Ribonucleotide triphosphate (rNTP) incorporation in DNA is a general phenomenon in many species. The rNTPs are misincorporated by DNA polymerases and become embedded ribonucleotide monophosphates (rNMPs) in DNA. Revealing patterns and preferences of embedded rNMPs is an important topic in the field of genome stability and DNA biology. Hence, we developed the RibosePreferenceAnalysis software to identify rNTP incorporation preferences and study the genomic contexts of the embedded rNMPs. This software is an easy-to-use tool for researchers who are interested in embedded rNMP data and provides useful results to study rNTP incorporation, embedded rNMP removal, and rNMP functionality.