Abstract
BackgroundSingle-cell RNA sequencing (scRNA-Seq) is an increasingly popular platform to study heterogeneity at the single-cell level. Computational methods to process scRNA-Seq data are not very accessible to bench scientists as they require a significant amount of bioinformatic skills.ResultsWe 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-expression normalization, imputation, gene filtering, cell clustering, differential gene expression analysis, pathway/ontology enrichment analysis, protein network interaction visualization, and pseudo-time cell series construction.ConclusionsGranatum enables broad adoption of scRNA-Seq technology by empowering 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
Highlights
Single-cell RNA sequencing is an increasingly popular platform to study heterogeneity at the single-cell level
We have developed Granatum, a fully interactive graphical scRNA-Seq analysis tool
Clustering methods The following description of clustering algorithms assumes that n is the number of genes, m is the number of samples, and k is the number of clusters
Summary
Single-cell RNA sequencing (scRNA-Seq) is an increasingly popular platform to study heterogeneity at the single-cell level. Existing workflows that can be used to analyze scRNA-Seq data, such as Singular (Fluidigm, Inc., South San Francisco, CA, USA), Cell Ranger (10x Genomics Inc., Pleasanton, CA, USA), and Scater [7], all require some non-graphical interactions They may not provide a comprehensive set of scRNA-Seq analysis methods. Granatum takes its name from the Latin word for pomegranate, whose copious seeds resemble individual cells This tool employs an easy-touse web browser interface for a wide range of methods suitable for scRNA-Seq analysis: removal of batch effects, removal of outlier cells, normalization of expression levels, imputation for dropout events, filtering of under-informative genes, clustering of cells, identification of differentially expressed genes, identification of
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