Authors: A.I. Luppi, Z-Q. Liu, J.Y. Hansen, R. Cofre, M. Niu, E. Kuzmin, S. Froudist-Walsh, N. Palomero-Gallagher, & B. Misic.
This repository provides code to reproduce the main results of Luppi et al., "Benchmarking macaque brain gene expression for horizontal and vertical translation." bioRxiv (2024) (preprint).
It was developed in MATLAB 2019a by Andrea Luppi from the the Network Neuroscience Lab at the Montreal Neurological Institute, McGill University.
This code relies on MATLAB code from the BrainSpace Toolbox for MATLAB by Vos de Wael et al. (2020) Communications Biology. The essential functions are included in this repo to ensure standalone functionality. For additional plotting functionality, also include in your MATLAB path the ENIGMA Toolbox by Lariviere et al. (2021) Nature Methods.
The study investigates the spatial correspondence of cortical patterns of gene expression in the macaque, against (i) protein density in the macaque cortex (vertical translation); and (ii) gene expression in the human cortex (horizontal translation).
The main file is Luppi_macaque_brain_gene_translation_code_4GitHub.m This script should work out of the box, if run from the parent directory. To run, ensure you are in the main directory of the repo.
The data folder contains all the data you need to make this code run.
The utils folder contains support functions called by the main script, including some third-party code.