GitHub
Plotrr
Plotrr: Functions for making visual exploratory data analysis with nested data easier. - Published in JOSS (2017)
AHGestimation
AHGestimation: An R package for computing robust, mass preserving hydraulic geometries and rating curves - 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)
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)
sboxgates
sboxgates: A program for finding low gate count implementations of S-boxes - Published in JOSS (2021)
EFAshiny
EFAshiny: An User-Friendly Shiny Application for Exploratory Factor Analysis - Published in JOSS (2018)
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)
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)
Computing diffusion coefficients in macromolecular simulations
Computing diffusion coefficients in macromolecular simulations: the Diffusion Coefficient Tool for VMD - Published in JOSS (2019)
model-traits
model-traits: Model attribute definitions for scientific simulations in C++ - Published in JOSS (2021)
Phylen
Phylen: automatic phylogenetic reconstruction using the EggNOG database - Published in JOSS (2018)
simode
simode: R Package for Statistical Inference of Ordinary Differential Equations using Separable Integral-Matching - Published in JOSS (2019)
reper
reper: Genome-wide identification, classification and quantification of repetitive elements without an assembled genome - Published in JOSS (2018)
ADaPT-ML
ADaPT-ML: A Data Programming Template for Machine Learning - Published in JOSS (2022)
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)
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)
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)
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)
neurone_loader
neurone_loader: A Python module for loading EEG data recorded with Bittium NeurOne - Published in JOSS (2019)
ALVA
ALVA: An adaptive MATLAB package for layered viscoelastic analysis - Published in JOSS (2020)
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)
pypbomb
pypbomb: A Python package with tools for the design of detonation tubes - Published in JOSS (2022)
ACEInhibPKPD
ACEInhibPKPD: An open-source MATLAB app for a pharmacokinetic/pharmacodynamic model of ACE inhibition - Published in JOSS (2017)
PDF Entity Annotation Tool (PEAT)
PDF Entity Annotation Tool (PEAT) - Published in JOSS (2025)
FijiRelax
FijiRelax: Fast and noise-corrected estimation of MRI relaxation maps in 3D + t - Published in JOSS (2023)
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)
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)
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)
xesn
xesn: Echo state networks powered by Xarray and Dask - Published in JOSS (2024)
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)
Deident
Deident: An R package for data anonymization - Published in JOSS (2025)
SIRITVIS
SIRITVIS: Social Interaction Research Insights Topic Visualisation - Published in JOSS (2024)
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)
tfaip - a Generic and Powerful Research Framework for Deep Learning based on Tensorflow
tfaip - a Generic and Powerful Research Framework for Deep Learning based on Tensorflow - Published in JOSS (2021)
bioregistry
📮 An integrative registry of biological databases, ontologies, and nomenclatures.
Correlation
Correlation: An Analysis Tool for Liquids and for Amorphous Solids - Published in JOSS (2021)
Armadillo
Armadillo: a template-based C++ library for linear algebra - Published in JOSS (2016)
PDOPT
PDOPT: A Python library for Probabilistic Design space exploration and OPTimisation - Published in JOSS (2024)
GGoutlieR
GGoutlieR: an R package to identify and visualize unusual geo-genetic patterns of biological samples - Published in JOSS (2023)
AutoRA
AutoRA: Automated Research Assistant for Closed-Loop Empirical Research - Published in JOSS (2024)
proEQUIB
proEQUIB: IDL Library for Plasma Diagnostics and Abundance Analysis - Published in JOSS (2018)
An Open-Source Tool for Generating Domain-Specific Accelerators for Resource-Constrained Computing
An Open-Source Tool for Generating Domain-Specific Accelerators for Resource-Constrained Computing - Published in JOSS (2024)
mimosa
mimosa: A Modern Graphical User Interface for 2-level Mixed Models - Published in JOSS (2020)
fib-tf
fib-tf: A TensorFlow-based Cardiac Electrophysiology Simulator - Published in JOSS (2018)
FGTpartitioner
FGTpartitioner: A rapid method for parsimonious delimitation of ancestry breakpoints in large genome-wide SNP datasets - Published in JOSS (2020)
arcos and arcospy
arcos and arcospy: R and Python packages for accessing the DEA ARCOS database from 2006 - 2014 - Published in JOSS (2020)
Kanapy
Kanapy: A Python package for generating complex synthetic polycrystalline microstructures - Published in JOSS (2019)
Agents.jl
Agents.jl: agent-based modeling framework in Julia - Published in JOSS (2019)
bmi-topography
Fetch and cache land elevation data from OpenTopography through an API, BMI, or CLI
Overlapping
Overlapping: a R package for Estimating Overlapping in Empirical Distributions - Published in JOSS (2018)
Baargin
Baargin: a Nextflow workflow for the automatic analysis of bacterial genomics data with a focus on Antimicrobial Resistance - Published in JOSS (2023)
HRnV-Calc
HRnV-Calc: A Software for Heart Rate n-Variability and Heart Rate Variability Analysis - Published in JOSS (2023)
Reference Point Calculator (RPC)
Reference Point Calculator (RPC): A Shiny app for exploration of limit reference points for fisheries management - Published in JOSS (2023)
OmniTrax
OmniTrax: A deep learning-driven multi-animal tracking and pose-estimation add-on for Blender - Published in JOSS (2024)
ALPPACA - A tooL for Prokaryotic Phylogeny And Clustering Analysis
ALPPACA - A tooL for Prokaryotic Phylogeny And Clustering Analysis - Published in JOSS (2022)
SHGYield
SHGYield - Published in JOSS (2017)
tsfeaturex
tsfeaturex: An R Package for Automating Time Series Feature Extraction - Published in JOSS (2019)
Chromatiblock
Chromatiblock: scalable whole-genome visualization of structural differences in prokaryotes - Published in JOSS (2020)
Translational Informatics Management System (TIMS)
Translational Informatics Management System (TIMS): Towards OMICS based clinical data management for long term curation of clinical studies - Published in JOSS (2019)
ExoTiC-ISM
ExoTiC-ISM: A Python package for marginalised exoplanet transit parameters across a grid of systematic instrument models - Published in JOSS (2020)
idvf
idvf: Iterative Inversion of Deformation Vector Field with Adaptive Bi-residual Feedback Control - Published in JOSS (2019)
EllipticForest
EllipticForest: A Direct Solver Library for Elliptic Partial Differential Equations on Adaptive Meshes - Published in JOSS (2024)