Comparison of visualization tools for single-cell RNAseq data
Comparison of visualization tools for single-cell RNAseq data
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DOI：
10.1093/nargab/lqaa052
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发表时间：
2020-09-01
影响因子：
4.6
通讯作者：
Kiselev, Vladimir Yu
中科院分区：
文献类型：
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作者：
Cakir, Batuhan;Prete, Martin;Kiselev, Vladimir Yu
在过去的十年中，单细胞RNAseq（scRNAseq）数据集的规模已经从单个细胞增长到数百万个细胞。由于scRNAseq数据的高维性，将其可视化并以科学报告或文章出版格式共享并不总是可行的。最近，许多互动分析和可视化工具已经开发出来，以解决这个问题，并促进科学界的知识转让。在这项研究中，我们回顾了几个目前可用的scRNAseq可视化工具，并对允许在网络上可视化数据并与他人共享的子集进行了基准测试。我们考虑了随着单元格数量的增加，准备数据集以进行共享所需的内存和时间，并额外审查了Web界面中可用的用户体验和功能。为了解决格式兼容性问题，我们还开发了一个用户友好的R包sceasy，它允许用户将自己的scRNASeq数据集转换为特定的数据格式以进行可视化。
In the last decade, single cell RNAseq (scRNAseq) datasets have grown in size from a single cell to millions of cells. Due to its high dimensionality, it is not always feasible to visualize scRNAseq data and share it in a scientific report or an article publication format. Recently, many interactive analysis and visualization tools have been developed to address this issue and facilitate knowledge transfer in the scientific community. In this study, we review several of the currently available scRNAseq visualization tools and benchmark the subset that allows to visualize the data on the web and share it with others. We consider the memory and time required to prepare datasets for sharing as the number of cells increases, and additionally review the user experience and features available in the web interface. To address the problem of format compatibility we have also developed a user-friendly R package, sceasy, which allows users to convert their own scRNAseq datasets into a specific data format for visualization.