eQTL searching with biocXqtl

Vincent J. Carey, stvjc at channing.harvard.edu

January 06, 2026

Introduction

eQTLs are genetic loci exhibiting association with gene expression.

Consortia have produced catalogs of eQTLs based on various cohorts and experimental procedures.

• EBI eQTL catalog
• eQTLGen; a related project with single-cell experiments is sc-eqtlGen

biocXqtl facilitates flexible analyses for genetics of variation in molecular phenotypes. In this vignette we review analytic results for 455 GEUVADIS samples.

tensorQTL example

library(biocXqtl)

## Warning: package 'GenomicRanges' was built under R version 4.5.2

## Warning: replacing previous import 'BiocGenerics::type' by 'arrow::type' when
## loading 'biocXqtl'

library(arrow)

## Warning: package 'arrow' was built under R version 4.5.2

library(dplyr)
library(DT)
tens = example_tensorQTL()
tens |> arrange(pval_nominal) |> head(10) |> 
    as.data.frame() |> datatable()