Sean Davis

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

A community-maintained repository of cancer clinical knowledge bases and databases focused on cancer variants.

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

The bridge between the NCBI Gene Expression Omnibus and Bioconductor

Computable build reports, package metadata, and download stats from the Bioconductor project

A brief introduction to agentic coding principles and practice

Convert, explore, and manipulate GFF and GTF files (used in bioinformatics) using a sqlite-based approach

Elastic, reproducible, and reusable genomic data science tools from R backed by cloud resources

A model context protocol (MCP) server for the EBI Ontology Lookup Service (OLS)

Git mirror of Bioconductor SRAdb package

An opinionated, agentic life-OS for Claude Code — a markdown vault with daily/weekly/quarterly review skills baked in. Includes the feedback layer most templates skip.

R Interface to the NCBI SRA metadata

Community-maintained list of resources that the CI4CC organization and the larger cancer informatics community have found useful or are developing.

workshop platform provider for running docker containers on kubernetes

Tools for producing pseudo-cgh of next-generation sequencing data

Fork of https://code.google.com/p/ngs-analysis

Machine learning use cases for teaching

Overview repo for the omicidx project -- start here!

Develop and host GitHub actions for Bioconductor

Software for manipulating and visualizing Complete Genomics data, with a focus on cancer

An instructional/experiential book using R and Bioconductor.

docker image containing postgresql and zombodb (pre-installed)

Curated Metagenomics Data Nextflow workflows

Generated knowledge graph of biomedical LLM agent systems

A lightweight introduction to NextFlow, a workflow description language and engine for (mainly) bioinformatics workflows. Leverages notebooks for easy teaching.

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Next Gen Sequencing Utilities

Introduction to R

gpt-examples

fastapi google oauth example

Book -- Implementing AI at an Academic Medical Center

Github mirror of the GEOmetadb bioconductor package

NGS pipelines

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Python web api for nextflow web callbacks

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

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

My .emacs.d directory

Access the NIH ClinicalTrials.gov REST API

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Learning and teaching materials for R and Bioconductor

GeneTrack is a genomic data visualization software

Tools for next-generation sequencing in use at the CCR/NCI

An R data package for the COSMIC database

An agentic scriptorium for scholarly writing — coordinated AI capabilities for manuscripts, grants, and reviews.

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R package for accessing NCBI EUtilities

Python wrapper -- and more -- for Aaron Quinlan's BEDTools (bioinformatics tools)

Collection of emacs extensions specifically collected for python development, with workflow guidelines!

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Bioconductor Spatial Data and Image Analysis Hackathon — Venice, April 2026 — manuscript source (Quarto)

Design patterns of agentic AI in scholarly writing — narrative-review paper + lit review wiki. PRISMA-trAIce-compliant; senior author Sean Davis, Claude (Anthropic) as postdoc-equivalent collaborator.

React Application to robustly check if drugs are FDA approved.

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

Longitudinal Bioc build database

An introduction to RNA-seq file formats, quality control, and visualization targeted to a biologist audience

The bridge between refine.bio and Bioconductor

Terraform for allowing gcp Vertex AI for a user

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An example RNAseq pipeline with snakemake on the NIH biowulf cluster

A curated list of awesome deep learning applications in the field of computational biology

Project for publishing from Bioconductor to F1000R and back

SV detection from paired end reads mapping

Mysqldump, writing in postgresql format

The missing package manager for OS X.

AJAX Genome Browser

Definitions for a reStructuredText code-block directive using pygments, and scripts to render HTML and LaTeX.

HTML5 canvas genomic graphics library

python access to UCSC genomes database

A quick & dirty git-powered Sinatra wiki

A JavaScript visualization library for HTML and SVG.

Tools for the NIH's Helix and Biowulf system

Various teaching material

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

A simple xml-to-csv parser for Foundation Medicine XML reports

:clipboard: A Python Parser for PubMed Open-Access XML Subset and MEDLINE XML Dataset

Bioconductor Hubs API

worker for running curatedmetagenomicsdata nextflow pipelines

University of Colorado Cancer Center COE data

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Website for the Human Microbiome Compendium

A DSL for data-driven computational pipelines

Docker Containers for Bioconductor - NEW!

Animal Image Shared Resource PACS/Viewer

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File system based on the SSH File Transfer Protocol

ATACseqQC tutorials for BioC 2019 workshop

A small website generator for a conference that uses a google sheet to populate abstracts.

OpenAlex research-intelligence pipeline + UCCC cancer-center dashboard, API, and full-text search

Public repository for cFMD - curatedFoodMetagenomicData

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

Sources for a Bioc2026 workshop on ontology for genomic data science with ontoProc2

Visualizations for the CFDE Marker Paper 2026

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

Chat-first exploration of Colorado cancer data — public ECCO API → DuckDB snapshot → Gemini + Vega-Lite tools

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Capture information regarding CU clinical genomics efforts

Prefect/Python ELT for CFDE evaluation data (data layer for seandavi/cfde-atlas)

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The ACME Bioconductor Package

Small app for taking a short list of pubmed ids, fetching icite data, and then chatting with it.

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ETL processing for the output from pipeline processing of cmgd

SQLMesh is a data transformation framework that brings the benefits of DevOps to data teams. It enables data scientists, analysts, and engineers to efficiently run and deploy data transformations written in SQL or Python.

Simple traefik and oauth proxy for backend cfde app. Temporary fix.

Maintain a time series dataset of r universe builds.

Colorado Cancer Catchment information portal

GitHub copilot skill to generate a repository summary for funder

ETL for icc-eval-core metrics collection

Categorized views of R package repositories

Repository for allowing autonomous coding agents to experiment and build

Sample Metadata Curation for curatedMetagenomicData

pg_lake: Postgres with Iceberg and data lake access

Random code experiments

R client for accessing the omicidx database

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Template for building a bioconductor workshop package using github actions

Telemetry for curated metagenomics workflows

Migrate annotationhub and experimenthub sqlite databases to postgres

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Apogee: An AI-Powered Grant Evaluation Ecosystem

Pipelines for cmgd data engineering

Reporting infrastructure for CFDE Centers, DCCs, and Partnerships

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Testing scripts for Bioconductor codespaces

Serve multiple R2 buckets from the same Worker, with different settings

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Notebooks for fun

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Example project demonstrating how to implement GraphRAG

Course materials for Anschutz School of Medicine Frontier of AI in Medicine course

Animation engine for explanatory math videos

(WIP) Tools for collecting and reporting CFDE metrics

Examples for deploying applications with PGO, the Postgres Operator from Crunchy Data

Formatted datasets for Machine Learning With R by Brett Lantz

Intro to R for BigCare 2024

Web portal and API for the Curated Metagenomics Data project

R for Reproducible Scientific Analysis

R vignettes/pkgdown for elementary statistics for a summer course

Tooling for working with clinvar in Bioconductor

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Files for manuscript Resources for Interpreting Variants in Precision Genomic Oncology Applications

'Small project to set up an existing project for using VertexAI using terraform and then testing via python'

Example repo for authenticating to GCP from ghactions

A curated list of static web site generators.

Bibliometrics for Bioconductor package publications

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Notebooks using the Hugging Face libraries 🤗

blog

Brief introduction to SQL using quarto, duckdb, and R

An open source sandbox project exploring dbt workflows via a fictional sandwich shop's data.

Brief overview of JSON data and web tech for course at CUNY

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Polars integration for Dagster

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dadbod.vim: Modern database interface for Vim

For submitting and tracking Orchestra training platform contributions

Home page for CSHL Statistical Methods for Genome Scale Data, 2023 edition

load flatiron zip file deliveries to slowflake data warehouse

Repository holding a wiki for Research Computing tutorials

A launch point for your personal nvim configuration

B2AITeamingScratchpad

CLI tool for dbt users adopting analytics engineering best practices.

ncbi_mesh_parser

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Web services for interrogating various omics-related resources and returning results as json responses.

A LaTeX class implementing the new NIH Biographical Sketch Format

A package to transform all OBO ontologies into KGX TSV format and OBO json, and put the transformed graph in KGhub

A collection of Python clients and accessory scripts for interacting with the Cromwell

RAD Lab enables users to deploy infrastructure on Google Cloud Platform (GCP) to support specific use cases. Infrastructure is created and managed through Terraform in conjunction with support scripts written in Python. The templates, code, and documentation for each use case are bundled into modules.

Bioc2022 brief talk on ontology and ontoProc

Automatically exported from code.google.com/p/gitinspector

Tooing to extract and pubmed and medline to cloud

Random notes/notebook

Collection of terraform examples

Dynamic Open API (Swagger) Client for R

CU Anschutz Course IMMU6110, introduction to bioinformatics for Department of Immunology and Microbiology

Demo for Flask, Django, and Starlette OAuth clients with Authlib>=v0.13

just a simple POC using pulumi for GCP at Anschutz

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Code for classifying unstructured text to tissue ontology terms using natural language processing and machine learning.

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University of Colorado Cancer Center Reporter

SQL database, API, and related functions for curatedMetagenomicData

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R Package Client for Curated Metagenomics Web Portal and API

template for vue frontends

API for linked biological knowledge

Data Ingestion Pipeline for Monarch

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Curated applications for Kubernetes

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