MPRAnalyze

MPRAnalyze is a statistical framework to analyze Massively Parallel Reporter Assay (MPRA) count data. MPRAs enable the measurement of regulatory function for thousands of DNA sequences in a single experiment. The tool provides a unified framework for quantifying the regulatory activity of sequences, comparing activities across different conditions, and accommodating the evolving nature of the field. MPRAnalyze is demonstrated to be accurate and applicable through simulations and analyses of published data.

Topic

Transcription factors and regulatory sites;Functional, regulatory and non-coding RNA;RNA-Seq

Detail

  • Operation: Quantification;Enrichment analysis;Community profiling

  • Software interface: Command-line user interface

  • Language: R

  • License: The GNU General Public License v3.0

  • Cost: Free

  • Version name: 1.20.0

  • Credit: The National Human Genome Research Institute (NHGRI).

  • Input: -

  • Output: -

  • Contact: Tal Ashuach tal_ashuach@berkeley.edu

  • Collection: -

  • Maturity: Stable

Publications

  • MPRAnalyze: statistical framework for massively parallel reporter assays.
  • Ashuach T, et al. MPRAnalyze: statistical framework for massively parallel reporter assays. MPRAnalyze: statistical framework for massively parallel reporter assays. 2019; 20:183. doi: 10.1186/s13059-019-1787-z
  • https://doi.org/10.1186/S13059-019-1787-Z
  • PMID: 31477158
  • PMC: PMC6717970

Download and documentation

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