{"id":"https://openalex.org/W2463616135","doi":"https://doi.org/10.1093/bioinformatics/btw405","title":"MetaCycle: an integrated R package to evaluate periodicity in large scale data","display_name":"MetaCycle: an integrated R package to evaluate periodicity in large scale data","publication_year":2016,"publication_date":"2016-07-04","ids":{"openalex":"https://openalex.org/W2463616135","doi":"https://doi.org/10.1093/bioinformatics/btw405","mag":"2463616135","pmid":"https://pubmed.ncbi.nlm.nih.gov/27378304"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btw405","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btw405","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/32/21/3351/7889685/btw405.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":null,"license_id":null,"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":"bronze","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/32/21/3351/7889685/btw405.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5100630676","display_name":"Gang Wu","orcid":"https://orcid.org/0000-0002-4526-2034"},"institutions":[{"id":"https://openalex.org/I4210125521","display_name":"Translational Therapeutics (United States)","ror":"https://ror.org/02z3rcy16","country_code":"US","type":"company","lineage":["https://openalex.org/I4210125521"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Gang Wu","raw_affiliation_strings":["1 Department of Systems Pharmacology and Translational Therapeutics, Institute for Translational Medicine and Therapeutics"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Department of Systems Pharmacology and Translational Therapeutics, Institute for Translational Medicine and Therapeutics","institution_ids":["https://openalex.org/I4210125521"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5044447178","display_name":"Ron C. Anafi","orcid":"https://orcid.org/0000-0003-4643-5854"},"institutions":[{"id":"https://openalex.org/I4210154614","display_name":"SleepMed","ror":"https://ror.org/04bxj6908","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I4210154614"]},{"id":"https://openalex.org/I79576946","display_name":"University of Pennsylvania","ror":"https://ror.org/00b30xv10","country_code":"US","type":"education","lineage":["https://openalex.org/I79576946"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Ron C. Anafi","raw_affiliation_strings":["2 Division of Sleep Medicine","3 Center for Sleep and Circadian Neurobiology, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"2 Division of Sleep Medicine","institution_ids":["https://openalex.org/I4210154614"]},{"raw_affiliation_string":"3 Center for Sleep and Circadian Neurobiology, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA","institution_ids":["https://openalex.org/I79576946"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101469963","display_name":"Michael E. Hughes","orcid":"https://orcid.org/0000-0002-8828-3732"},"institutions":[{"id":"https://openalex.org/I208333798","display_name":"University of Missouri\u2013St. Louis","ror":"https://ror.org/037cnag11","country_code":"US","type":"education","lineage":["https://openalex.org/I208333798"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Michael E. Hughes","raw_affiliation_strings":["4 Department of Biology, University of Missouri\u2013St. Louis, St. Louis, MO 63121, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"4 Department of Biology, University of Missouri\u2013St. Louis, St. Louis, MO 63121, USA","institution_ids":["https://openalex.org/I208333798"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5013614373","display_name":"Karl Kornacker","orcid":null},"institutions":[{"id":"https://openalex.org/I52357470","display_name":"The Ohio State University","ror":"https://ror.org/00rs6vg23","country_code":"US","type":"education","lineage":["https://openalex.org/I52357470"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Karl Kornacker","raw_affiliation_strings":["5 Emeritus Professor of Sensory Biophysics, the Ohio State University, Columbus, OH 43210, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"5 Emeritus Professor of Sensory Biophysics, the Ohio State University, Columbus, OH 43210, USA","institution_ids":["https://openalex.org/I52357470"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5035012559","display_name":"John B. Hogenesch","orcid":"https://orcid.org/0000-0002-9138-8973"},"institutions":[{"id":"https://openalex.org/I4210125521","display_name":"Translational Therapeutics (United States)","ror":"https://ror.org/02z3rcy16","country_code":"US","type":"company","lineage":["https://openalex.org/I4210125521"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"John B. Hogenesch","raw_affiliation_strings":["1 Department of Systems Pharmacology and Translational Therapeutics, Institute for Translational Medicine and Therapeutics"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Department of Systems Pharmacology and Translational Therapeutics, Institute for Translational Medicine and Therapeutics","institution_ids":["https://openalex.org/I4210125521"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5035012559"],"corresponding_institution_ids":["https://openalex.org/I4210125521"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":16.5403,"has_fulltext":true,"cited_by_count":599,"citation_normalized_percentile":{"value":0.9938079,"is_in_top_1_percent":true,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":90,"max":100},"biblio":{"volume":"32","issue":"21","first_page":"3351","last_page":"3353"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12946","display_name":"Fractal and DNA sequence analysis","score":0.23980000615119934,"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/T12946","display_name":"Fractal and DNA sequence analysis","score":0.23980000615119934,"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/T12254","display_name":"Machine Learning in Bioinformatics","score":0.08829999715089798,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.06780000030994415,"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/suite","display_name":"Suite","score":0.8368492722511292},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7862425446510315},{"id":"https://openalex.org/keywords/r-package","display_name":"R package","score":0.691780686378479},{"id":"https://openalex.org/keywords/series","display_name":"Series (stratigraphy)","score":0.5331714749336243},{"id":"https://openalex.org/keywords/scale","display_name":"Scale (ratio)","score":0.5296962857246399},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.4759387969970703},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.3525657057762146},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.24178946018218994}],"concepts":[{"id":"https://openalex.org/C79581498","wikidata":"https://www.wikidata.org/wiki/Q1367530","display_name":"Suite","level":2,"score":0.8368492722511292},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7862425446510315},{"id":"https://openalex.org/C2984074130","wikidata":"https://www.wikidata.org/wiki/Q73539779","display_name":"R package","level":2,"score":0.691780686378479},{"id":"https://openalex.org/C143724316","wikidata":"https://www.wikidata.org/wiki/Q312468","display_name":"Series (stratigraphy)","level":2,"score":0.5331714749336243},{"id":"https://openalex.org/C2778755073","wikidata":"https://www.wikidata.org/wiki/Q10858537","display_name":"Scale (ratio)","level":2,"score":0.5296962857246399},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.4759387969970703},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.3525657057762146},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.24178946018218994},{"id":"https://openalex.org/C62520636","wikidata":"https://www.wikidata.org/wiki/Q944","display_name":"Quantum mechanics","level":1,"score":0.0},{"id":"https://openalex.org/C151730666","wikidata":"https://www.wikidata.org/wiki/Q7205","display_name":"Paleontology","level":1,"score":0.0},{"id":"https://openalex.org/C95457728","wikidata":"https://www.wikidata.org/wiki/Q309","display_name":"History","level":0,"score":0.0},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.0},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.0},{"id":"https://openalex.org/C166957645","wikidata":"https://www.wikidata.org/wiki/Q23498","display_name":"Archaeology","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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":"D013223","descriptor_name":"Statistics as Topic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D013223","descriptor_name":"Statistics as Topic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D013223","descriptor_name":"Statistics as Topic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":4,"locations":[{"id":"doi:10.1093/bioinformatics/btw405","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btw405","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/32/21/3351/7889685/btw405.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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:27378304","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/27378304","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:pubmedcentral.nih.gov:5079475","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/5079475","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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"Text"},{"id":"pmh:oai:open-archive.highwire.org:bioinfo:32/21/3351","is_oa":false,"landing_page_url":"http://bioinformatics.oxfordjournals.org/cgi/content/short/32/21/3351","pdf_url":null,"source":{"id":"https://openalex.org/S4406923041","display_name":"HighWire Press Open Archive","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"TEXT"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btw405","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btw405","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/32/21/3351/7889685/btw405.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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G5333873862","display_name":null,"funder_award_id":"DARPA-D12AP00025","funder_id":"https://openalex.org/F4320332180","funder_display_name":"Defense Advanced Research Projects Agency"},{"id":"https://openalex.org/G7035006519","display_name":null,"funder_award_id":"D12AP00025","funder_id":"https://openalex.org/F4320332180","funder_display_name":"Defense Advanced Research Projects Agency"},{"id":"https://openalex.org/G7479834065","display_name":null,"funder_award_id":"R01 NS054794","funder_id":"https://openalex.org/F4320337359","funder_display_name":"National Institute of Neurological Disorders and Stroke"}],"funders":[{"id":"https://openalex.org/F4320332180","display_name":"Defense Advanced Research Projects Agency","ror":"https://ror.org/02caytj08"},{"id":"https://openalex.org/F4320332815","display_name":"Advanced Research Projects Agency","ror":"https://ror.org/02caytj08"},{"id":"https://openalex.org/F4320337359","display_name":"National Institute of Neurological Disorders and Stroke","ror":"https://ror.org/01s5ya894"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2463616135.pdf","grobid_xml":"https://content.openalex.org/works/W2463616135.grobid-xml"},"referenced_works_count":15,"referenced_works":["https://openalex.org/W1533179050","https://openalex.org/W1945100066","https://openalex.org/W1971883897","https://openalex.org/W1985332662","https://openalex.org/W2049047355","https://openalex.org/W2056395995","https://openalex.org/W2122135124","https://openalex.org/W2128397850","https://openalex.org/W2135657996","https://openalex.org/W2137810258","https://openalex.org/W2141526271","https://openalex.org/W2167325131","https://openalex.org/W2997000181","https://openalex.org/W4205470728","https://openalex.org/W6680046297"],"related_works":["https://openalex.org/W4231704780","https://openalex.org/W2083794993","https://openalex.org/W352609212","https://openalex.org/W1511772879","https://openalex.org/W4200340037","https://openalex.org/W4379115841","https://openalex.org/W608917066","https://openalex.org/W4283652261","https://openalex.org/W585424826","https://openalex.org/W564602992"],"abstract_inverted_index":{"Detecting":[0],"periodicity":[1,49],"in":[2,29,50],"large":[3],"scale":[4],"data":[5,102],"remains":[6],"a":[7,30,75],"challenge.":[8],"While":[9],"efforts":[10],"have":[11],"been":[12],"made":[13],"to":[14,46,61],"identify":[15],"best":[16],"of":[17,77],"breed":[18],"algorithms,":[19],"relatively":[20],"little":[21],"research":[22],"has":[23,54],"gone":[24],"into":[25],"integrating":[26,80],"these":[27],"methods":[28],"generalizable":[31],"method.":[32],"Here,":[33],"we":[34],"present":[35],"MetaCycle,":[36],"an":[37],"R":[38],"package":[39,87],"that":[40],"incorporates":[41],"ARSER,":[42],"JTK_CYCLE":[43],"and":[44,58,64,79,95],"Lomb-Scargle":[45],"conveniently":[47],"evaluate":[48],"time-series":[51,66],"data.":[52],"MetaCycle":[53,86],"two":[55],"functions,":[56],"meta2d":[57],"meta3d,":[59],"designed":[60],"analyze":[62],"two-dimensional":[63],"three-dimensional":[65],"datasets,":[67],"respectively.":[68],"Meta2d":[69],"implements":[70],"N-version":[71],"programming":[72],"concepts":[73],"using":[74],"suite":[76],"algorithms":[78],"their":[81],"results.":[82],"AVAILABILITY":[83],"AND":[84],"IMPLEMENTATION:":[85],"is":[88],"available":[89,104],"on":[90],"the":[91],"CRAN":[92],"repository":[93],"(https://cran.r-project.org/web/packages/MetaCycle/index.html)":[94],"GitHub":[96],"(https://github.com/gangwug/MetaCycle).":[97],"CONTACT:":[98],"hogenesch@gmail.comSupplementary":[99],"information:":[100],"Supplementary":[101],"are":[103],"at":[105],"Bioinformatics":[106],"online.":[107]},"counts_by_year":[{"year":2026,"cited_by_count":35},{"year":2025,"cited_by_count":76},{"year":2024,"cited_by_count":92},{"year":2023,"cited_by_count":79},{"year":2022,"cited_by_count":82},{"year":2021,"cited_by_count":75},{"year":2020,"cited_by_count":64},{"year":2019,"cited_by_count":41},{"year":2018,"cited_by_count":30},{"year":2017,"cited_by_count":18},{"year":2016,"cited_by_count":5},{"year":2015,"cited_by_count":1},{"year":2012,"cited_by_count":1}],"updated_date":"2026-06-24T13:16:06.693445","created_date":"2025-10-10T00:00:00"}
