Additional Projects

htseq-count-cluster: HTSeq-count parallelization for HPC.

pymerlin: Python genetics workflow around MERLIN-style linkage analysis.

netZooPy: Network biology software contribution for PANDA and related network methods.

beRi: R environment, installation, and package management system for R.

BASHful: Bash scripts for computational biology project setup, document conversion, and workflow helpers.

OpenOmics: API for unified access to public multi-omics resources.

rinse: CLI for installing and switching R versions.

vcf-prepping: HPC scripts for VCF file manipulation and preparation.

renv: Python-style virtual environment manager for R.

rut: CLI utilities for R package and .Rprofile management.

edgePy: Python implementation of edgeR-style differential expression analysis.

ood-template-editor: Template editor for Open OnDemand app development.

cheaha-notes: Documentation site for using the UAB Cheaha compute cluster.

ood-flask-template: Flask template for Open OnDemand applications.

ood-gradio-chatbot: Open OnDemand app for launching local LLM chatbot access on HPC.

qsubmitter: R package for submitting jobs to remote SGE clusters.

jekyll-club-website: Jekyll theme for student organizations and clubs.

github-templates: Reusable GitHub repository templates for READMEs, issues, pull requests, and workflows.

uab-brand-yml: Brand configuration file for University of Alabama at Birmingham projects.

jekyll-coders-delight: Minimal Jekyll theme for code-friendly blogs with syntax highlighting and responsive design.

pkgmkr: R package scaffold generator with Git, license, README, and pkgdown setup.

repo-notes-template: Template for repo-local research notes.

flask-demo: Demo Flask template with login flow, test coverage, and simple local setup.

phd-research-template: Template for planning computational biology research projects.

base-repository-template: Base repository scaffold.

awesome-reproducible-R: Curated resources for reproducible research in R.

workshop-cheatsheet: LaTeX cheatsheet template adapted for Git and Bash workshop handouts.

cookiecutter-computational-biology: Cookiecutter template for computational biology projects.

gbs-guide: Graduate biomedical sciences guide and resource.

panda-gpu-tutorial: GPU-enabled PANDA tutorial for regulatory network modeling.

teaching-template: Template for teaching materials.

ggpubr-tutorial: Tutorial materials for publication-style R visualization.

py4ds: Python-for-data-science learning material.

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.

swc-r-reproducible-scientific-analysis: Reproducible R lesson material.

awesome-edu-perks: Curated education-related software and resources.

BioHackathons: Shared infrastructure for scientific hackathons.

awesome-academic-websites: Curated academic website examples.

ideas-for-collaboration: Public collaboration idea bank.

helpful-llm-science-prompts: Prompt patterns for scientific work.

awesome-rshiny: Curated R Shiny learning resources, examples, and tools.

hackathon-website-template: Template for hackathon websites.

git-status-checker: Utility for checking Git repository status.

harlem: R package of visualization palettes inspired by Harlem Renaissance art.

documenteR: R documentation helper tooling.

gumdrops: Small utility project.

pwdgen: Command-line password generator with configurable length and character exclusions.

myrandomutils: Personal Python utility package for small reusable helper functions.

shinySCP: Shiny project around single-cell proteomics.

nba-draft-combine-anthro: Website for browsing NBA draft combine anthropometric data in one place.

slayinthegame: Jekyll website and theme project inspired by Clean Blog.

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.

shinyPubMed: Shiny app for exploring PubMed abstracts.

docarie: Quarto documentation site for bioinformatics tools and computational biology workflows.

shinyMyGene: Shiny interface around gene-query workflows.