xQTL-AD-Loci-Explore

Interactive Shiny app for browsing xQTL evidence at Alzheimer's disease GWAS loci.

Live app: https://jenny-empawi.shinyapps.io/xQTL-AD-loci-Explore/

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Overview

This app visualises results from the FunGen-xQTL consortium ADSP Functional Genomics pipeline, linking AD GWAS variants to molecular QTL evidence across brain cell types.

Data contents (current build)

• 4,817 rows — one per variant × gene pair with xQTL evidence
• Sources: Brain eQTL · Brain pQTL · Brain gpQTL · Excitatory / Inhibitory / Oligodendrocyte / OPC / Astrocyte / Microglia / Bulk Immune eQTL · MiGA eQTL (GFM, GTS, SVZ, THA)
• Trans xQTL: 2,263 loci with at least one trans-acting gene

Features

• Filter by chromosome, GWAS study, significance level, confidence level, cell type, and functional evidence (TWAS / MR / cTWAS)
• Toggle individual cell-type columns on/off
• Side detail panel per variant — shows evidence contexts, cell type breakdown, and trans xQTL target genes
• Download filtered results as CSV

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Repository structure

File/Folder	Description
app.R	Shiny app source (R)
data.csv	Processed display data (generated from flat file pipeline)
DEPLOY.md	Step-by-step deployment instructions
data/	Jupyter notebook + Excel summary table

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Updating the data

Re-run AD_loci_xQTL_table_updated.ipynb on the cluster with the latest flat file, then re-deploy to shinyapps.io:

rsconnect::deployApp(appDir = ".", appName = "xQTL-AD-loci-Explore", account = "jenny-empawi")

See DEPLOY.md for full instructions.

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Citation / Contact

FunGen-xQTL Consortium · ADSP Functional Genomics