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    25 repositories

    • BioModelComparison

      Public
      Comparing different model architectures and training methods on simple biological and medical datasets.
      Jupyter Notebook
      •
      MIT License
      •1•5•0•0•Updated Feb 16, 2026Feb 16, 2026

    • BNP-FRET-Binned

      Public
      Julia
      •
      MIT License
      •2•0•0•0•Updated Dec 10, 2025Dec 10, 2025

    • SP2T.jl

      Public
      Julia
      •
      MIT License
      •0•3•0•0•Updated Sep 28, 2025Sep 28, 2025

    • WidefieldMotionModels

      Public
      MATLAB
      •
      MIT License
      •0•0•0•0•Updated Jul 25, 2025Jul 25, 2025

    • bnp-step

      Public
      Jupyter Notebook
      •5•1•0•0•Updated Mar 28, 2025Mar 28, 2025

    • BindingKinetics

      Public
      A repository for our work on analyzing binding kinetics from DNA origami experiments.
      Python
      •
      MIT License
      •0•0•0•0•Updated Feb 7, 2025Feb 7, 2025

    • PotentialsFromFRET

      Public
      Code for inferring continuous potentials from FRET data
      Python
      •
      MIT License
      •0•1•0•0•Updated Nov 20, 2024Nov 20, 2024

    • BayesianDeconvolution

      Public
      Julia
      •1•8•0•0•Updated Nov 5, 2024Nov 5, 2024

    • B-SIM

      Public
      Physically Accurate Structured Illumination Microscopy Reconstruction
      Julia
      •
      MIT License
      •3•2•0•0•Updated Nov 4, 2024Nov 4, 2024

    • GPDiffusionMapping

      Public
      Code for our diffusion coefficient mapping project.
      Python
      •
      MIT License
      •1•1•0•0•Updated Oct 26, 2024Oct 26, 2024

    • BNP-Track

      Public
      MATLAB
      •2•6•2•0•Updated Jul 26, 2024Jul 26, 2024

    • FluorophoreCounter

      Public
      Python
      •
      MIT License
      •0•1•0•0•Updated May 28, 2024May 28, 2024

    • NatComm_FRET_Benchmark

      Public
      Simulation Datasets and HMM Analysis Code for Nature Communication Matters Arising
      Julia
      •0•0•0•0•Updated Mar 27, 2024Mar 27, 2024

    • AvoidingMatrixExponential

      Public
      Python
      •1•0•0•0•Updated Dec 12, 2023Dec 12, 2023

    • Bayes-smRD

      Public
      MATLAB
      •1•1•0•0•Updated Aug 7, 2023Aug 7, 2023

    • RunOnHPC

      Public
      Use these bash scripts to automatically run multiple jobs on Agave.
      Shell
      •
      MIT License
      •0•0•0•0•Updated Jun 16, 2023Jun 16, 2023

    • how_many_submissions

      Public
      Jupyter Notebook
      •1•0•0•0•Updated May 2, 2023May 2, 2023

    • gene_exp_nonpara

      Public
      nonparametric inference of gene networks from smFISH
      MATLAB
      •
      MIT License
      •1•0•0•0•Updated Dec 11, 2022Dec 11, 2022

    • BNP-MFT

      Public
      MATLAB
      •1•0•0•0•Updated Oct 12, 2022Oct 12, 2022

    • GPPotentialLearner

      Public
      Code for inferring potential energy landscapes from trajectory information, as shown in iScience and JCP.
      Python
      •
      MIT License
      •0•0•0•0•Updated Sep 30, 2022Sep 30, 2022

    • cluster-hacks

      Public
      Where we keep a list of handy tricks/templates.
      Shell
      •1•1•0•1•Updated Sep 29, 2022Sep 29, 2022

    • BNP-LA

      Public
      Bayesian nonparametric lifetime analysis for single confocal spot / pixel
      MATLAB
      •
      MIT License
      •1•0•0•0•Updated Sep 20, 2022Sep 20, 2022

    • BNP-FLIM

      Public
      Bayesian parametric analysis of wide-field FLIM data
      MATLAB
      •
      MIT License
      •1•0•0•0•Updated Sep 10, 2022Sep 10, 2022

    • BNP-FRET

      Public
      A package to analyze single photon smFRET data in a Bayesian nonparametrics (BNP) paradigm while including all the sources of noise.
      Julia
      •
      MIT License
      •2•0•0•0•Updated Aug 6, 2022Aug 6, 2022

    • PresseLib

      Public
      MATLAB
      •1•0•0•0•Updated Jul 9, 2021Jul 9, 2021