GO.groups               GO terms and genes
OU.invgamma.like.norm   Calculate the likelihood of normalized
                        comparative data as OUs with inverse gamma
                        distributed rates
OU.invgamma.sim.group   Simulate phylogenetic comparative data as OUs
                        with inverse gamma distributed rates
OU.vcv                  The variance covariance matrix for an
                        Ornstein-Uhlenbeck process
compute.sqrt.dist       Compute the vector of branch scaling parameters
dmvnorminvgamma         Compute the pdf for multi-variate
                        normal-inverse-gamma random variates
dnorminvgamma           Compute the pdf for normal-inverse-gamma random
                        variates
good.groups             Find groups represented in the data
mean_invgamma           The mean of the inverse gamma distribution
normalize.vcv           Compute the variance-covariance matrix of
                        normalized phylogenetic data
norminvgamma.shift.like.norm
                        Calculate the likelihood of normalized
                        comparative data as Brownian motions with
                        inverse gamma distributed rates
norminvgamma.shift.sim.group
                        Simulate phylogenetic comparative data as
                        Brownian motions with inverse gamma distributed
                        rates
plot_logfoldchange      Plot densities of expression differences,
                        possibly normalized
plot_wAICbarplot        Plot a barplot of AIC weights for each model
                        and each gene group
read.exp                Read gene expression data from a file, sorted
                        by a phylogenetic tree
read.groups             Read in the members of a gene group
remove.from.genome      Remove genes from a specified group from the
                        data
rnorminvgamma           Draw normal-inverse-gamma distributed random
                        variates
test.groups             Test all possible single-rate shift Brownian
                        motion models and an Ornstein-Uhlenbeck model
                        for an arbitrary number of predefined gene
                        groups.
test.subtrees           Test all possible single-rate shift Brownian
                        motion models and an Ornstein-Uhlenbeck model
var_invgamma            The variance of the inverse gamma distribution
yeast.homozygote        Yeast homozygote transcription profiles
yeast.hybrid            Yeast hybrid transcription profiles
yeast.tree              Phylogenetic tree of yeast species
