Asc-Seurat: analytical single-cell Seurat-based web application

Abstract Background Single-cell RNA sequencing (scRNA-seq) has revolutionized the study of transcriptomes, arising as a powerful tool for discovering and characterizing cell types and their developmental trajectories. However, scRNA-seq analysis is complex, requiring a continuous, iterative process...

Descripción completa

Guardado en:

Detalles Bibliográficos
Autores principales:	W. J. Pereira, F. M. Almeida, D. Conde, K. M. Balmant, P. M. Triozzi, H. W. Schmidt, C. Dervinis, G. J. Pappas, M. Kirst
Formato:	article
Lenguaje:	EN
Publicado:	BMC 2021
Materias:	Single-cell RNA sequencing scRNA-seq Web application Gene expression Computer applications to medicine. Medical informatics R858-859.7 Biology (General) QH301-705.5
Acceso en línea:	https://doaj.org/article/4b03afee582043438c940730d80ff4fb
Etiquetas:	Agregar Etiqueta Sin Etiquetas, Sea el primero en etiquetar este registro!

id	oai:doaj.org-article:4b03afee582043438c940730d80ff4fb
record_format	dspace
spelling	oai:doaj.org-article:4b03afee582043438c940730d80ff4fb2021-11-21T12:09:15ZAsc-Seurat: analytical single-cell Seurat-based web application10.1186/s12859-021-04472-21471-2105https://doaj.org/article/4b03afee582043438c940730d80ff4fb2021-11-01T00:00:00Zhttps://doi.org/10.1186/s12859-021-04472-2https://doaj.org/toc/1471-2105Abstract Background Single-cell RNA sequencing (scRNA-seq) has revolutionized the study of transcriptomes, arising as a powerful tool for discovering and characterizing cell types and their developmental trajectories. However, scRNA-seq analysis is complex, requiring a continuous, iterative process to refine the data and uncover relevant biological information. A diversity of tools has been developed to address the multiple aspects of scRNA-seq data analysis. However, an easy-to-use web application capable of conducting all critical steps of scRNA-seq data analysis is still lacking. Summary We present Asc-Seurat, a feature-rich workbench, providing an user-friendly and easy-to-install web application encapsulating tools for an all-encompassing and fluid scRNA-seq data analysis. Asc-Seurat implements functions from the Seurat package for quality control, clustering, and genes differential expression. In addition, Asc-Seurat provides a pseudotime module containing dozens of models for the trajectory inference and a functional annotation module that allows recovering gene annotation and detecting gene ontology enriched terms. We showcase Asc-Seurat’s capabilities by analyzing a peripheral blood mononuclear cell dataset. Conclusions Asc-Seurat is a comprehensive workbench providing an accessible graphical interface for scRNA-seq analysis by biologists. Asc-Seurat significantly reduces the time and effort required to analyze and interpret the information in scRNA-seq datasets.W. J. PereiraF. M. AlmeidaD. CondeK. M. BalmantP. M. TriozziH. W. SchmidtC. DervinisG. J. PappasM. KirstBMCarticleSingle-cell RNA sequencingscRNA-seqWeb applicationGene expressionComputer applications to medicine. Medical informaticsR858-859.7Biology (General)QH301-705.5ENBMC Bioinformatics, Vol 22, Iss 1, Pp 1-14 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Single-cell RNA sequencing scRNA-seq Web application Gene expression Computer applications to medicine. Medical informatics R858-859.7 Biology (General) QH301-705.5
spellingShingle	Single-cell RNA sequencing scRNA-seq Web application Gene expression Computer applications to medicine. Medical informatics R858-859.7 Biology (General) QH301-705.5 W. J. Pereira F. M. Almeida D. Conde K. M. Balmant P. M. Triozzi H. W. Schmidt C. Dervinis G. J. Pappas M. Kirst Asc-Seurat: analytical single-cell Seurat-based web application
description	Abstract Background Single-cell RNA sequencing (scRNA-seq) has revolutionized the study of transcriptomes, arising as a powerful tool for discovering and characterizing cell types and their developmental trajectories. However, scRNA-seq analysis is complex, requiring a continuous, iterative process to refine the data and uncover relevant biological information. A diversity of tools has been developed to address the multiple aspects of scRNA-seq data analysis. However, an easy-to-use web application capable of conducting all critical steps of scRNA-seq data analysis is still lacking. Summary We present Asc-Seurat, a feature-rich workbench, providing an user-friendly and easy-to-install web application encapsulating tools for an all-encompassing and fluid scRNA-seq data analysis. Asc-Seurat implements functions from the Seurat package for quality control, clustering, and genes differential expression. In addition, Asc-Seurat provides a pseudotime module containing dozens of models for the trajectory inference and a functional annotation module that allows recovering gene annotation and detecting gene ontology enriched terms. We showcase Asc-Seurat’s capabilities by analyzing a peripheral blood mononuclear cell dataset. Conclusions Asc-Seurat is a comprehensive workbench providing an accessible graphical interface for scRNA-seq analysis by biologists. Asc-Seurat significantly reduces the time and effort required to analyze and interpret the information in scRNA-seq datasets.
format	article
author	W. J. Pereira F. M. Almeida D. Conde K. M. Balmant P. M. Triozzi H. W. Schmidt C. Dervinis G. J. Pappas M. Kirst
author_facet	W. J. Pereira F. M. Almeida D. Conde K. M. Balmant P. M. Triozzi H. W. Schmidt C. Dervinis G. J. Pappas M. Kirst
author_sort	W. J. Pereira
title	Asc-Seurat: analytical single-cell Seurat-based web application
title_short	Asc-Seurat: analytical single-cell Seurat-based web application
title_full	Asc-Seurat: analytical single-cell Seurat-based web application
title_fullStr	Asc-Seurat: analytical single-cell Seurat-based web application
title_full_unstemmed	Asc-Seurat: analytical single-cell Seurat-based web application
title_sort	asc-seurat: analytical single-cell seurat-based web application
publisher	BMC
publishDate	2021
url	https://doaj.org/article/4b03afee582043438c940730d80ff4fb
work_keys_str_mv	AT wjpereira ascseuratanalyticalsinglecellseuratbasedwebapplication AT fmalmeida ascseuratanalyticalsinglecellseuratbasedwebapplication AT dconde ascseuratanalyticalsinglecellseuratbasedwebapplication AT kmbalmant ascseuratanalyticalsinglecellseuratbasedwebapplication AT pmtriozzi ascseuratanalyticalsinglecellseuratbasedwebapplication AT hwschmidt ascseuratanalyticalsinglecellseuratbasedwebapplication AT cdervinis ascseuratanalyticalsinglecellseuratbasedwebapplication AT gjpappas ascseuratanalyticalsinglecellseuratbasedwebapplication AT mkirst ascseuratanalyticalsinglecellseuratbasedwebapplication
_version_	1718419183223439360

Asc-Seurat: analytical single-cell Seurat-based web application

Ejemplares similares