RgammaMLE               RgammaMLE fits a gamma distribution to a
                        specified data vector using maximum likelihood.
Rnorm                   Rnorm fits a normal distribution to a specified
                        data vector using maximum likelihood.
Rnorm.exp               Rnorm.exp fits a normal+exponential
                        distribution to a specified data vector using
                        maximum likelihood.
averagePlot             Returns the average profile of tiling array
                        probe intensity values or wiggle-like count
                        data centered on a set of genomic positions
                        (specified by 'Peaks').
breakTranscriptsOnGenes
                        breakTranscriptsOnGenes Breaks transcripts on
                        genes
combineTranscripts      combineTranscripts Combines transnscipts.
countMappableReadsInInterval
                        countMappableReadsInInterval counts the number
                        of mappable reads in a set of genomic features.
detectTranscripts       detectTranscripts detects transcripts de novo
                        using a two-state hidden Markov model (HMM).
evaluateHMMInAnnotations
                        evaluateHMM Evaluates HMM calling.
expressedGenes          Function identifies expressed features using
                        the methods introduced in Core, Waterfall, Lis;
                        Science, Dec. 2008.
getCores                Returns the number of cores.
getTxDensity            getTxDensity Calculates transcript density.
groHMM-package          groHMM: GRO-seq Analysis Pipeline
limitToXkb              limitToXkb truncates a set of genomic itnervals
                        at a constant, maximum size.
makeConsensusAnnotations
                        makeConsensusAnnotations Makes a consensus
                        annotation
metaGene                Returns a histogram of the number of reads in
                        each section of a moving window centered on a
                        certain feature.
metaGeneMatrix          Returns a matrix, with rows representing read
                        counts across a specified gene, or other
                        features of interest.
metaGene_nL             Returns a histogram of the number of reads in
                        each section of a moving window of #' variable
                        size across genes.
pausingIndex            Returns the pausing index for different genes.
                        TODO: DESCRIBE THE PAUSING INDEX.
polymeraseWave          Given GRO-seq data, identifies the location of
                        the polymerase 'wave' in up- or down- regulated
                        genes.
readBed                 readBed Returns a GenomicRanges object
                        constrcuted from the specified bed file.
runMetaGene             Runs metagene analysis for sense and antisense
                        direction.
tlsDeming               A 'total least squares' implementation using
                        demming regression.
tlsLoess                A 'total least squares'-like hack for LOESS.
                        Works by rotating points 45 degrees, fitting
                        LOESS, and rotating back.
tlsSvd                  A 'total least squares' implementation using
                        singular value demposition.
windowAnalysis          windowAnalysis Returns a vector of integers
                        representing the counts of reads in a moving
                        window.
writeWiggle             writeWiggle writes a wiggle track or BigWig
                        file suitable for uploading to the UCSC genome
                        browser.
