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

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. Bioconductor Paper

Hosted, reproducible training environments for hands-on bioinformatics education — one-click workspaces the community can teach and learn in. Open

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

Append NIH iCite metrics to a set of PubMed IDs. Open

Robustly check whether a drug is FDA approved. Open

Public datasets and derived files, served from R2. Open

Manuscript-as-software: the manubot pattern, ergonomically, on Quarto. Docs

Coordinated AI capabilities for manuscripts, grants, and review. Docs

An MCP server for the EBI Ontology Lookup Service. GitHub

A brief introduction to agentic coding principles and practice. GitHub

Design patterns of agentic AI in scholarly writing. GitHub

An opinionated, agentic life-OS for Claude Code. GitHub

Build reports, package metadata, and download stats for Bioconductor. Docs Paper

Query and download data and metadata from the NCI Genomic Data Commons in R. Docs Paper

Interpret RNA-seq experiments by comparing them to models built from public data. Bioconductor Paper

Query NCBI Sequence Read Archive metadata from R through a SQLite database. Bioconductor Paper

Query NCBI GEO sample metadata from R through a SQLite database. Bioconductor Paper

Data structures and tools for Illumina methylation arrays in R. Bioconductor

Enrichment calling for tiling microarrays such as ChIP-chip and DNase-chip. Bioconductor Paper

A community list of cancer clinical knowledge bases and databases. GitHub

Observability and web callbacks for Nextflow workflows. GitHub

Bulk access to NCI State Cancer Profiles data. GitHub Paper

Spec-first, ontology-grounded reproduction of sample-level metadata. GitHub

A knowledge graph of biomedical LLM agent systems. Open