Genomic architecture

This repository contains the code used for the analyses described in our manuscript "Polygenic architecture of human neuroanatomical diversity" (Preprint: https://www.biorxiv.org/content/10.1101/592337v3).

We used this code to analyse the genomic architecture of neuroanatomical diversity using magnetic resonance imaging and SNP data from > 26,000 individuals.

Project organisation

The project organisation is inspired by that of the Data Science Cookie Cutter. Raw data is stored in /data/raw and converted depending on its particularities to a dataset that is stored in /data/derived. Here, the dataset /data/derived/test is provided as illustration and for testing purposes.

Instructions

Load git submodules

git submodule init
git submodule update

Install bioconda

conda config --add channels bioconda
conda config --add channels r
conda config --add channels conda-forge
conda config --add channels defaults

Create a conda environment (recommended)

conda create --name genomic-architecture python=3
conda activate genomic-architecture

Install requirements

conda install --file requirements.txt
conda install --file requirements_r.txt

Run analyses for test dataset

python3 src/00.run_all.py src/config/test.yml