OfflineMOT
OfflineMOT: A Python package for multiple objects detection and tracking from bird view stationary drone videos - Published in JOSS (2022)
PII-Codex
PII-Codex: a Python library for PII detection, categorization, and severity assessment - Published in JOSS (2023)
SkyPortal
SkyPortal: An Astronomical Data Platform - Published in JOSS (2019)
SphericalScattering
SphericalScattering: A Julia Package for Electromagnetic Scattering from Spherical Objects - Published in JOSS (2023)
Bacting
Bacting: a next generation, command line version of Bioclipse - Published in JOSS (2021)
patRoon 2.0
patRoon 2.0: Improved non-target analysis workflows including automated transformation product screening - Published in JOSS (2022)
EFAtools
EFAtools: An R package with fast and flexible implementations of exploratory factor analysis tools - Published in JOSS (2020)
daiquiri
daiquiri: Data Quality Reporting for Temporal Datasets - Published in JOSS (2022)
mcboost
mcboost: Multi-Calibration Boosting for R - Published in JOSS (2021)
`NGSTrefftz`
`NGSTrefftz`: Add-on to NGSolve for Trefftz methods - Published in JOSS (2022)
rsimsum
rsimsum: Summarise results from Monte Carlo simulation studies - Published in JOSS (2018)
CluSim
CluSim: a python package for calculating clustering similarity - Published in JOSS (2019)
ASTE
ASTE: An artificial solver testing environment for partitioned coupling with preCICE - Published in JOSS (2024)
Singularity-EOS
Singularity-EOS: Performance Portable Equations of State and Mixed Cell Closures - Published in JOSS (2024)
CalibrateEmulateSample.jl
CalibrateEmulateSample.jl: Accelerated Parametric Uncertainty Quantification - Published in JOSS (2024)
adaptr
adaptr: an R package for simulating and comparing adaptive clinical trials - Published in JOSS (2022)
gemlog
gemlog: Data Conversion for the Open-Source Gem Infrasound Logger - Published in JOSS (2023)
SMART
SMART: Spatial Modeling Algorithms for Reactions and Transport - Published in JOSS (2023)
PyProBE
PyProBE: Python Processing for Battery Experiments - Published in JOSS (2025)
SetVis
SetVis: Visualizing Large Numbers of Sets and Intersections - Published in JOSS (2024)
py_neuromodulation
py_neuromodulation: Signal processing and decoding for neural electrophysiological recordings - Published in JOSS (2025)
Empirical and non-parametric copula models with the cort R package
Empirical and non-parametric copula models with the cort R package - Published in JOSS (2020)
PhaseFieldX
PhaseFieldX: An Open-Source Framework for Advanced Phase-Field Simulations - Published in JOSS (2025)
FaaSr
FaaSr: R Package for Function-as-a-Service Cloud Computing - Published in JOSS (2024)
Contextualized
Contextualized: Heterogeneous Modeling Toolbox - Published in JOSS (2024)
simpleCache
simpleCache: R caching for reproducible, distributed, large-scale projects - Published in JOSS (2018)
BCEA
BCEA: An R Package for Cost-Effectiveness Analysis - Published in JOSS (2022)
OPEM
OPEM : Open Source PEM Cell Simulation Tool - Published in JOSS (2018)
Hexatomic
Hexatomic: An extensible, OS-independent platform for deep multi-layer linguistic annotation of corpora - Published in JOSS (2023)
LIBSsa
LIBSsa: an open source software for analyzing LIBS spectra - Published in JOSS (2024)
Osprey
Osprey: Hyperparameter Optimization for Machine Learning - Published in JOSS (2016)
Crowsetta
Crowsetta: A Python tool to work with any format for annotating animal vocalizations and bioacoustics data. - Published in JOSS (2023)
phylogram
phylogram: an R package for phylogenetic analysis with nested lists - Published in JOSS (2018)
pref_voting
pref_voting: The Preferential Voting Tools package for Python - Published in JOSS (2025)
Pyrgg
Pyrgg: Python Random Graph Generator - Published in JOSS (2017)
Snk
Snk: A Snakemake CLI and Workflow Management System - Published in JOSS (2024)
TopSearch
TopSearch: a Python package for topographical analysis of machine learning models and physical systems - Published in JOSS (2024)
gridwxcomp
gridwxcomp: A Python package to evaluate and interpolate biases between station and gridded weather data - Published in JOSS (2025)
cottoncandy
cottoncandy: scientific python package for easy cloud storage - Published in JOSS (2018)
ThermoParser
ThermoParser: Streamlined Analysis of Thermoelectric Properties - Published in JOSS (2024)
dorado
dorado: A Python package for simulating passive particle transport in shallow-water flows - Published in JOSS (2020)
wdpar
wdpar: Interface to the World Database on Protected Areas - Published in JOSS (2022)
ggvoronoi
ggvoronoi: Voronoi Diagrams and Heatmaps with ggplot2 - Published in JOSS (2018)
RIAssigner
RIAssigner: A package for gas chromatographic retention index calculation - Published in JOSS (2022)
byteparsing
byteparsing: a functional parser combinator for mixed ASCII/binary data - Published in JOSS (2023)
Hoki
Hoki: Making BPASS accessible through Python - Published in JOSS (2020)
PyVOLCANS
PyVOLCANS: A Python package to flexibly explore similarities and differences between volcanic systems - Published in JOSS (2021)
unxt
unxt: A Python package for unit-aware computing with JAX - Published in JOSS (2025)
Suppdata
Suppdata: Downloading Supplementary Data from Published Manuscripts - Published in JOSS (2018)
Fast and flexible simulation and parameter estimation for synthetic biology using bioscrape
Fast and flexible simulation and parameter estimation for synthetic biology using bioscrape - Published in JOSS (2023)
pyMechT
pyMechT: A Python package for mechanics of soft tissues - Published in JOSS (2025)
fleck
fleck: Fast approximate light curves for starspot rotational modulation - Published in JOSS (2020)
Manif
Manif: A micro Lie theory library for state estimation in robotics applications - Published in JOSS (2020)
pygtc
pygtc: beautiful parameter covariance plots (aka. Giant Triangle Confusograms) - Published in JOSS (2016)
Nominally
Nominally: A Name Parser for Record Linkage - Published in JOSS (2021)
COMPAS
COMPAS: A rapid binary population synthesis suite - Published in JOSS (2022)
Koverage
Koverage: Read-coverage analysis for massive (meta)genomics datasets - Published in JOSS (2024)
jointVIP
jointVIP: Prioritizing variables in observational study design with joint variable importance plot in R - Published in JOSS (2024)
EcoLogits
EcoLogits: Evaluating the Environmental Impacts of Generative AI - Published in JOSS (2025)
pactus
pactus: A Python framework for trajectory classification - Published in JOSS (2023)
Multilocus sequence typing by blast from de novo assemblies against PubMLST
Multilocus sequence typing by blast from de novo assemblies against PubMLST - Published in JOSS (2016)
ewstools
ewstools: A Python package for early warning signals of bifurcations in time series data - Published in JOSS (2023)
CurvilinearGrids.jl
CurvilinearGrids.jl: A Julia package for curvilinear coordinate transformations - Published in JOSS (2024)
piar
piar: Price Index Aggregation in R - Published in JOSS (2024)
pyndl
pyndl: Naïve Discriminative Learning in Python - 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)
(py)oscode
(py)oscode: fast solutions of oscillatory ODEs - Published in JOSS (2020)
Connectome Mapper 3
Connectome Mapper 3: A Flexible and Open-Source Pipeline Software for Multiscale Multimodal Human Connectome Mapping - Published in JOSS (2022)
AIBECS.jl
AIBECS.jl: A tool for exploring global marine biogeochemical cycles. - Published in JOSS (2022)
BlueCelluLab
BlueCelluLab: Biologically Detailed Neural Network Experimentation API - Published in JOSS (2024)
cvCovEst
cvCovEst: Cross-validated covariance matrix estimator selection and evaluation in R - Published in JOSS (2021)
Lumen
Lumen: A software for the interactive visualization of probabilistic models together with data - Published in JOSS (2021)
servir-aces
servir-aces: A Python Package for Training Machine Learning Models for Remote Sensing Applications - Published in JOSS (2024)
bsym
bsym: A basic symmetry module - Published in JOSS (2017)
DetecTree
DetecTree: Tree detection from aerial imagery in Python - Published in JOSS (2020)
AeroAcoustics.jl
AeroAcoustics.jl: A Julia package for aeroacoustics - Published in JOSS (2024)
dtrackr
dtrackr: An R package for tracking the provenance of data - Published in JOSS (2022)
The Pencil Code, a modular MPI code for partial differential equations and particles
The Pencil Code, a modular MPI code for partial differential equations and particles: multipurpose and multiuser-maintained - Published in JOSS (2021)
PlantSimEngine
PlantSimEngine: A Simulation Engine For The Soil-Plant-Atmosphere System - Published in JOSS (2023)
scribl
scribl: A system for the semantic capture of relationships in biological literature - Published in JOSS (2024)
datastructures
datastructures: An R package for organisation and storage of data - Published in JOSS (2018)
deeplenstronomy
deeplenstronomy: A dataset simulation package for strong gravitational lensing - Published in JOSS (2021)
CheckQC
CheckQC: Quick quality control of Illumina sequencing runs - Published in JOSS (2018)
SeismicMesh
SeismicMesh: Triangular meshing for seismology - Published in JOSS (2021)
SIRUS.jl
SIRUS.jl: Interpretable Machine Learning via Rule Extraction - Published in JOSS (2023)
rempsyc
rempsyc: Convenience functions for psychology - Published in JOSS (2023)
SESAMI APP
SESAMI APP: An Accessible Interface for Surface Area Calculation of Materials from Adsorption Isotherms - Published in JOSS (2023)
catwoman
catwoman: A transit modelling Python package for asymmetric light curves - Published in JOSS (2022)
Cacatoo
Cacatoo: building, exploring, and sharing spatially structured models of biological systems - Published in JOSS (2022)
ngsPETSc
ngsPETSc: A coupling between NETGEN/NGSolve and PETSc - Published in JOSS (2024)
OpenTerrace
OpenTerrace: A fast, flexible and extendable Python framework for thermal energy storage packed bed simulations - Published in JOSS (2024)
The Dusty Evolved Star Kit (DESK)
The Dusty Evolved Star Kit (DESK): A Python package for fitting the Spectral Energy Distribution of Evolved Stars - Published in JOSS (2020)
solid_dmft
solid_dmft: gray-boxing DFT+DMFT materials simulations with TRIQS - Published in JOSS (2022)
21cmSense v2
21cmSense v2: A modular, open-source 21 cm sensitivity calculator - Published in JOSS (2024)
RFBzero
RFBzero: A Python package for zero-dimensional simulation of redox flow battery cycling - Published in JOSS (2024)
rcites
rcites: An R package to access the CITES Speciesplus database - Published in JOSS (2018)
CATS
CATS: The Climate Aware Task Scheduler - Published in JOSS (2025)