Repository Index

CASSIA: A Multi-Agent LLM-Based Single-Cell Cell Type Annotation Framework

• ai4science
• llm
• multiagent-systems
• prompt-engineering

Cumo (pronounced like "koomo") is CUDA aware numerical library whose interface is highly compatible with Ruby Numo

• ruby
• cuda
• numo
• scicentific-computing

Rails frontend to The Genome Institute's drug gene interaction database.

A math and collisions library for Lua.

• math
• intersection
• lua

🔟 Implementation of rational number arithmetic for .NET with arbitrary precision.

• arbitrary-precision
• biginteger
• bigrational
• c-sharp

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

NeoDTI: Neural integration of neighbor information from a heterogeneous network for discovering new drug-target interactions

• computational-biology
• bioinformatics
• graph-convolution
• deep-learning

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

MAT is library for working with multi-dimensional arrays which supports efficient interfacing to foreign and CUDA code. BLAS and CUBLAS bindings are available.

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

C# math expression library with symbolic computation support

• csharp
• dotnet
• expression-parser
• math

Elixir library implementing a parallel matrix multiplication algorithm and other utilities for working with matrices. Used for benchmarking computationally intensive concurrent code.

Minerva Story is an image viewer that is designed specifically to make it easy for non-expert users to interact with complex tissue images.

• minerva
• microscopy
• ome
• immunofluorescence

Arbitrary Big Integer Library for Pascal

• intx
• biginteger
• pascal
• fpc

High-Dimensional Gene Expression and Morphology Profiles of Cells across 28,000 Genetic and Chemical Perturbations

Tool for precise, interactive, fast and scalable FISH spot detection

Zero-dependency 128-bit fixed-point decimal for Go. Exact SQL NUMERIC / PostgreSQL semantics, no heap allocation, no panics — built for money, ledgers and banking arithmetic.

• decimal
• fixed-point
• go
• golang

An extensible .NET genetic algorithm library for optimization and artificial intelligence - Evolutionary computation and complex problem solving made simple

• artificial-intelligence
• csharp
• dotnet
• evolutionary-algorithm

A Julia GraphQL client for seamless integration with a server

MCP server for spatial transcriptomics analysis through natural language interfaces.

• bioinformatics
• cell-communication
• deconvolution
• machine-learning

Predicting Cell Health with Morphological Profiles

• carpenter-lab
• morphological-profiling
• crispr
• cell-painting

💬 Trace citation chains for any concept across research papers and render them as an interactive graph.

• academic-research
• bibliography
• citation-graph
• cli

A foundation model-driven whole slide image-scale cell phenotyping method with QuPath integration Resources

• bioimage-analysis
• cell-classification
• computer-vision
• digital-pathology

Multigrate: multiomic data integration for single-cell genomics