A selective review of recent developments in spatially variable gene detection for spatial transcriptomics

With the emergence of advanced spatial transcriptomic technologies, there has been a surge in research papers dedicated to analyzing spatial transcriptomics data, resulting in significant contributions to our understanding of biology. The initial stage of downstream analysis of spatial transcriptomi...

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Autores principales: Adhikari, Sikta Das, Yang, Jiaxin, Wang, Jianrong, Cui, Yuehua
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Cornell University 2023
Materias:
Article
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10690303/
https://www.ncbi.nlm.nih.gov/pubmed/38045476
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author Adhikari, Sikta Das
Yang, Jiaxin
Wang, Jianrong
Cui, Yuehua
author_facet Adhikari, Sikta Das
Yang, Jiaxin
Wang, Jianrong
Cui, Yuehua
author_sort Adhikari, Sikta Das
collection PubMed
description With the emergence of advanced spatial transcriptomic technologies, there has been a surge in research papers dedicated to analyzing spatial transcriptomics data, resulting in significant contributions to our understanding of biology. The initial stage of downstream analysis of spatial transcriptomic data has centered on identifying spatially variable genes (SVGs) or genes expressed with specific spatial patterns across the tissue. SVG detection is an important task since many downstream analyses depend on these selected SVGs. Over the past few years, a plethora of new methods have been proposed for the detection of SVGs, accompanied by numerous innovative concepts and discussions. This article provides a selective review of methods and their practical implementations, offering valuable insights into the current literature in this field.
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spelling pubmed-106903032023-12-02 A selective review of recent developments in spatially variable gene detection for spatial transcriptomics Adhikari, Sikta Das Yang, Jiaxin Wang, Jianrong Cui, Yuehua ArXiv Article With the emergence of advanced spatial transcriptomic technologies, there has been a surge in research papers dedicated to analyzing spatial transcriptomics data, resulting in significant contributions to our understanding of biology. The initial stage of downstream analysis of spatial transcriptomic data has centered on identifying spatially variable genes (SVGs) or genes expressed with specific spatial patterns across the tissue. SVG detection is an important task since many downstream analyses depend on these selected SVGs. Over the past few years, a plethora of new methods have been proposed for the detection of SVGs, accompanied by numerous innovative concepts and discussions. This article provides a selective review of methods and their practical implementations, offering valuable insights into the current literature in this field. Cornell University 2023-11-23 /pmc/articles/PMC10690303/ /pubmed/38045476 Text en https://creativecommons.org/licenses/by/4.0/This work is licensed under a Creative Commons Attribution 4.0 International License (https://creativecommons.org/licenses/by/4.0/) , which allows reusers to distribute, remix, adapt, and build upon the material in any medium or format, so long as attribution is given to the creator. The license allows for commercial use.
spellingShingle Article
Adhikari, Sikta Das
Yang, Jiaxin
Wang, Jianrong
Cui, Yuehua
A selective review of recent developments in spatially variable gene detection for spatial transcriptomics
title A selective review of recent developments in spatially variable gene detection for spatial transcriptomics
title_full A selective review of recent developments in spatially variable gene detection for spatial transcriptomics
title_fullStr A selective review of recent developments in spatially variable gene detection for spatial transcriptomics
title_full_unstemmed A selective review of recent developments in spatially variable gene detection for spatial transcriptomics
title_short A selective review of recent developments in spatially variable gene detection for spatial transcriptomics
title_sort selective review of recent developments in spatially variable gene detection for spatial transcriptomics
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10690303/
https://www.ncbi.nlm.nih.gov/pubmed/38045476
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