Abstract
Abstract
Background:
The development of single-cell technologies yields large datasets of information as diverse and multimodal as transcriptomes, immunophenotypes, and spatial position from tissue sections in the so-called ’spatial transcriptomics’. Currently however, user-friendly, powerful, and free algorithmic tools for straightforward analysis of spatial transcriptomic datasets are scarce.
Results:
Here, we introduce Single-Cell Spatial Explorer, an open-source software for multimodal exploration of spatial transcriptomics, examplified with 9 human and murine tissues datasets from 4 different technologies.
Conclusions:
Single-Cell Spatial Explorer is a very powerful, versatile, and interoperable tool for spatial transcriptomics analysis.
Publisher
Springer Science and Business Media LLC
Subject
Applied Mathematics,Computer Science Applications,Molecular Biology,Biochemistry,Structural Biology
Reference19 articles.
1. Butler A, Hoffman P, Smibert P, Papalexi E, Satija R. Integrating single-cell transcriptomic data across different conditions, technologies, and species. Nat Biotechnol. 2018;36:411–20.
2. Cerapio J-P, Perrier M, Balança C-C, Gravelle P, Pont F, Devaud C, Franchini D-M, Féliu V, Tosolini M, Valle C, et al. Phased differentiation of $$\gamma$$$$\delta$$ t and t cd8 tumor-infiltrating lymphocytes revealed by single-cell transcriptomics of human cancers. Oncoimmunology. 2021;10(1):1939518.
3. Chen TJ, Kotecha N. Cytobank: providing an analytics platform for community cytometry data analysis and collaboration. Berlin: Springer; 2014. p. 127–57.
4. Cho C-S, Xi J, Si Y, Park S-R, Hsu J-E, Kim M, Jun G, Kang HM, Lee JH. Microscopic examination of spatial transcriptome using seq-scope. Cell. 2021;184(13):3559–72.
5. Deng Y, Bartosovic M, Kukanja P, Zhang D, Liu Y, Su G, Enninful A, Bai Z, Castelo-Branco G, Fan R. Spatial-cut &tag: spatially resolved chromatin modification profiling at the cellular level. Science. 2022;375(6581):681–6.
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