{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,27]],"date-time":"2026-02-27T00:22:56Z","timestamp":1772151776429,"version":"3.50.1"},"reference-count":9,"publisher":"Oxford University Press (OUP)","issue":"6","license":[{"start":{"date-parts":[[2018,8,23]],"date-time":"2018-08-23T00:00:00Z","timestamp":1534982400000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"name":"Max-Planck Society"},{"DOI":"10.13039\/501100004189","name":"MPG","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100004189","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Excellence Cluster Cardio-Pulmonary System"},{"name":"ECCPS"},{"DOI":"10.13039\/501100001659","name":"Deutsche Forschungsgemeinschaft","doi-asserted-by":"publisher","award":["KLIFO309"],"award-info":[{"award-number":["KLIFO309"]}],"id":[{"id":"10.13039\/501100001659","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2019,3,15]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:sec><jats:title>Motivation<\/jats:title><jats:p>High throughput (HT) screens in the omics field are typically analyzed by automated pipelines that generate static visualizations and comprehensive spreadsheet data for scientists. However, exploratory and hypothesis driven data analysis are key aspects of the understanding of biological systems, both generating extensive need for customized and dynamic visualization.<\/jats:p><\/jats:sec><jats:sec><jats:title>Results<\/jats:title><jats:p>Here we describe WIlsON, an interactive workbench for analysis and visualization of multi-omics data. It is primarily intended to empower screening platforms to offer access to pre-calculated HT screen results to the non-computational scientist. Facilitated by an open file format, WIlsON supports all types of omics screens, serves results via a web-based dashboard, and enables end users to perform analyses and generate publication-ready plots.<\/jats:p><\/jats:sec><jats:sec><jats:title>Availability and implementation<\/jats:title><jats:p>We implemented WIlsON in R with a focus on extensibility using the modular Shiny and Plotly frameworks. A demo of the interactive workbench without limitations may be accessed at http:\/\/loosolab.mpi-bn.mpg.de. A standalone Docker container as well as the source code of WIlsON are freely available from our Docker hub https:\/\/hub.docker. com\/r\/loosolab\/wilson, CRAN https:\/\/cran.r-project.org\/web\/packages\/wilson\/, and GitHub repository https:\/\/github.molgen.mpg.de\/loosolab\/wilson-apps, respectively.<\/jats:p><\/jats:sec>","DOI":"10.1093\/bioinformatics\/bty711","type":"journal-article","created":{"date-parts":[[2018,8,22]],"date-time":"2018-08-22T19:19:20Z","timestamp":1534965560000},"page":"1055-1057","source":"Crossref","is-referenced-by-count":26,"title":["WIlsON: Web-based Interactive Omics VisualizatioN"],"prefix":"10.1093","volume":"35","author":[{"given":"Hendrik","family":"Schultheis","sequence":"first","affiliation":[{"name":"Max Planck Institute for Heart and Lung Research, Bioinformatics Core Unit (BCU), 61231 Bad Nauheim, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Carsten","family":"Kuenne","sequence":"additional","affiliation":[{"name":"Max Planck Institute for Heart and Lung Research, Bioinformatics Core Unit (BCU), 61231 Bad Nauheim, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jens","family":"Preussner","sequence":"additional","affiliation":[{"name":"Max Planck Institute for Heart and Lung Research, Bioinformatics Core Unit (BCU), 61231 Bad Nauheim, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Rene","family":"Wiegandt","sequence":"additional","affiliation":[{"name":"Max Planck Institute for Heart and Lung Research, Bioinformatics Core Unit (BCU), 61231 Bad Nauheim, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Annika","family":"Fust","sequence":"additional","affiliation":[{"name":"Max Planck Institute for Heart and Lung Research, Bioinformatics Core Unit (BCU), 61231 Bad Nauheim, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Mette","family":"Bentsen","sequence":"additional","affiliation":[{"name":"Max Planck Institute for Heart and Lung Research, Bioinformatics Core Unit (BCU), 61231 Bad Nauheim, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Mario","family":"Looso","sequence":"additional","affiliation":[{"name":"Max Planck Institute for Heart and Lung Research, Bioinformatics Core Unit (BCU), 61231 Bad Nauheim, Germany"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2018,8,23]]},"reference":[{"key":"2023013107261017100_bty711-B1","doi-asserted-by":"crossref","first-page":"1367","DOI":"10.1038\/nbt.1511","article-title":"MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification","volume":"26","author":"Cox","year":"2008","journal-title":"Nat. Biotechnol"},{"key":"2023013107261017100_bty711-B2","doi-asserted-by":"crossref","first-page":"52995","DOI":"10.18632\/oncotarget.18031","article-title":"Pulmonary endothelial cell DNA methylation signature in pulmonary arterial hypertension","volume":"8","author":"Hautefort","year":"2017","journal-title":"Oncotarget"},{"key":"2023013107261017100_bty711-B3","doi-asserted-by":"crossref","first-page":"e0187457.","DOI":"10.1371\/journal.pone.0187457","article-title":"ExpressionDB: an open source platform for distributing genome-scale datasets","volume":"12","author":"Hughes","year":"2017","journal-title":"PLoS One"},{"key":"2023013107261017100_bty711-B4","doi-asserted-by":"crossref","first-page":"550.","DOI":"10.1186\/s13059-014-0550-8","article-title":"Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2","volume":"15","author":"Love","year":"2014","journal-title":"Genome Biol"},{"key":"2023013107261017100_bty711-B5","doi-asserted-by":"crossref","first-page":"447","DOI":"10.1093\/bioinformatics\/btw624","article-title":"The START App: a web-based RNAseq analysis and visualization resource","volume":"33","author":"Nelson","year":"2017","journal-title":"Bioinformatics"},{"key":"2023013107261017100_bty711-B6","doi-asserted-by":"crossref","first-page":"51","DOI":"10.1186\/s13072-015-0045-1","article-title":"ADMIRE: analysis and visualization of differential methylation in genomic regions using the Infinium HumanMethylation450 Assay","volume":"8","author":"Preussner","year":"2015","journal-title":"Epigenet. 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