SpatialDE: identification of spatially variable genes

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 develop SpatialDE, a statistical test to identify genes with spatial patterns of expression variation from multiplexed i...

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Detalles Bibliográficos
Autores principales: Svensson, Valentine, Teichmann, Sarah A, Stegle, Oliver
Formato: Online Artículo Texto
Lenguaje:English
Publicado: 2018
Materias:
Article
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6350895/
https://www.ncbi.nlm.nih.gov/pubmed/29553579
http://dx.doi.org/10.1038/nmeth.4636
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author Svensson, Valentine
Teichmann, Sarah A
Stegle, Oliver
author_facet Svensson, Valentine
Teichmann, Sarah A
Stegle, Oliver
author_sort Svensson, Valentine
collection PubMed
description 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 develop 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.
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spelling pubmed-63508952019-01-29 SpatialDE: identification of spatially variable genes Svensson, Valentine Teichmann, Sarah A Stegle, Oliver Nat Methods Article 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 develop 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. 2018-03-19 2018-05 /pmc/articles/PMC6350895/ /pubmed/29553579 http://dx.doi.org/10.1038/nmeth.4636 Text en Users may view, print, copy, and download text and data-mine the content in such documents, for the purposes of academic research, subject always to the full Conditions of use:http://www.nature.com/authors/editorial_policies/license.html#terms
spellingShingle Article
Svensson, Valentine
Teichmann, Sarah A
Stegle, Oliver
SpatialDE: identification of spatially variable genes
title SpatialDE: identification of spatially variable genes
title_full SpatialDE: identification of spatially variable genes
title_fullStr SpatialDE: identification of spatially variable genes
title_full_unstemmed SpatialDE: identification of spatially variable genes
title_short SpatialDE: identification of spatially variable genes
title_sort spatialde: identification of spatially variable genes
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6350895/
https://www.ncbi.nlm.nih.gov/pubmed/29553579
http://dx.doi.org/10.1038/nmeth.4636
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AT teichmannsaraha spatialdeidentificationofspatiallyvariablegenes
AT stegleoliver spatialdeidentificationofspatiallyvariablegenes

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