ArticleBioinformatics (Oxford, England)2024
Scope+: an open source generalizable architecture for single-cell RNA-seq atlases at sample and cell levels.
Article in Bioinformatics (Oxford, England), 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.
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Who cites it
1 citing paper in PubMed.
- Transformative advances in single-cell omics: a comprehensive review of foundation models, multimodal integration and computational ecosystems.Journal of translational medicine · 2025Review
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10 authors.
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Abstract
summaryWith 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 optimized 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.
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