graphsim
graphsim: An R package for simulating gene expression data from graph structures of biological pathways - Published in JOSS (2020)
Netgraph
Netgraph: Publication-quality Network Visualisations in Python - Published in JOSS (2023)
OApackage
OApackage: A Python package for generation and analysis of orthogonal arrays, optimal designs and conference designs - Published in JOSS (2019)
spgrep
spgrep: On-the-fly generator of space-group irreducible representations - Published in JOSS (2023)
fractopo
fractopo: A Python package for fracture network analysis - Published in JOSS (2023)
gym-electric-motor (GEM)
gym-electric-motor (GEM): A Python toolbox for the simulation of electric drive systems - Published in JOSS (2021)
AtlasReader
AtlasReader: A Python package to generate coordinate tables, region labels, and informative figures from statistical MRI images - Published in JOSS (2019)
BibDedupe
BibDedupe: An Open-Source Python Library for Bibliographic Record Deduplication - Published in JOSS (2024)
PyCPD
PyCPD: Pure NumPy Implementation of the Coherent Point Drift Algorithm - Published in JOSS (2022)
Monte Carlo / Dynamic Code (MC/DC)
Monte Carlo / Dynamic Code (MC/DC): An accelerated Python package for fully transient neutron transport and rapid methods development - Published in JOSS (2024)
Tools21cm
Tools21cm: A python package to analyse the large-scale 21-cm signal from the Epoch of Reionization and Cosmic Dawn - Published in JOSS (2020)
egobox, a Rust toolbox for efficient global optimization
egobox, a Rust toolbox for efficient global optimization - Published in JOSS (2022)
Stingray 2
Stingray 2: A fast and modern Python library for spectral timing - Published in JOSS (2024)
DataInterpolations.jl
DataInterpolations.jl: Fast Interpolations of 1D data - Published in JOSS (2024)
Blimpy
Blimpy: Breakthrough Listen I/O Methods for Python - Published in JOSS (2019)
sjmisc
sjmisc: Data and Variable Transformation Functions - Published in JOSS (2018)
see
see: An R Package for Visualizing Statistical Models - Published in JOSS (2021)
PyPulseq
PyPulseq: A Python Package for MRI Pulse Sequence Design - Published in JOSS (2019)
EPyT
EPyT: An EPANET-Python Toolkit for Smart Water Network Simulations - Published in JOSS (2023)
AMLTK
AMLTK: A Modular AutoML Toolkit in Python - Published in JOSS (2024)
AMReX
AMReX: a framework for block-structured adaptive mesh refinement - Published in JOSS (2019)
UltraNest - a robust, general purpose Bayesian inference engine
UltraNest - a robust, general purpose Bayesian inference engine - Published in JOSS (2021)
Pylinac
Pylinac: Image analysis for routine quality assurance in radiotherapy - Published in JOSS (2023)
Bempp-cl
Bempp-cl: A fast Python based just-in-time compiling boundary element library. - Published in JOSS (2021)
The Causal Testing Framework
The Causal Testing Framework - Published in JOSS (2025)
The pdb2sql Python Package
The pdb2sql Python Package: Parsing, Manipulation and Analysis of PDB Files Using SQL Queries - Published in JOSS (2020)
Pyglmnet
Pyglmnet: Python implementation of elastic-net regularized generalized linear models - Published in JOSS (2020)
fqfa
fqfa: A pure Python package for genomic sequence files - Published in JOSS (2020)
py-pde
py-pde: A Python package for solving partial differential equations - Published in JOSS (2020)
ETHOS.FINE
ETHOS.FINE: A Framework for Integrated Energy System Assessment - Published in JOSS (2025)
Efficient Polyhedral Gravity Modeling in Modern C++ and Python
Efficient Polyhedral Gravity Modeling in Modern C++ and Python - Published in JOSS (2024)
Micro Manager
Micro Manager: a Python package for adaptive and flexible two-scale coupling - Published in JOSS (2023)
https://github.com/juliageo/cftime.jl
Julia library for decoding time units conforming to the Climate and Forecasting (CF) netCDF conventions.
Turftopic
Turftopic: Topic Modelling with Contextual Representations from Sentence Transformers - Published in JOSS (2025)
OnlineStats.jl
OnlineStats.jl: A Julia package for statistics on data streams - Published in JOSS (2020)
DeepRank2
DeepRank2: Mining 3D Protein Structures with Geometric Deep Learning - Published in JOSS (2024)
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)
PAM
PAM: Population Activity Modeller - Published in JOSS (2024)
SNEWPY
SNEWPY: A Data Pipeline from Supernova Simulations to Neutrino Signals - Published in JOSS (2021)
Methods and Algorithms for Correlation Analysis in R
Methods and Algorithms for Correlation Analysis in R - Published in JOSS (2020)
JetNet
JetNet: A Python package for accessing open datasets and benchmarking machine learning methods in high energy physics - Published in JOSS (2023)
Larq
Larq: An Open-Source Library for Training Binarized Neural Networks - Published in JOSS (2020)
ezc3d
ezc3d: An easy C3D file I/O cross-platform solution for C++, Python and MATLAB - Published in JOSS (2021)
CMinx
CMinx: A CMake Documentation Generator - Published in JOSS (2022)
JMcDM
JMcDM: A Julia package for multiple-criteria decision-making tools - Published in JOSS (2021)
CellPyLib
CellPyLib: A Python Library for working with Cellular Automata - Published in JOSS (2021)
tidyhydat
tidyhydat: Extract and Tidy Canadian Hydrometric Data - Published in JOSS (2017)
DSSE
DSSE: An environment for simulation of reinforcement learning-empowered drone swarm maritime search and rescue missions - Published in JOSS (2024)
metrica
metrica: an R package to evaluate prediction performance of regression and classification point-forecast models - Published in JOSS (2022)
PDFIO
PDFIO: PDF Reader Library for native Julia - Published in JOSS (2019)
pyodesys
pyodesys: Straightforward numerical integration of ODE systems from Python - Published in JOSS (2018)
FOXES
FOXES: Farm Optimization and eXtended yield Evaluation Software - Published in JOSS (2023)
https://github.com/connor-makowski/type_enforced
A pure python type enforcer for annotations. Enforce types in python functions and methods.
drms
drms: A Python package for accessing HMI and AIA data - Published in JOSS (2019)
Spectral Connectivity
Spectral Connectivity: a python package for computing multitaper spectral estimates and frequency-domain brain connectivity measures on the CPU and GPU - Published in JOSS (2022)
scene_synthesizer
scene_synthesizer: A Python Library for Procedural Scene Generation in Robot Manipulation - Published in JOSS (2025)
Finch
Finch: a tool adding dynamic abundance filtering to genomic MinHashing - Published in JOSS (2018)
TimeseriesSurrogates.jl
TimeseriesSurrogates.jl: a Julia package for generating surrogate data - Published in JOSS (2022)
Gridap
Gridap: An extensible Finite Element toolbox in Julia - Published in JOSS (2020)
Generative DAGs as an Interface Into Probabilistic Programming with the R Package causact
Generative DAGs as an Interface Into Probabilistic Programming with the R Package causact - Published in JOSS (2022)
Frites
Frites: A Python package for functional connectivity analysis and group-level statistics of neurophysiological data - Published in JOSS (2022)
qicharts2
qicharts2: Quality Improvement Charts for R - Published in JOSS (2018)
Gala
Gala: A Python package for galactic dynamics - Published in JOSS (2017)
measr
measr: Bayesian psychometric measurement using Stan - Published in JOSS (2023)
Manopt.jl
Manopt.jl: Optimization on Manifolds in Julia - Published in JOSS (2022)
FDApy
FDApy: a Python package for functional data - Published in JOSS (2025)
oce
oce: an R package for Oceanographic Analysis - Published in JOSS (2022)
Sciris
Sciris: Simplifying scientific software in Python - Published in JOSS (2023)
kuibit
kuibit: Analyzing Einstein Toolkit simulations with Python - Published in JOSS (2021)
coalitions
coalitions: Coalition probabilities in multi-party democracies - Published in JOSS (2018)
pymdp
pymdp: A Python library for active inference in discrete state spaces - Published in JOSS (2022)
Mechkit
Mechkit: A continuum mechanics toolkit in Python - Published in JOSS (2022)
mTRFpy
mTRFpy: A Python package for temporal response function analysis - Published in JOSS (2023)
LiberTEM
LiberTEM: Software platform for scalable multidimensional data processing in transmission electron microscopy - Published in JOSS (2020)
schwimmbad
schwimmbad: A uniform interface to parallel processing pools in Python - Published in JOSS (2017)
FSharpGephiStreamer
FSharpGephiStreamer: An idiomatic bridge between F# and network visualization - Published in JOSS (2019)
cffr
cffr: Generate Citation File Format Metadata for R Packages - Published in JOSS (2021)
PDR
PDR: The Planetary Data Reader - Published in JOSS (2024)
REDCapTidieR
REDCapTidieR: Extracting complex REDCap databases into tidy tables - Published in JOSS (2024)
GSODR
GSODR: Global Summary Daily Weather Data in R - Published in JOSS (2017)
GeophysicalModelGenerator.jl
GeophysicalModelGenerator.jl: A Julia package to visualise geoscientific data and create numerical model setups - Published in JOSS (2024)
SpeedyWeather.jl
SpeedyWeather.jl: Reinventing atmospheric general circulation models towards interactivity and extensibility - Published in JOSS (2024)
PyRolL - An Extensible OpenSource Framework for Rolling Simulation
PyRolL - An Extensible OpenSource Framework for Rolling Simulation - Published in JOSS (2024)
ZOSPy
ZOSPy: optical ray tracing in Python through OpticStudio - Published in JOSS (2024)
Rdataretriever
Rdataretriever: R Interface to the Data Retriever - Published in JOSS (2021)
Open OnDemand
Open OnDemand: A web-based client portal for HPC centers - Published in JOSS (2018)
ODES
ODES: a high level interface to ODE and DAE solvers - Published in JOSS (2018)
UnROOT
UnROOT: an I/O library for the CERN ROOT file format written in Julia - Published in JOSS (2022)
LISC
LISC: A Python Package for Scientific Literature Collection and Analysis - Published in JOSS (2019)
OpenRepGrid
OpenRepGrid: An R Package for the Analysis of Repertory Grid Data - Published in JOSS (2024)
Φ-ML
Φ-ML: Intuitive Scientific Computing with Dimension Types for Jax, PyTorch, TensorFlow & NumPy - Published in JOSS (2024)
pulse
pulse: A python package based on FEniCS for solving problems in cardiac mechanics - Published in JOSS (2019)