{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,11,21]],"date-time":"2025-11-21T06:39:12Z","timestamp":1763707152293,"version":"3.45.0"},"reference-count":34,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2025,11,21]],"date-time":"2025-11-21T00:00:00Z","timestamp":1763683200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["frontiersin.org"],"crossmark-restriction":true},"short-container-title":["Front. Bioinform."],"abstract":"<jats:p>\n                    Dual RNA-sequencing enables simultaneous profiling of protein-coding and non-coding transcripts from two interacting organisms, an essential capability when physical separation is difficult, such as in host-parasite or cross-kingdom interactions (e.g., plant-plant or host-pathogen systems). By allowing\n                    <jats:italic>in silico<\/jats:italic>\n                    separation of mixed reads, dual RNA-seq reveals the transcriptomic dynamics of both partners during interaction. However, existing analysis workflows often require programming expertise, limiting accessibility. We present inDAGO, a free, open-source, cross-platform graphical user interface designed for biologists without coding skills. inDAGO supports both bulk and dual RNA sequencing, with dual RNA sequencing further accommodating both sequential and combined approaches. The interface guides users through key analysis steps, including quality control, read alignment, read summarization, exploratory data analysis, and identification of differentially expressed genes, while generating intermediate outputs and publication-ready plots. Optimized for speed and efficiency, inDAGO performs complete analyses on a standard laptop (16 GB RAM) without requiring high-performance computing. We validated inDAGO using diverse real datasets to demonstrate its reliability and usability. inDAGO, available on CRAN (\n                    <jats:ext-link>https:\/\/cran.r-project.org\/web\/packages\/inDAGO\/<\/jats:ext-link>\n                    ) and GitHub (\n                    <jats:ext-link>https:\/\/github.com\/inDAGOverse\/inDAGO<\/jats:ext-link>\n                    ), lowers the technical barrier to dual RNA-seq by enabling robust, reproducible analyses, even for users without coding experience.\n                  <\/jats:p>","DOI":"10.3389\/fbinf.2025.1696823","type":"journal-article","created":{"date-parts":[[2025,11,21]],"date-time":"2025-11-21T06:30:57Z","timestamp":1763706657000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":0,"title":["inDAGO: a user-friendly interface for seamless dual and bulk RNA-Seq analysis"],"prefix":"10.3389","volume":"5","author":[{"given":"Gaetano","family":"Aufiero","sequence":"first","affiliation":[]},{"given":"Carmine","family":"Fruggiero","sequence":"additional","affiliation":[]},{"given":"Nunzio","family":"D\u2019Agostino","sequence":"additional","affiliation":[]}],"member":"1965","published-online":{"date-parts":[[2025,11,21]]},"reference":[{"key":"B1","doi-asserted-by":"publisher","first-page":"W537","DOI":"10.1093\/nar\/gky379","article-title":"The galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2018 update","volume":"46","author":"Afgan","year":"2018","journal-title":"Nucleic Acids Res."},{"key":"B2","doi-asserted-by":"publisher","first-page":"R106","DOI":"10.1186\/gb-2010-11-10-r106","article-title":"Differential expression analysis for sequence count data","volume":"11","author":"Anders","year":"2010","journal-title":"Genome Biol."},{"key":"B3","doi-asserted-by":"publisher","first-page":"2114","DOI":"10.1093\/bioinformatics\/btu170","article-title":"Trimmomatic: a flexible trimmer for illumina sequence data","volume":"30","author":"Bolger","year":"2014","journal-title":"Bioinformatics"},{"key":"B4","doi-asserted-by":"publisher","first-page":"94","DOI":"10.1186\/1471-2105-11-94","article-title":"Evaluation of statistical methods for normalization and differential expression in mRNA-Seq experiments","volume":"11","author":"Bullard","year":"2010","journal-title":"BMC Bioinforma."},{"key":"B5","unstructured":"Shiny: web application framework for R\n          \n          \n            \n              Chang\n              W.\n            \n            \n              Cheng\n              J.\n            \n            \n              Allaire\n              J.\n            \n            \n              Sievert\n              C.\n            \n            \n              Schloerke\n              B.\n            \n            \n              Xie\n              Y.\n            \n          \n          \n          2025"},{"key":"B6","doi-asserted-by":"publisher","first-page":"1438","DOI":"10.12688\/f1000research.8987.2","article-title":"From reads to genes to pathways: differential expression analysis of RNA-seq experiments using rsubread and the edgeR quasi-likelihood pipeline","volume":"5","author":"Chen","year":"2016","journal-title":"F1000Res"},{"key":"B7","doi-asserted-by":"publisher","first-page":"gkaf018","DOI":"10.1093\/nar\/gkaf018","article-title":"edgeR v4: powerful differential analysis of sequencing data with expanded functionality and improved support for small counts and larger datasets","volume":"53","author":"Chen","year":"2025","journal-title":"Nucleic Acids Res."},{"key":"B8","doi-asserted-by":"publisher","first-page":"2938","DOI":"10.1093\/bioinformatics\/btx364","article-title":"UpSetR: an R package for the visualization of intersecting sets and their properties","volume":"33","author":"Conway","year":"2017","journal-title":"Bioinformatics"},{"key":"B9","doi-asserted-by":"publisher","first-page":"15","DOI":"10.1093\/bioinformatics\/bts635","article-title":"STAR: ultrafast universal RNA-seq aligner","volume":"29","author":"Dobin","year":"2013","journal-title":"Bioinformatics"},{"key":"B10","unstructured":"RNAseQC: helper functions for conducting quality control of RNAseq data\n          \n          \n            \n              Dufort\n              M.\n            \n          \n          \n          2025"},{"key":"B11","doi-asserted-by":"publisher","first-page":"e20190215","DOI":"10.1590\/1678-4685-GMB-2019-0215","article-title":"The combined analysis as the best strategy for dual RNA-seq mapping","volume":"42","author":"Espindula","year":"2019","journal-title":"Genet. 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