Spatially Resolved Transcriptomics Mining in 3D and Virtual Reality Environments with VR-Omics (Software and Data)

Here, we summarise available data and source code regarding the publication "Spatially Resolved Transcriptomics Mining in 3D and Virtual Reality Environments with VR-Omics". Abstract Spatially resolved transcriptomics (SRT) technologies produce complex, multi-dimensional data sets of gene expression information that can be obtained at subcellular spatial resolution. While several computational tools are available to process and analyse SRT data, no platforms facilitate the visualisation and interaction with SRT data in an immersive manner. Here we present VR-Omics, a computational platform that supports the analysis, visualisation, exploration, and interpretation SRT data compatible with any SRT technology. VR-Omics is the first tool capable of analysing and visualising data generated by multiple SRT platforms in both 2D desktop and virtual reality environments. It incorporates an in-built workflow to automatically pre-process and spatially mine the data within a user-friendly graphical user interface. Benchmarking VR-Omics against other comparable software demonstrates its seamless end-to-end analysis of SRT data, hence making SRT data processing and mining universally accessible. VR-Omics is an open-source software freely available at: https://ramialison-lab.github.io/pages/vromics.html or below.

本节综述了关于《在三维与虚拟现实环境中利用VR-Omics进行空间解析转录组学挖掘》一文的可用数据与源代码。摘要中提到，空间解析转录组学（SRT）技术能够生成复杂的、多维度的基因表达信息数据集，该数据集可达到亚细胞的空间分辨率。尽管存在多种计算工具用于处理和分析SRT数据，但尚无平台能够以沉浸式的方式促进对SRT数据的可视化与交互。本文介绍的VR-Omics即为一款计算平台，它支持对与任何SRT技术兼容的SRT数据进行分析、可视化、探索与解读。VR-Omics是首个能够分析并可视化由多个SRT平台生成数据的工具，无论是在2D桌面还是虚拟现实环境中均能胜任。该平台内置工作流程，能够自动在用户友好的图形用户界面中对数据进行预处理和空间挖掘。将VR-Omics与其他同类软件进行基准测试，证明了其在SRT数据端到端分析方面的无缝性能，从而使得SRT数据处理和挖掘变得普遍可及。VR-Omics是一款开源软件，可在以下链接免费获取：https://ramialison-lab.github.io/pages/vromics.html 或下方。