My work has focused on analyzing still and time-lapse microscopy data. Selected projects:
MotilityTools
An R package for analyzing cell migration data. Currently, in progress, this package will provide users with a set of functions that make analyzing motility data fast and easy. It enables users to simulate random cell migration in any number of dimensions. A snapshot of a 2D simulation for cell types with different motility parameters is depicted below. Click the image to try it in interactive mode.
SimplifyStats
An R package for simplifying pairwise hypothesis testing (available on CRAN and GitHub)
Bioi
An R package for performing single linkage clustering on spatial coordinates and for connected components analysis.
evolution
An R package for simulating gene sequence evolution.
Agent-based model of collective cell migration
This agent-based model of collective cell migration, implemented in Python, suggests that small changes in the ability of a cell to remain polarized can have a large effect on wound closure rates.