{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,7]],"date-time":"2026-06-07T09:31:39Z","timestamp":1780824699130,"version":"3.54.1"},"reference-count":15,"publisher":"Oxford University Press (OUP)","issue":"7","license":[{"start":{"date-parts":[[2019,11,25]],"date-time":"2019-11-25T00:00:00Z","timestamp":1574640000000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100005010","name":"Fondazione AIRC per la Ricerca sul Cancro","doi-asserted-by":"publisher","award":["IG-2017-20162"],"award-info":[{"award-number":["IG-2017-20162"]}],"id":[{"id":"10.13039\/501100005010","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100010663","name":"European Research Council","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100010663","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100010663","name":"ERC","doi-asserted-by":"publisher","award":["341131"],"award-info":[{"award-number":["341131"]}],"id":[{"id":"10.13039\/100010663","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2020,4,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title\/>\n                    <jats:p>Despite the growing availability of sophisticated bioinformatic methods for the analysis of single-cell RNA-seq data, few tools exist that allow biologists without extensive bioinformatic expertise to directly visualize and interact with their own data and results. Here, we present Cerebro (cell report browser), a Shiny- and Electron-based standalone desktop application for macOS and Windows which allows investigation and inspection of pre-processed single-cell transcriptomics data without requiring bioinformatic experience of the user. Through an interactive and intuitive graphical interface, users can (i) explore similarities and heterogeneity between samples and cell clusters in two-dimensional or three-dimensional projections such as t-SNE or UMAP, (ii) display the expression level of single genes or gene sets of interest, (iii) browse tables of most expressed genes and marker genes for each sample and cluster and (iv) display trajectories calculated with Monocle 2. We provide three examples prepared from publicly available datasets to show how Cerebro can be used and which are its capabilities. Through a focus on flexibility and direct access to data and results, we think Cerebro offers a collaborative framework for bioinformaticians and experimental biologists that facilitates effective interaction to shorten the gap between analysis and interpretation of the data.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>The Cerebro application, additional documentation, and example datasets are available at https:\/\/github.com\/romanhaa\/Cerebro. Similarly, the cerebroApp R package is available at https:\/\/github.com\/romanhaa\/cerebroApp. All components are released under the MIT License.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Supplementary information<\/jats:title>\n                    <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btz877","type":"journal-article","created":{"date-parts":[[2019,11,22]],"date-time":"2019-11-22T15:10:46Z","timestamp":1574435446000},"page":"2311-2313","source":"Crossref","is-referenced-by-count":65,"title":["Cerebro: interactive visualization of scRNA-seq data"],"prefix":"10.1093","volume":"36","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-3528-9276","authenticated-orcid":false,"given":"Roman","family":"Hillje","sequence":"first","affiliation":[{"name":"Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS , 20139 Milan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5076-2316","authenticated-orcid":false,"given":"Pier Giuseppe","family":"Pelicci","sequence":"additional","affiliation":[{"name":"Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS , 20139 Milan"},{"name":"Department of Oncology and Hemato-Oncology, Universit\u00e0 Degli Studi di Milano , Milan 20122, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8746-4179","authenticated-orcid":false,"given":"Lucilla","family":"Luzi","sequence":"additional","affiliation":[{"name":"Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS , 20139 Milan"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2019,11,25]]},"reference":[{"key":"2023062300072749300_btz877-B2","doi-asserted-by":"crossref","first-page":"411","DOI":"10.1038\/nbt.4096","article-title":"Integrating single-cell transcriptomic data across different conditions, technologies, and species","volume":"36","author":"Butler","year":"2018","journal-title":"Nat. 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