mpra

mpra provides preprocessing, statistical analysis, and experimental design evaluation for massively parallel reporter assays (MPRAs) to quantify functional effects of noncoding genetic variation.

Key Features:

• Data Management: Handles MPRA datasets from raw counts through analysis-ready formats for downstream processing.
• Count Preprocessing: Implements normalization and transformation steps for barcode and count data prior to statistical analysis.
• Differential Analysis: Performs differential expression analysis to identify differences in reporter activity between experimental conditions.
• mpralm method: Provides the calibrated mpralm statistical approach tailored for MPRA data and evaluated across multiple datasets.
• Barcode Summarization: Investigates theoretical and empirical properties of barcode summarization techniques and their impact on results.
• Power Analysis: Conducts power analysis demonstrating that replicate number strongly influences power (recommending at least four replicates per condition) while sequencing depth has a lesser impact.

Scientific Applications:

• Functional assessment of noncoding variants: Identify and quantify the regulatory impact of noncoding genetic variation using reporter activity measurements.
• Gene regulation and expression studies: Characterize activity of regulatory sequences and condition-specific effects on expression.
• Genomics, epigenetics, and disease mechanisms: Support investigations linking noncoding variation to regulatory mechanisms, disease biology, and personalized medicine.

Methodology:

Computational methods explicitly include count preprocessing with normalization and transformation, differential expression analysis, the calibrated mpralm statistical method, theoretical and empirical evaluation of barcode summarization, and power analysis assessing replicate number (≥4 recommended) versus sequencing depth.