Clustering of Single Cell Sequencing Copy Number Profiles to Identify Clones

calc_bins2regions | Converts list of bins from binning scheme to regions. |

calc_centroareas | Calculates centromere regions (areas). |

calc_pinmat | Select features and generate the incidence table. |

calc_ploidies | Calculates ploidies for samples passed in 'segment_df'. |

calc_regions2bins | Converts regions to list of bins from binning scheme. |

case_filenames | Constructs names for various output files based on... |

chrom_numeric | Converts chrom name to numeric and adds 'chrom.numeric'... |

find_clones | Identify nodes in a hierarchical tree which qualify as... |

find_subclones | Identify subclones in a clonal branch of a hierarchical tree. |

fisher_dist | Calculates a distance matrix given Fisher FDR true p-values. |

fisher_fdr | Compute FDRs for Fisher's test p-values. |

hclust_tree | Build the hierarchical clustering tree. |

segment_varbin_files | Generate the segmented profile for each cell. |

sgains_pipeline | Integration with 'sGAINS' tool. |

sim_fisher_wrapper | Simulate the Fisher's test p-values. |

tree_py | Builds HC tree representation based on the distance matrix... |

varbin_input_files | Collects all bin count files from given directory |

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