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)
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)
StatAid
StatAid: An R package with a graphical user interface for data analysis - Published in JOSS (2020)
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)
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)
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)
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)
SeroTools
SeroTools: a Python package for Salmonella serotype data analysis - Published in JOSS (2020)
Multi-attribute task builder
Multi-attribute task builder - Published in JOSS (2019)
AHGestimation
AHGestimation: An R package for computing robust, mass preserving hydraulic geometries and rating curves - Published in JOSS (2024)
Plotrr
Plotrr: Functions for making visual exploratory data analysis with nested data easier. - Published in JOSS (2017)
microPIECE - microRNA pipeline enhanced by CLIP experiments
microPIECE - microRNA pipeline enhanced by CLIP experiments - Published in JOSS (2018)
Delta-Rice
Delta-Rice: A HDF5 Compression Plugin optimized for Digitized Detector Data - Published in JOSS (2024)
NBI
NBI: A library for Nystrom Boundary Integral calculations - 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)
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)
DWBuilder
DWBuilder: A code to generate ferroelectric/ferroelastic domain walls and multi-material atomic interface structures - Published in JOSS (2024)
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)
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)
Text detection in screen images with a Convolutional Neural Network
Text detection in screen images with a Convolutional Neural Network - Published in JOSS (2017)
wolfexplorer
wolfexplorer: a tool for visualization and exploration of complex multi-year multi-specimen datasets - Published in JOSS (2018)
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)
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)
simode
simode: R Package for Statistical Inference of Ordinary Differential Equations using Separable Integral-Matching - Published in JOSS (2019)
model-traits
model-traits: Model attribute definitions for scientific simulations in C++ - Published in JOSS (2021)
fastSF
fastSF: A parallel code for computing the structure functions of turbulence - Published in JOSS (2021)
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)
Py-school-match
Py-school-match: Matching algorithms to assign students to schools - Published in JOSS (2019)
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)
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)
ALVA
ALVA: An adaptive MATLAB package for layered viscoelastic analysis - Published in JOSS (2020)
neurone_loader
neurone_loader: A Python module for loading EEG data recorded with Bittium NeurOne - Published in JOSS (2019)
Mobile Gaze Mapping
Mobile Gaze Mapping: A Python package for mapping mobile gaze data to a fixed target stimulus - Published in JOSS (2018)
OrpailleCC
OrpailleCC: a Library for Data Stream Analysis on Embedded Systems - Published in JOSS (2019)
PDF Entity Annotation Tool (PEAT)
PDF Entity Annotation Tool (PEAT) - Published in JOSS (2025)
pypbomb
pypbomb: A Python package with tools for the design of detonation tubes - Published in JOSS (2022)
CGIMP
CGIMP: Real-time exploration and covariate projection for self-organizing map datasets - Published in JOSS (2019)
Lepton
Lepton: An automaton for Literate Executable Papers - Published in JOSS (2019)
ACEInhibPKPD
ACEInhibPKPD: An open-source MATLAB app for a pharmacokinetic/pharmacodynamic model of ACE inhibition - Published in JOSS (2017)
biotmle
biotmle: Targeted Learning for Biomarker Discovery - Published in JOSS (2017)
KMC_Lattice v2.0
KMC_Lattice v2.0: An Object-Oriented C\texttt{++} Library for Custom Kinetic Monte Carlo Simulations - Published in JOSS (2019)
FijiRelax
FijiRelax: Fast and noise-corrected estimation of MRI relaxation maps in 3D + t - Published in JOSS (2023)
itrm
itrm: Interactive Terminal Utilities - Published in JOSS (2024)
Finding and removing introns from RNA-Seq de novo assemblies with IntronSeeker
Finding and removing introns from RNA-Seq de novo assemblies with IntronSeeker - Published in JOSS (2024)
lightkurve
A friendly package for Kepler & TESS time series analysis in Python.
PyIRD: A Python-Based Data Reduction Pipeline for Subaru/IRD and REACH
PyIRD: A Python-Based Data Reduction Pipeline for Subaru/IRD and REACH - Published in JOSS (2026)
xesn
xesn: Echo state networks powered by Xarray and Dask - Published in JOSS (2024)
solposx: A Python package for determining solar position and atmospheric refraction
solposx: A Python package for determining solar position and atmospheric refraction - Published in JOSS (2025)
Deident
Deident: An R package for data anonymization - Published in JOSS (2025)
feign
feign: a Python package to estimate geometric efficiency in passive gamma spectroscopy measurements of nuclear fuel - Published in JOSS (2019)
logKDE
logKDE: log-transformed kernel density estimation - Published in JOSS (2018)
SIRITVIS
SIRITVIS: Social Interaction Research Insights Topic Visualisation - Published in JOSS (2024)
BioPandas: Working with molecular structures in pandas DataFrames
BioPandas: Working with molecular structures in pandas DataFrames - Published in JOSS (2017)
Scan Session Tool
Scan Session Tool: (f)MRI scan session documentation and archiving - Published in JOSS (2024)
GiNaCDE
GiNaCDE: the high-performance F-expansion and First Integral Methods with C++ library for solving Nonlinear Differential Equations - Published in JOSS (2022)