MPRAlib

MPRAlib is a Python library and CLI for processing MPRA (Massively Parallel Reporter Assay) data.

Citation

If you use MPRAlib in your work please cite out recent preprint:

Uniform processing and analysis of IGVF massively parallel reporter assay data with MPRAsnakeflow Jonathan D. Rosen, Arjun Devadas Vasanthakumari, Kilian Salomon, Nikola de Lange, Pyaree Mohan Dash, Pia Keukeleire, Ali Hassan, Alejandro Barrera, Martin Kircher, Michael I. Love, Max Schubach bioRxiv (2025). 2025.09.25.678548

Installation

PyPI

pip install mpralib

Conda

From the bioconda channel

conda install -c bioconda mpralib

Usage

Command Line Interface

Use the mpralib command to access various functionalities.

Validate a file

MPRAlib provides a CLI tool for validating MPRA data files against supported schemas.

mpralib validate-file <schema> --input <input_file>

• <schema>: One of reporter-sequence-design, reporter-barcode-to-element-mapping, reporter-experiment-barcode, reporter-experiment, reporter-element, reporter-variant, reporter-genomic-element, reporter-genomic-variant
• <input_file>: Path to your data file (e.g., .tsv.gz, .bed.gz)

Example:

mpralib validate-file reporter-sequence-design --input data/reporter_sequence_design.example.tsv.gz

Python API

In general MPRAlib is ment to be used as a library. Please have a look at our notebook mpralib.ipynb for a more detailed example.

License

MIT License

Links

• Documentation
• Issues