The quantitative polymerase chain reaction (qPCR) is a versatile and popular assay for quantifying nucleic acids. With the recent expansion of the number of reactions per assay, there is a need for an accurate method to report the data suitable for automation. This book will describe such a method, based on machine learning analysis, and implement it with publicly available tools. This book is intended for researchers and will provide a detailed introduction to the programming language R, including references for the most common functions. This book will provide an advanced strategy for the objective analysis of qPCR data suitable for experts in the field and an introduction to qPCR and computational analysis for students.