GitHub
Mashtree
Mashtree: a rapid comparison of whole genome sequence files - Published in JOSS (2019)
FuzzyClass
FuzzyClass: A family of Fuzzy and Non-Fuzzy probabilistic-based classifiers - Published in JOSS (2023)
ppiclF
ppiclF: A Parallel Particle-In-Cell Library in Fortran - Published in JOSS (2019)
A flexible search system for high-accuracy identification of biological entities and molecules
A flexible search system for high-accuracy identification of biological entities and molecules - Published in JOSS (2021)
walkr
walkr: MCMC Sampling from Non-Negative Convex Polytopes - Published in JOSS (2017)
sandpyper
sandpyper: A Python package for UAV-SfM beach volumetric and behavioural analysis - Published in JOSS (2021)
KADE
KADE: A desktop application for Q methodology - Published in JOSS (2019)
Biosiglive
Biosiglive: an Open-Source Python Package for Real-time Biosignal Processing - Published in JOSS (2023)
DynaMo
DynaMo: Dynamic Body Shape and Motion Capture with Intel RealSense Cameras - Published in JOSS (2019)
PyZFS
PyZFS: A Python package for first-principles calculations of zero-field splitting tensors - Published in JOSS (2020)
ur-scape
ur-scape: harnessing data for stakeholder participation in city-making processes - Published in JOSS (2022)
Krang
Krang: Kerr Raytracer for Analytic Null Geodesics - Published in JOSS (2024)
HARDy
HARDy: Handling Arbitrary Recognition of Data in Python - Published in JOSS (2022)
xraybinaryorbit
xraybinaryorbit: A Python Package for Analyzing Orbital Modulations in X-ray Binaries - Published in JOSS (2024)
taurenmd
taurenmd: A command-line interface for analysis of Molecular Dynamics simulations. - Published in JOSS (2020)
latentcor
latentcor: An R Package for estimating latent correlations from mixed data types - Published in JOSS (2021)
stardate
stardate: Combining dating methods for better stellar ages - Published in JOSS (2019)
Fireworks
Fireworks: Reproducible Machine Learning and Preprocessing with PyTorch - Published in JOSS (2019)
ESVM
ESVM: an open-source finite volume Electrostatic Vlasov-Maxwell code - Published in JOSS (2021)
ParticlePhaseSpace
ParticlePhaseSpace: A python package for streamlined import, analysis, and export of particle phase space data - Published in JOSS (2023)
ConTEXT Explorer
ConTEXT Explorer: a web-based text analysis tool for exploring and visualizing concepts across time - Published in JOSS (2021)
perfectns
perfectns: perfect dynamic and standard nested sampling for spherically symmetric likelihoods and priors - Published in JOSS (2018)
org.biojava
:book::microscope::coffee: BioJava is an open-source project dedicated to providing a Java library for processing biological data.
boxmot
BoxMOT: Pluggable SOTA multi-object tracking modules modules for segmentation, object detection and pose estimation models
pySLM2
pySLM2: A full-stack python package for holographic beam shaping - Published in JOSS (2024)
PyTransport
PyTransport: A Python package for the calculation of inflationary correlation functions - Published in JOSS (2018)
tbeptools
tbeptools: An R package for synthesizing estuarine data for environmental research - Published in JOSS (2021)
MorphoMetriX
MorphoMetriX: a photogrammetric measurement GUI for morphometric analysis of megafauna - Published in JOSS (2020)
pyGOURGS - global optimization of n-ary tree representable problems using uniform random global search
pyGOURGS - global optimization of n-ary tree representable problems using uniform random global search - Published in JOSS (2020)
PCRedux
PCRedux: A Quantitative PCR Machine Learning Toolkit - Published in JOSS (2022)
CNATool - Complex Network Analysis Tool
CNATool - Complex Network Analysis Tool - Published in JOSS (2023)
malan
malan: MAle Lineage ANalysis - Published in JOSS (2018)
SEEDPOD Ground Risk
SEEDPOD Ground Risk: A Python application and library for Uncrewed Aerial Systems ground risk analysis and risk-aware path finding - Published in JOSS (2022)
INCHEM-Py
INCHEM-Py: An open source Python box model for indoor air chemistry - Published in JOSS (2021)
Prest
Prest: Open-Source Software for Computational Revealed Preference Analysis - Published in JOSS (2018)
pfla
pfla: A Python Package for Dental Facial Analysis using Computer Vision and Statistical Shape Analysis - Published in JOSS (2018)
pymeasure
Scientific measurement library for instruments, experiments, and live-plotting
terratools: A Python package to analyse TERRA mantle convection simulations
terratools: A Python package to analyse TERRA mantle convection simulations - Published in JOSS (2025)
ClimDown
ClimDown: Climate Downscaling in R - Published in JOSS (2018)
COSplay
COSplay: Contrast Optimized Stimulation Player - Published in JOSS (2019)
hf_hydrodata
hf_hydrodata: A Python package for accessing hydrologic simulations and observations across the United States - Published in JOSS (2024)
G'MIC
G'MIC: An Open-Source Self-Extending Framework for Image Processing - Published in JOSS (2025)
TimeStruct.jl -- flexible multi-horizon time modelling in optimization models
TimeStruct.jl -- flexible multi-horizon time modelling in optimization models - Published in JOSS (2025)
Histogram-weighted Networks for Feature Extraction, Connectivity and Advanced Analysis in Neuroscience
Histogram-weighted Networks for Feature Extraction, Connectivity and Advanced Analysis in Neuroscience - Published in JOSS (2017)
pysersic
pysersic: A Python package for determining galaxy structural properties via Bayesian inference, accelerated with jax - Published in JOSS (2023)
xml2jupyter
xml2jupyter: Mapping parameters between XML and Jupyter widgets - Published in JOSS (2019)
epipack
epipack: An infectious disease modeling package for Python - Published in JOSS (2021)
lightcurver
lightcurver: A Python Pipeline for Precise Photometry of Multiple-Epoch Wide-Field Images - Published in JOSS (2024)
DynamicOED.jl
DynamicOED.jl: A Julia package for solving optimum experimental design problems - Published in JOSS (2024)
MFEM/MGIS, a HPC mini-application targeting nonlinear thermo-mechanical simulations of nuclear fuels at mesoscale
MFEM/MGIS, a HPC mini-application targeting nonlinear thermo-mechanical simulations of nuclear fuels at mesoscale - Published in JOSS (2025)
TsgFEM
TsgFEM: Tensegrity Finite Element Method - Published in JOSS (2022)
Git-RDM
Git-RDM: A research data management plugin for the Git version control system - Published in JOSS (2016)
SonoUno development
SonoUno development: a User-Centered Sonification software for data analysis - Published in JOSS (2024)
nap
nap: A molecular dynamics package with parameter-optimization programs for classical and machine-learning potentials - Published in JOSS (2021)
SuperNOVA
SuperNOVA: Semi-Parametric Identification and Estimation of Interaction and Effect Modification in Mixed Exposures using Stochastic Interventions in R - Published in JOSS (2023)
helayo
helayo: Reconstructing Sanskrit texts from manuscript witnesses - Published in JOSS (2022)
CoreRobotics
CoreRobotics: An object-oriented C++ library with cross-language wrappers for cross-platform robot control - Published in JOSS (2018)
rFBP
rFBP: Replicated Focusing Belief Propagation algorithm - Published in JOSS (2020)
LabelProp
LabelProp: A semi-automatic segmentation tool for 3D medical images - Published in JOSS (2025)
haldensify
haldensify: Highly adaptive lasso conditional density estimation in R - Published in JOSS (2022)
PyNGHam
PyNGHam: A Python library of the NGHam protocol - Published in JOSS (2023)
q2-sample-classifier
q2-sample-classifier: machine-learning tools for microbiome classification and regression - Published in JOSS (2018)
graphenv
graphenv: a Python library for reinforcement learning on graph search spaces - Published in JOSS (2022)
Recan
Recan: Python tool for analysis of recombination events in viral genomes - Published in JOSS (2020)
Syn-CpG-Spacer
Syn-CpG-Spacer: A Panel web app for synonymous recoding of viral genomes with CpG dinucleotides - Published in JOSS (2024)
PyLogGrid
PyLogGrid: A Python package for fluid dynamics on logarithmic lattices - Published in JOSS (2024)
CBX
CBX: Python and Julia Packages for Consensus-Based Interacting Particle Methods - Published in JOSS (2024)
bleiglas
bleiglas: An R package for interpolation and visualisation of spatiotemporal data with 3D tessellation - Published in JOSS (2021)
WDPM
WDPM: the Wetland DEM Ponding Model - Published in JOSS (2021)
COVID-19 Lung Segmentation
COVID-19 Lung Segmentation - Published in JOSS (2021)
ros_control
ros_control: A generic and simple control framework for ROS - Published in JOSS (2017)
treemaker
treemaker: A Python tool for constructing a Newick formatted tree from a set of classifications. - Published in JOSS (2018)
diman
diman: A Clojure Package for Dimensional Analysis - Published in JOSS (2022)
dropout
dropout: an R Package for Addressing Dropouts, Missing Values, and Sectional Challenges in Survey Data Analysis - Published in JOSS (2024)
FIPS
FIPS: An R Package for Biomathematical Modelling of Human Fatigue Related Impairment - Published in JOSS (2020)
seg1d
seg1d: A Python package for Automated segmentation of one-dimensional (1D) data - Published in JOSS (2020)
pudu
pudu: A Python library for agnostic feature selection and explainability of Machine Learning spectroscopic problems - Published in JOSS (2023)
MDPax: GPU-accelerated MDP solvers in Python with JAX
MDPax: GPU-accelerated MDP solvers in Python with JAX - Published in JOSS (2025)
rOPTRAM
rOPTRAM: Deriving Soil Moisture from Satellite Imagery in R - Published in JOSS (2024)
gcamreport
gcamreport: An R tool to process and standardize GCAM outputs - Published in JOSS (2024)
WODEN
WODEN: A CUDA-enabled package to simulate low-frequency radio interferometric data - Published in JOSS (2022)
ELECTRIC
ELECTRIC: Electric fields Leveraged from multipole Expansion Calculations in Tinker Rapid Interface Code - Published in JOSS (2020)
dsBinVal
dsBinVal: Conducting distributed ROC analysis using DataSHIELD - Published in JOSS (2023)
CrystalGrowthTracker
CrystalGrowthTracker: A Python package to analyse crystal face advancement rates from time lapse synchrotron radiography - Published in JOSS (2022)
popkinmocks
popkinmocks: mock IFU datacubes for modelling stellar populations and kinematics - Published in JOSS (2023)
Corekaburra
Corekaburra: pan-genome post-processing using core gene synteny - Published in JOSS (2022)
Halotools
Halotools: A New Release Adding Intrinsic Alignments to Halo-Based Methods - Published in JOSS (2025)
easyvvuq
Python 3 framework to facilitate verification, validation and uncertainty quantification (VVUQ) for a wide variety of simulations.
Open Source Optical Coherence Tomography Software
Open Source Optical Coherence Tomography Software - Published in JOSS (2020)
DICaugment
DICaugment: A Python Package for 3D Medical Imaging Augmentation - Published in JOSS (2024)
PyMap3D
PyMap3D: 3-D coordinate conversions for terrestrial and geospace environments - Published in JOSS (2018)