GranatumX: A Community-engaging, Modularized, and Flexible Webtool for Single-cell Data Analysis

• Published in: Genomics, proteomics & bioinformatics Vol. 19; no. 3; pp. 452 - 460
• Main Authors: Garmire, David G., Zhu, Xun, Mantravadi, Aravind, Huang, Qianhui, Yunits, Breck, Liu, Yu, Wolfgruber, Thomas, Poirion, Olivier, Zhao, Tianying, Arisdakessian, Cédric, Stanojevic, Stefan, Garmire, Lana X.
• Format: Journal Article
• Language: English
• Published: China Elsevier B.V 01.06.2021; Department of Electrical Engineering&Computer Science,University of Michigan,Ann Arbor,MI 48109,USA%Epidemiology Program,University of Hawaii Cancer Center,Honolulu,HI 96813,USA%Department of Biostatistics,University of Michigan,Ann Arbor,MI 48109,USA%Department of Computational Medicine and Bioinformatics,University of Michigan,Ann Arbor,MI 48105,USA%Molecular Biosciences and Bioengineering Graduate Program,University of Hawaii at Manoa,Honolulu,HI 96822,USA%Epidemiology Program,University of Hawaii Cancer Center,Honolulu,HI 96813,USA; Molecular Biosciences and Bioengineering Graduate Program,University of Hawaii at Manoa,Honolulu,HI 96822,USA; Elsevier
• Subjects: Analysis; Computational Biology - methods; Data Analysis; Ecosystem; Module; Pipeline; Sequence Analysis, RNA - methods; Single-Cell Analysis - methods; Single-cell RNA sequencing; Software; Web Server; Webtool; Module; Single-cell RNA sequencing; Analysis; Pipeline; Webtool
• ISSN: 1672-0229; 2210-3244
• DOI: 10.1016/j.gpb.2021.07.005

We present GranatumX, a next-generation software environment for single-cell RNA sequencing (scRNA-seq) data analysis. GranatumX is inspired by the interactive webtool Granatum. GranatumX enables biologists to access the latest scRNA-seq bioinformatics methods in a web-based graphical environment. It also offers software developers the opportunity to rapidly promote their own tools with others in customizable pipelines. The architecture of GranatumX allows for easy inclusion of plugin modules, named Gboxes, which wrap around bioinformatics tools written in various programming languages and on various platforms. GranatumX can be run on the cloud or private servers and generate reproducible results. It is a community-engaging, flexible, and evolving software ecosystem for scRNA-seq analysis, connecting developers with bench scientists. GranatumX is freely accessible at http://garmiregroup.org/granatumx/app.