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

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

Publication date: Dec 20, 2024

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. 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 data are available at Bioinformatics online.

Concepts Keywords
Atlases Analysis
Covidscope Architecture
Efficient Atlas
Tutorials Atlases
Cell
Covid
Covidscope
Https
Level
Meta
Open
Portal
Rna
Scope+
Single

Semantics

Type Source Name
disease IDO cell
disease MESH COVID-19
disease IDO blood
drug DRUGBANK Coenzyme M

Original Article

(Visited 1 times, 1 visits today)