BGGM
BGGM: Bayesian Gaussian Graphical Models in R - Published in JOSS (2020)
MiscMetabar
MiscMetabar: an R package to facilitate visualization and reproducibility in metabarcoding analysis - Published in JOSS (2023)
BayesO
BayesO: A Bayesian optimization framework in Python - Published in JOSS (2023)
partition
partition: A fast and flexible framework for data reduction in R - Published in JOSS (2020)
Autorank
Autorank: A Python package for automated ranking of classifiers - Published in JOSS (2020)
Ambit – A FEniCS-based cardiovascular multi-physics solver
Ambit – A FEniCS-based cardiovascular multi-physics solver - Published in JOSS (2024)
hydroscoper
hydroscoper: R interface to the Greek National Data Bank for Hydrological and Meteorological Information - Published in JOSS (2018)
Shapelets
Shapelets: A Python package implementing shapelet functions and their applications - Published in JOSS (2024)
ProbNumDiffEq.jl
ProbNumDiffEq.jl: Probabilistic Numerical Solvers for Ordinary Differential Equations in Julia - Published in JOSS (2024)
The UCSCXenaTools R package
The UCSCXenaTools R package: a toolkit for accessing genomics data from UCSC Xena platform, from cancer multi-omics to single-cell RNA-seq - Published in JOSS (2019)
SysIdentPy
SysIdentPy: A Python package for System Identification using NARMAX models - Published in JOSS (2020)
JAXbind
JAXbind: Bind any function to JAX - Published in JOSS (2024)
scPCA
scPCA: A toolbox for sparse contrastive principal component analysis in R - Published in JOSS (2020)
pypromice
pypromice: A Python package for processing automated weather station data - Published in JOSS (2023)
PythonicDISORT
PythonicDISORT: A Python reimplementation of the Discrete Ordinate Radiative Transfer package DISORT - Published in JOSS (2024)
TransBigData
TransBigData: A Python package for transportation spatio-temporal big data processing, analysis and visualization - Published in JOSS (2022)
mikropml
mikropml: User-Friendly R Package for Supervised Machine Learning Pipelines - Published in JOSS (2021)
PyBCI
PyBCI: A Python Package for Brain-Computer Interface (BCI) Design - Published in JOSS (2023)
finreportr
finreportr: Financial Data from U.S. Securities and Exchange Commission - Published in JOSS (2016)
OpenTripPlanner for R
OpenTripPlanner for R - Published in JOSS (2019)
ASSUME - Agent-based Simulation for Studying and Understanding Market Evolution
ASSUME - Agent-based Simulation for Studying and Understanding Market Evolution - Published in JOSS (2025)
hal9001
hal9001: Scalable highly adaptive lasso regression in R - Published in JOSS (2020)
ReferenceSeeker
ReferenceSeeker: rapid determination of appropriate reference genomes - Published in JOSS (2020)
MemCNN
MemCNN: A Python/PyTorch package for creating memory-efficient invertible neural networks - Published in JOSS (2019)
SleepECG
SleepECG: a Python package for sleep staging based on heart rate - Published in JOSS (2023)
pycoQC, interactive quality control for Oxford Nanopore Sequencing
pycoQC, interactive quality control for Oxford Nanopore Sequencing - Published in JOSS (2019)
AixWeather
AixWeather: A Weather Data Generation Tool for Building Energy System Simulations. Pull, Transform, Export. - Published in JOSS (2025)
getCRUCLdata
getCRUCLdata: Use and Explore CRU CL v. 2.0 Climatology Elements in R - Published in JOSS (2017)
Building, Importing, and Exporting GEXF Graph Files with rgexf
Building, Importing, and Exporting GEXF Graph Files with rgexf - Published in JOSS (2021)
SampleDB
SampleDB: A sample and measurement metadata database - Published in JOSS (2021)
Af-analysis
Af-analysis: a Python package for Alphafold analysis - Published in JOSS (2025)
stacks
stacks: Stacked Ensemble Modeling with Tidy Data Principles - Published in JOSS (2022)
Teaspoon
Teaspoon: A Python Package for Topological Signal Processing - Published in JOSS (2025)
BayesianNetwork
BayesianNetwork: Interactive Bayesian Network Modeling and Analysis - Published in JOSS (2018)
Fast Resampling and Monte Carlo Methods in Python
Fast Resampling and Monte Carlo Methods in Python - Published in JOSS (2023)
modelStudio
modelStudio: Interactive Studio with Explanations for ML Predictive Models - Published in JOSS (2019)
Tashaphyne
Tashaphyne: A Python package for Arabic Light Stemming - Published in JOSS (2024)
verdata
verdata: An R package for analyzing data from the Truth Commission in Colombia - Published in JOSS (2024)
The Spreadsheet Energy System Model Generator (SESMG)
The Spreadsheet Energy System Model Generator (SESMG): A tool for the optimization of urban energy systems - Published in JOSS (2023)
biopeaks
biopeaks: a graphical user interface for feature extraction from heart- and breathing biosignals - Published in JOSS (2020)
quickBayes
quickBayes: An analytical approach to Bayesian marginal likelihoods - Published in JOSS (2025)
BAMnostic
BAMnostic: an OS-agnostic toolkit for genomic sequence analysis - Published in JOSS (2018)
GaussianRandomFields.jl
GaussianRandomFields.jl: A Julia package to generate and sample from Gaussian random fields - Published in JOSS (2023)
Pyafscgap.org
Pyafscgap.org: Open source multi-modal Python-based tools for NOAA AFSC RACE GAP - Published in JOSS (2023)
liionpack
liionpack: A Python package for simulating packs of batteries with PyBaMM - Published in JOSS (2022)
Fasten
Fasten: a toolkit for streaming operations on fastq files - Published in JOSS (2024)
rdflib
RDFLib is a Python library for working with RDF, a simple yet powerful language for representing information.
PlanetMapper
PlanetMapper: A Python package for visualising, navigating and mapping Solar System observations - Published in JOSS (2023)
netrd
netrd: A library for network reconstruction and graph distances - Published in JOSS (2021)
bayes-toolbox
bayes-toolbox: A Python package for Bayesian statistics - Published in JOSS (2023)
archetypal
archetypal: A Python package for collecting, simulating, converting and analyzing building archetypes - Published in JOSS (2020)
Thermosteam
Thermosteam: BioSTEAM's Premier Thermodynamic Engine - Published in JOSS (2020)
EoN (Epidemics on Networks)
EoN (Epidemics on Networks): a fast, flexible Python package for simulation, analytic approximation, and analysis of epidemics on networks - Published in JOSS (2019)
PyKoopman
PyKoopman: A Python Package for Data-Driven Approximation of the Koopman Operator - Published in JOSS (2024)
FitBenchmarking
FitBenchmarking: an open source Python package comparing data fitting software - Published in JOSS (2021)
NodePy
NodePy: A package for the analysis of numerical ODE solvers - Published in JOSS (2020)
DAPPER
DAPPER: Data Assimilation with Python: a Package for Experimental Research - Published in JOSS (2024)
idf-analysis
idf-analysis: Heavy rainfall intensity as a function of duration and return period - Published in JOSS (2025)
modisfast
modisfast: An R package for fast and efficient access to MODIS, VIIRS and GPM Earth Observation data - Published in JOSS (2024)
UQTestFuns
UQTestFuns: A Python3 library of uncertainty quantification (UQ) test functions - Published in JOSS (2023)
Pooltool
Pooltool: A Python package for realistic billiards simulation - Published in JOSS (2024)
dantro
dantro: a Python package for handling, transforming, and visualizing hierarchically structured data - Published in JOSS (2020)
The vtreat R package
The vtreat R package: a statistically sound data processor for predictive modeling - Published in JOSS (2018)
PYDAQ
PYDAQ: Data Acquisition and Experimental Analysis with Python - Published in JOSS (2023)
Elektra
Elektra: universal framework to access configuration parameters - Published in JOSS (2016)
TipToft
TipToft: detecting plasmids contained in uncorrected long read sequencing data - Published in JOSS (2019)
XRTpy
XRTpy: A Hinode-X-Ray Telescope Python Package - Published in JOSS (2024)
pyOptSparse
pyOptSparse: A Python framework for large-scale constrained nonlinear optimization of sparse systems - Published in JOSS (2020)
FastVPINNs
FastVPINNs: An efficient tensor-based Python library for solving partial differential equations using hp-Variational Physics Informed Neural Networks - Published in JOSS (2024)
HW2D
HW2D: A reference implementation of the Hasegawa-Wakatani model for plasma turbulence in fusion reactors - Published in JOSS (2023)
Multiblock PLS
Multiblock PLS: Block dependent prediction modeling for Python - Published in JOSS (2019)
signnet
signnet: An R package for analyzing signed networks - Published in JOSS (2023)
LobsterPy
LobsterPy: A package to automatically analyze LOBSTER runs - Published in JOSS (2024)
Bodge
Bodge: Python package for efficient tight-binding modeling of superconducting nanostructures - Published in JOSS (2024)
CADET-Core 5.0
CADET-Core 5.0: High-Performance Solver for Advanced Biotechnology Process Modeling - Published in JOSS (2025)
mcsm-benchs: Benchmarking methods for multi-component signal processing
mcsm-benchs: Benchmarking methods for multi-component signal processing - Published in JOSS (2025)
forestatrisk
forestatrisk: a Python package for modelling and forecasting deforestation in the tropics - Published in JOSS (2021)
yadg
yadg: yet another datagram - Published in JOSS (2022)
eddy
eddy: Extracting Protoplanetary Disk Dynamics with Python - Published in JOSS (2019)
DeepReg
DeepReg: a deep learning toolkit for medical image registration - Published in JOSS (2020)
piglot
piglot: an Open-source Package for Derivative-free Optimisation of Numerical Responses - Published in JOSS (2024)
Generating fragment density plots in R/Bioconductor with VplotR
Generating fragment density plots in R/Bioconductor with VplotR - Published in JOSS (2021)
rr2
rr2: An R package to calculate $R^2$s for regression models - Published in JOSS (2018)
ParaMonte
ParaMonte: A high-performance serial/parallel Monte Carlo simulation library for C, C++, Fortran - Published in JOSS (2021)
spINAR
spINAR: An R Package for Semiparametric and Parametric Estimation and Bootstrapping of Integer-Valued Autoregressive (INAR) Models - Published in JOSS (2024)
rf
rf: Receiver function calculation in seismology - Published in JOSS (2020)
MapReader
MapReader: Open software for the visual analysis of maps - Published in JOSS (2024)
Pyret
Pyret: A Python package for analysis of neurophysiology data - Published in JOSS (2017)
ComplexRegions.jl
ComplexRegions.jl: A Julia package for regions in the complex plane - Published in JOSS (2019)
Fastsubtrees
Fastsubtrees: simple and efficient subtrees extractions in Python with applications to NCBI taxonomy - Published in JOSS (2022)
ddtlcm
ddtlcm: An R package for overcoming weak separation in Bayesian latent class analysis via tree-regularization - Published in JOSS (2024)
WordTokenizers.jl
WordTokenizers.jl: Basic tools for tokenizing natural language in Julia - Published in JOSS (2020)
Bluebonnet
Bluebonnet: Scaling solutions for production analysis from unconventional oil and gas wells - Published in JOSS (2023)
solids4foam
solids4foam: A toolbox for performing solid mechanics and fluid-solid interaction simulations in OpenFOAM - Published in JOSS (2025)
msmhelper
msmhelper: A Python package for Markov state modeling of protein dynamics - Published in JOSS (2023)
Metaheuristics
Metaheuristics: A Julia Package for Single- and Multi-Objective Optimization - Published in JOSS (2022)