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... |

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. |

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