RNA-seq analysis is an essential component of modern biological research. While the use of RNA-seq to determine the gene expression of a sample is a powerful method for gaining insight into biological processes, the interpretation of the results obtained can be challenging when faced with data analyses. Here, we present BioJupies Generator, a user-friendly Jupyter Notebooks generator that enables users to quickly generate customized Jupyter Notebooks containing RNA-seq data analyses. By combining an intuitive user interface for notebook generation with options to generate custom analysis scripts, the application is designed to address the computational needs of both experimental and computational biologists.