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@Murali-group T. M. Murali's Research Group at Virginia Tech

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    25 repositories

    • Beeline

      Public
      BEELINE: evaluation of algorithms for gene regulatory network inference
      Python
      •
      GNU General Public License v3.0
      •61•207•38•19•Updated Mar 1, 2026Mar 1, 2026

    • Murali-group.github.io

      Public
      Website for our group
      HTML
      •
      MIT License
      •0•0•0•2•Updated Feb 20, 2026Feb 20, 2026

    • SynVerse

      Public
      Universal prediction of drug synergies
      Python
      •
      GNU General Public License v3.0
      •1•1•0•0•Updated Jan 28, 2026Jan 28, 2026

    • BoolODE

      Public
      Git Repo for simulating Boolean Models
      Python
      •
      GNU General Public License v3.0
      •19•37•9•8•Updated Nov 7, 2025Nov 7, 2025

    • provenance-tracing

      Public
      GNU General Public License v3.0
      •0•0•0•0•Updated Oct 27, 2025Oct 27, 2025

    • graph-split

      Public
      A module to split a graph in different ways (for deep learning applications)
      Python
      •
      GNU General Public License v3.0
      •2•0•0•1•Updated Jun 30, 2025Jun 30, 2025

    • ICoN

      Public
      Integration using Co-attention across Biological Networks
      Python
      •
      GNU General Public License v3.0
      •2•1•0•0•Updated Feb 6, 2025Feb 6, 2025

    • GraphSpace

      Public
      The interactive graph sharing website.
      Python
      •
      GNU General Public License v2.0
      •44•35•82•22•Updated Aug 6, 2023Aug 6, 2023

    • halp

      Public
      Hypergraph Algorithms Package
      Python
      •
      GNU General Public License v3.0
      •23•100•4•3•Updated Jul 6, 2023Jul 6, 2023

    • annotation_prediction

      Public
      Algorithms for predicting gene and protein annotations, e.g., to the GO and to the HPO.
      Python
      •
      GNU General Public License v3.0
      •3•2•0•2•Updated Jul 6, 2023Jul 6, 2023

    • SARS-CoV-2-network-analysis

      Public
      Software framework for analysis of SARS-CoV-2 molecular networks
      Jupyter Notebook
      •
      GNU General Public License v3.0
      •3•6•6•4•Updated Jul 6, 2023Jul 6, 2023

    • tox_signaling_networks

      Public
      Code for building and evaluating toxicant signaling networks.
      Python
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Jun 5, 2023Jun 5, 2023

    • BeeHive

      Public
      A general platform for multiple types of network biology workflows
      HTML
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Dec 15, 2022Dec 15, 2022

    • CyGraphSpace

      Public
      A GraphSpace app for Cytoscape
      Java
      •
      GNU General Public License v3.0
      •2•1•11•3•Updated Nov 16, 2022Nov 16, 2022

    • PathLinker-Cytoscape

      Public
      Cytoscape plugin for PathLinker
      Java
      •
      GNU General Public License v3.0
      •5•3•6•0•Updated Oct 26, 2022Oct 26, 2022

    • GRN-tutorial

      Public
      Tutorial on inferring gene regulatory networks from single-cell data
      Jupyter Notebook
      •
      GNU General Public License v3.0
      •0•2•8•0•Updated Jul 18, 2022Jul 18, 2022

    • Flud

      Public
      An interactive game to lay out graphs.
      JavaScript
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Nov 8, 2021Nov 8, 2021

    • supervised-grns

      Public
      Supervised inference of gene regulatory networks from single-cell RNA-sequencing data
      Python
      •
      GNU General Public License v3.0
      •0•0•2•2•Updated Jun 23, 2021Jun 23, 2021

    • multi-species-GOA-prediction

      Public
      Software for predicting GO annotations using a multi-species network.
      Python
      •
      GNU General Public License v3.0
      •0•0•1•0•Updated Jan 29, 2021Jan 29, 2021

    • PathLinker

      Public
      Connect the dots in networks.
      Python
      •
      GNU General Public License v3.0
      •10•20•7•1•Updated Aug 28, 2020Aug 28, 2020

    • RegLinker

      Public
      Connect the dots in protein interaction networks ... using regular expressions!
      Python
      •
      GNU General Public License v3.0
      •1•0•0•0•Updated May 19, 2020May 19, 2020

    • networkx

      Public
      Official NetworkX source code repository.
      Python
      •
      Other
      •3.5k•0•0•0•Updated Oct 22, 2019Oct 22, 2019

    • crossplan

      Public
      The CrossPlan software for systematically planning genetic cross experiments
      Python
      •
      GNU General Public License v3.0
      •1•1•1•0•Updated Mar 2, 2018Mar 2, 2018

    • 2017-ICSB-graphspace-tutorial

      Public
      Materials for the tutorial on GraphSpace at 2017 ICSB
      Jupyter Notebook
      •
      GNU General Public License v3.0
      •0•3•1•0•Updated Aug 7, 2017Aug 7, 2017

    • PathLinker-PathVisio

      Public
      A plugin to PathVisio that implements and provides an inteface to the PathLinker algorithm
      Java
      •0•0•2•0•Updated Nov 19, 2016Nov 19, 2016