Intron-Exon Retention Estimator

addAnnotation | Adding sample annotations to a 'SummarizedExperiment' object |

annotateU12 | Annotate the U12 (and U2) type introns |

attributes | Extracting values of useful attributes of... |

boxplot-method | boxplot - method |

buildSsTypePwms | Building Position Weight Matrices for Splice Sites of U12 and... |

counts-method | Counts - method |

DEXSeqIntEREst | DEXSeq test for IntEREst object |

eBayesInterest | Limma based statistical test |

exactTestInterest | Exact test |

getRepeatTable | Get table of regions with repetetive DNA sequences |

glmInterest | generalized linear model likelihood ratio tests |

interest | Wrapper function: Parallel run |

IntEREst-package | IntEREst |

interestResult | Building SummarizedExperiment object from results in... |

interest.sequential | Wrapup function: Sequential running |

intexIndex | Extract index of intron or exon rows |

lfc | Log fold change |

mdsChr22Obj | Object of SummarizedExperiment type for MDS data |

mergeInterestResult | merge two SummarizedExperiment objects into one |

plot-method | plot - method |

pwmU12db | PWM of U12 and U2-type introns splice sites |

qlfInterest | quasi-likelihood F-test |

readInterestResults | Read interest/interest.sequential results text files |

referencePrepare | Creates reference file |

subInterestResult | Extract subset of object |

treatInterest | Differential retention test relative to a threshold |

u12 | U12 data |

u12Boxplot | U12 boxplot |

u12BoxplotNb | boxplot U12 introns retention levels (or flanking exons... |

u12DensityPlot | Density plot of fld changes of intron retention and exon-exon... |

u12Index | Extract index of U12 introns rows |

u12NbIndex | Extract index of U2 introns (up/down)stream of U12 introns... |

unionRefTr | Union introns/exons of transcripts |

updateRowDataCol | Updating contents of 'rowData' of 'SummarizedExperiment'... |

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