qcelemental
Periodic table, physical constants, and molecule parsing for quantum chemistry.
Computer-Aided Generation of N-shift RWS
Computer-Aided Generation of N-shift RWS - Published in JOSS (2023)
3D ultrasound file reading and coordinate transformations
3D ultrasound file reading and coordinate transformations - Published in JOSS (2019)
LearnSAT
LearnSAT: A SAT Solver for Education - Published in JOSS (2018)
igneous-pipeline
Scalable Neuroglancer compatible Downsampling, Meshing, Skeletonizing, Contrast Normalization, Transfers and more.
localcovid19now
localcovid19now: processing and mapping COVID-19 case data at subnational scales - Published in JOSS (2023)
cowfootR: An R Package for Dairy Farm Carbon Footprint Assessment
cowfootR: An R Package for Dairy Farm Carbon Footprint Assessment - Published in JOSS (2026)
DiscreteEntropy.jl
DiscreteEntropy.jl: Entropy Estimation of Discrete Random Variables with Julia - Published in JOSS (2024)
LorenzCycleToolkit
LorenzCycleToolkit: A Comprehensive Python Tool for Analyzing Atmospheric Energy Cycles - Published in JOSS (2024)
kimimaro
Skeletonize densely labeled 3D image segmentations with TEASAR. (Medial Axis Transform)
oemof.solph
A model generator for energy system modelling and optimisation (LP/MILP).
BayesMFSurv
BayesMFSurv: An R Package to Estimate Bayesian Split-Population Survival Models With (and Without) Misclassified Failure Events - Published in JOSS (2020)
RECOLO
RECOLO: A Python package for the reconstruction of surface pressure loads from kinematic fields using the virtual fields method - Published in JOSS (2022)
ORIS
ORIS: An interactive software tool for prediction of replication origin in prokaryotic genomes - Published in JOSS (2019)
mbir
mbir: Magnitude-Based Inferences - Published in JOSS (2019)
SeleDiff
SeleDiff: A fast and scalable tool for estimating and testing selection differences between populations - Published in JOSS (2019)
FlexWing-ROM
FlexWing-ROM: A matlab framework for data-driven reduced-order modeling of flexible wings - Published in JOSS (2022)
GKNAP
GKNAP: A Java and C++ package for solving the multidimensional knapsack problem - Published in JOSS (2019)
chronovise
chronovise: Measurement-Based Probabilistic Timing Analysis framework - Published in JOSS (2018)
sdmbench
sdmbench: R package for benchmarking species distribution models - Published in JOSS (2018)
skijumpdesign
skijumpdesign: A Ski Jump Design Tool for Specified Equivalent Fall Height - Published in JOSS (2018)
p2smi: A toolkit enabling SMILES generation and property analysis for noncanonical and cyclized peptides
p2smi: A toolkit enabling SMILES generation and property analysis for noncanonical and cyclized peptides - Published in JOSS (2025)
cellanneal
cellanneal: A user-friendly deconvolution software for transcriptomics data - Published in JOSS (2024)
GGMnonreg
GGMnonreg: Non-Regularized Gaussian Graphical Models in R - Published in JOSS (2021)
IBCAO_py
IBCAO_py: A matplotlib library for using the International Bathymetric Chart of the Arctic Ocean with cartopy and matplotlib - Published in JOSS (2017)
SubZero
SubZero: a discrete element sea ice model that simulates floes as evolving concave polygons - Published in JOSS (2023)
The Climate Equity Reference Calculator
The Climate Equity Reference Calculator - Published in JOSS (2019)
niacin
niacin: A Python package for text data enrichment - Published in JOSS (2020)
Solar Data Tools: a Python library for automated analysis of unlabeled PV data
Solar Data Tools: a Python library for automated analysis of unlabeled PV data - Published in JOSS (2025)
SpatialGEV
SpatialGEV: Fast Bayesian inference for spatial extreme value models in R - Published in JOSS (2024)
MG-MAMPOSSt, a Fortran code to test gravity at galaxy-cluster scales
MG-MAMPOSSt, a Fortran code to test gravity at galaxy-cluster scales - Published in JOSS (2023)
Reorient
Reorient: A Web tool for reorienting and cropping MRI data. - Published in JOSS (2020)
Bernadette
Bernadette: Bayesian Inference and Model Selection for Stochastic Epidemics in R - Published in JOSS (2023)
BCImat
BCImat: a Matlab-based framework for Intracortical Brain-Computer Interfaces and their simulation with an artificial spiking neural network - Published in JOSS (2022)
BluVision Macro - a software for automated powdery mildew and rust disease quantification on detached leaves.
BluVision Macro - a software for automated powdery mildew and rust disease quantification on detached leaves. - Published in JOSS (2020)
GMP-Featurizer
GMP-Featurizer: A parallelized Python package for efficiently computing the Gaussian Multipole features of atomic systems - Published in JOSS (2023)
memochange
memochange: An R package for estimation procedures and tests for persistent time series - Published in JOSS (2019)
fibergen
fibergen: An introductory tool for FFT-based material homogenization - Published in JOSS (2019)
profileR
profileR: An R package for profile analysis - Published in JOSS (2020)
geneXplainR
geneXplainR: An R interface for the geneXplain platform - Published in JOSS (2017)
simpeg
Simulation and Parameter Estimation in Geophysics - A python package for simulation and gradient based parameter estimation in the context of geophysical applications.
scikit-finite-diff, a new tool for PDE solving
scikit-finite-diff, a new tool for PDE solving - Published in JOSS (2019)
MetalWalls
MetalWalls: A classical molecular dynamics software dedicated to the simulation of electrochemical systems - Published in JOSS (2020)
An easy-to-use p5.js 3D object picker for visual artists
An easy-to-use p5.js 3D object picker for visual artists - Published in JOSS (2017)
fuse
fuse: An R package for ensemble Hydrological Modelling - Published in JOSS (2016)
PyThia
PyThia: A Python package for Uncertainty Quantification based on non-intrusive polynomial chaos expansions - Published in JOSS (2023)
tsp ("Teaspoon")
tsp ("Teaspoon"): A library for ground temperature data - Published in JOSS (2022)
molify: Molecular Structure Interface
molify: Molecular Structure Interface - Published in JOSS (2025)
PyAstroPol
PyAstroPol: A Python package for the instrumental polarization analysis of the astronomical optics. - Published in JOSS (2020)
OTTO
OTTO: A Python package to simulate, solve and visualize the source-tracking POMDP - Published in JOSS (2022)
genieR
genieR: An R package for inference of demographic history of phylogenies - Published in JOSS (2019)
HyperNaut
HyperNaut: a navigator for the hyperbolic plane - Published in JOSS (2019)
Dark-field X-ray microscopy visualization
Dark-field X-ray microscopy visualization - Published in JOSS (2023)
oplab-pipeline
parsers for navigation data for oplab_standard and acfr_standard formats
CORA and LOGIGRAM
CORA and LOGIGRAM: A Duo of Python Packages for Combinational Regularity Analysis (CORA) - Published in JOSS (2023)
Correlation Trait Loci (CTL) mapping
Correlation Trait Loci (CTL) mapping: phenotype network inference subject to genotype - Published in JOSS (2016)
SymbiotaR2
SymbiotaR2: An R Package for Accessing Symbiota2 Data - Published in JOSS (2020)
mwarp1d
mwarp1d: Manual one-dimensional data warping in Python and PyQt - Published in JOSS (2019)
onsetsync
onsetsync: An R Package for Onset Synchrony Analysis - Published in JOSS (2024)
FRIDGe
FRIDGe: Fast Reactor Input Deck Generator - Published in JOSS (2019)
SIAL
SIAL: A simple image analysis library for wet-lab scientists - Published in JOSS (2020)
Tabbed: A Python package for reading variably structured text files at scale
Tabbed: A Python package for reading variably structured text files at scale - Published in JOSS (2025)
discourseGT
discourseGT: An R package to analyze discourse networks in educational contexts - Published in JOSS (2023)
BeeNestABM
BeeNestABM: An open-source agent-based model of spatiotemporal distribution of bumblebees in nests - Published in JOSS (2018)
BetterReg
BetterReg: An R package for Useful Regression Statistics - Published in JOSS (2022)
MaDaTS
MaDaTS: Managing Data on Tiered Storage for Scientific Workflows - Published in JOSS (2018)
qlass: A Python Package for Variational Quantum Algorithms on Photonic Devices
qlass: A Python Package for Variational Quantum Algorithms on Photonic Devices - Published in JOSS (2026)
GASTLI
GASTLI: A Python package for coupled interior–atmosphere modelling of volatile-rich planets - Published in JOSS (2025)
EMViz (Early Music Visualization)
EMViz (Early Music Visualization): MATLAB runtime application - Published in JOSS (2019)
WEPPCLIFF
WEPPCLIFF: A command-line tool to process climate inputs for soil loss models - Published in JOSS (2020)
SPyCi-PDB
SPyCi-PDB: A modular command-line interface for back-calculating experimental datatypes of protein structures. - Published in JOSS (2023)
fissa
A Python toolbox for Fast Image Signal Separation Analysis, designed for Calcium Imaging data.
feos
FeOs - A Framework for Equations of State and Classical Density Functional Theory
Ising_OPV v4.0
Ising_OPV v4.0: Experimental Tomography Data Import, Interpretation, and Analysis - Published in JOSS (2018)
Ratel: Performance portable solid mechanics with libCEED and PETSc
Ratel: Performance portable solid mechanics with libCEED and PETSc - Published in JOSS (2026)
home2park
home2park: An R package to assess the spatial provision of urban parks - Published in JOSS (2021)
PXO (Poly-XTAL Operations)
PXO (Poly-XTAL Operations): MATLAB Codebase to Generate, Analyse and Export Complex 2D Spatio-Temporally Gradient Grain Structures - Published in JOSS (2021)
Open-Source Hypothalamic-ForniX (OSHy-X) Atlases and Segmentation Tool for 3T and 7T
Open-Source Hypothalamic-ForniX (OSHy-X) Atlases and Segmentation Tool for 3T and 7T - Published in JOSS (2022)
LightTwinSVM
LightTwinSVM: A Simple and Fast Implementation of Standard Twin Support Vector Machine Classifier - Published in JOSS (2019)
bbousuite
bbousuite: A set of R packages to facilitate analysis of boreal caribou survival and recruitment data - Published in JOSS (2025)