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)
Simple-Web-Server
Simple-Web-Server: a fast and flexible HTTP/1.1 C++ client and server library - Published in JOSS (2019)
ELECTRIC
ELECTRIC: Electric fields Leveraged from multipole Expansion Calculations in Tinker Rapid Interface Code - Published in JOSS (2020)
WODEN
WODEN: A CUDA-enabled package to simulate low-frequency radio interferometric data - Published in JOSS (2022)
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.
STARRED
STARRED: a two-channel deconvolution method with Starlet regularization - Published in JOSS (2023)
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)
MCycle
MCycle: A Python package for 1D sizing and analysis of thermodynamic power cycles - Published in JOSS (2018)
medoutcon
medoutcon: Nonparametric efficient causal mediation analysis with machine learning in R - Published in JOSS (2022)
scTree
scTree: An R package to generate antibody-compatible classifiers from single-cell sequencing data - Published in JOSS (2020)
Mold
Mold: a LAMMPS package to compute interfacial free energies and nucleation rates - Published in JOSS (2024)
CVtreeMLE
CVtreeMLE: Efficient Estimation of Mixed Exposures using Data Adaptive Decision Trees and Cross-Validated Targeted Maximum Likelihood Estimation in R - Published in JOSS (2023)
cde - R package to retrieve data from the Environment Agency Catchment Data Explorer site
cde - R package to retrieve data from the Environment Agency Catchment Data Explorer site - Published in JOSS (2019)
SWAMPE
SWAMPE: A Shallow-Water Atmospheric Model in Python for Exoplanets - Published in JOSS (2022)
Xenomapper: Mapping reads in a mixed species context
Xenomapper: Mapping reads in a mixed species context - Published in JOSS (2016)
MicroBenthos
MicroBenthos: a modeling framework for microbial benthic ecology - Published in JOSS (2018)
LGP
LGP: A robust Linear Genetic Programming implementation on the JVM using Kotlin. - Published in JOSS (2019)
Learning Simulator
Learning Simulator: A simulation software for animal and human learning - Published in JOSS (2021)
ParticleTracker
ParticleTracker: a gui based particle tracking software - Published in JOSS (2021)
Dryft
Dryft: A Python and MATLAB package to correct drifting ground reaction force signals during treadmill running - Published in JOSS (2019)
Quilë
Quilë: C++ genetic algorithms scientific library - Published in JOSS (2023)
mhealthtools
mhealthtools: A Modular R Package for Extracting Features from Mobile and Wearable Sensor Data - Published in JOSS (2020)
MM-PoE
MM-PoE: Multiple Choice Reasoning via. Process of Elimination using Multi-Modal Models - Published in JOSS (2025)
acronym
acronym: An Automatic Reduction Pipeline for Astronomical Images - Published in JOSS (2017)
CycloPhaser
CycloPhaser: A Python Package for Detecting Extratropical Cyclone Life Cycles - Published in JOSS (2025)
MetObs - a Python toolkit for using non-traditional meteorological observations
MetObs - a Python toolkit for using non-traditional meteorological observations - Published in JOSS (2024)
psychTestR
psychTestR: An R package for designing and conducting behavioural psychological experiments - Published in JOSS (2020)
Open-Unmix - A Reference Implementation for Music Source Separation
Open-Unmix - A Reference Implementation for Music Source Separation - Published in JOSS (2019)
The DynaGUI package
The DynaGUI package - Published in JOSS (2020)
mnt.pyfiction
An open-source design automation framework for Field-coupled Nanotechnologies
dtaidistance
Time series distances: Dynamic Time Warping (fast DTW implementation in C)
Phylogemetric
Phylogemetric: A Python library for calculating phylogenetic network metrics - Published in JOSS (2016)
deepmd-kit
A deep learning package for many-body potential energy representation and molecular dynamics
whampy
whampy: Python Package to Interact with, Visualize, and Analyze the Wisconsin H-Alpha Mapper - Sky Survey - Published in JOSS (2019)
LinguiPhyR
LinguiPhyR: A Package for Linguistic Phylogenetic Analysis in R - Published in JOSS (2024)
NEMESISPY
NEMESISPY: A Python package for simulating and retrieving exoplanetary spectra - Published in JOSS (2024)
Sinaps
Sinaps: A Python library to simulate voltage dynamics and ionic electrodiffusion in neurons - Published in JOSS (2022)
cosasi
cosasi: Graph Diffusion Source Inference in Python - Published in JOSS (2022)
directChillFoam
directChillFoam: an OpenFOAM application for direct-chill casting - Published in JOSS (2023)
SenAOReFoc
SenAOReFoc: A Closed-Loop Sensorbased Adaptive Optics and Remote Focusing Control Software - Published in JOSS (2022)
atems
atems: Analysis tools for TEM images of carbonaceous particles - Published in JOSS (2024)
pyBEMT
pyBEMT: An implementation of the Blade Element Momentum Theory in Python - Published in JOSS (2020)
DeepSynth
DeepSynth: Scaling Neural Program Synthesis with Distribution-based Search - Published in JOSS (2022)
EdgeVPN.io
EdgeVPN.io: Seamless Software-defined Layer 2 Virtual Networking for Edge Computing - Published in JOSS (2024)
NLMech
NLMech: Implementation of finite difference/meshfree discretization of nonlocal fracture models - Published in JOSS (2021)
QMRTools
QMRTools: a Mathematica toolbox for quantitative MRI analysis. - Published in JOSS (2019)
DBSP_DRP
DBSP_DRP: A Python package for automated spectroscopic data reduction of DBSP data - Published in JOSS (2022)
AtomNeb Python Package, an addendum to AtomNeb
AtomNeb Python Package, an addendum to AtomNeb: IDL Library for Atomic Data of Ionized Nebulae - Published in JOSS (2020)
pypots
A Python toolkit/library for reality-centric machine/deep learning and data mining on partially-observed time series, including SOTA neural network models for scientific analysis tasks of imputation/classification/clustering/forecasting/anomaly detection/cleaning on incomplete industrial (irregularly-sampled) multivariate TS with NaN missing values
UFig v1: The ultra-fast image generator
UFig v1: The ultra-fast image generator - Published in JOSS (2025)
xgboost
Scalable, Portable and Distributed Gradient Boosting (GBDT, GBRT or GBM) Library, for Python, R, Java, Scala, C++ and more. Runs on single machine, Hadoop, Spark, Dask, Flink and DataFlow
pysrim
pysrim: Automation, Analysis, and Plotting of SRIM Calculations - Published in JOSS (2018)
Shiny tools for management rules
Shiny tools for management rules: interactive applications that aid in conservation strategies for North Atlantic right whales - Published in JOSS (2023)
Synaptus
Synaptus: A Matlab/Octave toolbox for synthetic aperture ultrasound imaging - Published in JOSS (2022)
The 3D Slicer RVXLiverSegmentation plug-in for interactive liver anatomy reconstruction from medical images
The 3D Slicer RVXLiverSegmentation plug-in for interactive liver anatomy reconstruction from medical images - Published in JOSS (2022)
AliasFinder
AliasFinder: A Python script to search for the true planetary frequency within radial velocity data - Published in JOSS (2020)
TSE
TSE: A triple stellar evolution code - Published in JOSS (2024)
MSMExplorer
MSMExplorer: Data Visualizations for Biomolecular Dynamics - Published in JOSS (2017)
Bayesian model reconstruction based on spectral line observations with pomme
Bayesian model reconstruction based on spectral line observations with pomme - Published in JOSS (2024)
Excimontec v1.0
Excimontec v1.0: An Open-Source Software Tool for Kinetic Monte Carlo Simulations of Organic Electronic Devices - Published in JOSS (2020)
geocat-viz
GeoCAT-viz contains tools to help plot geoscience data, including convenience and plotting functions that are used to facilitate plotting geosciences data with Matplotlib, Cartopy, and other visualization packages.
ShUShER
ShUShER: private browser-based placement of sensitive genome samples on phylogenetic trees - Published in JOSS (2021)
pollucheck v1.0
pollucheck v1.0: A package to explore open-source air pollution data - Published in JOSS (2021)
FEniCS-arclength
FEniCS-arclength: A numerical continuation package in FEniCS for nonlinear problems in solid mechanics - Published in JOSS (2024)
GENRE (GPU Elastic-Net REgression)
GENRE (GPU Elastic-Net REgression): A CUDA-Accelerated Package for Massively Parallel Linear Regression with Elastic-Net Regularization - Published in JOSS (2020)
SeqIKPy: a Python package for inverse kinematics in insects
SeqIKPy: a Python package for inverse kinematics in insects - Published in JOSS (2026)
Taxonomy Resolver
Taxonomy Resolver: A Python package for building and filtering taxonomy trees - Published in JOSS (2025)
napari-clusters-plotter
A napari plugin for clustering objects according to their properties.
UPOsHam
UPOsHam: A Python package for computing unstable periodic orbits in two-degree-of-freedom Hamiltonian systems - Published in JOSS (2020)
MSG
MSG: A software package for interpolating stellar spectra in pre-calculated grids - Published in JOSS (2023)
papaya2
papaya2: 2D Irreducible Minkowski Tensor computation - Published in JOSS (2020)
Virtual Engineering: Python framework for engineering process design
Virtual Engineering: Python framework for engineering process design - Published in JOSS (2025)
HuracanPy
HuracanPy: A Python package for reading and analysing cyclone tracks - Published in JOSS (2025)
ecopath_matlab
ecopath_matlab: A Matlab-based implementation of the Ecopath food web algorithm - Published in JOSS (2017)
Umami
Umami: A Python toolkit for jet flavour tagging - Published in JOSS (2024)
Paraqus
Paraqus: Exporting Finite Element Simulation Results from Abaqus to VTK - Published in JOSS (2025)
The ppmData R-package for setting up spatial point process models
The ppmData R-package for setting up spatial point process models - Published in JOSS (2023)
Eyestream
Eyestream: An Open WebSocket-based Middleware for Serializing and Streaming Eye Tracker Event Data from Gazepoint GP3 HD Research Hardware - Published in JOSS (2019)
Estimating statistics from multi-state models using simulation with multistateutils
Estimating statistics from multi-state models using simulation with multistateutils - Published in JOSS (2018)
pypsa
PyPSA: Python for Power System Analysis
datasets
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