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Related Experiment Video

Updated: Sep 20, 2025

Spatial Profiling of Protein and RNA Expression in Tissue: An Approach to Fine-Tune Virtual Microdissection
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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.

BMC Genomics
|June 10, 2022
PubMed
Summary
This summary is machine-generated.

spatialLIBD is a new R/Bioconductor package for interactively exploring spatial transcriptomics data. It visualizes gene expression and clusters from the 10x Visium platform, aiding tissue-specific biological process understanding.

Keywords:
10x Genomics VisiumInteractive visualizationSpatially-resolved transcriptomics

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Area of Science:

  • Genomics
  • Bioinformatics
  • Computational Biology

Background:

  • Spatially-resolved transcriptomics enables high-throughput, transcriptome-wide gene expression quantification with spatial coordinates.
  • Mapping gene activity in intact tissues enhances understanding of tissue-specific biological processes.
  • Interactive visualization tools are crucial for interpreting novel spatial transcriptomics data.

Purpose of the Study:

  • To introduce spatialLIBD, an R/Bioconductor package for interactive exploration of spatial transcriptomics data.
  • To provide tools for accessing, visualizing, and inspecting spatial gene expression data and identified clusters.
  • To enable analysis on a user's computer or via a web application.

Main Methods:

  • Development of the spatialLIBD R/Bioconductor package.
  • Implementation of functions for interactive data access and visualization.
  • Compatibility with 10x Genomics Visium platform data and the Bioconductor ecosystem.

Main Results:

  • spatialLIBD allows interactive exploration of spatially-resolved transcriptomics data.
  • The package visualizes gene expression and clusters from the 10x Visium platform.
  • Analysis can be performed locally or through a web application.

Conclusions:

  • spatialLIBD is available as an R/Bioconductor package.
  • It is compatible with SpatialExperiment and the broader Bioconductor ecosystem.
  • Facilitates analysis and interactive exploration of Visium platform spatial data.