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OneStopRNAseq: A Web Application for Comprehensive and Efficient Analyses of RNA-Seq Data

Over the past decade, a large amount of RNA sequencing (RNA-seq) data were deposited in public repositories, and more are being produced at an unprecedented rate. However, there are few open source tools with point-and-click interfaces that are versatile and offer streamlined comprehensive analysis...

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Detalles Bibliográficos
Autores principales: Li, Rui, Hu, Kai, Liu, Haibo, Green, Michael R., Zhu, Lihua Julie
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2020
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7650687/
https://www.ncbi.nlm.nih.gov/pubmed/33023248
http://dx.doi.org/10.3390/genes11101165
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author Li, Rui
Hu, Kai
Liu, Haibo
Green, Michael R.
Zhu, Lihua Julie
author_facet Li, Rui
Hu, Kai
Liu, Haibo
Green, Michael R.
Zhu, Lihua Julie
author_sort Li, Rui
collection PubMed
description Over the past decade, a large amount of RNA sequencing (RNA-seq) data were deposited in public repositories, and more are being produced at an unprecedented rate. However, there are few open source tools with point-and-click interfaces that are versatile and offer streamlined comprehensive analysis of RNA-seq datasets. To maximize the capitalization of these vast public resources and facilitate the analysis of RNA-seq data by biologists, we developed a web application called OneStopRNAseq for the one-stop analysis of RNA-seq data. OneStopRNAseq has user-friendly interfaces and offers workflows for common types of RNA-seq data analyses, such as comprehensive data-quality control, differential analysis of gene expression, exon usage, alternative splicing, transposable element expression, allele-specific gene expression quantification, and gene set enrichment analysis. Users only need to select the desired analyses and genome build, and provide a Gene Expression Omnibus (GEO) accession number or Dropbox links to sequence files, alignment files, gene-expression-count tables, or rank files with the corresponding metadata. Our pipeline facilitates the comprehensive and efficient analysis of private and public RNA-seq data.
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spelling pubmed-76506872020-11-10 OneStopRNAseq: A Web Application for Comprehensive and Efficient Analyses of RNA-Seq Data Li, Rui Hu, Kai Liu, Haibo Green, Michael R. Zhu, Lihua Julie Genes (Basel) Article Over the past decade, a large amount of RNA sequencing (RNA-seq) data were deposited in public repositories, and more are being produced at an unprecedented rate. However, there are few open source tools with point-and-click interfaces that are versatile and offer streamlined comprehensive analysis of RNA-seq datasets. To maximize the capitalization of these vast public resources and facilitate the analysis of RNA-seq data by biologists, we developed a web application called OneStopRNAseq for the one-stop analysis of RNA-seq data. OneStopRNAseq has user-friendly interfaces and offers workflows for common types of RNA-seq data analyses, such as comprehensive data-quality control, differential analysis of gene expression, exon usage, alternative splicing, transposable element expression, allele-specific gene expression quantification, and gene set enrichment analysis. Users only need to select the desired analyses and genome build, and provide a Gene Expression Omnibus (GEO) accession number or Dropbox links to sequence files, alignment files, gene-expression-count tables, or rank files with the corresponding metadata. Our pipeline facilitates the comprehensive and efficient analysis of private and public RNA-seq data. MDPI 2020-10-02 /pmc/articles/PMC7650687/ /pubmed/33023248 http://dx.doi.org/10.3390/genes11101165 Text en © 2020 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (http://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Li, Rui
Hu, Kai
Liu, Haibo
Green, Michael R.
Zhu, Lihua Julie
OneStopRNAseq: A Web Application for Comprehensive and Efficient Analyses of RNA-Seq Data
title OneStopRNAseq: A Web Application for Comprehensive and Efficient Analyses of RNA-Seq Data
title_full OneStopRNAseq: A Web Application for Comprehensive and Efficient Analyses of RNA-Seq Data
title_fullStr OneStopRNAseq: A Web Application for Comprehensive and Efficient Analyses of RNA-Seq Data
title_full_unstemmed OneStopRNAseq: A Web Application for Comprehensive and Efficient Analyses of RNA-Seq Data
title_short OneStopRNAseq: A Web Application for Comprehensive and Efficient Analyses of RNA-Seq Data
title_sort onestoprnaseq: a web application for comprehensive and efficient analyses of rna-seq data
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7650687/
https://www.ncbi.nlm.nih.gov/pubmed/33023248
http://dx.doi.org/10.3390/genes11101165
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