A broader inventory of public software, tutorials, templates, and community resources. Selected work appears on the Projects page.
beRi: R environment, installation, and package management system for R.
renv: Python-style virtual environment manager for R.
rinse: CLI for installing and switching R versions.
rut: CLI utilities for R package and .Rprofile management.
OpenOmics: API for unified access to public multi-omics resources.
edgePy: Python implementation of edgeR-style differential expression analysis.
pymerlin: Python genetics workflow around MERLIN-style linkage analysis.
netZooPy: Network biology software contribution for PANDA and related network methods.
BASHful: Bash scripts for computational biology project setup, document conversion, and workflow helpers.
vcf-prepping: HPC scripts for VCF file manipulation and preparation.
htseq-count-cluster: HTSeq-count parallelization for HPC.
ood-gradio-chatbot: Open OnDemand app for launching local LLM chatbot access on HPC.
ood-template-editor: Template editor for Open OnDemand app development.
ood-flask-template: Flask template for Open OnDemand applications.
cheaha-notes: Documentation site for using the UAB Cheaha compute cluster.
qsubmitter: R package for submitting jobs to remote SGE clusters.
awesome-reproducible-R: Curated resources for reproducible research in R.
phd-research-template: Template for planning computational biology research projects.
cookiecutter-computational-biology: Cookiecutter template for computational biology projects.
base-repository-template: Base repository scaffold.
repo-notes-template: Template for repo-local research notes.
pkgmkr: R package scaffold generator with Git, license, README, and pkgdown setup.
flask-demo: Demo Flask template with login flow, test coverage, and simple local setup.
github-templates: Reusable GitHub repository templates for READMEs, issues, pull requests, and workflows.
jekyll-coders-delight: Minimal Jekyll theme for code-friendly blogs with syntax highlighting and responsive design.
workshop-cheatsheet: LaTeX cheatsheet template adapted for Git and Bash workshop handouts.
cookiecutter-pypackage-travisci: Cookiecutter template for Python packages with Travis CI.
panda-gpu-tutorial: GPU-enabled PANDA tutorial for regulatory network modeling.
swc-r-reproducible-scientific-analysis: Reproducible R lesson material.
ggpubr-tutorial: Tutorial materials for publication-style R visualization.
py4ds: Python-for-data-science learning material.
teaching-template: Template for teaching materials.
computational-biology-starter-kit: Starter kit for computational biology tooling and practices.
grad-school-app-toolkit: Templates, examples, and guides for graduate school applications in STEM and biomedical sciences.
gbs-guide: Graduate biomedical sciences guide and resource.
BioHackathons: Shared infrastructure for scientific hackathons.
hackathon-website-template: Template for hackathon websites.
awesome-academic-websites: Curated academic website examples.
awesome-edu-perks: Curated education-related software and resources.
awesome-rshiny: Curated R Shiny learning resources, examples, and tools.
helpful-llm-science-prompts: Prompt patterns for scientific work.
ideas-for-collaboration: Public collaboration idea bank.
harlem: R package of visualization palettes inspired by Harlem Renaissance art.
documenteR: R documentation helper tooling.
git-status-checker: Utility for checking Git repository status.
myrandomutils: Personal Python utility package for small reusable helper functions.
gumdrops: Small utility project.
pwdgen: Command-line password generator with configurable length and character exclusions.
docarie: Quarto documentation site for bioinformatics tools and computational biology workflows.
nba-draft-combine-anthro: Website for browsing NBA draft combine anthropometric data in one place.
r3frag.me: Astro-based static site for publishing short scientific, artistic, and threaded fragments.
escapism: Interactive p5.js beach scene designed as a calming web experience.
slayinthegame: Jekyll website and theme project inspired by Clean Blog.
shinyPubMed: Shiny app for exploring PubMed abstracts.
shinyMyGene: Shiny interface around gene-query workflows.
shinySCP: Shiny project around single-cell proteomics.