This repository contains scripts for data processing, analysis and figure generation for our paper introducing SAIGE-QTL, a new method for single-cell eQTL mapping:
Zhou*, Cuomo*, et al. Efficient and accurate mixed model association tool for single-cell eQTL analysis, medRxiv, 2024.
The following folders contain scripts for data processing and analysis.
A short description can be found below:
- Plotting notebooks: notebooks to reproduce all figures, main and supplementary.
- SAIGE-QTL runners: example scripts to run SAIGE-QTL on HPC.
- downstream analyses: scripts to summarise data and results using R.
- preprocessing scripts: scripts for preprocessing and input files generation.
- TensorQTL runners: preprocessing scripts and runners for TensorQTL on HPC.
- SMR: summary-based Mendelian Randomisation.