Software
Computational Tools
RNA Analysis Software
Open-source tools for RNA variant discovery, RNA editing, and transcriptome-scale analysis.
I develop production-ready bioinformatics methods in Python, including packaging and distribution workflows for reproducible research software. I am also proficient in R and Bash for scalable analysis pipelines and rapid prototyping.
View GitHub ProfileisoLASER
Role: Lead developer
isoLASER performs variant calling, haplotyping, and allele-specific splicing analysis in long-read RNA-sequencing data. This one-stop solution enables classification of genetically regulated splicing events, revealing transcriptome-wide regulation patterns and disease-relevant isoform regulation, including the HLA gene family and Alzheimer's disease risk genes. Built in Python and available on GitHub and PyPI.
scAllele
Role: Lead developer
scAllele is an integrative tool that performs high-confidence calls of small variants in single-cell RNA-sequencing data. It also enables allele-specific splicing analysis, a feature not previously used at single-cell resolution, allowing identification of cell-type and cancer-specific splicing regulation in our studies. Built in Python and available on GitHub and PyPI.
L-GIREMI
Role: Contributor
L-GIREMI uses a robust statistical approach based on mutual information for detecting A-to-I RNA editing in long-read RNA sequencing data, unveiling insights about the distribution of editing sites on individual RNA molecules. Built in Python and available on GitHub.
BEAPR
Role: Contributor
BEAPR identifies allele-specific binding events in eCLIP-seq data to functionally characterize genetic variants. By modeling crosslinking-induced sequence propensity and variation between replicated experiments, BEAPR achieves high-accuracy calls and identifies clinically relevant variants. Built in C++ and R and available on GitHub.