Please use this identifier to cite or link to this item: http://hdl.handle.net/1822/59408

TitleDEWE: a novel tool for executing differential expression RNA-Seq workflows in biomedical research
Author(s)López-Fernández, Hugo
Blanco-Míguez, Aitor
Fdez-Riverola, Florentino
Sánchez, Borja
Lourenço, Anália
KeywordsDifferential expression
RNA-Seq
Open-source software
Workflow management
Translational application
Issue date2019
PublisherElsevier
JournalComputers in Biology and Medicine
CitationLópez-Fernández, Hugo; Blanco-Míguez, Aitor; Fdez-Riverola, Florentino; Sánchez, Borja; Lourenço, Anália, DEWE: A novel tool for executing differential expression RNA-Seq workflows in biomedical research. Computers in Biology and Medicine, 107, 197-205, 2019
Abstract(s)Background Transcriptomics profiling aims to identify and quantify all transcripts present within a cell type or tissue at a particular state, and thus provide information on the genes expressed in specific experimental settings, differentiation or disease conditions. RNA-Seq technology is becoming the standard approach for such studies, but available analysis tools are often hard to install, configure and use by users without advanced bioinformatics skills. Methods Within reason, DEWE aims to make RNA-Seq analysis as easy for non-proficient users as for experienced bioinformaticians. DEWE supports two well-established and widely used differential expression analysis workflows: using Bowtie2 or HISAT2 for sequence alignment; and, both applying StringTie for quantification, and Ballgown and edgeR for differential expression analysis. Also, it enables the tailored execution of individual tools as well as helps with the management and visualisation of differential expression results. Results DEWE provides a user-friendly interface designed to reduce the learning curve of less knowledgeable users while enabling analysis customisation and software extension by advanced users. Docker technology helps overcome installation and configuration hurdles. In addition, DEWE produces high quality and publication-ready outputs in the form of tab-delimited files and figures, as well as helps researchers with further analyses, such as pathway enrichment analysis. Conclusions The abilities of DEWE are exemplified here by practical application to a comparative analysis of monocytes and monocyte-derived dendritic cells, a study of clinical relevance. DEWE installers and documentation are freely available at https://www.sing-group.org/dewe.
TypeArticle
URIhttp://hdl.handle.net/1822/59408
DOI10.1016/j.compbiomed.2019.02.021
ISSN0010-4825
e-ISSN0010-4825
Publisher versionhttps://www.journals.elsevier.com/computers-in-biology-and-medicine
Peer-Reviewedyes
AccessOpen access
Appears in Collections:CEB - Publicações em Revistas/Séries Internacionais / Publications in International Journals/Series

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