qPCR is today the preferred method for quantitative nucleic acid analysis, and is being extensively used in routine as well as research. Proper usage of qPCR requires careful planning of the experiment including optimized design, followed by elimination of systematic noise by proper handling of controls and references, and mining of the data. This complex flow is made easy with GenEx 5.3. With GenEx a small pilot study is easily planned that will identify the sources of confounding variation to the data, aiding the design of the main experiment and estimating the number of subjects needed to secure sufficient statistical power. The measured data including relevant experimental settings and sample/assay information are then imported directly into GenEx from Roche, Agilent, Eppendorf, Bio-Rad, Life Technologies, Illumina and Fluidigm qPCR instruments eliminating the risk of introducing error by manually entering experimental parameters, where noise is reduced by proper normalization with standards and references, and prepared for statistical analysis. Then, with few clicks with the mouse on user friendly and clear panels, groups are compared using statistical tests, or patterns revealed based on powerful classification tools. All results are presented in clear and intuitive high resolved graphs ready for publication.