GitHub
pyransac3d
A python tool for fitting primitives 3D shapes in point clouds using RANSAC algorithm
amici
High-performance sensitivity analysis for large ordinary differential equation models
https://github.com/cytoscape/cytoscape.js
Graph theory (network) library for visualisation and analysis
PySWMM
PySWMM: The Python Interface to Stormwater Management Model (SWMM) - Published in JOSS (2020)
gladia-torchaudio
Data manipulation and transformation for audio signal processing, powered by PyTorch
ogs6py and VTUinterface
ogs6py and VTUinterface: streamlining OpenGeoSys workflows in Python - Published in JOSS (2021)
eights
eights: BS 8888:2011 first angle projection drawings from FreeCAD 3D model - Published in JOSS (2019)
“Blaster” – a graphical user interface for common sequence analysis tools
“Blaster” – a graphical user interface for common sequence analysis tools - Published in JOSS (2019)
Multivariate Covariance Generalized Linear Models in Python
Multivariate Covariance Generalized Linear Models in Python: The mcglm library - Published in JOSS (2024)
YAD
YAD: A Learning-based Inductive Logic Programming Tool - Published in JOSS (2018)
CytobankAPIstats
CytobankAPIstats: Computes Signaling and Population Statistics for Cytometry Data on Cytobank using 'CytobankAPI' - Published in JOSS (2019)
TidyTensor
TidyTensor: Utilities for multidimensional arrays as named hierarchical structures - Published in JOSS (2021)
Bramble
Bramble: adaptive common neighbor analysis (CNA) for the recognition of surface topologies in nanoparticles - Published in JOSS (2023)
ordPens
ordPens: An R package for Selection, Smoothing and Principal Components Analysis for Ordinal Variables - Published in JOSS (2021)
catalystcoop.pudl
The Public Utility Data Liberation Project provides analysis-ready energy system data to climate advocates, researchers, policymakers, and journalists.
BayesFlow
BayesFlow: Amortized Bayesian Workflows With Neural Networks - Published in JOSS (2023)
compas-cra
Coupled Rigid-Block Analysis: Stability-Aware Design of Complex Discrete-Element Assemblies
pastas
Pastas is an open-source Python framework for the analysis of groundwater time series.
edsnlp
Modular, fast NLP framework, compatible with Pytorch and spaCy, offering tailored support for French clinical notes.
Algorithms for SEM-EDS Mineral Dust Classification
Algorithms for SEM-EDS Mineral Dust Classification - Published in JOSS (2025)
fff_segmenter
fff_segmenter: A signal segmentation script for acoustic FFF fabrication data in MATLAB - Published in JOSS (2024)
OpenEPSim
OpenEPSim: An Open Exclusion Process Simulation Tool - Published in JOSS (2018)
Bioassays
Bioassays: a new package in R for analyzing cellular assays - Published in JOSS (2020)
CRED
CRED: a rapid peak caller for Chem-seq data - Published in JOSS (2019)
YoungTab
YoungTab - Published in JOSS (2017)
Habfuzz
Habfuzz: A tool to calculate the instream hydraulic habitat suitability using fuzzy logic and fuzzy Bayesian inference - Published in JOSS (2016)
BCEA
Bayesian Cost Effectiveness Analysis. Given the results of a Bayesian model (possibly based on MCMC) in the form of simulations from the posterior distributions of suitable variables of costs and clinical benefits for two or more interventions, produces a health economic evaluation. Compares one of the interventions (the "reference") to the others ("comparators"). Produces many summary and plots to analyse the results
esmvaltool
ESMValTool: A community diagnostic and performance metrics tool for routine evaluation of Earth system models in CMIP
NiTransforms
NiTransforms: A Python tool to read, represent, manipulate, and apply $n$-dimensional spatial transforms - Published in JOSS (2021)
@kit-data-manager/react-pid-component
The PID-Component is a web component that can be used to display PIDs, ORCiDs, and possibly other identifiers in a user-friendly way. It is easily extensible to support other identifier types.
parcels
Main code for Parcels - a highly customisable Lagrangian simulation framework
DEVSIM
DEVSIM: A TCAD Semiconductor Device Simulator - Published in JOSS (2022)
pettingzoo
An API standard for multi-agent reinforcement learning environments, with popular reference environments and related utilities
flaml
A fast library for AutoML and tuning. Join our Discord: https://discord.gg/Cppx2vSPVP.
esmvalcore
ESMValCore: A community tool for pre-processing data from Earth system models in CMIP and running analysis scripts.
heat
Distributed tensors and Machine Learning framework with GPU and MPI acceleration in Python
specreduce
Tools for the reduction of spectroscopic observations from Optical and NIR instruments
cebra
Learnable latent embeddings for joint behavioral and neural analysis - Official implementation of CEBRA
CITapp - a response time-based Concealed Information Test lie detector web application
CITapp - a response time-based Concealed Information Test lie detector web application - Published in JOSS (2019)
fitODBOD
fitODBOD: An R Package to Model Binomial Outcome Data using Binomial Mixture and Alternate Binomial Distributions. - Published in JOSS (2019)
gofcat
gofcat: An R package for goodness-of-fit of categorical response models - Published in JOSS (2022)
Discrete Laplace mixture model with applications in forensic genetics
Discrete Laplace mixture model with applications in forensic genetics - Published in JOSS (2018)
Automated Sleep Stage Scoring Using k-Nearest Neighbors Classifier
Automated Sleep Stage Scoring Using k-Nearest Neighbors Classifier - Published in JOSS (2020)
serverless-benchmarks
SeBS: serverless benchmarking suite for automatic performance analysis of FaaS platforms.
deltascf-aims
An application to automate core level spectroscopy simulations in FHI-aims
datalad-next
DataLad extension for new functionality and improved user experience
andes
Python toolbox / library for power system transient dynamics simulation with symbolic modeling and numerical analysis 🔥
KrylovKit
Krylov methods for linear problems, eigenvalues, singular values and matrix functions
geostatspy
GeostatsPy Python package for spatial data analytics and geostatistics. Started as a reimplementation of GSLIB, Geostatistical Library (Deutsch and Journel, 1992) from Fortran to Python, Geostatistics in a Python package. Now with many additional methods. I hope this resources is helpful, Prof. Michael Pyrcz
dm-meltingpot
A suite of test scenarios for multi-agent reinforcement learning.
splashsurf
Surface reconstruction library and CLI for particle data from SPH simulations, written in Rust.
ersilia
The Ersilia Model Hub, a repository of AI/ML models for infectious and neglected disease research.
scikit-activeml
scikit-activeml: Python library for active learning on top of scikit-learn
mmgis
Multi-Mission Geographical Information System - Web-based Mapping and Spatial Data Infrastructure for Planetary Science Operations - https://nasa-ammos.github.io/MMGIS/
Altair
Altair: Interactive Statistical Visualizations for Python - Published in JOSS (2018)
fuxictr
A configurable, tunable, and reproducible library for CTR prediction https://fuxictr.github.io
Catalyst
Chemical reaction network and systems biology interface for scientific machine learning (SciML). High performance, GPU-parallelized, and O(1) solvers in open source software.
mermaid
Generation of diagrams like flowcharts or sequence diagrams from text in a similar manner as markdown
quantus
Quantus is an eXplainable AI toolkit for responsible evaluation of neural network explanations
pyiron
pyiron - an integrated development environment (IDE) for computational materials science.
DEPP - Differential Evolution Parallel Program
DEPP - Differential Evolution Parallel Program - Published in JOSS (2020)
autoStreamTree
autoStreamTree: Genomic variant data fitted to geospatial networks - Published in JOSS (2024)
PyMS
PyMS: Python for Mycorrhizal Symbiosis data analysis - Published in JOSS (2019)
TEfits
TEfits: Nonlinear regression for time-evolving indices - Published in JOSS (2020)
SeqPeelSort
SeqPeelSort: a spike sorting algorithm for single sensillum recordings - Published in JOSS (2018)
scikit-maad
Open-source and modular toolbox for quantitative soundscape analysis in Python
cytoscape-expand-collapse
A Cytoscape.js extension to expand/collapse nodes for better management of complexity of compound graphs
pytest
The pytest framework makes it easy to write small tests, yet scales to support complex functional testing