Skip to main content

BRIE-kit: Preprocessing tool kit of BRIE in splicing analysis

Project description

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.

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


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:

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 install

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


  • Type command line briekit-event -h

Detailed manual

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


Yuanhua Huang and Guido Sanguinetti. BRIE: transcriptome-wide splicing quantification in single cells. Genome Biology, 2017; 18(1):123.

Project details

Download files

Download the file for your platform. If you're not sure which to choose, learn more about installing packages.

Source Distribution

briekit-0.2.2.tar.gz (41.8 kB view hashes)

Uploaded source

Supported by

AWS AWS Cloud computing Datadog Datadog Monitoring Fastly Fastly CDN Google Google Object Storage and Download Analytics Microsoft Microsoft PSF Sponsor Pingdom Pingdom Monitoring Sentry Sentry Error logging StatusPage StatusPage Status page