GitHub
kramersmoyal
kramersmoyal: Kramers--Moyal coefficients for stochastic processes - Published in JOSS (2019)
pyhector
pyhector: A Python interface for the simple climate model Hector - Published in JOSS (2017)
MembraneAnalysis.jl
MembraneAnalysis.jl: A Julia package for analyzing molecular dynamics simulations of lipid membranes - Published in JOSS (2023)
mrivis
mrivis: Medical image visualization library for neuroscience in python - Published in JOSS (2018)
`hessQuik`
`hessQuik`: Fast Hessian computation of composite functions - Published in JOSS (2022)
Ngesh
Ngesh: a Python library for synthetic phylogenetic data - Published in JOSS (2021)
The nnlib2 library and nnlib2Rcpp R package for implementing neural networks
The nnlib2 library and nnlib2Rcpp R package for implementing neural networks - Published in JOSS (2021)
OpenSCM Two Layer Model
OpenSCM Two Layer Model: A Python implementation of the two-layer climate model - Published in JOSS (2021)
SPICY
SPICY: a Python toolbox for meshless assimilation from image velocimetry using radial basis functions - Published in JOSS (2024)
Olaf
Olaf: a lightweight, portable audio search system - Published in JOSS (2023)
multimatch-gaze
multimatch-gaze: The MultiMatch algorithm for gaze path comparison in Python - Published in JOSS (2019)
SALSA
SALSA: A Python Package for Constructing Synthetic Quasar Absorption Line Catalogs from Astrophysical Hydrodynamic Simulations - Published in JOSS (2020)
AirTrafficSim
AirTrafficSim: An open-source web-based air traffic simulation platform. - Published in JOSS (2023)
VineCopulas
VineCopulas: an open-source Python package for vine copula modelling - Published in JOSS (2024)
transformers
🤗 Transformers: the model-definition framework for state-of-the-art machine learning models in text, vision, audio, and multimodal models, for both inference and training.
Evoke
Evoke: A Python package for evolutionary signalling games - Published in JOSS (2024)
anadrofish
anadrofish: Anadromous fish population responses to dams - Published in JOSS (2025)
SurvivalVolume
SurvivalVolume: interactive volume threshold survival graphs - Published in JOSS (2016)
DREiMac
DREiMac: Dimensionality Reduction with Eilenberg-MacLane Coordinates - Published in JOSS (2023)
HoverFast
HoverFast: an accurate, high-throughput, clinically deployable nuclear segmentation tool for brightfield digital pathology images - Published in JOSS (2024)
RandomForestsGLS
RandomForestsGLS: An R package for Random Forests for dependent data - Published in JOSS (2022)
IDESolver
IDESolver: a general purpose integro-differential equation solver - Published in JOSS (2018)
Osier
Osier: A Python package for multi-objective energy system optimization - Published in JOSS (2024)
MMM
MMM: A C++ library for simulating large herbivores - Published in JOSS (2021)
xinvert
xinvert: A Python package for inversion problems in geophysical fluid dynamics - Published in JOSS (2023)
Katsu
Katsu: A Python package for Mueller and Stokes simulation and polarimetry - Published in JOSS (2025)
kokkos-fft
kokkos-fft: A shared-memory FFT for the Kokkos ecosystem - Published in JOSS (2025)
Xponge
Xponge: A Python package to perform pre- and post-processing of molecular simulations - Published in JOSS (2022)
CLAIRE
CLAIRE: Constrained Large Deformation Diffeomorphic Image Registration on Parallel Computing Architectures - Published in JOSS (2021)
umami
umami: A Python package for Earth surface dynamics objective function construction - Published in JOSS (2019)
SONIC
SONIC: Software for Optical Navigation and Instrument Calibration - Published in JOSS (2024)
Stokesian Dynamics in Python
Stokesian Dynamics in Python - Published in JOSS (2024)
studentlife
studentlife: Tidy Handling and Navigation of a Valuable Mobile-Health Dataset - Published in JOSS (2019)
lazyllm-llamafactory
Unified Efficient Fine-Tuning of 100+ LLMs & VLMs (ACL 2024)
<code>biopixR</code>
<code>biopixR</code>: Extracting Insights from Biological Images - Published in JOSS (2024)
astrosource
astrosource: automating optical astronomy measurement, calibration and analysis for variable stellar sources from provided photometry - Published in JOSS (2021)
Persistable
Persistable: persistent and stable clustering - Published in JOSS (2023)
Logodetect
Logodetect: One-shot detection of logos in image and video data - Published in JOSS (2022)
labjack-controller
labjack-controller: Robust and Easy Data Collection with Labjack T-Series DAQs in Python - Published in JOSS (2019)
Reasons
Reasons: A digital argument mapping library for modern browsers - Published in JOSS (2019)
ALUES
ALUES: R package for Agricultural Land Use Evaluation System - Published in JOSS (2022)
ratesb_python: A Python Package for Analyzing Rate Laws in Biological Models
ratesb_python: A Python Package for Analyzing Rate Laws in Biological Models - Published in JOSS (2025)
GECo
GECo: A collection of solvers for the self-gravitating Vlasov equations - Published in JOSS (2023)
WorldDynamics.jl
WorldDynamics.jl: A Julia Package for Developing and Simulating Integrated Assessment Models - Published in JOSS (2024)
RELSAD
RELSAD: A Python package for reliability assessment of modern distribution systems - Published in JOSS (2022)
PAS
PAS: a Python Anesthesia Simulator for drug control - Published in JOSS (2023)
lmfit
Non-Linear Least Squares Minimization, with flexible Parameter settings, based on scipy.optimize, and with many additional classes and methods for curve fitting.
PETRARCH2
PETRARCH2: Another Event Coding Program - Published in JOSS (2017)
thresholdmodeling
thresholdmodeling: A Python package for modeling excesses over a threshold using the Peak-Over-Threshold Method and the Generalized Pareto Distribution - Published in JOSS (2020)
MDCraft
MDCraft: A Python assistant for performing and analyzing molecular dynamics simulations of soft matter systems - Published in JOSS (2024)
BioSimSpace
BioSimSpace: An interoperable Python framework for biomolecular simulation - Published in JOSS (2019)
usearch
Fast Open-Source Search & Clustering engine × for Vectors & Arbitrary Objects × in C++, C, Python, JavaScript, Rust, Java, Objective-C, Swift, C#, GoLang, and Wolfram 🔍
aion
aion: An R Package to Represent Archaeological Time Series - Published in JOSS (2024)
Effluent
Effluent: A Python package for modelling effluent discharge - Published in JOSS (2023)
chombo-discharge
chombo-discharge: An AMR code for gas discharge simulations in complex geometries - Published in JOSS (2023)
Viime
Viime: Visualization and Integration of Metabolomics Experiments - Published in JOSS (2020)
AutoEncoderToolkit.jl
AutoEncoderToolkit.jl: A Julia package for training (Variational) Autoencoders - Published in JOSS (2024)
TLViz
TLViz: Visualising and analysing tensor decomposition models with Python - Published in JOSS (2022)
Cellocity
Cellocity: A Python package for analysis of confluent cell layer dynamics - Published in JOSS (2021)
Torque-limited simple pendulum
Torque-limited simple pendulum: A toolkit for getting familiar with control algorithms in underactuated robotics - Published in JOSS (2022)
qtl2pleio
qtl2pleio: Testing pleiotropy vs. separate QTL in multiparental populations - Published in JOSS (2019)
Oceananigans.jl
Oceananigans.jl: Fast and friendly geophysical fluid dynamics on GPUs - Published in JOSS (2020)
SAMBA
SAMBA: A Trainable Segmentation Web-App with Smart Labelling - Published in JOSS (2024)
Opfi
Opfi: A Python package for identifying gene clusters in large genomics and metagenomics data sets - Published in JOSS (2021)
sbp-env
sbp-env: A Python Package for Sampling-based Motion Planner and Samplers - Published in JOSS (2021)
EphemerisSources.jl
EphemerisSources.jl: Idiomatic Ephemeris Sourcing and Parsing in Julia - Published in JOSS (2024)
Comet Time Series Visualizer
Comet Time Series Visualizer: CometTS - Published in JOSS (2019)
SDGdetector
SDGdetector: an R-based text mining tool for quantifying efforts toward Sustainable Development Goals - Published in JOSS (2023)
Embeddings.jl
Embeddings.jl: easy access to pretrained word embeddings from Julia - Published in JOSS (2019)
lbh15
lbh15: a Python package for standard use and implementation of physical data of heavy liquid metals used in nuclear reactors - Published in JOSS (2024)
VIEWpoly
VIEWpoly: a visualization tool to integrate and explore results of polyploid genetic analysis - Published in JOSS (2022)
prisonbrief
prisonbrief: An R package that returns tidy data from the World Prison Brief website - Published in JOSS (2018)
EWDM
EWDM: A wavelet-based method for estimating directional spectra of ocean waves - Published in JOSS (2025)
ShOpt.jl
ShOpt.jl: A Julia Package for Empirical Point Spread Function Characterization of JWST NIRCam Data - Published in JOSS (2024)
PyGRB
PyGRB: A pure Python gamma-ray burst analysis package. - Published in JOSS (2020)
GraphSL
GraphSL: An Open-Source Library for Graph Source Localization Approaches and Benchmark Datasets - Published in JOSS (2024)
AxoPy
AxoPy: A Python Library for Implementing Human-Computer Interface Experiments - Published in JOSS (2019)
pyCADMium
pyCADMium: Chemical Atoms in Diatomic Molecules. A prolate spheroidal Python module for embedding calculations - Published in JOSS (2022)
'StreamPoseML' An End-to-End Open-Source Web Application and Python Toolkit for Real-Time Video Pose Classification and Machine Learning
'StreamPoseML' An End-to-End Open-Source Web Application and Python Toolkit for Real-Time Video Pose Classification and Machine Learning - Published in JOSS (2024)
The SAGE Rejected Article Tracker
The SAGE Rejected Article Tracker - Published in JOSS (2021)
Binette
Binette: a fast and accurate bin refinement tool to construct high quality Metagenome Assembled Genomes. - Published in JOSS (2024)
UWGeodynamics
UWGeodynamics: A teaching and research tool for numerical geodynamic modelling - Published in JOSS (2019)
PyKronecker
PyKronecker: A Python Library for the Efficient Manipulation of Kronecker Products and Related Structures - Published in JOSS (2023)
NeuroAnalyzer
NeuroAnalyzer: Julia toolbox for analyzing neurophysiological data - Published in JOSS (2025)
X-PSI
X-PSI: A Python package for neutron star X-ray pulse simulation and inference - Published in JOSS (2023)
bíogo/ncbi
bíogo/ncbi: interfaces to NCBI services for the Go language - Published in JOSS (2017)
covidregionaldata
covidregionaldata: Subnational data for COVID-19 epidemiology - Published in JOSS (2021)
libscientific
libscientific: A Powerful C Library for Multivariate Analysis - Published in JOSS (2023)
PFEIFER
PFEIFER: Preprocessing Framework for Electrograms Intermittently Fiducialized from Experimental Recordings - Published in JOSS (2018)
pathways
pathways: life cycle assessment of energy transition scenarios - Published in JOSS (2024)
NCBImeta
NCBImeta: efficient and comprehensive metadata retrieval from NCBI databases - Published in JOSS (2020)
Aletheia
Aletheia: an open-source toolbox for steganalysis - Published in JOSS (2024)