Abstract
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.
Original language | English (US) |
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Article number | 434 |
Journal | BMC genomics |
Volume | 23 |
Issue number | 1 |
DOIs | |
State | Published - Dec 2022 |
Keywords
- 10x Genomics Visium
- Interactive visualization
- Spatially-resolved transcriptomics
ASJC Scopus subject areas
- Genetics
- Biotechnology