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

• DOI: 10.1186/s12864-022-08601-w
• Publication Date: 2022-06-10T18:08:00Z
• Authors: Brenda Pardo; Abby Spangler; Lukas M. Weber; Stephanie C. Page; Stephanie C. Hicks; Andrew E. Jaffe; Keri Martinowich; Kristen R. Maynard; Leonardo Collado-...
• Keywords: Bioconductor; R package

Abstract Background Spatially-resolved transcriptomics has now enabled the quantification of high-throughput and transcriptome-wide gene expression in intact tissue while also retaining spatial coordinates. Incorporating precise mapping activity advances our understanding tissue-specific biological processes. In order to interpret these novel data types, interactive visualization tools are necessary. Results We describe spatialLIBD , an R/Bioconductor package interactively explore spatially-resolved generated with 10x Genomics Visium platform. The contains functions access, visualize, inspect observed data-driven clusters identified supervised or unsupervised analyses, either on user’s computer through a web application. Conclusions is available at https://bioconductor.org/packages/spatialLIBD . It fully compatible SpatialExperiment Bioconductor ecosystem. Its functionality facilitates analyzing exploring from