goldmine: Genomic context annotation for any set of genomic ranges using UCSC Genome Browser tables

Global functions | |
---|---|

addGenes | Man page Source code |

addNearest | Man page Source code |

calcOverlapForReport | Source code |

calcOverlapForReportExons | Source code |

calcPercentOverlap | Source code |

drawGenomePool | Man page Source code |

get3primeUTROverlap | Source code |

getBrowserURLs | Source code |

getCpgFeatures | Man page Source code |

getDistTSE | Source code |

getDistTSECenter | Source code |

getDistTSS | Source code |

getDistTSSCenter | Source code |

getDownstreamOverlap | Source code |

getExonOverlap | Source code |

getFeatures | Man page Source code |

getFreqCpG | Source code |

getGeneModels | Man page Source code |

getGenes | Man page Source code |

getGenicOverlap | Source code |

getGenicOverlapGenes | Source code |

getRepeatPercent | Source code |

getRepeatPercentFast | Source code |

getTableHeaderFromSQL | Source code |

getUCSCTable | Man page Source code |

getUpstreamOverlap | Source code |

ggnice | Man page Source code |

gmWrite | Man page Source code |

goldmine | Man page Source code |

goldmine-package | Man page |

makeDT | Man page Source code |

makeGRanges | Man page Source code |

parseExons | Source code |

read.table.ucsc | Source code |

read.table.ucsc.big | Source code |

readRepeatMasker | Source code |

readUCSCAnnotation | Man page Source code |

sortDT | Man page Source code |

sortGRanges | Man page Source code |

syncUCSCTable | Source code |

writeBEDFromGRanges | Man page Source code |

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