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    16 repositories

    • Mase-phi

      Public
      Marker selection strategies for ctDNA guided by phylogenetic inference
      Python
      •
      MIT License
      •1•2•0•0•Updated Jan 31, 2025Jan 31, 2025

    • TUSV-INT

      Public
      Python
      •0•0•0•0•Updated Jan 29, 2025Jan 29, 2025

    • TUSV-ext

      Public
      Python
      •
      MIT License
      •5•21•1•0•Updated Jan 24, 2025Jan 24, 2025

    • Sc-TUSV-ext

      Public
      Sc-TUSV-ext: Tumor evolutionary tree reconstruction from single-cell DNA-seq data of single nucleotide variants (SNV), copy number alterations (CNA) and structural variants (SV).
      Python
      •0•2•0•0•Updated Nov 21, 2024Nov 21, 2024

    • StudyDesignOptimization

      Public
      Jupyter Notebook
      •0•0•0•0•Updated Oct 21, 2024Oct 21, 2024

    • MosaicSim

      Public
      Jupyter Notebook
      •
      MIT License
      •1•5•1•0•Updated Sep 6, 2023Sep 6, 2023

    • SimGenome

      Public
      Simulation of the somatic variations (structural variations, copy number variations and single nucleotide variations) in whole genome based on tumor phylogenetic trees. SimGenome is the simulation method used in TUSV-ext project.
      Python
      •0•2•0•0•Updated Jun 19, 2023Jun 19, 2023

    • ConTreeDP

      Public
      Consensus method for tumor history tree based on directed partitions using dynamic programming
      Python
      •
      Creative Commons Zero v1.0 Universal
      •0•5•0•0•Updated Oct 24, 2022Oct 24, 2022

    • RADs

      Public
      Jupyter Notebook
      •2•11•0•0•Updated Mar 13, 2022Mar 13, 2022

    • JointClustering

      Public
      The joint clustering method for single cell miFISH and single cell whole genome copy numbers
      Python
      •
      Creative Commons Zero v1.0 Universal
      •0•4•0•0•Updated Nov 18, 2021Nov 18, 2021

    • RAD

      Public
      Robust and Accurate Deconvolution
      matrix-factorizationnmfdeconvolutiontumor-heterogeneityrad
      Jupyter Notebook
      •
      MIT License
      •3•13•0•0•Updated Oct 18, 2020Oct 18, 2020

    • NND

      Public
      Neural network deconvolution
      neural-networkmatrix-factorizationnmfdeconvolution
      Jupyter Notebook
      •
      MIT License
      •1•8•0•0•Updated Sep 10, 2020Sep 10, 2020

    • FISH_deconvolution

      Public
      code implementing methods for pooling bulk and single cell data and FISH data for copy number deconvolution
      Python
      •1•10•0•0•Updated Jan 31, 2020Jan 31, 2020

    • cancer-phylogenetics-prognostic-prediction

      Public
      Improving Personalized Prediction of Cancer Prognoses with Clonal Evolution Models
      cancer-genomicssurvival-analysissurvival-predictionevolutionary-modelscancer-prognoses
      Python
      •4•22•0•0•Updated Sep 23, 2019Sep 23, 2019

    • BrM-Phylo

      Public
      Phylogenies of Breast Cancer Brain Metastases
      matrix-factorizationbreast-cancertumor-heterogeneitydeconvolutionphylogenies
      Python
      •
      MIT License
      •1•3•0•0•Updated Sep 20, 2019Sep 20, 2019

    • SCS_deconvolution

      Public
      code implementing methods for pooling bulk and single cell data for copy number deconvolution
      Python
      •4•4•0•0•Updated Feb 14, 2019Feb 14, 2019
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