Software

Declaration on Use of AI

For research software, I have used Large Language Models (LLMs) for autocompletion and limited code generation. All such code has been manually reviewed line by line to ensure correctness and functionality. Software intended for non-research purposes, particularly GUI tools, may involve extensive vibe coding; such software is explicitly labeled with on this page and in the README of the corresponding software repository. All vibe-coded software has been tested against manually curated test cases.

Genetics

• collapse-bubble: Pangenome structural variations merging and deduplication.
• HarmoniSV: A toolkit to harmonize and filter structural variations across methods and samples.
• CrossLD: Cross-dataset linkage disequilibrium analysis.

Gene therapy

• COVER: Analytical tools for common variants-assisted genome-editing remedy.

Wet lab

• GelTyper: Automatic genotyping from DNA gel electrophoresis images.
• CagePlate: A Windows GUI tool for mouse management and genotyping.

Miscellaneous

• doctk: A lightweight desktop utility for everyday document-processing tasks.
• slurmtk: Lightweight Slurm tools for resource monitoring and remote development.