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@IlyaLab Shmulevich Lab, Institute for Systems Biology

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    42 repositories

    • KGBN

      Public
      Jupyter Notebook
      •5•4•0•0•Updated Jan 16, 2026Jan 16, 2026

    • tbccsi

      Public
      Tile based classification of cell segmented images (TBCCSI)
      Python
      •
      MIT License
      •0•0•0•0•Updated Jan 8, 2026Jan 8, 2026

    • LogicModelMerger

      Public
      Jupyter Notebook
      •1•2•0•0•Updated Jul 24, 2025Jul 24, 2025

    • TextureAnalysis

      Public
      Python
      •
      Apache License 2.0
      •0•0•0•0•Updated Jun 5, 2025Jun 5, 2025

    • wsinfer

      Public
      🔥 🚀 Blazingly fast pipeline for patch-based classification in whole slide images
      Python
      •
      Apache License 2.0
      •12•0•0•0•Updated Dec 9, 2024Dec 9, 2024

    • gssnng

      Public
      Gene Set Scoring on the Nearest Neighbor Graph (gssnng) for Single Cell RNA-seq (scRNA-seq) using AnnData h5ad files.
      Jupyter Notebook
      •
      MIT License
      •4•12•5•0•Updated Oct 1, 2024Oct 1, 2024

    • KG_predict_DrugResponse

      Public
      Jupyter Notebook
      •1•1•0•0•Updated Jul 18, 2024Jul 18, 2024

    • GRN_modeling

      Public
      Jupyter Notebook
      •0•2•0•0•Updated Mar 26, 2024Mar 26, 2024

    • t2d-dt-modeling

      Public
      Type 2 Diabetes digital twins - modeling and knowledge graph analysis
      Jupyter Notebook
      •1•1•0•0•Updated Nov 14, 2023Nov 14, 2023

    • BigGIM

      Public
      Jupyter Notebook
      •
      MIT License
      •2•2•0•0•Updated Aug 7, 2023Aug 7, 2023

    • SL-Cloud

      Public
      Jupyter Notebook
      •
      Apache License 2.0
      •4•0•0•0•Updated Mar 3, 2023Mar 3, 2023

    • digital_twin_graph_utils

      Public
      HTML
      •0•0•0•0•Updated Dec 14, 2022Dec 14, 2022

    • CellReprogramming

      Public
      Jupyter Notebook
      •
      Apache License 2.0
      •1•2•0•0•Updated Sep 14, 2022Sep 14, 2022

    • ABM-DTwinMelanoma

      Public
      0•0•0•0•Updated Jan 21, 2022Jan 21, 2022

    • FMStates

      Public
      Jupyter Notebook
      •1•0•0•0•Updated Dec 22, 2021Dec 22, 2021

    • Pan-Cancer-Cell-Cell-Comm-Net

      Public
      The Pan-Cancer cell-cell communication network, data, scripts, results.
      HTML
      •0•1•0•0•Updated Jul 16, 2021Jul 16, 2021

    • BooleanNetworkReservoirComputers

      Public
      Generate and run Boolean Network Reservoir Computers. Code used in Entropy manuscript.
      Python
      •0•1•0•0•Updated Nov 6, 2018Nov 6, 2018

    • FamSuite

      Public
      Python
      •0•0•0•0•Updated Mar 3, 2018Mar 3, 2018

    • CombiningDependentPvaluesUsingEBM

      Public
      Python, R and Matlab implementation of Brown's Method to combine dependent P-values
      R
      •
      Apache License 2.0
      •9•25•0•0•Updated Feb 12, 2018Feb 12, 2018

    • ISB-LSDF

      Public
      ISB CGC Webapp
      JavaScript
      •
      Apache License 2.0
      •10•0•11•0•Updated Apr 27, 2016Apr 27, 2016

    • M2C

      Public
      Multiscale Mutation Clustering Algorithm
      Python
      •2•3•0•0•Updated Mar 31, 2016Mar 31, 2016

    • visquick

      Public
      JavaScript
      •
      BSD 3-Clause "New" or "Revised" License
      •1•1•0•0•Updated Jan 4, 2016Jan 4, 2016

    • epept

      Public
      Automatically exported from code.google.com/p/epept
      MATLAB
      •3•2•0•0•Updated Jan 4, 2016Jan 4, 2016

    • systemsbiology-visualizations

      Public
      Automatically exported from code.google.com/p/systemsbiology-visualizations
      JavaScript
      •6•0•0•0•Updated Dec 23, 2015Dec 23, 2015

    • dodoma

      Public
      Automatically exported from code.google.com/p/dodoma
      JavaScript
      •1•1•0•0•Updated Dec 21, 2015Dec 21, 2015

    • hukilau

      Public archive
      Automatically exported from code.google.com/p/hukilau
      Java
      •1•1•0•0•Updated Dec 21, 2015Dec 21, 2015

    • molotov

      Public archive
      Automatically exported from code.google.com/p/molotov
      C++
      •1•1•0•0•Updated Dec 21, 2015Dec 21, 2015

    • CloudForest

      Public
      Ensembles of decision trees in go/golang.
      Go
      •
      Other
      •92•3•0•0•Updated Sep 21, 2015Sep 21, 2015

    • kramtools

      Public
      C
      •
      MIT License
      •0•2•0•0•Updated Mar 26, 2015Mar 26, 2015

    • rf-ace

      Public
      (backup fork since google code is going down)
      C++
      •3•12•0•0•Updated Mar 12, 2015Mar 12, 2015