spatialLIBD: an R/Bioconductor package to visualize spatially-resolved transcriptomics data

Background Spatially-resolved transcriptomics has now enabled the quantification of high-throughput and transcriptome-wide gene expression in intact tissue while also retaining the spatial coordinates. Incorporating the precise spatial mapping of gene activity advances our understanding of intact ti...

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Bibliographic Details
Published in:BMC genomics Vol. 23; no. 1; pp. 434 - 5
Main Authors: Pardo, Brenda, Spangler, Abby, Weber, Lukas M., Page, Stephanie C., Hicks, Stephanie C., Jaffe, Andrew E., Martinowich, Keri, Maynard, Kristen R., Collado-Torres, Leonardo
Format: Journal Article
Language:English
Published: London BioMed Central 10.06.2022
BioMed Central Ltd
Springer Nature B.V
BMC
Subjects:
10x Genomics Visium
Analysis
Animal Genetics and Genomics
Applications programs
Biological activity
Biomedical and Life Sciences
Brain
Cell cycle
Clustering
Data analysis
Ecosystem
Gene expression
Gene mapping
Genomes
Genomics
Geospatial data
Health aspects
Interactive visualization
Life Sciences
Methods
Microarrays
Microbial Genetics and Genomics
Open source software
Plant Genetics and Genomics
Proteomics
R (Programming language)
Software
Spatial data
Spatially-resolved transcriptomics
Transcriptome
Transcriptomes
Transcriptomic methods
Transcriptomics
Visualization
Visualization (Computers)
Websites
United States
Spatially-resolved transcriptomics
Interactive visualization
10x Genomics Visium
ISSN:1471-2164, 1471-2164
Online Access:Get full text
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Summary:Background Spatially-resolved transcriptomics has now enabled the quantification of high-throughput and transcriptome-wide gene expression in intact tissue while also retaining the spatial coordinates. Incorporating the precise spatial mapping of gene activity advances our understanding of intact tissue-specific biological processes. In order to interpret these novel spatial data types, interactive visualization tools are necessary. Results We describe spatialLIBD , an R/Bioconductor package to interactively explore spatially-resolved transcriptomics data generated with the 10x Genomics Visium platform. The package contains functions to interactively access, visualize, and inspect the observed spatial gene expression data and data-driven clusters identified with supervised or unsupervised analyses, either on the user’s computer or through a web application. Conclusions spatialLIBD is available at https://bioconductor.org/packages/spatialLIBD . It is fully compatible with SpatialExperiment and the Bioconductor ecosystem. Its functionality facilitates analyzing and interactively exploring spatially-resolved data from the Visium platform.
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ISSN:1471-2164
1471-2164
DOI:10.1186/s12864-022-08601-w