Scopeþ: an open source generalizable architecture for single-cell RNA-seq atlases at sample and cell levels

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 optimized and scalable architecture, named Scopeþ, 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. Scopeþ 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 Scopeþ architecture with their atlases can be found at https://hiyin.github.io/scopeplus-user-tutorial/. Scopeþ source code can be found at https://doi.org/10.5281/zenodo.14174632 and https://github.com/hiyin/scopeplus.