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    • Python
      1000Updated Mar 18, 2026Mar 18, 2026
    • Snakemake workflow that runs PyClone-VI clustering and then PhyClone phylogenetic reconstruction.
      Python
      GNU General Public License v3.0
      0100Updated Jan 24, 2026Jan 24, 2026
    • PhyClone

      Public
      Accurate Bayesian reconstruction of cancer phylogenies from bulk sequencing.
      Python
      GNU General Public License v3.0
      1500Updated Jan 22, 2026Jan 22, 2026
    • Fast method for inferring cancer clonal population structure from SNV data.
      Python
      GNU General Public License v3.0
      1371240Updated Jan 20, 2026Jan 20, 2026
    • serval

      Public
      Python
      Other
      0000Updated Nov 21, 2025Nov 21, 2025
    • FISHsim

      Public
      Python
      GNU General Public License v3.0
      1100Updated Jul 3, 2025Jul 3, 2025
    • pgsm

      Public
      Python
      21200Updated May 12, 2025May 12, 2025
    • Pipeline for running Hierachical UMI model
      Python
      0000Updated Apr 2, 2025Apr 2, 2025
    • ESQmodel

      Public
      A biologically informed evaluation of 2-D cell segmentation quality in multiplexed tissue images.
      Python
      MIT License
      0210Updated Jul 6, 2023Jul 6, 2023
    • Code repo for our publication
      R
      MIT License
      0100Updated Feb 16, 2023Feb 16, 2023
    • scg

      Public
      Software for inference of clonal genotypes using targeted single cell (nucleus) sequencing.
      Python
      GNU General Public License v3.0
      2110Updated Jun 15, 2022Jun 15, 2022
    • A spatially aware Bayesian clustering approach that allows for the incorporation of prior biological knowledge.
      Python
      MIT License
      0520Updated May 24, 2022May 24, 2022
    • HTML
      0000Updated Oct 14, 2021Oct 14, 2021
    • Experiments for Particle Gibbs Feature Allocation paper
      Python
      0000Updated Jun 25, 2021Jun 25, 2021
    • pgfa

      Public
      Particle Gibbs Feature Allocation
      Python
      0000Updated Jun 8, 2021Jun 8, 2021
    • Jupyter Notebook
      2000Updated May 6, 2021May 6, 2021
    • Notes from the CONTRA cancer evolution workshop
      Tcl
      1710Updated Apr 8, 2021Apr 8, 2021
    • pyclone

      Public
      Probabilistic model for inferring clonal population structure from deep NGS sequencing.
      Python
      Other
      35120210Updated Aug 19, 2020Aug 19, 2020
    • pydp

      Public
      Python
      GNU General Public License v3.0
      4300Updated Jul 28, 2020Jul 28, 2020
    • Automatically exported from code.google.com/p/joint-snv-mix
      C
      1170Updated Jan 4, 2017Jan 4, 2017
    • FlowVB

      Public
      Gating Flow Cytometry Data with Variational Bayes
      Python
      1100Updated Feb 8, 2011Feb 8, 2011
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