{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,1]],"date-time":"2026-07-01T04:23:05Z","timestamp":1782879785145,"version":"3.54.5"},"reference-count":16,"publisher":"Oxford University Press (OUP)","issue":"11","license":[{"start":{"date-parts":[[2020,10,17]],"date-time":"2020-10-17T00:00:00Z","timestamp":1602892800000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001809","name":"The National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["31771373"],"award-info":[{"award-number":["31771373"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100012600","name":"ShanghaiTech University","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100012600","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2021,7,12]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Summary<\/jats:title>\n                    <jats:p>Mutational signatures are recurring DNA alteration patterns caused by distinct mutational events during the evolution of cancer. In recent years, several bioinformatics tools are available for mutational signature analysis. However, most of them focus on specific type of mutation or have limited scope of application. A pipeline tool for comprehensive mutational signature analysis is still lacking. Here we present Sigflow pipeline, which provides an one-stop solution for de novo signature extraction, reference signature fitting, signature stability analysis, sample clustering based on signature exposure in different types of genome DNA alterations including single base substitution, doublet base substitution, small insertion and deletion and copy number alteration. A Docker image is constructed to solve the complex and time-consuming installation issues, and this enables reproducible research by version control of all dependent tools along with their environments. Sigflow pipeline can be applied to both human and mouse genomes.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>Sigflow is an open source software under academic free license v3.0 and it is freely available at https:\/\/github.com\/ShixiangWang\/sigflow or https:\/\/hub.docker.com\/r\/shixiangwang\/sigflow.<\/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\/btaa895","type":"journal-article","created":{"date-parts":[[2020,10,3]],"date-time":"2020-10-03T07:13:02Z","timestamp":1601709182000},"page":"1590-1592","source":"Crossref","is-referenced-by-count":53,"title":["Sigflow: an automated and comprehensive pipeline for cancer genome mutational signature analysis"],"prefix":"10.1093","volume":"37","author":[{"given":"Shixiang","family":"Wang","sequence":"first","affiliation":[{"name":"School of Life Science and Technology, ShanghaiTech University , Shanghai 201203, China"},{"name":"Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences , Shanghai 200031, China"},{"name":"University of Chinese Academy of Sciences , Beijing 100049, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ziyu","family":"Tao","sequence":"additional","affiliation":[{"name":"School of Life Science and Technology, ShanghaiTech University , Shanghai 201203, China"},{"name":"Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences , Shanghai 200031, China"},{"name":"University of Chinese Academy of Sciences , Beijing 100049, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tao","family":"Wu","sequence":"additional","affiliation":[{"name":"School of Life Science and Technology, ShanghaiTech University , Shanghai 201203, China"},{"name":"Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences , Shanghai 200031, China"},{"name":"University of Chinese Academy of Sciences , Beijing 100049, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7736-0077","authenticated-orcid":false,"given":"Xue-Song","family":"Liu","sequence":"additional","affiliation":[{"name":"School of Life Science and Technology, ShanghaiTech University , Shanghai 201203, China"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2020,10,17]]},"reference":[{"key":"2023051709443411100_btaa895-B1","doi-asserted-by":"crossref","first-page":"246","DOI":"10.1016\/j.celrep.2012.12.008","article-title":"Deciphering signatures of mutational processes operative in human cancer","volume":"3","author":"Alexandrov","year":"2013","journal-title":"Cell Rep"},{"key":"2023051709443411100_btaa895-B2","doi-asserted-by":"crossref","first-page":"94","DOI":"10.1038\/s41586-020-1943-3","article-title":"The repertoire of mutational signatures in human cancer","volume":"578","author":"Alexandrov","year":"2020","journal-title":"Nature"},{"key":"2023051709443411100_btaa895-B3","doi-asserted-by":"crossref","first-page":"77","DOI":"10.1093\/bib\/bbx082","article-title":"Computational approaches for discovery of mutational signatures in cancer","volume":"20","author":"Baez-Ortega","year":"2019","journal-title":"Brief Bioinform"},{"key":"2023051709443411100_btaa895-B4","doi-asserted-by":"crossref","first-page":"685","DOI":"10.1186\/s12864-019-6041-2","article-title":"SigProfilerMatrixGenerator: a tool for visualizing and exploring patterns of small mutational events","volume":"20","author":"Bergstrom","year":"2019","journal-title":"BMC Genomics"},{"key":"2023051709443411100_btaa895-B5","doi-asserted-by":"crossref","first-page":"517","DOI":"10.1038\/nm.4292","article-title":"HRDetect is a predictor of BRCA1 and BRCA2 deficiency based on mutational signatures","volume":"23","author":"Davies","year":"2017","journal-title":"Nat. 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