{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,11]],"date-time":"2026-04-11T16:09:52Z","timestamp":1775923792347,"version":"3.50.1"},"reference-count":14,"publisher":"Oxford University Press (OUP)","issue":"5","license":[{"start":{"date-parts":[[2023,4,12]],"date-time":"2023-04-12T00:00:00Z","timestamp":1681257600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100014989","name":"Chan Zuckerberg Initiative","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100014989","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"NIH","doi-asserted-by":"publisher","award":["R01-HG009937"],"award-info":[{"award-number":["R01-HG009937"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2023,5,4]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Motivation<\/jats:title>\n                    <jats:p>Enrichment analysis is a widely utilized technique in genomic analysis that aims to determine if there is a statistically significant association between two sets of genomic features. To conduct this type of hypothesis testing, an appropriate null model is typically required. However, the null distribution that is commonly used can be overly simplistic and may result in inaccurate conclusions.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>bootRanges provides fast functions for generation of block bootstrapped genomic ranges representing the null hypothesis in enrichment analysis. As part of a modular workflow, bootRanges offers greater flexibility for computing various test statistics leveraging other Bioconductor packages. We show that shuffling or permutation schemes may result in overly narrow test statistic null distributions and over-estimation of statistical significance, while creating new range sets with a block bootstrap preserves local genomic correlation structure and generates more reliable null distributions. It can also be used in more complex analyses, such as accessing correlations between cis-regulatory elements (CREs) and genes across cell types or providing optimized thresholds, e.g. log fold change (logFC) from differential analysis.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>bootRanges is freely available in the R\/Bioconductor package nullranges hosted at https:\/\/bioconductor.org\/packages\/nullranges.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btad190","type":"journal-article","created":{"date-parts":[[2023,4,12]],"date-time":"2023-04-12T09:23:55Z","timestamp":1681291435000},"source":"Crossref","is-referenced-by-count":19,"title":["bootRanges: flexible generation of null sets of genomic ranges for hypothesis testing"],"prefix":"10.1093","volume":"39","author":[{"given":"Wancen","family":"Mu","sequence":"first","affiliation":[{"name":"Department of Biostatistics, University of North Carolina , Chapel Hill 27514, United States"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4051-3217","authenticated-orcid":false,"given":"Eric S","family":"Davis","sequence":"additional","affiliation":[{"name":"Curriculum in Bioinformatics and Computational Biology, University of North Carolina, Chapel Hill 27514, United States"}]},{"given":"Stuart","family":"Lee","sequence":"additional","affiliation":[{"name":"Genentech, South San Francisco , Western California 94080, United States"}]},{"given":"Mikhail G","family":"Dozmorov","sequence":"additional","affiliation":[{"name":"Department of Biostatistics, Virginia Commonwealth University , Richmond, VA 23284, United States"},{"name":"Department of Pathology, Virginia Commonwealth University , Richmond, VA 23284, United States"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2123-0051","authenticated-orcid":false,"given":"Douglas H","family":"Phanstiel","sequence":"additional","affiliation":[{"name":"Curriculum in Bioinformatics and Computational Biology, University of North Carolina, Chapel Hill 27514, United States"},{"name":"Thurston Arthritis Research Center, University of North Carolina , Chapel Hill 27514, United States"},{"name":"Department of Cell Biology and Physiology, University of North Carolina , Chapel Hill 27514, United States"},{"name":"Lineberger Comprehensive Cancer Center, University of North Carolina , Chapel Hill 27514, United States"},{"name":"Curriculum in Genetics and Molecular Biology, University of North Carolina , Chapel Hill 27514, United States"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8401-0545","authenticated-orcid":false,"given":"Michael I","family":"Love","sequence":"additional","affiliation":[{"name":"Department of Biostatistics, University of North Carolina , Chapel Hill 27514, United States"},{"name":"Curriculum in Bioinformatics and Computational Biology, University of North Carolina, Chapel Hill 27514, United States"},{"name":"Lineberger Comprehensive Cancer Center, University of North Carolina , Chapel Hill 27514, United States"},{"name":"Department of Genetics, University of North Carolina , Chapel Hill 27514, United States"}]}],"member":"286","published-online":{"date-parts":[[2023,4,12]]},"reference":[{"key":"2023050421470981300_btad190-B1","doi-asserted-by":"crossref","first-page":"424","DOI":"10.1038\/s41588-018-0046-7","article-title":"Shared genetic effects on chromatin and gene expression indicate a role for enhancer priming in immune response","volume":"50","author":"Alasoo","year":"2018","journal-title":"Nat Genet"},{"key":"2023050421470981300_btad190-B2","doi-asserted-by":"crossref","first-page":"1660","DOI":"10.1214\/10-AOAS363","article-title":"Subsampling methods for genomic 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