GitHub
pykeen
🤖 A Python library for learning and evaluating knowledge graph embeddings
gdess
gdess: A framework for evaluating simulated atmospheric CO₂ in Earth System Models - Published in JOSS (2022)
hopit
hopit: An R Package for Analysis of Reporting Behavior Using Generalized Ordered Probit Models - Published in JOSS (2019)
GO-RXR
GO-RXR: Global Optimization of Resonant X-ray Reflectometry - Published in JOSS (2025)
airflow-provider-vineyard
vineyard (v6d): an in-memory immutable data manager. (Project under CNCF, TAG-Storage)
wristpy: Fast, User-Friendly Python Processing of Wrist-worn Accelerometer Data
wristpy: Fast, User-Friendly Python Processing of Wrist-worn Accelerometer Data - Published in JOSS (2025)
Ellip: An Elliptic Integral Library for Rust
Ellip: An Elliptic Integral Library for Rust - Published in JOSS (2026)
hebbRNN
hebbRNN: A Reward-Modulated Hebbian Learning Rule for Recurrent Neural Networks - Published in JOSS (2016)
FASMA 2.0
FASMA 2.0: A Python package for stellar parameters and chemical abundances - Published in JOSS (2020)
getTBinR
getTBinR: an R package for accessing and summarising the World Health Organisation Tuberculosis data - Published in JOSS (2019)
shipgrav
shipgrav: A Python package for marine gravimetry - Published in JOSS (2024)
PyCVI
PyCVI: A Python package for internal Cluster Validity Indices, compatible with time-series data - Published in JOSS (2024)
lattice-symmetries
lattice-symmetries: A package for working with quantum many-body bases - Published in JOSS (2021)
Cthulhu
Cthulhu: An Open Source Molecular and Atomic Cross Section Computation Code for Substellar Atmospheres - Published in JOSS (2024)
The stantargets R package
The stantargets R package: a workflow framework for efficient reproducible Stan-powered Bayesian data analysis pipelines - Published in JOSS (2021)
strucscan
strucscan: A lightweight Python-based framework for high-throughput material simulation - Published in JOSS (2022)
IGRINS RV
IGRINS RV: A Python Package for Precision Radial Velocities with Near-Infrared Spectra - Published in JOSS (2021)
ScenTrees.jl
ScenTrees.jl: A Julia Package for Generating Scenario Trees and Scenario Lattices for Multistage Stochastic Programming - Published in JOSS (2020)
WGS2NCBI - Toolkit for preparing genomes for submission to NCBI
WGS2NCBI - Toolkit for preparing genomes for submission to NCBI - Published in JOSS (2019)
hmis
hmis: A python tool to visualize and analyze HMIS data - Published in JOSS (2017)
remBoot
remBoot: An R package for Random Encounter Modelling - Published in JOSS (2017)
DscoreApp
DscoreApp: An user-friendly web application for computing the Implicit Association Test D-score - Published in JOSS (2019)
RTMsim - A Julia module for filling simulations in Resin Transfer Moulding with the Finite Area Method
RTMsim - A Julia module for filling simulations in Resin Transfer Moulding with the Finite Area Method - Published in JOSS (2023)
MiNAA
MiNAA: Microbiome Network Alignment Algorithm - Published in JOSS (2024)
minorbsem
minorbsem: An R package for structural equation models that account for the influence of minor factors - Published in JOSS (2023)
CliquePercolation
CliquePercolation: An R Package for conducting and visualizing results of the clique percolation network community detection algorithm - Published in JOSS (2021)
tissueloc
tissueloc: Whole slide digital pathology image tissue localization - Published in JOSS (2019)
TrackSegNet
TrackSegNet: a tool for trajectory segmentation into diffusive states using supervised deep learning - Published in JOSS (2024)
COSMO
COSMO: Accelerated ADMM-based solver for convex conic optimisation problems (LP, QP, SOCP, SDP, ExpCP, PowCP). Automatic chordal decomposition of sparse semidefinite programs.
VCC
VCC: A framework for building containerized reproducible cluster software environments - Published in JOSS (2017)
MultichannelGPR
MultichannelGPR: A MATLAB tool for Ground Penetrating Radar data processing - Published in JOSS (2024)
Genotify
Genotify: Fast, lightweight gene lookup and summarization - Published in JOSS (2018)
microViz
microViz: an R package for microbiome data visualization and statistics - Published in JOSS (2021)
NLSIG-COVID19Lab
NLSIG-COVID19Lab: A modern logistic-growth tool (nlogistic-sigmoid) for descriptively modelling the dynamics of the COVID-19 pandemic process - Published in JOSS (2021)
Masks2Metrics (M2M)
Masks2Metrics (M2M): A Matlab Toolbox for Gold Standard Morphometrics - Published in JOSS (2018)
EMBERS
EMBERS: Experimental Measurement of BEam Responses with Satellites - Published in JOSS (2020)
AIgarMIC
AIgarMIC: a Python package for automated interpretation of agar dilution minimum inhibitory concentration assays - Published in JOSS (2024)
umpire
An application-focused API for memory management on NUMA & GPU architectures
cdcam
cdcam: Cambridge Digital Communications Assessment Model - Published in JOSS (2020)
GMSimViz
GMSimViz: Automated 3D Visualization of Ground Motion Simulation with Generic Mapping Tools (GMT) - Published in JOSS (2019)
ysoisochrone
ysoisochrone: A Python package to estimate masses and ages for YSOs - Published in JOSS (2025)
fairchem-core
FAIR Chemistry's library of machine learning methods for chemistry
<strong>geospaNN</strong>: A Python package for geospatial neural networks
<strong>geospaNN</strong>: A Python package for geospatial neural networks - Published in JOSS (2026)
E2EDNA 2.0
E2EDNA 2.0: Python Pipeline for Simulating DNA Aptamers with Ligands - Published in JOSS (2022)
gwdegree
gwdegree: Improving interpretation of geometrically-weighted degree estimates in exponential random graph models - Published in JOSS (2016)
NodeLab
NodeLab: A MATLAB package for meshfree node-generation and adaptive refinement - Published in JOSS (2019)
CheSweet
CheSweet: An application to predict glycan’s chemicals shifts - Published in JOSS (2018)
SlicerITKUltrasound
SlicerITKUltrasound: A 3D Slicer extension for scan conversion of B-mode and next-generation ultrasound imaging modalities - Published in JOSS (2017)
tesliper
tesliper: a theoretical spectroscopist's little helper - Published in JOSS (2022)
BioSigKit
BioSigKit: A Matlab Toolbox and Interface for Analysis of BioSignals - Published in JOSS (2018)
Rule-based integration
Rule-based integration: An extensive system of symbolic integration rules - Published in JOSS (2018)
zfit
Model manipulation and fitting library based on TensorFlow and optimised for simple and direct manipulation of probability density functions. Its main focus is on scalability, parallelisation and user friendly experience.
Tidytacos
Tidytacos: An R package for analyses on taxonomic composition of microbial communities - Published in JOSS (2025)
Simulated Diffusion in Realistic Imaging Features of Tissue (Sim-DRIFT)
Simulated Diffusion in Realistic Imaging Features of Tissue (Sim-DRIFT) - Published in JOSS (2023)
obscura
obscura: A modular C++ tool and library for the direct detection of (sub-GeV) dark matter via nuclear and electron recoils - Published in JOSS (2021)
BoltzMM
BoltzMM: an R package for maximum pseudolikelihood estimation of fully-visible Boltzmann machines - Published in JOSS (2019)
StoSpa2
StoSpa2: A C++ software package for stochastic simulations of spatially extended systems - Published in JOSS (2020)
NoisySignalIntegration.jl
NoisySignalIntegration.jl: A Julia package for uncertainty evaluation of numeric integrals - Published in JOSS (2021)
js-emass
js-emass: A flexible JavaScript implementation of the emass algorithm - Published in JOSS (2018)
PyAFBF
PyAFBF: a Python library for sampling image textures from the anisotropic fractional Brownian field. - Published in JOSS (2022)
particle
Package to deal with particles, the PDG particle data table, PDGIDs, etc.
Port
Port: A software tool for digital data donation - Published in JOSS (2023)
Parent-map
Parent-map: analysis of parental contributions to evolved or engineered protein or DNA sequences - Published in JOSS (2021)
tcherry
tcherry: Learning the structure of tcherry trees - Published in JOSS (2019)
StatAid
StatAid: An R package with a graphical user interface for data analysis - Published in JOSS (2020)
DeBEIR
DeBEIR: A Python Package for Dense Bi-Encoder Information Retrieval - Published in JOSS (2023)
PoUnce
PoUnce: A framework for automatized uncertainty quantification simulations on high-performance clusters - Published in JOSS (2023)
A News Verification Browser for the Detection of Clickbait, Satire, and Falsified News
A News Verification Browser for the Detection of Clickbait, Satire, and Falsified News - Published in JOSS (2019)
Artery.FE
Artery.FE: An implementation of the 1D blood flow equations in FEniCS - Published in JOSS (2018)
openEyeTrack - A high speed multi-threaded eye tracker for head-fixed applications
openEyeTrack - A high speed multi-threaded eye tracker for head-fixed applications - Published in JOSS (2019)
BracketingNonlinearSolve
High-performance and differentiation-enabled nonlinear solvers (Newton methods), bracketed rootfinding (bisection, Falsi), with sparsity and Newton-Krylov support.
maxsmooth
maxsmooth: Derivative Constrained Function Fitting - Published in JOSS (2020)
SG-t-SNE-Π
SG-t-SNE-Π: Swift Neighbor Embedding of Sparse Stochastic Graphs - Published in JOSS (2019)
c-lasso - a Python package for constrained sparse and robust regression and classification
c-lasso - a Python package for constrained sparse and robust regression and classification - Published in JOSS (2021)
`QuasinormalModes.jl`
`QuasinormalModes.jl`: A Julia package for computing discrete eigenvalues of second order ODEs - Published in JOSS (2022)
PyGModels
PyGModels: A Python package for exploring Probabilistic Graphical Models with Graph Theoretical Structures - Published in JOSS (2021)
SeroTools
SeroTools: a Python package for Salmonella serotype data analysis - Published in JOSS (2020)
covtobed
covtobed: a simple and fast tool to extract coverage tracks from BAM files - Published in JOSS (2020)
Finnish Media Scrapers
Finnish Media Scrapers - Published in JOSS (2021)
NBI
NBI: A library for Nystrom Boundary Integral calculations - Published in JOSS (2024)
Delta-Rice
Delta-Rice: A HDF5 Compression Plugin optimized for Digitized Detector Data - Published in JOSS (2024)
AHGestimation
AHGestimation: An R package for computing robust, mass preserving hydraulic geometries and rating curves - Published in JOSS (2024)
Multi-attribute task builder
Multi-attribute task builder - Published in JOSS (2019)