| addDummyProb | Create a dummy GRanges object as a placeholder in case nbh_em... |
| addPseudoAlignment | Add a psuedoalignment as a placeholder for the chromosome... |
| annotateRIP | Annotate RIP peaks with genomic information and perform GO... |
| binCount | Count reads in nonoverlapping bins across a chromosome |
| combineAlignGals | Combine alignment files into a single GAlignments 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... |
| empiricalFDR | Compute empirical false discovery rate |
| evalBinSize | Evaluate bin size using Shimazaki cost function |
| exportGRanges | Export GRanges object in a specified format |
| galp2gal | Convert GAlignmentPairs to GAlignments |
| getAlignGal | Import and processs in BAM/SAM/BED format |
| logScoreWithControl | Compute RIPScore based on RIP and control posteriors and test... |
| logScoreWithoutControl | Compute RIPScore based on RIP posteriors alone and test for... |
| mainSeek | Train HMM paramters on each chromosome independently from the... |
| mainSeekSingleChrom | Automatic bin size selection, bin count, and HMM parameters... |
| nbh | Generic function of negative binomial HMM |
| nbh_chk | Check the parameters of the negative binomial HMM |
| nbh_em | Expectation conditional maximization of negative binomial HMM... |
| nbh_gen | Simulate data from a negative binomial HMM. |
| nbh.GRanges | Optimize HMM parameters based on the read counts on a... |
| nbh_init | Initialize negative binomial HMM parameters using negative... |
| nbh.integer | HMM posterior decoding and NB parameter optimization |
| nbh_vit | Derive maximum likelihood hidden state sequence using Viterbi... |
| nbm_chk | Check the parameters of the negative binomial mixture model |
| nbm_em | Expectation conditional maximization of likelihood for... |
| 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... |
| ripSeek | HMM-based de novo RIP predictions using alignment data |
| RIPSeeker-package | RIPSeeker: a statistical package for identifying... |
| rulebaseRIPSeek | Compute the RPKM and foldchange between two conditions for... |
| scoreMergedBins | Average log odd scores over bins being merged into a single... |
| 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. |
