Scientific Software
Updated 6 months ago

graphlayouts — Peer-reviewed • Rank 19.0 • Science 100%

graphlayouts: Layout algorithms for network visualizations in R - Published in JOSS (2023)

Scientific Software · Peer-reviewed
Scientific Software
Updated 6 months ago

graphsim — Peer-reviewed • Rank 14.3 • Science 98%

graphsim: An R package for simulating gene expression data from graph structures of biological pathways - Published in JOSS (2020)

Updated 6 months ago

cytoscape-fcose • Rank 27.5 • Science 75%

fCoSE: a fast Compound Spring Embedder

Scientific Software
Updated 6 months ago

graphenv — Peer-reviewed • Rank 6.1 • Science 93%

graphenv: a Python library for reinforcement learning on graph search spaces - Published in JOSS (2022)

Artificial Intelligence and Machine Learning (33%)
Scientific Software · Peer-reviewed
Scientific Software
Updated 6 months ago

cosasi — Peer-reviewed • Rank 5.7 • Science 93%

cosasi: Graph Diffusion Source Inference in Python - Published in JOSS (2022)

Updated 6 months ago

tractor.base • Rank 15.7 • Science 77%

Magnetic resonance imaging and tractography with R

Updated 6 months ago

cytoscape.js-cise • Rank 5.3 • Science 85%

An implementation of the circular layout algorithm by Dogrusoz et al. as a Cytoscape.js extension

Updated 6 months ago

kglab • Rank 15.8 • Science 67%

Graph Data Science: an abstraction layer in Python for building knowledge graphs, integrated with popular graph libraries – atop Pandas, NetworkX, RAPIDS, RDFlib, pySHACL, PyVis, morph-kgc, pslpython, pyarrow, etc.

Scientific Software
Updated 6 months ago

BisPy — Peer-reviewed • Rank 4.4 • Science 77%

BisPy: Bisimulation in Python - Published in JOSS (2021)

Updated 6 months ago

suitesparse • Rank 15.5 • Science 59%

The official SuiteSparse library: a suite of sparse matrix algorithms authored or co-authored by Tim Davis, Texas A&M University.

Updated 6 months ago

AtiyahBott • Rank 3.0 • Science 67%

An implementation of the Atiyah-Bott formula for the moduli space of genus 0 stable maps.

Updated 6 months ago

graphtage • Rank 15.7 • Science 44%

A semantic diff utility and library for tree-like files such as JSON, JSON5, XML, HTML, YAML, and CSV.

Updated 6 months ago

phd-dissertation • Rank 1.9 • Science 54%

My "Efficient Materials Informatics between Rockets and Electrons" PhD Dissertation in Materials Science and Engineering, defended on May 20th 2024, concisely spanning 352 pages and 109 figures.

Updated 6 months ago

iGraphMatch • Rank 10.6 • Science 36%

Tools to find the correspondences between vertices in different graphs.

Updated 5 months ago

https://github.com/cqcl/portgraph • Rank 16.8 • Science 26%

Directed graph with first-level ports in Rust.

Updated 5 months ago

https://github.com/jmrozanec/ts2g2 • Rank 1.1 • Science 36%

Generate graphs from time series and time series from graphs.

Scientific Software
Updated 6 months ago

SPbLA — Peer-reviewed • Rank 3.9 • Science 26%

SPbLA: The Library of GPGPU-powered Sparse Boolean Linear Algebra Operations - Published in JOSS (2022)

Scientific Software
Updated 6 months ago

IGraph/M — Peer-reviewed • Science 95%

IGraph/M: graph theory and network analysis for Mathematica - Published in JOSS (2023)

Updated 5 months ago

https://github.com/kahypar/mt-kahypar • Science 49%

Mt-KaHyPar (Multi-Threaded Karlsruhe Hypergraph Partitioner) is a shared-memory multilevel graph and hypergraph partitioner equipped with parallel implementations of techniques used in the best sequential partitioning algorithms. Mt-KaHyPar can partition extremely large hypergraphs very fast and with high quality.

Updated 6 months ago

sssnet_signed_clustering • Science 36%

Official code for the SDM2022 paper -- SSSNET: Semi-Supervised Signed Network Clustering.

Updated 6 months ago

cytoscape-layout-utilities • Science 75%

Miscellaneous utilities for placement of nodes or components complementary to a main layout algorithm

Updated 5 months ago

matlab-igraph: bringing igraph to MATLAB • Science 98%

matlab-igraph: bringing igraph to MATLAB - Published in JOSS (2025)

Updated 4 months ago

https://github.com/gscholze/graphcream • Science 13%

using graphs to choose ice cream flavors

Updated 6 months ago

teexgraph • Science 57%

C++ library for large-scale network analysis and computation

Updated 6 months ago

global-chem • Science 57%

A Knowledge Graph of Common Chemical Names to their Molecular Definition

Updated 6 months ago

gpugraphlayout • Science 67%

An experimental GPU accelerated implementation of ForceAtlas2

Updated 6 months ago

feasible-edge-replacements • Science 54%

Classes and algorithms for recursive amoeba trees and general framework for feasible edge replacements.

Updated 5 months ago

https://github.com/alondmnt/scom • Science 13%

algorithm for detecting Spatially Co-evolving Orthologous Modules

Updated 6 months ago

idron • Science 44%

Inferring Distance Rankings on Networks

Updated 6 months ago

community-aware-graph-transformer • Science 67%

Community-aware Graph Transformer (CGT) is a novel Graph Transformer model that utilizes community structures to address node degree biases in message-passing mechanism and developed by NS Lab @ CUK based on pure PyTorch backend.

Updated 5 months ago

https://github.com/amr-yasser226/pagerank-power-method • Science 26%

Modular Python implementation of the PageRank algorithm via the power method, with discrete‑math foundations, end‑to‑end code, and experimental validation.

Updated 6 months ago

graphsbase.jl • Science 44%

Basic interface and structures for the JuliaGraphs ecosystem

Updated 6 months ago

hypergraphx • Science 67%

HGX is a multi-purpose, open-source Python library for higher-order network analysis

Updated 6 months ago

orbweaver • Science 26%

Orbweaver is an R package that optimizes the processing of graph data structures.