CollapseReplicates      Combine Replicates in an ExpressionSet
CombinatorialSignificance
                        Compute the Statistical Significance of Each
                        Replicate Combination
DiffGenes               Differential Gene Expression Analysis
DivergenceExpressionSetExample
                        An Example DivergenceExpressionSet Data Set
EarlyConservationTest   Perform Reductive Early Conservation Test
EnrichmentTest          Phylostratum or Divergence Stratum Enrichment
                        of a given Gene Set based on Fisher's Test
Expressed               Filter for Expressed Genes
FlatLineTest            Perform Flat Line Test
GroupDiffs              Quantify the significant differences between
                        gene expression distributions of age groups
MatchMap                Match a Phylostratigraphic Map or Divergence
                        Map with a ExpressionMatrix
PhyloExpressionSetExample
                        An Example PhyloExpressionSet Data Set
PlotBarRE               Plot Mean Relative Expression Levels as Barplot
PlotCIRatio             Plot Transcriptome Index using bootstrapping
                        and confidence intervals
PlotCategoryExpr        Plot the Expression Levels of each Age or
                        Divergence Category as Boxplot, Violinplot, or
                        Dotplot
PlotContribution        Plot Cumuative Transcriptome Index
PlotCorrelation         Plot the Correlation Between Phylostrata and
                        Divergence Strata
PlotDistribution        Plot the Frequency Distribution of Phylostrata
                        or Divergence Strata
PlotEnrichment          Plot the Phylostratum or Divergence Stratum
                        Enrichment of a given Gene Set
PlotGeneSet             Plot the Expression Profiles of a Gene Set
PlotGroupDiffs          Plot the significant differences between gene
                        expression distributions of PS or DS groups
PlotMeans               Plot Mean Expression Profiles
PlotMedians             Plot Median Expression Profiles
PlotPattern             Plot the Transcriptome Age Index or
                        Transcriptome Divergence Index
PlotRE                  Plot Relative Expression Levels
PlotReplicateQuality    Plot the Quality of Biological Replicates
PlotSelectedAgeDistr    Plot the PS or DS distribution of a selected
                        set of genes
PlotSignature           Plot evolutionary signatures across
                        transcriptomes
PlotVars                Plot Variance of Expression Profiles
RE                      Transform to Relative Expression Levels
REMatrix                Compute a Relative Expression Matrix
ReductiveHourglassTest
                        Perform the Reductive Hourglass Test
ReverseHourglassTest    Perform the Reverse Hourglass Test
SelectGeneSet           Select a Subset of Genes in an ExpressionSet
TAI                     Compute the Transcriptome Age Index (TAI)
TDI                     Compute the Transcriptome Divergence Index
                        (TDI)
TPI                     Compute the Transcriptome Polymorphism Index
                        (TPI)
age.apply               Age Category Specific apply Function
bar.colors              Color palette for barplots
bootMatrix              Compute a Permutation Matrix for Test
                        Statistics
ecScore                 Compute the Hourglass Score for the
                        EarlyConservationTest
geom.mean               Geometric Mean
harm.mean               Harmonic Mean
is.ExpressionSet        Test ExpressionSet Standard
omitMatrix              Compute TAI or TDI Profiles Omitting a Given
                        Gene
pMatrix                 Compute Partial TAI or TDI Values
pStrata                 Compute Partial Strata Values
pTAI                    Compute the Phylostratum Contribution to the
                        Global Transcriptome Age Index
pTDI                    Compute the Divergence Stratum Contribution to
                        the Global Transcriptome Divergence Index
reversehourglassScore   Compute the Reverse Hourglass Score for the
                        Reverse Hourglass Test
rhScore                 Compute the Hourglass Score for the Reductive
                        Hourglass Test
taxid                   Retrieve taxonomy categories from NCBI Taxonomy
taxonomy                Retrieving Taxonomic Information of a Query
                        Organism
tf                      Transform Gene Expression Levels
