News and events from BioInfoRx and the communities
February 24, 2023

News: RNASequest: An end-to-end reproducible RNAseq data analysis and publishing framework

BioInfoRx and Biogen have collaborated to release RNASequest, a new RNA sequencing (RNA-seq) analysis and publishing framework. The framework has been published in the Journal of Molecular Biology and is available as open-source software to support reproducibility and the widespread adoption of RNAseq data analysis. RNASequest is a customizable and user-friendly framework that integrates with Quickomics, an omics data visualization tool, to provide a three-in-one ecosystem for RNAseq data analysis, app management, and result publishing. Quickomics, another open-source tool from our group, was published in Bioinfomatics in 2021.

RNASequest automates the differential gene expression analysis step and includes a built-in covariate testing module, making statistical model design easier. The framework also comes with a web-based tool, ShinyOne, to manage apps powered by Quickomics and reports generated by running the pipeline on multiple projects in one place. RNASequest presents results in multiple user-friendly formats, including an online Bookdown, a slide deck, and an interactive app, making it accessible to a wide range of researchers with varying levels of bioinformatics expertise.

RNASequest was designed with usability in mind, and we wanted to make it easy for researchers to use and adapt it to their own needs. By releasing it as open-source software on Github (, we hope to encourage crowd contribution and enable researchers to use it for their private data analysis. Researchers can explore demo datasets processed by RNASequest hosted online, and follow the online tutorial to learn how to use the pipeline.

For researchers who require expert support for RNASequest and QuickOmics, BioInfoRx offers RNA-Seq data analysis and visualization services with these advanced tools through the BxGenomics product.

For further information, please contact us at (608) 467-4936 or