GitHub
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
Baargin
Baargin: a Nextflow workflow for the automatic analysis of bacterial genomics data with a focus on Antimicrobial Resistance - Published in JOSS (2023)
Overlapping
Overlapping: a R package for Estimating Overlapping in Empirical Distributions - Published in JOSS (2018)
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)
SHGYield
SHGYield - Published in JOSS (2017)
ALPPACA - A tooL for Prokaryotic Phylogeny And Clustering Analysis
ALPPACA - A tooL for Prokaryotic Phylogeny And Clustering Analysis - Published in JOSS (2022)
Chromatiblock
Chromatiblock: scalable whole-genome visualization of structural differences in prokaryotes - 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)
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)
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)
EllipticForest
EllipticForest: A Direct Solver Library for Elliptic Partial Differential Equations on Adaptive Meshes - Published in JOSS (2024)
The hhi Package
The hhi Package: Streamlined Calculation and Visualization of Herfindahl-Hirschman Index Scores - Published in JOSS (2018)
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)
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)
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)
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)
MCSD
MCSD: A MATLAB Tool for Monte-Carlo Simulations of Diffusion in biological Tissues - Published in JOSS (2018)
VBLinLogit
VBLinLogit: Variational Bayesian linear and logistic regression - 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)
BrightEyes-MCS
BrightEyes-MCS: a control software for multichannel scanning microscopy - Published in JOSS (2024)
densify
densify: An R package to reduce empty cells in data frames of typological linguistic data - 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
fMRIStroke
fMRIStroke: A preprocessing pipeline for fMRI Data from Stroke patients - Published in JOSS (2024)
Foam
Foam: A Python package for forward asteroseismic modelling of gravity modes - 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.
vbvs.concurrent
vbvs.concurrent: Fitting Methods for the Functional Linear Concurrent Model - Published in JOSS (2016)
AtomNeb
AtomNeb: IDL Library for Atomic Data of Ionized Nebulae - Published in JOSS (2019)
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)
RBF
RBF: An R package to compute a robust backfitting estimator for additive models - Published in JOSS (2021)
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)
MeMC
MeMC: A package for Monte Carlo simulations of spherical shells - Published in JOSS (2022)
limHaloPT
limHaloPT: A Numerical Package for Accurate Modeling of Line Intensity Power Spectrum - Published in JOSS (2022)
skpro
A unified framework for tabular probabilistic regression, time-to-event prediction, and probability distributions in python
SimplyAgree
SimplyAgree: An R package and jamovi Module for Simplifying Agreement and Reliability Analyses - Published in JOSS (2022)
Sensie
Sensie: Probing the sensitivity of neural networks - Published in JOSS (2020)
Minimalist And Customisable Optimisation Package
Minimalist And Customisable Optimisation Package - Published in JOSS (2021)
ChiRP
ChiRP: Chinese Restaurant Process Mixtures for Regression and Clustering - Published in JOSS (2019)
qcelemental
Periodic table, physical constants, and molecule parsing for quantum chemistry.
Computer-Aided Generation of N-shift RWS
Computer-Aided Generation of N-shift RWS - Published in JOSS (2023)
3D ultrasound file reading and coordinate transformations
3D ultrasound file reading and coordinate transformations - Published in JOSS (2019)
LearnSAT
LearnSAT: A SAT Solver for Education - Published in JOSS (2018)
igneous-pipeline
Scalable Neuroglancer compatible Downsampling, Meshing, Skeletonizing, Contrast Normalization, Transfers and more.
localcovid19now
localcovid19now: processing and mapping COVID-19 case data at subnational scales - Published in JOSS (2023)
cowfootR: An R Package for Dairy Farm Carbon Footprint Assessment
cowfootR: An R Package for Dairy Farm Carbon Footprint Assessment - Published in JOSS (2026)
LorenzCycleToolkit
LorenzCycleToolkit: A Comprehensive Python Tool for Analyzing Atmospheric Energy Cycles - Published in JOSS (2024)
DiscreteEntropy.jl
DiscreteEntropy.jl: Entropy Estimation of Discrete Random Variables with Julia - Published in JOSS (2024)
kimimaro
Skeletonize densely labeled 3D image segmentations with TEASAR. (Medial Axis Transform)
oemof.solph
A model generator for energy system modelling and optimisation (LP/MILP).
SeleDiff
SeleDiff: A fast and scalable tool for estimating and testing selection differences between populations - Published in JOSS (2019)
ORIS
ORIS: An interactive software tool for prediction of replication origin in prokaryotic genomes - Published in JOSS (2019)
BayesMFSurv
BayesMFSurv: An R Package to Estimate Bayesian Split-Population Survival Models With (and Without) Misclassified Failure Events - Published in JOSS (2020)
RECOLO
RECOLO: A Python package for the reconstruction of surface pressure loads from kinematic fields using the virtual fields method - Published in JOSS (2022)
mbir
mbir: Magnitude-Based Inferences - Published in JOSS (2019)
FlexWing-ROM
FlexWing-ROM: A matlab framework for data-driven reduced-order modeling of flexible wings - Published in JOSS (2022)
GKNAP
GKNAP: A Java and C++ package for solving the multidimensional knapsack problem - Published in JOSS (2019)
chronovise
chronovise: Measurement-Based Probabilistic Timing Analysis framework - Published in JOSS (2018)
sdmbench
sdmbench: R package for benchmarking species distribution models - Published in JOSS (2018)
p2smi: A toolkit enabling SMILES generation and property analysis for noncanonical and cyclized peptides
p2smi: A toolkit enabling SMILES generation and property analysis for noncanonical and cyclized peptides - Published in JOSS (2025)
SubZero
SubZero: a discrete element sea ice model that simulates floes as evolving concave polygons - Published in JOSS (2023)
cellanneal
cellanneal: A user-friendly deconvolution software for transcriptomics data - Published in JOSS (2024)
IBCAO_py
IBCAO_py: A matplotlib library for using the International Bathymetric Chart of the Arctic Ocean with cartopy and matplotlib - Published in JOSS (2017)
GGMnonreg
GGMnonreg: Non-Regularized Gaussian Graphical Models in R - Published in JOSS (2021)
The Climate Equity Reference Calculator
The Climate Equity Reference Calculator - Published in JOSS (2019)