Projects
Open Source Software
I build and maintain open-source tools for problems Iโve hit myself in cancer genomics and drug-sensitivity workflows. Both are actively used outside my own projects, so I keep them documented and maintained.
vcf-reformatter
Rust Package for VCF to TSV Conversion
VEP-annotated VCF files are dense and awkward to filter or join with other tabular data. vcf-reformatter parses them into a clean, analyzable TSV, handling multi-transcript annotations and multi-allelic sites correctly. Written in Rust for speed: reduces preprocessing time by 90% over the R/Python scripts it replaced.
~1,000 downloads on Bioconda ยท 47 GitHub stars
Rust Genomics VCF TSV Variant annotation
drugsens
CRAN Package for Drug Sensitivity Analysis
Turns high-content confocal imaging of 3D drug-sensitivity assays into dose-response curves and statistics, without a manual imaging pipeline: image processing, curve fitting, and reporting in one R workflow. Built from the same assay pipeline behind the DRUGSENS platform published in npj Precision Oncology.
R Image Analysis Statistics CRAN
CRAN | GitHub | Documentation
Working on an open bioinformatics tool, or hitting the same VCF or drug-sensitivity bottlenecks these solve? Iโm happy to help or take contributions: reach out.