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    24 repositories

    • Self-Organization-Through-Local-Cell-Cell-Communication-Drives-Intestinal-Epithelial-Zonation

      Public
      This is the repo of the code containing the necessary functions to reproduce the analyses and figure panels presented in our paper "Self-Organization through lo…
      Python
      •0•0•0•0•Updated Apr 6, 2026Apr 6, 2026

    • bioIB

      Public
      bioIB package for scRNA-seq analysis
      Jupyter Notebook
      •1•7•1•0•Updated Dec 22, 2025Dec 22, 2025

    • prototype-equivalences

      Public
      The official implementation of smooth prototype equivalences (SPE), used to classify and characterize observations from empirical vector field data.
      machine-learningdynamical-systemsprototype-methods
      machine-learningdynamical-systemsprototype-methodsvector-fieldinvariant-setsnormalizing-flowlimit-cycle
      Jupyter Notebook
      •
      MIT License
      •0•2•0•0•Updated Nov 18, 2025Nov 18, 2025

    • SwaGen

      Public
      A graph neural network-based generative model to enhance swarm durability against threats.
      Jupyter Notebook
      •
      MIT License
      •1•1•0•0•Updated Nov 9, 2025Nov 9, 2025

    • Neighborhood-Informed-Positional-Information

      Public
      Python
      •0•0•0•0•Updated Sep 15, 2025Sep 15, 2025

    • coupling-signaling-adhesion

      Public
      Jupyter Notebook
      •0•0•0•0•Updated Jul 23, 2025Jul 23, 2025

    • Annotatability

      Public
      Annotatability, a method to identify meaningful patterns in single-cell genomics data through annotation-trainability analysis, which estimates annotation congr…
      Python
      •
      MIT License
      •2•19•0•0•Updated Jun 23, 2025Jun 23, 2025

    • Overfitness

      Public
      Python
      •
      MIT License
      •0•0•0•0•Updated May 26, 2025May 26, 2025

    • Annotatability_notebooks

      Public
      Reproducibility of "Annotatability" results
      Jupyter Notebook
      •1•0•0•0•Updated Dec 2, 2024Dec 2, 2024

    • trendy

      Public
      Temporal regression of effective nonlinear dynamics.
      Python
      •0•1•0•0•Updated Sep 12, 2024Sep 12, 2024

    • gep-dynamics

      Public
      Examining the dynamics of Gene Expression Programs (a.k.a. metagenes) at different time scales
      Jupyter Notebook
      •
      Other
      •0•0•0•0•Updated Aug 12, 2024Aug 12, 2024

    • biolord

      Public
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •6•95•0•2•Updated Aug 12, 2024Aug 12, 2024

    • sift-sc-reproducibility

      Public
      reproducibility code for SiFT manuscript https://doi.org/10.1101/2023.01.18.524512
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •0•0•0•0•Updated Jun 25, 2024Jun 25, 2024

    • biolord_reproducibility

      Public
      Reproducibility repository for the biolord publication.
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •1•5•0•0•Updated Apr 26, 2024Apr 26, 2024

    • scPrisma

      Public
      scPrisma is a spectral analysis method, for pseudotime reconstruction, informative genes inference, filtering, and enhancement of underlying cyclic signals
      Jupyter Notebook
      •
      MIT License
      •2•19•0•0•Updated Mar 31, 2024Mar 31, 2024

    • trajectory_reconstruction_tradeoff

      Public
      Jupyter Notebook
      •
      MIT License
      •0•0•0•0•Updated Mar 20, 2024Mar 20, 2024

    • time-warp-attend

      Public
      Jupyter Notebook
      •1•3•0•0•Updated Mar 6, 2024Mar 6, 2024

    • bio_disorder

      Public
      Jupyter Notebook
      •0•0•0•0•Updated Feb 7, 2024Feb 7, 2024

    • sift-sc

      Public
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •1•5•1•0•Updated Dec 11, 2023Dec 11, 2023

    • biolord_immune_bcells

      Public
      Train a bioLORD model with developing human immune across tissue (B-cells)
      Jupyter Notebook
      •1•0•0•0•Updated Aug 31, 2023Aug 31, 2023

    • pareto_interactions_py

      Public
      Jupyter Notebook
      •1•2•0•0•Updated Mar 23, 2023Mar 23, 2023

    • phase2vec

      Public
      Embeddings for dynamical systems
      Jupyter Notebook
      •3•10•1•0•Updated Mar 13, 2023Mar 13, 2023

    • scsim-ext

      Public
      Extension of scsim single-cell RNA-sequencing data simulations.
      Jupyter Notebook
      •
      MIT License
      •7•2•0•0•Updated Feb 9, 2023Feb 9, 2023

    • scPrisma_notebooks

      Public
      Tutorials and running examples of scPrisma workflow.
      Jupyter Notebook
      •0•0•0•0•Updated Jan 25, 2023Jan 25, 2023
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