j-bac / GTEx_analysis

GTEx analysis

To reproduce analyses, first download the data from GTEx website and GENCODE or from the drive folder

Then create the conda environment with:

conda env create -f gtex.yml

The analysis is then reproduced by running two notebooks and one script in the analysis folder. If preferred, notebooks can be executed as scripts using nbconvert. The full pipeline is then performed by:

conda activate gtex
jupyter nbconvert --execute --to notebook 0_load_data_subset.ipynb
Rscript 1_yarn_normalize.R
jupyter nbconvert --execute --to notebook 2_specificity_analysis.ipynb