EasyqpcR

EasyqpcR computes amplification efficiencies, relative quantities with standard errors, and normalized relative quantities using reference-gene selection to provide accurate qPCR-based gene expression quantification.

Key Features:

• Data Import and Management: Imports qPCR data files into Bioconductor-compatible data structures.
• Hellemans et al. (2007) algorithms: Implements the qPCR analysis algorithms published by Hellemans et al. (2007).
• Amplification Efficiency Calculation: Calculates amplification efficiencies for qPCR assays.
• Relative Quantities and Standard Errors: Computes relative quantities (RQs) of gene expression and their associated standard errors.
• Normalization Using Best Reference Genes: Identifies optimal reference genes using the SLqPCR package and applies them for normalization.
• Normalized Relative Quantities (NRQs): Calculates normalized relative quantities scaled to user-defined controls with standard errors.

Scientific Applications:

• Gene Expression Analysis: Provides efficiency-corrected and normalized quantification for accurate gene expression studies.
• Validation Studies: Supplies amplification efficiencies and error estimates to support validation of qPCR results against other assays.
• Comparative Genomics: Enables comparison of gene expression across species, tissues, or experimental conditions using normalized data.

Methodology:

Implements algorithms from Hellemans et al. (2007); calculates amplification efficiencies, relative quantities, and standard errors; selects reference genes via SLqPCR for normalization; computes NRQs scaled to user-defined controls; integrates with Bioconductor data structures.