Ancestral recombination graph (ARG) data structure and operations.

Project description

arg-needle-lib

This repository contains arg-needle-lib, which implements an ARG data structure and ARG-based analyses such as genealogy-wide association.

Quickstart

Install the Python module from PyPI

Most functionality is available through a Python module which can be installed with:

pip install arg-needle-lib

This Python module is currently available on Linux and macOS.

Documentation

Please see the ARG-Needle manual for all usage instructions and documentation.

License

arg-needle-lib is distributed under the GNU General Public License v3.0 (GPLv3). For any questions or comments on arg-needle-lib, please contact Pier Palamara using <lastname>@stats.ox.ac.uk.

Acknowledgements

arg-needle-lib is developed by (in alphabetical order) Arjun Biddanda, Fergus Cooper, Árni Freyr Gunnarsson, Pier Francesco Palamara, Sinan Shi, Brian C. Zhang, and Jiazheng Zhu.

Reference

If you use this software, please cite:

B. C. Zhang, A. Biddanda, Á. F. Gunnarsson, F. Cooper, P. F. Palamara, Biobank-scale inference of ancestral recombination graphs enables genealogical analysis of complex traits. Nature Genetics, 2023.

arg-needle-lib Release Notes

v1.0.2 (2023-09-29)

Breaking changes

None

Other changes

Improve documentation.
Build Python wheels for macOS arm64 (Apple Silicon)
Build wheels for Python 3.12

v1.0.1 (2023-07-14)

Breaking changes

None

Other changes

Clean-up and release of the source code.
Improved mutation class.
Added from-to parameters to some functions.

v1.0.0 (2023-03-07)

Initial PyPI release of arg-needle-lib.

Project details

Release history Release notifications | RSS feed

This version

1.0.2

Sep 29, 2023

1.0.1

Jul 14, 2023

1.0.0

Mar 7, 2023

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