Overview

This application provides an interactive browser for single-cell expression quantitative trait loci (sc-eQTLs) mapped across multiple tissues and cell types.

Features

• Browsable, filterable table of LD-clumped independent eQTL signals
• Regional Manhattan plots of nominal eQTL associations
• Variance-explained analysis across all cell types
• Genotype-expression boxplots for top effector cell types

Data

eQTLs were mapped using TensorQTL on pseudobulked single-cell RNA-seq data. Independent signals were identified via conditional analysis and LD-clumped.

Security

This application runs on institutional infrastructure behind a firewall. No data leaves the server. Optional login authentication via shinymanager can be enabled for additional access control.

How to use

1. Use the sidebar filters to narrow down eQTLs by gene, tissue, cell type category, annotation level, or q-value.
2. Browse the table and sort by any column.
3. Click on a row to visualise the eQTL:
• Left panel: Regional Manhattan plot showing all nominal associations in a window around the lead variant.
• Right panel: Variance-explained scatter plot (R² vs median expression) across cell types, plus genotype boxplots for the top effector cell types.
4. Use the download button to export the filtered table as CSV.

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Built with R Shiny + bslib + DT + ggplot2