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Giotto: a toolbox for integrative analysis and visualization of spatial expression data
- Source :
- Genome Biology, Vol 22, Iss 1, Pp 1-31 (2021)
- Publication Year :
- 2021
- Publisher :
- BMC, 2021.
-
Abstract
- Abstract 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.
- Subjects :
- Biology (General)
QH301-705.5
Genetics
QH426-470
Subjects
Details
- Language :
- English
- ISSN :
- 1474760X
- Volume :
- 22
- Issue :
- 1
- Database :
- Directory of Open Access Journals
- Journal :
- Genome Biology
- Publication Type :
- Academic Journal
- Accession number :
- edsdoj.4e88a78b4f8948f69e0ebf5aa8ff65bc
- Document Type :
- article
- Full Text :
- https://doi.org/10.1186/s13059-021-02286-2