OneStopRNAseq: A Web Application for Comprehensive and Efficient Analyses of RNA-Seq Data
UMass Chan Affiliations
Department of Molecular, Cell and Cancer BiologyDocument Type
Journal ArticlePublication Date
2020-10-02Keywords
GSEARNA-seq
allele–specific expression quantification
alternative-splicing analysis
differential exon usage
differential gene expression
differential transposable element expression analysis
pipeline
quality control
visualization
web application
workflow
Bioinformatics
Computational Biology
Databases and Information Systems
Genomics
Health Information Technology
Nucleic Acids, Nucleotides, and Nucleosides
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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.Source
Li R, Hu K, Liu H, Green MR, Zhu LJ. OneStopRNAseq: A Web Application for Comprehensive and Efficient Analyses of RNA-Seq Data. Genes (Basel). 2020 Oct 2;11(10):1165. doi: 10.3390/genes11101165. PMID: 33023248; PMCID: PMC7650687. Link to article on publisher's site
DOI
10.3390/genes11101165Permanent Link to this Item
http://hdl.handle.net/20.500.14038/41621PubMed ID
33023248Related Resources
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© 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/).Distribution License
http://creativecommons.org/licenses/by/4.0/ae974a485f413a2113503eed53cd6c53
10.3390/genes11101165
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Except where otherwise noted, this item's license is described as © 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/).