Cellenium-a scalable and interactive visual analytics app for exploring multimodal single-cell data.

Autor:	Jahn C; Scientific Solutions, Bayer AG, Berlin 13353, Germany., Ibrahim M; Biomedical Data Science, Bayer AG, Wuppertal 42113, Germany., Busch J; Scientific Solutions, Bayer AG, Berlin 13353, Germany., Lin Q; Scientific Solutions, Bayer AG, Berlin 13353, Germany., Manchanda H; Biomedical Data Science I, Bayer AG, Berlin 13353, Germany., Mohr H; Scientific Solutions, Bayer AG, Berlin 13353, Germany., Plischke D; Scientific Solutions, Bayer AG, Berlin 13353, Germany., Roider HG; Biomedical Data Science I, Bayer AG, Berlin 13353, Germany., Steffen A; Scientific Solutions, Bayer AG, Berlin 13353, Germany.
Jazyk:	angličtina
Zdroj:	Bioinformatics (Oxford, England) [Bioinformatics] 2023 Jun 01; Vol. 39 (6).
DOI:	10.1093/bioinformatics/btad349
Abstrakt:	Summary: Multimodal single-cell sequencing data provide detailed views into the molecular biology of cells. To allow for interactive analyses of such rich data and to readily derive insights from it, new analysis solutions are required. In this work, we present Cellenium, our new scalable visual analytics web application that enables users to semantically integrate and organize all their single-cell RNA-, ATAC-, and CITE-sequencing studies. Users can then find relevant studies and analyze single-cell data within and across studies. An interactive cell annotation feature allows for adding user-defined cell types. Availability and Implementation: Source code and documentation are freely available under an MIT license and are available on GitHub (https://github.com/Bayer-Group/cellenium). The server backend is implemented in PostgreSQL, Python 3, and GraphQL, the frontend is written in ReactJS, TypeScript, and Mantine css, and plots are generated using plotlyjs, seaborn, vega-lite, and nivo.rocks. The application is dockerized and can be deployed and orchestrated on a standard workstation via docker-compose. (© The Author(s) 2023. Published by Oxford University Press.)
Databáze:	MEDLINE
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