Repositories list

• spras-benchmarking

  Public
  Benchmarking datasets and analysis using SPRAS

  snakemakepathway-reconstructionspras

  Jupyter Notebook

  •

  MIT License

  •10•1•13•5•Updated Feb 22, 2026Feb 22, 2026

• spras

  Public
  Signaling Pathway Reconstruction Analysis Streamliner (SPRAS)

  snakemakenetworkomics+ 2pathway-reconstructionspras

  Python

  •

  MIT License

  •25•19•130•44•Updated Feb 20, 2026Feb 20, 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

  Reed-CompBio/rwr’s past year of commit activity
  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

  Reed-CompBio/protein-function-prediction’s past year of commit activity
  A tool to predict protein functions (Gene Ontology) via protein-protein and ontology networks

  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+ 3cytoscapejsprotein-protein-interactionnetwork-biology

  JavaScript

  •

  GNU General Public License v3.0

  •5•2•27•10•Updated Jul 15, 2025Jul 15, 2025

• growing-dags-rs

  Public

  Reed-CompBio/growing-dags-rs’s past year of commit activity
  A Growing DAGs reimplementation.

  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+ 2graph-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