SEQUIN is a web-based application (app) that allows fast and intuitive analysis of RNA-sequencing data derived for model organisms, tissues, and single cells. Integrated app functions enable uploading datasets, quality control, gene set enrichment, data visualization, and differential gene expression analysis. We also developed the iPSC Profiler, a practical gene module scoring tool that helps to measure and compare pluripotent and differentiated cell types. Benchmarking to other commercial and non-commercial products underscored several advantages of SEQUIN. Freely available to the public, SEQUIN empowers scientists using interdisciplinary methods to investigate and present transcriptome data firsthand with state-of-the-art statistical methods. SEQUIN helps to democratize and increase the throughput of interrogating biological questions using next-generation sequencing data with single-cell resolution. See also the Github repository: https://github.com/ncats/public_sequin