GranatumX: A Community-Engaging, Modularized, and Flexible Webtool for Single-Cell Data Analysis

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.

Advanced Single-Cell Omics Technologies and Informatics Tools for Genomics, Proteomics, and Bioinformatics Analysis

“…Ge et al identified different biomarkers during Cashmere goat hair follicle development, which has implications for Cashmere goat breeding in the future [21] . Meanwhile, a webserver, GranatumX was also presented in this special issue, which enables biologists to access the latest single-cell bioinformatics methods in a web-based graphical environment [22] . On the other hand, as a method-oriented work, the computational model proposed by Zhong et al [23] can explore the gene–gene associations based on scRNA-seq data for critical transition prediction.…”