Resource Development


rhapsodi is an R software package designed to work with low coverage single-cell DNA sequencing data from many gametes. Specifically, rhapsodi performs three sequential tasks:

  1. Phasing the haplotypes of the diploid donor from which the gametes originate
  2. Imputing the missing gamete genotypes
  3. Detecting gamete-specific meiotic crossovers

rhapsodi can be installed directly from GitHub and has been extensively benchmarked as presented in our preprint, Strict adherence to Mendel’s First Law across a large sample of human sperm genomes


In relation to my work in undergrad, I have recently begun developing an open-source, documented, and reproducible Python program that replaces the manual analyses used in the paper. Now all these analyses can be automatically performed and figures can be created, all in a fraction of the time.

Computational Human Genome Variation Modules

As part of the Johns Hopkins Center for Educational Resources (CER) Technology Fellowship, of which I am a co-fellow, and supervised by Dr. McCoy, we are developing computational modules for an undergraduate course on human genome variation. The course introduces students who have little to no coding experience to the analysis of human genomic data in the context of published papers and conclusions relevant to the course material. The computational modules that we are developing are comprehensive resources that provide biological background on each week’s topic, explore data, and then discuss the biological implications of the exploratory analysis. We expect that these modules will increase student participation and understanding. All materials will be publicly available through the lab’s website so other institutions and instructors may adapt them for their courses.