Research Department, Biogen, Inc., 225 Binney St, Cambridge, MA 02142, USA.
BioInfoRx, Inc., 510 Charmany Dr, Suite 275A, Madison, WI 53719, USA.
J Mol Biol. 2022 Jun 15;434(11):167425. doi: 10.1016/j.jmb.2021.167425. Epub 2021 Dec 28.
CellDepot containing over 270 datasets from 8 species and many tissues serves as an integrated web application to empower scientists in exploring single-cell RNA-seq (scRNA-seq) datasets and comparing the datasets among various studies through a user-friendly interface with advanced visualization and analytical capabilities. To begin with, it provides an efficient data management system that users can upload single cell datasets and query the database by multiple attributes such as species and cell types. In addition, the graphical multi-logic, multi-condition query builder and convenient filtering tool backed by MySQL database system, allows users to quickly find the datasets of interest and compare the expression of gene(s) across these. Moreover, by embedding the cellxgene VIP tool, CellDepot enables fast exploration of individual dataset in the manner of interactivity and scalability to gain more refined insights such as cell composition, gene expression profiles, and differentially expressed genes among cell types by leveraging more than 20 frequently applied plotting functions and high-level analysis methods in single cell research. In summary, the web portal available at http://celldepot.bxgenomics.com, prompts large scale single cell data sharing, facilitates meta-analysis and visualization, and encourages scientists to contribute to the single-cell community in a tractable and collaborative way. Finally, CellDepot is released as open-source software under MIT license to motivate crowd contribution, broad adoption, and local deployment for private datasets.
CellDepot 包含来自 8 个物种和多种组织的超过 270 个数据集，是一个集成的网络应用程序，通过用户友好的界面、高级可视化和分析功能，为科学家探索单细胞 RNA-seq（scRNA-seq）数据集并比较各种研究中的数据集提供支持。首先，它提供了一个高效的数据管理系统，用户可以上传单细胞数据集，并通过物种和细胞类型等多个属性查询数据库。此外，图形化的多逻辑、多条件查询构建器和方便的过滤工具，由 MySQL 数据库系统支持，使用户能够快速找到感兴趣的数据集，并比较这些数据集之间基因的表达情况。此外，通过嵌入 cellxgene VIP 工具，CellDepot 能够以交互性和可扩展性的方式快速探索单个数据集，从而获得更精细的见解，例如细胞组成、基因表达谱以及不同细胞类型之间的差异表达基因，利用单细胞研究中 20 多种常用的绘图功能和高级分析方法。总之，该网站（http://celldepot.bxgenomics.com）提供了大规模的单细胞数据共享，促进了元分析和可视化，并鼓励科学家以可管理和协作的方式为单细胞社区做出贡献。最后，CellDepot 作为 MIT 许可证下的开源软件发布，以激发人群的贡献、广泛采用和针对私人数据集的本地部署。
