Starred repositories
AI agents, automations and apps that run your operations. Model agnostic.
Swap GPT for any LLM by changing a single line of code. Xinference lets you run open-source, speech, and multimodal models on cloud, on-prem, or your laptop — all through one unified, production-re…
Multiplatform plotting library based on the Grammar of Graphics
Interactive Data Visualization in the browser, from Python
spatial transcriptomics analysis pipeline
Technology-invariant pipeline for spatial omics analysis that scales to millions of cells (Xenium / Visium HD / MERSCOPE / CosMx / PhenoCycler / MACSima / etc)
rapids-singlecell: GPU-accelerated framework for scRNA analysis
Graph-based foundation model for spatial transcriptomics data. Zero-shot spatial domain inference, batch-effect correction, and many other features.
Scripts and utilities for automatic processing & management of Illumina NGS sequencing data within the Bioinformatics Core Facility at the University of Manchester
is an open-source LIMS (laboratory Information Management System) for Next Generation Sequencing sample management, statistics and reports, and bioinformatics analysis service management.
A Python package to manage protein design workflows on computing clusters and local machines. Documentation can be found here: https://protflow.readthedocs.io/en/latest/
This is the development home of the workflow management system Snakemake. For general information, see
Define and run multi-container applications with Docker
Single-cell analysis in Python. Scales to >100M cells.
Autonomous agentic system for supervised machine learning model development.
🦖 ClawBio — The first bioinformatics-native AI agent skill library. Local-first. Reproducible. Built on OpenClaw.
The official repository for NOVA, a deep learning framework designed for high-throughput organellar phenotyping of perturbed human neurons using AI-driven methodologies
Use Garry Tan's exact Claude Code setup: 23 opinionated tools that serve as CEO, Designer, Eng Manager, Release Manager, Doc Engineer, and QA
A Zotero plugin for syncing items and notes into Notion
A general, evolvable, and distributed agent framework & harness for data science.
f.k.a. Awesome ChatGPT Prompts. Share, discover, and collect prompts from the community. Free and open source — self-host for your organization with complete privacy.
A curated list of awesome AI tools, libraries, papers, datasets, and frameworks that accelerate scientific discovery — from physics and chemistry to biology, materials, and beyond.
Combining multimodality histopathology images for integrated cancer research
a generalist algorithm for cellular segmentation with human-in-the-loop capabilities