Repeated Evolution in Cancer (REVOLVER)

Breast.fit | Fit from the Yates et al. cohort of Breast cancers, with... |

CRC | Colorectal Cancer Data by Cross et al. |

CRC.cohort | Colorectal Cancer Data by Cross et al., in the cohort format... |

jamPDF | PDF jamming function |

plot.rev_cohort | Plot data and trees for a REVOLVER cohort. |

plot.rev_cohort_fit | Plot fits from a REVOLVER cohort. |

plot.rev_phylo | S3 method calling 'revolver_plt_tree'. |

print.rev_cohort | Print a '"rev_cohort"' object |

print.rev_cohort_fit | Print a REVOLVER cohort object with fits. |

print.rev_phylo | Print a '"rev_phylo"' object. |

revolver_analyzer | Wrapper for a full analysis with REVOLVER This is convenient... |

revolver_check_cohort | Check basic inconsistencies in a REVOLVER cohort. |

revolver_cluster | Compute hierarchical clustering for a REVOLVER cohort |

revolver_cohort | Construct a REVOLVER cohort object (S3 class '"rev_cohort"'). |

revolver_compute_CLtrees | Compute/ add mutation trees to a REVOLVER cohort. |

revolver_compute_phylogenies | Compute/ add CCF-based phylogenies to a REVOLVER cohort. |

revolver_deletePatients | Subset the patients in the cohort to match the input list. |

revolver_DETindex | helper function to calculate diversity indices |

revolver_dumpStatistics | Dump statistics for fit to an Excel file. |

revolver_evo_distance | Compute REVOLVER's evolutionary distance h(P_i, P_j). |

revolver_fit | REVOLVER fit function. |

revolver_infoclustering | Compute possible clusterings for standard parameters. |

revolver_jackknife | Computation of fit confidence with the jackknife. |

revolver_phylogeny | REVOLVER constructor for an object of type "rev_phylo": a... |

revolver_plt_compare_dendrograms | Plot the comparison among REVOLVER's clusters and the one... |

revolver_plt_dendrogram | Plot the dendrogram for REVOLVER's clusters. |

revolver_plt_DET_index | Plot the DET index, via non parametric bootstrap. |

revolver_plt_DET_index_driver | Plot the DET index of each driver from the data (empirical). |

revolver_plt_evodistance | Plot REVOLVER's evolutionary distance, in a heatmap. |

revolver_plt_fit_by_group | Plot model fit grouped by cluster. |

revolver_plt_fit_patient | Plot the tree fit for a patient. |

revolver_plt_group_trajectories | Plot the consensus model of the trajectories/ |

revolver_plt_itransfer_patient | Plot the information transfer from a patient's fit. |

revolver_plt_jackknife_coclust | Plot jackknife statistics for co-clustering (heatmap). |

revolver_plt_jackknife_coclust_bplot | Plot jackknife statistics for co-clustering (boxplot). |

revolver_plt_jackknife_edge_counts | Plot jackknife statistics for the number of patients with an... |

revolver_plt_jackknife_edge_prb | Plot jackknife statistics for edge detection probability. |

revolver_plt_patient_data | Plot a patient's data |

revolver_plt_patient_trees | Plot a the top-scoring trees for a patient. |

revolver_plt_patient_trees_scores | Plot the scores for the trees of each patient. |

revolver_plt_penalty_barplot | Plot a barplot of the penalty per patient. |

revolver_plt_penalty_matrix | Plot a pheatmap of the penalty (patients per alterations) . |

revolver_plt_rbannerplot | Bannerplot for REVOLVER's clusters. |

revolver_plt_rclusters | Plot the features of REVOLVER's clusters, in a heatmap. |

revolver_plt_trajectories_patient | Plot the trajectories in a patient's fit model. |

revolver_plt_tree | Plot a phylogenetic or a mutation tree for a patient. |

revolver_removeDriver | Remove a driver event from a cohort. |

revolver_report_fit_patient | Generate PDF report for a patient's fit |

revolver_report_patient | Generate PDF report for a patient's data and trees |

revolver_subsetDrivers | Subset the drivers in the cohort to match the input list. |

stats.rev_phylo | Compute statistics for a '"rev_phylo"' tree. |

summary.rev_phylo | Summary of a '"rev_phylo"' object. |

TRACERx | TRACERx mutation and CNAs Data by Jamal-Hanjani et al.,... |

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