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    21 repositories

    • PhyClone

      Public
      Accurate Bayesian reconstruction of cancer phylogenies from bulk sequencing.
      Python
      •
      GNU General Public License v3.0
      •1•5•2•0•Updated Dec 18, 2025Dec 18, 2025

    • cfclone-smk

      Public
      Python
      •1•0•0•0•Updated Dec 10, 2025Dec 10, 2025

    • PhyClone-Workflow

      Public
      Snakemake workflow that runs PyClone-VI clustering and then PhyClone phylogenetic reconstruction.
      Python
      •
      GNU General Public License v3.0
      •0•1•0•0•Updated Nov 25, 2025Nov 25, 2025

    • serval

      Public
      Python
      •
      Other
      •0•0•0•0•Updated Nov 21, 2025Nov 21, 2025

    • pyclone-vi

      Public
      Fast method for inferring cancer clonal population structure from SNV data.
      Python
      •
      GNU General Public License v3.0
      •13•66•24•0•Updated Sep 1, 2025Sep 1, 2025

    • FISHsim

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

    • pgsm

      Public
      Python
      •2•12•0•0•Updated May 12, 2025May 12, 2025

    • humi_pipeline

      Public
      Pipeline for running Hierachical UMI model
      Python
      •0•1•0•0•Updated Apr 2, 2025Apr 2, 2025

    • ESQmodel

      Public
      A biologically informed evaluation of 2-D cell segmentation quality in multiplexed tissue images.
      Python
      •
      MIT License
      •0•2•1•0•Updated Jul 6, 2023Jul 6, 2023

    • single_cell_FL

      Public
      Code repo for our publication
      R
      •
      MIT License
      •0•0•0•0•Updated 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
      •2•1•1•0•Updated Jun 15, 2022Jun 15, 2022

    • SpatialSort

      Public
      A spatially aware Bayesian clustering approach that allows for the incorporation of prior biological knowledge.
      Python
      •
      MIT License
      •1•5•2•0•Updated May 24, 2022May 24, 2022

    • Roth-Lab.github.io

      Public
      HTML
      •0•0•0•0•Updated Oct 14, 2021Oct 14, 2021

    • pgfa_experiments

      Public
      Experiments for Particle Gibbs Feature Allocation paper
      Python
      •0•0•0•0•Updated Jun 25, 2021Jun 25, 2021

    • pgfa

      Public
      Particle Gibbs Feature Allocation
      Python
      •0•1•0•0•Updated Jun 8, 2021Jun 8, 2021

    • merfish-segmentation

      Public
      Jupyter Notebook
      •2•0•0•0•Updated May 6, 2021May 6, 2021

    • contra_workshop

      Public
      Notes from the CONTRA cancer evolution workshop
      Tcl
      •1•7•1•0•Updated Apr 8, 2021Apr 8, 2021

    • pyclone

      Public
      Probabilistic model for inferring clonal population structure from deep NGS sequencing.
      Python
      •
      Other
      •36•116•21•0•Updated Aug 19, 2020Aug 19, 2020

    • pydp

      Public
      Python
      •
      GNU General Public License v3.0
      •5•3•0•0•Updated Jul 28, 2020Jul 28, 2020

    • JointSNVMix

      Public
      Automatically exported from code.google.com/p/joint-snv-mix
      C
      •1•1•7•0•Updated Jan 4, 2017Jan 4, 2017

    • FlowVB

      Public
      Gating Flow Cytometry Data with Variational Bayes
      Python
      •1•1•0•0•Updated Feb 8, 2011Feb 8, 2011