singlecellVR: Interactive Visualization of Single-Cell Data in Virtual Reality

Abstract

Single-cell assays have transformed our ability to model heterogeneity within cell populations. As these assays have advanced in their ability to measure various aspects of molecular processes in cells, computational methods to analyze and meaningfully visualize such data have required matched innovation. Independently, Virtual Reality (VR) has recently emerged as a powerful technology to dynamically explore complex data and shows promise for adaptation to challenges in single-cell data visualization. However, adopting VR for single-cell data visualization has thus far been hindered by expensive prerequisite hardware or advanced data preprocessing skills. To address current shortcomings, we present singlecellVR, a user-friendly web application for visualizing single-cell data, designed for cheap and easily available virtual reality hardware (e.g., Google Cardboard, ∼$8). singlecellVR can visualize data from a variety of sequencing-based technologies including transcriptomic, epigenomic, and proteomic data as well as combinations thereof. Analysis modalities supported include approaches to clustering as well as trajectory inference and visualization of dynamical changes discovered through modelling RNA velocity. We provide a companion software package, scvr to streamline data conversion from the most widely-adopted single-cell analysis tools as well as a growing database of pre-analyzed datasets to which users can contribute.

transomics2cytoscape: An automated software for interpretable 2.5-dimensional visualization of trans-omic networks

“…In addition, a paper on visualization methods for interpreting genome-wide association study data in VR has already been published 27 . VR for visualization of single-cell data has also been presented 28 . It is worth keeping an eye on the trend of developments regarding what humans can find by wearing headsets and moving around in a large-scale network and related omics data.…”

Bioinformatics and the Metaverse: Are We Ready?

“…CellexalVR ( Legetth et al, 2021 ) is a VR application that does this while providing other tools to comprehensively visualize and analyze single-cell data. Others include Thiea ( Bressan et al, 2021 ) which will also handle volumetric data, and singlecellVR ( Stein et al, 2021 ) which offers visualization using Google Cardboard.…”

A Brave New World: Virtual Reality and Augmented Reality in Systems Biology

“…A recent tool, CellexalVR, allows visual exploration and analysis of such dimensionality reduction plots and associated metadata in immersive VR (Legetth et al, 2021). Other tools for the same purpose include starmapVR (Yang et al, 2020), singlecellVR (Stein et al, 2021) and Theia (Bressan et al, 2021). These platforms often include additional modalities such as on-thefly clustering, or visualization of dynamic changes in RNA velocity.…”

“…These platforms often include additional modalities such as on-thefly clustering, or visualization of dynamic changes in RNA velocity. While singlecellVR and starmapVR are web applications that enable visualizations using low-cost and easily available VR hardware such as Google Cardboard (Yang et al, 2020;Stein et al, 2021), CellexalVR involves GPUaccelerated performance and in-session on-the-fly calculations. StarmapVR further enables simultaneous visualization of spatial transcriptomics data from matching histological images.…”