Software

I develop open-source tools for analyzing and visualizing cancer genomes and creating cancer vaccines GitHub.

Transcriptome Explorer

A web app for visualization of gene isoforms derived from long-read sequencing

fishplot

An R package for drawing "fish plots" that visualize changes in the clonal architecture of a tumor over time. BMC Genomics, 2016.

SciClone

Github Paper

An R package for inferring the clonal architecture of tumors, and tracking their evolution over time. PLoS Computational Biology, 2014.

VAtools

Github Docs Paper (submitted)

submitted to JOSS, 2026.

pVACtools

Github Docs Paper

A Computational Toolkit to Identify and Visualize Cancer Neoantigens. Cancer Immunol Res, 2020.

bam-readcount

Github Paper

Rapid generation of base-pair-resolution sequence metrics from BAM files. Journal of Open Source Software, 2022.

ReadDepth

Github Paper

A parallel R package for detecting copy-number alterations from short sequencing reads. PLoS ONE, 2011.

copyCat

Github

A parallel R package for detecting somatic copy-number alterations from whole-genome sequencing data.

RMEmod

Github Paper

A tool for discovering functional modules by identifying recurrent and mutually exclusive mutational patterns in tumors. BMC Medical Genomics, 2011.

Contributions

Other tools I've contributed to:

pVACview - neoantigen prediction and prioritization for personalized cancer vaccines.
WashU Analysis workflows - End-to-end CWL workflows for turning genomic data into insight.
ImmunoNX - a bioinformatics workflow to support personalized neoantigen vaccine trials.
MGIbio Docker containers - Dozens of docker containers that make bioinformatics software available in the cloud
Genome Modeling System - a knowledge-management platform for genomics.
DGIdb - a drug/gene interaction database.
VarScan 2 - somatic mutation and copy-number discovery from exome data.