{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,28]],"date-time":"2026-03-28T08:23:11Z","timestamp":1774686191560,"version":"3.50.1"},"reference-count":51,"publisher":"Oxford University Press (OUP)","issue":"10","license":[{"start":{"date-parts":[[2020,1,31]],"date-time":"2020-01-31T00:00:00Z","timestamp":1580428800000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100022719","name":"Darwin Trust of Edinburgh","doi-asserted-by":"crossref","id":[{"id":"10.13039\/501100022719","id-type":"DOI","asserted-by":"crossref"}]},{"name":"Medical Research Council University Unit programme grant","award":["MC_ UU_00007\/2"],"award-info":[{"award-number":["MC_ UU_00007\/2"]}]},{"name":"MRC Career Development Award","award":["MR\/S007644\/1"],"award-info":[{"award-number":["MR\/S007644\/1"]}]},{"name":"University of Edinburgh Simons Initiative for the Developing Brain"},{"DOI":"10.13039\/501100015504","name":"SIDB","doi-asserted-by":"crossref","id":[{"id":"10.13039\/501100015504","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/100014370","name":"Simons Foundation Autism Research Initiative","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100014370","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100014370","name":"SFARI","doi-asserted-by":"publisher","award":["MC_ UU_00007\/2"],"award-info":[{"award-number":["MC_ UU_00007\/2"]}],"id":[{"id":"10.13039\/100014370","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2020,5,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Motivation<\/jats:title>\n                    <jats:p>Hi-C is currently the method of choice to investigate the global 3D organization of the genome. A major limitation of Hi-C is the sequencing depth required to robustly detect loops in the data. A popular approach used to mitigate this issue, even in single-cell Hi-C data, is genome-wide averaging (piling-up) of peaks, or other features, annotated in high-resolution datasets, to measure their prominence in less deeply sequenced data. However, current tools do not provide a computationally efficient and versatile implementation of this approach.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>Here, we describe coolpup.py\u2014a versatile tool to perform pile-up analysis on Hi-C data. We demonstrate its utility by replicating previously published findings regarding the role of cohesin and CTCF in 3D genome organization, as well as discovering novel details of Polycomb-driven interactions. We also present a novel variation of the pile-up approach that can aid the statistical analysis of looping interactions. We anticipate that coolpup.py will aid in Hi-C data analysis by allowing easy to use, versatile and efficient generation of pile-ups.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>Coolpup.py is cross-platform, open-source and free (MIT licensed) software. Source code is available from https:\/\/github.com\/Phlya\/coolpuppy and it can be installed from the Python Packaging Index.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btaa073","type":"journal-article","created":{"date-parts":[[2020,1,27]],"date-time":"2020-01-27T07:08:22Z","timestamp":1580108902000},"page":"2980-2985","source":"Crossref","is-referenced-by-count":211,"title":["<i>Coolpup.py:<\/i>\n                    versatile pile-up analysis of Hi-C data"],"prefix":"10.1093","volume":"36","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-4892-4208","authenticated-orcid":false,"given":"Ilya M","family":"Flyamer","sequence":"first","affiliation":[{"name":"MRC Human Genetics Unit , Institute of Genetics and Molecular Medicine, The University of Edinburgh, Edinburgh, EH4 2XU, UK"}]},{"given":"Robert S","family":"Illingworth","sequence":"additional","affiliation":[{"name":"MRC Centre for Regenerative Medicine , Institute for Regeneration and Repair, The University of Edinburgh, Edinburgh, EH16 4UU, UK"}]},{"given":"Wendy A","family":"Bickmore","sequence":"additional","affiliation":[{"name":"MRC Human Genetics Unit , Institute of Genetics and Molecular Medicine, The University of Edinburgh, Edinburgh, EH4 2XU, UK"}]}],"member":"286","published-online":{"date-parts":[[2020,1,31]]},"reference":[{"key":"2023013111540228000_btaa073-B1","doi-asserted-by":"crossref","first-page":"311","DOI":"10.1093\/bioinformatics\/btz540","article-title":"Cooler: scalable storage for Hi-C data and other genomically labeled arrays","volume":"36","author":"Abdennur","year":"2019","journal-title":"Bioinformatics"},{"key":"2023013111540228000_btaa073-B2","author":"Abdennur","year":"2018"},{"key":"2023013111540228000_btaa073-B3","doi-asserted-by":"crossref","first-page":"585","DOI":"10.1101\/gad.256354.114","article-title":"Two distinct modes for propagation of histone PTMs across the cell cycle","volume":"29","author":"Alabert","year":"2015","journal-title":"Genes Dev"},{"key":"2023013111540228000_btaa073-B4","doi-asserted-by":"crossref","first-page":"31","DOI":"10.1002\/jcp.25062","article-title":"C-ing the genome: a compendium of chromosome conformation capture methods to study higher-order chromatin organization","volume":"231","author":"Barutcu","year":"2016","journal-title":"J. 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