Metadata-Version: 1.0
Name: brie
Version: 0.1.4
Summary: BRIE: Bayesian regression for isoform estimate
Home-page: http://brie-rna.sourceforge.net
Author: Yuanhua Huang
Author-email: yuanhua@ebi.ac.uk
License: Apache-2.0
Description: BRIE: Bayesian Regression for Isoform Estimate
        ==============================================
        
        About BRIE
        ----------
        
        BRIE (Bayesian regression for isoform estimate) is a Bayesian method to 
        estimate isoform proportions from RNA-seq data. Currently, BRIE could take 
        sequence features to automatically learn informative prior of exon inclusion 
        ratio in  exon-skippiing events. This informative prior is very important when 
        limited data is available. In Bulk RNA-seq experiment, we could easily increase 
        the amplification to get more sequencing reads to improve the accuracy of 
        isoform estimate. However, in single cell RNA-seq (scRNA-seq) experiments, the 
        initial molecular is very limited, which always results some genes with very 
        low coverage or even drop-out. In scRNA-seq, the BRIE method, by integrating 
        informative prior, e.g. learned from sequence feature, could provide accurate 
        and reproducible estimates of splicing in single cells, as well as sensitive 
        differential analyses.
        
        
        BRIE provides following functions through command line:
        
        1. ``brie``: Estimate isoform proportions and FPKM, and calculate weights for 
        regulatory features.
        
        2. ``brie-diff``: Calculate Bayes factor of differential splicing between 
        multiple cells pair-wisely. 
        
        3. ``brie-event``: Extract the splicing events from gene annotation file in 
        gff3/gtf formate. (**Only supported in Python2**, see this issue_)
        
        4. ``brie-factor``: Fetch genentic features from genome sequence reference file 
        in fasta formate.
        
        .. _issue: https://github.com/huangyh09/brie/issues/12
        
        Quick Start
        -----------
        
        **Installation**: 
        
        - ``pip install brie``
        - or download this repository, and type ``python setup.py install``; 
        - add ``--user`` if you don't have root permission and you don't use Anaconda_.
        
        .. _Anaconda: https://www.continuum.io/anaconda-overview
        
        **Arguments**
        
        - Type command line ``brie -h``
        
        
        Detailed manual
        ---------------
        
        See the documentation_ on how to install, to use, to find the annotation data 
        etc.
        
        .. _documentation: http://brie-rna.sourceforge.net
        
        
        References
        ----------
        
        Yuanhua Huang and Guido Sanguinetti. `BRIE: transcriptome-wide splicing quantification in single cells <https://genomebiology.biomedcentral.com/articles/10.1186/s13059-017-1248-5>`_. 
        \ **Genome Biology**\, 2017; 18(1):123.
        
Keywords: splicing isoform estimate,Bayesian regression,single cell RNA-seq,Markov chain Monte Carlo
Platform: UNKNOWN
