mmdetection-competition • Science 44%

hgu • Science 44%

Project

dgmf • Science 52%

This repository holds the Dependency Graph Mining Framework (DGMF). DGMF offers fast, comparable depedency graph generation for multiple repositories.

knowledgeui • Science 57%

Application to Interact with a Knowledge Base in a Triple Store

parrotsdl-mmdetection3d • Science 54%

parrotsdl-mmaction2 • Science 54%

mmtracking • Science 54%

passwords-package • Science 44%

Password Generator and Strength Checker python package

fedsa_public • Science 67%

Field Effect Detection by Spectral Analysis, FEDSA, public repository.

hermes-plugins • Science 44%

Plugins for applying HERMES to publish Carpentries lessons

cyrcular-calling-main • Science 67%

ttsceleb • Science 54%

A TTS app where you can clone the voices of any person you wish.

ieeh-power-system-data-model • Science 75%

A hierarchical data model for the description of electrical power systems.

NonSysId: Nonlinear System Identification with Improved Model Term Selection for NARMAX Models • Science 93%

NonSysId: Nonlinear System Identification with Improved Model Term Selection for NARMAX Models - Published in JOSS (2025)

https://github.com/kunpengren/demolinux • Science 13%

THz Image Explorer - An Interactive Cross-Platform Open-Source THz Image Analysis Tool • Science 93%

THz Image Explorer - An Interactive Cross-Platform Open-Source THz Image Analysis Tool - Published in JOSS (2025)

https://github.com/kunpengren/slimchain • Science 13%

Source code for the VLDB21 paper "SlimChain: Scaling Blockchain Transactions through Off-Chain Storage and Parallel Processing"

https://github.com/kunpengren/starter-academic • Science 13%

phylo2vec • Science 67%

Phylo2Vec: a vector representation for binary trees

PyDrugLogics: A Python Package for Predicting Drug Synergies Using Boolean Models • Science 93%

PyDrugLogics: A Python Package for Predicting Drug Synergies Using Boolean Models - Published in JOSS (2025)

https://github.com/kunpengren/sui-networks • Science 13%

A local multiple validator nodes sui network with fauce service

https://github.com/kunpengren/verismart-benchmarks • Science 10%

MetaSpread: A cancer growth and metastatic spread simulation program in Python • Science 93%

MetaSpread: A cancer growth and metastatic spread simulation program in Python - Published in JOSS (2025)

mlr3extralearners: Expanding the mlr3 Ecosystem with Community-Driven Learner Integration • Science 95%

mlr3extralearners: Expanding the mlr3 Ecosystem with Community-Driven Learner Integration - Published in JOSS (2025)

deepinv • Science 54%

DeepInverse: a PyTorch library for solving imaging inverse problems using deep learning

mlgidGUI - an annotation program for 2D scattering data • Science 93%

mlgidGUI - an annotation program for 2D scattering data - Published in JOSS (2025)

STON: SofTware for petrOgraphic visualisatioN • Science 87%

STON: SofTware for petrOgraphic visualisatioN - Published in JOSS (2025)

optimeo • Science 67%

OPTIMEO is a package doubled by a web application that helps you optimize your experimental process by generating a Design of Experiment, generating new experiments using Bayesian Optimization (BO), and analyzing the results of your experiments using Machine Learning models.

PathFinder: A Matlab/Octave package for oscillatory integration • Science 93%

PathFinder: A Matlab/Octave package for oscillatory integration - Published in JOSS (2025)

NeuroCAPs — Peer-reviewed • Science 93%

NeuroCAPs: A Python Package for Performing Co-Activation Patterns Analyses on Resting-State and Task-Based fMRI Data - Published in JOSS (2025)

ActiSleep Tracker — Peer-reviewed • Science 93%

ActiSleep Tracker: a Python-based dashboard for adjusting automatic sleep predictions of actigraphy data - Published in JOSS (2025)

HINA — Peer-reviewed • Science 98%

HINA: A Learning Analytics Tool for Heterogenous Interaction Network Analysis in Python - Published in JOSS (2025)

calzone-tool • Science 44%

Evaluating the Calibration of Probabilistic Models

https://github.com/kunpengren/wormhole-token • Science 13%

PANKH: An unsteady potential flow solver for hovering airfoils • Science 93%

PANKH: An unsteady potential flow solver for hovering airfoils - Published in JOSS (2025)

https://github.com/kunpengren/zclaim • Science 10%

Cross-chain private transactions between Zcash chains

elasticipy • Science 49%

A python toolkit to perform common tensor operations in Continuum Mechanics

https://github.com/kurokida/jspsych • Science 23%

A JavaScript library for creating and running behavioral experiments in a web browser

eitprocessing • Science 44%

Software for electrical impedance tomography data loading, visualization and processing

https://github.com/kunpai/ecs272-final-project • Science 10%

Final project for ECS272 class - InfoVis

sata • Science 67%

opensim-creator • Science 49%

A UI for building OpenSim models

https://github.com/kunpai/ecs289g-alignment-term-project • Science 13%

https://github.com/kunpai/MARS • Science 26%

PyMetric: A Geometry Informed Array Mathematics Package • Science 87%

PyMetric: A Geometry Informed Array Mathematics Package - Published in JOSS (2026)

SPAC: A Python Package for Spatial Single-Cell Analysis of Multiplexed Imaging • Science 87%

SPAC: A Python Package for Spatial Single-Cell Analysis of Multiplexed Imaging - Published in JOSS (2026)

https://github.com/kunpai/llm-inference-cpp • Science 26%

Script to run LLM inference using C++

pyforce: Python Framework for data-driven model Order Reduction of multi-physiCs problEms • Science 87%

pyforce: Python Framework for data-driven model Order Reduction of multi-physiCs problEms - Published in JOSS (2026)

vkcompviz • Science 44%

Vulkan image and data processing framework capable of running a cascade of compute shaders and displaying or storing the result.

https://github.com/kundupro/packages-genmeta • Science 36%

constrainthg • Science 67%

General system simulation using constraint hypergraphs

https://github.com/kundupro/attributablefraction • Science 13%

https://github.com/kundupro/advanced_data_science-i • Science 13%

https://github.com/kundajelab/atacseq-dnaseseq-chrombpnet-modelzoo-pipeline • Science 13%

itwinai • Science 44%

Advanced AI workflows for scientific digital twins

hermes-rheo • Science 49%

Python package designed to complement and extend the piblin library, offering a set of transforms tailored for analysis of rheological data

https://github.com/kundajelab/affinity_distillation • Science 36%

SatRbedo: An R package for retrieving snow and ice albedo from optical satellite imagery • Science 87%

SatRbedo: An R package for retrieving snow and ice albedo from optical satellite imagery - Published in JOSS (2026)

torch_blue: A Flexible Python Package for Bayesian Neural Networks in PyTorch • Science 87%

torch_blue: A Flexible Python Package for Bayesian Neural Networks in PyTorch - Published in JOSS (2026)

https://github.com/spectralmatch/spectralmatch • Science 49%

Relative radiometric normalization toolkit for raster mosaics and time series

https://github.com/kundajelab/ctcfmutants • Science 13%

FAIRmaterials: Ontology Tools with Data FAIRification in Development • Science 87%

FAIRmaterials: Ontology Tools with Data FAIRification in Development - Published in JOSS (2026)

tools4rdf • Science 44%

Collection of tools for working with RDF data

$\mathcal{H}$-HIGNN Toolkit: A Software for Efficient and Scalable Simulation of Large-Scale Particulate Suspensions Using GNNs and $\mathcal{H}$-Matrices • Science 90%

$\mathcal{H}$-HIGNN Toolkit: A Software for Efficient and Scalable Simulation of Large-Scale Particulate Suspensions Using GNNs and $\mathcal{H}$-Matrices - Published in JOSS (2026)

aiida-aimall: A Python package for automating workflows for AIMAll software • Science 87%

aiida-aimall: A Python package for automating workflows for AIMAll software - Published in JOSS (2026)

https://github.com/kundajelab/pylearn2 • Science 10%

A Machine Learning library based on Theano

https://github.com/kundupro/codejavaapp • Science 13%

https://github.com/kundajelab/synapse-backup-syncer • Science 13%

Create and sync backups to Synapse

OnlinePCA.jl: A Julia Package for Out-of-core and Sparse Principal Component Analysis • Science 87%

OnlinePCA.jl: A Julia Package for Out-of-core and Sparse Principal Component Analysis - Published in JOSS (2026)

OnlineNMF.jl: A Julia Package for Out-of-core and Sparse Non-negative Matrix Factorization • Science 87%

OnlineNMF.jl: A Julia Package for Out-of-core and Sparse Non-negative Matrix Factorization - Published in JOSS (2026)

https://github.com/kundajelab/anvil-variant-scoring • Science 13%

https://github.com/kundajelab/coessentiality • Science 13%

Companion to "A genome-wide almanac of co-essential modules assigns function to uncharacterized genes" (https://doi.org/10.1101/827071)

https://github.com/kundajelab/3dchromatin_replicateqc • Science 10%

Software to compute reproducibility and quality scores for Hi-C data

Reyna: A minimal overhead polytopal discontinuous Galerkin finite element library • Science 87%

Reyna: A minimal overhead polytopal discontinuous Galerkin finite element library - Published in JOSS (2026)

A Python API for OTTER • Science 87%

A Python API for OTTER - Published in JOSS (2026)

c3dr • Science 67%

Read and write C3D motion capture data in R

rydiqule • Science 75%

Rydberg Sensor Interactive Quantum Physics Module

MieSimulatorGUI: A user-friendly tool to compute and visualize light scattering by spherical dielectric particles • Science 87%

MieSimulatorGUI: A user-friendly tool to compute and visualize light scattering by spherical dielectric particles - Published in JOSS (2026)

Dyad: a binary-star dynamics and statistics library for Python • Science 87%

Dyad: a binary-star dynamics and statistics library for Python - Published in JOSS (2026)

pyfive: A pure-Python HDF5 reader • Science 92%

pyfive: A pure-Python HDF5 reader - Published in JOSS (2026)

r.earthworks • Science 67%

An add-on tool for computational terrain modeling in GRASS

BiGSTARS.jl: A Julia package for bi-global stability analysis for rotating stratified flows • Science 87%

BiGSTARS.jl: A Julia package for bi-global stability analysis for rotating stratified flows - Published in JOSS (2026)

regularizedoptimization.jl • Science 67%

Algorithms for regularized optimization

https://github.com/kundajelab/cardiogenesis_repo • Science 23%

Cardiogenesis Repo

anvay: A Web-based Tool for Interpretive Topic Modelling in Bengali • Science 87%

anvay: A Web-based Tool for Interpretive Topic Modelling in Bengali - Published in JOSS (2026)

Htool-DDM: A C++ library for parallel solvers and compressed linear systems. • Science 92%

Htool-DDM: A C++ library for parallel solvers and compressed linear systems. - Published in JOSS (2026)

KinOpt: A Python package for chemical kinetics analysis and optimization • Science 87%

KinOpt: A Python package for chemical kinetics analysis and optimization - Published in JOSS (2026)

https://github.com/kundajelab/chromdragonn • Science 23%

Code for the paper "Integrating regulatory DNA sequence and gene expression to predict genome-wide chromatin accessibility across cellular contexts"

FluxOptics.jl: A Differentiable Wave Optics Framework for Inverse Design in Julia • Science 87%

FluxOptics.jl: A Differentiable Wave Optics Framework for Inverse Design in Julia - Published in JOSS (2026)

https://github.com/kundajelab/bpnet-manuscript • Science 10%

BPNet manuscript code.

Graphorge: An open-source forge of graph neural networks • Science 87%

Graphorge: An open-source forge of graph neural networks - Published in JOSS (2026)

tangram, an open platform for modular, real-time air traffic management research • Science 96%

tangram, an open platform for modular, real-time air traffic management research - Published in JOSS (2025)

simulist • Science 67%

An R package for simulating line lists

https://github.com/kundajelab/neural_motif_discovery • Science 10%

Framework for interrogating transcription-factor motifs and their syntax/grammars from neural-network interpretations

powerfactory-tools • Science 75%

A Python toolbox for the (external) control of DIgSILENT PowerFactory.

times_model • Science 23%

The Integrated MARKAL-EFOM System (TIMES) - a bottom-up optimization model for energy-environment systems

https://github.com/kundajelab/pybigwig • Science 23%

A python extension for quick access to bigWig files

nepcmforcedconvectionpimplefoam • Science 54%

baysc: An R package for Bayesian survey clustering • Science 87%

baysc: An R package for Bayesian survey clustering - Published in JOSS (2026)

https://github.com/kundajelab/libbigwig • Science 23%

A C library for handling bigWig files