HPDplot                 Plotting fixed effects for all genes for a
                        single combination of factors
HPDplotBygene           Plots qPCR analysis results for individual
                        genes.
HPDplotBygeneBygroup    Plots qPCR analysis results for individual
                        genes
HPDpoints               HPDplot, HPDpoints
HPDsummary              Summarizes and plots results of mcmc.qpcr
                        function series.
MCMC.qpcr               Bayesian analysis of qRT-PCR data
PrimEff                 Determines qPCR amplification efficiencies from
                        dilution series
amp.eff                 amplification efficiencies and experimental Cq1
                        (optional column)
beckham.data            Cellular heat stress response data.
beckham.eff             amplification efficiencies for beckham.data
coral.stress            RT-qPCR of stress response in coral Porites
                        astreoides
cq2counts               Prepares qRT-PCR data for mcmc.qpcr analysis
cq2genorm               Reformats raw Ct data for geNorm analysis
                        (non-parametric selection of stable control
                        genes) as implemented in selectHKgenes function
                        (package SLqPCR)
cq2log                  Prepares qRT-PCR data for mcmc.qpcr analysis
                        using lognormal and "classic"
                        (normalization-based) models
diagnostic.mcmc         Plots three diagnostic plots to check the
                        validity of the assumptions of linear model
                        analysis.
dilutions               Data to determine amplification efficiency
getNormalizedData       Extracts qPCR model predictions
mcmc.converge.check     MCMC diagnostic plots
mcmc.pval               calculates p-value based on Bayesian z-score or
                        MCMC sampling
mcmc.qpcr               Analyzes qRT-PCR data using generalized linear
                        mixed model
mcmc.qpcr.classic       Analyzes qRT-PCR data using "classic" model,
                        based on multigene normalization.
mcmc.qpcr.lognormal     Fits a lognormal linear mixed model to qRT-PCR
                        data.
normalize.qpcr          Internal function called by mcmc.qpcr.classic
outlierSamples          detects outlier samples in qPCR data
padj.hpdsummary         Adjusts p-values within an HPDsummary() object
                        for multiple comparisons
padj.qpcr               Calculates adjusted p-values corrected for
                        multiple comparisons
softNorm                Accessory function to mcmc.qpcr() to perform
                        soft normalization
summaryPlot             Wrapper function for ggplot2 to make bar and
                        line graphs of mcmc.qpcr() results
trellisByGene           For two-way designs, plots mcmc.qpcr model
                        predictions gene by gene
