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

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ID: 278316
2024
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Abstract
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.To fill the gap, we developed SpatialView, an open-source web browser-based interactive application for visualizing data and results from multiple 10x 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.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/.Supplementary data are available at Bioinformatics online.
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mohanty2024spatialviewbioinformatics Use this key to autocite in the manuscript while using SciMatic Manuscript Manager or Thesis Manager
Authors Chitrasen Mohanty, Aman Prasad, Lingxin Cheng, Lisa M Arkin, Bridget E Shields, Beth Drolet, Christina Kendziorski
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Journal Bioinformatics
Year 2024
DOI
btae117
URL
Keywords
Deep learning agent-based models surrogate modeling emulation spatio-temporal emergence

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