GEOquery
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 Paper
Sean Davis
Physician-scientist — open software and data for cancer research.
- MD, PhD · Professor of Medicine and Biomedical Informatics, University of Colorado Anschutz Medical Campus
- Rifkin Bennis Chair of Cancer Informatics
- Associate Director for Informatics and Data Science, University of Colorado Cancer Center
For almost two decades I've built open tools, curated the public biomedical record, and now build AI agents that help researchers find and use it. Core Bioconductor packages I steward bridge the field's largest data archives: in 2025, GEOquery alone was downloaded 314,396 times from 112,736 distinct IP addresses.
Selected work
Community resources, core software, and data infrastructure.
OmicIDX
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
CFDE Atlas
A knowledge base and conversational agent over the NIH Common Fund Data Ecosystem — ask across programs, grants, and datasets in plain language. Open
curatedMetagenomicData
Uniformly processed human microbiome data with curated, standardized metadata — a widely used resource in the Bioconductor ecosystem. Bioconductor Paper
Orchestra
Hosted, reproducible training environments for hands-on bioinformatics education — one-click workspaces the community can teach and learn in. Open
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
More software
A selection — the full list lives on GitHub.
AI & agentic tooling
quartobot 5★
Manuscript-as-software: the manubot pattern, ergonomically, on Quarto.
scriptorium 3★
Coordinated AI capabilities for manuscripts, grants, and review.
ols-mcp-server 26★
An MCP server for the EBI Ontology Lookup Service.
agentic-coding-intro 46★
A brief introduction to agentic coding principles and practice.
agentic-writing-patterns 2★
Design patterns of agentic AI in scholarly writing.
lifeos-template 24★
An opinionated, agentic life-OS for Claude Code.
Bioconductor & data tools
BiocPkgTools 22★
Build reports, package metadata, and download stats for Bioconductor.
GenomicDataCommons
Query and download data and metadata from the NCI Genomic Data Commons in R.
GenomicSuperSignature
Interpret RNA-seq experiments by comparing them to models built from public data.
SRAdb
Query NCBI Sequence Read Archive metadata from R through a SQLite database.
GEOmetadb
Query NCBI GEO sample metadata from R through a SQLite database.
methylumi
Data structures and tools for Illumina methylation arrays in R.
ACME
Enrichment calling for tiling microarrays such as ChIP-chip and DNase-chip.
awesome-cancer-variant-resources 335★
A community list of cancer clinical knowledge bases and databases.
nextflow_telemetry 5★
Observability and web callbacks for Nextflow workflows.
state-cancer-profile-scraper 5★
Bulk access to NCI State Cancer Profiles data.
metacurator
Spec-first, ontology-grounded reproduction of sample-level metadata.
biomedical-agent-kg 9★
A knowledge graph of biomedical LLM agent systems.
Apps
Full project directory — every project in one place, with where each one is hosted.
Writing
Books, manuscripts, and methods.
Book
Data Science for Biologists: A Hands-On Introduction with R and Bioconductor
An instructional book grown from ~100 trainees across four course offerings.
Book
Implementing AI at an Academic Medical Center
A working book on AI governance and adoption in academic medicine.
Publications
Peer-reviewed publications across genomics, informatics, and cancer data science. Full record on ORCID.
Notes — release notes, build logs, and short technical pieces on the tools, data, and methods behind this work.
Talks & teaching
Lectures from the Frontiers of AI in Medicine course and invited talks.
talks.seandavis.net — the full archive, 2022–present, mostly AI/ML in medicine and data science.