ChIPseqSet-class        Class '"ChIPseqSet"'
MixModel-class          Class '"MixModel"'
MixModelBayes-class     Class '"MixModelBayes"'
MixModelML-class        Class '"MixModelML"'
MixtureComponent-class
                        Class '"MixtureComponent"'
bayesMixModel           Fits a Bayesian mixture model using Markov
                        Chain Monte Carlo (MCMC) methods
calculateCrossCorrelation
                        Calculate the cross correlation for a given
                        GRanges object.
eSet                    Example gene expression data set.
fpkm                    Example RNA-seq data set.
getAlignmentQuality     Calculation of basic alignments statistics
integrateData           Calculates a normalized correlation score from
                        ChIP-seq and microarray gene expression data.
mappedReads             Mapped reads obtained from a anti-histone
                        ChIP-seq experiment.
matchProbeToPromoter    A function assigning promoter regions to given
                        probe IDs.
mlMixModel              Fits a mixture model using the maximum
                        likelihood principle.
normalize               Normalization of ChIP-seq and other count data
normalizeChIP           Normalization of ChIP-seq count data.
                        (deprecated)
plotChains              Produces trace plots for a Bayesian mixture
                        model
plotClassification      Plot classification obtained from a mixture
                        model.
plotComponents          Plots the mixture density together with the
                        densities of all single components.
summarizeReads          Count reads lying within given regions.
transToTSS              A data frame with Ensemble transcript IDs and
                        transcriptional start sites.
