awesome-single-cell
The field's reference list of software and data resources for single-cell analysis — one of the most-starred curated resources in computational biology.GitHub
Physician-scientist — open software and data for cancer research.
For over a decade I've built open tools, curated the public biomedical record, and now build AI agents that help researchers find and use it. The resources I maintain are used widely across genomics, and core Bioconductor packages I steward bridge the field's largest data archives.
The field's reference list of software and data resources for single-cell analysis — one of the most-starred curated resources in computational biology.GitHub
The bridge between the NCBI Gene Expression Omnibus and Bioconductor — a foundational R package I've maintained for years, used across the genomics community.Docs
A continuously refreshed index of the world's public sequencing metadata — SRA, GEO, and BioProject — served as open columnar snapshots and a query API.Docs
A knowledge base and conversational agent over the NIH Common Fund Data Ecosystem — ask across programs, grants, and datasets in plain language.Open
Uniformly processed human microbiome data with curated, standardized metadata — a widely used resource in the Bioconductor ecosystem.Open
Hosted, reproducible training environments for hands-on bioinformatics education — one-click workspaces the community can teach and learn in.Open
Manuscript-as-software: the manubot pattern, ergonomically, on Quarto.
Coordinated AI capabilities for manuscripts, grants, and review.
An MCP server for the EBI Ontology Lookup Service.
A brief introduction to agentic coding principles and practice.
Design patterns of agentic AI in scholarly writing.
An opinionated, agentic life-OS for Claude Code.
Build reports, package metadata, and download stats for Bioconductor.
A community list of cancer clinical knowledge bases and databases.
Observability and web callbacks for Nextflow workflows.
Bulk access to NCI State Cancer Profiles data.
Spec-first, ontology-grounded reproduction of sample-level metadata.
A knowledge graph of biomedical LLM agent systems.
Data Science for Biologists: A Hands-On Introduction with R and Bioconductor
An instructional book grown from ~100 trainees across four course offerings.
Implementing AI at an Academic Medical Center
A working book on AI governance and adoption in academic medicine.
Peer-reviewed publications across genomics, informatics, and cancer data science.
Notes — release notes, build logs, and short technical pieces on the tools, data, and methods behind this work.
LLMs with Retrieval-Augmented Generation (RAG)
How retrieval grounds large language models, with a NotebookLM walkthrough.
A Brief History of AI in Medicine
From early expert systems to modern foundation models, for a clinical audience.
Lightweight Comparative Analysis of Data Formats
Trade-offs across common storage formats for scientific data at scale.
Language for Computers: Word Embeddings
Word embeddings as the representational basis for large language models.
All talks & teaching — a 2022–2025 archive, mostly AI/ML in medicine and data science.
Much of the data-infrastructure work above lives under an open program,Cancer Data Science — OmicIDX, CFDE Atlas, curated datasets, and more.
cancerdatasci.orgI'm a physician-scientist and Professor of Medicine at the University of Colorado Anschutz Medical Campus, where I'm Associate Director for Informatics and Data Science in the Comprehensive Cancer Center and Deputy Director of the Center for Health AI.
I build open data infrastructure and AI tooling for cancer research, maintain long-standing software in the Bioconductor project, and help lead community open-science efforts. Reach me through any of the channels below.