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

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

multimodars: A Rust-powered toolkit for multi-modality cardiac image fusion and registration • Rank 3.3 • Science 87%

multimodars: A Rust-powered toolkit for multi-modality cardiac image fusion and registration - Published in JOSS (2026)

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

CoSim Toolbox - Making HELICS Co-Simulations Easier • Rank 3.3 • Science 87%

CoSim Toolbox - Making HELICS Co-Simulations Easier - Published in JOSS (2026)

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

InspectorCell — Peer-reviewed • Rank 3.2 • Science 87%

InspectorCell: Finding Ground Truth in Multiplexed Microscopy Images - Published in JOSS (2022)

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

hawen — Peer-reviewed • Rank 1.1 • Science 89%

hawen: time-harmonic wave modeling and inversion using hybridizable discontinuous Galerkin discretization - Published in JOSS (2021)

imea — Peer-reviewed • Rank 1.1 • Science 89%

imea: A Python package for extracting 2D and 3D shape measurements from images - Published in JOSS (2021)

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.

Tagging Latency Estimator — Peer-reviewed • Rank 3.0 • Science 87%

Tagging Latency Estimator: A Standalone Software for Estimating Latency of Event-Related Potentials in P300-based Brain-Computer Interfaces - Published in JOSS (2023)

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

galsbi: A Python package for the GalSBI galaxy population model • Rank 3.0 • Science 87%

galsbi: A Python package for the GalSBI galaxy population model - Published in JOSS (2025)

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

HLAfreq: Download and combine HLA allele frequency data • Rank 2.8 • Science 87%

HLAfreq: Download and combine HLA allele frequency data - Published in JOSS (2026)

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

DASF — Peer-reviewed • Rank 2.6 • Science 87%

DASF: A data analytics software framework for distributed environments - Published in JOSS (2022)

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

CN-AeroModels — Peer-reviewed • Rank 2.5 • Science 87%

CN-AeroModels: A C++ implementation of aerodynamic models for wind propulsion systems of cargo ships - Published in JOSS (2024)

BigX — Peer-reviewed • Rank 2.5 • Science 87%

BigX: A geographical dataset visualisation tool - Published in JOSS (2020)

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

diff_classifier: Parallelization of multi-particle tracking video analyses • Rank 2.4 • Science 87%

diff_classifier: Parallelization of multi-particle tracking video analyses - Published in JOSS (2019)

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%

robotkube • Rank 4.3 • Science 85%

Orchestrating Large-Scale Cooperative Multi-Robot Systems with Kubernetes and ROS

tensorwaves • Rank 12.3 • Science 77%

Python fitter package for multiple computational back-ends

skada • Rank 12.3 • Science 77%

Domain adaptation toolbox compatible with scikit-learn and pytorch

pyhmmer • Rank 22.3 • Science 67%

Cython bindings and Python interface to HMMER3.

mss • Rank 12.3 • Science 77%

A QT application, a OGC web map server, a collaboration server to plan atmospheric research flights.

fastcrypto • Rank 22.3 • Science 67%

Common cryptographic library used in software at Mysten Labs.

qc-procrustes • Rank 12.3 • Science 77%

Python library for finding the optimal transformation(s) that makes two matrices as close as possible to each other.

gbd-tools • Rank 12.3 • Science 77%

Management of Benchmark Instances and Instance Attributes

iga • Rank 4.2 • Science 85%

IGA is the InvenioRDM GitHub Archiver, a standalone program as well as a GitHub Action that lets you automatically archive GitHub software releases in an InvenioRDM repository.

kitsune • Rank 4.2 • Science 85%

Kitsune is a next-generation data steward and harmonization tool.

pysdc • Rank 12.2 • Science 77%

pySDC is a Python implementation of the spectral deferred correction (SDC) approach and its flavors, esp. the multilevel extension MLSDC and PFASST.

pytextrank • Rank 22.2 • Science 67%

Python implementation of TextRank algorithms ("textgraphs") for phrase extraction

epiparameter • Rank 12.2 • Science 77%

R package with classes and helper functions for working with epidemiological parameters and access to a library of epidemiological parameters for infectious diseases

calphy • Rank 12.2 • Science 77%

A Python library and command line interface for automated free energy calculations

SumOfSquares • Rank 12.2 • Science 77%

Sum of Squares Programming for Julia

albumentations • Rank 30.2 • Science 59%

Fast and flexible image augmentation library. Paper about the library: https://www.mdpi.com/2078-2489/11/2/125

pylipd • Rank 12.2 • Science 77%

Development repository for Python LiPD utilities

torch-pme • Rank 14.2 • Science 75%

Particle-mesh based calculations of long-range interactions in PyTorch

proglearn • Rank 12.2 • Science 77%

NeuroData's package for exploring and using progressive learning algorithms

gdal • Rank 30.1 • Science 59%

GDAL is an open source MIT licensed translator library for raster and vector geospatial data formats.

https://github.com/hpcaitech/colossalai • Rank 30.1 • Science 59%

Making large AI models cheaper, faster and more accessible

imaris_extensions • Rank 4.1 • Science 85%

Algorithmic and Utility Extensions for the Imaris Program

llview • Rank 4.1 • Science 85%

HPC Monitoring Tool

pyoptas • Rank 12.1 • Science 77%

OpTaS: An optimization-based task specification library for trajectory optimization and model predictive control.

onnx2tf • Rank 22.1 • Science 67%

Self-Created Tools to convert ONNX files (NCHW) to TensorFlow/TFLite/Keras format (NHWC). The purpose of this tool is to solve the massive Transpose extrapolation problem in onnx-tensorflow (onnx-tf). I don't need a Star, but give me a pull request.

STUMPY — Peer-reviewed • Rank 12.1 • Science 77%

STUMPY: A Powerful and Scalable Python Library for Time Series Data Mining - Published in JOSS (2019)

rJavaEnv • Rank 12.1 • Science 77%

Java Environments for R Projects

nrel-sup3r • Rank 12.1 • Science 77%

The Super-Resolution for Renewable Resource Data (sup3r) software uses generative adversarial networks to create synthetic high-resolution wind and solar spatiotemporal data from coarse low-resolution inputs.

input4mips_cvs • Rank 4.0 • Science 85%

Controlled Vocabularies (CVs) for use in input4MIPs

spyglass-neuro • Rank 14.0 • Science 75%

Neuroscience data analysis framework for reproducible research built by Loren Frank Lab at UCSF

nf-core • Rank 22.0 • Science 67%

Python package with helper tools for the nf-core community.

selfie • Rank 12.0 • Science 77%

An educational software system of a tiny self-compiling C compiler, a tiny self-executing RISC-V emulator, and a tiny self-hosting RISC-V hypervisor.

cadet-process • Rank 12.0 • Science 77%

A Framework for Modelling and Optimizing Advanced Chromatographic Processes

citations • Rank 4.0 • Science 85%

Citation manager support for GAP. This helps with citations for reports, papers, data, and presentations!

rbaps • Rank 4.0 • Science 85%

R implementation of the BAPS software for Bayesian Analysis of Population Structure

gnss-lib-py • Rank 14.0 • Science 75%

Modular Python tool for parsing, analyzing, and visualizing Global Navigation Satellite Systems (GNSS) data and state estimates

cutadapt • Rank 22.0 • Science 67%

Cutadapt removes adapter sequences from sequencing reads