neos • Rank 10.8 • Science 85%

Upstream optimisation for downstream inference

shapely • Rank 31.8 • Science 64%

Manipulation and analysis of geometric objects

OTTO — Peer-reviewed • Rank 2.8 • Science 93%

OTTO: A Python package to simulate, solve and visualize the source-tracking POMDP - Published in JOSS (2022)

Dark-field X-ray microscopy visualization — Peer-reviewed • Rank 2.8 • Science 93%

Dark-field X-ray microscopy visualization - Published in JOSS (2023)

genieR — Peer-reviewed • Rank 2.8 • Science 93%

genieR: An R package for inference of demographic history of phylogenies - Published in JOSS (2019)

HyperNaut — Peer-reviewed • Rank 2.8 • Science 93%

HyperNaut: a navigator for the hyperbolic plane - Published in JOSS (2019)

PyAstroPol — Peer-reviewed • Rank 2.8 • Science 93%

PyAstroPol: A Python package for the instrumental polarization analysis of the astronomical optics. - Published in JOSS (2020)

qonnx • Rank 18.7 • Science 77%

QONNX: Arbitrary-Precision Quantized Neural Networks in ONNX

oplab-pipeline • Rank 10.7 • Science 85%

parsers for navigation data for oplab_standard and acfr_standard formats

mwarp1d — Peer-reviewed • Rank 2.7 • Science 93%

mwarp1d: Manual one-dimensional data warping in Python and PyQt - Published in JOSS (2019)

CORA and LOGIGRAM — Peer-reviewed • Rank 2.7 • Science 93%

CORA and LOGIGRAM: A Duo of Python Packages for Combinational Regularity Analysis (CORA) - Published in JOSS (2023)

onsetsync — Peer-reviewed • Rank 2.7 • Science 93%

onsetsync: An R Package for Onset Synchrony Analysis - Published in JOSS (2024)

SymbiotaR2 — Peer-reviewed • Rank 2.7 • Science 93%

SymbiotaR2: An R Package for Accessing Symbiota2 Data - Published in JOSS (2020)

Correlation Trait Loci (CTL) mapping — Peer-reviewed • Rank 2.7 • Science 93%

Correlation Trait Loci (CTL) mapping: phenotype network inference subject to genotype - Published in JOSS (2016)

FRIDGe — Peer-reviewed • Rank 0.7 • Science 95%

FRIDGe: Fast Reactor Input Deck Generator - Published in JOSS (2019)

BeeNestABM — Peer-reviewed • Rank 0.7 • Science 95%

BeeNestABM: An open-source agent-based model of spatiotemporal distribution of bumblebees in nests - Published in JOSS (2018)

MaDaTS — Peer-reviewed • Rank 0.7 • Science 95%

MaDaTS: Managing Data on Tiered Storage for Scientific Workflows - Published in JOSS (2018)

Tabbed: A Python package for reading variably structured text files at scale • Rank 0.7 • Science 95%

Tabbed: A Python package for reading variably structured text files at scale - Published in JOSS (2025)

BetterReg — Peer-reviewed • Rank 0.7 • Science 95%

BetterReg: An R package for Useful Regression Statistics - Published in JOSS (2022)

SIAL — Peer-reviewed • Rank 0.7 • Science 95%

SIAL: A simple image analysis library for wet-lab scientists - Published in JOSS (2020)

discourseGT — Peer-reviewed • Rank 0.7 • Science 95%

discourseGT: An R package to analyze discourse networks in educational contexts - Published in JOSS (2023)

qlass: A Python Package for Variational Quantum Algorithms on Photonic Devices • Rank 8.7 • Science 87%

qlass: A Python Package for Variational Quantum Algorithms on Photonic Devices - Published in JOSS (2026)

aucmedi • Rank 10.7 • Science 85%

a framework for Automated Classification of Medical Images

SPyCi-PDB — Peer-reviewed • Rank 2.6 • Science 93%

SPyCi-PDB: A modular command-line interface for back-calculating experimental datatypes of protein structures. - Published in JOSS (2023)

EMViz (Early Music Visualization) — Peer-reviewed • Rank 2.6 • Science 93%

EMViz (Early Music Visualization): MATLAB runtime application - Published in JOSS (2019)

GASTLI — Peer-reviewed • Rank 2.6 • Science 93%

GASTLI: A Python package for coupled interior–atmosphere modelling of volatile-rich planets - Published in JOSS (2025)

WEPPCLIFF — Peer-reviewed • Rank 2.6 • Science 93%

WEPPCLIFF: A command-line tool to process climate inputs for soil loss models - Published in JOSS (2020)

fissa • Rank 10.6 • Science 85%

A Python toolbox for Fast Image Signal Separation Analysis, designed for Calcium Imaging data.

feos • Rank 18.6 • Science 77%

FeOs - A Framework for Equations of State and Classical Density Functional Theory

Ising_OPV v4.0 — Peer-reviewed • Rank 2.6 • Science 93%

Ising_OPV v4.0: Experimental Tomography Data Import, Interpretation, and Analysis - Published in JOSS (2018)

ikpy • Rank 18.6 • Science 77%

IKPy, an Universal Inverse Kinematics library

ccdproc • Rank 18.5 • Science 77%

Astropy affiliated package for reducing optical/IR CCD data

nc-time-axis • Rank 18.5 • Science 77%

Provides support for a cftime axis in matplotlib

PXO (Poly-XTAL Operations) — Peer-reviewed • Rank 2.5 • Science 93%

PXO (Poly-XTAL Operations): MATLAB Codebase to Generate, Analyse and Export Complex 2D Spatio-Temporally Gradient Grain Structures - Published in JOSS (2021)

enetLTS — Peer-reviewed • Rank 2.5 • Science 93%

enetLTS: Robust and Sparse Methods for High Dimensional Linear, Binary, and Multinomial Regression - Published in JOSS (2023)

bbousuite — Peer-reviewed • Rank 2.5 • Science 93%

bbousuite: A set of R packages to facilitate analysis of boreal caribou survival and recruitment data - Published in JOSS (2025)

LightTwinSVM — Peer-reviewed • Rank 2.5 • Science 93%

LightTwinSVM: A Simple and Fast Implementation of Standard Twin Support Vector Machine Classifier - Published in JOSS (2019)

home2park — Peer-reviewed • Rank 2.5 • Science 93%

home2park: An R package to assess the spatial provision of urban parks - Published in JOSS (2021)

Open-Source Hypothalamic-ForniX (OSHy-X) Atlases and Segmentation Tool for 3T and 7T — Peer-reviewed • Rank 2.5 • Science 93%

Open-Source Hypothalamic-ForniX (OSHy-X) Atlases and Segmentation Tool for 3T and 7T - Published in JOSS (2022)

SeqPanther — Peer-reviewed • Rank 2.5 • Science 93%

SeqPanther: Sequence manipulation and mutation statistics toolset - Published in JOSS (2023)

Reel1.0 - A visualization tool for evaluating powder diffraction refinements — Peer-reviewed • Rank 2.5 • Science 93%

Reel1.0 - A visualization tool for evaluating powder diffraction refinements - Published in JOSS (2021)

filter-functions • Rank 10.4 • Science 85%

Efficient numerical calculation of generalized filter functions

gmm_diag and gmm_full — Peer-reviewed • Rank 2.4 • Science 93%

gmm_diag and gmm_full: C++ classes for multi-threaded Gaussian mixture models and Expectation-Maximisation - Published in JOSS (2017)

scikit-mobility • Rank 18.4 • Science 77%

scikit-mobility: mobility analysis in Python

traits • Rank 18.4 • Science 77%

R package for accessing species trait data from multiple databases

proj • Rank 18.3 • Science 77%

PROJ - Cartographic Projections and Coordinate Transformations Library

EAGO • Rank 10.3 • Science 85%

A development environment for robust and global optimization

Scikit-Topt: A Python Library for Algorithm Development in Topology Optimization • Rank 8.3 • Science 87%

Scikit-Topt: A Python Library for Algorithm Development in Topology Optimization - Published in JOSS (2025)

Bloch: a strongly typed, hardware-agnostic, hybrid quantum programming language • Rank 3.3 • Science 92%

Bloch: a strongly typed, hardware-agnostic, hybrid quantum programming language - Published in JOSS (2026)

hermit-kernel • Rank 18.3 • Science 77%

A Rust-based, lightweight unikernel.

Fraggler — Peer-reviewed • Rank 2.3 • Science 93%

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

einprot — Peer-reviewed • Rank 2.3 • Science 93%

einprot: flexible, easy-to-use, reproducible workflows for statistical analysis of quantitative proteomics data - Published in JOSS (2023)

BioDeg — Peer-reviewed • Rank 2.3 • Science 93%

BioDeg: A finite element software for the simulation of the corrosion and biodegradation process in metallic biomaterials - Published in JOSS (2022)

ivprobit — Peer-reviewed • Rank 2.3 • Science 93%

ivprobit:An R package to estimate the instrumental variables probit model - Published in JOSS (2018)

The Biddy BDD package — Peer-reviewed • Rank 2.3 • Science 93%

The Biddy BDD package - Published in JOSS (2019)

rGUIDANCE – alignment confidence score computation in R — Peer-reviewed • Rank 2.3 • Science 93%

rGUIDANCE – alignment confidence score computation in R - Published in JOSS (2019)

MOAFS — Peer-reviewed • Rank 2.3 • Science 93%

MOAFS: A Massive Online Analysis library for feature selection in data streams - Published in JOSS (2020)

grapesAgri1 — Peer-reviewed • Rank 2.3 • Science 93%

grapesAgri1: Collection of Shiny Apps for Data Analysis in Agriculture - Published in JOSS (2021)

rocrate • Rank 18.3 • Science 77%

Python library for RO-Crate

pyrho • Rank 18.3 • Science 77%

higlass • Rank 18.2 • Science 77%

Fast, flexible and extensible genome browser.

BrainGlobe Atlas API — Peer-reviewed • Rank 18.2 • Science 77%

BrainGlobe Atlas API: a common interface for neuroanatomical atlases - Published in JOSS (2020)

SARAS — Peer-reviewed • Rank 2.2 • Science 93%

SARAS: A general-purpose PDE solver for fluid dynamics - Published in JOSS (2021)

HARE — Peer-reviewed • Rank 2.2 • Science 93%

HARE: A Python workflow for analyzing genomic feature enrichment in GWAS datasets - Published in JOSS (2024)

J2suscep — Peer-reviewed • Rank 2.2 • Science 93%

J2suscep: Calculation of magnetic exchange coupling and temperature dependence of magnetic susceptibility - Published in JOSS (2021)

subMALDI — Peer-reviewed • Rank 2.2 • Science 93%

subMALDI: an open framework R package for processing irregularly-spaced mass spectrometry data - Published in JOSS (2021)

discretize • Rank 18.2 • Science 77%

Discretization tools for finite volume and inverse problems.

pyabsa • Rank 18.2 • Science 77%

Sentiment Analysis, Text Classification, Text Augmentation, Text Adversarial defense, etc.;

stacomiR — Peer-reviewed • Rank 2.1 • Science 93%

stacomiR : a common tool for monitoring fish migration - Published in JOSS (2019)

datasailr - An R Package for Row by Row Data Processing, Using DataSailr Script — Peer-reviewed • Rank 2.1 • Science 93%

datasailr - An R Package for Row by Row Data Processing, Using DataSailr Script - Published in JOSS (2021)

CART — Peer-reviewed • Rank 2.1 • Science 93%

CART: A Tool for Making Paper Relevancy Screening Easier - Published in JOSS (2024)

NEEP — Peer-reviewed • Rank 2.1 • Science 93%

NEEP: null empirically estimated p-values for high-throughput molecular survival analysis - Published in JOSS (2020)

mikecalsetup — Peer-reviewed • Rank 2.1 • Science 93%

mikecalsetup: an open-source python tool for automatically creating calibration setups of MIKE SHE models in PEST or OSTRICH - Published in JOSS (2023)

dms-viz — Peer-reviewed • Rank 2.1 • Science 93%

dms-viz: Structure-informed visualiz ations for deep mutational scanning and other mutation-based datasets - Published in JOSS (2024)

chise • Rank 10.0 • Science 85%

A web application to visualize and edit the pathway models represented by SBGN Process Description Notation

EPICpy — Peer-reviewed • Rank 0.0 • Science 95%

EPICpy: A Python Interface for EPIC Computational Cognitive Modeling - Published in JOSS (2022)

rehype-citation • Rank 18.0 • Science 77%

Rehype plugin to add citation and bibliography from bibtex files

pysteps • Rank 18.0 • Science 77%

Python framework for short-term ensemble prediction systems.

LiGuard — Peer-reviewed • Rank 1.9 • Science 93%

LiGuard: Interactively and Rapidly Create Point-Cloud and Image Processing Pipelines - Published in JOSS (2025)

miditok • Rank 17.9 • Science 77%

MIDI / symbolic music tokenizers for Deep Learning models 🎶

openfold • Rank 17.9 • Science 77%

Trainable, memory-efficient, and GPU-friendly PyTorch reproduction of AlphaFold 2

graphannis • Rank 17.9 • Science 77%

This is a new backend implementation of the ANNIS linguistic search and visualization system.

tableone • Rank 17.9 • Science 77%

Create "Table 1" for research papers in Python

cchdo.hydro • Rank 9.9 • Science 85%

The big ol CCHDO netCDF-CF project

qbraid • Rank 17.9 • Science 77%

A platform-agnostic quantum runtime framework

biolink-model • Rank 17.8 • Science 77%

Schema and generated objects for biolink data model and upper ontology

riversCentralAsia — Peer-reviewed • Rank 1.8 • Science 93%

riversCentralAsia: An R package to support data pre- and postprocessing for hydrological modelling with RS MINERVE - Published in JOSS (2023)

KinESim — Peer-reviewed • Rank 1.8 • Science 93%

KinESim: Pre-equilibrium kinetic simulation of electrochemical reactions - Published in JOSS (2019)

DataRepExp — Peer-reviewed • Rank 1.8 • Science 93%

DataRepExp: a R shiny Application that makes Data FAIR for Data Repositories - Published in JOSS (2024)

SIMIO-continuum — Peer-reviewed • Rank 1.8 • Science 93%

SIMIO-continuum: Connecting simulations to ALMA observations - Published in JOSS (2024)

OpenPelt — Peer-reviewed • Rank 1.8 • Science 93%

OpenPelt: Python Framework for Thermoelectric Temperature Control System Development - Published in JOSS (2022)

whalestrike — Peer-reviewed • Rank 1.8 • Science 93%

whalestrike: An R package for simulating ship strikes on whales - Published in JOSS (2024)

qrules • Rank 17.7 • Science 77%

Rule-based particle reaction problem solver on a quantum number level

cf-units • Rank 17.7 • Science 77%

Units of measure as required by the Climate and Forecast (CF) Metadata Conventions

pytreedb • Rank 9.7 • Science 85%

Python package providing a file and object-based database to store tree objects.

cooler • Rank 17.7 • Science 77%

A cool place to store your Hi-C

GPJax — Peer-reviewed • Rank 17.6 • Science 77%

GPJax: A Gaussian Process Framework in JAX - Published in JOSS (2022)

ACHR.cu — Peer-reviewed • Rank 1.6 • Science 93%

ACHR.cu: GPU-accelerated sampling of metabolic networks - Published in JOSS (2019)

Mapelia and friends — Peer-reviewed • Rank 1.6 • Science 93%

Mapelia and friends: create 3D models from maps - Published in JOSS (2018)

pyransac3d • Rank 17.6 • Science 77%

A python tool for fitting primitives 3D shapes in point clouds using RANSAC algorithm