coding

In graduate school I discovered the power of using computers to make my life easier. I’ve been using R since my undergraduate days for data analysis, statistics, and general-purpose programming. As a data science intern at Continuum Analytics, I learned to flex my Python skills. I’ve recently taken up Go as well, have some experience with Julia, and have done some bash scripting in the past.

code profile

Click here for my github page.

tracking software

I use OpenCV in Python to track the fish in all my experiments. This makes data collection fast, repeatable, and precise.

The graphic below represents ~3.5 million measurements of fish locations and heading angles for one of my experiments. Darker hexagons represent regions of the tank where the fish spent more time:

tracking

Python video coder

I created a GUI python program for coding behavior data for an experiment in the Cummings lab. It allows the user to identify the location of different types of fish in a video and record the number and type of behaviors observed. I also wrote code in R that parses the resulting json data automatically creates various graphs of interest.

graphics

I find myself dissatisfied with the plotting defaults and types of plots that can be produced with base R, so I created a plotting package that implements (1) good defaults for various types of graphs and (2) adds new types of graphs with an emphasis on categorical x continuous data. See here for my thoughts and best practices for creating graphics.

example_plot

For ggplot2 users, you can find a clean theme and some nice color scales here.

analysis of RNA-seq data

I have some experience analyzing data from RNA-seq studies. See the code here.

other code

I’ve written code to do various other tasks, like coordinating two computers to show video on three-four screens simultaneously, brew beer according to a precise temperature series, scramble video stimuli for use in behavior trials (see below), and various other things.

blocks