OncoSimulR

Description

Functions for forward population genetic simulation in asexual populations, with special focus on cancer progression. Fitness can be an arbitrary function of genetic interactions between multiple genes or modules of genes, including epistasis, order restrictions in mutation accumulation, and order effects. Fitness (including just birth, just death, or both birth and death) can also be a function of the relative and absolute frequencies of other genotypes (i.e., frequency-dependent fitness). Mutation rates can differ between genes, and we can include mutator/antimutator genes (to model mutator phenotypes). Simulating multi-species scenarios and therapeutic interventions, including adaptive therapy, is also possible. Simulations use continuous-time models and can include driver and passenger genes and modules. Also included are functions for: simulating random DAGs of the type found in Oncogenetic Trees, Conjunctive Bayesian Networks, and other cancer progression models; plotting and sampling from single or multiple realizations of the simulations, including single-cell sampling; plotting the parent-child relationships of the clones; generating random fitness landscapes (Rough Mount Fuji, House of Cards, additive, NK, Ising, and Eggbox models) and plotting them.

Code

Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.

Topics

People

• Ramon Diaz-Uriarte author maintainer
• Guillaume Achaz contributor
• Harry Annoni contributor
• Rafael Barrero Rodriguez contributor
• Tim Beissbarth contributor
• Christian Bender contributor
• Yolanda Benitez Quesada contributor
• Sophie Brouillet contributor
• Marta Couce Iglesias contributor
• Cristina Devesa contributor
• Sara Dorado Alfaro contributor
• Niklas Endres contributor
• Asier Fernandez Pato contributor
• Luca Ferretti contributor
• Holger Froehlich contributor
• Jorge Garcia Calleja contributor
• Silvia Garcia Cobos contributor
• Guillermo Garcia Hoyos contributor
• Alberto Gonzalez Klein author
• Guillermo Gorines Cordero contributor
• Miguel Hernandez del Valle contributor
• Alejandro Herrador contributor
• Alvaro Huertas Garcia contributor
• Javier Lopez Cano author
• Esperanza Lopez Lopez contributor
• Ivan Lorca Alonso contributor
• Claudio Lottaz contributor
• Carlos Madariaga Aramendi contributor
• Matthias Maneck contributor
• Florian Markowetz contributor
• Alejandro Martin Mu~noz contributor
• Sebastian Matuszewski contributor
• Diego Ma~nanes Cayero contributor
• Juan Antonio Miguel Gonzalez author
• Javier Mu~noz Haro author
• Francisco Mu~noz Lopez contributor
• Theresa Niederberger contributor
• Rosalia Palomino Cabrera contributor
• Alberto Manuel Parra Perez contributor
• Arash Partow contributor
• Pablo Perez contributor
• Alvaro Quevedo contributor
• Ana Rodriguez Ronchel contributor
• David Roncero Moro~no contributor
• Lucia Sanchez Garcia contributor
• Sergio Sanchez-Carrillo author
• Silvia Talavera Marcos contributor
• Mark Taylor contributor
• Achim Tresch contributor
• Wolodzko Tymoteusz contributor
• Alejandro de los Reyes Benitez contributor
• Ana del Ramo Galian contributor