The DOI matches its Crossref record; 51 of the 51 references it cites were found in a registry or an index.
Giotto: a toolbox for integrative analysis and visualization of spatial expression data
Open accessAbstract
Spatial transcriptomic and proteomic technologies have provided new opportunities to investigate cells in their native microenvironment. Here we present Giotto, a comprehensive and open-source toolbox for spatial data analysis and visualization. The analysis module provides end-to-end analysis by implementing a wide range of algorithms for characterizing tissue composition, spatial expression patterns, and cellular interactions. Furthermore, single-cell RNAseq data can be integrated for spatial cell-type enrichment analysis. The visualization module allows users to interactively visualize analysis outputs and imaging features. To demonstrate its general applicability, we apply Giotto to a wide range of datasets encompassing diverse technologies and platforms.
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Cites
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Cited by
Spatiotemporal transcriptomic atlas of mouse organogenesis using DNA nanoball-patterned arrays
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Museum of spatial transcriptomics
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Best practices for single-cell analysis across modalities
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“Tangram 224 , GridNet 230 and eggplant 231 generate common coordinate frameworks across samples to mitigate this issue 232 .”
BackgroundIntegrating single-cell and spatial transcriptomics to elucidate intercellular tissue dynamics
Longo, S. K., Guo, M. G., Ji, A. L., & Khavari, P. A. (2021) · Nature Reviews Genetics · doi:10.1038/s41576-021-00370-8 · Cited by 1,059
Metadata
- Authors
- Dries, R., Zhu, Q., Dong, R., Eng, C.-H. L., Li, H., Liu, K., Fu, Y., Zhao, T., Sarkar, A., Bao, F., George, R. E., Pierson, N., Cai, L., & Yuan, G.-C.
- Venue
- Genome Biology
- Published
- 2021-03-08
- Volume
- 22
- Issue
- 1
- Pages
- 78-78
- ISSN
- 1465-6906 (ISSN-L)
- 1474-760X
- OpenAlex
- W3134482219
- Cited by
- 917
- References
- 51
- FWCI
- 37.64
- Type
- journal article
- Language
- en
- Open access
- gold
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- Dries, R., Zhu, Q., Dong, R., Eng, C.-H. L., Li, H., Liu, K., Fu, Y., Zhao, T., Sarkar, A., Bao, F., George, R. E., Pierson, N., Cai, L., & Yuan, G.-C. (2021). Giotto: a toolbox for integrative analysis and visualization of spatial expression data. Genome Biology. https://doi.org/10.1186/s13059-021-02286-2
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