RT Journal Article
SR Electronic
T1 spatialLIBD: an R/Bioconductor package to visualize spatially-resolved transcriptomics data
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 2021.04.29.440149
DO 10.1101/2021.04.29.440149
A1 Brenda Pardo
A1 Abby Spangler
A1 Lukas M. Weber
A1 Stephanie C. Hicks
A1 Andrew E. Jaffe
A1 Keri Martinowich
A1 Kristen R. Maynard
A1 Leonardo Collado-Torres
YR 2021
UL http://biorxiv.org/content/early/2021/04/30/2021.04.29.440149.abstract
AB 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.Supplementary information Supplementary data are available at Bioinformatics online.Competing Interest StatementThe authors have declared no competing interest.