agricola
agricola is a Python package and command-line tool for conducting genome-wide association studies (GWAS) in admixed populations. Inspired by regenie and Tractor, agricola provides a scalable, local-ancestry–aware framework that handles relatedness, population structure, and ancestry effect heterogeneity.
Full documentation can be found here
Why agricola?
Admixed individuals have unique LD patterns that can improve signal localization and improve power for population-specific causal variants. However, standard GWAS tools fail to adjust for local ancestry or model effect heterogeneity in admixed individuals.
Tools like Tractor and SAIGE-Tractor address this gap. agricola follows the same conceptual approach-performing single-variant association tests with explicit local ancestry adjustment-but combines it with:
- Accelerated linear algebra via JAX
- CUDA GPU, TPU, or CPU support for flexible compute environments
- Efficient local ancestry queries using lanctools
- Multi-phenotype modeling
- Adjustment for sample relatedness
Installation
Requirements: Python 3.10+
Install via pip:
pip install agricola
For GPU or TPU support:
pip install agricola[cuda]
pip install agricola[tpu]
1 maintainer
Download files
Download the file for your platform. If you're not sure which to choose, learn more about installing packages.
Source Distribution
Built Distribution
Filter files by name, interpreter, ABI, and platform.
If you're not sure about the file name format, learn more about wheel file names.
Copy a direct link to the current filters
File details
Details for the file agricola-0.8.0.tar.gz.
File metadata
- Download URL: agricola-0.8.0.tar.gz
- Upload date:
- Size: 26.8 kB
- Tags: Source
- Uploaded using Trusted Publishing? No
- Uploaded via:
uv/0.11.28 {"installer":{"name":"uv","version":"0.11.28","subcommand":["publish"]},"python":null,"implementation":{"name":null,"version":null},"distro":{"name":"Ubuntu","version":"24.04","id":"noble","libc":null},"system":{"name":null,"release":null},"cpu":null,"openssl_version":null,"setuptools_version":null,"rustc_version":null,"ci":true}
File hashes
| Algorithm | Hash digest | |
|---|---|---|
| SHA256 |
f008ac62a2cb6ae589582d75af26276eeee90a559645d413a3c746cab02b3428
|
|
| MD5 |
25c037f2c44c30e44d345d6e2076dfa5
|
|
| BLAKE2b-256 |
8b467017bbfeedfd78ee6657a5c7326c58ffac294ef8bc91865b9b9cdc9ccb3a
|
File details
Details for the file agricola-0.8.0-py3-none-any.whl.
File metadata
- Download URL: agricola-0.8.0-py3-none-any.whl
- Upload date:
- Size: 26.3 kB
- Tags: Python 3
- Uploaded using Trusted Publishing? No
- Uploaded via:
uv/0.11.28 {"installer":{"name":"uv","version":"0.11.28","subcommand":["publish"]},"python":null,"implementation":{"name":null,"version":null},"distro":{"name":"Ubuntu","version":"24.04","id":"noble","libc":null},"system":{"name":null,"release":null},"cpu":null,"openssl_version":null,"setuptools_version":null,"rustc_version":null,"ci":true}
File hashes
| Algorithm | Hash digest | |
|---|---|---|
| SHA256 |
b1ee5158e3465b99fcb8cb65c0e7616f7fd0a7f052f585e13d69252bd897b7bc
|
|
| MD5 |
e69668772321ca4431bdf003c2563b2a
|
|
| BLAKE2b-256 |
3d92418312f21be9232e2ed707a0e345fb0f7530c566a00a53d70a3155173bd6
|
