jaxQTL¤

jaxQTL is a JAX-based command-line tool and Python library for cell-type-specific eQTL mapping from donor-level single-cell pseudobulk expression. It provides Poisson and Negative Binomial count models, while also supporting Gaussian molecular phenotypes.

Try the quickstart Install jaxQTL Browse the Python API

Install¤

pip install jaxqtl
jaxqtl --help

Run the tutorial¤

The Quickstart runs ten genes from the bundled pseudobulk data and shows how to inspect the results. Choose SPA + ACAT for fast gene-level testing without permutations, or Beta permutation for permutation calibration. SPA is strongly recommended with score-test ACAT because ACAT is sensitive to variant p-value calibration.

To analyze your own data, follow the single-cell workflow from pseudobulk preparation through multiple-testing correction. The task guides cover cis, nominal, trans, and expression-PC workflows.

Support and citation¤

Report bugs and feature requests through the GitHub issue tracker. See Citation when using jaxQTL in published work.