Optimising expression quantitative trait locus mapping workflows for single-cell studies

This repository contains scripts for the analysis of both real and simulated single-cell RNA-seq data for our paper:

Cuomo*, Alvari*, Azodi* et al, Optimizing expression quantitative trait locus mapping workflows for single-cell studies, Genome Biology (2021).

Analysis Scripts

The following folders contain scripts to reproduce the figures and analyses presented in the paper. In particular:

• Plotting Notebooks contains notebooks to reproduce our figures (both main and supplementary).

• Simulation Scripts contains scripts to estimate parameters from real data and then set up simulations). For an introduction to splatPop for simulating population scale single-cell RNA-seq data, see the vignette. splatPop is now out as a preprint!

Software Requirements

• splatter v1.17.1
• VariantAnnotation v1.36.0
• tidyverse v1.3.1
• SingleCellExperiment v1.12.0
• fitdistrplus v1.1-3
• scater v1.18.6
• data.table v1.14.0