madminer • Rank 14.1 • Science 77%

Machine learning–based inference toolkit for particle physics

rust-kmedoids • Rank 14.1 • Science 77%

k-Medoids clustering in Rust with the FasterPAM algorithm

monai • Rank 27.1 • Science 64%

AI Toolkit for Healthcare Imaging

wpextract • Rank 6.1 • Science 85%

Create datasets from WordPress sites for research or archiving

metric-temporal-logic • Rank 14.1 • Science 77%

Python library for working with Metric Temporal Logic (MTL)

dace • Rank 19.1 • Science 72%

DaCe - Data Centric Parallel Programming

variation-normalization • Rank 14.1 • Science 77%

Services and guidelines for normalizing variants

aimsim • Rank 16.0 • Science 75%

A Python toolbox to work with molecular similarity

ampform • Rank 14.0 • Science 77%

Automatically generate symbolic amplitude models for Partial Wave Analysis

movement • Rank 14.0 • Science 77%

A Python toolbox for analysing animal body movements across space and time

eazy • Rank 14.0 • Science 77%

Pythonic photometric redshift tools based on EAZY

SSMSE — Peer-reviewed • Rank 6.0 • Science 85%

SSMSE: An R package for Management Strategy Evaluation with Stock Synthesis Operating Models - Published in JOSS (2023)

MadNLP • Rank 14.0 • Science 77%

A solver for nonlinear programming with GPU support

pygeohydro • Rank 13.9 • Science 77%

A part of HyRiver software stack for accessing hydrology data through web services

cheminformatics-microservice • Rank 5.9 • Science 85%

This set of essential and valuable microservices is designed to be accessed via API calls to support cheminformatics.

numexpr • Rank 31.9 • Science 59%

Fast numerical array expression evaluator for Python, NumPy, Pandas, PyTables and more

speasy • Rank 13.9 • Science 77%

Space Physics made EASY! A simple Python package to deal with main Space Physics WebServices (CDA,SSC,AMDA,..)

pyEQL — Peer-reviewed • Rank 13.9 • Science 77%

pyEQL: A Python interface for water chemistry - Published in JOSS (2024)

rosella • Rank 13.9 • Science 77%

Metagenomic Binning Algorithm

ldtk • Rank 13.9 • Science 77%

Python toolkit for calculating stellar limb darkening profiles and model-specific coefficients using the stellar atmosphere spectrum library by Husser et al. (2013). Described in Parviainen & Aigrain, MNRAS 453, 3821–3826 (2015).

deeplabcut-live • Rank 13.9 • Science 77%

SDK for running DeepLabCut on a live video stream

sepia • Rank 5.8 • Science 85%

Simulation-Enabled Prediction, Inference, and Analysis: physics-informed statistical learning.

pylint • Rank 36.8 • Science 54%

It's not just a linter that annoys you!

Clapeyron • Rank 13.8 • Science 77%

Clapeyron provides a framework for the development and use of fluid-thermodynamic models, including SAFT, cubic, activity, multi-parameter, and COSMO-SAC.

georasters • Rank 13.8 • Science 77%

GeoRasters is a Python module that provides a fast and flexible tool to work with GIS raster files.

xarrayutils • Rank 13.8 • Science 77%

carlos • Rank 5.7 • Science 85%

CARLA Open Simulation Architecture

AdditiveFOAM — Peer-reviewed • Rank 5.7 • Science 85%

AdditiveFOAM: A Continuum Multiphysics Code for Additive Manufacturing - Published in JOSS (2025)

nobrainer • Rank 13.7 • Science 77%

A framework for developing neural network models for 3D image processing.

gosling.js • Rank 13.7 • Science 77%

Grammar of Scalable Linked Interactive Nucleotide Graphics

python-novice-gdp-penguins • Rank 5.7 • Science 85%

rewrite of inflammation lesson using pandas

yt_astro_analysis • Rank 13.7 • Science 77%

yt astrophysical analysis modules

partseg • Rank 13.7 • Science 77%

Tool for segmentation in bioimaging

great-tables • Rank 23.7 • Science 67%

Make awesome display tables using Python

gimmemotifs • Rank 13.6 • Science 77%

Suite of motif tools, including a motif prediction pipeline for ChIP-seq experiments. See full GimmeMotifs documentation for detailed installation instructions and usage examples.

RxInfer — Peer-reviewed • Rank 13.6 • Science 77%

RxInfer: A Julia package for reactive real-time Bayesian inference - Published in JOSS (2023)

openfermion • Rank 13.6 • Science 77%

Python package for compiling and analyzing quantum algorithms to simulate electronic structures.

LightKrylov: Lightweight implementation of Krylov subspace techniques in modern Fortran • Rank 3.6 • Science 87%

LightKrylov: Lightweight implementation of Krylov subspace techniques in modern Fortran - Published in JOSS (2026)

cytoscape.js-undo-redo • Rank 15.5 • Science 75%

A Cytoscape.js extension to provide an undo-redo framework

cabinetry • Rank 13.5 • Science 77%

design and steer profile likelihood fits

ChaosTools • Rank 13.5 • Science 77%

Tools for the exploration of chaos and nonlinear dynamics

viresclient • Rank 13.5 • Science 77%

viresclient is a Python package for easy access to Swarm & Aeolus products as xarray.Dataset

t-elf • Rank 5.5 • Science 85%

Tensor Extraction of Latent Features (T-ELF). Within T-ELF's arsenal are non-negative matrix and tensor factorization solutions, equipped with automatic model determination (also known as the estimation of latent factors - rank) for accurate data modeling. Our software suite encompasses cutting-edge data pre-processing and post-processing modules.

nltk • Rank 36.5 • Science 54%

NLTK Source

tuv-x • Rank 5.4 • Science 85%

Photolysis rate constant calculator

pysisyphus • Rank 13.4 • Science 77%

Python suite for optimization of stationary points on ground- and excited states PES and determination of reaction paths.

mail-deduplicate • Rank 13.4 • Science 77%

📧 CLI to deduplicate mails from mail boxes

cadquery • Rank 23.4 • Science 67%

A python parametric CAD scripting framework based on OCCT

mgviz • Rank 5.3 • Science 85%

Multi-Mission Geographic Information System (MMGIS) Global Navigation Satellite System (GNSS) Visualizer

cytoscape-view-utilities • Rank 15.3 • Science 75%

A Cytoscape.js extension to provide miscellenaous view utilities such as hiding and highlighting nodes/edges

cheetah-accelerator • Rank 13.3 • Science 77%

Fast and differentiable particle accelerator optics simulation for reinforcement learning and optimisation applications.

mpskit.jl • Rank 13.3 • Science 77%

A Julia package dedicated to simulating quantum many-body systems using Matrix Product States (MPS)

cytoscape.js-cise • Rank 5.3 • Science 85%

An implementation of the circular layout algorithm by Dogrusoz et al. as a Cytoscape.js extension

vak • Rank 13.3 • Science 77%

A neural network framework for researchers studying acoustic communication

gllvm • Rank 13.3 • Science 77%

Generalized Linear Latent Variable Models

openprompt • Rank 18.3 • Science 72%

An Open-Source Framework for Prompt-Learning.

corpus-annotation-graph-builder • Rank 5.2 • Science 85%

Corpus Annotation Graph builder (CAG) is an architectural framework that employs the build-and-annotate pattern for creating a graph.

fitz-main-website • Rank 5.2 • Science 85%

A simple Laravel front end for the production version of the Fitzwilliam Museum website.

BSplineKit • Rank 13.2 • Science 77%

A collection of B-spline tools in Julia

shotgun-metagenomics-analysis • Rank 5.2 • Science 85%

Analysis of metagenomic shotgun sequences including assembly, speciation, ARG discovery and more

atropos • Rank 13.1 • Science 77%

An NGS read trimming tool that is specific, sensitive, and speedy. (production)

scri • Rank 13.1 • Science 77%

Python/numba code for manipulating time-dependent functions of spin-weighted spherical harmonics on future null infinity

mnt-opdom-explorer • Rank 5.1 • Science 85%

Explore Operational Domains of SiDB logic gates

aguaclara • Rank 13.1 • Science 77%

An open-source Python package for designing and performing research on AguaClara water treatment plants.

The Experiment Factory — Peer-reviewed • Rank 13.0 • Science 77%

The Experiment Factory: Reproducible Experiment Containers - Published in JOSS (2018)

scalene • Rank 26.0 • Science 64%

Scalene: a high-performance, high-precision CPU, GPU, and memory profiler for Python with AI-powered optimization proposals

pira • Rank 5.0 • Science 85%

PIRA - Automatic Instrumentation Refinement

oac • Rank 4.9 • Science 85%

OpenAirClim

DEEPaaS API — Peer-reviewed • Rank 12.9 • Science 77%

DEEPaaS API: a REST API for Machine Learning and Deep Learning models - Published in JOSS (2019)

reactionmechanismgenerator • Rank 12.9 • Science 77%

Python version of the amazing Reaction Mechanism Generator (RMG).

torchao • Rank 25.9 • Science 64%

PyTorch native quantization and sparsity for training and inference

modepy • Rank 12.8 • Science 77%

Modes and nodes for high-order discretizations

pyo3 • Rank 35.8 • Science 54%

Rust bindings for the Python interpreter

multinma • Rank 12.8 • Science 77%

Network meta-analysis of individual and aggregate data in Stan

mdocean • Rank 4.8 • Science 85%

Multidisciplinary Design Optimization (MDO) to optimize an ocean wave energy converter

astrophot • Rank 12.8 • Science 77%

A fast, flexible, automated, and differentiable astronomical image 2D forward modelling tool for precise parallel multi-wavelength photometry

DynamicalSystemsBase • Rank 12.8 • Science 77%

Definition of dynamical systems types and API for DynamicalSystems.jl

base-repo • Rank 4.7 • Science 85%

Basic repository service used as central component of the KIT DM 2.0 infrastructure.

annogesic • Rank 12.7 • Science 77%

ANNOgesic - A Swiss army knife for the RNA-Seq based annotation of bacterial/archaeal genomes

litstudy • Rank 12.7 • Science 77%

LitStudy: Using the power of Python to automate scientific literature analysis from the comfort of a Jupyter notebook

tensorcircuit-ng • Rank 12.6 • Science 77%

The next-gen tensor network based quantum software framework: superseding the original TensorCircuit

locuszoom • Rank 14.6 • Science 75%

A Javascript/d3 embeddable plugin for interactively visualizing statistical genetic data from customizable sources.

catd_snakemake • Rank 4.6 • Science 85%

Snakemake pipeline for benchmarking cell-type deconvolution methods and deconvolving real bulk RNA-seq data with the use of scRNA-seq datasets

deepxde • Rank 12.6 • Science 77%

A library for scientific machine learning and physics-informed learning

eht-imaging • Rank 12.6 • Science 77%

Imaging, analysis, and simulation software for radio interferometry

pymwp • Rank 4.6 • Science 85%

A static analyzer of variable value growth for C programs.

assist • Rank 12.5 • Science 77%

ASSIST is a software package for ephemeris-quality integrations of test particles.

ml-pls • Rank 12.5 • Science 77%

PLS regression algorithm

datefixR • Rank 12.5 • Science 77%

🗓 Standardize messy date data into consistent, machine-readable, formats

snakefmt • Rank 22.5 • Science 67%

The uncompromising Snakemake code formatter

molstar • Rank 22.5 • Science 67%

A comprehensive macromolecular library

statsmodels • Rank 35.5 • Science 54%

Statsmodels: statistical modeling and econometrics in Python

MuData • Rank 12.5 • Science 77%

MuData-compatible storage for bioconductor's MultiAssayExperiment

hypatia.jl • Rank 12.5 • Science 77%

interior point solver for general convex conic optimization problems

llnl-thicket • Rank 14.4 • Science 75%

lab.js • Rank 12.4 • Science 77%

Online research made easy

cblaster • Rank 12.4 • Science 77%

Find clustered hits from a BLAST search

aviary-genome • Rank 12.4 • Science 77%

A hybrid assembly and MAG recovery pipeline (and more!)

conda • Rank 35.3 • Science 54%

A system-level, binary package and environment manager running on all major operating systems and platforms.

ADNLPModels • Rank 12.3 • Science 77%