Genes Under Selection In Tumors

append.info | Merge selection coefficients, spatial concentration,... |

check.gene.consv.all | Retreve fitch rate for each position of a protein. |

check.gene.mut | Retreve somatic mutations of a gene from one or more tumor... |

compute.fitch.stats | Compute statistics related to evolutionary conservation |

compute.selection | Estimate selection coefficients of missense mutations and... |

compute.selection.stats | Compute statistics related to somatic selection |

compute.spatial.stats | Compute statistics related to mutational spatial... |

condense.type | Combine reciprocal mutation types |

correct.small.sample.bias | Correct biases for genes with too few somatic variants. |

find.outliers | Find hypo- and hyper-mutated samples |

find_peaks | Detect mutational hotspots |

get.exp | Get expected counts of variants for a vector of gene symbols |

get.opt.genes | Estimate selection coefficients |

gust | Perform GUST classification of oncogens, tumor suppressor... |

initialize.gust | Prepare data for GUST classification return a list of data... |

make.prediction | Predict oncogenes, tumor suppressor genes and passenger... |

organize.obs | Organize a collection of variants in a gene into counts |

parse.aggregated.mut | Parse the VCF file to aggregate variants by genes and... |

plot.multiple | Plot distribution of somatic mutations of multiple genes. |

plot.mut | Plot distribution of somatic mutations. |

plot.this.one | Plot distribution of somatic mutations of a gene. |

prob | optimization function to estimate independent probabilities... |

prob.joint | optimization function to estimate joint probabilities of... |

prob.joint.indel | optimization function to estimate joint probabilities of... |

reformat | Reformat a data frame to be suitable for modeling. |

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