GitHub
FGTpartitioner
FGTpartitioner: A rapid method for parsimonious delimitation of ancestry breakpoints in large genome-wide SNP datasets - 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
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)
Reference Point Calculator (RPC)
Reference Point Calculator (RPC): A Shiny app for exploration of limit reference points for fisheries management - Published in JOSS (2023)
HRnV-Calc
HRnV-Calc: A Software for Heart Rate n-Variability and Heart Rate Variability Analysis - Published in JOSS (2023)
OmniTrax
OmniTrax: A deep learning-driven multi-animal tracking and pose-estimation add-on for Blender - Published in JOSS (2024)
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)
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)
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)
idvf
idvf: Iterative Inversion of Deformation Vector Field with Adaptive Bi-residual Feedback Control - Published in JOSS (2019)
XLUR
XLUR: A land use regression wizard for ArcGIS Pro - Published in JOSS (2020)
argodata
argodata: An R interface to oceanographic data from the International Argo Program - Published in JOSS (2021)
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)
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)
CSaransh
CSaransh : Software Suite to Study Molecular Dynamics Simulations of Collision Cascades - Published in JOSS (2019)
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)
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)
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)
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)
ORMIR_XCT
ORMIR_XCT: A Python package for high resolution peripheral quantitative computed tomography image processing - Published in JOSS (2024)
densify
densify: An R package to reduce empty cells in data frames of typological linguistic data - 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.
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)
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)
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)
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)
skpro
A unified framework for tabular probabilistic regression, time-to-event prediction, and probability distributions in python
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)
Sensie
Sensie: Probing the sensitivity of neural networks - Published in JOSS (2020)
SimplyAgree
SimplyAgree: An R package and jamovi Module for Simplifying Agreement and Reliability Analyses - Published in JOSS (2022)
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).
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)
mbir
mbir: Magnitude-Based Inferences - Published in JOSS (2019)
RECOLO
RECOLO: A Python package for the reconstruction of surface pressure loads from kinematic fields using the virtual fields method - Published in JOSS (2022)
SeleDiff
SeleDiff: A fast and scalable tool for estimating and testing selection differences between populations - 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)
GGMnonreg
GGMnonreg: Non-Regularized Gaussian Graphical Models in R - Published in JOSS (2021)
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)