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)

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)

Phasik — Peer-reviewed • Rank 6.4 • Science 89%

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

chatAI4R: Interactive Artificial Intelligence toolkit for Data Science in R • Rank 8.4 • Science 87%

chatAI4R: Interactive Artificial Intelligence toolkit for Data Science in R - Published in JOSS (2026)

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)

Solshade: Terrain-aware Solar Illumination Modelling using Digital Elevation Models and Orbital Geometry • Rank 6.4 • Science 89%

Solshade: Terrain-aware Solar Illumination Modelling using Digital Elevation Models and Orbital Geometry - Published in JOSS (2026)

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)

FAME-Core — Peer-reviewed • Rank 6.3 • Science 89%

FAME-Core: An open Framework for distributed Agent-based Modelling of Energy systems - Published in JOSS (2023)

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.

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)

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)

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

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

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)

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

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

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

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

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)

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

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

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

SARAS: A general-purpose PDE solver for fluid dynamics - 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)

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

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

GIMS — Peer-reviewed • Rank 6.2 • Science 89%

GIMS: Graphical Interface for Materials Simulations - 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.;

Groundhog - A general-purpose geotechnical Python package • Rank 8.2 • Science 87%

Groundhog - A general-purpose geotechnical Python package - Published in JOSS (2026)

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)

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)

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

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

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)

chise • Rank 10.0 • Science 85%

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

AMIRIS — Peer-reviewed • Rank 6.0 • Science 89%

AMIRIS: Agent-based Market model for the Investigation of Renewable and Integrated energy Systems - Published in JOSS (2023)

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

PileupCaller: A command-line tool to sample genotypes from low-coverage sequencing data of ancient DNA • Rank 8.0 • Science 87%

PileupCaller: A command-line tool to sample genotypes from low-coverage sequencing data of ancient DNA - Published in JOSS (2026)

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

ado: a Python framework for computational experimentation and benchmarking • Rank 7.9 • Science 87%

ado: a Python framework for computational experimentation and benchmarking - Published in JOSS (2026)

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

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

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

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)

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

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

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

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

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

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

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

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

qrules • Rank 17.7 • Science 77%

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

APAV — Peer-reviewed • Rank 7.7 • Science 87%

APAV: An Open-Source Python Package for Mass Spectrum Analysis in Atom Probe Tomography - Published in JOSS (2023)

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

REMix — Peer-reviewed • Rank 5.7 • Science 89%

REMix: A GAMS-based framework for optimizing energy system models - Published in JOSS (2024)

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

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

Copernicus Seasonal Forecast Tools Package: Bridging Seasonal Climate Predictions and Impact Models for Operational Risk Assessment • Rank 5.6 • Science 89%

Copernicus Seasonal Forecast Tools Package: Bridging Seasonal Climate Predictions and Impact Models for Operational Risk Assessment - Published in JOSS (2026)

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

amici • Rank 17.6 • Science 77%

High-performance sensitivity analysis for large ordinary differential equation models

Melissa — Peer-reviewed • Rank 5.6 • Science 89%

Melissa: coordinating large-scale ensemble runs for deep learning and sensitivity analyses - Published in JOSS (2023)

https://github.com/cytoscape/cytoscape.js • Rank 35.6 • Science 59%

Graph theory (network) library for visualisation and analysis

io.nextflow:nextflow • Rank 17.5 • Science 77%

A DSL for data-driven computational pipelines

hepunits • Rank 17.5 • Science 77%

Units and constants in the HEP system of units

IdentityByDescentDispersal.jl: Inferring dispersal rates with identity-by-descent blocks • Rank 2.5 • Science 92%

IdentityByDescentDispersal.jl: Inferring dispersal rates with identity-by-descent blocks - Published in JOSS (2026)

pysradb • Rank 17.5 • Science 77%

Package for fetching metadata and downloading data from SRA/ENA/GEO

PySWMM — Peer-reviewed • Rank 17.4 • Science 77%

PySWMM: The Python Interface to Stormwater Management Model (SWMM) - Published in JOSS (2020)

gladia-torchaudio • Rank 30.4 • Science 64%

Data manipulation and transformation for audio signal processing, powered by PyTorch

interpax • Rank 17.4 • Science 77%

Interpolation and function approximation with JAX

pyunicorn • Rank 17.4 • Science 77%

Unified Complex Network and Recurrence Analysis Toolbox

Bramble — Peer-reviewed • Rank 1.4 • Science 93%

Bramble: adaptive common neighbor analysis (CNA) for the recognition of surface topologies in nanoparticles - Published in JOSS (2023)

eights — Peer-reviewed • Rank 1.4 • Science 93%

eights: BS 8888:2011 first angle projection drawings from FreeCAD 3D model - Published in JOSS (2019)

ogs6py and VTUinterface — Peer-reviewed • Rank 1.4 • Science 93%

ogs6py and VTUinterface: streamlining OpenGeoSys workflows in Python - Published in JOSS (2021)

Multivariate Covariance Generalized Linear Models in Python — Peer-reviewed • Rank 1.4 • Science 93%

Multivariate Covariance Generalized Linear Models in Python: The mcglm library - Published in JOSS (2024)

TidyTensor — Peer-reviewed • Rank 1.4 • Science 93%

TidyTensor: Utilities for multidimensional arrays as named hierarchical structures - Published in JOSS (2021)

CytobankAPIstats — Peer-reviewed • Rank 1.4 • Science 93%

CytobankAPIstats: Computes Signaling and Population Statistics for Cytometry Data on Cytobank using 'CytobankAPI' - Published in JOSS (2019)

YAD — Peer-reviewed • Rank 1.4 • Science 93%

YAD: A Learning-based Inductive Logic Programming Tool - Published in JOSS (2018)

“Blaster” – a graphical user interface for common sequence analysis tools — Peer-reviewed • Rank 1.4 • Science 93%

“Blaster” – a graphical user interface for common sequence analysis tools - Published in JOSS (2019)

ordPens — Peer-reviewed • Rank 1.4 • Science 93%

ordPens: An R package for Selection, Smoothing and Principal Components Analysis for Ordinal Variables - Published in JOSS (2021)

catalystcoop.pudl • Rank 17.3 • Science 77%

The Public Utility Data Liberation Project provides analysis-ready energy system data to climate advocates, researchers, policymakers, and journalists.

bioframe • Rank 17.3 • Science 77%

Genomic interval operations on Pandas DataFrames

BayesFlow — Peer-reviewed • Rank 17.3 • Science 77%

BayesFlow: Amortized Bayesian Workflows With Neural Networks - Published in JOSS (2023)

compas-cra • Rank 9.3 • Science 85%

Coupled Rigid-Block Analysis: Stability-Aware Design of Complex Discrete-Element Assemblies

pastas • Rank 17.3 • Science 77%

Pastas is an open-source Python framework for the analysis of groundwater time series.

pyFBS — Peer-reviewed • Rank 5.2 • Science 89%

pyFBS: A Python package for Frequency Based Substructuring - Published in JOSS (2022)