Analysis scripts for seismic

seismic is a computationally efficient, powerful, and interpretable approach for identifying associations between complex traits and cell type-specific expression using GWAS summary statistics and single-cell RNA-seq data. This repository contains all code and scripts required for reproducing the results and figures of the paper, Disentangling associations between complex traits and cell types with seismic.

All data for reproducing the analyses can be found on zenodo. We recommend downloading these files and unzipping into this base directory before proceeding. All file paths will assume that downloaded all_data file from zenodo is unzipped and placed under this repo's parent directory.

Scripts are located in the src folder and are divided into the following directories:

• analysis: scripts for performing seismic analysis on various datasets.
• causal-sim: scripts for simulating trait-specific gene expression in cell groups and evaluating the performance of different cell type-trait association detection methods
• data-cleaning: scripts for preparing the expression data sets from raw data downloaded directly from their respective sources
• extra: scripts for extra experiments that analyze the performance of seismic
• method-compare: scripts for running other methods for baseline comparison
• null-sim: scripts for performing null simulations to assess the calibration of different cell type-trait association frameworks
• plot-figure: scripts for generating all the figures in the paper
• runtime: scripts for evaluating the runtime performance of seismic and other cell type-trait association frameworks
• tools: accessory scripts to facilitate data processing, annotation, and analysis

Basic setup

The seismic framework is available as an R package seismicGWAS. Please refer to the package and accompanying vignette for more about usage, requirements, and installation. To quickly install the package in R use devtools:

devtools::install_github("ylaboratory/seismicGWAS")

Other requirements including other tool prerequisites are located in the README files in respective subdirectories.

We refer users to the seismicGWAS repo for detailed instructions on how to preprocess your own data and run seismic on your own data.