Bioinformatics and genomics software

  1. Aneuvis is a github web application for analyzing chromosomal variation in single cells. A local Desktop app created using electronJS is available for Mac. Code: github   Paper: github   Tutorial: aneuvis   Website: github

  2. Oncomix is an R package for identifying oncogene candidates based on gene expression patterns in tumor and adjacent normal tissue. Code: github oncomix   Paper: github   Press: github

  3. ReceptLoss is an R package for identifying tumor suppressor candidates based on gene expression patterns in tumor and adjacent normal tissue. Code: github

Other sofware

  1. abbreviatoR is a github web application for automatically generating an alphabetized list of abbreviations for a thesis or manuscript. Just copy-paste from Word or Excel into the text box! Code: github Website: github

  2. mnemonifAI is a github web application that automatically generates mnemonics from 2 text inputs. Data is stored on a Google Sheets backend. Website: github

  3. The clinical flow tracking sheet tracks clinic progress in real time. Designed for use in the ECHO free clinic. Created using sheets & sheets . Website: github

Data-containing software packages

  1. knudson is an github data package that contains a machine-readable form of Table 1 from Alfred Knudson’s classic paper describing the two-hit cancer hypothesis (Knudson, 1971). A vignette recreates Figure 1 from the data in Table 1. Code: github   Talk @ SatRday Neuchâtel (03/2020): knudson

  2. pecase is an github data package containing a list of all winners of the presidential early career award for scientists and engineers from 1996 through 2017. Code: github

  3. hotdog is an R package containing data from Nathan’s Hot Dog Eating contest from 2002-2019.

Data visualization

  • Medical care in pregnancy - A timeline displaying the diseases, interventions, immunizations, and required screenings (y-axis) across the various weeks of pregnancy (x axis). Made with github + ppt . Code: github


  • Parasite lifecycle in humans - Where do parasites travel in the human body? Beginning with the mode of transmission (“0”), shows the order of infection (“1”, “2”, etc.) within organs with commonly-tested parasites on USMLE. Made using github + ppt + ppt


  • Metabolic networks in microbial communities - Inspired by this talk (@ 2:56) ) ppt


  • Motor spinal cord tract - A schematic of the descending (i.e. motor) spinal cord tract. Tip: Remember ‘motwor’ for the two-neuron motor system. ppt

sp cord mtr

  • Sensory spinal cord tracts - A schematic of the two major ascending (i.e. sensory) spinal cord tracts. The dorsal column-medial lemniscal (DCML) pathway carries fine touch, vibration, and proprioception. The spinothalamic (ST) track can be subdivided (not shown) into anterior (crude touch/pressure) and lateral (pain/temp) ST tracks. Tip: Remember ‘sensothree’ for the three-neuron sensory system. ppt

sp cord sens

  • Mood and psychotic disorders - visualization comparing and contrasting mood (e.g. major depressive disorder + bipolar I) and psychotic (e.g. schizophrenia) disorders. ppt

psych disorders

ss and rd

ego def

  • Hemoglobinopathies - diagram demonstrating the relationship of hemoglobinopathies to the hemoglobin molecule (heme + globin). Made using ppt .

ss and rd


  • Dietary sugars - diagram demonstrating the different types of dietary sugars, and how they are each composed of 3 sugar building blocks (Fructose, Glucose, and Galactose). ppt

dietary sugars


  • Extrapyramidal Side Effects (EPS) of Antipsychotics - diagram demonstrating the different extrapyramidal side effects and treatments associated with taking antipsychotic medications. Mnemonics included. ppt


Other Contributions

  1. Automated emails and scheduler for Jacobi’s MSTP Continuity clinic - Helped repair automated weekly email software (original code by Tommy Wilson, MD, PhD) - javascript, google apps script

Open source contributions

  1. Awesome reproducible research list on github