Welcome to BrainGENIE!

Developed using
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R version 3.5.2 (2018-12-20)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS Mojave 10.14.5
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Clone this repository with:

git clone https://github.com/hessJ/BrainGENIE

Install dependencies for BrainGENIE with the command in console:

Rscript install.R

Current: Download paired blood & brain normalized (residual) gene expression data from GTEx version 10 release:

https://zenodo.org/records/17068862/files/braingenie_gtexv10_dataset.tar.gz?download=1

Old: Download paired blood & brain normalized (residual) gene expression data from GTEx version 8 release:

https://zenodo.org/record/6350240/files/normalized_expression_dat_gtexv8.tar.gz?download=1

Extract the data from the compressed tar archive with the following command in terminal:

tar -xzvf braingenie_gtexv10_dataset.tar.gz <-- Current

tar -xzvf normalized_expression_dat_gtexv8.tar.gz <-- Old

Vignette for getting started:

https://github.com/hessJ/BrainGENIE/wiki/How-to-run-BrainGENIE

#### Normalization of transcriptome-wide gene expression data from GTEx v8:
1. Kept genes with ≥5 read counts ≥10 samples &  RPKM ≥ 0.1 in ≥10 samples
2. Quantile normalization of RPKM values
3. Inverse normal transformation
4. Regressed covariates out of expression data, used residuals for model training cross-validation
 - Brain: Age, sex, top three genotype-based principal components, PCR method, platform, ischemic time, RIN, and death record by Hardy  scale.
 - Blood: Age, sex, top three genotype-based principal components, top three CIBERSORT principal components, PCR method, platform, ischemic time, RIN, and death record by Hardy  scale.