KMC_Lattice v2.0
KMC_Lattice v2.0: An Object-Oriented C\texttt{++} Library for Custom Kinetic Monte Carlo Simulations - Published in JOSS (2019)
biotmle
biotmle: Targeted Learning for Biomarker Discovery - Published in JOSS (2017)
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)
feign
feign: a Python package to estimate geometric efficiency in passive gamma spectroscopy measurements of nuclear fuel - Published in JOSS (2019)
Deident
Deident: An R package for data anonymization - Published in JOSS (2025)
logKDE
logKDE: log-transformed kernel density estimation - Published in JOSS (2018)
SIRITVIS
SIRITVIS: Social Interaction Research Insights Topic Visualisation - Published in JOSS (2024)
HierarchyCraft: A Benchmark Builder for Hierarchical Reasoning
HierarchyCraft: A Benchmark Builder for Hierarchical Reasoning - Published in JOSS (2026)
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)
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)
GiNaCDE
GiNaCDE: the high-performance F-expansion and First Integral Methods with C++ library for solving Nonlinear Differential Equations - Published in JOSS (2022)
bioregistry
📮 An integrative registry of biological databases, ontologies, and nomenclatures.
Armadillo
Armadillo: a template-based C++ library for linear algebra - Published in JOSS (2016)
Correlation
Correlation: An Analysis Tool for Liquids and for Amorphous Solids - Published in JOSS (2021)
PDOPT
PDOPT: A Python library for Probabilistic Design space exploration and OPTimisation - Published in JOSS (2024)
arcos and arcospy
arcos and arcospy: R and Python packages for accessing the DEA ARCOS database from 2006 - 2014 - Published in JOSS (2020)
mimosa
mimosa: A Modern Graphical User Interface for 2-level Mixed Models - Published in JOSS (2020)
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)
GGoutlieR
GGoutlieR: an R package to identify and visualize unusual geo-genetic patterns of biological samples - Published in JOSS (2023)
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)
AutoRA
AutoRA: Automated Research Assistant for Closed-Loop Empirical Research - Published in JOSS (2024)
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)
OmniTrax
OmniTrax: A deep learning-driven multi-animal tracking and pose-estimation add-on for Blender - Published in JOSS (2024)
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)
tsfeaturex
tsfeaturex: An R Package for Automating Time Series Feature Extraction - Published in JOSS (2019)
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)
Chromatiblock
Chromatiblock: scalable whole-genome visualization of structural differences in prokaryotes - Published in JOSS (2020)
EllipticForest
EllipticForest: A Direct Solver Library for Elliptic Partial Differential Equations on Adaptive Meshes - Published in JOSS (2024)
Torsional Axisymmetric Core Oscillations Visualiser (TACO-VIS)
Torsional Axisymmetric Core Oscillations Visualiser (TACO-VIS): A Python module for animating torsional wave data for fluid planetary cores - Published in JOSS (2020)
ExoTiC-ISM
ExoTiC-ISM: A Python package for marginalised exoplanet transit parameters across a grid of systematic instrument models - 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)
idvf
idvf: Iterative Inversion of Deformation Vector Field with Adaptive Bi-residual Feedback Control - Published in JOSS (2019)
The hhi Package
The hhi Package: Streamlined Calculation and Visualization of Herfindahl-Hirschman Index Scores - Published in JOSS (2018)
argodata
argodata: An R interface to oceanographic data from the International Argo Program - Published in JOSS (2021)
fellingdater
fellingdater: a toolkit to estimate, report and combine felling dates derived from historical tree-ring series - Published in JOSS (2024)
prospect
prospect: an R package to link leaf optical properties with their chemical and structural properties with the leaf model PROSPECT - Published in JOSS (2024)
JCOL
JCOL: A Java package for solving the graph coloring problem - Published in JOSS (2020)
XLUR
XLUR: A land use regression wizard for ArcGIS Pro - Published in JOSS (2020)
SCALAR - A Platform for Real-time Machine Learning Competitions on Data Streams
SCALAR - A Platform for Real-time Machine Learning Competitions on Data Streams - Published in JOSS (2020)
CSaransh
CSaransh : Software Suite to Study Molecular Dynamics Simulations of Collision Cascades - Published in JOSS (2019)
RCaNmodel
RCaNmodel: An R package for Chance and Necessity modelling - Published in JOSS (2023)
VBLinLogit
VBLinLogit: Variational Bayesian linear and logistic regression - Published in JOSS (2019)
MCSD
MCSD: A MATLAB Tool for Monte-Carlo Simulations of Diffusion in biological Tissues - Published in JOSS (2018)
PDLSM-FEM
PDLSM-FEM: Solver of Coupled Peridynamics Least Squares Minimization with Finite Element Method - Published in JOSS (2021)
KLRfome - Kernel Logistic Regression on Focal Mean Embeddings
KLRfome - Kernel Logistic Regression on Focal Mean Embeddings - Published in JOSS (2019)
mitiq
Mitiq is an open source toolkit for implementing error mitigation techniques on most current intermediate-scale quantum computers.
gnark-crypto
gnark-crypto provides elliptic curve and pairing-based cryptography on BN, BLS12, BLS24 and BW6 curves. It also provides various algorithms (algebra, crypto) of particular interest to zero knowledge proof systems.
FluxCalR
FluxCalR: a R package for calculating CO~2~ and CH~4~ fluxes from static chambers - Published in JOSS (2019)
densify
densify: An R package to reduce empty cells in data frames of typological linguistic data - Published in JOSS (2024)
BrightEyes-MCS
BrightEyes-MCS: a control software for multichannel scanning microscopy - Published in JOSS (2024)
ORMIR_XCT
ORMIR_XCT: A Python package for high resolution peripheral quantitative computed tomography image processing - Published in JOSS (2024)
mlonmcu
Tool for the deployment and analysis of TinyML applications on TFLM and MicroTVM backends
qsim
Fast C++ and Python library for state-vector simulation of quantum circuits.
ck
Collective Knowledge (CK), Collective Mind (CM/CMX) and MLPerf automations: community-driven projects to facilitate collaborative and reproducible research and to learn how to run AI, ML, and other emerging workloads more efficiently and cost-effectively across diverse models, datasets, software, and hardware using MLPerf methodology and benchmarks
kep_solver
kep_solver: A Python package for kidney exchange programme exploration - Published in JOSS (2022)
Foam
Foam: A Python package for forward asteroseismic modelling of gravity modes - Published in JOSS (2024)
fMRIStroke
fMRIStroke: A preprocessing pipeline for fMRI Data from Stroke patients - Published in JOSS (2024)
BellDiagonalQudits
BellDiagonalQudits: A package for entanglement analyses of mixed maximally entangled qudits - Published in JOSS (2023)
herbie-data
Download numerical weather prediction datasets (HRRR, RAP, GFS, IFS, etc.) from NOMADS, NODD partners (Amazon, Google, Microsoft), ECMWF open data, and the University of Utah Pando Archive System.
Fitting a Gamma-Gompertz survival model to capture-recapture data collected on free-ranging animal populations
Fitting a Gamma-Gompertz survival model to capture-recapture data collected on free-ranging animal populations - Published in JOSS (2018)
vbvs.concurrent
vbvs.concurrent: Fitting Methods for the Functional Linear Concurrent Model - Published in JOSS (2016)
MitoHEAR
MitoHEAR: an R package for the estimation and downstream statistical analysis of the mitochondrial DNA heteroplasmy calculated from single-cell datasets - Published in JOSS (2022)
AtomNeb
AtomNeb: IDL Library for Atomic Data of Ionized Nebulae - Published in JOSS (2019)
RBF
RBF: An R package to compute a robust backfitting estimator for additive models - Published in JOSS (2021)
limHaloPT
limHaloPT: A Numerical Package for Accurate Modeling of Line Intensity Power Spectrum - Published in JOSS (2022)
MeMC
MeMC: A package for Monte Carlo simulations of spherical shells - Published in JOSS (2022)
skpro
A unified framework for tabular probabilistic regression, time-to-event prediction, and probability distributions in python
elsa
elsa: an elegant framework for tomographic reconstruction - Published in JOSS (2024)
Sensie
Sensie: Probing the sensitivity of neural networks - Published in JOSS (2020)
ChiRP
ChiRP: Chinese Restaurant Process Mixtures for Regression and Clustering - Published in JOSS (2019)
SimplyAgree
SimplyAgree: An R package and jamovi Module for Simplifying Agreement and Reliability Analyses - Published in JOSS (2022)
Minimalist And Customisable Optimisation Package
Minimalist And Customisable Optimisation Package - Published in JOSS (2021)