MPRAscore: robust and non-parametric analysis of massively parallel reporter assays.

Niroula A, Ajore R, Nilsson B

Bioinformatics 35 (24) 5351-5353 [2019-12-15; online 2019-07-31]

Massively parallel reporter assays (MPRA) enable systematic screening of DNA sequence variants for effects on transcriptional activity. However, convenient analysis tools are still needed. 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. Source code (C++), precompiled binaries and data used in the paper at and Supplementary data are available at Bioinformatics online.

Abhishek Niroula

DDLS Fellow

PubMed 31359027

DOI 10.1093/bioinformatics/btz591

Crossref 10.1093/bioinformatics/btz591

pii: 5540322

Publications 9.5.0