GitHub
pysr3
pysr3: A Python Package for Sparse Relaxed Regularized Regression - Published in JOSS (2023)
Gillespie.jl: Stochastic Simulation Algorithm in Julia
Gillespie.jl: Stochastic Simulation Algorithm in Julia - Published in JOSS (2016)
RadGEEToolbox: Streamlined Multispectral & SAR Analysis for Google Earth Engine
RadGEEToolbox: Streamlined Multispectral & SAR Analysis for Google Earth Engine - Published in JOSS (2025)
Mandyoc
Mandyoc: A finite element code to simulate thermochemical convection in parallel - Published in JOSS (2022)
AXITOM
AXITOM: A Python package for reconstruction of axisymmetric tomograms acquired by a conical beam - Published in JOSS (2019)
fastPLI
fastPLI: A Fiber Architecture Simulation Toolbox for 3D-PLI - Published in JOSS (2021)
SiSyPHE
SiSyPHE: A Python package for the Simulation of Systems of interacting mean-field Particles with High Efficiency - Published in JOSS (2021)
cuIBM
cuIBM: a GPU-based immersed boundary method code - Published in JOSS (2017)
electiondata
electiondata: a Python package for consolidating, checking, analyzing, visualizing and exporting election results - Published in JOSS (2022)
surtvep
surtvep: An R package for estimating time-varying effects - Published in JOSS (2024)
A Fast Iterative Method Python package
A Fast Iterative Method Python package - Published in JOSS (2021)
PetIBM
PetIBM: toolbox and applications of the immersed-boundary method on distributed-memory architectures - Published in JOSS (2018)
QuantNBody
QuantNBody: a Python package for quantum chemistry and physics to build and manipulate many-body operators and wave functions. - Published in JOSS (2022)
JeFaPaTo - A joint toolbox for blinking analysis and facial features extraction
JeFaPaTo - A joint toolbox for blinking analysis and facial features extraction - Published in JOSS (2024)
bbsAssistant
bbsAssistant: An R package for downloading and handling data and information from the North American Breeding Bird Survey - Published in JOSS (2019)
polypy - Analysis Tools for Solid State Molecular Dynamics and Monte Carlo Trajectories
polypy - Analysis Tools for Solid State Molecular Dynamics and Monte Carlo Trajectories - Published in JOSS (2021)
POSSA
POSSA: Power simulation for sequential analyses and multiple hypotheses - Published in JOSS (2022)
lhorizon
lhorizon: geometry and targeting via JPL Horizons - Published in JOSS (2021)
PxMCMC
PxMCMC: A Python package for proximal Markov Chain Monte Carlo - Published in JOSS (2023)
tacmagic
tacmagic: Positron emission tomography analysis in R - Published in JOSS (2019)
SCAS dashboard
SCAS dashboard: A tool to intuitively and interactively analyze Slurm cluster usage - Published in JOSS (2024)
GLUE Code
GLUE Code: A framework handling communication and interfaces between scales - Published in JOSS (2022)
CoralP
CoralP: Flexible visualization of the human phosphatome - Published in JOSS (2019)
flory
flory: A Python package for finding coexisting phases in multicomponent mixtures - Published in JOSS (2025)
D3mirt
D3mirt: Descriptive Three-Dimensional Multidimensional Item Response Theory for R - Published in JOSS (2024)
dms-view
dms-view: Interactive visualization tool for deep mutational scanning data - Published in JOSS (2020)
aweSOM
aweSOM: a CPU/GPU-accelerated Self-organizing Map and Statistically Combined Ensemble Framework for Machine-learning Clustering Analysis - Published in JOSS (2025)
PlanktonIndividuals.jl
PlanktonIndividuals.jl: A GPU supported individual-based phytoplankton life cycle model - Published in JOSS (2022)
xpecgen
xpecgen: A program to calculate x-ray spectra generated in tungsten anodes - Published in JOSS (2016)
4DModeller
4DModeller: a spatio-temporal modelling package - Published in JOSS (2025)
scikit-hubness
scikit-hubness: Hubness Reduction and Approximate Neighbor Search - Published in JOSS (2020)
DoSOCS
DoSOCS: A System for SPDX 2.0 Document Creation and Storage - Published in JOSS (2016)
Web-based text anonymization with Node.js
Web-based text anonymization with Node.js: Introducing NETANOS (Named entity-based Text Anonymization for Open Science) - Published in JOSS (2017)
QMix
QMix: A Python package for simulating the quasiparticle tunneling currents in SIS junctions - Published in JOSS (2019)
Eir
Eir: A Python Package for Epidemic Simulation - Published in JOSS (2021)
Thresholdmann
Thresholdmann: A Web tool for interactively creating adaptive thresholds to segment MRI data. - Published in JOSS (2024)
Local clustering
Local clustering - Published in JOSS (2018)
arcesetc
arcesetc: ARC Echelle Spectrograph Exposure Time Calculator - Published in JOSS (2019)
PRDA
PRDA: An R package for Prospective and Retrospective Design Analysis - Published in JOSS (2021)
aesop
aesop: ARC Echelle Spectroscopic Observation Pipeline - Published in JOSS (2018)
HOOMD-TF
HOOMD-TF: GPU-Accelerated, Online Machine Learning in the HOOMD-blue Molecular Dynamics Engine - Published in JOSS (2020)
Rescal-snow
Rescal-snow: Simulating snow dunes with cellular automata - Published in JOSS (2019)
swisslandstats-geopy
swisslandstats-geopy: Python tools for the land statistics datasets from the Swiss Federal Statistical Office - Published in JOSS (2019)
CEGO
CEGO: C++11 Evolutionary Global Optimization - Published in JOSS (2019)
ViMag
ViMag: A Visual Vibration Analysis Toolbox - Published in JOSS (2023)
dcTensor
dcTensor: An R package for discrete matrix/tensor decomposition - Published in JOSS (2023)
geoclaw-landspill
geoclaw-landspill: an oil land-spill and overland flow simulator for pipeline rupture events - Published in JOSS (2021)
PyStack3D
PyStack3D: A python package for fast image stack correction - Published in JOSS (2024)
Minerva
Minerva: a light-weight, narrative image browser for multiplexed tissue images - Published in JOSS (2020)
refsplitr
refsplitr: Author name disambiguation, author georeferencing, and mapping of coauthorship networks with Web of Science data - Published in JOSS (2020)
pyPhenology
pyPhenology: A python framework for plant phenology modelling - Published in JOSS (2018)
grapherator
grapherator: A Modular Multi-Step Graph Generator - Published in JOSS (2018)
molic
molic: An R package for multivariate outlier detection in contingency tables - Published in JOSS (2019)
concstats
concstats: Market Structure, Concentration and Inequality Measures, with R - Published in JOSS (2023)
mmaqshiny v1.0
mmaqshiny v1.0: R-Shiny package to explore Air-Quality Mobile-Monitoring data - Published in JOSS (2020)
MimiBRICK.jl
MimiBRICK.jl: A Julia package for the BRICK model for sea-level change in the Mimi integrated modeling framework - Published in JOSS (2022)
JOAN
JOAN: a framework for human-automated vehicle interaction experiments in a virtual reality driving simulator - Published in JOSS (2023)
DESPASITO
DESPASITO: A Python Package for SAFT EOS Parametrization and Thermodynamic Calculations - Published in JOSS (2025)
LBR-Stack
LBR-Stack: ROS 2 and Python Integration of KUKA FRI for Med and IIWA Robots - Published in JOSS (2024)
Efficiently Learning Relative Similarity Embeddings with Crowdsourcing
Efficiently Learning Relative Similarity Embeddings with Crowdsourcing - Published in JOSS (2023)
sahi
Framework agnostic sliced/tiled inference + interactive ui + error analysis plots
Scanbuddy: fMRI motion plotting and SNR estimation at scan acquisition
Scanbuddy: fMRI motion plotting and SNR estimation at scan acquisition - Published in JOSS (2025)
findSVI
findSVI: an R package to calculate the Social Vulnerability Index at multiple geographical levels - Published in JOSS (2024)
Annotate-Lab
Annotate-Lab: Simplifying Image Annotation - Published in JOSS (2024)
PyGeoPressure
PyGeoPressure: Geopressure Prediction in Python - Published in JOSS (2018)
basilisk
basilisk: a Bioconductor package for managing Python environments - Published in JOSS (2022)
VPsearch
VPsearch: fast exact sequence similarity search for genomic sequences - Published in JOSS (2022)
GCIdentifier.jl
GCIdentifier.jl: A Julia package for identifying molecular fragments from SMILES - Published in JOSS (2024)
HistoJS
HistoJS: Web-Based Analytical Tool for Advancing Multiplexed Images - Published in JOSS (2024)
ronswanson
ronswanson: Building Table Models for 3ML - Published in JOSS (2023)
SBIAX
SBIAX: Density-estimation simulation-based inference in JAX - Published in JOSS (2025)
DWIQC
DWIQC: A Python package for preprocessing and quality assurance of diffusion weighted images - Published in JOSS (2025)
partycls
partycls: A Python package for structural clustering - Published in JOSS (2021)
strandCheckR
strandCheckR: An R package for quantifying and removing double strand sequences for strand-specific RNA-seq - Published in JOSS (2019)
Pyripherals
Pyripherals: A Python Package for Communicating with Peripheral Electronic Devices - Published in JOSS (2022)
carl
carl: a likelihood-free inference toolbox - Published in JOSS (2016)
The PHITS Tools Python package for parsing, organizing, and analyzing results from the PHITS radiation transport and DCHAIN activation codes
The PHITS Tools Python package for parsing, organizing, and analyzing results from the PHITS radiation transport and DCHAIN activation codes - Published in JOSS (2025)
SIMsalabim
SIMsalabim: An open-source drift-diffusion simulator for semiconductor devices - Published in JOSS (2022)
BCAWT
BCAWT: Automated tool for codon usage bias analysis for molecular evolution - Published in JOSS (2019)
occupationMeasurement
occupationMeasurement: A Comprehensive Toolbox for Interactive Occupation Coding in Surveys - Published in JOSS (2023)
FixedPointFinder
FixedPointFinder: A Tensorflow toolbox for identifying and characterizing fixed points in recurrent neural networks - Published in JOSS (2018)
gcamfaostat
gcamfaostat: An R package to prepare, process, and synthesize FAOSTAT data for global agroeconomic and multisector dynamic modeling - Published in JOSS (2024)
pyemgpipeline
pyemgpipeline: A Python package for electromyography processing - Published in JOSS (2022)
starry_process
starry_process: Interpretable Gaussian processes for stellar light curves - Published in JOSS (2021)
Eniric
Eniric: Extended NIR Information Content - Published in JOSS (2019)
GPUE
GPUE: Graphics Processing Unit Gross--Pitaevskii Equation solver - Published in JOSS (2018)
dfreproject: A Python package for astronomical reprojection
dfreproject: A Python package for astronomical reprojection - Published in JOSS (2025)
iRF
iRF: extracting interactions from random forests - Published in JOSS (2018)
One4All
One4All: An Open Source Portal to Validate and Share Microplastics Data and Beyond - Published in JOSS (2024)
hilbertmodgroup
hilbertmodgroup: Reduction algorithms and framework for Hilbert Modular Groups - Published in JOSS (2022)
SideScanSonarEditor: A Python package for annotation of side-scan sonar data
SideScanSonarEditor: A Python package for annotation of side-scan sonar data - Published in JOSS (2025)
AstroPaint
AstroPaint: A Python Package for Painting Halo Catalogs into Celestial Maps - Published in JOSS (2020)
inAccessMod
inAccessMod: An R package to automate data downloading and processing for AccessMod - Published in JOSS (2024)
Hypredrive
Hypredrive: High-level interface for solving linear systems with hypre - Published in JOSS (2024)
MACE
MACE: a Machine-learning Approach to Chemistry Emulation - Published in JOSS (2025)
Sigma
Sigma: Uncertainty Propagation for C++ - Published in JOSS (2025)