Black-it 93% confidence

Black-it: A Ready-to-Use and Easy-to-Extend Calibration Kit for Agent-based Models - Published in JOSS (2022)

GrainLearning 93% confidence

GrainLearning: A Bayesian uncertainty quantification toolbox for discrete and continuum numerical models of granular materials - Published in JOSS (2024)

SCIMAP 93% confidence

SCIMAP: A Python Toolkit for Integrated Spatial Analysis of Multiplexed Imaging Data - Published in JOSS (2024)

stabm 87% confidence

stabm: Stability Measures for Feature Selection - Published in JOSS (2021)

IFermi 87% confidence

IFermi: A python library for Fermi surface generation and analysis - Published in JOSS (2021)

BioSimSpace 87% confidence

BioSimSpace: An interoperable Python framework for biomolecular simulation - Published in JOSS (2019)

pyliqtr 87% confidence

Lincoln Laboratory Quantum Algorithm Test and Research

Augur 87% confidence

Augur: a bioinformatics toolkit for phylogenetic analyses of human pathogens - Published in JOSS (2021)

DetectorChecker 87% confidence

DetectorChecker: analyzing patterns of defects in detector screens - Published in JOSS (2020)

pyveg 87% confidence

pyveg: A Python package for analysing the time evolution of patterned vegetation using Google Earth Engine - Published in JOSS (2020)

ParticleTracking 87% confidence

ParticleTracking: A GUI and library for particle tracking on stereo camera images - Published in JOSS (2025)

PyMarket - A simple library for simulating markets in Python 87% confidence

PyMarket - A simple library for simulating markets in Python - Published in JOSS (2020)

Visions 87% confidence

Visions: An Open-Source Library for Semantic Data - Published in JOSS (2020)

matador 87% confidence

matador: a Python library for analysing, curating and performing high-throughput density-functional theory calculations - Published in JOSS (2020)

fMRIStroke 87% confidence

fMRIStroke: A preprocessing pipeline for fMRI Data from Stroke patients - Published in JOSS (2024)

multipers 87% confidence

multipers: Multiparameter Persistence for Machine Learning - Published in JOSS (2024)

HOOMD-TF 87% confidence

HOOMD-TF: GPU-Accelerated, Online Machine Learning in the HOOMD-blue Molecular Dynamics Engine - Published in JOSS (2020)

Grama 87% confidence

Grama: A Grammar of Model Analysis - Published in JOSS (2020)

archetypal 87% confidence

archetypal: A Python package for collecting, simulating, converting and analyzing building archetypes - Published in JOSS (2020)

pylustrator 87% confidence

pylustrator: code generation for reproducible figures for publication - Published in JOSS (2020)

FiLiP 87% confidence

FiLiP: A python software development kit (SDK) for accelerating the development of services based on FIWARE IoT platform - Published in JOSS (2024)

Fraggler 87% confidence

Fraggler: A Python Package and CLI Tool for Automated Fragment Analysis - Published in JOSS (2024)

dea-coastlines 87% confidence

Extracting tidally-constrained annual shorelines and robust rates of coastal change from freely available Earth observation data at continental scale

posebench 87% confidence

Comprehensive benchmarking of protein-ligand structure prediction methods. (ICML 2024 AI4Science)

GeneScape 87% confidence

GeneScape: A Python package for gene ontology visualization - Published in JOSS (2024)

SCAS dashboard 87% confidence

SCAS dashboard: A tool to intuitively and interactively analyze Slurm cluster usage - Published in JOSS (2024)

RidePy 87% confidence

RidePy: A fast and modular framework for simulating ridepooling systems - Published in JOSS (2024)

Ryacas 87% confidence

Ryacas: A computer algebra system in R - Published in JOSS (2019)

rtweet 87% confidence

rtweet: Collecting and analyzing Twitter data - Published in JOSS (2019)

biomedical-qa-system 87% confidence

imager 87% confidence

imager: an R package for image processing based on CImg - Published in JOSS (2019)

phylosmith 87% confidence

phylosmith: an R-package for reproducible and efficient microbiome analysis with phyloseq-objects - Published in JOSS (2019)

sbp-env 87% confidence

sbp-env: A Python Package for Sampling-based Motion Planner and Samplers - Published in JOSS (2021)

abbreviationes 87% confidence

Automated pipeline for expanding medieval Latin abbreviations encoded in TEI using finetuned ByT5. Drop your TEI files, run five scripts, and get a Hugging Face dataset plus a lightweight LoRA adapter for ByT5 that turns graphemic ATR output into expanded text.

ZodiPy 87% confidence

ZodiPy: A Python package for zodiacal light simulations - Published in JOSS (2024)

Systems Neuro Browser (SNUB) 87% confidence

Systems Neuro Browser (SNUB) - Published in JOSS (2024)

refmap 87% confidence

Jobflow 87% confidence

Jobflow: Computational Workflows Made Simple - Published in JOSS (2024)

otoole 87% confidence

otoole: OSeMOSYS Tools for Energy Work - Published in JOSS (2023)

Snowdrop 87% confidence

Snowdrop: Python Package for DSGE Modeling - Published in JOSS (2025)

MAHOS 87% confidence

MAHOS: Measurement Automation Handling and Orchestration System - Published in JOSS (2023)

embedding-atlas 87% confidence

Embedding Atlas is a tool that provides interactive visualizations for large embeddings. It allows you to visualize, cross-filter, and search embeddings and metadata.

NOMAD 87% confidence

NOMAD: A distributed web-based platform for managing materials science research data - Published in JOSS (2023)

macro 87% confidence

[ICC '21] MACRO: Megastructure Assembly via Collaborative Robots in Orbits

spike 87% confidence

spike: A Tool to Drizzle HST, JWST, and Roman PSFs for Improved Analyses - Published in JOSS (2025)

pycrop2ml 87% confidence

CropML Python library

sfctools - A toolbox for stock-flow consistent, agent-based models 87% confidence

sfctools - A toolbox for stock-flow consistent, agent-based models - Published in JOSS (2023)

pynguin 87% confidence

The PYthoN General UnIt Test geNerator is a test-generation tool for Python

fRAT 87% confidence

fRAT: an interactive, Python-based tool for region-of-interest summaries of functional imaging data - Published in JOSS (2023)

greenlight-gym2 87% confidence

Reinforcement learning environment for controlling greenhouse crop production systems. The greenhouse dynamics are based on GreenLight..

HylleraasMD 87% confidence

HylleraasMD: Massively parallel hybrid particle-field molecular dynamics in Python - Published in JOSS (2023)

The Causal Testing Framework 87% confidence

The Causal Testing Framework - Published in JOSS (2025)

Melodie 87% confidence

Melodie: Agent-based Modeling in Python - Published in JOSS (2023)

bittrex 87% confidence

bittrex: An R client for the Bittrex Crypto-Currency Exchange - Published in JOSS (2017)

FDApy 87% confidence

FDApy: a Python package for functional data - Published in JOSS (2025)

RCaNmodel 87% confidence

RCaNmodel: An R package for Chance and Necessity modelling - Published in JOSS (2023)

ALNS 87% confidence

ALNS: a Python implementation of the adaptive large neighbourhood search metaheuristic - Published in JOSS (2023)

Corekaburra 87% confidence

Corekaburra: pan-genome post-processing using core gene synteny - Published in JOSS (2022)

giotto-deep 87% confidence

giotto-deep: A Python Package for Topological Deep Learning - Published in JOSS (2022)

Mechkit 87% confidence

Mechkit: A continuum mechanics toolkit in Python - Published in JOSS (2022)

malan 87% confidence

malan: MAle Lineage ANalysis - Published in JOSS (2018)

Generative DAGs as an Interface Into Probabilistic Programming with the R Package causact 87% confidence

Generative DAGs as an Interface Into Probabilistic Programming with the R Package causact - Published in JOSS (2022)

mitolina 87% confidence

mitolina: MITOchondrial LINeage Analysis - Published in JOSS (2019)

Connectome Mapper 3 87% confidence

Connectome Mapper 3: A Flexible and Open-Source Pipeline Software for Multiscale Multimodal Human Connectome Mapping - Published in JOSS (2022)

Sinaps 87% confidence

Sinaps: A Python library to simulate voltage dynamics and ionic electrodiffusion in neurons - Published in JOSS (2022)

PiSCAT 87% confidence

PiSCAT: A Python Package for Interferometric Scattering Microscopy - Published in JOSS (2022)

CoperniFUS 87% confidence

CoperniFUS: A flexible Python-based GUI for stereotaxic Focused UltraSound (FUS) experiment planning - Published in JOSS (2025)

patRoon 2.0 87% confidence

patRoon 2.0: Improved non-target analysis workflows including automated transformation product screening - Published in JOSS (2022)

xcp_d 87% confidence

Post-processing of fMRIPrep, NiBabies, and HCP outputs

bmm 87% confidence

bmm: Bayesian Map-matching - Published in JOSS (2022)

CluSim 87% confidence

CluSim: a python package for calculating clustering similarity - Published in JOSS (2019)

VeridicalFlow 87% confidence

VeridicalFlow: a Python package for building trustworthy data science pipelines with PCS - Published in JOSS (2022)

OpenRepGrid 87% confidence

OpenRepGrid: An R Package for the Analysis of Repertory Grid Data - Published in JOSS (2024)

Contextualized 71% confidence

Contextualized: Heterogeneous Modeling Toolbox - Published in JOSS (2024)

emba 71% confidence

emba: R package for analysis and visualization of biomarkers in boolean model ensembles - Published in JOSS (2020)

pylimer-tools 71% confidence

A collection of utility python functions for handling bead-spring polymer networks and LAMMPS output in Python

NetworkSedimentTransporter 64% confidence

NetworkSedimentTransporter: A Landlab component for bed material transport through river networks - Published in JOSS (2020)

GraphCalc 64% confidence

GraphCalc: A Python Package for Computing Graph Invariants in Automated Conjecturing Systems - Published in JOSS (2025)

Segmenteverygrain 64% confidence

Segmenteverygrain: A Python module for segmentation of grains in images - Published in JOSS (2025)

GCol 64% confidence

GCol: A High-Performance Python Library for Graph Colouring - Published in JOSS (2025)

Mesa 3 64% confidence

Mesa 3: Agent-based modeling with Python in 2025 - Published in JOSS (2025)

Teaspoon 64% confidence

Teaspoon: A Python Package for Topological Signal Processing - Published in JOSS (2025)

AdOpT-NET0 64% confidence

AdOpT-NET0: A technology-focused Python package for the optimization of multi-energy systems - Published in JOSS (2025)

PhyloX 64% confidence

PhyloX: A Python package for complete phylogenetic network workflows - Published in JOSS (2024)

ChainoPy 64% confidence

ChainoPy: A Python Library for Discrete Time Markov Chain Based Stochastic Analysis - Published in JOSS (2024)

Phasik 64% confidence

Phasik: a Python package to identify system states in partially temporal networks - Published in JOSS (2023)

Spikeometric 64% confidence

Spikeometric: Linear Non-Linear Cascade Spiking Neural Networks with Pytorch Geometric - Published in JOSS (2023)

VisWaterNet 64% confidence

VisWaterNet: A Python package for visualization of water distribution networks - Published in JOSS (2023)

PhaseTypeR 64% confidence

PhaseTypeR: an R package for phase-type distributions in population genetics - Published in JOSS (2023)

radioactivedecay 64% confidence

radioactivedecay: A Python package for radioactive decay calculations - Published in JOSS (2022)

nsink 64% confidence

nsink: An R package for flow path nitrogen removal estimation - Published in JOSS (2022)

sknet 64% confidence

sknet: A Python framework for Machine Learning in Complex Networks - Published in JOSS (2021)

OpenOmics 64% confidence

OpenOmics: A bioinformatics API to integrate multi-omics datasets and interface with public databases. - Published in JOSS (2021)

The targets R package 64% confidence

The targets R package: a dynamic Make-like function-oriented pipeline toolkit for reproducibility and high-performance computing - Published in JOSS (2021)

secuTrialR 64% confidence

secuTrialR: Seamless interaction with clinical trial databases in R - Published in JOSS (2020)

High-Dimensional Integrator 64% confidence

High-Dimensional Integrator - Published in JOSS (2017)

matchms - processing and similarity evaluation of mass spectrometry data. 64% confidence

matchms - processing and similarity evaluation of mass spectrometry data. - Published in JOSS (2020)

Rclean 64% confidence

Rclean: A Tool for Writing Cleaner, More Transparent Code - Published in JOSS (2020)

EoN (Epidemics on Networks) 64% confidence

EoN (Epidemics on Networks): a fast, flexible Python package for simulation, analytic approximation, and analysis of epidemics on networks - Published in JOSS (2019)

momepy 64% confidence

momepy: Urban Morphology Measuring Toolkit - Published in JOSS (2019)