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Cerebro: interactive visualization of scRNA-seq data.

Roman Hillje1, Pier Giuseppe Pelicci1,2, Lucilla Luzi1

  • 1Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, 20139 Milan.

Bioinformatics (Oxford, England)
|November 26, 2019
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Summary

Cerebro is a desktop application that allows biologists to visualize and interact with single-cell RNA sequencing data without needing bioinformatic expertise. It facilitates exploration of cell clusters, gene expression, and trajectories, bridging the gap between analysis and interpretation.

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Area of Science:

  • Bioinformatics
  • Computational Biology
  • Genomics

Background:

  • Sophisticated bioinformatic tools for single-cell RNA sequencing (scRNA-seq) data analysis are available.
  • However, a gap exists for biologists lacking extensive computational expertise to directly visualize and interact with their scRNA-seq data and results.

Purpose of the Study:

  • To present Cerebro, a user-friendly desktop application for interactive visualization and exploration of scRNA-seq data.
  • To enable biologists to analyze their data without requiring advanced bioinformatic skills.

Main Methods:

  • Cerebro is a standalone desktop application built with Shiny and Electron for macOS and Windows.
  • It offers an intuitive graphical interface for data exploration.
  • Features include visualization of sample/cluster similarities (t-SNE, UMAP), gene expression, marker genes, and trajectories (Monocle 2).

Main Results:

  • Cerebro allows users to explore similarities and heterogeneity between samples and cell clusters.
  • Users can visualize gene expression patterns and identify marker genes.
  • The application supports the visualization of calculated cell trajectories.

Conclusions:

  • Cerebro provides a flexible and accessible framework for investigating scRNA-seq data.
  • It facilitates collaboration between bioinformaticians and experimental biologists.
  • The tool aims to shorten the gap between data analysis and biological interpretation.