https://github.com/huangyh09/brie

BRIE: Bayesian Regression for Isoform Estimate in Single Cells
https://github.com/huangyh09/brie

alternative-splicing differential-momentum-gene differential-splicing isoform-quantification rna-seq single-cell variantional-inference

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BRIE: Bayesian Regression for Isoform Estimate in Single Cells

• Host: GitHub
• URL: https://github.com/huangyh09/brie
• Owner: huangyh09
• License: apache-2.0
• Created: 2016-12-14T14:34:06.000Z (over 9 years ago)
• Default Branch: master
• Last Pushed: 2024-06-17T03:35:13.000Z (almost 2 years ago)
• Last Synced: 2025-09-14T04:51:34.991Z (9 months ago)
• Topics: alternative-splicing, differential-momentum-gene, differential-splicing, isoform-quantification, rna-seq, single-cell, variantional-inference
• Language: Python
• Homepage: https://brie.readthedocs.io
• Size: 1.72 MB
• Stars: 42
• Watchers: 8
• Forks: 15
• Open Issues: 27
• Metadata Files:
  • Readme: README.rst
  • License: LICENSE

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README

          
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.. |PyPI| image:: https://img.shields.io/pypi/v/brie.svg

    :target: https://pypi.org/project/brie

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   :target: https://brie.readthedocs.io

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   :target: https://travis-ci.org/huangyh09/brie

BRIE: Bayesian Regression for Isoform Estimate

==============================================

Top News

--------

* [29/05/2022] We have released v2.2 that fully supports counting droplet-based 

  data for both Skipping Exon events and other types of splcing events. See the

  `brie-count manual `_

* [29/05/2022] We have include small-sized test data sets (15MB) for both 

  smart-seq2 and 10x Genomics. See data in `brie-tutorials/tests repo 

  `_

About BRIE

----------

Welcome to the new BRIE (>=2.0 or BRIE2), Bayesian Regression for Isoform 

Estimate, a scalable Bayesian method to accurately identify splicing phenotypes 

in single-cell RNA-seq experiments and quantify isoform proportions and their 

uncertainty.

BRIE2 supports the analysis of splicing processes at two molecular levels, 

either between alternative splicing isoforms or between unspliced and spliced 

RNAs. In either case, it returns cell-by-event or cell-by-gene matrices of PSI 

value and its 95% confidence interval (quantification) and the statistics for 

detecting DAS and DMG on each event or gene:

1. **Differential alternative splicing (DAS):** This task is to quantify the 

   proportions of alternative splicing isoforms and to detect DAS between groups

   of cells or along with a continuous covariate, e.g., pseudotime. 

   BRIE2 is designed for two-isoform splicing events with a focus on exon 

   skipping, but in principle also applicable for mutual exclusion, 

   intron-retaining, alternative poly-A site, 3' splice site and 5' splice site.

2. **Differential momentum genes (DMG):** This task is to quantify the 

   proportions of unspliced and spliced RNAs in each gene and each cell. 

   Similar to DAS, the DMG is a principled selection of genes that capture 

   heterogeneity in transcriptional kinetics between cell groups, e.g., cell 

   types, or continuous cell covariates, hence may enhance the RNA velocity 

   analyses by focusing on dynamics informed genes.

Installation

============

BRIE2 is available through PyPI_. To install, type the following command 

line, and add ``-U`` for upgrading:

.. code-block:: bash

  pip install -U brie

Alternatively, you can install from this GitHub repository for the latest (often 

development) version with the following command line

.. code-block:: bash

  pip install -U git+https://github.com/huangyh09/brie

In either case, add ``--user`` if you don't have the write permission for your 

Python environment.

For more instructions, see the installation_ manual.

.. _PyPI: https://pypi.org/project/brie

.. _installation: https://brie.readthedocs.io/en/latest/install.html

Manual and examples

===================

* The full manual is at https://brie.readthedocs.io 

* More examples and tutorials: https://github.com/huangyh09/brie-tutorials

In short, there are two steps for running BRIE2. 

First, obtain cell-by-gene or cell-by-event count matrices for each isoform. 

For the exon-skipping event, you can run ``brie-count``, which will return count 

matrices and hdf5 file for AnnData. 

For spliced and unspliced matrices, we listed a few options in the manual_.

Then you can use ``brie-quant`` to perform quantification of splicing ratio and 

detect differential alternative splicing or differential momentum genes. 

Type command line ``brie-count -h`` and ``brie-quant -h`` to see the full 

arguments.

.. _manual: https://brie.readthedocs.io/en/latest/quick_start.html#step1-read-counts

References

==========

* Yuanhua Huang and Guido Sanguinetti. `BRIE2: computational identification of 

  splicing phenotypes from single-cell transcriptomic experiments

  `_.

  \ **Genome Biology**\, 2021; 22(1):251.

* Yuanhua Huang and Guido Sanguinetti. `BRIE: transcriptome-wide splicing 

  quantification in single cells 

  `_. 

  \ **Genome Biology**\, 2017; 18(1):123.