GitHub
MCycle
MCycle: A Python package for 1D sizing and analysis of thermodynamic power cycles - Published in JOSS (2018)
scTree
scTree: An R package to generate antibody-compatible classifiers from single-cell sequencing data - Published in JOSS (2020)
Xenomapper: Mapping reads in a mixed species context
Xenomapper: Mapping reads in a mixed species context - Published in JOSS (2016)
CVtreeMLE
CVtreeMLE: Efficient Estimation of Mixed Exposures using Data Adaptive Decision Trees and Cross-Validated Targeted Maximum Likelihood Estimation in R - Published in JOSS (2023)
cde - R package to retrieve data from the Environment Agency Catchment Data Explorer site
cde - R package to retrieve data from the Environment Agency Catchment Data Explorer site - Published in JOSS (2019)
medoutcon
medoutcon: Nonparametric efficient causal mediation analysis with machine learning in R - Published in JOSS (2022)
Mold
Mold: a LAMMPS package to compute interfacial free energies and nucleation rates - Published in JOSS (2024)
SWAMPE
SWAMPE: A Shallow-Water Atmospheric Model in Python for Exoplanets - Published in JOSS (2022)
MicroBenthos
MicroBenthos: a modeling framework for microbial benthic ecology - Published in JOSS (2018)
LGP
LGP: A robust Linear Genetic Programming implementation on the JVM using Kotlin. - Published in JOSS (2019)
Learning Simulator
Learning Simulator: A simulation software for animal and human learning - Published in JOSS (2021)
Dryft
Dryft: A Python and MATLAB package to correct drifting ground reaction force signals during treadmill running - Published in JOSS (2019)
Quilë
Quilë: C++ genetic algorithms scientific library - Published in JOSS (2023)
ParticleTracker
ParticleTracker: a gui based particle tracking software - Published in JOSS (2021)
mhealthtools
mhealthtools: A Modular R Package for Extracting Features from Mobile and Wearable Sensor Data - Published in JOSS (2020)
MM-PoE
MM-PoE: Multiple Choice Reasoning via. Process of Elimination using Multi-Modal Models - Published in JOSS (2025)
acronym
acronym: An Automatic Reduction Pipeline for Astronomical Images - Published in JOSS (2017)
CycloPhaser
CycloPhaser: A Python Package for Detecting Extratropical Cyclone Life Cycles - Published in JOSS (2025)
MetObs - a Python toolkit for using non-traditional meteorological observations
MetObs - a Python toolkit for using non-traditional meteorological observations - Published in JOSS (2024)
psychTestR
psychTestR: An R package for designing and conducting behavioural psychological experiments - Published in JOSS (2020)
Open-Unmix - A Reference Implementation for Music Source Separation
Open-Unmix - A Reference Implementation for Music Source Separation - Published in JOSS (2019)
The DynaGUI package
The DynaGUI package - Published in JOSS (2020)
mnt.pyfiction
An open-source design automation framework for Field-coupled Nanotechnologies
dtaidistance
Time series distances: Dynamic Time Warping (fast DTW implementation in C)
Phylogemetric
Phylogemetric: A Python library for calculating phylogenetic network metrics - Published in JOSS (2016)
deepmd-kit
A deep learning package for many-body potential energy representation and molecular dynamics
whampy
whampy: Python Package to Interact with, Visualize, and Analyze the Wisconsin H-Alpha Mapper - Sky Survey - Published in JOSS (2019)
LinguiPhyR
LinguiPhyR: A Package for Linguistic Phylogenetic Analysis in R - Published in JOSS (2024)
NEMESISPY
NEMESISPY: A Python package for simulating and retrieving exoplanetary spectra - Published in JOSS (2024)
Sinaps
Sinaps: A Python library to simulate voltage dynamics and ionic electrodiffusion in neurons - Published in JOSS (2022)
cosasi
cosasi: Graph Diffusion Source Inference in Python - Published in JOSS (2022)
atems
atems: Analysis tools for TEM images of carbonaceous particles - Published in JOSS (2024)
SenAOReFoc
SenAOReFoc: A Closed-Loop Sensorbased Adaptive Optics and Remote Focusing Control Software - Published in JOSS (2022)
directChillFoam
directChillFoam: an OpenFOAM application for direct-chill casting - Published in JOSS (2023)
pyBEMT
pyBEMT: An implementation of the Blade Element Momentum Theory in Python - Published in JOSS (2020)
DeepSynth
DeepSynth: Scaling Neural Program Synthesis with Distribution-based Search - Published in JOSS (2022)
EdgeVPN.io
EdgeVPN.io: Seamless Software-defined Layer 2 Virtual Networking for Edge Computing - Published in JOSS (2024)
NLMech
NLMech: Implementation of finite difference/meshfree discretization of nonlocal fracture models - Published in JOSS (2021)
DBSP_DRP
DBSP_DRP: A Python package for automated spectroscopic data reduction of DBSP data - Published in JOSS (2022)
QMRTools
QMRTools: a Mathematica toolbox for quantitative MRI analysis. - Published in JOSS (2019)
AtomNeb Python Package, an addendum to AtomNeb
AtomNeb Python Package, an addendum to AtomNeb: IDL Library for Atomic Data of Ionized Nebulae - Published in JOSS (2020)
pypots
A Python toolkit/library for reality-centric machine/deep learning and data mining on partially-observed time series, including SOTA neural network models for scientific analysis tasks of imputation/classification/clustering/forecasting/anomaly detection/cleaning on incomplete industrial (irregularly-sampled) multivariate TS with NaN missing values
xgboost
Scalable, Portable and Distributed Gradient Boosting (GBDT, GBRT or GBM) Library, for Python, R, Java, Scala, C++ and more. Runs on single machine, Hadoop, Spark, Dask, Flink and DataFlow
Shiny tools for management rules
Shiny tools for management rules: interactive applications that aid in conservation strategies for North Atlantic right whales - Published in JOSS (2023)
Synaptus
Synaptus: A Matlab/Octave toolbox for synthetic aperture ultrasound imaging - Published in JOSS (2022)
The 3D Slicer RVXLiverSegmentation plug-in for interactive liver anatomy reconstruction from medical images
The 3D Slicer RVXLiverSegmentation plug-in for interactive liver anatomy reconstruction from medical images - Published in JOSS (2022)
TSE
TSE: A triple stellar evolution code - Published in JOSS (2024)
AliasFinder
AliasFinder: A Python script to search for the true planetary frequency within radial velocity data - Published in JOSS (2020)
MSMExplorer
MSMExplorer: Data Visualizations for Biomolecular Dynamics - Published in JOSS (2017)
Bayesian model reconstruction based on spectral line observations with pomme
Bayesian model reconstruction based on spectral line observations with pomme - Published in JOSS (2024)
Excimontec v1.0
Excimontec v1.0: An Open-Source Software Tool for Kinetic Monte Carlo Simulations of Organic Electronic Devices - Published in JOSS (2020)
geocat-viz
GeoCAT-viz contains tools to help plot geoscience data, including convenience and plotting functions that are used to facilitate plotting geosciences data with Matplotlib, Cartopy, and other visualization packages.
pollucheck v1.0
pollucheck v1.0: A package to explore open-source air pollution data - Published in JOSS (2021)
GENRE (GPU Elastic-Net REgression)
GENRE (GPU Elastic-Net REgression): A CUDA-Accelerated Package for Massively Parallel Linear Regression with Elastic-Net Regularization - Published in JOSS (2020)
FEniCS-arclength
FEniCS-arclength: A numerical continuation package in FEniCS for nonlinear problems in solid mechanics - Published in JOSS (2024)
ShUShER
ShUShER: private browser-based placement of sensitive genome samples on phylogenetic trees - Published in JOSS (2021)
SeqIKPy: a Python package for inverse kinematics in insects
SeqIKPy: a Python package for inverse kinematics in insects - Published in JOSS (2026)
Taxonomy Resolver
Taxonomy Resolver: A Python package for building and filtering taxonomy trees - Published in JOSS (2025)
napari-clusters-plotter
A napari plugin for clustering objects according to their properties.
UPOsHam
UPOsHam: A Python package for computing unstable periodic orbits in two-degree-of-freedom Hamiltonian systems - Published in JOSS (2020)
MSG
MSG: A software package for interpolating stellar spectra in pre-calculated grids - Published in JOSS (2023)
papaya2
papaya2: 2D Irreducible Minkowski Tensor computation - Published in JOSS (2020)
Virtual Engineering: Python framework for engineering process design
Virtual Engineering: Python framework for engineering process design - Published in JOSS (2025)
HuracanPy
HuracanPy: A Python package for reading and analysing cyclone tracks - Published in JOSS (2025)
Estimating statistics from multi-state models using simulation with multistateutils
Estimating statistics from multi-state models using simulation with multistateutils - Published in JOSS (2018)
The ppmData R-package for setting up spatial point process models
The ppmData R-package for setting up spatial point process models - Published in JOSS (2023)
Eyestream
Eyestream: An Open WebSocket-based Middleware for Serializing and Streaming Eye Tracker Event Data from Gazepoint GP3 HD Research Hardware - Published in JOSS (2019)
ecopath_matlab
ecopath_matlab: A Matlab-based implementation of the Ecopath food web algorithm - Published in JOSS (2017)
Paraqus
Paraqus: Exporting Finite Element Simulation Results from Abaqus to VTK - Published in JOSS (2025)
Umami
Umami: A Python toolkit for jet flavour tagging - Published in JOSS (2024)
pypsa
PyPSA: Python for Power System Analysis
datasets
🤗 The largest hub of ready-to-use datasets for AI models with fast, easy-to-use and efficient data manipulation tools
TextWiller
TextWiller: Collection of functions for text mining, specially devoted to the Italian language - Published in JOSS (2019)
CoastalLens
CoastalLens: A MATLAB UAV Video Stabilization & Rectification Framework - Published in JOSS (2024)
Oetqf: A Julia package for quasi-dynamic earthquake cycle simulation
Oetqf: A Julia package for quasi-dynamic earthquake cycle simulation - Published in JOSS (2025)
VlaPy
VlaPy: A Python package for Eulerian Vlasov-Poisson-Fokker-Planck Simulations - Published in JOSS (2020)
Surjectors
Surjectors: surjection layers for density estimation with normalizing flows - Published in JOSS (2024)
MyPTV
MyPTV: A Python Package for 3D Particle Tracking - Published in JOSS (2022)
PyBWE
PyBWE: Python tools for Bandwidth Extrapolation of planetary radar signals - Published in JOSS (2024)
DuoDIC
DuoDIC: 3D Digital Image Correlation in MATLAB - Published in JOSS (2022)
pytransform3d
pytransform3d: 3D Transformations for Python - Published in JOSS (2019)
QuaCa
QuaCa: an open-source library for fast calculations of steady-state quantum friction - Published in JOSS (2023)
hei
hei: Calculate Healthy Eating Index (HEI) Scores - Published in JOSS (2017)
plotastic
plotastic: Bridging Plotting and Statistics in Python - Published in JOSS (2024)
TraitDB
TraitDB: Web application database of phenotypic trait data. - Published in JOSS (2019)
MAHOS
MAHOS: Measurement Automation Handling and Orchestration System - Published in JOSS (2023)
MetaGenePipe
MetaGenePipe: An Automated, Portable Pipeline for Contig-based Functional and Taxonomic Analysis - Published in JOSS (2023)
morphMan
morphMan: Automated manipulation of vascular geometries - Published in JOSS (2019)
JetFuelBurn: A Python package for calculating fuel burn of commercial aircraft
JetFuelBurn: A Python package for calculating fuel burn of commercial aircraft - Published in JOSS (2026)
QXTools
QXTools: A Julia framework for distributed quantum circuit simulation - Published in JOSS (2022)
GORILLA
GORILLA: Guiding-center ORbit Integration with Local Linearization Approach - Published in JOSS (2023)
PostcodesioR
PostcodesioR: An R package for UK geocoding - Published in JOSS (2023)
3D reconstruction toolbox for behavior tracked with multiple cameras
3D reconstruction toolbox for behavior tracked with multiple cameras - Published in JOSS (2020)
ElGateau
ElGateau: A Library for Using the Elgato Stream Deck for Experimental Psychology Research - Published in JOSS (2018)