The contents of this repository contain code for redoing analyses of Bergmann et al. The code is split into two parts:
- Bioinformatics analyses (primarily in R) in the `Bioinformatics' folder
This folder contains code used to process the data, as well as various code for loading and analysnig the data, producing plots etc.
- A custom MATLAB package for loading and interogating the spatial data in the `SpatialModelling' folder.
This is code for loading in and visualising gene expression in 1D/2D/3D, as well as projecting other sources of data on to the embryos.
To run these datasets processed data can be downloaded from XXXX or by running the shell script in the Data folder and unzipping the contents.