DivergenceExpressionSetExample
                        A standard DivergenceExpressionSet example
EarlyConservationTest   Perform the Reductive Early Conservation Test
FlatLineTest            Perform the Flat Line Test
MatchMap                Match a Phylostratigraphic Map or Divergence
                        Map with a ExpressionMatrix
PhyloExpressionSetExample
                        A standard PhyloExpressionSet example
PlotBarRE               Plot the mean relative expression levels as
                        barplot
PlotCorrelation         Plot the correlation between Phylostrata and
                        Divergence-Strata of a given PhyloExpressionSet
                        and DivergenceExpressionSet
PlotDistribution        Plot the frequency distribution of Phylostrata
                        or Divergence-Strata
PlotMeans               Plot the Mean Expression Profiles of
                        Phylostrata or Divergence-Strata
PlotPattern             Plot the Transcriptome Age Index or
                        Transcriptome Divergence Index
PlotRE                  Plot relative expression levels
RE                      Transform to relative expression levels
REMatrix                Compute relative expression profiles for
                        Phylostrata or Divergence-Strata available in a
                        PhyloExpressionSet or DivergenceExpressionSet
ReductiveHourglassTest
                        Perform the Reductive Hourglass Test
TAI                     Compute the Transcriptome Age Index (TAI)
TDI                     Compute the Transcriptome Divergence Index
                        (TDI)
age.apply               Age class specific apply function
bar.colors              Color palette for barplots
bootMatrix              Compute a permutation matrix for test
                        statistics
combinatorialSignificance
                        Compute the statistical significance of each
                        replicate combination
ecScore                 Compute the Hourglass Score for the
                        EarlyConservationTest
is.ExpressionSet        Testing the validaty of a PhyloExpressionSet or
                        DivergenceExpressionSet standard
omitMatrix              Compute TAI or TDI profiles omitting a given
                        gene
pMatrix                 Compute the partial TAI or TDI values for each
                        single gene in a standard PhyloExpressionSet or
                        DivergenceExpressionSet object
rhScore                 Compute the Hourglass Score for the Reductive
                        Hourglass Test
tf                      Transform the gene expression set of a given
                        PhyloExpressionSet or DivergenceExpressionSet
