Single-cell spatial explorer: easy exploration of spatial and multimodal transcriptomics

BACKGROUND: The development of single-cell technologies yields large datasets of information as diverse and multimodal as transcriptomes, immunophenotypes, and spatial position from tissue sections in the so-called ’spatial transcriptomics’. Currently however, user-friendly, powerful, and free algor...

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Autores principales: Pont, Frédéric, Cerapio, Juan Pablo, Gravelle, Pauline, Ligat, Laetitia, Valle, Carine, Sarot, Emeline, Perrier, Marion, Lopez, Frédéric, Laurent, Camille, Fournié, Jean Jacques, Tosolini, Marie
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2023
Materias:
Software
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9881287/
https://www.ncbi.nlm.nih.gov/pubmed/36707753
http://dx.doi.org/10.1186/s12859-023-05150-1
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author Pont, Frédéric
Cerapio, Juan Pablo
Gravelle, Pauline
Ligat, Laetitia
Valle, Carine
Sarot, Emeline
Perrier, Marion
Lopez, Frédéric
Laurent, Camille
Fournié, Jean Jacques
Tosolini, Marie
author_facet Pont, Frédéric
Cerapio, Juan Pablo
Gravelle, Pauline
Ligat, Laetitia
Valle, Carine
Sarot, Emeline
Perrier, Marion
Lopez, Frédéric
Laurent, Camille
Fournié, Jean Jacques
Tosolini, Marie
author_sort Pont, Frédéric
collection PubMed
description BACKGROUND: The development of single-cell technologies yields large datasets of information as diverse and multimodal as transcriptomes, immunophenotypes, and spatial position from tissue sections in the so-called ’spatial transcriptomics’. Currently however, user-friendly, powerful, and free algorithmic tools for straightforward analysis of spatial transcriptomic datasets are scarce. RESULTS: Here, we introduce Single-Cell Spatial Explorer, an open-source software for multimodal exploration of spatial transcriptomics, examplified with 9 human and murine tissues datasets from 4 different technologies. CONCLUSIONS: Single-Cell Spatial Explorer is a very powerful, versatile, and interoperable tool for spatial transcriptomics analysis.
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spelling pubmed-98812872023-01-28 Single-cell spatial explorer: easy exploration of spatial and multimodal transcriptomics Pont, Frédéric Cerapio, Juan Pablo Gravelle, Pauline Ligat, Laetitia Valle, Carine Sarot, Emeline Perrier, Marion Lopez, Frédéric Laurent, Camille Fournié, Jean Jacques Tosolini, Marie BMC Bioinformatics Software BACKGROUND: The development of single-cell technologies yields large datasets of information as diverse and multimodal as transcriptomes, immunophenotypes, and spatial position from tissue sections in the so-called ’spatial transcriptomics’. Currently however, user-friendly, powerful, and free algorithmic tools for straightforward analysis of spatial transcriptomic datasets are scarce. RESULTS: Here, we introduce Single-Cell Spatial Explorer, an open-source software for multimodal exploration of spatial transcriptomics, examplified with 9 human and murine tissues datasets from 4 different technologies. CONCLUSIONS: Single-Cell Spatial Explorer is a very powerful, versatile, and interoperable tool for spatial transcriptomics analysis. BioMed Central 2023-01-27 /pmc/articles/PMC9881287/ /pubmed/36707753 http://dx.doi.org/10.1186/s12859-023-05150-1 Text en © The Author(s) 2023 https://creativecommons.org/licenses/by/4.0/Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) . The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/ (https://creativecommons.org/publicdomain/zero/1.0/) ) applies to the data made available in this article, unless otherwise stated in a credit line to the data.
spellingShingle Software
Pont, Frédéric
Cerapio, Juan Pablo
Gravelle, Pauline
Ligat, Laetitia
Valle, Carine
Sarot, Emeline
Perrier, Marion
Lopez, Frédéric
Laurent, Camille
Fournié, Jean Jacques
Tosolini, Marie
Single-cell spatial explorer: easy exploration of spatial and multimodal transcriptomics
title Single-cell spatial explorer: easy exploration of spatial and multimodal transcriptomics
title_full Single-cell spatial explorer: easy exploration of spatial and multimodal transcriptomics
title_fullStr Single-cell spatial explorer: easy exploration of spatial and multimodal transcriptomics
title_full_unstemmed Single-cell spatial explorer: easy exploration of spatial and multimodal transcriptomics
title_short Single-cell spatial explorer: easy exploration of spatial and multimodal transcriptomics
title_sort single-cell spatial explorer: easy exploration of spatial and multimodal transcriptomics
topic Software
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9881287/
https://www.ncbi.nlm.nih.gov/pubmed/36707753
http://dx.doi.org/10.1186/s12859-023-05150-1
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