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

David G Garmire; Xun Zhu; Aravind Mantravadi; Qianhui Huang; Breck Yunits; Yu Liu; Thomas Wolfgruber; Olivier Poirion; Tianying Zhao; Cédric Arisdakessian; Stefan Stanojevic; Lana X Garmire

doi:10.1016/j.gpb.2021.07.005

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

Genomics Proteomics Bioinformatics. 2021 Jun;19(3):452-460. doi: 10.1016/j.gpb.2021.07.005. Epub 2021 Dec 30.

Authors

Affiliations

¹ Department of Electrical Engineering & Computer Science, University of Michigan, Ann Arbor, MI 48109, USA.
² Epidemiology Program, University of Hawaii Cancer Center, Honolulu, HI 96813, USA.
³ Department of Biostatistics, University of Michigan, Ann Arbor, MI 48109, USA.
⁴ Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48105, USA.
⁵ Molecular Biosciences and Bioengineering Graduate Program, University of Hawaii at Manoa, Honolulu, HI 96822, USA.
⁶ 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.
⁷ Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48105, USA. Electronic address: lgarmire@med.umich.edu.

Abstract

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.

Keywords: Analysis; Module; Pipeline; Single-cell RNA sequencing; Webtool.

Publication types

Research Support, N.I.H., Extramural

MeSH terms

Computational Biology / methods
Data Analysis*
Ecosystem
Sequence Analysis, RNA / methods
Single-Cell Analysis* / methods
Software

Abstract

Publication types

MeSH terms

Grants and funding