Copy Number Profiling using Sequencing and CBS

BayesCptCI | Bayesian Point-wise Confidence Interval for Change-Point... |

CombineCaseControlC | Combine case and control reads |

CombineReadsAcrossRuns | Combine multiple read lists |

getAutoGridSize | Get Automatic Grid Sizes |

getCountsInWindow | Get number of reads in fixed-width window |

hppSimulate | Simulate a homogeneous Poisson Process |

JSSim_Meta | Meta File for Simulated Datasets |

JSSim_NormalSim1 | Simulated normal sample dataset 1 |

JSSim_NormalSim2 | Simulated normal sample dataset 2 |

JSSim_SpikeMat | True Signal Spike for the Simulated Dataset |

JSSim_TumorSim1 | Simulated Tumor sample dataset 1 |

JSSim_TumorSim2 | Simulated Tumor sample dataset 2 |

nhppRateEstimate | Estimate the rate of non-homogeneous PP with data |

nhppSimConstWindowAnalysis | Analyze the performance on simulation with constant signal... |

nhppSimConstWindowGen | Simulate a Non-Homogeneous PP with constant window spike |

nhppSimulate | Simulate a non-homogeneous Poisson Process |

nhppSpike | Spike rates of NHPP |

nhppSpikeConstWindow | Spike NHPP rate with constant window width |

readInput | Manage reading and merging of raw datasets. Main file input |

readListInputFile | Read meta file containing list of raw data files |

readSeq | Wrapper for managing the reading of different raw data... |

readSeqChiang | Read data formatted as in Chiang (2009) |

readSeqELANDPaired | Read raw data formatted as in paired ELAND output |

relCNComp | Compute the Relative Copy Number |

ScanBIC | Compute the modified BIC for change-point models |

ScanCBS | Main CBS Algorithm for Change-Point Detection |

ScanCBSPlot | Main Plotting of the scan statistic segmentation |

ScanCBSSimPlot | Plotting for CBS results of Simulated Data |

ScanIterateGrid | Main Scan with Iterative Grid Search |

ScanStatNewComp | Main new window scan statistics computation |

ScanStatRefineComp | Main refining window scan statistics computation |

SegSeqResProcess | Read and Process result of SegSeq |

seqCBS-package | Scan Statistics CNV detection using sequencing data |

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