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BetaBinomial\n\n![tests](https://github.com/muhammedhasan/betabinomial/actions/workflows/python-app.yml/badge.svg)\n[![pypi](https://img.shields.io/pypi/v/betabinomial.svg)](https://pypi.python.org/pypi/betabinomial)\n[![Documentation Status](https://readthedocs.org/projects/betabinomial/badge/?version=latest)](https://betabinomial.readthedocs.io/en/latest/?badge=latest)\n\nImplementation of Beta-Binomial (https://en.wikipedia.org/wiki/Beta-binomial_distribution) in python for parameters inference with moment method estimation and statistical testing on count data.\n\n[Documentation](https://betabinomial.readthedocs.io/en/latest/)\n\n## Installation\n\n```\npip install betabinomial\n```\n\n## Example\n\n```python\nimport numpy as np\nfrom betabinomial import BetaBinomial, pval_adj\n\n\nbb = BetaBinomial()\n\n# total counts\nn = np.array([\n  [5, 2, 5, 6, 6],\n  [8, 8, 0, 9, 1],\n  [8, 2, 6, 1, 7]\n])\n# event count\nk = np.array([\n  [3, 1, 4, 1, 2],\n  [8, 7, 0, 9, 1],\n  [0, 0, 0, 0, 2]\n])\n\n# Infer `alpha` and `beta` parameters from counts\nbb.infer(k, n)\n\nbb.alpha\n# [[ 11.45811965]\n#  [121.01628682]\n#  [0.43620744]]\n\nbb.beta\n# [[13.332114  ]\n#  [ 4.97492014]\n#  [ 5.41047636]]\n\n# Statistical testing with inferred `alpha` and `beta`\npval = bb.pval(k, n, alternative='two-sided')\n# array([[0.33287737, 0.44653957, 0.06266123, 0.35378069, 0.85568061],\n#        [0.        , 0.53825136, 0.        , 0.        , 0.        ],\n#       [0.67209923, 0.26713023, 0.57287758, 0.14921533, 0.10535054]])\n\n# Adjust p-value with multiple testing correction\npadj = pval_adj(pval)\n# array([[0.53067103, 0.60891759, 0.18798369, 0.53067103, 0.85568061],\n#        [0.        , 0.6610126 , 0.        , 0.        , 0.        ],\n#        [0.72010631, 0.50086919, 0.6610126 , 0.31974714, 0.26337634]])\n```\n\n## Citation\n\nIf you use this package in academic publication, please cite:\n```\n@article{celik2022analysis,\n  title={Analysis of alternative polyadenylation from long-read or short-read RNA-seq with LAPA},\n  author={Celik, Muhammed Hasan and Mortazavi, Ali},\n  journal={bioRxiv},\n  year={2022},\n  publisher={Cold Spring Harbor Laboratory}\n}\n```\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fmuhammedhasan%2Fbetabinomial","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fmuhammedhasan%2Fbetabinomial","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fmuhammedhasan%2Fbetabinomial/lists"}