{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,2,22]],"date-time":"2025-02-22T00:45:46Z","timestamp":1740185146121,"version":"3.37.3"},"reference-count":3,"publisher":"Oxford University Press (OUP)","issue":"16","license":[{"start":{"date-parts":[[2020,11,27]],"date-time":"2020-11-27T00:00:00Z","timestamp":1606435200000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000026","name":"National Institute on Drug Abuse","doi-asserted-by":"publisher","award":["R01042691","R01DA047063","R01DA047820"],"award-info":[{"award-number":["R01042691","R01DA047063","R01DA047820"]}],"id":[{"id":"10.13039\/100000026","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2021,8,25]]},"abstract":"Abstract<\/jats:title>\n \n Motivation<\/jats:title>\n High-quality\u00a0imaging analyses have been proposed to drive innovation in biomedical and biological research. However, the application of images remains underexploited because of the limited capacity of human vision and the challenges in extracting quantitative information from images. Computationally extracting quantitative information from images is critical to overcoming this limitation. Here, we present a novel R package, i2d, to simulate data from an image based on digital convolution.<\/jats:p>\n <\/jats:sec>\n \n Results<\/jats:title>\n The R package i2d allows users to transform an image into a simulated dataset that can be used to extract and analyze complex information in biomedical and biological research. The package also includes three novel and efficient methods for graph clustering based on simulated data, which can be used to dissect complex gene networks into sub-clusters that have similar biological functions.<\/jats:p>\n <\/jats:sec>\n \n Availability and implementation<\/jats:title>\n The code, the documentation, a tutorial and example data are available on an open source at: github.com\/XiaoyuLiang\/i2d.<\/jats:p>\n <\/jats:sec>\n \n Supplementary information<\/jats:title>\n Supplementary data are available at Bioinformatics online.<\/jats:p>\n <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btaa991","type":"journal-article","created":{"date-parts":[[2020,11,17]],"date-time":"2020-11-17T04:16:08Z","timestamp":1605586568000},"page":"2497-2498","source":"Crossref","is-referenced-by-count":0,"title":["i2d: an R package for simulating data from images and the implications in biomedical research"],"prefix":"10.1093","volume":"37","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-7796-2441","authenticated-orcid":false,"given":"Xiaoyu","family":"Liang","sequence":"first","affiliation":[{"name":"Department of Psychiatry, Yale School of Medicine , New Haven, CT 06511, USA"},{"name":"VA Connecticut Healthcare System , West Haven, CT 06516, USA"}]},{"given":"Ying","family":"Hu","sequence":"additional","affiliation":[{"name":"Center for Biomedical Bioinformatics and Information Technology, National Cancer Institute , Rockville, MD 20852, USA"}]},{"given":"Chunhua","family":"Yan","sequence":"additional","affiliation":[{"name":"Center for Biomedical Bioinformatics and Information Technology, National Cancer Institute , Rockville, MD 20852, USA"}]},{"given":"Ke","family":"Xu","sequence":"additional","affiliation":[{"name":"Department of Psychiatry, Yale School of Medicine , New Haven, CT 06511, USA"},{"name":"VA Connecticut Healthcare System , West Haven, CT 06516, USA"}]}],"member":"286","published-online":{"date-parts":[[2020,11,27]]},"reference":[{"key":"2023051609060283700_btaa991-B1","first-page":"1","article-title":"The igraph software package for complex network research","volume":"1695","author":"Csardi","year":"2006","journal-title":"Int. J. Complex Syst"},{"year":"2018","author":"Ooms","key":"2023051609060283700_btaa991-B2"},{"key":"2023051609060283700_btaa991-B3","doi-asserted-by":"crossref","first-page":"979","DOI":"10.1093\/bioinformatics\/btq046","article-title":"EBImage\u2014an R package for image processing with applications to cellular phenotypes","volume":"26","author":"Pau","year":"2010","journal-title":"Bioinformatics"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/academic.oup.com\/bioinformatics\/advance-article-pdf\/doi\/10.1093\/bioinformatics\/btaa991\/34875676\/btaa991.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/37\/16\/2497\/50339506\/btaa991.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/37\/16\/2497\/50339506\/btaa991.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,5,16]],"date-time":"2023-05-16T09:10:57Z","timestamp":1684228257000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/37\/16\/2497\/6007260"}},"subtitle":[],"editor":[{"given":"Wren","family":"Jonathan","sequence":"additional","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2020,11,27]]},"references-count":3,"journal-issue":{"issue":"16","published-print":{"date-parts":[[2021,8,25]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btaa991","relation":{},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"type":"print","value":"1367-4803"},{"type":"electronic","value":"1367-4811"}],"subject":[],"published-other":{"date-parts":[[2021,8,15]]},"published":{"date-parts":[[2020,11,27]]}}}