smolyax — Peer-reviewed • Science 98%

smolyax: a high-performance implementation of the Smolyak interpolation operator in JAX - Published in JOSS (2025)

graflo • Science 67%

A framework for transforming tabular (CSV, SQL) and hierarchical data (JSON, XML) into property graphs and ingesting them into graph databases (ArangoDB, Neo4j)

Parallel-CDM — Peer-reviewed • Science 98%

Parallel-CDM: Parallel Implementation of Continuum Damage Mechanics Simulations using FEM and MATLAB - Published in JOSS (2025)

ChemInformant — Peer-reviewed • Science 98%

ChemInformant: A Robust and Workflow-Centric Python Client for High-Throughput PubChem Access - Published in JOSS (2025)

cactus • Science 44%

Chromatin ACcessibility and Transcriptomics Unifying Software

SDA — Peer-reviewed • Science 93%

SDA: a symbolic differential algebra package in C++ - Published in JOSS (2025)

voice — Peer-reviewed • Science 93%

voice: A Comprehensive R Package for Audio Analysis - Published in JOSS (2025)

BayesReconPy — Peer-reviewed • Science 93%

BayesReconPy: A Python package for forecast reconciliation - Published in JOSS (2025)

SOAP — Peer-reviewed • Science 93%

SOAP: A Python Package for Calculating the Properties of Galaxies and Halos Formed in Cosmological Simulations - Published in JOSS (2025)

tensorflow • Science 49%

PolytopeWalk — Peer-reviewed • Science 93%

PolytopeWalk: Sparse MCMC Sampling over Polytopes - Published in JOSS (2025)

The Population Synthesis Toolkit (PST) Python Library — Peer-reviewed • Science 98%

The Population Synthesis Toolkit (PST) Python Library - Published in JOSS (2025)

PyStarshade — Peer-reviewed • Science 93%

PyStarshade: Simulating High-Contrast Imaging of Exoplanets with Starshades - Published in JOSS (2025)

PAAT — Peer-reviewed • Science 93%

PAAT: Physical Activity Analysis Toolbox for the analysis of hip-worn raw accelerometer data in Python - Published in JOSS (2025)

my-first-github-repository • Science 44%

EvoVis — Peer-reviewed • Science 67%

EvoVis: Dashboard for Visualizing Evolutionary Neural Architecture Search Algorithms - Published in JOSS (2025)

ExcelToShiny — Peer-reviewed • Science 93%

ExcelToShiny: An R Package for Automating Shiny Dashboard Creation from Excel Templates - Published in JOSS (2025)

VectoRose — Peer-reviewed • Science 98%

VectoRose: A new package for analysing and visualising 3D non-unit vectors in Python - Published in JOSS (2025)

bisonpicsuite — Peer-reviewed • Science 93%

bisonpicsuite: A set of R packages to estimate wood bison population parameters from remote camera data. - Published in JOSS (2025)

gaia — Peer-reviewed • Science 100%

gaia: An R package to estimate crop yield responses to temperature and precipitation - Published in JOSS (2025)

example-parcel • Science 44%

Stylescape Example | Parcel

lookahead • Science 57%

An ML-based framework for DeFi attack detection (based on adversarial contracts)

private-gpt-tweaks • Science 44%

Lighter — Peer-reviewed • Science 93%

Lighter: Configuration-Driven Deep Learning - Published in JOSS (2025)

3DQLayers — Peer-reviewed • Science 98%

3DQLayers: Volumetric Layer Based Analysis for Quantitative Renal MRI - Published in JOSS (2025)

TurboFlow — Peer-reviewed • Science 93%

TurboFlow: Meanline Modelling of Axial Turbines - Published in JOSS (2025)

ce597_cfd_openfoam • Science 67%

Repository for the CFD with OpenFOAM course

PointClouds.jl — Peer-reviewed • Science 96%

PointClouds.jl: Fast & flexible processing of lidar data - Published in JOSS (2025)

dpest — Peer-reviewed • Science 98%

dpest: Streamlining Creation of PEST input files for DSSAT Crop Model Calibration - Published in JOSS (2025)

MEDUSA — Peer-reviewed • Science 93%

MEDUSA: An R tool to model equity and distributional impacts - Published in JOSS (2025)

AutoUncertainties — Peer-reviewed • Science 93%

AutoUncertainties: A Python Package for Uncertainty Propagation - Published in JOSS (2025)

Solar Data Tools — Peer-reviewed • Science 96%

Solar Data Tools: a Python library for automated analysis of unlabeled PV data - Published in JOSS (2025)

medRCT — Peer-reviewed • Science 93%

medRCT: Causal mediation analysis estimating interventional effects mapped to a target trial in R - Published in JOSS (2025)

Syclops — Peer-reviewed • Science 96%

Syclops: A Modular Pipeline for Procedural Generation of Synthetic Data - Published in JOSS (2025)

RiverFlowDynamics v1.0 — Peer-reviewed • Science 92%

RiverFlowDynamics v1.0: A Landlab component for computing two-dimensional river flow dynamics - Published in JOSS (2025)

https://github.com/jboynyc/textnets-binder • Science 13%

Mozzie — Peer-reviewed • Science 98%

Mozzie: a computationally efficient simulator for the spatio-temporal modelling of mosquitoes - Published in JOSS (2025)

REMORA — Peer-reviewed • Science 93%

REMORA: Regional Modeling of Oceans Refined Adaptively (built on AMReX) - Published in JOSS (2025)

ICAT — Peer-reviewed • Science 96%

ICAT: The Interactive Corpus Analysis Tool - Published in JOSS (2025)

Giga Connectome — Peer-reviewed • Science 98%

Giga Connectome: a BIDS-app for time series and functional connectome extraction - Published in JOSS (2025)

AI-ANNE — Peer-reviewed • Science 93%

AI-ANNE: (A) (N)eural (N)et for (E)xploration - Published in JOSS (2025)

<code>diverse-seq</code> — Peer-reviewed • Science 93%

<code>diverse-seq</code>: an application for alignment-free selecting and clustering biological sequences - Published in JOSS (2025)

elfe3D v1.0.1 — Peer-reviewed • Science 93%

elfe3D v1.0.1: Modelling with the total electric field approach using finite elements in 3D - Published in JOSS (2025)

AquaCrop.jl — Peer-reviewed • Science 93%

AquaCrop.jl: A Process-Based Model of Crop Growth - Published in JOSS (2025)

SAnTex — Peer-reviewed • Science 93%

SAnTex: A Python-based Library for Seismic Anisotropy Calculation - Published in JOSS (2025)

2021-03-25-um-scientific-python • Science 54%

2021-06-21-um-scientific-computing • Science 54%

MDPSolver — Peer-reviewed • Science 93%

MDPSolver: An Efficient Solver for Markov Decision Processes - Published in JOSS (2025)

2021-03-04-um-scientific-r • Science 54%

EKF_CAL — Peer-reviewed • Science 98%

EKF_CAL: Extended Kalman Filter-based Calibration and Localization - Published in JOSS (2025)

corrp — Peer-reviewed • Science 93%

corrp: An R package for multiple correlation-like analysis and clustering in mixed data - Published in JOSS (2025)

popclass — Peer-reviewed • Science 100%

popclass: A Python Package for Classifying Microlensing Events - Published in JOSS (2025)

remotePARTS — Peer-reviewed • Science 93%

remotePARTS: Spatiotemporal autoregression analyses for large data sets - Published in JOSS (2025)

https://github.com/jboynyc/shifterator • Science 13%

Interpretable data visualizations for understanding how texts differ at the word level

target-methylseq-qc — Peer-reviewed • Science 98%

target-methylseq-qc: a lightweight pipeline for collecting metrics from targeted sequence mapping files. - Published in JOSS (2025)

CUDA-METRO — Peer-reviewed • Science 93%

CUDA-METRO: Parallel Metropolis Monte Carlo for 2D Atomistic Spin Texture Simulation - Published in JOSS (2025)

ez-zarr — Peer-reviewed • Science 98%

ez-zarr: A Python package for easy access and visualisation of OME-Zarr filesets - Published in JOSS (2025)

pooledpeaks — Peer-reviewed • Science 93%

pooledpeaks: Open-Source Fragment Scoring and Analysis Workflow for Population Genetic Analyses of Microsatellite Markers in Pooled Samples - Published in JOSS (2025)

ParquetDB — Peer-reviewed • Science 93%

ParquetDB: A Lightweight Python Parquet-Based Database - Published in JOSS (2025)

AutoEIS — Peer-reviewed • Science 98%

AutoEIS: Automated equivalent circuit modeling from electrochemical impedance spectroscopy data using statistical machine learning - Published in JOSS (2025)

https://github.com/lymdlut/pix2seq • Science 10%

Pix2Seq - A general framework for turning RGB pixels into semantically meaningful sequences

PathSim - A System Simulation Framework — Peer-reviewed • Science 98%

PathSim - A System Simulation Framework - Published in JOSS (2025)

BESMARTS — Peer-reviewed • Science 93%

BESMARTS: A toolkit for data-driven force field design using binary-encoded SMARTS - Published in JOSS (2025)

EXP — Peer-reviewed • Science 98%

EXP: a Python/C++ package for basis function expansion methods in galactic dynamics - Published in JOSS (2025)

Minterpy — Peer-reviewed • Science 93%

Minterpy: multivariate polynomial interpolation in Python - Published in JOSS (2025)

Topography-based surface water modeling in Julia, with support for infiltration and temporal developments — Peer-reviewed • Science 67%

Topography-based surface water modeling in Julia, with support for infiltration and temporal developments - Published in JOSS (2025)

DIFFICE-jax — Peer-reviewed • Science 93%

DIFFICE-jax: Differentiable neural-network solver for data assimilation of ice shelves in JAX - Published in JOSS (2025)

pengWann — Peer-reviewed • Science 98%

pengWann: Descriptors of chemical bonding from Wannier functions - Published in JOSS (2025)

Pydre — Peer-reviewed • Science 100%

Pydre: A Python package for driving simulation data reduction - Published in JOSS (2025)

apoptosis-project • Science 54%

OPTIMUS — Peer-reviewed • Science 93%

OPTIMUS: A Multidimensional Global Optimization Package - Published in JOSS (2025)

ReadmeReady — Peer-reviewed • Science 93%

ReadmeReady: Free and Customizable Code Documentation with LLMs - A Fine-Tuning Approach - Published in JOSS (2025)

assert-has-float16array-support • Science 44%

Detect native Float16Array support.

rjaf — Peer-reviewed • Science 95%

rjaf: Regularized Joint Assignment Forest with Treatment Arm Clustering - Published in JOSS (2025)

LongMemory.jl — Peer-reviewed • Science 100%

LongMemory.jl: Generating, Estimating, and Forecasting Long Memory Models in Julia - Published in JOSS (2025)

QuantumACES.jl — Peer-reviewed • Science 98%

QuantumACES.jl: design noise characterisation experiments for quantum computers - Published in JOSS (2025)

rtn_scheduling • Science 67%

Nexarag: Democratizing Reproducible Knowledge Graph Contexts for LLM Research • Science 87%

Nexarag: Democratizing Reproducible Knowledge Graph Contexts for LLM Research - Published in JOSS (2026)

a-voronov.github.io • Science 44%

stats-strided-dnanstdevtk • Science 57%

Calculate the standard deviation of a double-precision floating-point strided array ignoring NaN values and using a one-pass textbook algorithm.

spatiomic • Science 67%

A Python package for unsupervised analysis of spatial (prote)omics data.

DemeterWatch — Peer-reviewed • Science 95%

DemeterWatch: A Java tool to detect Law of Demeter violations in Java collections - Published in JOSS (2025)

humanmobility • Science 52%

variantcalling • Science 65%

Nextflow DSL2 pipeline to call variants on long read alignment.

2025-07-22-ornl • Science 44%

antares-hep • Science 67%

Automated Numerical To Analytical REconstruction Software

nf-core-ameta • Science 57%

An nf-core compliant version of aMeta; An ancient metagenomic profiling Snakemake workflow

gadd • Science 54%

Genetic Algorithm-based Dynamical Decoupling with Qiskit

performposeone • Science 44%

Perform Pose

linjiao.info • Science 54%

dd_autostitch • Science 44%

Algorithm for autostitching DD images

find_citations • Science 44%

featuretracerecording • Science 75%

Feature Trace Recording in Haskell

superverse • Science 44%

globalhealthinequalities • Science 44%

2025-07-22-otago-git • Science 44%

COHESIVM — Peer-reviewed • Science 98%

COHESIVM: Combinatorial h+/e- Sample Investigation using Voltaic Measurements - Published in JOSS (2025)

simpleharvest • Science 44%

a (very) simple spatially explicit forest harvest module to interface with LandR

top-ai-ml-algos-paper-code-and-more • Science 44%

AI/ML - Miscellaneous and More

ScatteringOptics.jl — Peer-reviewed • Science 95%

ScatteringOptics.jl: An Interstellar Scattering Framework in the Julia Programming Language - Published in JOSS (2025)