{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,7,30]],"date-time":"2025-07-30T11:43:58Z","timestamp":1753875838295,"version":"3.41.2"},"reference-count":8,"publisher":"Oxford University Press (OUP)","issue":"5","license":[{"start":{"date-parts":[[2024,5,8]],"date-time":"2024-05-08T00:00:00Z","timestamp":1715126400000},"content-version":"vor","delay-in-days":7,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001659","name":"Deutsche Forschungsgemeinschaft","doi-asserted-by":"publisher","award":["192904750-SFB 992","TI688\/1\u20131"],"award-info":[{"award-number":["192904750-SFB 992","TI688\/1\u20131"]}],"id":[{"id":"10.13039\/501100001659","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2024,5,2]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>To study gene regulation through transcription factors and chromatin modifiers, a variety of genome-wide techniques are used. Recently, CUT&amp;RUN-based technologies have become popular, but a pipeline for the comprehensive analysis of CUT&amp;RUN datasets is currently lacking. Here, we present the \u201cgreenPipes\u201d package, which includes fine-tuned parameters specifically for bioinformatic analyses of greenCUT&amp;RUN and CUT&amp;RUN datasets. greenPipes provides additional functionalities for data analysis and data integration with other -omics technologies, which are either not available in other pipelines developed for CUT&amp;RUN datasets or scattered in the literature as individual packages.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>Source code and a manual of the greenPipes are freely available on GitHub website (https:\/\/github.com\/snizam001\/greenPipes). The test datasets, comprehensive annotation files, and other datasets are available at https:\/\/osf.io\/ruhj9\/.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Contact<\/jats:title>\n                  <jats:p>n.sheikh@dkfz-heidelberg.de or m.timmers@dkfz-heidelberg.de<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Supplementary information<\/jats:title>\n                  <jats:p>The handbook of greenPipes is available online at Bioinformatics as Supplementary text.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btae307","type":"journal-article","created":{"date-parts":[[2024,5,8]],"date-time":"2024-05-08T18:22:40Z","timestamp":1715192560000},"source":"Crossref","is-referenced-by-count":0,"title":["greenPipes: an integrated data analysis pipeline for greenCUT&amp;RUN and CUT&amp;RUN genome-localization datasets"],"prefix":"10.1093","volume":"40","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-4586-5898","authenticated-orcid":false,"given":"Sheikh","family":"Nizamuddin","sequence":"first","affiliation":[{"name":"Department of Urology, Medical Center-University of Freiburg , Freiburg, 79016, Germany"},{"name":"German Cancer Consortium (DKTK), partnersite Freiburg, a partnership between the DKFZ and Medical Center-University of Freiburg , Germany"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7062-1417","authenticated-orcid":false,"given":"H T Marc","family":"Timmers","sequence":"additional","affiliation":[{"name":"Department of Urology, Medical Center-University of Freiburg , Freiburg, 79016, Germany"},{"name":"German Cancer Consortium (DKTK), partnersite Freiburg, a partnership between the DKFZ and Medical Center-University of Freiburg , Germany"}]}],"member":"286","published-online":{"date-parts":[[2024,5,8]]},"reference":[{"key":"2024052304525582700_btae307-B1","doi-asserted-by":"crossref","first-page":"276","DOI":"10.1038\/s41587-020-0439-x","article-title":"The nf-core framework for community-curated bioinformatics pipelines","volume":"38","author":"Ewels","year":"2020","journal-title":"Nat Biotechnol"},{"key":"2024052304525582700_btae307-B2","first-page":"D58","article-title":"EnhancerAtlas 2.0: an updated resource with enhancer annotation in 586 tissue\/cell types across nine species","volume":"48","author":"Gao","year":"2020","journal-title":"Nucleic Acids Res"},{"key":"2024052304525582700_btae307-B3","doi-asserted-by":"crossref","first-page":"248","DOI":"10.1093\/bioinformatics\/btw615","article-title":"Improved methods for multi-trait fine mapping of pleiotropic risk 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