Projects

ProxiomeVis

An interactive Python Shiny application for processed Pixelgen Proximity Network Assay data. ProxiomeVis brings cell annotations, protein abundance, pairwise molecular proximity, and three-dimensional graph layouts into one workflow for quality assessment, clustering, colocalization, differential analysis, patch analysis, visualization, and export.

The application uses scoped data retrieval, DuckDB queries, and Parquet caching to make large proximity datasets practical to explore without requiring users to write analysis code.

scChromatic

An R package for persistent, reproducible color semantics in single-cell and other categorical biological visualizations. scChromatic stores label-to-color mappings as auditable data objects, supports relationship-aware and hierarchical color assignment, preserves important colors with explicit locks, and includes accessibility diagnostics and redundant encodings.

Documentation · Source code

ViewBS

A toolkit for visualizing high-throughput bisulfite sequencing data. ViewBS provides practical summaries and publication-ready views of DNA methylation patterns across samples, genomic regions, and experimental comparisons.

Source code · Publication

Reproducible sequencing workflows

I design and maintain production-oriented workflows for single-cell sequencing, multimodal assays, and Oxford Nanopore direct-RNA analysis. This work combines workflow engines, HPC scheduling, containers, structured quality control, automated tests, and user-facing documentation to connect research methods with reliable operations.

Current interests include isoform-aware transcript analysis, direct-RNA modification calling, and reproducible integration of short- and long-read evidence.