BASS: multi-scale and multi-sample analysis enables accurate cell type clustering and spatial domain detection in spatial transcriptomic studies

Spatial transcriptomic studies are reaching single-cell spatial resolution, with data often collected from multiple tissue sections. Here, we present a computational method, BASS, that enables multi-scale and multi-sample analysis for single-cell resolution spatial transcriptomics. BASS performs cel...

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Veröffentlicht in:Genome Biology Jg. 23; H. 1; S. 168
Hauptverfasser: Li, Zheng, Zhou, Xiang
Format: Journal Article
Sprache:Englisch
Veröffentlicht: London BioMed Central 04.08.2022
Springer Nature B.V
BMC
Schlagworte:
Animal Genetics and Genomics
Bayes Theorem
Bayesian analysis
Bayesian theory
Bioinformatics
Biomedical and Life Sciences
Cell type
Cluster Analysis
Clustering analysis
Computer applications
cortex
data collection
Datasets
domain
Evolutionary Biology
Gene expression
genome
Human Genetics
Hypothalamus
landscapes
Life Sciences
Localization
Method
Microbial Genetics and Genomics
Multi-sample analysis
Multi-scale analysis
Performance evaluation
Plant Genetics and Genomics
Simulation
Spatial discrimination
Spatial domain
Spatial transcriptomics
Transcriptome
Transcriptomics
Bayesian hierarchical model
BASS
Multi-scale analysis
Spatial domain
Spatial transcriptomics
Clustering analysis
Tissue section
Cell type
Multi-sample analysis
ISSN:1474-760X, 1474-7596, 1474-760X
Online-Zugang:Volltext
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Beschreibung
Zusammenfassung:Spatial transcriptomic studies are reaching single-cell spatial resolution, with data often collected from multiple tissue sections. Here, we present a computational method, BASS, that enables multi-scale and multi-sample analysis for single-cell resolution spatial transcriptomics. BASS performs cell type clustering at the single-cell scale and spatial domain detection at the tissue regional scale, with the two tasks carried out simultaneously within a Bayesian hierarchical modeling framework. We illustrate the benefits of BASS through comprehensive simulations and applications to three datasets. The substantial power gain brought by BASS allows us to reveal accurate transcriptomic and cellular landscape in both cortex and hypothalamus.
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ISSN:1474-760X
1474-7596
1474-760X
DOI:10.1186/s13059-022-02734-7