{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,4]],"date-time":"2026-02-04T17:10:12Z","timestamp":1770225012158,"version":"3.49.0"},"reference-count":31,"publisher":"Oxford University Press (OUP)","issue":"2","license":[{"start":{"date-parts":[[2019,8,2]],"date-time":"2019-08-02T00:00:00Z","timestamp":1564704000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"name":"National Institute of Allergy and Infectious Diseases to the ImmGen Consortium","award":["AI072073"],"award-info":[{"award-number":["AI072073"]}]},{"name":"National Institute of Allergy and Infectious Diseases to the ImmGen Consortium","award":["AI116834-03S1"],"award-info":[{"award-number":["AI116834-03S1"]}]},{"DOI":"10.13039\/100000002","name":"NIH","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2020,1,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>Visualization of multiple genomic data generally requires the use of public or commercially hosted browsers. Flexible visualization of chromatin interaction data as genomic features and network components offer informative insights to gene expression. An open source application for visualizing HiC and chromatin conformation-based data as 2D-arcs accompanied by interactive network analyses is valuable.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>DNA Rchitect is a new tool created to visualize HiC and chromatin conformation-based contacts at high (Kb) and low (Mb) genomic resolutions. The user can upload their pre-filtered HiC experiment in bedpe format to the DNA Rchitect web app that we have hosted or to a version they themselves have deployed. Using DNA Rchitect, the uploaded data allows the user to visualize different interactions of their sample, perform simple network analyses, while also offering visualization of other genomic data types. The user can then download their results for additional network functionality offered in network based programs such as Cytoscape.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>DNA Rchitect is freely available both as a web application written primarily in R available at http:\/\/shiny.immgen.org\/DNARchitect\/ and as an open source released under an MIT license at: https:\/\/github.com\/alosdiallo\/DNA_Rchitect.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btz608","type":"journal-article","created":{"date-parts":[[2019,8,1]],"date-time":"2019-08-01T19:11:49Z","timestamp":1564686709000},"page":"644-646","source":"Crossref","is-referenced-by-count":6,"title":["DNA Rchitect: an R based visualizer for network analysis of chromatin interaction data"],"prefix":"10.1093","volume":"36","author":[{"given":"R N","family":"Ramirez","sequence":"first","affiliation":[{"name":"Department of Immunology, Harvard Medical School , Boston, MA, 02115, USA"}]},{"given":"K","family":"Bedirian","sequence":"additional","affiliation":[{"name":"Department of Immunology, Harvard Medical School , Boston, MA, 02115, USA"},{"name":"Electrical and Computer Engineering Department, American University of Beirut , Beirut, Lebanon"}]},{"given":"S M","family":"Gray","sequence":"additional","affiliation":[{"name":"Department of Immunology, Harvard Medical School , Boston, MA, 02115, USA"}]},{"given":"A","family":"Diallo","sequence":"additional","affiliation":[{"name":"Department of Immunology, Harvard Medical School , Boston, MA, 02115, USA"}]}],"member":"286","published-online":{"date-parts":[[2019,8,2]]},"reference":[{"key":"2023013112070042500_btz608-B1","author":"Almende","year":"2019"},{"key":"2023013112070042500_btz608-B2","doi-asserted-by":"crossref","first-page":"772.","DOI":"10.1038\/nrg.2016.147","article-title":"Organization and function of the 3D genome","volume":"17","author":"Bonev","year":"2016","journal-title":"Nat. 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