Starred repositories
CASSIA: A Multi-Agent LLM-Based Single-Cell Cell Type Annotation Framework
SpotSweeper-py: Python version of SpotSweeper package
Inferring allele-specific copy number aberrations and tumor phylogeography from spatially resolved transcriptomics
List of Spatial Transcriptomics related Tools organized per category
This is a pipeline for analysing high-dimensional tissue data in a HPC environment. It includes tools for analysing IMC data in the Scanpy ecosystem, but also several image-based analysis tools. Cu…
Evolvable, distributed agent framework & harness for data science.
Use Garry Tan's exact Claude Code setup: 23 opinionated tools that serve as CEO, Designer, Eng Manager, Release Manager, Doc Engineer, and QA
🦖 ClawBio — The first bioinformatics-native AI agent skill library. Local-first. Reproducible. Built on OpenClaw.
Centralising our llm client for agentic work.
Open-source AI research assistant for biomedicine — chat to run RNA-seq, drug discovery, clinical analysis, and more. Built on Claude Code with 140 K-Dense scientific skills, real-time dashboard, a…
Professional Antigravity Account Manager & Switcher. One-click seamless account switching for Antigravity Tools. Built with Tauri v2 + React (Rust).专业的 Antigravity 账号管理与切换工具。为 Antigravity 提供一键无缝账号切…
Paper2Agent is a multi-agent AI system that automatically transforms research papers into interactive AI agents with minimal human input.
An easy-to-use PyTorch library for Pathology Image ANalysis Orchestrator (PIANO), including generating patches from whole slide images, using pathology foundation models to create features, and so on.
Python library for processing whole slide images (WSIs) in sdpc format
Autonomous agentic system for supervised machine learning model development.
Biomni-Web: A General-Purpose Biomedical AI Agent with Custom UI
Universal SEO skill for Claude Code. 19 sub-skills, 12 subagents, 3 extensions (DataForSEO, Firecrawl, Banana). Technical SEO, E-E-A-T, schema, GEO/AEO, backlinks, local SEO, maps intelligence, Goo…
Coarse-graining of large single-cell RNA-seq data into metacells
Democratizing AI scientists with ToolUniverse
Design notes, architecture, and trade-offs for MyInvestPilot — an AI-native investment OS built with agent-driven development, DSL engine, and solo company tech stack.
Comprehensive open-source library of AI research and engineering skills for any AI model. Package the skills and your claude code/codex/gemini agent will be an AI research agent with full horsepowe…
a set of SKILLS.md for doing bioinformatics with agents like claude code
Benchmarking methods for identification of spatially variable genes