SpatialView: an interactive web application for visualization of multiple samples in spatial transcriptomics experiments.

Autor:	Mohanty C; Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI 53726, United States., Prasad A; Department of Dermatology, University of Pennsylvania, Philadelphia, PA 19104, United States., Cheng L; Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI 53726, United States., Arkin LM; Department of Dermatology, University of Wisconsin-Madison, Madison, WI 53715, United States., Shields BE; Department of Dermatology, University of Wisconsin-Madison, Madison, WI 53715, United States., Drolet B; Department of Dermatology, University of Wisconsin-Madison, Madison, WI 53715, United States., Kendziorski C; Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI 53726, United States.
Jazyk:	angličtina
Zdroj:	Bioinformatics (Oxford, England) [Bioinformatics] 2024 Mar 04; Vol. 40 (3).
DOI:	10.1093/bioinformatics/btae117
Abstrakt:	Motivation: Spatial transcriptomics (ST) experiments provide spatially localized measurements of genome-wide gene expression allowing for an unprecedented opportunity to investigate cellular heterogeneity and organization within a tissue. Statistical and computational frameworks exist that implement robust methods for pre-processing and analyzing data in ST experiments. However, the lack of an interactive suite of tools for visualizing ST data and results currently limits the full potential of ST experiments. Results: To fill the gap, we developed SpatialView, an open-source web browser-based interactive application for visualizing data and results from multiple 10× Genomics Visium ST experiments. We anticipate SpatialView will be useful to a broad array of clinical and basic science investigators utilizing ST to study disease. Availability and Implementation: SpatialView is available at https://github.com/kendziorski-lab/SpatialView (and https://doi.org/10.5281/zenodo.10223907); a demo application is available at https://www.biostat.wisc.edu/˜kendzior/spatialviewdemo/. (Published by Oxford University Press 2024.)
Databáze:	MEDLINE
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