Granatum: a graphical single-cell RNA-Seq analysis pipeline for genomics scientists

Abstract

Background: Single-cell RNA sequencing (scRNA-Seq) is an increasingly popular platform to study heterogeneity at the single-cell level. Computational methods to process scRNA-Seq have limited accessibility to bench scientists as they require significant amounts of bioinformatics skills. Results: We have developed Granatum, a web-based scRNA-Seq analysis pipeline to make analysis more broadly accessible to researchers. Without a single line of programming code, users can click through the pipeline, setting parameters and visualizing results via the interactive graphical interface. Granatum conveniently walks users through various steps of scRNA-Seq analysis. It has a comprehensive list of modules, including plate merging and batch-effect removal, outlier-sample removal, gene filtering, gene-expression normalization, cell clustering, differential gene expression analysis, pathway/ontology enrichment analysis, protein-network interaction visualization, and pseudo-time cell series construction. Conclusions: Granatum enables broad adoption of scRNA-Seq technology by empowering the bench scientists with an easy-to-use graphical interface for scRNA-Seq data analysis. The package is freely available for research use at http://garmiregroup.org/granatum/app