Code

ecDNA simulator#240

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Merged

mattjones315 merged 42 commits intomasterYosefLab/Cassiopeia:masterfrom ecdna-simulatorYosefLab/Cassiopeia:ecdna-simulatorCopy head branch name to clipboardMay 8, 2024

+1,766-202,252

Commits

Commits on Jul 18, 2022

• inited ecdna birth death simulator.py

  

  Matthew Gregory Jones

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  Matthew Gregory Jones

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Commits on Jul 27, 2022

• updated BirthDeathFitnessSimulator for more flexibility

  jpdsilva

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Commits on Aug 12, 2022

• ecDNABirthDeathSimulator is broken / in process of

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  jpdsilva

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• i don't think ecDNABirthDeathSimulator compiles, trying to add random seg. to it

  jpdsilva

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• added ecdna simulator first pass, some tests started

  

  Matthew Gregory Jones

  authored and

  Matthew Gregory Jones

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• added ecdna simulator first pass, some tests started

  

  Matthew Gregory Jones

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  Matthew Gregory Jones

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Commits on Aug 22, 2022

• debugging ecDNABirthDeathSimulator.py

  jpdsilva

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• continuing to debug / clean up ecDNABirthDeathSimulator.py, working on neutral model tests in notebooks

  jpdsilva

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• Delete ecDNABirthDeathSimulator_v2.py

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Commits on Aug 24, 2022

• added unit tests for ecDNABirthDeathSimulator.py

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  jpdsilva

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• Merge branch 'ecdna-simulator' of https://github.com/YosefLab/Cassiopeia into ecdna-simulator

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  jpdsilva

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Commits on Aug 26, 2022

• added CN-depdt fitness with epistasis

  jpdsilva

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• small notes indicating where we want to make changes

  

  Matthew Gregory Jones

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  Matthew Gregory Jones

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Commits on Aug 31, 2022

• implemented populate tree from simulation

  

  Matthew Gregory Jones

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  Matthew Gregory Jones

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• wrote more tests

  

  Matthew Gregory Jones

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  Matthew Gregory Jones

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Commits on Sep 1, 2022

• adding metadata to tree and cleaning up ecDNA_sim_test

  jpdsilva

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• edits to notebook

  jpdsilva

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• Merge branch 'ecdna-simulator' of https://github.com/YosefLab/Cassiopeia into ecdna-simulator

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Commits on Sep 5, 2022

• added functionality for simulating cooperativity

  

  Matthew Gregory Jones

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  Matthew Gregory Jones

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• updated simulation for cooperativity

  

  Matthew Gregory Jones

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  Matthew Gregory Jones

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Commits on Sep 7, 2022

• bug fix in cooperativity sim

  

  Matthew Gregory Jones

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  Matthew Gregory Jones

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• added tests for cosegregation

  

  Matthew Gregory Jones

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  Matthew Gregory Jones

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Commits on Sep 30, 2022

• added binomial noise model

  

  Matthew Gregory Jones

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  Matthew Gregory Jones

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Commits on Dec 1, 2022

• sped up simulator

  

  Matthew Gregory Jones

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  Matthew Gregory Jones

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Commits on Apr 12, 2023

• updates for ecDNA drug perturbation simulation

  

  Matthew Gregory Jones

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  Matthew Gregory Jones

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Commits on Apr 12, 2024

• cleanup

  mattjones315

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• Merge branch 'master' of github.com:YosefLab/Cassiopeia into ecdna-simulator

  mattjones315

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• updated format

  mattjones315

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Commits on Apr 13, 2024

• fixed tests

  mattjones315

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• reverted back to PriorityQueue

  mattjones315

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• moved ecDNA simulator back to PriorityQueue

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Commits on Apr 14, 2024

• rebuilding docs

  mattjones315

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• added ecDNA simulator to user guide

  mattjones315

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• added ecDNA simulator to user guide

  mattjones315

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• added ecDNA notebook

  mattjones315

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• added ecDNA notebook

  mattjones315

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Commits on Apr 15, 2024

• updated notebooks

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• updated notebooks

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Commits on May 8, 2024

• updated formatting issues and docs in birthdeathfitnessimulator

  mattjones315

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• covered edge case where no birth scale is in initial tree

  mattjones315

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• updated docs

  mattjones315

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• removed old unused code

  mattjones315

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