Repositories list

• Newsletter-Bibliography

  Public
  LaTeX bibliography of the "This week in Math Onco" newsletter (https://mathematical-oncology.org/newsletter)

  TeX

  •0•2•0•0•Updated Oct 22, 2024Oct 22, 2024

• IMAT

  Public
  IMO Methods & Tools Lecture Series

  0•0•0•0•Updated Oct 21, 2024Oct 21, 2024

• NeoPredPipe

  Public
  Neoantigens prediction pipeline for multi- or single-region vcf files using ANNOVAR and netMHCpan.

  Python

  •

  GNU Lesser General Public License v3.0

  •28•106•1•1•Updated Sep 2, 2024Sep 2, 2024

• valis

  Public
  Virtual Alignment of pathoLogy Image Series

  Python

  •

  MIT License

  •29•121•61•1•Updated Aug 20, 2024Aug 20, 2024

• HAL

  Public
  HAL (Hybrid Automata Library) is the one-stop shop for all of your hybrid modeling needs

  Java

  •

  MIT License

  •12•37•1•0•Updated Aug 19, 2024Aug 19, 2024

• DRL_Personalized_AT

  Public
  Mathematical Model-Driven Deep Learning Enables Personalized Adaptive Therapy

  Jupyter Notebook

  •2•1•0•0•Updated Aug 19, 2024Aug 19, 2024

• Mistic

  Public
  Multiplexed image tSNE visualizer

  Python

  •

  MIT License

  •6•36•0•0•Updated Jul 3, 2024Jul 3, 2024

• Mistic_code_live_cell_imaging

  Public
  Python

  •0•0•0•0•Updated Jul 2, 2024Jul 2, 2024

• CellCycle4DataIntegration

  Public
  Cell identity revealed by precise cell cycle state mapping links data modalities

  XSLT

  •0•0•0•0•Updated Jun 21, 2024Jun 21, 2024

• Lenia-in-HAL

  Public
  Repository for Lenia framework, implemented in Hybrid Automata Library (HAL)

  Java

  •

  MIT License

  •0•6•0•0•Updated Jun 11, 2024Jun 11, 2024

• PARPi_Model

  Public
  Jupyter Notebook

  •0•1•0•0•Updated Apr 9, 2024Apr 9, 2024

• multiMets

  Public
  grows and seeds multiple metastases and treats them with different therapeutic strategies

  Java

  •

  MIT License

  •0•0•0•0•Updated Feb 8, 2024Feb 8, 2024

• onubogu_spatial_analysis_of_recurrent_glioblastoma

  Public
  Code used in Spatial analysis of recurrent glioblastoma reveals perivascular niche organization.

  Jupyter Notebook

  •

  MIT License

  •0•0•0•0•Updated Jan 23, 2024Jan 23, 2024

• densityDependentSelection

  Public
  HTML

  •0•0•0•0•Updated Jul 5, 2023Jul 5, 2023

• ploidyEvolution

  Public
  A general N-compartment model of ploidy states is developed and analyzed.

  R

  •

  BSD 2-Clause "Simplified" License

  •1•1•7•0•Updated Feb 7, 2023Feb 7, 2023

• MIEmodel

  Public
  Simplified version of a deterministic framework for modeling whole chromosome missegregations. This model is more amendable to theoretical analysis to investigate conditions for missegregation-induced extinction (MIE).

  R

  •

  GNU General Public License v3.0

  •1•1•0•0•Updated Sep 13, 2022Sep 13, 2022

• HomeostaticEpidermis

  Public
  Homeostatic Epidermis – PNAS Full Codebase

  Java

  •0•0•0•0•Updated Aug 12, 2022Aug 12, 2022

• Curvogram

  Public
  Method for plotting histograms on a curve using a West Transform

  Jupyter Notebook

  •

  BSD 3-Clause "New" or "Revised" License

  •2•10•0•0•Updated Apr 26, 2022Apr 26, 2022

• strobl2021_space_modulates_competition_AT

  Public
  This repository contains the code and data for our publication Strobl et al (2022). Spatial structure impacts adaptive therapy by shaping intra-tumoral competition. Commun Med 2, 46, available at: https://rdcu.be/cL5bi.

  Jupyter Notebook

  •3•4•0•0•Updated Apr 25, 2022Apr 25, 2022

• AT_costOfResistance_LVModel

  Public
  This repository contains the code to generate the figures in our research paper: Strobl et al (2020), Turnover modulates the need for a cost of resistance in adaptive therapy published in Cancer Research.

  Jupyter Notebook

  •

  GNU General Public License v3.0

  •1•2•0•0•Updated Mar 22, 2022Mar 22, 2022

• gatenbee_2022_immunosuppressive_niche

  Public
  Code to used to simulate eco-evolutionary tumor-immune dynamics as described in https://www.researchsquare.com/article/rs-799879/v1

  Shell

  •

  MIT License

  •1•0•0•0•Updated Feb 4, 2022Feb 4, 2022

• staged-recipes

  Public
  A place to submit conda recipes before they become fully fledged conda-forge feedstocks

  Python

  •

  BSD 3-Clause "New" or "Revised" License

  •4.9k•0•0•0•Updated Jan 25, 2022Jan 25, 2022

• EvoFreq

  Public
  Evolutionary frequency visualization tool of temporal data

  R

  •

  GNU General Public License v3.0

  •3•21•3•1•Updated Jan 25, 2022Jan 25, 2022

• Gattaca

  Public
  Base pair resolution mutation tracking for somatic evolution studies using agent based simulations

  GNU General Public License v3.0

  •0•2•0•0•Updated Dec 20, 2021Dec 20, 2021

• flipflopspatialmodel

  Public
  GNU General Public License v3.0

  •0•0•0•0•Updated Aug 31, 2021Aug 31, 2021

• flipflopblood

  Public
  Whole Blood Simulations of Hematopoietic Stem Cells

  Java

  •

  GNU General Public License v3.0

  •1•3•0•0•Updated Aug 31, 2021Aug 31, 2021

• IsoMaTrix

  Public
  A framework to visualize the isoclines of matrix games and quantify uncertainty in structured populations (MATLAB, Java)

  Java

  •1•9•0•0•Updated Apr 29, 2021Apr 29, 2021

• adaptivePGG

  Public
  C++ code developed to study the emergence of dimorphic populations in nonlinear public good games

  MATLAB

  •

  GNU General Public License v3.0

  •3•0•0•0•Updated Apr 8, 2021Apr 8, 2021

• multiscaleGBM

  Public
  Java

  •

  MIT License

  •0•1•0•0•Updated Feb 9, 2021Feb 9, 2021

• tissue-structure-modulates-evolution

  Public
  Code repository associated with the paper "Tissue structure modulates evolution: premalignant sweeps precede neutral expansion"

  Java

  •

  GNU General Public License v3.0

  •2•2•0•0•Updated Jan 16, 2021Jan 16, 2021