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

Forskningsoutput: TidskriftsbidragArtikel i vetenskaplig tidskrift

Abstract

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.

Detaljer

Författare
Enheter & grupper
Externa organisationer
  • Broad Institute
Forskningsområden

Ämnesklassifikation (UKÄ) – OBLIGATORISK

  • Bioinformatik och systembiologi
  • Medicinsk genetik
Originalspråkengelska
Sidor (från-till)5351-5353
Antal sidor3
TidskriftBioinformatics (Oxford, England)
Volym35
Utgåva nummer24
StatusPublished - 2019 dec 15
PublikationskategoriForskning
Peer review utfördJa