{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,3]],"date-time":"2026-07-03T20:15:39Z","timestamp":1783109739333,"version":"3.54.6"},"reference-count":14,"publisher":"Oxford University Press (OUP)","issue":"22","license":[{"start":{"date-parts":[[2022,9,29]],"date-time":"2022-09-29T00:00:00Z","timestamp":1664409600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"RIKEN Center for Integrative Medical Sciences"},{"DOI":"10.13039\/501100001700","name":"Ministry of Education, Culture, Sports, Science and Technology","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100001700","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100014989","name":"Chan Zuckerberg Initiative","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100014989","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Seed Networks Incentive for the Human Cell Atlas","award":["CZF2019-0024446"],"award-info":[{"award-number":["CZF2019-0024446"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022,11,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>Cell type-specific activities of cis-regulatory elements (CRE) are central to understanding gene regulation and disease predisposition. Single-cell RNA 5\u2032end sequencing (sc-end5-seq) captures the transcription start sites (TSS) which can be used as a proxy to measure the activity of transcribed CREs (tCREs). However, a substantial fraction of TSS identified from sc-end5-seq data may not be genuine due to various artifacts, hindering the use of sc-end5-seq for de novo discovery of tCREs.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>We developed SCAFE\u2014Single-Cell Analysis of Five-prime Ends\u2014a software suite that processes sc-end5-seq data to de novo identify TSS clusters based on multiple logistic regression. It annotates tCREs based on the identified TSS clusters and generates a tCRE-by-cell count matrix for downstream analyses. The software suite consists of a set of flexible tools that could either be run independently or as pre-configured workflows.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>SCAFE is implemented in Perl and R. The source code and documentation are freely available for download under the MIT License from https:\/\/github.com\/chung-lab\/SCAFE. Docker images are available from https:\/\/hub.docker.com\/r\/cchon\/scafe. The submitted software version and test data are archived at https:\/\/doi.org\/10.5281\/zenodo.7023163 and https:\/\/doi.org\/10.5281\/zenodo.7024060, respectively.<\/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\/btac644","type":"journal-article","created":{"date-parts":[[2022,9,28]],"date-time":"2022-09-28T20:50:37Z","timestamp":1664398237000},"page":"5126-5128","source":"Crossref","is-referenced-by-count":22,"title":["SCAFE: a software suite for analysis of transcribed cis-regulatory elements in single cells"],"prefix":"10.1093","volume":"38","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-9261-711X","authenticated-orcid":false,"given":"Jonathan","family":"Moody","sequence":"first","affiliation":[{"name":"RIKEN Center for Integrative Medical Sciences , Yokohama City, Kanagawa 230-0045, Japan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tsukasa","family":"Kouno","sequence":"additional","affiliation":[{"name":"RIKEN Center for Integrative Medical Sciences , Yokohama City, Kanagawa 230-0045, Japan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6986-8479","authenticated-orcid":false,"given":"Jen-Chien","family":"Chang","sequence":"additional","affiliation":[{"name":"RIKEN Center for Integrative Medical Sciences , Yokohama City, Kanagawa 230-0045, Japan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8128-6201","authenticated-orcid":false,"given":"Yoshinari","family":"Ando","sequence":"additional","affiliation":[{"name":"RIKEN Center for Integrative Medical Sciences , Yokohama City, Kanagawa 230-0045, Japan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7202-7243","authenticated-orcid":false,"given":"Piero","family":"Carninci","sequence":"additional","affiliation":[{"name":"RIKEN Center for Integrative Medical Sciences , Yokohama City, Kanagawa 230-0045, Japan"},{"name":"Human Technopole , Milan 20157, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4037-3533","authenticated-orcid":false,"given":"Jay W","family":"Shin","sequence":"additional","affiliation":[{"name":"RIKEN Center for Integrative Medical Sciences , Yokohama City, Kanagawa 230-0045, Japan"},{"name":"Genome Institute of Singapore, A*STAR Singapore , 60 Biopolis Street, Genome, #02-01, Singapore"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3741-7577","authenticated-orcid":false,"given":"Chung-Chau","family":"Hon","sequence":"additional","affiliation":[{"name":"RIKEN Center for Integrative Medical Sciences , Yokohama City, Kanagawa 230-0045, Japan"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2022,9,29]]},"reference":[{"key":"2022112014191347200_btac644-B1","doi-asserted-by":"crossref","first-page":"505","DOI":"10.1038\/s41592-018-0014-2","article-title":"Comprehensive comparative analysis of 5\u2019-end RNA-sequencing methods","volume":"15","author":"Adiconis","year":"2018","journal-title":"Nat. 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