SunPy
SunPy: A Python package for Solar Physics - Published in JOSS (2020)
PyVista
PyVista: 3D plotting and mesh analysis through a streamlined interface for the Visualization Toolkit (VTK) - Published in JOSS (2019)
sourmash v4
sourmash v4: A multitool to quickly search, compare, and analyze genomic and metagenomic data sets - Published in JOSS (2024)
SpiceyPy
SpiceyPy: a Pythonic Wrapper for the SPICE Toolkit - Published in JOSS (2020)
mlpack 4
mlpack 4: a fast, header-only C++ machine learning library - Published in JOSS (2023)
NiaPy
NiaPy: Python microframework for building nature-inspired algorithms - Published in JOSS (2018)
DrWatson
DrWatson: the perfect sidekick for your scientific inquiries - Published in JOSS (2020)
icepyx
icepyx: querying, obtaining, analyzing, and manipulating ICESat-2 datasets - Published in JOSS (2023)
bayestestR
bayestestR: Describing Effects and their Uncertainty, Existence and Significance within the Bayesian Framework - Published in JOSS (2019)
Extracting, Computing and Exploring the Parameters of Statistical Models using R
Extracting, Computing and Exploring the Parameters of Statistical Models using R - Published in JOSS (2020)
ReproZip
ReproZip: The Reproducibility Packer - Published in JOSS (2016)
dust_extinction
dust_extinction: Interstellar Dust Extinction Models - Published in JOSS (2024)
DynamicalSystems.jl
DynamicalSystems.jl: A Julia software library for chaos and nonlinear dynamics - Published in JOSS (2018)
ggeffects
ggeffects: Tidy Data Frames of Marginal Effects from Regression Models - Published in JOSS (2018)
Physics-Informed Neural networks for Advanced modeling
Physics-Informed Neural networks for Advanced modeling - Published in JOSS (2023)
FURY
FURY: advanced scientific visualization - Published in JOSS (2021)
Visions
Visions: An Open-Source Library for Semantic Data - Published in JOSS (2020)
effectsize
effectsize: Estimation of Effect Size Indices and Standardized Parameters - Published in JOSS (2020)
performance
performance: An R Package for Assessment, Comparison and Testing of Statistical Models - Published in JOSS (2021)
insight
insight: A Unified Interface to Access Information from Model Objects in R - Published in JOSS (2019)
EZyRB
EZyRB: Easy Reduced Basis method - Published in JOSS (2018)
datawizard
datawizard: An R Package for Easy Data Preparation and Statistical Transformations - Published in JOSS (2022)
FiLiP
FiLiP: A python software development kit (SDK) for accelerating the development of services based on FIWARE IoT platform - Published in JOSS (2024)
Stingray 2
Stingray 2: A fast and modern Python library for spectral timing - Published in JOSS (2024)
see
see: An R Package for Visualizing Statistical Models - Published in JOSS (2021)
modelbased
modelbased: An R package to make the most out of your statistical models through marginal means, marginal effects, and model predictions - Published in JOSS (2025)
Methods and Algorithms for Correlation Analysis in R
Methods and Algorithms for Correlation Analysis in R - Published in JOSS (2020)
TimeseriesSurrogates.jl
TimeseriesSurrogates.jl: a Julia package for generating surrogate data - Published in JOSS (2022)
Open OnDemand
Open OnDemand: A web-based client portal for HPC centers - Published in JOSS (2018)
SLEPLET
SLEPLET: Slepian Scale-Discretised Wavelets in Python - Published in JOSS (2023)
Underworld2
Underworld2: Python Geodynamics Modelling for Desktop, HPC and Cloud - Published in JOSS (2020)
FTorch
FTorch: a library for coupling PyTorch models to Fortran - Published in JOSS (2025)
SWMManywhere
SWMManywhere: Synthesise Urban Drainage Network Models Anywhere in the World - Published in JOSS (2025)
FuseMedML
FuseMedML: a framework for accelerated discovery in machine learning based biomedicine - Published in JOSS (2023)
SummationByPartsOperators.jl
SummationByPartsOperators.jl: A Julia library of provably stable discretization techniques with mimetic properties - Published in JOSS (2021)
Bacting
Bacting: a next generation, command line version of Bioclipse - Published in JOSS (2021)
RIAssigner
RIAssigner: A package for gas chromatographic retention index calculation - Published in JOSS (2022)
TransitionsInTimeseries.jl
TransitionsInTimeseries.jl: A performant, extensible and reliable software for reproducible detection and prediction of transitions in timeseries - Published in JOSS (2024)
HRV
HRV: a Pythonic package for Heart Rate Variability Analysis - Published in JOSS (2020)
RSMTool
RSMTool: collection of tools building and evaluating automated scoring models - Published in JOSS (2016)
parafields
parafields: A generator for distributed, stationary Gaussian processes - Published in JOSS (2023)
Kepler Mapper
Kepler Mapper: A flexible Python implementation of the Mapper algorithm. - Published in JOSS (2019)
chemotools
chemotools: A Python Package that Integrates Chemometrics and scikit-learn - Published in JOSS (2024)
CHAMP is a HPC Access and Metadata Portal
CHAMP is a HPC Access and Metadata Portal - Published in JOSS (2022)
Taguette
Taguette: open-source qualitative data analysis - Published in JOSS (2021)
The Babelizer
The Babelizer: language interoperability for model coupling in the geosciences - Published in JOSS (2022)
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.
WorldDynamics.jl
WorldDynamics.jl: A Julia Package for Developing and Simulating Integrated Assessment Models - Published in JOSS (2024)
UWGeodynamics
UWGeodynamics: A teaching and research tool for numerical geodynamic modelling - Published in JOSS (2019)
Ipyannotator
Ipyannotator: the infinitely hackable annotation framework - Published in JOSS (2022)
Thresholdmann
Thresholdmann: A Web tool for interactively creating adaptive thresholds to segment MRI data. - Published in JOSS (2024)
kima
kima: Exoplanet detection in radial velocities - Published in JOSS (2018)
MSMetaEnhancer
MSMetaEnhancer: A Python package for mass spectra metadata annotation - Published in JOSS (2022)
q2-sample-classifier
q2-sample-classifier: machine-learning tools for microbiome classification and regression - Published in JOSS (2018)
Reorient
Reorient: A Web tool for reorienting and cropping MRI data. - Published in JOSS (2020)
graphannis
This is a new backend implementation of the ANNIS linguistic search and visualization system.
amici
High-performance sensitivity analysis for large ordinary differential equation models
pytest
The pytest framework makes it easy to write small tests, yet scales to support complex functional testing
parpe
Parameter estimation for dynamical models using high-performance computing, batch and mini-batch optimizers, and dynamic load balancing.
DynamicalSystemsBase
Definition of dynamical systems types and API for DynamicalSystems.jl
pysdc
pySDC is a Python implementation of the spectral deferred correction (SDC) approach and its flavors, esp. the multilevel extension MLSDC and PFASST.
@citation-js/cli
Core functionality of Citation.js, as well as the original plugins (CSL, BibTeX, RIS, DOI, Wikidata, and BibJSON)
lida
Automatic Generation of Visualizations and Infographics using Large Language Models
itk
Insight Toolkit (ITK) -- Official Repository. ITK builds on a proven, spatially-oriented architecture for processing, segmentation, and registration of scientific images in two, three, or more dimensions.
avogadro
Avogadro libraries provide 3D rendering, visualization, analysis and data processing useful in computational chemistry, molecular modeling, bioinformatics, materials science, and related areas.
Sundials
Julia interface to Sundials, including a nonlinear solver (KINSOL), ODE's (CVODE and ARKODE), and DAE's (IDA) in a SciML scientific machine learning enabled manner
optivorbis
🗜️ Library and application for lossless, format-preserving, two-pass optimization and repair of Vorbis data, reducing its size without altering any audio information.
novu
The open-source notification Inbox infrastructure. E-mail, SMS, Push and Slack Integrations.
jellyfish
🪼 a python library for doing approximate and phonetic matching of strings.