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

Image credit: bioRxiv

Abstract

Motivation. 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 tissuespecific 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. Availability. spatialLIBD is available at bioconductor.org/packages/spatialLIBD.

Publication
bioRxiv
Brenda Pardo
Brenda Pardo
LCG-UNAM 2020-2021