Repositories list

• Beeline

  Public
  BEELINE: evaluation of algorithms for gene regulatory network inference

  Python

  •

  GNU General Public License v3.0

  •53•170•33•19•Updated Aug 25, 2024Aug 25, 2024

• BoolODE

  Public
  Git Repo for simulating Boolean Models

  Python

  •

  GNU General Public License v3.0

  •15•32•9•8•Updated Jun 11, 2024Jun 11, 2024

• ICoN

  Public
  Integration using Co-attention across Biological Networks

  Python

  •

  GNU General Public License v3.0

  •1•1•0•0•Updated Mar 7, 2024Mar 7, 2024

• GraphSpace

  Public
  The interactive graph sharing website.

  Python

  •

  GNU General Public License v2.0

  •41•30•82•22•Updated Aug 6, 2023Aug 6, 2023

• halp

  Public
  Hypergraph Algorithms Package

  Python

  •

  GNU General Public License v3.0

  •21•95•4•2•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

  •4•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

• Murali-group.github.io

  Public
  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•1•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

  •9•17•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

  •3.2k•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