Scope+: An open source generalizable architecture for single-cell RNA-seq atlases at sample and cell levels

Danqing Yin; Yue Cao; Junyi Chen; Candice L Y Mak; Ken H O Yu; Jiaxuan Zhang; Jia Li; Yingxin Lin; Joshua W K Ho; Jean Y H Yang

doi:10.1093/bioinformatics/btae727

Scope+: An open source generalizable architecture for single-cell RNA-seq atlases at sample and cell levels

Bioinformatics. 2024 Dec 20:btae727. doi: 10.1093/bioinformatics/btae727. Online ahead of print.

Authors

Danqing Yin^{1

2}, Yue Cao^{1

3

4

5}, Junyi Chen^{1

2}, Candice L Y Mak¹, Ken H O Yu^{1

2}, Jiaxuan Zhang⁶, Jia Li^{6

7}, Yingxin Lin^{1

3

4

5}, Joshua W K Ho^{1

2}, Jean Y H Yang^{1

3

4

5}

Affiliations

¹ Laboratory of Data Discovery for Health Limited (D24H), Hong Kong SAR, China.
² School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong SAR, China.
³ Charles Perkins Centre, University of Sydney, NSW 2006, Australia.
⁴ School of Mathematics and Statistics, University of Sydney, NSW 2006, Australia.
⁵ Sydney Precision Data Science Centre, University of Sydney, NSW 2006, Australia.
⁶ Guangzhou National Laboratory, Guangzhou International Bio Island, 510005, China Guangzhou Guangdong Province, China.
⁷ State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University.

PMID: 39705183
DOI: 10.1093/bioinformatics/btae727

Abstract

Summary: With the recent advancement in single-cell RNA-sequencing technologies and the increased availability of integrative tools, challenges arise in easy and fast access to large collections of cell atlas. Existing cell atlas portals rarely are open sourced and adaptable, and do not support meta-analysis at cell level. Here, we present an open source, highly optimised and scalable architecture, named Scope+, to allow quick access, meta-analysis and cell-level selection of the atlas data. We applied this architecture to our well-curated 5 million COVID-19 blood and immune cells, as a portal called Covidscope. We achieved efficient access to atlas-scale data via three strategies, such as cell-as-unit data modelling, novel database optimization techniques and innovative software architectural design. Scope+ serves as an open source architecture for researchers to build on with their own atlas.

Availability and implementation: The COVID-19 web portal, data and meta-analysis are available on Covidscope (https://covidsc.d24h.hk/). User tutorials on how to implement Scope+ architecture with their atlases can be found at https://hiyin.github.io/scopeplus-user-tutorial/. Scope+ source code can be found at https://doi.org/10.5281/zenodo.14174632 and https://github.com/hiyin/scopeplus.

Supplementary information: Supplementary data are available at Bioinformatics online.