RSeQC

Requirements

• Python 3.9 or later
• pip

Check your Python and pip installations:

python3 --version
python3 -m pip --version

Example:

Python 3.11.13
pip 25.3 from /path/to/lib/python3.11/site-packages/pip (python 3.11)

If pip is not installed, follow the official installation instructions:

https://pip.pypa.io/en/stable/installation/

(Optional) Create a Virtual Environment

Using a virtual environment is recommended to keep RSeQC and its dependencies isolated from other Python packages.

Create a new environment:

python3 -m venv rseqc_env

Activate it:

Linux/macOS

source rseqc_env/bin/activate

Windows (PowerShell)

rseqc_env\Scripts\Activate.ps1

Install RSeQC

Install the latest stable release from PyPI

python3 -m pip install rseqc

Install the latest development version from GitHub

python3 -m pip install git+https://github.com/liguowang/RSeQC.git

You can also install a specific branch, tag, or commit.

Install a specific branch:

python3 -m pip install git+https://github.com/liguowang/RSeQC.git@main

Install a specific release tag:

python3 -m pip install git+https://github.com/liguowang/RSeQC.git@v5.0.6

Upgrade RSeQC

Upgrade an existing installation from PyPI:

python3 -m pip install --upgrade rseqc

To upgrade a GitHub installation:

python3 -m pip install --upgrade git+https://github.com/liguowang/RSeQC.git

Uninstall RSeQC

Remove RSeQC:

python3 -m pip uninstall rseqc

Verify the Installation

Check that RSeQC is installed correctly:

bam_stat.py --help

or

python3 -c "from importlib.metadata import version; print('RSeQC', version('RSeQC'))"

License

RSeQC is licensed under the GNU General Public License v3.0 or later (GPL-3.0-or-later).

See the LICENSE file included with this project for the complete license text.

Documentation

Documentation and tutorials are available at:

1. http://rseqc.sourceforge.net/
2. https://www.lwang.org/RSeQC/

References

1. Wang L, Wang S, Li W. RSeQC: quality control of RNA-seq experiments. Bioinformatics. 2012;28(16):2184-2185. doi:10.1093/bioinformatics/bts356
2. Wang L, Nie J, Sicotte H, et al. Measure transcript integrity using RNA-seq data. BMC Bioinformatics. 2016;17:58. doi:10.1186/s12859-016-0922-z