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 and also supports Gaussian molecular phenotypes.

Zhang, Z., Kim, A., Suboc, N., Mancuso, N., and Gazal, S. (2025). Efficient count-based models improve power and robustness for large-scale single-cell eQTL mapping. medRxiv (https://www.medrxiv.org/content/10.1101/2025.01.18.25320755v2)

Read the documentation

Installation

jaxQTL requires Python 3.11 or newer.

pip install jaxqtl
jaxqtl --help

Quick example

From a repository checkout, run a cis scan over the bundled tutorial data:

jaxqtl cis \
  --bfile tutorial/input/chr22_N100 \
  --pheno tutorial/input/CD4_NC.N100.bed.gz \
  --covar tutorial/input/donor_features.tsv \
  --gene-list tutorial/input/genelist_10 \
  --model nb \
  --test score \
  --set-offset-from-libsize \
  --normalize-covar \
  --nperm 1000 \
  --out tutorial/output/quickstart

The command writes tutorial/output/quickstart.cis.score.perm.parquet.gz.

The documentation covers the single-cell cis-eQTL workflow, the tutorial, input formats, mapping workflows, and output interpretation.

Development

See the development setup for environment, test, and documentation build instructions.

Citation and support

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

Download files

Download the file for your platform. If you're not sure which to choose, learn more about installing packages.

Source Distribution

jaxqtl-0.2.0.tar.gz (52.9 kB view details)

Uploaded Aug 24, 2026 Source

Built Distribution

If you're not sure about the file name format, learn more about wheel file names.

The dropdown lists show the available interpreters, ABIs, and platforms. Enable javascript to be able to filter the list of wheel files.

jaxqtl-0.2.0-py3-none-any.whl (66.7 kB view details)

Uploaded Aug 24, 2026 Python 3

File details

Details for the file jaxqtl-0.2.0.tar.gz.

File metadata

Download URL: jaxqtl-0.2.0.tar.gz
Upload date: Aug 24, 2026
Size: 52.9 kB
Tags: Source
Uploaded using Trusted Publishing? Yes
Uploaded via: twine/7.0.0 CPython/3.13.14

File hashes

Hashes for jaxqtl-0.2.0.tar.gz
Algorithm	Hash digest
SHA256	`cda23fad96f24437c4ccd839dcf191885772914b0547b2eb1275f4ab574a2cdf`
MD5	`66746a6e1be7bd218e8ce1605c30d9e9`
BLAKE2b-256	`50d272f351564c92fa0a1976eecb79ca47c2bea5d31d8431ec0e3cf718e1317d`

See more details on using hashes here.

Provenance

The following attestation bundles were made for jaxqtl-0.2.0.tar.gz:

Publisher: release.yml on mancusolab/jaxqtl

Attestations: Values shown here reflect the state when the release was signed and may no longer be current.

Statement:
- Statement type: https://in-toto.io/Statement/v1
- Predicate type: https://docs.pypi.org/attestations/publish/v1
- Subject name: jaxqtl-0.2.0.tar.gz
- Subject digest: cda23fad96f24437c4ccd839dcf191885772914b0547b2eb1275f4ab574a2cdf
- Sigstore transparency entry: 2581882698
- Sigstore integration time: Aug 24, 2026
Source repository:
- Permalink: mancusolab/jaxqtl@1e31bb9ec239ef6a8d9ea1f55b26bb0ccbef4843
- Branch / Tag: refs/heads/main
- Owner: https://github.com/mancusolab
- Access: public
Publication detail:
- Token Issuer: https://token.actions.githubusercontent.com
- Runner Environment: github-hosted
- Publication workflow: release.yml@1e31bb9ec239ef6a8d9ea1f55b26bb0ccbef4843
- Trigger Event: workflow_dispatch