Tools & Workflows

Software and tools I use for biomedical informatics and genomics research.

AI & Development

Claude (Anthropic) - Primary assistant for coding, analysis planning, and reviewing technical writing. Claude Code accelerates pipeline development and debugging.

GitHub - Version control for all projects.

Data Analysis

Python - Primary language. Heavy use of polars, numpy, scipy, statsmodels.

R - Secondary for specialized packages (MatchIt for matching, SAIGE for genetic association testing).

Jupyter - Notebooks for exploratory analysis and reproducible reporting.

Genomics & Bioinformatics

GATK - Variant calling pipelines, parallelized with GNU parallel for performance.

PLINK2 - Genetic data QC and association testing.

SAIGE - Mixed model association testing for biobank-scale data.

bcftools/samtools - VCF manipulation and processing.

Computing Infrastructure

Google Cloud - dsub for batch job orchestration on workflows at scale.

Verily Workbench - Secure analysis environment for All of Us data.

GNU parallel - Simple but powerful parallelization.

Writing & Organization

Notion - Research notes, literature tracking, project management.

Zotero - Reference management integrated with Scholia.fyi for literature review workflows.

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This page inspired by uses.tech. Last updated January 2026.