RIPSeeker-package       RIPSeeker: a statistical package for
                        identifying protein-associated transcripts from
                        RIP-seq experiments
addDummyProb            Create a dummy GRanges object as a placeholder
                        in case nbh_em fails (Internal function)
addPseudoAlignment      Add a psuedoalignment as a placeholder for the
                        chromosome (Internal function)
annotateRIP             Annotate RIP peaks with genomic information and
                        perform GO enrichement
binCount                Count reads in nonoverlapping bins across a
                        chromosome
combineAlignGals        Combine alignment files into a single
                        GappedAlignment object
combineRIP              Combined predictions from (presumably)
                        biological replicates.
computeLogOdd           Compute the log odd ratio of RIP over
                        background.
computeRPKM             Compute RPKM based on gene annotations
disambiguateMultihits   Assign each multihit to a unique region based
                        on the posterior for the read-enriched hidden
                        state
empiricalFDR            Compute empirical false discovery rate
evalBinSize             Evaluate bin size using Shimazaki cost function
exportGRanges           Export GRanges object in a specified format
galp2gal                Convert GappedAlignmentPairs to
                        GappedAlignments
getAlignGal             Import and processs in BAM/SAM/BED format
logScoreWithControl     Compute RIPScore based on RIP and control
                        posteriors and test for significance
logScoreWithoutControl
                        Compute RIPScore based on RIP posteriors alone
                        and test for significance
mainSeek                Train HMM paramters on each chromosome
                        independently from the alignments.
mainSeekSingleChrom     Automatic bin size selection, bin count, and
                        HMM parameters optimization on read count
                        vector from a single chromosome (Internal
                        function)
nbh                     Generic function of negative binomial HMM
nbh.GRanges             Optimize HMM parameters based on the read
                        counts on a chromosome
nbh.integer             HMM posterior decoding and NB parameter
                        optimization
nbh_chk                 Check the parameters of the negative binomial
                        HMM
nbh_em                  Expectation conditional maximization of
                        negative binomial HMM parameters using
                        forward-backward algorithm
nbh_gen                 Simulate data from a negative binomial HMM.
nbh_init                Initialize negative binomial HMM parameters
                        using negative binomial mixture model
nbh_vit                 Derive maximum likelihood hidden state sequence
                        using Viterbi algorithm
nbm_chk                 Check the parameters of the negative binomial
                        mixture model
nbm_em                  Expectation conditional maximization of
                        likelihood for negative binomial mixture model
plotCoverage            Plot read coverage for a GRanges object
plotStrandedCoverage    Plot strand-specific read coverage for a
                        GRanges object
randindx                Generates random indexes with a specified
                        probability distribution
ripSeek                 HMM-based de novo RIP predictions using
                        alignment data
rulebaseRIPSeek         Compute the RPKM and foldchange between two
                        conditions for the annotated genes
scoreMergedBins         Average log odd scores over bins being merged
                        into a single region
seekRIP                 Identify significant peaks
selectBinSize           Select optimal bin size based on Shimazaki
                        formula
statdis                 Returns the stationary distribution of a Markov
                        chain.
viewRIP                 Visualize peaks from UCSC genome browser.
