OSMnx
OSMnx: A Python package to work with graph-theoretic OpenStreetMap street networks - Published in JOSS (2017)
pycopancore
reference implementation of the copan:CORE World-Earth modelling framework
torch-geometric-signed-directed
PyTorch Geometric Signed Directed is a signed/directed graph neural network extension library for PyTorch Geometric. The paper is accepted by LoG 2023.
pybel
🌶️ An ecosystem in Python for working with the Biological Expression Language (BEL)
https://github.com/benchmark-urbanism/cityseer-api
Computational tools for urban analysis
how_attentive_are_gats
Code for the paper "How Attentive are Graph Attention Networks?" (ICLR'2022)
noria-ontology
The NORIA-O project is a data model for IT networks, events and operations information. The ontology is developed using web technologies (e.g. RDF, OWL, SKOS) and is intended as a structure for realizing an IT Service Management (ITSM) Knowledge Graph (KG) for Anomaly Detection (AD) and Risk Management applications. The model has been developed in collaboration with operational teams, and in connection with third parties linked vocabularies.
SGCP
SGCP: a spectral self-learning method for clustering genes in co-expression networks
math-text-semantic-networks
Python code for construction and analysis of semantic networks from text.
Economiccomplexity
Economiccomplexity: Computational Methods for Economic Complexity - Published in JOSS (2020)
AgentPy
AgentPy: A package for agent-based modeling in Python - Published in JOSS (2021)
bottleneck
Code for the paper: "On the Bottleneck of Graph Neural Networks and Its Practical Implications"
pynets
A Reproducible Workflow for Structural and Functional Connectome Ensemble Learning
https://github.com/cumbof/honto
A novel method for assessing and measuring homophily in networks
splitp
Python package that implements split- and rank-based tools for inferring phylogenies, such as flattenings and subflattenings.
Mangal.jl and EcologicalNetworks.jl
Mangal.jl and EcologicalNetworks.jl: Two complementary packages for analyzing ecological networks in Julia - Published in JOSS (2021)
connectivity-search-manuscript
Manuscript describing Hetnet Connectivity Search
https://github.com/benmaier/tacoma
Temporal networks in Python. Provides fast tools to analyze temporal contact networks and simulate dynamic processes on them using Gillespie's SSA.
https://github.com/cdpxe/nefias
Network Forensic & Anomaly Detection System; tailored for covert channel/network steganography detection
RandomWalkRestartMH
A package to perform Random Walk with Restart on different types of networks
rsetse
This package is used to calculate the Strain Elevation Tension Spring embedding (SETSe) for networks in R
https://github.com/alan-turing-institute/netts
Toolbox for creating networks capturing semantic content of speech transcripts.
linkcomm
Tools for Generating, Visualising, and Analysing Link Communities in Networks
https://github.com/benmaier/smallworld
Generate and analyze small-world networks according to the revised Watts-Strogatz model where the randomization at β = 1 is truly equal to the Erdős-Rényi network model.
https://github.com/aspuru-guzik-group/qtorch
qTorch (Quantum Tensor Contraction Handler) https://arxiv.org/abs/1709.03636 -> for quantum simulation using tensor networks
https://github.com/benmaier/biasedrandomwalks
Provides classes around biased random walks on networks.
https://github.com/aida-ugent/debayes
DeBayes: a Bayesian Method for Debiasing Network Embeddings (ICML 2020).
https://github.com/cbg-ethz/graphclust_neurips
Network-Based Clustering of Pan-Cancer Data Accounting for Clinical Covariates
dseco
The DSecO project is a data model for representing and reasoning on Domain Name System (DNS) data. The ontology is developed using web technologies (e.g. RDF, OWL, SKOS) and is intended as a structure for realizing a DNS Knowledge Graph (KG) for administration and security assessment applications.
https://github.com/barahona-research-group/hcga
Highly Comparative Graph Analysis - Code for network phenotyping
https://github.com/byt3n33dl3/crackmapexec
A swiss army Knife for Penetration testing Networks and Active Directory.
https://github.com/centre-for-humanities-computing/embedding-explorer
Tools for interactive visual exploration of semantic embeddings.
MultilayerGraphs.jl
MultilayerGraphs.jl: Multilayer Network Science in Julia - Published in JOSS (2023)
https://github.com/byt3n33dl3/swissnet
CrackMapExec Swiss army Knife Dismantling
https://github.com/byt3n33dl3/thc-nikto
Nikto the Alienware, scanning for misconfigurations and Information disclosures on WebApp.
diseasemodulediscovery
A pipeline for network-based disease module identification.
SNaQ
Julia package for the inference of semi-directed phylogenetic networks under pseudolikelihood model
tiledmultigpuvisualization
Using tiled display systems for the interactive visualization of GPGPU computed data
connectivity-search-analyses
hetnet connectivity search research notebooks (previously hetmech)
https://github.com/cran-task-views/networkanalysis
CRAN Task View: Network Analysis
https://github.com/biophys-turin/biophys-turin.github.io
Official site of Biophys group at Unito
https://github.com/benmaier/sixdegrees
Sample from a variety of small-world network models in Python and C++. This includes a model with modular hierarchical community structure.
https://github.com/amr-yasser226/pagerank-power-method
Modular Python implementation of the PageRank algorithm via the power method, with discrete‑math foundations, end‑to‑end code, and experimental validation.