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    103 repositories

    • cnplot

      Public
      A dedicated plotting library for copy numbers
      Python
      •
      MIT License
      •0•0•0•0•Updated Nov 12, 2026Nov 12, 2026

    • phyloGMM

      Public
      a phylogenetic mixture model for simultaneous inference of cell types and transitions from single-cell lineage tracing data
      C++
      •0•0•0•0•Updated Nov 7, 2026Nov 7, 2026

    • SUMMIT

      Public
      SUMMIT: Scalable Unified Metastatic Migration Inference on Trees
      Python
      •0•0•0•0•Updated Nov 6, 2026Nov 6, 2026

    • troupe

      Public
      Code for Tree-informed Rate Optimization Using Potency Enforcement and associated experiments
      Python
      •0•1•0•0•Updated Nov 5, 2026Nov 5, 2026

    • troupe-experiments

      Public
      Python
      •0•0•0•0•Updated Nov 5, 2026Nov 5, 2026

    • Universal-Genotyping-Pipeline

      Public
      Python
      •1•0•0•0•Updated Oct 30, 2026Oct 30, 2026

    • MGW

      Public
      Python
      •3•10•0•0•Updated Oct 7, 2026Oct 7, 2026

    • hatchet

      Public
      HATCHet (Holistic Allele-specific Tumor Copy-number Heterogeneity) is an algorithm that infers allele and clone-specific CNAs and WGDs jointly across multiple t…
      Roff
      •
      BSD 3-Clause "New" or "Revised" License
      •34•73•56•5•Updated Sep 29, 2026Sep 29, 2026

    • dialect

      Public
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •0•3•0•0•Updated Sep 26, 2026Sep 26, 2026

    • LAML-Pro

      Public
      C++
      •2•4•1•1•Updated Aug 6, 2026Aug 6, 2026

    • spatial_anomaly_detection

      Public
      Jupyter Notebook
      •
      MIT License
      •0•0•1•0•Updated Mar 12, 2026Mar 12, 2026

    • MET-MAP

      Public
      Reproducibility repository for Multi-GASTON applied on spatial metabolomics data
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •0•6•0•0•Updated Mar 11, 2026Mar 11, 2026

    • Multi-GASTON

      Public
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •1•8•0•0•Updated Mar 8, 2026Mar 8, 2026

    • fastBE

      Public
      ultrafast phylogenetic reconstruction from bulk DNA sequencing data
      Jupyter Notebook
      •0•6•0•0•Updated Feb 18, 2026Feb 18, 2026

    • GASTON

      Public
      GASTON: deep learning algorithm learns "topography" of a tissue slice from spatial transcriptomics data
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •16•77•1•1•Updated Dec 1, 2025Dec 1, 2025

    • LAML-Pro-experiments

      Public
      HTML
      •0•0•0•0•Updated Nov 29, 2025Nov 29, 2025

    • MOSAICField

      Public
      Source code for MOSAICField multimodal spatial alignment and morphological mapping
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •2•4•0•0•Updated Nov 21, 2025Nov 21, 2025

    • Phyllochron

      Public
      Phyllochron is an ILP method that solves the Maximum Likelihood Longitudinal Assignment Problem under the Longitudinally Observed Perfect Phylogeny Model.
      Jupyter Notebook
      •
      MIT License
      •0•2•0•0•Updated Nov 20, 2025Nov 20, 2025

    • GASTON-Mix

      Public
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •1•10•0•0•Updated Oct 16, 2025Oct 16, 2025

    • HiRef

      Public
      Hierarchical Refinement: Optimal Transport to Infinity and Beyond
      Jupyter Notebook
      •2•20•0•0•Updated Sep 29, 2025Sep 29, 2025

    • LAML

      Public
      LAML is a maximum likelihood algorithm to infer cell phylogeny from dynamic lineage tracing data
      single-cellphylogenymaximum-likelihood-estimation
      single-cellphylogenymaximum-likelihood-estimationtree-inferencelineage-tracing
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •1•12•2•0•Updated Sep 23, 2025Sep 23, 2025

    • HM-OT

      Public
      Hidden Markov Optimal Transport: learning the sequence of latent cell-states and transitions in transcriptomic time-series.
      Jupyter Notebook
      •2•10•0•0•Updated Aug 24, 2025Aug 24, 2025

    • CalicoST

      Public
      Inferring allele-specific copy number aberrations and tumor phylogeography from spatially resolved transcriptomics
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •4•52•13•3•Updated Aug 18, 2025Aug 18, 2025

    • chimeric-epistasis

      Public
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •0•0•0•0•Updated Aug 4, 2025Aug 4, 2025

    • laml-experiments

      Public
      experiments for the LAML paper
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •0•2•0•0•Updated Jun 1, 2025Jun 1, 2025

    • copulacci

      Public
      Jupyter Notebook
      •1•6•1•0•Updated May 29, 2025May 29, 2025

    • FRLC

      Public
      Low-rank optimal transport through factor relaxation with latent coupling.
      Jupyter Notebook
      •1•5•0•0•Updated May 20, 2025May 20, 2025

    • raphael-group.github.io

      Public
      Raphael group website.
      HTML
      •2•0•0•0•Updated Apr 11, 2025Apr 11, 2025

    • dialog

      Public
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •0•0•0•0•Updated Apr 7, 2025Apr 7, 2025

    • tree-labeling-polytope

      Public
      Python
      •1•2•0•0•Updated Mar 21, 2025Mar 21, 2025
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