Repository Index

A formalization of geometry in Coq based on Tarski's axiom system

• formalization
• coq
• geometry
• tarski-axiom

TranslatedAcademic research library for DSH — search, cite, approve imports, hand off notes. Also: a research literature library plugin for DeepSeek Harness: search papers, include sources, approve imports into the library, and hand off note leads to other plugins in the same session.

• academic
• agentero
• ai-agents
• citations

Cancer Imaging Phenomics Toolkit (CaPTk) is a software platform to perform image analysis and predictive modeling tasks. Documentation: https://cbica.github.io/CaPTk

• cancer-imaging-research
• radiomics
• radiomics-features
• machine-learning

Wrapper for RDKit's RunReactants to improve stereochemistry handling

scPerturb: A resource and a python/R tool for single-cell perturbation data

• cite-seq
• database
• perturbation
• scatac-seq

AI-based pathology predicts origins for cancers of unknown primary - Nature

• histology
• pathology
• wsi-images
• histopathology

Open source tumor evidence matching for sequencing labs and hospitals without molecular tumor boards. Research prototype; oncologist review required.

• bioinformatics
• cancer-research
• computational-biology
• drug-repurposing

Open-source software for exploring and analyzing large, high-dimensional image-derived data.

• cellprofiler-analyst
• cellprofiler
• image-analysis
• machine-learning

A python Two Source Energy Balance model for estimation of evapotranspiration with remote sensing data

• source-energy-balance
• canopy
• soil
• radiometric-temperatures

OpenBioLink is a resource and evaluation framework for evaluating link prediction models on heterogeneous biomedical graph data.

🏃 The go-to single-cell Foundation Model

• batch-correction
• cell-biology
• celltype-annotation
• denoising

TransformerCPI: Improving compound–protein interaction prediction by sequence-based deep learning with self-attention mechanism and label reversal experiments(BIOINFORMATICS 2020) https://doi.org/10.1093/bioinformatics/btaa524

• self-attention
• compound-protein-interaction
• transformercpi
• structure-free-virtual-sreening

The source code for the Menge crowd simulation framework

Safe Bayesian Optimization

• gaussian-processes
• optimization
• robotics
• reinforcement-learning

OFF, Open source Finite volume Fluid dynamics code

• fluid-dynamics
• fortran
• oop
• cfd

FastGenericNew: high-performance generic instantiation for .NET, replacing Activator.CreateInstance<

• activator
• createinstance
• csharp
• csharp-library

⚡ Open-source software for deep learning-based digital pathology

• deep-learning
• machine-learning
• digital-pathology
• computational-pathology

Easy link prediction tool

• python
• network-analysis
• link-prediction
• research

Extensive math expression evaluator library for JavaScript and Node.js

• typescript
• interpreter
• javascript
• calculator

Variations on Kirby & Paris' hydra battles and other entertaining math in Coq (collaborative, documented, includes exercises) [maintainer=@Casteran]

• coq
• hydra-battles
• ordinal-notations
• formal-proofs

Fast detection of repackaged Android applications based on the comparison of resource files included into the package.

• android
• android-security
• repackaging-detection
• java

PyTorch implementation of the MIDAS algorithm for single-cell multimodal data integration (Nature Biotechnology 2024).

• deep-generative-model
• deep-learning
• single-cell-data-integration
• single-cell-multiomics

Peax is a tool for interactive visual pattern search and exploration in epigenomic data based on unsupervised representation learning with autoencoders

• epigenomics
• pattern-search
• data-visualization
• interactive-machine-learning

A open source ballistics calculator

• ballistics
• vala
• gtk3
• meson