Tool to pull gene expression from Allen Brain Institute API in Common Coordinate Framework v2 space. This code was used to obtain gene expression data for Brynildsen et al. 2020 (https://www.pnas.org/content/early/2020/07/20/2003601117).
View code/misc/packages.R to find the prerequisite packages.
Open the file pipeline.R. Set the variable basedir to a string with the local path to this repository. Then run pipeline.R in order to sequentially execute the following scripts:
- packages.R: load all packages
- directories.R: establish results folder directory structure
- process.R: create connectivity matrix and get region names. These connectivity matrices are from Oh et al. 2014, and the static data files Connectome_Contra.csv and Connectome_Ipsi.csv were generated by Mike Henderson at the University of Pennsylvania (see my other repository connectome_diffusion).
- process_ontology.R: download ABA brain structure ontology
- download_gene_expression.R: download each gene's expression for the structures in the connectivity matrix one at a time from Allen Brain API
- probenormalization_selection.R: normalize each probe's expression with a sigmoid function and average expression across all available probes for each gene
Please direct any questions to Eli D0T Cornblath @t pennmedicine dºt upenn do† edu