A Method to Search for Differentially Expressed Genes and to Detect Recurrent Chromosomal Copy Number Aberrations

bott | Example of sequencing data to test the rankReads function. |

calcSRmat | Calculation of the sorted rank matrix from the dataset |

calcSRmatMod | Calculation of the sorted rank matrix from the dataset |

cghData | Example of aCGH "data file" for the fcros package. |

cghInfo | Example of aCGH "info file" for the fcros package. |

chrMerge | Using a C code for merging chromosome segments |

chrPlot | Plot a chromosome data |

chrPlot2 | Plot a chromosome segmentation results |

chrSegment | Segmentation of a chromosome data |

dataSummary | Summarization of the detection results for a list of... |

fc2Calc | Calculation of fold change using pairwise comparison values |

fcros | Search for differentially expressed genes/probes |

fcros2 | Search for differentially expressed genes/probes |

fcrosFCmat | Calculation of a matrix of fold changes using pairwise... |

fcrosMod | Search for differentially expressed genes or to detect... |

fcros-package | A Method to Search for Differentially Expressed Genes and to... |

fcrosRead | Read a tab delimited text file |

fcrosTopN | Search for the top N changed genes or probes |

fcrosTtest | Student t-test for detecting differentially expressed genes |

fcrosWrite | Writing the fcros() or pfco() results in a tab delimited text... |

fdata | Example of dataset for the fcros package. |

fvalTopN | Search for the top N changed genes or probes using f-values |

fvalVolcanoPlot | Performs a volcano plot of the FCROS/PFCO statistics |

histoPlot | Histogram plot function of the fcros package results |

moyStdCalc | Calculation of the mean and the standard deviation of the... |

pfco | Searching for differentially expressed genes/probes using an... |

pfcoMod | Searching for differentially expressed genes or detecting... |

pvalTopN | Search for the top N changed genes or probes using p-values |

pvalVolcanoPlot | Performs a volcano plot of the FCROS/PFCO statistics |

rankReads | This function computes a score to assess the significance of... |

rmatCalc | Calculation of the FC matrix using pairwise comparisons |

rmatTrim | Calculation of the reduced matrix containing sorted rank... |

scoreThr | Determine numerically a threshold for the ranking score |

tcnReads | Performs a total count normalization of reads |

tprobaCalc | Calculation of the Student one sample test probabilities |

varBeta | Compute variance of a beta distribution from data |

voomReads | Transformation of read count values |

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