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

Abstract

We present GranatumX, the next-generation software environment for single-cell data analysis. It enables biologists access to the latest single-cell bioinformatics methods in a 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", that wrap around bioinformatics tools written in various programming languages. GranatumX can be run in the cloud or private servers, and generate reproducible results. It is expected to become a community-engaging, flexible, and evolving software ecosystem for scRNA-Seq analysis, connecting developers with bench scientists. GranatumX is freely accessible at: MainSingle-cell RNA sequencing (scRNA-Seq) technologies have advanced our understanding of cell-level biology significantly 1 . Many exciting scientific discoveries are attributed to new experimental technologies and sophisticated computational methods 2,3 . Despite the progress on both sides, it has become obvious that an increasingly larger gap exists between the wet-lab biology and the bioinformatics community. Although some analytical packages such as SINCERA 4 , Seurat 5 , and Scanpy 6 provide complete scRNA-Seq pipelines, they require users to be familiar with their corresponding programming language (typically R or Python) and/or command line interface, hindering a wide adoption experimental biologists. A few platforms, such as ASAP 7 and our own tool Granatum 8 , provide an intuitive graphical user interface. However, these platforms are not modularized and lack the flexibility to incorporate a continuously growing list of new computational tools. Furthermore, these tools have limited scalability and cannot handle extremely large datasets. Here we present GranatumX, the new generation of scRNA-Seq analysis platform that aims to solve these issues systematically. Its architecture facilitates the rapid incorporation of cutting-edge tools and enables the handling of large datasets very efficiently.The objective of GranatumX is to provide scRNA-Seq biologists better access to bioinformatics tools and ability to conduct single cell data analysis independently ( Figure 1). Currently other single-cell RNA-Seq platforms usually only provide a fixed set of methods implemented by the authors themselves. Adding new methods developed by the community is difficult, due to programming language lock-in as well as monolithic code architectures. As a solution, GranatumX uses the plugin framework that provides an easy and unified approach to add new methods. The plugin system is developer code/scripting language agnostic. It also eliminates inter-module incompatibilities, by isolating the dependencies of each module ( Figure 2A). As a data portal, GranatumX provides a graphical user interface (GUI) that requires no programming experience. Its web-based GUI can be accessed on various devices including desktop, tablets, and smartphones ( Figure 2A). In addition ...

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Modeling population heterogeneity from microbial communities to immune response in cells

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