MPRAnalyze

MPRAnalyze provides a statistical framework to analyze MPRA count data, quantify enhancer activity, and perform rigorous statistical tests to identify and compare regulatory element function.

Key Features:

• Quantification of Enhancer Activity: Enables direct quantification of enhancer activity from MPRA count data.
• Classification and Comparative Analysis: Facilitates classification of active versus inactive enhancers and comparison of enhancer activities across experimental conditions and biological contexts.
• Statistical Modeling: Constructs a nested pair of generalized linear models (GLMs) that relate DNA and RNA observations and can be adjusted for diverse experimental designs.
• Rigorous Statistical Testing: Implements a comprehensive suite of statistical testing schemes to assess enhancer function and activity.

Scientific Applications:

• Regulatory Function Studies: Supports studies aimed at elucidating the regulatory functions of DNA sequences.
• Comparative Enhancer Analysis: Quantifies and compares enhancer activities across different biological conditions or experimental setups.
• Regulatory Element Identification: Identifies active regulatory elements within complex genomic datasets.
• Validation of Simulations: Enables validation of simulated MPRA experiments against published data.

Methodology:

MPRAnalyze fits a nested pair of generalized linear models (GLMs) to MPRA count data to relate DNA and RNA observations and applies statistical testing schemes.