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

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

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

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

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

A knowledge graph of biomedical LLM agent systems. Open