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:
Rosen JD, Vasanthakumari AD, Salomon K, de Lange N, Dash PM, Keukeleire P, Hassan A, Barrera A, Krupkin B, Oualline G, Kircher M, Love MI, Schubach M. Uniform processing and analysis of IGVF massively parallel reporter assay data with MPRAsnakeflow. Genome Research (2025). doi: 10.1101/gr.281462.125
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 ofreporter-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
1 maintainer
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