# RIPSeeker: a statistical package for identifying protein-associated transcripts from RIP-seq experiments

## Documentation for package ‘RIPSeeker’ version 1.8.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

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 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 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 GAlignmentPairs to GAlignments
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
RIPSeeker | RIPSeeker: a statistical package for identifying protein-associated transcripts from RIP-seq experiments
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.