{"id":"https://openalex.org/W3174992442","doi":"https://doi.org/10.1093/bioinformatics/btab459","title":"JBrowseR: an R interface to the JBrowse 2 genome browser","display_name":"JBrowseR: an R interface to the JBrowse 2 genome browser","publication_year":2021,"publication_date":"2021-06-29","ids":{"openalex":"https://openalex.org/W3174992442","doi":"https://doi.org/10.1093/bioinformatics/btab459","mag":"3174992442","pmid":"https://pubmed.ncbi.nlm.nih.gov/34196689"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btab459","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btab459","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/37/21/3914/41091620/btab459.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/37/21/3914/41091620/btab459.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5028316698","display_name":"Elliot A. Hershberg","orcid":"https://orcid.org/0000-0003-2068-3366"},"institutions":[{"id":"https://openalex.org/I95457486","display_name":"University of California, Berkeley","ror":"https://ror.org/01an7q238","country_code":"US","type":"education","lineage":["https://openalex.org/I95457486"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Elliot A Hershberg","raw_affiliation_strings":["Department of Bioengineering, University of California , Berkeley, Berkeley, CA 94720, USA"],"affiliations":[{"raw_affiliation_string":"Department of Bioengineering, University of California , Berkeley, Berkeley, CA 94720, USA","institution_ids":["https://openalex.org/I95457486"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5043892950","display_name":"Garrett Stevens","orcid":"https://orcid.org/0000-0002-9781-5323"},"institutions":[{"id":"https://openalex.org/I95457486","display_name":"University of California, Berkeley","ror":"https://ror.org/01an7q238","country_code":"US","type":"education","lineage":["https://openalex.org/I95457486"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Garrett Stevens","raw_affiliation_strings":["Department of Bioengineering, University of California , Berkeley, Berkeley, CA 94720, USA"],"affiliations":[{"raw_affiliation_string":"Department of Bioengineering, University of California , Berkeley, Berkeley, CA 94720, USA","institution_ids":["https://openalex.org/I95457486"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5027393785","display_name":"Colin Diesh","orcid":"https://orcid.org/0000-0003-2629-7570"},"institutions":[{"id":"https://openalex.org/I95457486","display_name":"University of California, Berkeley","ror":"https://ror.org/01an7q238","country_code":"US","type":"education","lineage":["https://openalex.org/I95457486"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Colin Diesh","raw_affiliation_strings":["Department of Bioengineering, University of California , Berkeley, Berkeley, CA 94720, USA"],"affiliations":[{"raw_affiliation_string":"Department of Bioengineering, University of California , Berkeley, Berkeley, CA 94720, USA","institution_ids":["https://openalex.org/I95457486"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5023203915","display_name":"Peter Xie","orcid":null},"institutions":[{"id":"https://openalex.org/I95457486","display_name":"University of California, Berkeley","ror":"https://ror.org/01an7q238","country_code":"US","type":"education","lineage":["https://openalex.org/I95457486"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Peter Xie","raw_affiliation_strings":["Department of Bioengineering, University of California , Berkeley, Berkeley, CA 94720, USA"],"affiliations":[{"raw_affiliation_string":"Department of Bioengineering, University of California , Berkeley, Berkeley, CA 94720, USA","institution_ids":["https://openalex.org/I95457486"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5064655588","display_name":"Teresa De Jesus Martinez","orcid":"https://orcid.org/0000-0002-1947-9539"},"institutions":[{"id":"https://openalex.org/I95457486","display_name":"University of California, Berkeley","ror":"https://ror.org/01an7q238","country_code":"US","type":"education","lineage":["https://openalex.org/I95457486"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Teresa De Jesus Martinez","raw_affiliation_strings":["Department of Bioengineering, University of California , Berkeley, Berkeley, CA 94720, USA"],"affiliations":[{"raw_affiliation_string":"Department of Bioengineering, University of California , Berkeley, Berkeley, CA 94720, USA","institution_ids":["https://openalex.org/I95457486"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5053277772","display_name":"Robert Buels","orcid":"https://orcid.org/0000-0002-9605-5895"},"institutions":[{"id":"https://openalex.org/I95457486","display_name":"University of California, Berkeley","ror":"https://ror.org/01an7q238","country_code":"US","type":"education","lineage":["https://openalex.org/I95457486"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Robert Buels","raw_affiliation_strings":["Department of Bioengineering, University of California , Berkeley, Berkeley, CA 94720, USA"],"affiliations":[{"raw_affiliation_string":"Department of Bioengineering, University of California , Berkeley, Berkeley, CA 94720, USA","institution_ids":["https://openalex.org/I95457486"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5052076713","display_name":"Lincoln Stein","orcid":"https://orcid.org/0000-0002-1983-4588"},"institutions":[{"id":"https://openalex.org/I112260969","display_name":"Ontario Institute for Cancer Research","ror":"https://ror.org/043q8yx54","country_code":"CA","type":"funder","lineage":["https://openalex.org/I112260969"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Lincoln Stein","raw_affiliation_strings":["Adaptive Oncology, Ontario Institute for Cancer Research , Toronto, ON M5G 0A3, Canada"],"affiliations":[{"raw_affiliation_string":"Adaptive Oncology, Ontario Institute for Cancer Research , Toronto, ON M5G 0A3, Canada","institution_ids":["https://openalex.org/I112260969"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5054625887","display_name":"Ian Holmes","orcid":"https://orcid.org/0000-0001-7639-5369"},"institutions":[{"id":"https://openalex.org/I95457486","display_name":"University of California, Berkeley","ror":"https://ror.org/01an7q238","country_code":"US","type":"education","lineage":["https://openalex.org/I95457486"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Ian Holmes","raw_affiliation_strings":["Department of Bioengineering, University of California , Berkeley, Berkeley, CA 94720, USA"],"affiliations":[{"raw_affiliation_string":"Department of Bioengineering, University of California , Berkeley, Berkeley, CA 94720, USA","institution_ids":["https://openalex.org/I95457486"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":8,"corresponding_author_ids":["https://openalex.org/A5054625887"],"corresponding_institution_ids":["https://openalex.org/I95457486"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":1.9521,"has_fulltext":true,"cited_by_count":26,"citation_normalized_percentile":{"value":0.86902029,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"37","issue":"21","first_page":"3914","last_page":"3915"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.998199999332428,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.998199999332428,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T11764","display_name":"Evolution and Genetic Dynamics","score":0.9872999787330627,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10885","display_name":"Gene expression and cancer classification","score":0.9810000061988831,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/genome-browser","display_name":"Genome browser","score":0.787118673324585},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7120104432106018},{"id":"https://openalex.org/keywords/interface","display_name":"Interface (matter)","score":0.6545288562774658},{"id":"https://openalex.org/keywords/web-browser","display_name":"Web browser","score":0.6541509628295898},{"id":"https://openalex.org/keywords/variety","display_name":"Variety (cybernetics)","score":0.6309431791305542},{"id":"https://openalex.org/keywords/visualization","display_name":"Visualization","score":0.6219286918640137},{"id":"https://openalex.org/keywords/download","display_name":"Download","score":0.6164867877960205},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.5861989855766296},{"id":"https://openalex.org/keywords/source-code","display_name":"Source code","score":0.5789143443107605},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.5563430786132812},{"id":"https://openalex.org/keywords/user-interface","display_name":"User interface","score":0.5306844711303711},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.46771612763404846},{"id":"https://openalex.org/keywords/code","display_name":"Code (set theory)","score":0.4587746858596802},{"id":"https://openalex.org/keywords/the-internet","display_name":"The Internet","score":0.3412379026412964},{"id":"https://openalex.org/keywords/genomics","display_name":"Genomics","score":0.26556694507598877},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.22178524732589722},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.15398645401000977},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.15190798044204712},{"id":"https://openalex.org/keywords/set","display_name":"Set (abstract data type)","score":0.11384811997413635},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.07920974493026733},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.07469344139099121}],"concepts":[{"id":"https://openalex.org/C2781148417","wikidata":"https://www.wikidata.org/wiki/Q5533486","display_name":"Genome browser","level":5,"score":0.787118673324585},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7120104432106018},{"id":"https://openalex.org/C113843644","wikidata":"https://www.wikidata.org/wiki/Q901882","display_name":"Interface (matter)","level":4,"score":0.6545288562774658},{"id":"https://openalex.org/C2983909278","wikidata":"https://www.wikidata.org/wiki/Q6368","display_name":"Web browser","level":3,"score":0.6541509628295898},{"id":"https://openalex.org/C136197465","wikidata":"https://www.wikidata.org/wiki/Q1729295","display_name":"Variety (cybernetics)","level":2,"score":0.6309431791305542},{"id":"https://openalex.org/C36464697","wikidata":"https://www.wikidata.org/wiki/Q451553","display_name":"Visualization","level":2,"score":0.6219286918640137},{"id":"https://openalex.org/C2780154274","wikidata":"https://www.wikidata.org/wiki/Q7126717","display_name":"Download","level":2,"score":0.6164867877960205},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.5861989855766296},{"id":"https://openalex.org/C43126263","wikidata":"https://www.wikidata.org/wiki/Q128751","display_name":"Source code","level":2,"score":0.5789143443107605},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.5563430786132812},{"id":"https://openalex.org/C89505385","wikidata":"https://www.wikidata.org/wiki/Q47146","display_name":"User interface","level":2,"score":0.5306844711303711},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.46771612763404846},{"id":"https://openalex.org/C2776760102","wikidata":"https://www.wikidata.org/wiki/Q5139990","display_name":"Code (set theory)","level":3,"score":0.4587746858596802},{"id":"https://openalex.org/C110875604","wikidata":"https://www.wikidata.org/wiki/Q75","display_name":"The Internet","level":2,"score":0.3412379026412964},{"id":"https://openalex.org/C189206191","wikidata":"https://www.wikidata.org/wiki/Q222046","display_name":"Genomics","level":4,"score":0.26556694507598877},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.22178524732589722},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.15398645401000977},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.15190798044204712},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.11384811997413635},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.07920974493026733},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.07469344139099121},{"id":"https://openalex.org/C157915830","wikidata":"https://www.wikidata.org/wiki/Q2928001","display_name":"Bubble","level":2,"score":0.0},{"id":"https://openalex.org/C129307140","wikidata":"https://www.wikidata.org/wiki/Q6795880","display_name":"Maximum bubble pressure method","level":3,"score":0.0},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.0},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0}],"mesh":[{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":4,"locations":[{"id":"doi:10.1093/bioinformatics/btab459","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btab459","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/37/21/3914/41091620/btab459.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:34196689","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/34196689","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics (Oxford, England)","raw_type":null},{"id":"pmh:oai:europepmc.org:7463232","is_oa":true,"landing_page_url":"http://europepmc.org/pmc/articles/PMC8570803","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Text"},{"id":"pmh:oai:pubmedcentral.nih.gov:8570803","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/8570803","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btab459","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btab459","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/37/21/3914/41091620/btab459.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1078007678","display_name":null,"funder_award_id":"HG004483","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G3354986905","display_name":null,"funder_award_id":"GM080203","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"}],"funders":[{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W3174992442.pdf","grobid_xml":"https://content.openalex.org/works/W3174992442.grobid-xml"},"referenced_works_count":9,"referenced_works":["https://openalex.org/W1993202658","https://openalex.org/W2021341670","https://openalex.org/W2099143842","https://openalex.org/W2122232025","https://openalex.org/W2128016314","https://openalex.org/W2268486506","https://openalex.org/W2336957559","https://openalex.org/W2765185461","https://openalex.org/W2946103575"],"related_works":["https://openalex.org/W2161951664","https://openalex.org/W1942786171","https://openalex.org/W3174992442","https://openalex.org/W4298080220","https://openalex.org/W2949621373","https://openalex.org/W4302610923","https://openalex.org/W2590969672","https://openalex.org/W4310490448","https://openalex.org/W2105114815","https://openalex.org/W2143797649"],"abstract_inverted_index":{"JBrowseR":[0],"is":[1,11],"available":[2,13],"for":[3],"download":[4],"from":[5,14],"CRAN,":[6],"and":[7],"the":[8,15],"source":[9],"code":[10],"openly":[12],"Github":[16],"repository":[17],"at":[18],"https://github.com/GMOD/JBrowseR/.":[19]},"counts_by_year":[{"year":2025,"cited_by_count":2},{"year":2024,"cited_by_count":9},{"year":2023,"cited_by_count":7},{"year":2022,"cited_by_count":7},{"year":2021,"cited_by_count":1}],"updated_date":"2026-04-21T08:09:41.155169","created_date":"2025-10-10T00:00:00"}