reflectorch: a deep learning package for X-ray and neutron reflectometry
reflectorch: a deep learning package for X-ray and neutron reflectometry - Published in JOSS (2025)
PyDTS: A Python Package for Discrete-Time Survival Analysis with Competing Risks and Optional Penalization
PyDTS: A Python Package for Discrete-Time Survival Analysis with Competing Risks and Optional Penalization - Published in JOSS (2025)
IAMReX: an adaptive framework for the multiphase flow and fluid-particle interaction problems
IAMReX: an adaptive framework for the multiphase flow and fluid-particle interaction problems - Published in JOSS (2025)
ggoncoplot: an R package for interactive visualisation of somatic mutation data from cancer patient cohorts
ggoncoplot: an R package for interactive visualisation of somatic mutation data from cancer patient cohorts - Published in JOSS (2025)
fgwqsr: An R package for Frequentist Grouped Weighted Quantile Sum Regression
fgwqsr: An R package for Frequentist Grouped Weighted Quantile Sum Regression - Published in JOSS (2025)
anesthetic: nested sampling visualisation
anesthetic: nested sampling visualisation - Published in JOSS (2019)
GroLink: A general application programming interface for the plant-modeling platform GroIMP
GroLink: A general application programming interface for the plant-modeling platform GroIMP - Published in JOSS (2025)
fathon: A Python package for a fast computation of detrendend fluctuation analysis and related algorithms
fathon: A Python package for a fast computation of detrendend fluctuation analysis and related algorithms - Published in JOSS (2020)
RxInfer: A Julia package for reactive real-time Bayesian inference
RxInfer: A Julia package for reactive real-time Bayesian inference - Published in JOSS (2023)
GasChromatographySimulator.jl
GasChromatographySimulator.jl - Published in JOSS (2022)
glottospace: R package for language mapping and geospatial analysis of linguistic and cultural data
glottospace: R package for language mapping and geospatial analysis of linguistic and cultural data - Published in JOSS (2022)
PyMPDATA v1: Numba-accelerated implementation of MPDATA with examples in Python, Julia and Matlab
PyMPDATA v1: Numba-accelerated implementation of MPDATA with examples in Python, Julia and Matlab - Published in JOSS (2022)
PySDM v1: particle-based cloud modeling package for warm-rain microphysics and aqueous chemistry
PySDM v1: particle-based cloud modeling package for warm-rain microphysics and aqueous chemistry - Published in JOSS (2022)
Qiskit Experiments: A Python package to characterize and calibrate quantum computers
Qiskit Experiments: A Python package to characterize and calibrate quantum computers - Published in JOSS (2023)
SwiftVISA: Controlling Instrumentation with a Swift-based Implementation of the VISA Communication Protocol
SwiftVISA: Controlling Instrumentation with a Swift-based Implementation of the VISA Communication Protocol - Published in JOSS (2023)
SPbLA: The Library of GPGPU-powered Sparse Boolean Linear Algebra Operations
SPbLA: The Library of GPGPU-powered Sparse Boolean Linear Algebra Operations - Published in JOSS (2022)
radioactivedecay: A Python package for radioactive decay calculations
radioactivedecay: A Python package for radioactive decay calculations - Published in JOSS (2022)
TorchMetrics - Measuring Reproducibility in PyTorch
TorchMetrics - Measuring Reproducibility in PyTorch - Published in JOSS (2022)
Kinematics-vis: A Visualization Tool for the Mathematics of Human Motion
Kinematics-vis: A Visualization Tool for the Mathematics of Human Motion - Published in JOSS (2021)
GSAreport: Easy to Use Global Sensitivity Reporting
GSAreport: Easy to Use Global Sensitivity Reporting - Published in JOSS (2022)
3D Line Radiative Transfer & Synthetic Observations with Magritte
3D Line Radiative Transfer & Synthetic Observations with Magritte - Published in JOSS (2022)
PyBioPAX: biological pathway exchange in Python
PyBioPAX: biological pathway exchange in Python - Published in JOSS (2022)
islatu: A Python package for the reduction of reflectometry data
islatu: A Python package for the reduction of reflectometry data - Published in JOSS (2022)
nsink: An R package for flow path nitrogen removal estimation
nsink: An R package for flow path nitrogen removal estimation - Published in JOSS (2022)
mctreesearch4j: A Monte Carlo Tree Search Implementation for the JVM
mctreesearch4j: A Monte Carlo Tree Search Implementation for the JVM - Published in JOSS (2022)
beamshapes: a Python package to generate directivity patterns for various sound source models
beamshapes: a Python package to generate directivity patterns for various sound source models - Published in JOSS (2022)
VTUFileHandler: A VTU library in the Julia language that implements an algebra for basic mathematical operations on VTU data
VTUFileHandler: A VTU library in the Julia language that implements an algebra for basic mathematical operations on VTU data - Published in JOSS (2022)
pyscreener: A Python Wrapper for Computational Docking Software
pyscreener: A Python Wrapper for Computational Docking Software - Published in JOSS (2022)
portalcasting: Supporting automated forecasting of rodent populations
portalcasting: Supporting automated forecasting of rodent populations - Published in JOSS (2022)
PopMedNet: A scalable and extensible open-source informatics platform designed to facilitate the implementation and operation of distributed health data networks
PopMedNet: A scalable and extensible open-source informatics platform designed to facilitate the implementation and operation of distributed health data networks - Published in JOSS (2022)
minimo: a linked data and metadata storage system for small labs
minimo: a linked data and metadata storage system for small labs - Published in JOSS (2021)
GRChombo: An adaptable numerical relativity code for fundamental physics
GRChombo: An adaptable numerical relativity code for fundamental physics - Published in JOSS (2021)
HOODESolver.jl: A Julia package for highly oscillatory problems
HOODESolver.jl: A Julia package for highly oscillatory problems - Published in JOSS (2021)
flowTorch - a Python library for analysis and reduced-order modeling of fluid flows
flowTorch - a Python library for analysis and reduced-order modeling of fluid flows - Published in JOSS (2021)
Makie.jl: Flexible high-performance data visualization for Julia
Makie.jl: Flexible high-performance data visualization for Julia - Published in JOSS (2021)
PolSAR tools: A QGIS plugin for generating SAR descriptors
PolSAR tools: A QGIS plugin for generating SAR descriptors - Published in JOSS (2021)
RivGraph: Automatic extraction and analysis of river and delta channel network topology
RivGraph: Automatic extraction and analysis of river and delta channel network topology - Published in JOSS (2021)
Kinetics Toolkit: An Open-Source Python Package to Facilitate Research in Biomechanics
Kinetics Toolkit: An Open-Source Python Package to Facilitate Research in Biomechanics - Published in JOSS (2021)
bwsample: Processing Best-Worst Scaling data
bwsample: Processing Best-Worst Scaling data - Published in JOSS (2021)
BrainGlobe Atlas API: a common interface for neuroanatomical atlases
BrainGlobe Atlas API: a common interface for neuroanatomical atlases - Published in JOSS (2020)
pyrexMD: Workflow-Orientated Python Package for Replica Exchange Molecular Dynamics
pyrexMD: Workflow-Orientated Python Package for Replica Exchange Molecular Dynamics - Published in JOSS (2021)
IndividualDisplacements.jl: a Julia package to simulate and study particle displacements within the climate system
IndividualDisplacements.jl: a Julia package to simulate and study particle displacements within the climate system - Published in JOSS (2021)
OpenOmics: A bioinformatics API to integrate multi-omics datasets and interface with public databases.
OpenOmics: A bioinformatics API to integrate multi-omics datasets and interface with public databases. - Published in JOSS (2021)
Chemiscope: interactive structure-property explorer for materials and molecules
Chemiscope: interactive structure-property explorer for materials and molecules - Published in JOSS (2020)
sntools: An event generator for supernova burst neutrinos
sntools: An event generator for supernova burst neutrinos - Published in JOSS (2021)
lidar: A Python package for delineating nested surface depressions from digital elevation data
lidar: A Python package for delineating nested surface depressions from digital elevation data - Published in JOSS (2021)
MLJ: A Julia package for composable machine learning
MLJ: A Julia package for composable machine learning - Published in JOSS (2020)
outsider: Install and run programs, outside of R, inside of R
outsider: Install and run programs, outside of R, inside of R - Published in JOSS (2020)
sbi: A toolkit for simulation-based inference
sbi: A toolkit for simulation-based inference - Published in JOSS (2020)
cerebra: A tool for fast and accurate summarizing of variant calling format (VCF) files
cerebra: A tool for fast and accurate summarizing of variant calling format (VCF) files - Published in JOSS (2020)
CategoricalTimeSeries.jl: A toolbox for categorical time-series analysis
CategoricalTimeSeries.jl: A toolbox for categorical time-series analysis - Published in JOSS (2021)
IPART: A Python Package for Image-Processing based Atmospheric River Tracking
IPART: A Python Package for Image-Processing based Atmospheric River Tracking - Published in JOSS (2020)
Sit2StandPy: An Open-Source Python Package for Detecting and Quantifying Sit-to-Stand Transitions Using an Accelerometer on the Lower Back
Sit2StandPy: An Open-Source Python Package for Detecting and Quantifying Sit-to-Stand Transitions Using an Accelerometer on the Lower Back - Published in JOSS (2020)
PyMarket - A simple library for simulating markets in Python
PyMarket - A simple library for simulating markets in Python - Published in JOSS (2020)
libRL: A Python library for the characterization of microwave absorption
libRL: A Python library for the characterization of microwave absorption - Published in JOSS (2019)
turtleFSI: A Robust and Monolithic FEniCS-based Fluid-Structure Interaction Solver
turtleFSI: A Robust and Monolithic FEniCS-based Fluid-Structure Interaction Solver - Published in JOSS (2020)
Oceananigans.jl: Fast and friendly geophysical fluid dynamics on GPUs
Oceananigans.jl: Fast and friendly geophysical fluid dynamics on GPUs - Published in JOSS (2020)
PySWMM: The Python Interface to Stormwater Management Model (SWMM)
PySWMM: The Python Interface to Stormwater Management Model (SWMM) - Published in JOSS (2020)
Pippin: A pipeline for supernova cosmology
Pippin: A pipeline for supernova cosmology - Published in JOSS (2020)
MaterialNet: A web-based graph explorer for materials science data
MaterialNet: A web-based graph explorer for materials science data - Published in JOSS (2020)
rtweet: Collecting and analyzing Twitter data
rtweet: Collecting and analyzing Twitter data - Published in JOSS (2019)
cmstatr: An R Package for Statistical Analysis of Composite Material Data
cmstatr: An R Package for Statistical Analysis of Composite Material Data - Published in JOSS (2020)
modelDown: automated website generator with interpretable documentation for predictive machine learning models
modelDown: automated website generator with interpretable documentation for predictive machine learning models - Published in JOSS (2019)
Delira: A High-Level Framework for Deep Learning in Medical Image Analysis
Delira: A High-Level Framework for Deep Learning in Medical Image Analysis - Published in JOSS (2019)
ccostr: An R package for estimating mean costs with censored data
ccostr: An R package for estimating mean costs with censored data - Published in JOSS (2019)
Annotation Sniffer: A tool to Extract Code Annotations Metrics
Annotation Sniffer: A tool to Extract Code Annotations Metrics - Published in JOSS (2020)
tabula: An R Package for Analysis, Seriation, and Visualization of Archaeological Count Data
tabula: An R Package for Analysis, Seriation, and Visualization of Archaeological Count Data - Published in JOSS (2019)
STUMPY: A Powerful and Scalable Python Library for Time Series Data Mining
STUMPY: A Powerful and Scalable Python Library for Time Series Data Mining - Published in JOSS (2019)
shinyssd v1.0: Species Sensitivity Distributions for Ecotoxicological Risk Assessment
shinyssd v1.0: Species Sensitivity Distributions for Ecotoxicological Risk Assessment - Published in JOSS (2019)
Ryacas: A computer algebra system in R
Ryacas: A computer algebra system in R - Published in JOSS (2019)
lightr: import spectral data and metadata in R
lightr: import spectral data and metadata in R - Published in JOSS (2019)
Pybotics: Python Toolbox for Robotics
Pybotics: Python Toolbox for Robotics - Published in JOSS (2019)
ggparliament: A ggplot2 extension for parliament plots in R
ggparliament: A ggplot2 extension for parliament plots in R - Published in JOSS (2019)
SBMLtoODEpy: A software program for converting SBML models into ODE models in Python
SBMLtoODEpy: A software program for converting SBML models into ODE models in Python - Published in JOSS (2020)
DEVSIM: A TCAD Semiconductor Device Simulator
DEVSIM: A TCAD Semiconductor Device Simulator - Published in JOSS (2022)
Grafoscopio: A moldable tool for literate computing and reproducible research
Grafoscopio: A moldable tool for literate computing and reproducible research - Published in JOSS (2017)
FAIRLinked: Data FAIRification Tools for Materials Data Science
FAIRLinked: Data FAIRification Tools for Materials Data Science - Published in JOSS (2026)
CGView.js: a JavaScript package for visualizing small genomes
CGView.js: a JavaScript package for visualizing small genomes - Published in JOSS (2026)
libqcpp: A C++14 sequence quality control library
libqcpp: A C++14 sequence quality control library - Published in JOSS (2017)
Vibrant: A Post-Processing Tool for Computational Vibrational Spectroscopy of Molecules, Liquids and Materials
Vibrant: A Post-Processing Tool for Computational Vibrational Spectroscopy of Molecules, Liquids and Materials - Published in JOSS (2026)
The Pulmonary Agent-based Infection simulator (PAI): A Multi-Scale Agent-Based Model of Pulmonary Host-Pathogen Interactions
The Pulmonary Agent-based Infection simulator (PAI): A Multi-Scale Agent-Based Model of Pulmonary Host-Pathogen Interactions - Published in JOSS (2026)
scpviz: A Python bioinformatics toolkit for Single-cell Proteomics and multi-omics analysis
scpviz: A Python bioinformatics toolkit for Single-cell Proteomics and multi-omics analysis - Published in JOSS (2026)
Singularity Registry: Open Source Registry for Singularity Images
Singularity Registry: Open Source Registry for Singularity Images - Published in JOSS (2017)
Capytaine: a Python-based linear potential flow solver
Capytaine: a Python-based linear potential flow solver - Published in JOSS (2019)
iscore
iScore: an MPI supported software for ranking protein-protein docking models based on a random walk graph kernel and support vector machines
macsyfinder
MacSyFinder - Detection of macromolecular systems in protein datasets using systems modelling and similarity search.
manifolds.jl
Manifolds.jl provides a library of manifolds aiming for an easy-to-use and fast implementation.
photutils
Astropy package for source detection and photometry. Maintainer: @larrybradley
deepdiff
DeepDiff: Deep Difference and search of any Python object/data. DeepHash: Hash of any object based on its contents. Delta: Use deltas to reconstruct objects by adding deltas together.
cazy-webscraper
Web scraper to retrieve protein data catalogued by the CAZy, UniProt, NCBI, GTDB and PDB websites/databases.
undate
A Python library for working with fuzzy, partial, or otherwise uncertain dates
widoco
Wizard for documenting ontologies. WIDOCO is a step by step generator of HTML templates with the documentation of your ontology. It uses the LODE environment to create part of the template.