Pydre — Peer-reviewed • Science 100%

Pydre: A Python package for driving simulation data reduction - Published in JOSS (2025)

https://github.com/caltechlibrary/2020-05-11-swc-online • Science 52%

May 2020 Software Carpentry Workshop

OPTIMUS — Peer-reviewed • Science 93%

OPTIMUS: A Multidimensional Global Optimization Package - Published in JOSS (2025)

ReadmeReady — Peer-reviewed • Science 93%

ReadmeReady: Free and Customizable Code Documentation with LLMs - A Fine-Tuning Approach - Published in JOSS (2025)

https://github.com/cair/tsetlinmachine • Science 49%

Code and datasets for the Tsetlin Machine

https://github.com/cafferychen777/cafferychen777 • Science 49%

rjaf — Peer-reviewed • Science 95%

rjaf: Regularized Joint Assignment Forest with Treatment Arm Clustering - Published in JOSS (2025)

https://github.com/bueler/glacier-fe-estimate • Science 46%

extend the Falk technique to Stokes glacier models of surface evolution

https://github.com/brugr9/uepluginvolumecreator • Science 49%

Unreal Engine Plugin: Volume Creator – Documentation

LongMemory.jl — Peer-reviewed • Science 100%

LongMemory.jl: Generating, Estimating, and Forecasting Long Memory Models in Julia - Published in JOSS (2025)

https://github.com/broadinstitute/dino4cells_analysis • Science 57%

https://github.com/broadinstitute/pbs-analysis • Science 57%

Scripts for analyzing ChIP-seq and related datatypes with binning and PBS

https://github.com/broadinstitute/strainge • Science 57%

strain-level analysis tools

QuantumACES.jl — Peer-reviewed • Science 98%

QuantumACES.jl: design noise characterisation experiments for quantum computers - Published in JOSS (2025)

https://github.com/broadinstitute/profiling-resistance-mechanisms • Science 57%

Predicting pharmacodynamic responses to cancer drugs using cell morphology

desirna • Science 67%

State of the art software for RNA sequence design. The first to solve the Eterna benchmark!

https://github.com/brainglobe/brainglobe-template-builder • Science 49%

Build unbiased anatomical templates from individual images

https://github.com/brainets/hosi_infogain • Science 49%

Script for "Higher-order and distributed synergistic functional interactions encode information gain in goal-directed learning"

csnet • Science 67%

https://github.com/bozenne/article-netbenefit-correction • Science 49%

Code and software for the article "Correcting the bias of the net benefit estimator due to right-censored observations" published in biometrical (link: https://doi.org/10.1002/bimj.202000001 ).

https://github.com/bootphon/speech-map • Science 49%

Mean Average Precision over words or n-grams with speech features

DemeterWatch — Peer-reviewed • Science 95%

DemeterWatch: A Java tool to detect Law of Demeter violations in Java collections - Published in JOSS (2025)

https://github.com/boothgroup/vayesta • Science 49%

A Python package for wave function-based quantum embedding

https://github.com/bodenmillergroup/imcdataanalysis • Science 49%

R based workflow for multiplexed imaging data

https://github.com/bioscan-ml/barcodebert • Science 49%

A pre-trained representation from a transformers model for inference on insect DNA barcoding data.

https://github.com/biont-training/hpc-workflows-en • Science 44%

https://github.com/biolink/resource-ingest-guide-schema • Science 44%

A LinkML schema for describing the scope, rationale, and modeling approach for ingesting content from a single source.

https://github.com/bioinfomachinelearning/multicom4 • Science 49%

The MULTICOM4 protein structure prediction system developed by the Bioinformatics and Machine Learning Lab at the University of Missouri - Columbia

https://github.com/biodt/uc-grassland • Science 49%

pDT grassland main repository

https://github.com/biodataanalysisgroup/virtual-tutorial-perturbation-modelling • Science 49%

https://github.com/bioconductor/bioconductor-training • Science 49%

Bioconductor teaching and education committee

https://github.com/bio-rsg/oceancolour • Science 49%

Package of custom functions for remote sensing data analysis

https://github.com/bin-cao/shapev • Science 49%

[JMI 2022 | Aggregate 2025] A package for searching equivalent values based on joined SHAP values

subjectivescalesmodels.jl • Science 44%

A Julia package for Beta-like regression models useful for subjective scales data (Likert scales, analog scales, ...)

https://github.com/berenslab/llm-excess-vocab • Science 49%

Delving into LLM-assisted writing in biomedical publications through excess vocabulary

https://github.com/benny0323/deep-learning-based-mia-tasks • Science 49%

⭐[A Deep Survey] Paper List For Metal Artifact Reduction including traditional and deepl leanring based methods. ℱℯℯ𝓁 𝒻𝓇ℯℯ to contribute!

https://github.com/beiko-lab/beiko-lab.github.io • Science 49%

COHESIVM — Peer-reviewed • Science 98%

COHESIVM: Combinatorial h+/e- Sample Investigation using Voltaic Measurements - Published in JOSS (2025)

https://github.com/bblodfon/pdac-efs-bench2024 • Science 49%

Feature Selection benchmark and analysis on multi-omics PDAC datasets

https://github.com/bayer-group/unidino • Science 49%

https://github.com/bartongroup/ligysis-web • Science 57%

https://github.com/baltic-coastal-monitoring-team/geopoint • Science 67%

GeoPOINT – Synthetic Point Generator for Geospatial Applications

ScatteringOptics.jl — Peer-reviewed • Science 95%

ScatteringOptics.jl: An Interstellar Scattering Framework in the Julia Programming Language - Published in JOSS (2025)

https://github.com/baaihealth/opencomplex2 • Science 49%

initial repo

https://github.com/awesomecosmos/aayushi-verma-cv • Science 49%

Aayushi Verma's Curriculum Vitae.

https://github.com/auroradysis/kerrp2p • Science 49%

KerrP2P is a software designed for forward ray tracing in Kerr spacetime. It is specifically tailored to efficiently calculate multiple null geodesics between designated "source" and "observer" points, locate apparent positions of the corresponding images, and quantify their shapes.

https://github.com/attpc/spyral • Science 49%

A Python analysis library for AT-TPC data

https://github.com/chendaniely/2022-01-06-ttt_demo • Science 44%

TTT workshop demo

https://github.com/astrazeneca/topmodel • Science 49%

Uses simulated time-to-event data to model efficacy by prevalence-adjusted nAb titres using a time-varying Cox model.

https://github.com/assert-kth/vrepair • Science 49%

open science repo of "Neural Transfer Learning for Repairing Security Vulnerabilities in C Code" https://arxiv.org/pdf/2104.08308

https://github.com/chen-yang-liu/git-rsclip • Science 49%

Git-RSCLIP pre-trained on 10 million Remote sensing image-text pairs

https://github.com/aspuru-guzik-group/pasithea • Science 57%

Deep Molecular Dreaming

https://github.com/chen-yang-liu/awesome-change-captioning • Science 49%

🔥Collection of resources and papers

https://github.com/arkokupski-wat/subjective_time_as_emergent_information_processing • Science 49%

The Brain's Clock: From the Phoenix Equation to Holographic Consciousness

https://github.com/arkokupski-wat/hypothesis-of-spontaneous-matter-antimatter-conversion • Science 49%

Hypothesis of Spontaneous Matter→Antimatter Conversion at Planck Densities

https://github.com/arkokupski-wat/g1g2-gravity-duality • Science 49%

🌌 G₁/G₂ Gravity Duality: Proves quantum & cosmic gravity are distinct phenomena.

PeakPerformance - A tool for Bayesian inference-based fitting of LC-MS/MS peaks — Peer-reviewed • Science 96%

PeakPerformance - A tool for Bayesian inference-based fitting of LC-MS/MS peaks - Published in JOSS (2024)

https://github.com/arkokupski-wat/modified-spacetime-hypothesis • Science 49%

The hypothesis treats spacetime not as a passive backdrop for matter, but as an equal partner in physical transformations. The inspiration stems from explosive chemistry—specifically, how the detonation of high-energy materials mixtures) converts condensed matter into expanding gases and energy.

https://github.com/aria-systems-group/regret_synthesis_toolbox • Science 49%

Source code for Regret synthesis for two-player turn-based game played on graphs - ICRA 22

https://github.com/arcadia-science/agent-literature-review • Science 49%

https://github.com/antoine-buetti/nf-core-tumorscope • Science 57%

https://github.com/anon0411/decoh_as_codom • Science 49%

Feedback-guided quantum circuits exploring codomain-zero as a structural condition. 구조 형성의 조건으로서 공역 0을 실험하는 피드백 기반 양자 회로.

https://github.com/annahedstroem/sanity-checks-revisited • Science 49%

[NeurIPS XAIA & Springer] Code and notebooks to paper "A Fresh Look at Sanity Checks for Saliency Maps"

https://github.com/anhph95/neslter-stingray • Science 49%

https://github.com/anananacr/bblib • Science 44%

beambusters library

https://github.com/ambco-iscte/jask • Science 49%

A Library for Generating Questions about Learners' Code in Java

https://github.com/amazon-science/mxeval • Science 46%

https://github.com/aloncrack7/data-degradation-detector • Science 49%

Library to make stimations on data degradation

https://github.com/aksw/frankgraphbench • Science 49%

The FranKGraphBench is a Framework to allow KG Aware RSs to be benchmarked in a reproducible and easy to implement manner. It was first created on Google Summer of Code 2023 for Data Integration between DBpedia and some standard RS datasets in a reproducible framework.

https://github.com/ajpelu/c_allocation_pine • Science 49%

https://github.com/erictleung/coursework • Science 10%

:notebook: Coursework for miscellaneous programming, web development, etc courses

dummydatarepo • Science 67%

https://github.com/cheminfo/jeol-data-test • Science 49%

https://github.com/aiformedresearch/synthetic_images_metrics_toolkit • Science 49%

SIM Toolkit: 2D and 3D synthetic image quality assessment using quantitative and qualitative metrics.

https://github.com/ai4bharat/fbi • Science 49%

FBI: Finding Blindspots in LLM Evaluations with Interpretable Checklists

https://github.com/agroboticsresearch/headland_trajectory_planning • Science 49%

This repo is includes headland space modeling and trajectory planning for autonomous agricultural vehicle in the orchard.

https://github.com/agda/agda2lambox • Science 57%

Compiling Agda's internal syntax to λ-box terms.

exocore • Science 44%

https://github.com/adrientaudiere/mitemaptools • Science 49%

https://github.com/erictleung/freecodecamp-news-analysis • Science 10%

:office: Code and notes on running various database management systems

https://github.com/adicksonlab/agdiff • Science 49%

Implementation of AGDIFF: Attention-Enhanced Diffusion for Molecular Geometry Prediction

https://github.com/adaptivemotorcontrollab/cellseg3d • Science 59%

A napari plugin for direct 3D cell segmentation -- taking you through training, inference, and review of masks

https://github.com/abhishektiwari/scholarimpact • Science 54%

ScholarImpact: A bibliometric tool to analyse, visualise, and share your research impact, output and scholarly influence using Google Scholar and OpenAlex data.

https://github.com/robelgium/msnoise • Science 59%

A Python Package for Monitoring Seismic Velocity Changes using Ambient Seismic Noise | http://www.msnoise.org

https://github.com/kmnhan/erlabpy • Science 54%

Complete python workflow for Angle-Resolved Photoemission Spectroscopy (ARPES)

Biosensor Framework — Peer-reviewed • Science 100%

Biosensor Framework: A C# Library for Affective Computing - Published in JOSS (2021)

https://github.com/openchemistry/tomviz • Science 46%

Cross platform, open source application for the processing, visualization, and analysis of 3D tomography data

https://github.com/chem-william/biotsavart • Science 49%

Implementation of Biot-Savart law

gaimerstablediffusion • Science 54%

https://github.com/smonto2/ptfa • Science 49%

https://github.com/patrickzib/dictionary • Science 49%

WEASEL 2.0 - A Random Dilated Dictionary Transform for Fast, Accurate and Constrained Memory Time Series Classification

https://github.com/ajshajib/dolphin • Science 49%

Automated pipeline for lens modelling based on lenstronomy

https://github.com/desbordante/desbordante-core • Science 49%

Desbordante is a high-performance data profiler that is capable of discovering many different patterns in data using various algorithms. It also allows to run data cleaning scenarios using these algorithms. Desbordante has a console version and an easy-to-use web application.

https://github.com/ibridges-for-irods/ibridges • Science 49%

A wrapper around the python-irodsclient to allow for easy interaction with iRODS servers.

peptipedia • Science 57%

https://github.com/georgedouzas/imbalanced-learn-extra • Science 49%

Implementation of novel oversampling algorithms.

magicbathynet • Science 49%

Quick start guide for benchmarking MagicBathyNet dataset in learning-based bathymetry and pixel-based classification using Remote Sensing imagery.

shadia • Science 59%

shadia: dam passage performance standard models for R

IDEAS • Science 49%

Modelica library allowing simultaneous transient simulation of thermal and electrical systems at both building and feeder level.

mena-fcv-economic-monitor • Science 44%