{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,29]],"date-time":"2026-05-29T19:04:32Z","timestamp":1780081472059,"version":"3.54.0"},"reference-count":10,"publisher":"Oxford University Press (OUP)","issue":"18","license":[{"start":{"date-parts":[[2018,4,26]],"date-time":"2018-04-26T00:00:00Z","timestamp":1524700800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"name":"Spanish MINECO\/FEDER","award":["TIN2015-71079-P"],"award-info":[{"award-number":["TIN2015-71079-P"]}]},{"name":"Maria de Maeztu Unit of Excellence"},{"name":"Catalan AGAUR","award":["SGR17-1020"],"award-info":[{"award-number":["SGR17-1020"]}]},{"name":"Catalan AGAUR","award":["FI-DGR 2015"],"award-info":[{"award-number":["FI-DGR 2015"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2018,9,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>Genomewide position-specific scores, such as those estimating conservation, constraint, fitness or mutation tolerance, are ubiquitous in current genome analyses. The diversity of sources and formats of these scores, as well as their size, increase the burden to use them. We present GenomicScores, a Bioconductor package that provides efficient storage and seamless access of genomewide position-specific scores from R, facilitating their use in genome analysis workflows.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>GenomicScores is implemented in R and available at https:\/\/bioconductor.org\/packages\/GenomicScores under the open source \u2018Artistic-2.0\u2019 license.<\/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\/bty311","type":"journal-article","created":{"date-parts":[[2018,4,25]],"date-time":"2018-04-25T19:59:04Z","timestamp":1524686344000},"page":"3208-3210","source":"Crossref","is-referenced-by-count":33,"title":["GenomicScores: seamless access to genomewide position-specific scores from R and Bioconductor"],"prefix":"10.1093","volume":"34","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-8687-4942","authenticated-orcid":false,"given":"Pau","family":"Puigdevall","sequence":"first","affiliation":[{"name":"Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona, Spain"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2229-4508","authenticated-orcid":false,"given":"Robert","family":"Castelo","sequence":"additional","affiliation":[{"name":"Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona, Spain"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2018,4,26]]},"reference":[{"key":"2023012704184725700_bty311-B1","doi-asserted-by":"crossref","first-page":"115.","DOI":"10.1038\/nmeth.3252","article-title":"Orchestrating high-throughput genomic analysis with bioconductor","volume":"12","author":"Huber","year":"2015","journal-title":"Nat. Methods"},{"key":"2023012704184725700_bty311-B2","doi-asserted-by":"crossref","first-page":"1581","DOI":"10.1038\/ng.3703","article-title":"M-CAP eliminates a majority of variants of uncertain significance in clinical exomes at high sensitivity","volume":"48","author":"Jagadeesh","year":"2016","journal-title":"Nat. Genet"},{"key":"2023012704184725700_bty311-B3","doi-asserted-by":"crossref","first-page":"310","DOI":"10.1038\/ng.2892","article-title":"A general framework for estimating the relative pathogenicity of human genetic variants","volume":"46","author":"Kircher","year":"2014","journal-title":"Nat. Genet"},{"key":"2023012704184725700_bty311-B4","doi-asserted-by":"crossref","first-page":"e1003118.","DOI":"10.1371\/journal.pcbi.1003118","article-title":"Software for computing and annotating genomic ranges","volume":"9","author":"Lawrence","year":"2013","journal-title":"PLOS Comp. Biol"},{"key":"2023012704184725700_bty311-B5","doi-asserted-by":"crossref","first-page":"285","DOI":"10.1038\/nature19057","article-title":"Analysis of protein-coding genetic variation in 60,706 humans","volume":"536","author":"Lek","year":"2016","journal-title":"Nature"},{"key":"2023012704184725700_bty311-B6","author":"Morgan","year":"2017"},{"key":"2023012704184725700_bty311-B7","doi-asserted-by":"crossref","first-page":"2076.","DOI":"10.1093\/bioinformatics\/btu168","article-title":"Variantannotation: a bioconductor package for exploration and annotation of genetic variants","volume":"30","author":"Obenchain","year":"2014","journal-title":"Bioinformatics"},{"key":"2023012704184725700_bty311-B8","volume-title":"R Internals","author":"R Core Team","year":"2018"},{"key":"2023012704184725700_bty311-B9","doi-asserted-by":"crossref","first-page":"1034","DOI":"10.1101\/gr.3715005","article-title":"Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes","volume":"15","author":"Siepel","year":"2005","journal-title":"Genome Res"},{"key":"2023012704184725700_bty311-B10","doi-asserted-by":"crossref","first-page":"3199","DOI":"10.5194\/gmd-9-3199-2016","article-title":"Bit Grooming: statistically accurate precision-preserving quantization with compression, evaluated in the netCDF Operators (NCO, v4.4.8+)","volume":"9","author":"Zender","year":"2016","journal-title":"Geosci. Model Dev"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/34\/18\/3208\/48920331\/bioinformatics_34_18_3208.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/34\/18\/3208\/48920331\/bioinformatics_34_18_3208.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,27]],"date-time":"2023-01-27T04:40:52Z","timestamp":1674794452000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/34\/18\/3208\/4987140"}},"subtitle":[],"editor":[{"given":"John","family":"Hancock","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2018,4,26]]},"references-count":10,"journal-issue":{"issue":"18","published-print":{"date-parts":[[2018,9,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/bty311","relation":{},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"value":"1367-4803","type":"print"},{"value":"1367-4811","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2018,9,15]]},"published":{"date-parts":[[2018,4,26]]}}}