{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,20]],"date-time":"2026-03-20T03:10:28Z","timestamp":1773976228992,"version":"3.50.1"},"reference-count":8,"publisher":"Oxford University Press (OUP)","issue":"3","license":[{"start":{"date-parts":[[2021,9,29]],"date-time":"2021-09-29T00:00:00Z","timestamp":1632873600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"name":"Research Council of Norway through its Centres of Excellence funding scheme","award":["262652"],"award-info":[{"award-number":["262652"]}]},{"name":"University of Oslo supported open access publication"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022,1,12]]},"abstract":"<jats:title>ABSTRACT<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Motivation<\/jats:title>\n                    <jats:p>Mapping of chromatin accessibility landscapes in single-cells and the integration with gene expression enables a better understanding of gene regulatory mechanisms defining cell identities and cell-fate determination in development and disease. Generally, raw data generated from single-cell Assay for Transposase-Accessible Chromatin sequencing (scATAC-seq) are deposited in repositories that are generally inaccessible due to lack of in-depth knowledge of computational programming.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>We have developed ShinyArchR.UiO, an R-based shiny app, that facilitates scATAC-seq data accessibility and visualization in a user-friendly, interactive and open-source web interface. ShinyArchR.UiO is an application that can streamline collaborative efforts for interpretation of massive chromatin accessibility datasets and allow for open access data sharing for wider audiences.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>https:\/\/Github.com\/EskelandLab\/ShinyArchRUiO and a demo server with a hematopoietic tutorial dataset https:\/\/cancell.medisin.uio.no\/ShinyArchR.UiO<\/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\/btab680","type":"journal-article","created":{"date-parts":[[2021,9,24]],"date-time":"2021-09-24T09:40:39Z","timestamp":1632476439000},"page":"834-836","source":"Crossref","is-referenced-by-count":8,"title":["ShinyArchR.UiO: user-friendly,integrative and open-source tool for visualization of single-cell ATAC-seq data using ArchR"],"prefix":"10.1093","volume":"38","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-1399-7503","authenticated-orcid":false,"given":"Ankush","family":"Sharma","sequence":"first","affiliation":[{"name":"Department of Biosciences, University of Oslo , 0316 Oslo, Norway"},{"name":"Department of Informatics, Institute of Basic Medical Sciences, University of Oslo , 0316 Oslo, Norway"},{"name":"Department of Molecular Medicine, Institute of Basic Medical Sciences, University of Oslo , 0317 Oslo, Norway"},{"name":"PharmaTox Strategic Research Initiative, Faculty of Mathematics and Natural Sciences, University of Oslo , 0316 Oslo, Norway"},{"name":"Centre for Cancer Cell Reprogramming, Institute of Clinical Medicine, Faculty of Medicine, University of Oslo , 0372 Oslo, Norway"}]},{"given":"Akshay","family":"Akshay","sequence":"additional","affiliation":[{"name":"Urology Research Laboratory, Department for BioMedical Research DBMR, University of Bern , 3012 Bern, Switzerland"}]},{"given":"Marie","family":"Rogne","sequence":"additional","affiliation":[{"name":"Department of Molecular Medicine, Institute of Basic Medical Sciences, University of Oslo , 0317 Oslo, Norway"},{"name":"Centre for Cancer Cell Reprogramming, Institute of Clinical Medicine, Faculty of Medicine, University of Oslo , 0372 Oslo, Norway"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2789-3171","authenticated-orcid":false,"given":"Ragnhild","family":"Eskeland","sequence":"additional","affiliation":[{"name":"Department of Molecular Medicine, Institute of Basic Medical Sciences, University of Oslo , 0317 Oslo, Norway"},{"name":"PharmaTox Strategic Research Initiative, Faculty of Mathematics and Natural Sciences, University of Oslo , 0316 Oslo, Norway"},{"name":"Centre for Cancer Cell Reprogramming, Institute of Clinical Medicine, Faculty of Medicine, University of Oslo , 0372 Oslo, Norway"}]}],"member":"286","published-online":{"date-parts":[[2021,9,29]]},"reference":[{"key":"2023020108484338200_btab680-B1","doi-asserted-by":"crossref","first-page":"1429","DOI":"10.1016\/j.csbj.2020.06.012","article-title":"Single-cell ATAC sequencing analysis: from data preprocessing to hypothesis generation","volume":"18","author":"Baek","year":"2020","journal-title":"Comput. Struct. Biotechnol. J"},{"key":"2023020108484338200_btab680-B2","doi-asserted-by":"crossref","first-page":"1213","DOI":"10.1038\/nmeth.2688","article-title":"Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position","volume":"10","author":"Buenrostro","year":"2013","journal-title":"Nat. Methods"},{"key":"2023020108484338200_btab680-B3","doi-asserted-by":"crossref","first-page":"486","DOI":"10.1038\/nature14590","article-title":"Single-cell chromatin accessibility reveals principles of regulatory variation","volume":"523","author":"Buenrostro","year":"2015","journal-title":"Nature"},{"key":"2023020108484338200_btab680-B4","doi-asserted-by":"crossref","first-page":"910","DOI":"10.1126\/science.aab1601","article-title":"Multiplex single cell profiling of chromatin accessibility by combinatorial cellular indexing","volume":"348","author":"Cusanovich","year":"2015","journal-title":"Science"},{"key":"2023020108484338200_btab680-B5","doi-asserted-by":"crossref","first-page":"403","DOI":"10.1038\/s41588-021-00790-6","article-title":"ArchR is a scalable software package for integrative single-cell chromatin accessibility analysis","volume":"53","author":"Granja","year":"2021","journal-title":"Nat. Genet"},{"key":"2023020108484338200_btab680-B6","year":"2020","journal-title":"R. RStudio"},{"key":"2023020108484338200_btab680-B7","doi-asserted-by":"crossref","first-page":"495","DOI":"10.1038\/nbt.3192","article-title":"Spatial reconstruction of single-cell gene expression data","volume":"33","author":"Satija","year":"2015","journal-title":"Nat. Biotechnol"},{"key":"2023020108484338200_btab680-B8","doi-asserted-by":"crossref","first-page":"1888","DOI":"10.1016\/j.cell.2019.05.031","article-title":"Comprehensive integration of single-cell data","volume":"177","author":"Stuart","year":"2019","journal-title":"Cell"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/academic.oup.com\/bioinformatics\/advance-article-pdf\/doi\/10.1093\/bioinformatics\/btab680\/40730412\/btab680.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/38\/3\/834\/49008050\/btab680.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/38\/3\/834\/49008050\/btab680.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,2,1]],"date-time":"2023-02-01T15:07:58Z","timestamp":1675264078000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/38\/3\/834\/6377776"}},"subtitle":[],"editor":[{"given":"Can","family":"Alkan","sequence":"additional","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2021,9,29]]},"references-count":8,"journal-issue":{"issue":"3","published-print":{"date-parts":[[2022,1,12]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btab680","relation":{"has-preprint":[{"id-type":"doi","id":"10.1101\/2021.06.21.449316","asserted-by":"object"}]},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"value":"1367-4803","type":"print"},{"value":"1367-4811","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2022,2,1]]},"published":{"date-parts":[[2021,9,29]]}}}