SpatialDE: identification of spatially variable genes.
Accepted version
Peer-reviewed
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Authors
Svensson, Valentine
Teichmann, Sarah A
Stegle, Oliver
Abstract
Technological advances have made it possible to measure spatially resolved gene expression at high throughput. However, methods to analyze these data are not established. Here we describe SpatialDE, a statistical test to identify genes with spatial patterns of expression variation from multiplexed imaging or spatial RNA-sequencing data. SpatialDE also implements 'automatic expression histology', a spatial gene-clustering approach that enables expression-based tissue histology.
Description
Keywords
Breast Neoplasms, Female, Gene Expression Regulation, Neoplastic, Humans, Models, Biological, Protein Transport, Single-Cell Analysis
Journal Title
Nature Methods
Conference Name
Journal ISSN
1548-7091
1548-7105
1548-7105
Volume Title
15
Publisher
Public Library of Science
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All rights reserved