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, Anthony Mathelier · 2024
Read Scope+: an open source generalizable architecture for single-cell RNA-seq atlases at sample and cell levels by 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, Anthony Mathelier (2024) in the Tower of Babel, a free online library of public-domain works preserved in clean, searchable text. No sign-up. The full text is served as a plain-text file at a predictable URL, where text is present: https://antarctic-labs.com/tower-of-babel/pmc-11755096.txt.
Description
Danqing Yin and co-authors present open-source software for exploring atlases of single-cell data, in this 2024 paper. Modern sequencing can read the gene activity of millions of individual cells, and researchers combine these into atlases for whole tissues or diseases. Browsing such mountains of data quickly, and comparing cells across studies, is hard, and most atlas websites are closed systems that others cannot adapt.
Their architecture, Scope+, attacks the problem with three tricks: modeling data cell by cell, tuned databases, and careful software design. They proved it on a curated collection of five million blood and immune cells from COVID-19 studies, launched as a public portal called Covidscope. Visitors can select cells at fine detail and run comparisons across samples. Because the code is open, other teams can build their own atlas portals on the same frame.
Catalog record
| CREATOR | 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, Anthony Mathelier |
|---|---|
| YEAR | 2024 |
| COLLECTION | PAPERS |
| FORMAT | TXT |
| FILE SIZE | 20 KB |
| VERSION | 1.0 |
| LICENSE | CC BY 4.0 |
| RIGHTS | CC BY |
| SOURCE | Europe PMC |