Research-intelligence & impact analytics for the Bioconductor ecosystem (DuckDB + Parquet, lake-sourced enrichment)

Curated Metagenomics Data Nextflow workflows

CDSCI data lake: shared DuckLake (Postgres catalog + R2) ingest for biomedical sources (RePORTER, iCite, ctgov, PMC, SCP, census, OpenAlex)

Personal portfolio hub for seandavis.net — open software and data for cancer research

Bioconductor's standalone package build system on GitHub Actions: configuration-driven build and check workflows for every package type, feeding the bioc-registry data plane

Next-generation bioconductor.org: static Astro build fed by a data pipeline over primary sources (r-universe, the site git repo, the bioc-prop data plane)

Serving side of bioconductor.org: Cloudflare Worker + R2 mirror

Bioconductor build manifest: one YAML per package the build system is authorized to build, plus the policy file. The trust root; changes by human PR.

The Bioconductor package registry: metadata, propagated versions, installable artifacts, provenance, and build/check state behind one HTTP API

Maintain a time series dataset of r universe builds.

A personal work queue over GitHub issues, PRs and manual tasks, with an append-only event log and an enforced state machine.

Community-curated list of software packages and data resources for single-cell, including RNA-seq, ATAC-seq, etc.

Spec-first toolkit for reproducing curated, ontology-grounded, sample-level metadata from publications, with a no-hallucination contract.

Python web api for nextflow web callbacks

How bioconductor.org is built, served, and being replaced — and the decisions behind it

Static SCIP code-intelligence indexer for R packages (tree-sitter, optional R runtime for deeper symbol resolution)

Shared, durable memory for coding agents (Claude Code, Codex, pi, omp and any MCP client) across projects and machines — MCP + CLI over SQLite

biocOnIce: a cloud-native biological annotation and data resource catalog for Bioconductor, served as Apache Iceberg tables behind icegate

cancerOnIce (Catchment Lake): population cancer data as Apache Iceberg tables keyed on geography and time, every source release kept queryable; served behind icegate

Overview repo for the omicidx project -- start here!

Bulk access and download state cancer profiles data. See the releases link for latest data.

R client for accessing the omicidx database

University of Colorado Cancer Center PubMed Grader — append NIH iCite metrics to a CSV of PubMed IDs and surface a summary dashboard.

CFDE evaluation metrics chatbot — ad hoc queries against grants, pubs, code, and analytics data, keyed by NIH core project

Book -- Implementing AI at an Academic Medical Center

An R package with over 50 highly cited, read-to-use, up-to-date COVID-19 pandemic data resources

Editable, version-controlled figures for Quarto: 18 agent-authorable formats (Excalidraw, Vega-Lite, Graphviz, PlantUML, ...) rendered at build time with caching and native figure semantics