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eQTL strategies in the lab

A lot of us have and will be mapping eQTLs across a number of projects. This is intended as resource to know which packages you should run and why, and points to the relevant instructions to get you started.

Matrix eQTL

Matrix eQTL package

For pseudobulk

SAIGE-QTL

SAIGE-QTL package

For single-cell expression profiles, and set-based tests (as well as single-variant ones)

RASQUAL

RASQUAL

For few individuals

CellRegMap

CellRegMap

for context-specific eQTLs