https://github.com/kumiori/indiscrete
How do elementary systems evolve, under irreversibility constraints?
https://github.com/kunalshah03/darknet
YOLOv4 / Scaled-YOLOv4 / YOLO - Neural Networks for Object Detection (Windows and Linux version of Darknet )
https://github.com/kundajelab/procapnet
Repository for modeling PRO-cap data with the BPNet-like model, ProCapNet.
https://github.com/kundajelab/immuneclip
CLIP-based model for aligning epitopes to immune receptors
https://github.com/kundajelab/chromdragonn
Code for the paper "Integrating regulatory DNA sequence and gene expression to predict genome-wide chromatin accessibility across cellular contexts"
https://github.com/kundajelab/3dchromatin_replicateqc
Software to compute reproducibility and quality scores for Hi-C data
https://github.com/kundajelab/coessentiality
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/synapse-backup-syncer
Create and sync backups to Synapse
https://github.com/kunpai/llm-inference-cpp
Script to run LLM inference using C++
https://github.com/kunpai/ecs272-final-project
Final project for ECS272 class - InfoVis
https://github.com/kurokida/jspsych
A JavaScript library for creating and running behavioral experiments in a web browser
https://github.com/kunpengren/ethlocal
Build a local private Ethereum Network by docker container
https://github.com/kurokio/soso-spase
For creating Science On Schema.Org (SOSO) markup in dataset landing pages to improve data discovery through search engines.
https://github.com/kurokio/spase-datacite
For creating and updating DataCite DOIs for SPASE records.
https://github.com/kurokio/ivoa-presentation-files
Contains the schema.org and DataCite JSONs resulting from new mappings with SPASE
https://github.com/lamastex/expositions
This is a set of mathematical, statistical and computational expositions
https://github.com/lamastex/jpautogradercomps
This is a repository for various components developed around semi/auto-grading a jupyter .ipynb notebook
https://github.com/lamastex/hawkesprocessesonmedia
Master's thesis of Alfred Lindstr\"om, Mathematics, Uppsala University, 2021 (exjobb of Combient Mix AB)
https://github.com/lamastex/2023-mastersthesis-axelsandstedt
Axel Sandstedt's Masters thesis
https://github.com/lamastex/spark-trend-calculus
To detect trends in time series using Andrew Morgan's trend calculus algorithms in Apache Spark and Scala from Antoine Amend's initial implementation
https://github.com/lamastex/scadamale
Scalable Data Science and Distributed Machine Learning Course Book written by Raazesh Sainudiin and his WASP AI-Track PhD Students
https://github.com/lczech/come_2017
Some sample files for the CoME2017 course to play around with.
https://github.com/lczech/ratatosk
Snakemake pipeline for phylogenetic placement of metagenomic sequences
https://github.com/lczech/grenepilot-paper
Scripts and analyses for the GrENE-net pilot dataset
https://github.com/lczech/grenedalf-paper
Code for tests and benchmarks of our paper on grenedalf
pyOMA2: A Python module for conducting operational modal analysis
pyOMA2: A Python module for conducting operational modal analysis - Published in JOSS (2025)
xeofs: Comprehensive EOF analysis in Python with xarray
xeofs: Comprehensive EOF analysis in Python with xarray - Published in JOSS (2024)
NOMAD: A distributed web-based platform for managing materials science research data
NOMAD: A distributed web-based platform for managing materials science research data - Published in JOSS (2023)
deepinv
DeepInverse: a PyTorch library for solving imaging inverse problems using deep learning
mlgidGUI - an annotation program for 2D scattering data
mlgidGUI - an annotation program for 2D scattering data - Published in JOSS (2025)
STON: SofTware for petrOgraphic visualisatioN
STON: SofTware for petrOgraphic visualisatioN - Published in JOSS (2025)
optimeo
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.
NeuroCAPs
NeuroCAPs: A Python Package for Performing Co-Activation Patterns Analyses on Resting-State and Task-Based fMRI Data - Published in JOSS (2025)
ActiSleep Tracker
ActiSleep Tracker: a Python-based dashboard for adjusting automatic sleep predictions of actigraphy data - Published in JOSS (2025)
HINA
HINA: A Learning Analytics Tool for Heterogenous Interaction Network Analysis in Python - Published in JOSS (2025)
PANKH: An unsteady potential flow solver for hovering airfoils
PANKH: An unsteady potential flow solver for hovering airfoils - Published in JOSS (2025)
elasticipy
A python toolkit to perform common tensor operations in Continuum Mechanics
PyMetric: A Geometry Informed Array Mathematics Package
PyMetric: A Geometry Informed Array Mathematics Package - Published in JOSS (2026)
SPAC: A Python Package for Spatial Single-Cell Analysis of Multiplexed Imaging
SPAC: A Python Package for Spatial Single-Cell Analysis of Multiplexed Imaging - Published in JOSS (2026)
pyforce: Python Framework for data-driven model Order Reduction of multi-physiCs problEms
pyforce: Python Framework for data-driven model Order Reduction of multi-physiCs problEms - Published in JOSS (2026)
vkcompviz
Vulkan image and data processing framework capable of running a cascade of compute shaders and displaying or storing the result.
hermes-rheo
Python package designed to complement and extend the piblin library, offering a set of transforms tailored for analysis of rheological data
SatRbedo: An R package for retrieving snow and ice albedo from optical satellite imagery
SatRbedo: An R package for retrieving snow and ice albedo from optical satellite imagery - Published in JOSS (2026)
Reyna: A minimal overhead polytopal discontinuous Galerkin finite element library
Reyna: A minimal overhead polytopal discontinuous Galerkin finite element library - Published in JOSS (2026)
MieSimulatorGUI: A user-friendly tool to compute and visualize light scattering by spherical dielectric particles
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
Dyad: a binary-star dynamics and statistics library for Python - Published in JOSS (2026)
pyfive: A pure-Python HDF5 reader
pyfive: A pure-Python HDF5 reader - Published in JOSS (2026)
KinOpt: A Python package for chemical kinetics analysis and optimization
KinOpt: A Python package for chemical kinetics analysis and optimization - Published in JOSS (2026)
search-query
Search Query: A Python package designed to load, lint, translate, save, improve, and automate academic literature search queries.
powerfactory-tools
A Python toolbox for the (external) control of DIgSILENT PowerFactory.
https://github.com/berkeleylab/fiats
A deep learning library for use in high-performance computing applications in modern Fortran
xr_fresh: Automated Time Series Feature Extraction for Remote Sensing & Gridded Data
xr_fresh: Automated Time Series Feature Extraction for Remote Sensing & Gridded Data - Published in JOSS (2025)
SpectralUnmixing
Spectral unmixing, oriented towards imaging spectroscopy data. Lots of flavors included.
MujocoROS2Control: Seamless MuJoCo Integration with ROS 2 for Robot Simulation and Control
MujocoROS2Control: Seamless MuJoCo Integration with ROS 2 for Robot Simulation and Control - Published in JOSS (2025)
HyRiver: Hydroclimate Data Retriever
HyRiver: Hydroclimate Data Retriever - Published in JOSS (2021)
dispersiveshallowwater.jl
A Julia library of structure-preserving numerical methods for dispersive wave equations
dataaimsr
dataaimsr: An R Client for the Australian Institute of Marine Science Data Platform API which provides easy access to AIMS Data Platform - Published in JOSS (2021)
https://github.com/kundajelab/fastism
In-silico Saturation Mutagenesis implementation with 10x or more speedup for certain architectures.
https://github.com/chroma-citi/namosim
A mobile-robot navigation planner for navigating among movable obstacles
