BioConductor package for Forward Genetic Simulation of Cancer Progresion with Epistasis Long Description (required)
An R/BioConductor package that provides 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. Mutation rates can differ between genes, and we can include mutator/antimutator genes (to model mutator phenotypes). 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, and additive models) and plotting them. cancer, mutation, simulation, evolution, mutator, epistasis, fitness landscape, cancer progression models https://github.com/rdiaz02/OncoSimul rdiaz02@gmail.com
Step 1: Use the attribute tree to add new attributes or remove pre-selected attributes to describe the simulator.
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Summary of Proposed Changes Step 2: Review list of proposed attribute addition(s) and subtraction(s).
Can't Find the Attribute You Are Looking For? If you would like to propose an attribute that you cannot find in the tree above, or if you would like to add a clarification to one or more attributes for this simulator (e.g. a specific file format for attribute /Output/File Format/Other), please list them in the Additional Comment box of the Submit tab .
Summary of Proposed Changes Current Citations/Applications Schoen D, Schultz S ,
Somatic mutation and evolution in plants ,
Annual Review of Ecology, Evolution, and Systematics, vol. 50, in press ,
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, Application
Diaz-Uriarte R, Vasallo C ,
Every which way? On predicting tumor evolution using cancer progression models ,
bioRxiv ,
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https://doi.org/10.1101/371039, , Application
[Pubmed ID: 28186227 ],
Diaz-Uriarte R ,
OncoSimulR: genetic simulation with arbitrary epistasis and mutator genes in asexual populations. ,
Bioinformatics ,
06-15-2017 ,
https://www.ncbi.nlm.nih.gov/pubmed/?term=28186227, Primary Citation
[Pubmed ID: 29048486 ],
Diaz-Uriarte R ,
Cancer progression models and fitness landscapes: a many-to-many relationship. ,
Bioinformatics ,
03-01-2018 ,
https://www.ncbi.nlm.nih.gov/pubmed/?term=29048486, , Application