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Updated: Jan 21, 2026

Massively Parallel Reporter Assays in Cultured Mammalian Cells
Published on: August 17, 2014
MPRAscore: robust and non-parametric analysis of massively parallel reporter assays
Abhishek Niroula1,2, Ram Ajore1, Björn Nilsson1,2
1Department of Laboratory Medicine, Lund University, 221 84 Lund, Sweden.
Motivation:
Massively parallel reporter assays (MPRA) enable systematic screening of DNA sequence variants for effects on transcriptional activity. However, convenient analysis tools are still needed.
Results:
We introduce MPRAscore, a novel tool to infer allele-specific effects on transcription from MPRA data. MPRAscore uses a weighted, variance-regularized method to calculate variant effect sizes robustly, and a permutation approach to test for significance without assuming normality or independence.
Availability And Implementation:
Source code (C++), precompiled binaries and data used in the paper at https://github.com/abhisheknrl/MPRAscore and https://www.ncbi.nlm.nih.gov/bioproject/PRJNA554195.
Supplementary Information:
Supplementary data are available at Bioinformatics online.
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