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SPICA: Swiss portal for immune cell analysis
Massimo Andreatta1,2, Fabrice P A David3, Christian Iseli3
1Ludwig Institute for Cancer Research, Lausanne Branch, and Department of Oncology, CHUV and University of Lausanne, Epalinges 1066, Switzerland.
Nucleic Acids Research
|November 8, 2021
Summary
The Swiss portal for immune cell analysis (SPICA) offers a unique resource for exploring immune cell data. It provides detailed atlases and allows users to analyze their own single-cell RNA sequencing data.
Area of Science:
- Immunology
- Bioinformatics
- Genomics
Background:
- Single-cell transcriptomics reveals immune cell heterogeneity.
- Existing databases lack high-resolution, cell type-specific immune atlases.
- Analyzing immune cell data requires specialized tools and curated references.
Purpose of the Study:
- To introduce the Swiss portal for immune cell analysis (SPICA), a web resource for immune cell single-cell RNA sequencing data.
- To provide curated, high-resolution reference atlases for immune cell states.
- To enable private analysis of user data within the context of existing atlases.
Main Methods:
- Development of a web-based portal (SPICA).
- Curation of cell type-specific reference atlases for immune cells.
- Integration of published single-cell RNA sequencing datasets.
- Implementation of a platform for private data analysis.
Main Results:
- SPICA hosts curated, high-resolution reference atlases for immune cell states.
- The portal includes published single-cell datasets analyzed against these atlases.
- Users can upload and privately analyze their own single-cell RNA sequencing data.
Conclusions:
- SPICA serves as a valuable resource for immune cell analysis using single-cell transcriptomics.
- The platform facilitates high-resolution exploration of immune cell heterogeneity.
- SPICA supports both public data exploration and private data analysis, fostering collaborative research.
