BYASE

A library that uses Bayesian inference to identify gene-level and isoform-level ASE (Allele-specific expression) in polyploid (diploid or higher) organisms from single-end or paired-end RNA-seq data.

Installation

BYASE is released as a Python package which requires Python 3.6 or higher to be installed on the computer.

To install BYASE, some Python packages that BYASE depends on should be installed first. In order to to successfully compile some of the packages, several system libraries should be pre-installed. For example, on Ubuntu 18.04, these libraries may need to be installed:

sudo apt install zlib1g-dev libbz2-dev liblzma-dev

Then, use pip to install dependent packages:

pip3 install --user numpy scipy pandas cython
pip3 install --user pymc3 pyarrow
pip3 install --user pysam htseq

Then, use pip to install BYASE:

pip3 install --user byase

After the installation, if you cannot run byase from the terminal, this is caused by the executable binary file byase not being found in the system path, you may need to run:

export PATH=~/.local/bin:$PATH

To use the plotting module, matplotlib should also be installed:

pip3 install --user matplotlib

If BYASE is run on a server or cluster system, the plotting module may not be used, then the installation of package matplotlib can be ignored, because some problem may be encountered during the installation of matplotlib on such systems.

Documentation

The documentation of BYASE can be found here.