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    38 repositories

    • spras

      Public
      Signaling Pathway Reconstruction Analysis Streamliner (SPRAS)
      snakemakenetworkomics
      snakemakenetworkomicspathway-reconstructionspras
      Python
      •
      MIT License
      •29•19•141•49•Updated Jun 28, 2026Jun 28, 2026

    • spras-benchmarking

      Public
      Benchmarking datasets and analysis using SPRAS
      snakemakepathway-reconstructionspras
      snakemakepathway-reconstructionspras
      13•2•19•10•Updated Jun 25, 2026Jun 25, 2026

    • BowTieBuilder-Algorithm

      Public
      This repository contains an implementation of the BowTieBuilder Algorithm.
      Jupyter Notebook
      •
      MIT License
      •2•1•0•0•Updated Jul 21, 2025Jul 21, 2025

    • rwr

      Public
      Random Walk w/ Restart (RWR) and variations for SPRAS.
      Python
      •
      MIT License
      •0•0•1•0•Updated Jul 20, 2025Jul 20, 2025

    • protein-function-prediction

      Public
      A tool to predict protein functions (Gene Ontology) via protein-protein and ontology networks
      gene-ontologyprotein-protein-interaction
      gene-ontologyprotein-protein-interaction
      Python
      •0•1•2•0•Updated Jul 15, 2025Jul 15, 2025

    • grphin

      Public
      HTML
      •
      MIT License
      •2•3•2•1•Updated Jul 15, 2025Jul 15, 2025

    • protein-weaver

      Public
      A web interface for ontology-based protein network visualization.
      neo4jgene-ontologyweb-tool
      neo4jgene-ontologyweb-toolcytoscapejsprotein-protein-interactionnetwork-biology
      JavaScript
      •
      GNU General Public License v3.0
      •5•2•27•10•Updated Jul 15, 2025Jul 15, 2025

    • growing-dags-rs

      Public
      A Growing DAGs reimplementation.
      signaling-pathways
      signaling-pathways
      Rust
      •0•0•0•0•Updated Jul 7, 2025Jul 7, 2025

    • all-pairs-shortest-paths

      Public
      APSP pathway reconstruction algorithm python implementation
      Python
      •
      MIT License
      •0•0•0•0•Updated Jun 23, 2025Jun 23, 2025

    • sp-orientation

      Public
      Shortest Paths-based Orientation PRA reimplementation
      Python
      •0•0•0•0•Updated Jun 16, 2025Jun 16, 2025

    • ResponseNet

      Public
      Implementation of the ResponseNet algorithm
      Python
      •
      GNU General Public License v3.0
      •1•1•1•0•Updated Jun 12, 2025Jun 12, 2025

    • zebrafish-gene-expression-patterns

      Public
      R
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated May 21, 2025May 21, 2025

    • github-tutorial

      Public
      0•0•0•0•Updated Jun 6, 2024Jun 6, 2024

    • growing-dags

      Public
      Python
      •1•0•0•0•Updated Sep 11, 2023Sep 11, 2023

    • nmii-contractility-regulators

      Public
      Python
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Sep 5, 2023Sep 5, 2023

    • random-walk-with-restart

      Public
      Jupyter Notebook
      •
      MIT License
      •1•0•0•0•Updated Aug 17, 2023Aug 17, 2023

    • graphlet-clustering

      Public
      Jupyter Notebook
      •
      GNU General Public License v3.0
      •0•1•0•0•Updated Aug 6, 2023Aug 6, 2023

    • TieDIE

      Public
      Tied Diffusion for Subnetwork Discovery (TieDIE)
      Python
      •
      Other
      •22•0•0•0•Updated Jun 21, 2023Jun 21, 2023

    • Graphery

      Public
      A graph tutorial website
      websitedjangovue
      websitedjangovuegraph-algorithmscomputational-biology
      Python
      •
      MIT License
      •3•12•34•21•Updated Mar 5, 2023Mar 5, 2023

    • pathway-reconciliation

      Public
      Python
      •
      GNU General Public License v3.0
      •0•3•0•0•Updated Oct 6, 2022Oct 6, 2022

    • GrapheryV2-Vue

      Public
      The frontend of Graphery, a graph algorithm tutorial & visualization website
      TypeScript
      •0•0•0•0•Updated Aug 2, 2022Aug 2, 2022

    • GrapheryV2-Django

      Public
      The backend of Graphery, a graph algorithm tutorial & visualization website
      Python
      •0•0•0•0•Updated Jul 31, 2022Jul 31, 2022

    • GrapheryExecutor

      Public
      Graphery Executor
      Python
      •
      MIT License
      •0•0•0•0•Updated Jul 31, 2022Jul 31, 2022

    • GrapheryRFCs

      Public
      MIT License
      •0•0•0•0•Updated Jul 28, 2022Jul 28, 2022

    • networkx

      Public
      Graphery networkx Wrapper
      Python
      •
      Other
      •3.5k•0•0•0•Updated Jun 22, 2022Jun 22, 2022

    • BIO331-F20

      Public
      Python
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Aug 25, 2021Aug 25, 2021

    • BIO331-Datasets

      Public
      Bio331 Fall 2020 -- Datasets
      GNU General Public License v3.0
      •0•1•0•0•Updated Aug 25, 2021Aug 25, 2021

    • pathway-parsers

      Public
      Signaling pathway database parsers
      Python
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Jul 20, 2021Jul 20, 2021

    • BIO331-F20-Lab6.2-community-detection

      Public archive
      Bio331 -- Fall 2020 -- Lab 6 Part 2
      Python
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Oct 13, 2020Oct 13, 2020

    • BIO331-F20-Lab6.1-GitHub

      Public archive
      Bio331 -- Fall 2020-- Lab 6 Part 1
      GNU General Public License v3.0
      •0•0•0•0•Updated Oct 13, 2020Oct 13, 2020
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