Advances in spatial transcriptomic data analysis
- Ruben Dries1,2,3,
- Jiaji Chen1,
- Natalie del Rossi4,
- Mohammed Muzamil Khan1,2,3,
- Adriana Sistig4 and
- Guo-Cheng Yuan4,5
- 1Department of Medicine, Boston University School of Medicine, Boston, Massachusetts 02118, USA;
- 2Bioinformatics Graduate Program, Boston University, Boston, Massachusetts 02215, USA;
- 3Section of Computational Biomedicine, Boston University School of Medicine, Boston, Massachusetts 02118, USA;
- 4Department of Genetics and Genomic Sciences, Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA;
- 5Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
Abstract
Spatial transcriptomics is a rapidly growing field that promises to comprehensively characterize tissue organization and architecture at the single-cell or subcellular resolution. Such information provides a solid foundation for mechanistic understanding of many biological processes in both health and disease that cannot be obtained by using traditional technologies. The development of computational methods plays important roles in extracting biological signals from raw data. Various approaches have been developed to overcome technology-specific limitations such as spatial resolution, gene coverage, sensitivity, and technical biases. Downstream analysis tools formulate spatial organization and cell–cell communications as quantifiable properties, and provide algorithms to derive such properties. Integrative pipelines further assemble multiple tools in one package, allowing biologists to conveniently analyze data from beginning to end. In this review, we summarize the state of the art of spatial transcriptomic data analysis methods and pipelines, and discuss how they operate on different technological platforms.
This article, published in Genome Research, is available under a Creative Commons License (Attribution 4.0 International), as described at http://creativecommons.org/licenses/by/4.0/.
