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    96 repositories

    • MOSAICField

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

    • MGW

      Public
      Jupyter Notebook
      •0•0•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

    • troupe

      Public
      All code for Tree-informed Rate Optimization Using Potency Enforcement and associated experiments
      Python
      •0•0•0•0•Updated Nov 20, 2025Nov 20, 2025

    • MET-MAP

      Public
      Reproducibility repository for Multi-GASTON applied on spatial metabolomics data
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •0•2•0•0•Updated Nov 5, 2025Nov 5, 2025

    • GASTON-Mix

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

    • HiRef

      Public
      Hierarchical Refinement: Optimal Transport to Infinity and Beyond
      Jupyter Notebook
      •1•12•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-estimationtree-inferencelineage-tracing
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •1•11•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
      •0•9•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•42•8•4•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

    • GASTON

      Public
      GASTON: deep learning algorithm learns "topography" of a tissue slice from spatial transcriptomics data
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •11•63•0•1•Updated Jun 16, 2025Jun 16, 2025

    • Multi-GASTON

      Public
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •0•7•0•0•Updated Jun 6, 2025Jun 6, 2025

    • laml-experiments

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

    • copulacci

      Public
      Jupyter Notebook
      •0•5•1•0•Updated May 29, 2025May 29, 2025

    • FRLC

      Public
      Low-rank optimal transport through factor relaxation with latent coupling.
      Jupyter Notebook
      •0•4•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

    • dialect

      Public
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •0•4•0•0•Updated Apr 3, 2025Apr 3, 2025

    • fastBE

      Public
      ultrafast phylogenetic reconstruction from bulk DNA sequencing data
      Jupyter Notebook
      •0•5•0•0•Updated Apr 1, 2025Apr 1, 2025

    • tree-labeling-polytope

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

    • DeST_OT

      Public
      Developmental Spatiotemporal Optimal Transport
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •1•13•0•0•Updated Mar 19, 2025Mar 19, 2025

    • lazac-copy-number

      Public
      fast and accurate phylogenetic reconstruction from copy number data
      C++
      •0•6•1•0•Updated Mar 6, 2025Mar 6, 2025

    • paste2

      Public
      Probabilistic Alignment of Spatial Transcriptomics Experiments v.2
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •2•41•10•0•Updated Mar 2, 2025Mar 2, 2025

    • 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 tumor samples from the same patient, and that leverages the relationships between clones in these samples.
      Roff
      •
      BSD 3-Clause "New" or "Revised" License
      •31•70•56•4•Updated Feb 26, 2025Feb 26, 2025

    • paste

      Public
      Probabilistic Alignment of Spatial Transcriptomics Experiments
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •19•96•7•0•Updated Feb 26, 2025Feb 26, 2025

    • spatial_anomaly_detection

      Public
      Jupyter Notebook
      •
      MIT License
      •0•0•1•0•Updated Jan 30, 2025Jan 30, 2025

    • startle

      Public
      cellular lineage reconstruction from lineage tracing data
      C++
      •
      MIT License
      •2•4•0•0•Updated Jan 29, 2025Jan 29, 2025

    • CARTA

      Public
      Jupyter Notebook
      •1•3•0•0•Updated Jan 27, 2025Jan 27, 2025

    • paste3

      Public
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •2•18•9•0•Updated Jan 10, 2025Jan 10, 2025