EMD
EMD: Empirical Mode Decomposition and Hilbert-Huang Spectral Analyses in Python - Published in JOSS (2021)
Council Data Project
Council Data Project: Software for Municipal Data Collection, Analysis, and Publication - Published in JOSS (2021)
statemodify
statemodify: a Python framework to facilitate accessible exploratory modeling for discovering drought vulnerabilities - Published in JOSS (2024)
predictNMB
predictNMB: An R package to estimate if or when a clinical prediction model is worthwhile - Published in JOSS (2023)
lattice_mc
lattice_mc: A Python Lattice-Gas Monte Carlo Module - Published in JOSS (2017)
IKPLS
IKPLS: Improved Kernel Partial Least Squares and Fast Cross-Validation Algorithms for Python with CPU and GPU Implementations Using NumPy and JAX - Published in JOSS (2024)
RNAsik
RNAsik: A Pipeline for complete and reproducible RNA-seq analysis that runs anywhere with speed and ease - Published in JOSS (2018)
iharm3D
iharm3D: Vectorized General Relativistic Magnetohydrodynamics - Published in JOSS (2021)
ASGarD
ASGarD: Adaptive Sparse Grid Discretization - Published in JOSS (2024)
nimbleHMC
nimbleHMC: An R package for Hamiltonian Monte Carlo sampling in nimble - Published in JOSS (2024)
py-opc
py-opc: operate the Alphasense OPC-N2 from a raspberry pi or other popular microcontrollers/microcomputers - Published in JOSS (2018)
The fqar package
The fqar package: R tools for analyzing floristic quality assessment data - Published in JOSS (2024)
excitingtools
excitingtools: An exciting Workflow Tool - Published in JOSS (2023)
Analysis of Prehistoric Iconography with the R package iconr
Analysis of Prehistoric Iconography with the R package iconr - Published in JOSS (2021)
PatchView
PatchView: A Python Package for Patch-clamp Data Analysis and Visualization - Published in JOSS (2022)
statConfR
statConfR: An R Package for Static Models of Decision Confidence and Metacognition - Published in JOSS (2025)
teiphy
teiphy: A Python Package for Converting TEI XML Collations to NEXUS and Other Formats - Published in JOSS (2022)
hectorui
hectorui: A web-based interactive scenario builder and visualization application for the Hector climate model - Published in JOSS (2020)
VisualTorch
VisualTorch: Streamlining Visualization for PyTorch Neural Network Architectures - Published in JOSS (2024)
MPIFiles.jl
MPIFiles.jl: A Julia Package for Magnetic Particle Imaging Files - Published in JOSS (2019)
archeoViz
archeoViz: an R package for the Visualisation, Exploration, and Web Communication of Archaeological Spatial Data - Published in JOSS (2023)
hoggorm
hoggorm: a python library for explorative multivariate statistics - Published in JOSS (2019)
SBArchOpt
SBArchOpt: Surrogate-Based Architecture Optimization - Published in JOSS (2023)
PAPRECA
PAPRECA: A parallel hybrid off-lattice kinetic Monte Carlo/molecular dynamics simulator - Published in JOSS (2024)
Spikeometric
Spikeometric: Linear Non-Linear Cascade Spiking Neural Networks with Pytorch Geometric - Published in JOSS (2023)
JaxLayerLumos: A JAX-based Differentiable Optical and Radio Frequency Simulator for Multilayer Structures
JaxLayerLumos: A JAX-based Differentiable Optical and Radio Frequency Simulator for Multilayer Structures - Published in JOSS (2025)
Hypothesize
Hypothesize: Robust Statistics for Python - Published in JOSS (2020)
Museo ToolBox
Museo ToolBox: A Python library for remote sensing including a new way to handle rasters. - Published in JOSS (2020)
stella
stella: Convolutional Neural Networks for Flare Identification in TESS - Published in JOSS (2020)
TessPy
TessPy: a python package for geographical tessellation - Published in JOSS (2022)
Project RACCOON
Project RACCOON: Automated construction of PDB files for polymers and polymer peptide conjugates - Published in JOSS (2024)
lintegrate
lintegrate: A C/Python numerical integration library for working in log-space - Published in JOSS (2022)
QMCPy: A Python Framework for (Quasi-)Monte Carlo Algorithms
QMCPy: A Python Framework for (Quasi-)Monte Carlo Algorithms - Published in JOSS (2026)
TREvoSim v3
TREvoSim v3: An individual based simulation for generating trees and character data - Published in JOSS (2024)
AutoBZ.jl
AutoBZ.jl: Automatic, adaptive Brillouin zone integration using Wannier interpolation - Published in JOSS (2024)
Pyoints
Pyoints: A Python package for point cloud, voxel and raster processing. - Published in JOSS (2019)
GraphNeT
GraphNeT: Graph neural networks for neutrino telescope event reconstruction - Published in JOSS (2023)
CLEAVING
CLEAVING: a LAMMPS package to compute surface free energies - Published in JOSS (2024)
LaplaceInterpolation.jl
LaplaceInterpolation.jl: A Julia package for fast interpolation on a grid - Published in JOSS (2022)
daiR
daiR: an R package for OCR with Google Document AI - Published in JOSS (2021)
py2lispIDyOM
py2lispIDyOM: A Python package for the information dynamics of music (IDyOM) model - Published in JOSS (2022)
Ethome
Ethome: tools for machine learning of animal behavior - Published in JOSS (2024)
PyTeNet
PyTeNet: A concise Python implementation of quantum tensor network algorithms - Published in JOSS (2018)
epimargin
epimargin: A Toolkit for Epidemiological Estimation, Prediction, and Policy Evaluation - Published in JOSS (2021)
yam
yam: Yet another monitoring tool using correlations of ambient noise - Published in JOSS (2023)
h5fortran
h5fortran: object-oriented polymorphic Fortran interface for HDF5 file IO - Published in JOSS (2021)
ReLax
ReLax: Efficient and Scalable Recourse Explanation Benchmarking using JAX - Published in JOSS (2024)
Stresslog: A Python package for modeling wellbore stability in inclined stress states
Stresslog: A Python package for modeling wellbore stability in inclined stress states - Published in JOSS (2025)
cofad
cofad: An R package and shiny app for contrast analysis - Published in JOSS (2021)
DeepOF
DeepOF: a Python package for supervised and unsupervised pattern recognition in mice motion tracking data - Published in JOSS (2023)
cifkit
cifkit: A Python package for coordination geometry and atomic site analysis - Published in JOSS (2024)
FlowerMD
FlowerMD: Flexible Library of Organic Workflows and Extensible Recipes for Molecular Dynamics - Published in JOSS (2023)
OpenTera
OpenTera: A Framework for Telehealth Applications - Published in JOSS (2023)
HiPart
HiPart: Hierarchical Divisive Clustering Toolbox - Published in JOSS (2023)
The jagstargets R package
The jagstargets R package: a reproducible workflow framework for Bayesian data analysis with JAGS - Published in JOSS (2021)
PyHOPE: A Python Toolkit for Three-Dimensional Unstructured High-Order Meshes
PyHOPE: A Python Toolkit for Three-Dimensional Unstructured High-Order Meshes - Published in JOSS (2025)
WRF-CMake
WRF-CMake: integrating CMake support into the Advanced Research WRF (ARW) modelling system - Published in JOSS (2019)
CausalTables.jl
CausalTables.jl: Simulating and storing data for statistical causal inference in Julia - Published in JOSS (2025)
PyNeuroTrace - Python code for neural activity time series
PyNeuroTrace - Python code for neural activity time series - Published in JOSS (2024)
High-performance neural population dynamics modeling enabled by scalable computational infrastructure
High-performance neural population dynamics modeling enabled by scalable computational infrastructure - Published in JOSS (2023)
SubsetTools
SubsetTools: A Python package to subset data to build and run ParFlow hydrologic models - Published in JOSS (2024)
OpenFEPOPS
OpenFEPOPS: A Python implementation of the FEPOPS molecular similarity technique - Published in JOSS (2023)
Scikit-Longitudinal
Scikit-Longitudinal: A Machine Learning Library for Longitudinal Classification in Python - Published in JOSS (2025)
RADWave
RADWave: Python code for ocean surface wave analysis by satellite radar altimeter - Published in JOSS (2020)
RHEIA
RHEIA: Robust design optimization of renewable Hydrogen and dErIved energy cArrier systems - Published in JOSS (2022)
NAIF PDS4 Bundler
NAIF PDS4 Bundler: A Python package to generate SPICE PDS4 archives - Published in JOSS (2022)
A Library of Lower Fidelity Dynamics Models (LFDMs) For On-Road Vehicle Dynamics Targeting Faster Than Real-Time Applications
A Library of Lower Fidelity Dynamics Models (LFDMs) For On-Road Vehicle Dynamics Targeting Faster Than Real-Time Applications - Published in JOSS (2024)
cgeniepy
cgeniepy: A Python package for analysing cGENIE Earth System Model output - Published in JOSS (2024)
Django Remote Submission
Django Remote Submission - Published in JOSS (2017)
Metagenomic classification with KrakenUniq on low-memory computers
Metagenomic classification with KrakenUniq on low-memory computers - Published in JOSS (2022)
Hypercomplex
Hypercomplex: abstract & fast header-only C++ template library for lattice-based cryptosystems in high-dimensional algebras - Published in JOSS (2023)
sierra-local
sierra-local: A lightweight standalone application for drug resistance prediction - Published in JOSS (2019)
A Short Introduction to PF
A Short Introduction to PF: A C++ Library for Particle Filtering - Published in JOSS (2020)
DeepBench
DeepBench: A simulation package for physical benchmarking data - Published in JOSS (2025)
DTCC Builder
DTCC Builder: A mesh generator for automatic, efficient, and robust mesh generation for large-scale city modeling and simulation - Published in JOSS (2023)
Psifr
Psifr: Analysis and visualization of free recall data - Published in JOSS (2020)
COINr
COINr: An R package for developing composite indicators - Published in JOSS (2022)
pycellga
pycellga: A Python package for improved cellular genetic algorithms - Published in JOSS (2025)
Moran Pycess
Moran Pycess: a Python package to simulate Moran processes driven by game theory - Published in JOSS (2020)
Pakman
Pakman: a modular, efficient and portable tool for approximate Bayesian inference - Published in JOSS (2020)
AdOpT-NET0
AdOpT-NET0: A technology-focused Python package for the optimization of multi-energy systems - Published in JOSS (2025)
Lcopt - An interactive tool for creating fully parameterised Life Cycle Assessment (LCA) foreground models
Lcopt - An interactive tool for creating fully parameterised Life Cycle Assessment (LCA) foreground models - Published in JOSS (2017)
orbitize! v3
orbitize! v3: Orbit fitting for the High-contrast Imaging Community - Published in JOSS (2024)
Neuropsydia.py
Neuropsydia.py: A Python Module for Creating Experiments, Tasks and Questionnaires - Published in JOSS (2017)
GAMA
GAMA: Genetic Automated Machine learning Assistant - Published in JOSS (2019)
Lerche
Lerche: Generating data file processors in Julia from EBNF grammars - Published in JOSS (2021)
perccalc
perccalc: An R package for estimating percentiles from categorical variables - Published in JOSS (2019)
PulPy
PulPy: A Python Toolkit for MRI RF and Gradient Pulse Design - Published in JOSS (2024)
survPen
survPen: an R package for hazard and excess hazard modelling with multidimensional penalized splines - Published in JOSS (2019)
Spruceup
Spruceup: fast and flexible identification, visualization, and removal of outliers from large multiple sequence alignments - Published in JOSS (2019)
gobbli
gobbli: A uniform interface to deep learning for text in Python - Published in JOSS (2021)
Wakeflow
Wakeflow: A Python package for semi-analytic models of planetary wakes - Published in JOSS (2023)
TDApplied
TDApplied: An R package for machine learning and inference with persistence diagrams - Published in JOSS (2024)
PWSpy
PWSpy: A Python library dedicated to the analysis of Partial Wave Spectroscopic Microscopy data. - Published in JOSS (2022)
bmm
bmm: Bayesian Map-matching - Published in JOSS (2022)
kdensity
kdensity: An R package for kernel density estimation with parametric starts and asymmetric kernels - Published in JOSS (2019)
ChebTools
ChebTools: C++11 (and Python) tools for working with Chebyshev expansions - Published in JOSS (2018)