viprs: Variational Inference of Polygenic Risk Scores

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viprs is a python package that implements variational inference techniques to estimate the posterior distribution of variant effect sizes conditional on the GWAS summary statistics. The package is designed to be fast and accurate, and to provide a variety of options for the user to customize the inference process. Highlighted features:

  • The coordinate ascent algorithms are written in C/C++ and cython for improved speed and efficiency.
  • The code is written in object-oriented form, allowing the user to extend and experiment with existing implementations.
  • Different priors on the effect size: Spike-and-slab, Sparse mixture, etc.
  • We also provide scripts for different hyperparameter tuning strategies, including: Grid search, Bayesian optimization, Bayesian model averaging.
  • Easy and straightforward interfaces for computing PRS from fitted models.
  • Implementation for a wide variety of evaluation metrics for both binary and continuous phenotypes.

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AI-DECLARATION: assist

This project is developed using AI-assisted technologies. Please review our AI Declaration for full transparency on automated pipelines.

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Avatar for shz9 from gravatar.com shz9

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Author: Shadi Zabad

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Python <3.14, >=3.10

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opt test docs

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Key dates

PyPI data
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  • Released:
Latest release

1 maintainer

PyPI data
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Avatar for shz9 from gravatar.com shz9

Credits

Author: Shadi Zabad

Requires

Python <3.14, >=3.10

Provides Extra

opt test docs

Classifiers

Report project as malware

Release files for viprs 0.1.4

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Source distribution (sdist)

Source distribution for viprs 0.1.4
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viprs-0.1.4.tar.gz 73.8 kB Details

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Table of built distributions (wheels) for viprs 0.1.4
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viprs-0.1.4-cp313-cp313-win_amd64.whl 408.8 kB CPython 3.13 CPython 3.13 Windows x86-64 Details
viprs-0.1.4-cp313-cp313-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl 2.6 MB CPython 3.13 CPython 3.13 Linux glibc 2.28+ x86-64, Linux glibc 2.27+ x86-64 Details
viprs-0.1.4-cp313-cp313-macosx_11_0_arm64.whl 311.5 kB CPython 3.13 CPython 3.13 macOS 11.0+ ARM64 Details
viprs-0.1.4-cp313-cp313-macosx_10_13_x86_64.whl 414.6 kB CPython 3.13 CPython 3.13 macOS 10.13+ x86-64 Details
viprs-0.1.4-cp312-cp312-win_amd64.whl 410.2 kB CPython 3.12 CPython 3.12 Windows x86-64 Details
viprs-0.1.4-cp312-cp312-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl 2.6 MB CPython 3.12 CPython 3.12 Linux glibc 2.27+ x86-64, Linux glibc 2.28+ x86-64 Details
viprs-0.1.4-cp312-cp312-macosx_11_0_arm64.whl 313.0 kB CPython 3.12 CPython 3.12 macOS 11.0+ ARM64 Details
viprs-0.1.4-cp312-cp312-macosx_10_13_x86_64.whl 416.4 kB CPython 3.12 CPython 3.12 macOS 10.13+ x86-64 Details
viprs-0.1.4-cp311-cp311-win_amd64.whl 405.2 kB CPython 3.11 CPython 3.11 Windows x86-64 Details
viprs-0.1.4-cp311-cp311-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl 2.6 MB CPython 3.11 CPython 3.11 Linux glibc 2.28+ x86-64, Linux glibc 2.27+ x86-64 Details
viprs-0.1.4-cp311-cp311-macosx_11_0_arm64.whl 312.1 kB CPython 3.11 CPython 3.11 macOS 11.0+ ARM64 Details
viprs-0.1.4-cp311-cp311-macosx_10_9_x86_64.whl 414.8 kB CPython 3.11 CPython 3.11 macOS 10.9+ x86-64 Details
viprs-0.1.4-cp310-cp310-win_amd64.whl 404.8 kB CPython 3.10 CPython 3.10 Windows x86-64 Details
viprs-0.1.4-cp310-cp310-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl 2.6 MB CPython 3.10 CPython 3.10 Linux glibc 2.28+ x86-64, Linux glibc 2.27+ x86-64 Details
viprs-0.1.4-cp310-cp310-macosx_11_0_arm64.whl 312.7 kB CPython 3.10 CPython 3.10 macOS 11.0+ ARM64 Details
viprs-0.1.4-cp310-cp310-macosx_10_9_x86_64.whl 415.5 kB CPython 3.10 CPython 3.10 macOS 10.9+ x86-64 Details

Total release size: 15.0 MB

Release files / viprs-0.1.4.tar.gz

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0.1.4 This release

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0.1.3

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0.1.2

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0.1.1

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0.1.0

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0.0.4

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0.0.3

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0.0.1

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