Related Experiment Video
Updated: Sep 20, 2025
Spatial Profiling of Protein and RNA Expression in Tissue: An Approach to Fine-Tune Virtual Microdissection
Published on: July 6, 2022
spatialLIBD: an R/Bioconductor package to visualize spatially-resolved transcriptomics data
Brenda Pardo1,2, Abby Spangler2, Lukas M Weber3
1Licenciatura de Ciencias Genómicas, Escuela Nacional de Estudios Superiores Unidad Juriquilla, Universidad Nacional Autónoma de México, Querétaro, 76230, Mexico.
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.
