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        "author": "Yuanhua Huang",
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        "description": "|PyPI| |Docs| |Build Status|\n\n.. |PyPI| image:: https://img.shields.io/pypi/v/brie.svg\n    :target: https://pypi.org/project/brie\n.. |Docs| image:: https://readthedocs.org/projects/brie/badge/?version=latest\n   :target: https://brie.readthedocs.io\n.. |Build Status| image:: https://travis-ci.org/huangyh09/brie.svg?branch=master\n   :target: https://travis-ci.org/huangyh09/brie\n\n\nBRIE: Bayesian Regression for Isoform Estimate\n==============================================\n\nAbout BRIE\n----------\n\nBRIE (Bayesian regression for isoform estimate) is a Bayesian method to \nestimate isoform proportions from RNA-seq data. Currently, BRIE could take \nsequence features to automatically learn informative prior of exon inclusion \nratio in  exon-skippiing events. This informative prior is very important when \nlimited data is available. In Bulk RNA-seq experiment, we could easily increase \nthe amplification to get more sequencing reads to improve the accuracy of \nisoform estimate. However, in single cell RNA-seq (scRNA-seq) experiments, the \ninitial molecular is very limited, which always results some genes with very \nlow coverage or even drop-out. In scRNA-seq, the BRIE method, by integrating \ninformative prior, e.g. learned from sequence feature, could provide accurate \nand reproducible estimates of splicing in single cells, as well as sensitive \ndifferential analyses.\n\n\nBRIE provides following functions through command line:\n\n1. ``brie``: Estimate isoform proportions and FPKM, and calculate weights for \nregulatory features.\n\n2. ``brie-diff``: Calculate Bayes factor of differential splicing between \nmultiple cells pair-wisely. \n\nQuick Start\n-----------\n\n**Installation**: \n\n- ``pip install brie``\n- or download this repository, and type ``python setup.py install``; \n- add ``--user`` if you don't have root permission and you don't use Anaconda_.\n\n.. _Anaconda: https://www.continuum.io/anaconda-overview\n\n**Arguments**\n\n- Type command line ``brie -h``\n\n\nDetailed manual\n---------------\n\nSee the documentation_ on how to install, to use, to find the annotation data \netc.\n\n.. _documentation: https://brie.readthedocs.io\n\n\nReferences\n----------\n\nYuanhua Huang and Guido Sanguinetti. `BRIE: transcriptome-wide splicing quantification in single cells <https://genomebiology.biomedcentral.com/articles/10.1186/s13059-017-1248-5>`_. \n\\ **Genome Biology**\\, 2017; 18(1):123.",
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