Cytosplore-Transcriptomics: a scalable inter-active framework for single-cell RNA sequencing data analysis

bioRxiv (Cold Spring Harbor Laboratory)

Abstract

Summary The ever-increasing number of analyzed cells in Single-cell RNA sequencing (scRNA-seq) experiments imposes several challenges on the data analysis. Current analysis methods lack scalability to large datasets hampering interactive visual exploration of the data. We present Cytosplore-Transcriptomics, a framework to analyze scRNA-seq data, including data preprocessing, visualization and downstream analysis. At its core, it uses a hierarchical, manifold preserving representation of the data that allows the inspection and annotation of scRNA-seq data at different levels of detail. Consequently, Cytosplore-Transcriptomics provides interactive analysis of the data using low-dimensional visualizations that scales to millions of cells. Availability Cytosplore-Transcriptomics can be freely downloaded from transcriptomics.cytosplore.org Contact b.p.f.lelieveldt@lumc.nl

Authors 6

1. Tamim Abdelaal Aachen Department of Radiology, Leiden University Medical Center Leiden Computational Biology Center

   Leiden University Medical Center · Delft University of Technology

   Affiliation as printed

   Delft Bioinformatics Lab, Delft University of Technology, 2628 XE Delft, The Netherlands

   Department of Radiology, Leiden University Medical Center, 2333ZC Leiden, The Netherlands

   Leiden Computational Biology Center, Leiden University Medical Center, 2333ZC Leiden, The Netherlands

   Delft Bioinformatics Lab, Delft University of Technology, 68 XE Delft, The Netherlands

   Leiden Computational Biology Center, Leiden University Medical Center, 2ZC Leiden, The Netherlands

2. Jeroen Eggermont Aachen Department of Radiology, Leiden University Medical Center

   Leiden University Medical Center

   Affiliation as printed

   Department of Radiology, Leiden University Medical Center, 2333ZC Leiden, The Netherlands

3. Thomas Höllt Aachen Leiden Computational Biology Center

   Leiden University Medical Center · Delft University of Technology

   Affiliation as printed

   Computer Graphics and Visualization, Delft University of Technology, 2628 XE Delft, The Netherlands

   Leiden Computational Biology Center, Leiden University Medical Center, 2333ZC Leiden, The Netherlands

   Leiden Computational Biology Center, Leiden University Medical Center, 2ZC Leiden, The Netherlands

4. Ahmed Essam Mahfouz Aachen Department of Human Genetics Leiden Computational Biology Center

   Leiden University Medical Center · Delft University of Technology

   Affiliation as printed

   Delft Bioinformatics Lab, Delft University of Technology, 2628 XE Delft, The Netherlands

   Department of Human Genetics, Leiden University Medical Center, 2333ZC Leiden, The Netherlands

   Leiden Computational Biology Center, Leiden University Medical Center, 2333ZC Leiden, The Netherlands

   Delft Bioinformatics Lab, Delft University of Technology, 68 XE Delft, The Netherlands

   Leiden Computational Biology Center, Leiden University Medical Center, 2ZC Leiden, The Netherlands

5. Marcel J. T. Reinders Aachen Leiden Computational Biology Center

   Leiden University Medical Center · Delft University of Technology

   Affiliation as printed

   Delft Bioinformatics Lab, Delft University of Technology, 2628 XE Delft, The Netherlands

   Leiden Computational Biology Center, Leiden University Medical Center, 2333ZC Leiden, The Netherlands

   Delft Bioinformatics Lab, Delft University of Technology, 68 XE Delft, The Netherlands

   Leiden Computational Biology Center, Leiden University Medical Center, 2ZC Leiden, The Netherlands

6. Boudewijn P. F. Lelieveldt corresponding Aachen Department of Radiology, Leiden University Medical Center

   Leiden University Medical Center · Delft University of Technology

   Affiliation as printed

   Delft Bioinformatics Lab, Delft University of Technology, 2628 XE Delft, The Netherlands

   Department of Radiology, Leiden University Medical Center, 2333ZC Leiden, The Netherlands

   Delft Bioinformatics Lab, Delft University of Technology, 68 XE Delft, The Netherlands