Granatum – a graphical single-cell RNA-seq analysis pipeline for genomics scientists

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 amount of bioinformatics skills.

Researchers from the University of Hawaii at Manoa have developed Granatum, a web browser based scRNA-seq analysis pipeline to make analysis more broadly accessible to researchers. Without a single line of programming code, a user can click through the pipeline, setting parameters and visualizing results via the interactive graphical interface. The pipeline conveniently walks the 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.

Granatum workflow


Granatum is built with the Shiny framework, which supports both front-end and the back-end. The user uploads one or more expression matrices with corresponding metadata for samples. The back-end stores data separately for each individual user, and invokes third-party libraries on demand.

Granatum enables much widely adoption of scRNA-seq technology by empowering the bench scientists with an easy to use graphical interface for scRNA-seq data analysis.

Availability – The code is freely available for research use at:

Zhu X, Wolfgruber T, Tasato A, Garmire L. (2017) Granatum: a graphical single-cell RNA-seq analysis pipeline for genomics scientists. bioRXiv [Epub ahead of print]. [abstract]

Leave a Reply

Your email address will not be published. Required fields are marked *


Time limit is exhausted. Please reload CAPTCHA.