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

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TY - JOUR

T1 - MPRAscore

T2 - robust and non-parametric analysis of massively parallel reporter assays

AU - Niroula, Abhishek

AU - Ajore, Ram

AU - Nilsson, Björn

PY - 2019/12/15

Y1 - 2019/12/15

N2 - 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.

AB - 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.

UR - http://www.scopus.com/inward/record.url?scp=85077774150&partnerID=8YFLogxK

U2 - 10.1093/bioinformatics/btz591

DO - 10.1093/bioinformatics/btz591

M3 - Article

C2 - 31359027

AN - SCOPUS:85077774150

VL - 35

SP - 5351

EP - 5353

JO - Bioinformatics

JF - Bioinformatics

SN - 1367-4803

IS - 24

ER -