The article introduces qBase, a free software program for the management and automated analysis of real-time quantitative PCR (qPCR) data. qBase addresses the limitations of existing software tools by implementing advanced models and algorithms for relative quantification and inter-run calibration, along with proper error propagation. The software is designed to handle multiple reference genes, gene-specific amplification efficiencies, and run-to-run differences. It includes features such as data import from various formats, quality control checks, and visualization of normalized relative quantities (NRQs). The article also provides a detailed description of the calculation methods and formulas used in qBase, along with experimental validation and a user-friendly tutorial. qBase is freely available for non-commercial research and aims to improve the accuracy and reliability of qPCR data analysis.The article introduces qBase, a free software program for the management and automated analysis of real-time quantitative PCR (qPCR) data. qBase addresses the limitations of existing software tools by implementing advanced models and algorithms for relative quantification and inter-run calibration, along with proper error propagation. The software is designed to handle multiple reference genes, gene-specific amplification efficiencies, and run-to-run differences. It includes features such as data import from various formats, quality control checks, and visualization of normalized relative quantities (NRQs). The article also provides a detailed description of the calculation methods and formulas used in qBase, along with experimental validation and a user-friendly tutorial. qBase is freely available for non-commercial research and aims to improve the accuracy and reliability of qPCR data analysis.