{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,26]],"date-time":"2026-02-26T20:34:21Z","timestamp":1772138061521,"version":"3.50.1"},"reference-count":10,"publisher":"Oxford University Press (OUP)","issue":"8","license":[{"start":{"date-parts":[[2023,8,7]],"date-time":"2023-08-07T00:00:00Z","timestamp":1691366400000},"content-version":"vor","delay-in-days":6,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Landes Initiative Rheinland-Pfalz and the Resilience, Adaptation, and Longevity"},{"DOI":"10.13039\/501100001659","name":"German Research Foundation","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100001659","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2023,8,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Summary<\/jats:title>\n                    <jats:p>Oxford Nanopore Technologies\u2019 (ONT) sequencing platform offers an excellent opportunity to perform real-time analysis during sequencing. This feature allows for early insights into experimental data and accelerates a potential decision-making process for further analysis, which can be particularly relevant in the clinical context. Although some tools for the real-time analysis of DNA-sequencing data already exist, there is currently no application available for differential transcriptome data analysis designed for scientists or physicians with limited bioinformatics knowledge. Here, we introduce NanopoReaTA, a user-friendly real-time analysis toolbox for RNA-sequencing data from ONT. Sequencing results from a running or finished experiment are processed through an R Shiny-based graphical user interface with an integrated Nextflow pipeline for whole transcriptome or gene-specific analyses. NanopoReaTA provides visual snapshots of a sequencing run in progress, thus enabling interactive sequencing and rapid decision making that could also be applied to clinical cases.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>Github https:\/\/github.com\/AnWiercze\/NanopoReaTA; Zenodo https:\/\/doi.org\/10.5281\/zenodo.8099825.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btad492","type":"journal-article","created":{"date-parts":[[2023,8,7]],"date-time":"2023-08-07T12:51:14Z","timestamp":1691412674000},"source":"Crossref","is-referenced-by-count":13,"title":["NanopoReaTA: a user-friendly tool for nanopore-seq real-time transcriptional analysis"],"prefix":"10.1093","volume":"39","author":[{"given":"Anna","family":"Wierczeiko","sequence":"first","affiliation":[{"name":"Institute of Human Genetics, University Medical Center of the Johannes Gutenberg University Mainz , Mainz 55131, Germany"}]},{"given":"Stefan","family":"Pastore","sequence":"additional","affiliation":[{"name":"Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Mainz , Mainz 55128, Germany"}]},{"given":"Stefan","family":"M\u00fcndnich","sequence":"additional","affiliation":[{"name":"Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Mainz , Mainz 55128, Germany"}]},{"given":"Anne M","family":"Busch","sequence":"additional","affiliation":[{"name":"Institute of Human Genetics, University Medical Center of the Johannes Gutenberg University Mainz , Mainz 55131, Germany"}]},{"given":"Vincent","family":"Dietrich","sequence":"additional","affiliation":[{"name":"Institute of Human Genetics, University Medical Center of the Johannes Gutenberg University Mainz , Mainz 55131, Germany"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0154-0928","authenticated-orcid":false,"given":"Mark","family":"Helm","sequence":"additional","affiliation":[{"name":"Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Mainz , Mainz 55128, Germany"}]},{"given":"Tamer","family":"Butto","sequence":"additional","affiliation":[{"name":"Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Mainz , Mainz 55128, Germany"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9513-0729","authenticated-orcid":false,"given":"Susanne","family":"Gerber","sequence":"additional","affiliation":[{"name":"Institute of Human Genetics, University Medical Center of the Johannes Gutenberg University Mainz , Mainz 55131, Germany"}]}],"member":"286","published-online":{"date-parts":[[2023,8,7]]},"reference":[{"key":"2023081801563852600_btad492-B9125817","doi-asserted-by":"crossref","DOI":"10.1186\/s13059-020-1935-5","article-title":"Opportunities and 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