spatialLIBD: an R/Bioconductor package to visualize spatially-resolved transcriptomics data.
BMC Genomics
; 23(1): 434, 2022 Jun 10.
Article
em En
| MEDLINE
| ID: mdl-35689177
ABSTRACT
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.Palavras-chave
Texto completo:
1
Coleções:
01-internacional
Base de dados:
MEDLINE
Assunto principal:
Ecossistema
/
Transcriptoma
Idioma:
En
Ano de publicação:
2022
Tipo de documento:
Article