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)
StoSpa2
StoSpa2: A C++ software package for stochastic simulations of spatially extended systems - Published in JOSS (2020)
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)
NoisySignalIntegration.jl
NoisySignalIntegration.jl: A Julia package for uncertainty evaluation of numeric integrals - Published in JOSS (2021)
BoltzMM
BoltzMM: an R package for maximum pseudolikelihood estimation of fully-visible Boltzmann machines - Published in JOSS (2019)
Simulated Diffusion in Realistic Imaging Features of Tissue (Sim-DRIFT)
Simulated Diffusion in Realistic Imaging Features of Tissue (Sim-DRIFT) - Published in JOSS (2023)
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)
StatAid
StatAid: An R package with a graphical user interface for data analysis - Published in JOSS (2020)
tcherry
tcherry: Learning the structure of tcherry trees - Published in JOSS (2019)
PoUnce
PoUnce: A framework for automatized uncertainty quantification simulations on high-performance clusters - Published in JOSS (2023)
DeBEIR
DeBEIR: A Python Package for Dense Bi-Encoder Information Retrieval - 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)
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)
Artery.FE
Artery.FE: An implementation of the 1D blood flow equations in FEniCS - Published in JOSS (2018)
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)
Cost-Effective Big Data Orchestration Using Dagster: A Multi-Platform Approach
Cost-Effective Big Data Orchestration Using Dagster: A Multi-Platform Approach - Published in JOSS (2026)
`QuasinormalModes.jl`
`QuasinormalModes.jl`: A Julia package for computing discrete eigenvalues of second order ODEs - Published in JOSS (2022)
ect: A Python Package for the Euler Characteristic Transform
ect: A Python Package for the Euler Characteristic Transform - Published in JOSS (2026)
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)
PyGModels
PyGModels: A Python package for exploring Probabilistic Graphical Models with Graph Theoretical Structures - Published in JOSS (2021)
Finnish Media Scrapers
Finnish Media Scrapers - Published in JOSS (2021)
Plotrr
Plotrr: Functions for making visual exploratory data analysis with nested data easier. - Published in JOSS (2017)
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)
Akmedoids R package for generating directionally-homogeneous clusters of longitudinal data sets
Akmedoids R package for generating directionally-homogeneous clusters of longitudinal data sets - Published in JOSS (2020)
Multi-attribute task builder
Multi-attribute task builder - Published in JOSS (2019)
microPIECE - microRNA pipeline enhanced by CLIP experiments
microPIECE - microRNA pipeline enhanced by CLIP experiments - Published in JOSS (2018)
AHGestimation
AHGestimation: An R package for computing robust, mass preserving hydraulic geometries and rating curves - Published in JOSS (2024)
DSWL package: a Python implementation of the Debiased Spatial Whittle Likelihood
DSWL package: a Python implementation of the Debiased Spatial Whittle Likelihood - Published in JOSS (2026)
BATMAN
BATMAN: Statistical analysis for expensive computer codes made easy - Published in JOSS (2018)
pySRURGS - a python package for symbolic regression by uniform random global search
pySRURGS - a python package for symbolic regression by uniform random global search - Published in JOSS (2019)
EFAshiny
EFAshiny: An User-Friendly Shiny Application for Exploratory Factor Analysis - Published in JOSS (2018)
sboxgates
sboxgates: A program for finding low gate count implementations of S-boxes - Published in JOSS (2021)
DWBuilder
DWBuilder: A code to generate ferroelectric/ferroelastic domain walls and multi-material atomic interface structures - Published in JOSS (2024)
MatDL
MatDL: A Lightweight Deep Learning Library in MATLAB - Published in JOSS (2017)
guitarsounds
guitarsounds: A Python package to visualize harmonic sounds for musical instrument design - Published in JOSS (2023)
wolfexplorer
wolfexplorer: a tool for visualization and exploration of complex multi-year multi-specimen datasets - Published in JOSS (2018)
Text detection in screen images with a Convolutional Neural Network
Text detection in screen images with a Convolutional Neural Network - Published in JOSS (2017)
pymsis
Python interface to the NRLMSIS codes for calculating atmospheric densities and constituents at satellite altitudes
COBRAPRO
COBRAPRO: A MATLAB toolbox for Physics-based Battery Modeling and Co-simulation Parameter Optimization - Published in JOSS (2025)
RENT
RENT: A Python Package for Repeated Elastic Net Feature Selection - Published in JOSS (2021)
lpcde
lpcde: Estimation and Inference for Local Polynomial Conditional Density Estimators - Published in JOSS (2025)
ReinforcementLearning
ReinforcementLearning: A Package to Perform Model-Free Reinforcement Learning in R - Published in JOSS (2019)
dfba
dfba: Software for efficient simulation of dynamic flux-balance analysis models in Python - Published in JOSS (2020)
A MATLAB toolbox to detect and analyze marine heatwaves
A MATLAB toolbox to detect and analyze marine heatwaves - Published in JOSS (2019)
AstronomicAL
AstronomicAL: an interactive dashboard for visualisation, integration and classification of data with Active Learning - Published in JOSS (2021)
The Generalized Green's function Cluster Expansion
The Generalized Green's function Cluster Expansion: A Python package for simulating polarons - Published in JOSS (2023)
Mantik
Mantik: A Workflow Platform for the Development of Artificial Intelligence on High-Performance Computing Infrastructures - Published in JOSS (2024)
Computing diffusion coefficients in macromolecular simulations
Computing diffusion coefficients in macromolecular simulations: the Diffusion Coefficient Tool for VMD - Published in JOSS (2019)
ADaPT-ML
ADaPT-ML: A Data Programming Template for Machine Learning - Published in JOSS (2022)
model-traits
model-traits: Model attribute definitions for scientific simulations in C++ - Published in JOSS (2021)
simode
simode: R Package for Statistical Inference of Ordinary Differential Equations using Separable Integral-Matching - Published in JOSS (2019)
Phylen
Phylen: automatic phylogenetic reconstruction using the EggNOG database - Published in JOSS (2018)
reper
reper: Genome-wide identification, classification and quantification of repetitive elements without an assembled genome - Published in JOSS (2018)
fastSF
fastSF: A parallel code for computing the structure functions of turbulence - Published in JOSS (2021)
IntrinsicTimescales.jl: A Julia package to estimate intrinsic (neural) timescales (INTs) from time-series data
IntrinsicTimescales.jl: A Julia package to estimate intrinsic (neural) timescales (INTs) from time-series data - Published in JOSS (2025)
Py-school-match
Py-school-match: Matching algorithms to assign students to schools - Published in JOSS (2019)
EndoMineR for the extraction of endoscopic and associated pathology data from medical reports
EndoMineR for the extraction of endoscopic and associated pathology data from medical reports - Published in JOSS (2018)
connected-components-3d
Connected components on discrete and continuous multilabel 3D & 2D images. Handles 26, 18, and 6 connected variants; periodic boundaries (4, 8, & 6)
Open Computational Chemistry (OCC) - A portable software library and program for quantum chemistry and crystallography
Open Computational Chemistry (OCC) - A portable software library and program for quantum chemistry and crystallography - Published in JOSS (2026)
virtualNicheR
virtualNicheR: generating virtual fundamental and realised niches for use in virtual ecology experiments - Published in JOSS (2019)
cwl_runner
Repository for the CWL standards. Use https://cwl.discourse.group/ for support 😊
Enhanced software and platform for the Town Energy Balance (TEB) model
Enhanced software and platform for the Town Energy Balance (TEB) model - Published in JOSS (2020)
Qiskit Experiments
Qiskit Experiments: A Python package to characterize and calibrate quantum computers - Published in JOSS (2023)
A Python module to combine $p$ values arising from discrete tests.
A Python module to combine $p$ values arising from discrete tests. - Published in JOSS (2024)
OrpailleCC
OrpailleCC: a Library for Data Stream Analysis on Embedded Systems - Published in JOSS (2019)
ALVA
ALVA: An adaptive MATLAB package for layered viscoelastic analysis - Published in JOSS (2020)
Mobile Gaze Mapping
Mobile Gaze Mapping: A Python package for mapping mobile gaze data to a fixed target stimulus - Published in JOSS (2018)
neurone_loader
neurone_loader: A Python module for loading EEG data recorded with Bittium NeurOne - Published in JOSS (2019)
datadriftR: An R package for data drift detection
datadriftR: An R package for data drift detection - Published in JOSS (2026)
ACEInhibPKPD
ACEInhibPKPD: An open-source MATLAB app for a pharmacokinetic/pharmacodynamic model of ACE inhibition - Published in JOSS (2017)
pypbomb
pypbomb: A Python package with tools for the design of detonation tubes - Published in JOSS (2022)
PDF Entity Annotation Tool (PEAT)
PDF Entity Annotation Tool (PEAT) - Published in JOSS (2025)
Lepton
Lepton: An automaton for Literate Executable Papers - Published in JOSS (2019)
CGIMP
CGIMP: Real-time exploration and covariate projection for self-organizing map datasets - Published in JOSS (2019)
FijiRelax
FijiRelax: Fast and noise-corrected estimation of MRI relaxation maps in 3D + t - Published in JOSS (2023)