BRIE-kit

Preprocessing tool kit of BRIE project in splicing analysis

Why BRIE-kit

The purpose of move some utility functions from BRIE main package into this tool kit is that brie-event is only supported by Python 2 (see issue). Therefore, we keep a few pre-processing tools into this package and BRIE main package can focus on splicing quantification and downstream analysis.

Therefore, use BRIE-kit in Python 2 environment only for full fucntions.

.. _BRIE: https://github.com/huangyh09/brie .. _issue: https://github.com/huangyh09/brie/issues/12

Supported fucntions

BRIE-kit provides following functions through command line, which are upgraded from BRIE main package:

1. briekit-event: Extract the splicing events from gene annotation file in gff3/gtf formate.

2. briekit-event-filter: Filter exon-skipping events by setting thresholds.

3. briekit-factor: Fetch genentic features from genome sequence reference file in fasta formate.

Quick Start

Installation

BRIE-kit is developed under Python 2.7 environment, and not full compatible with Python 3, so please use it in Python2 environment. If you are using Python3 in Anaconda 3, you can simply create a conda environment with Python=2.7:

.. code-block:: bash

conda create -n briekit python=2.7 numpy=1.13.0

source activate briekit

Once you are in a Python 2 environment, there are two ways to isntall:

• Opt 1: Type in terminal: pip install briekit. Add -U if you want to upgrade your earlier installation.
• Opt 2: Download the GitHub repository_, and type python setup.py install

Note, if you don't use Anaconda_ and don't have root permission, add --user, so you can install it in your folder.

.. _conda: https://conda.io/docs/user-guide/tasks/manage-environments.html .. _Anaconda: https://anaconda.org .. _repository: https://github.com/huangyh09/briekit

Arguments

• Type command line briekit-event -h

Detailed manual

See the Wiki_ documentation on how to install, to use, to find the annotation data etc.

.. _Wiki: https://github.com/huangyh09/briekit/wiki

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.