trud • Science 36%

R package wrapper for the NHS TRUD API

quanteda — Peer-reviewed • Science 95%

quanteda: An R package for the quantitative analysis of textual data - Published in JOSS (2018)

QuantumACES.jl — Peer-reviewed • Science 98%

QuantumACES.jl: design noise characterisation experiments for quantum computers - Published in JOSS (2025)

RelativisticDynamics.jl — Peer-reviewed • Science 93%

RelativisticDynamics.jl: Relativistic Spin-Orbital Dynamics in Julia - Published in JOSS (2023)

https://github.com/abuzarmahmood/pytau • Science 36%

Library to streamline batch-fitting of Bayesian changepoint models to neural population spiking data

Optimising Light Source Positioning for Even and Flux-Efficient Illumination — Peer-reviewed • Science 93%

Optimising Light Source Positioning for Even and Flux-Efficient Illumination - Published in JOSS (2019)

Implicit measures with reproducible results — Peer-reviewed • Science 87%

Implicit measures with reproducible results: The implicitMeasures package - Published in JOSS (2020)

A Julia package for bilevel optimization problems — Peer-reviewed • Science 98%

A Julia package for bilevel optimization problems - Published in JOSS (2019)

BotSlayer — Peer-reviewed • Science 87%

BotSlayer: real-time detection of bot amplification on Twitter - Published in JOSS (2019)

DemeterWatch — Peer-reviewed • Science 95%

DemeterWatch: A Java tool to detect Law of Demeter violations in Java collections - Published in JOSS (2025)

COHESIVM — Peer-reviewed • Science 98%

COHESIVM: Combinatorial h+/e- Sample Investigation using Voltaic Measurements - Published in JOSS (2025)

opensim-creator • Science 49%

A UI for building OpenSim models

jax-smfsb — Peer-reviewed • Science 87%

jax-smfsb: A Python library for stochastic systems biology modelling and inference - Published in JOSS (2025)

ProntoPCR: Efficient qPCR Data Analysis Software • Science 87%

ProntoPCR: Efficient qPCR Data Analysis Software - Published in JOSS (2026)

dolfin-adjoint 2018.1 — Peer-reviewed • Science 87%

dolfin-adjoint 2018.1: automated adjoints for FEniCS and Firedrake - Published in JOSS (2019)

eitprocessing • Science 44%

Software for electrical impedance tomography data loading, visualization and processing

mlgidGUI - an annotation program for 2D scattering data • Science 93%

mlgidGUI - an annotation program for 2D scattering data - Published in JOSS (2025)

elasticipy • Science 49%

A python toolkit to perform common tensor operations in Continuum Mechanics

RAFF.jl — Peer-reviewed • Science 93%

RAFF.jl: Robust Algebraic Fitting Function in Julia - Published in JOSS (2019)

Compare Expression Profiles for Pre-defined Gene Groups with C-REx — Peer-reviewed • Science 95%

Compare Expression Profiles for Pre-defined Gene Groups with C-REx - Published in JOSS (2019)

deepinv • Science 54%

DeepInverse: a PyTorch library for solving imaging inverse problems using deep learning

hammurabi X — Peer-reviewed • Science 89%

hammurabi X: a C++ package for simulating Galactic emissions - Published in JOSS (2020)

mlr3extralearners: Expanding the mlr3 Ecosystem with Community-Driven Learner Integration • Science 95%

mlr3extralearners: Expanding the mlr3 Ecosystem with Community-Driven Learner Integration - Published in JOSS (2025)

RHEOS.jl -- A Julia Package for Rheology Data Analysis — Peer-reviewed • Science 95%

RHEOS.jl -- A Julia Package for Rheology Data Analysis - Published in JOSS (2019)

quadcleanR — Peer-reviewed • Science 93%

quadcleanR: An R Package for the Cleanup and Visualization of Quadrat Data - Published in JOSS (2022)

EvoDynamics.jl — Peer-reviewed • Science 93%

EvoDynamics.jl: a framework for modeling eco-evolutionary dynamics - Published in JOSS (2022)

A reusable tree-based web-visualization to browse EDAM ontology, and contribute to it. — Peer-reviewed • Science 95%

A reusable tree-based web-visualization to browse EDAM ontology, and contribute to it. - Published in JOSS (2018)

dia — Peer-reviewed • Science 95%

dia: An R package for the National Oceanic and Atmospheric Administration dam impact analysis - Published in JOSS (2025)

IGraph/M — Peer-reviewed • Science 95%

IGraph/M: graph theory and network analysis for Mathematica - Published in JOSS (2023)

VOTCA — Peer-reviewed • Science 100%

VOTCA: multiscale frameworks for quantum and classical simulations in soft matter - Published in JOSS (2024)

bor — Peer-reviewed • Science 93%

bor: An R Package for Transforming Behavioral Observation Records into Data Matrices - Published in JOSS (2018)

WEdiff — Peer-reviewed • Science 87%

WEdiff: A Python and C++ package for automatic differentiation - Published in JOSS (2018)

Pyra — Peer-reviewed • Science 98%

Pyra: Automated EM27/SUN Greenhouse Gas Measurement Software - Published in JOSS (2023)

CLOOPSy - Copernicus Land cOver crOwdsourcing Platform for Sentinel-based mapping — Peer-reviewed • Science 89%

CLOOPSy - Copernicus Land cOver crOwdsourcing Platform for Sentinel-based mapping - Published in JOSS (2017)

carbonr — Peer-reviewed • Science 93%

carbonr: An R Package for Estimating Carbon-Equivalent Emissions - Published in JOSS (2024)

GRBoondi — Peer-reviewed • Science 98%

GRBoondi: A code for evolving Generalized Proca theories on arbitrary backgrounds - Published in JOSS (2024)

Pysewer — Peer-reviewed • Science 87%

Pysewer: A Python Library for Sewer Network Generation in Data Scarce Regions - Published in JOSS (2024)

BVPy — Peer-reviewed • Science 89%

BVPy: A FEniCS-based Python package to ease the expression and study of boundary value problems in Biology. - Published in JOSS (2021)

Jabberwocky — Peer-reviewed • Science 93%

Jabberwocky: an ontology-aware toolkit for manipulating text - Published in JOSS (2020)

validateHOT - an R package for the analysis of holdout/validation tasks and other choice modeling tools — Peer-reviewed • Science 98%

validateHOT - an R package for the analysis of holdout/validation tasks and other choice modeling tools - Published in JOSS (2025)

PhenoFeatureFinder — Peer-reviewed • Science 95%

PhenoFeatureFinder: a python package for linking developmental phenotypes to omics features - Published in JOSS (2024)

XCALibre.jl — Peer-reviewed • Science 93%

XCALibre.jl: A Julia XPU unstructured finite volume Computational Fluid Dynamics library - Published in JOSS (2025)

VibIR-Parallel-Compute — Peer-reviewed • Science 87%

VibIR-Parallel-Compute: Enhancing Vibration and Infrared Analysis in High-Performance Computing Environments - Published in JOSS (2025)

QGDipoles.jl — Peer-reviewed • Science 98%

QGDipoles.jl: A Julia package for calculating dipolar vortex solutions to the Quasi-Geostrophic equations - Published in JOSS (2025)

MDL Suite — Peer-reviewed • Science 95%

MDL Suite: A language, generator and compiler for describing mazes - Published in JOSS (2020)

G3F — Peer-reviewed • Science 93%

G3F: Global, Multidimensional Spectral Regression Analysis - Published in JOSS (2019)

ExTemp — Peer-reviewed • Science 93%

ExTemp: A computational and image-processing suite for extracting temporal barcodes - Published in JOSS (2020)

Ocellaris — Peer-reviewed • Science 89%

Ocellaris: a DG FEM solver for free-surface flows - Published in JOSS (2019)

MPA — Peer-reviewed • Science 93%

MPA: a novel cross-language API for time series analysis - Published in JOSS (2020)

Go-HEP — Peer-reviewed • Science 95%

Go-HEP: libraries for High Energy Physics analyses in Go - Published in JOSS (2017)

Production Function Estimation in R — Peer-reviewed • Science 87%

Production Function Estimation in R: The prodest Package - Published in JOSS (2017)

CRBHits — Peer-reviewed • Science 89%

CRBHits: From Conditional Reciprocal Best Hits to Codon Alignments and Ka/Ks in R - Published in JOSS (2020)

Temporalis — Peer-reviewed • Science 87%

Temporalis: an open source software for dynamic LCA - Published in JOSS (2018)

GeoClimate — Peer-reviewed • Science 95%

GeoClimate: a Geospatial processing toolbox for environmental and climate studies - Published in JOSS (2021)

passt — Peer-reviewed • Science 95%

passt: An R implementation of the Probability Associator Time (PASS-T) model - Published in JOSS (2020)

https://github.com/bc3lc/rhap • Science 49%

Econometric analysis to analyze health impacts attributable to indoor air pollution

vivid-volcano • Science 98%

A shiny app for custom analyzes of preprocessed omics data

Groupyr — Peer-reviewed • Science 93%

Groupyr: Sparse Group Lasso in Python - Published in JOSS (2021)

ScatteringOptics.jl — Peer-reviewed • Science 95%

ScatteringOptics.jl: An Interstellar Scattering Framework in the Julia Programming Language - Published in JOSS (2025)

automesh • Science 57%

Automatic mesh generation.

THz Image Explorer - An Interactive Cross-Platform Open-Source THz Image Analysis Tool • Science 93%

THz Image Explorer - An Interactive Cross-Platform Open-Source THz Image Analysis Tool - Published in JOSS (2025)

brains-py, A framework to support research on energy-efficient unconventional hardware for machine learning — Peer-reviewed • Science 93%

brains-py, A framework to support research on energy-efficient unconventional hardware for machine learning - Published in JOSS (2023)

NonSysId: Nonlinear System Identification with Improved Model Term Selection for NARMAX Models • Science 93%

NonSysId: Nonlinear System Identification with Improved Model Term Selection for NARMAX Models - Published in JOSS (2025)

GOBLIN Lite — Peer-reviewed • Science 93%

GOBLIN Lite: A National Land Balance Model for Assessment of Climate Mitigation Pathways for Ireland. - Published in JOSS (2024)

diwanalr — Peer-reviewed • Science 95%

diwanalr: An R data analysis package for diffusing-wave spectroscopy - Published in JOSS (2019)

FastTanhSinhQuadrature.jl: High-performance Tanh-Sinh numerical integration in Julia • Science 87%

FastTanhSinhQuadrature.jl: High-performance Tanh-Sinh numerical integration in Julia - Published in JOSS (2026)

HCP — Peer-reviewed • Science 87%

HCP: A Matlab package to create beautiful heatmaps with richly annotated covariates - Published in JOSS (2019)

Basicsums — Peer-reviewed • Science 87%

Basicsums: A Python package for computing structural sums and the effective conductivity of random composites - Published in JOSS (2019)

pyOMA2: A Python module for conducting operational modal analysis • Science 93%

pyOMA2: A Python module for conducting operational modal analysis - Published in JOSS (2025)

SpinVibe: Simulating spin-phonon coupling for molecular qubits • Science 87%

SpinVibe: Simulating spin-phonon coupling for molecular qubits - Published in JOSS (2026)

Biosensor Framework — Peer-reviewed • Science 100%

Biosensor Framework: A C# Library for Affective Computing - Published in JOSS (2021)

xr_fresh: Automated Time Series Feature Extraction for Remote Sensing & Gridded Data • Science 93%

xr_fresh: Automated Time Series Feature Extraction for Remote Sensing & Gridded Data - Published in JOSS (2025)

rmcmc • Science 57%

Robust Markov chain Monte Carlo methods in R

ParaDigMa: a Python toolbox for extracting Parkinson's disease digital biomarkers from daily life wrist sensor data • Science 92%

ParaDigMa: a Python toolbox for extracting Parkinson's disease digital biomarkers from daily life wrist sensor data - Published in JOSS (2026)

targene-pipeline • Science 44%

Nextflow pipeline for Targeted-Learning of genetic effects

PySGN: A Python package for constructing synthetic geospatial networks • Science 87%

PySGN: A Python package for constructing synthetic geospatial networks - Published in JOSS (2026)

Liblsl.dart: A Dart native API for Lab Streaming Layer (LSL) • Science 98%

Liblsl.dart: A Dart native API for Lab Streaming Layer (LSL) - Published in JOSS (2026)

Napari-3D-Counter: A manual cell counter for napari • Science 87%

Napari-3D-Counter: A manual cell counter for napari - Published in JOSS (2026)

biodiscvr: Biomarker Discovery Using Composite Value Ratios • Science 87%

biodiscvr: Biomarker Discovery Using Composite Value Ratios - Published in JOSS (2026)

PeakPerformance - A tool for Bayesian inference-based fitting of LC-MS/MS peaks — Peer-reviewed • Science 96%

PeakPerformance - A tool for Bayesian inference-based fitting of LC-MS/MS peaks - Published in JOSS (2024)

baysc: An R package for Bayesian survey clustering • Science 87%

baysc: An R package for Bayesian survey clustering - Published in JOSS (2026)

ccviR — Peer-reviewed • Science 98%

ccviR: an R package and Shiny app to implement the NatureServe Climate Change Vulnerability Index - Published in JOSS (2024)

Tools for Prototyping with 3D Ultrasonics in ROS — Peer-reviewed • Science 87%

Tools for Prototyping with 3D Ultrasonics in ROS - Published in JOSS (2019)

unsafe • Science 57%

A package for adding parametric uncertainty to the national structure inventory and estimating flood losses with uncertain depth-damage relationships

GAIM — Peer-reviewed • Science 89%

GAIM: A C++ library for Genetic Algorithms and Island Models - Published in JOSS (2019)

plasticparcels — Peer-reviewed • Science 93%

plasticparcels: A python package for marine plastic dispersal simulations and parameterisation development using parcels - Published in JOSS (2024)

search-query • Science 36%

Search Query: A Python package designed to load, lint, translate, save, improve, and automate academic literature search queries.

pypluto • Science 93%

A data analysis Python package for the PLUTO code

Reyna: A minimal overhead polytopal discontinuous Galerkin finite element library • Science 87%

Reyna: A minimal overhead polytopal discontinuous Galerkin finite element library - Published in JOSS (2026)

Kirstine.jl — Peer-reviewed • Science 100%

Kirstine.jl: A Julia Package for Bayesian Optimal Design of Experiments - Published in JOSS (2024)

GaPFlow: Gap-averaged flow simulations with Gaussian process regression • Science 87%

GaPFlow: Gap-averaged flow simulations with Gaussian process regression - Published in JOSS (2026)

ggpedigree • Science 36%

This is companion package to BGmisc for ggplot2

GEOS — Peer-reviewed • Science 95%

GEOS: A performance portable multi-physics simulation framework for subsurface applications - Published in JOSS (2024)

AssumpSure • Science 39%

OnlineNMF.jl: A Julia Package for Out-of-core and Sparse Non-negative Matrix Factorization • Science 87%

OnlineNMF.jl: A Julia Package for Out-of-core and Sparse Non-negative Matrix Factorization - Published in JOSS (2026)

OnlinePCA.jl: A Julia Package for Out-of-core and Sparse Principal Component Analysis • Science 87%

OnlinePCA.jl: A Julia Package for Out-of-core and Sparse Principal Component Analysis - Published in JOSS (2026)

BordAX: A High-Performance JAX Framework for Programmatic Reinforcement Learning • Science 87%

BordAX: A High-Performance JAX Framework for Programmatic Reinforcement Learning - Published in JOSS (2026)

materforge • Science 44%

rjaf — Peer-reviewed • Science 95%

rjaf: Regularized Joint Assignment Forest with Treatment Arm Clustering - Published in JOSS (2025)

survxai — Peer-reviewed • Science 93%

survxai: an R package for structure-agnostic explanations of survival models - Published in JOSS (2018)