Library to analyze count data of MPRA experiments.
Project description
MPRAlib
MPRAlib is a Python library and CLI for processing MPRA (Massively Parallel Reporter Assay) data.
Installation
PyPI
pip install MPRAlib
Conda
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
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