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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 https://github.com/abhisheknrl/MPRAscore and https://www.ncbi.nlm.nih.gov/bioproject/PRJNA554195. Supplementary data are available at Bioinformatics online.
PubMed 31359027
DOI 10.1093/bioinformatics/btz591
Crossref 10.1093/bioinformatics/btz591
pii: 5540322