      Compare the score distributions between 2 taxon
                        groups
createArchiPlot         Create protein's domain architecure plot
createDimRedPlotData    Generate data for dimension reduction plot
createGeneAgePlot       Create gene age plot
createLongMatrix        Create a long matrix format for all kinds of
                        input phylogenetic profiles
createPercentageDistributionData
                        Create data for percentage present taxa
                        distribution
createProfileFromOma    Create a phylogenetic profile from a raw OMA
                        dataframe
createUnrootedTree      Create unrooted tree from a taxonomy matrix
createVarDistPlot       Create distribution plot
createVariableDistributionData
                        Create data for additional variable
                        distribution
createVariableDistributionDataSubset
                        Create data for additional variable
                        distribution (for a subset data)
dataCustomizedPlot      Create data for customized profile plot
dataFeatureTaxGroup     Create data for feature distribution comparison
                        plot
dataMainPlot            Create data for main profile plot
dataVarDistTaxGroup     Create data for variable distribution
                        comparison plot
dimReduction            Perform dimension reduction 2D
distributionTest        Compare the distribution of 2 numeric vectors
estimateGeneAge         Calculate the phylogenetic gene age from the
                        phylogenetic profiles
fallbackUmap            Fallback for UMAP in case of insufficient
                        samples
fastaParser             Parse multi-fasta input file
featureDistTaxPlot      Create feature distribution comparison plot
filterProfileData       Filter phylogentic profiles
filteredProfile         An example of a filtered phylogenetic profile
finalProcessedProfile   An example of a final processed & filtered
                        phylogenetic profile
fromInputToProfile      Complete processing of raw input phylogenetic
                        profiles
fullProcessedProfile    An example of a fully processed phylogenetic
                        profile
geneAgePlotDf           Create data for plotting gene ages
generateSinglePlot      Create a single violin distribution plot
getAllDomainsOma        Create domain annotation dataframe from a raw
                        OMA dataframe
getAllFastaOma          Get all fasta sequences from a raw OMA
                        dataframe
getCommonAncestor       Get all taxa that share a common ancestor
getCoreGene             Identify core genes for a list of selected taxa
getDataClustering       Get data for calculating distance matrix from
                        phylogenetic profiles
getDataForOneOma        Get OMA info for a query protein and its
                        orthologs
getDendrogram           Plot dendrogram tree
getDistanceMatrix       Calculate the distance matrix
getDomainFolder         Get domain file from a folder for a seed
                        protein
getFastaFromFasInput    Get fasta sequences from main input file in
                        multi-fasta format
getFastaFromFile        Get fasta sequences from main input file in
                        multi-fasta format
getFastaFromFolder      Get fasta sequences
getIDsRank              Get taxonomy info for a list of taxa
getInputTaxaID          Get ID list of input taxa from the main input
getInputTaxaName        Get NCBI taxon names for a selected list of
                        taxa
getNameList             Get list of pre-installed NCBI taxon names
getOmaDataForOneOrtholog
                        Get taxonomy ID, sequence and annotation for
                        one OMA protein
getOmaDomainFromURL     Get domain annotation from OMA Browser
getOmaMembers           Get OMA members
getQualColForVector     Get color for a list of items
getSelectedFastaOma     Get selected fasta sequences from a raw OMA
                        dataframe
getSelectedTaxonNames   Get a subset of input taxa based on a selected
                        taxonomy rank
getTaxHierarchy         Get taxonomy hierarchy for a list of taxon IDs
getTaxonomyInfo         Get taxonomy info for a list of input taxa
getTaxonomyMatrix       Get taxonomy matrix
getTaxonomyRanks        Create a list containing all main taxanomy
                        ranks
gridArrangeSharedLegend
                        Plot Multiple Graphs with Shared Legend in a
                        Grid
groupLabelDimRedData    Reduce the number of labels for DIM reduction
                        plot based on the gene/taxon frequency
heatmapPlotting         Create profile heatmap plot
heatmapPlottingFast     Create profile heatmap plot using scattermore
highlightProfilePlot    Highlight gene and/or taxon of interest on the
                        phylogenetic profile plot
id2name                 Get taxon names for a list of taxon IDs
idList                  NCBI ID list for experimental data sets
joinPlotMergeLegends    Join multiple plots and merge legends
linearizeArchitecture   Linearize PFAM/SMART annotations by best
                        e-value/bitscore
mainLongRaw             An example of a raw long input file
mainTaxonomyRank        Get all NCBI taxonomy rank names
modifyFeatureName       Modify feature names
pairDomainPlotting      Create architecure plot for a pair of seed and
                        ortholog protein
parseDomainInput        Parse domain input file
parseInfoProfile        Parsing info for phylogenetic profiles
performPCA              Helper function to perform PCA
performUmap             Helper function to handle UMAP logic
plotDimRed              Create dimension reduction plot
plotDimRed3D            Create dimension reduction 3D plot
ppTaxonomyMatrix        An example of a taxonomy matrix
ppTree                  An example of a taxonomy tree in newick format
prepareDimRedData       Prepare data for dimension reduction
processNcbiTaxonomy     Pre-processing NCBI taxonomy data
processOrthoID          Process ortholog IDs
profileWithTaxonomy     An example of a raw long input file together
                        with the taxonomy info
qualitativeColours      Create qualitative colours
rankIndexing            Indexing all available ranks (including norank)
rankList                NCBI rank list for experimental data sets
reduceProfile           Reduce the filtered profile data into
                        supertaxon level
resolveOverlapFeatures
                        Modify domain dataframe to resolve overlapped
                        domains/features
runPhyloProfile         Run PhyloProfile app
singleDomainPlotting    Create architecure plot for a single protein
sortDomains             Sort one domain dataframe based on the other
                        domain dataframe
sortDomainsByList       Sort one domain dataframe based on list of
                        ordered feature types
sortInputTaxa           Sort list of (super)taxa based on a selected
                        reference (super)taxon
sortTaxaFromTree        Get sorted supertaxon list based on a rooted
                        taxonomy tree
taxa2dist               taxa2dist
taxonNamesReduced       NCBI Taxonomy reduced data set
taxonomyMatrix          Taxonomy matrix for experimental data sets
taxonomyTableCreator    Align NCBI taxonomy IDs of list of taxa into a
                        sorted rank list.
varDistTaxPlot          Create variable distribution comparison plot
wideToLong              Transform input file in wide matrix into long
                        matrix format
xmlParser               Parse orthoXML input file
