U.S. Department of Health and Human ServicesHHS National Institutes of HealthNIH National Center for Advancing Translational SciencesNCATS

SEQUIN is an R/Shiny framework for rapid and reproducible analysis of RNA-seq data

Posted on March 14th, 2023 by Hannah Baskir

Claire Weber 1 4, Marissa B. Hirst 2 4, Ben Ernest 2, Nicholas J. Schaub 3, Kelli M. Wilson 3, Ke Wang 3, Hannah M. Baskir 1, Pei-Hsuan Chu 1, Carlos A. Tristan 1, Ilyas SingeƧ 1 5

1National Center for Advancing Translational Sciences (NCATS), Division of Preclinical Innovation, Stem Cell Translation Laboratory (SCTL), National Institutes of Health (NIH), 9800 Medical Center Drive, Rockville, MD 20850, USA
2Rancho Biosciences, 16955 Via Del Campo, #200, San Diego, CA 92127, USA
3National Center for Advancing Translational Sciences (NCATS), National Institutes of Health (NIH), 9800 Medical Center Drive, Rockville, MD 20850, USA
4These authors contributed equally
5Lead contact


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 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. Hence, SEQUIN helps democratize and increase the throughput of interrogating biological questions using next-generation sequencing data with single-cell resolution.