{"id":"https://openalex.org/W2809708472","doi":"https://doi.org/10.1093/bioinformatics/bty546","title":"ShinyCNV: a Shiny/R application to view and annotate DNA copy number variations","display_name":"ShinyCNV: a Shiny/R application to view and annotate DNA copy number variations","publication_year":2018,"publication_date":"2018-06-29","ids":{"openalex":"https://openalex.org/W2809708472","doi":"https://doi.org/10.1093/bioinformatics/bty546","mag":"2809708472","pmid":"https://pubmed.ncbi.nlm.nih.gov/30561549"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/bty546","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bty546","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/35/1/126/48962677/bioinformatics_35_1_126.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/35/1/126/48962677/bioinformatics_35_1_126.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5011812481","display_name":"Zhaohui Gu","orcid":"https://orcid.org/0000-0003-1581-1327"},"institutions":[{"id":"https://openalex.org/I1313298211","display_name":"St. Jude Children's Research Hospital","ror":"https://ror.org/02r3e0967","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I1313298211","https://openalex.org/I2802152183"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Zhaohui Gu","raw_affiliation_strings":["Department of Pathology, St. Jude Children\u2019s Research Hospital, Memphis, TN, USA"],"raw_orcid":"https://orcid.org/0000-0003-1581-1327","affiliations":[{"raw_affiliation_string":"Department of Pathology, St. Jude Children\u2019s Research Hospital, Memphis, TN, USA","institution_ids":["https://openalex.org/I1313298211"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5048744038","display_name":"Charles G. Mullighan","orcid":"https://orcid.org/0000-0002-1871-1850"},"institutions":[{"id":"https://openalex.org/I1313298211","display_name":"St. Jude Children's Research Hospital","ror":"https://ror.org/02r3e0967","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I1313298211","https://openalex.org/I2802152183"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Charles G Mullighan","raw_affiliation_strings":["Department of Pathology, St. Jude Children\u2019s Research Hospital, Memphis, TN, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Pathology, St. Jude Children\u2019s Research Hospital, Memphis, TN, USA","institution_ids":["https://openalex.org/I1313298211"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5048744038"],"corresponding_institution_ids":["https://openalex.org/I1313298211"],"apc_list":{"value":3989,"currency":"USD","value_usd":3989},"apc_paid":null,"fwci":0.2765,"has_fulltext":true,"cited_by_count":9,"citation_normalized_percentile":{"value":0.47263868,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":97},"biblio":{"volume":"35","issue":"1","first_page":"126","last_page":"129"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11287","display_name":"Cancer Genomics and Diagnostics","score":0.586899995803833,"subfield":{"id":"https://openalex.org/subfields/1306","display_name":"Cancer Research"},"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/T11287","display_name":"Cancer Genomics and Diagnostics","score":0.586899995803833,"subfield":{"id":"https://openalex.org/subfields/1306","display_name":"Cancer Research"},"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/T11213","display_name":"Genomic variations and chromosomal abnormalities","score":0.32510000467300415,"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/T11642","display_name":"Genomics and Rare Diseases","score":0.01269999984651804,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7366605997085571},{"id":"https://openalex.org/keywords/copy-number-variation","display_name":"Copy-number variation","score":0.6375741958618164},{"id":"https://openalex.org/keywords/snp","display_name":"SNP","score":0.5824921727180481},{"id":"https://openalex.org/keywords/breakpoint","display_name":"Breakpoint","score":0.45358067750930786},{"id":"https://openalex.org/keywords/graphical-user-interface","display_name":"Graphical user interface","score":0.4345674514770508},{"id":"https://openalex.org/keywords/single-nucleotide-polymorphism","display_name":"Single-nucleotide polymorphism","score":0.36143386363983154},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.3502013087272644},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.21765825152397156},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.21577584743499756},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.17514950037002563},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.10384407639503479}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7366605997085571},{"id":"https://openalex.org/C120821319","wikidata":"https://www.wikidata.org/wiki/Q1501491","display_name":"Copy-number variation","level":4,"score":0.6375741958618164},{"id":"https://openalex.org/C139275648","wikidata":"https://www.wikidata.org/wiki/Q17134011","display_name":"SNP","level":5,"score":0.5824921727180481},{"id":"https://openalex.org/C206936463","wikidata":"https://www.wikidata.org/wiki/Q634179","display_name":"Breakpoint","level":4,"score":0.45358067750930786},{"id":"https://openalex.org/C37789001","wikidata":"https://www.wikidata.org/wiki/Q782543","display_name":"Graphical user interface","level":2,"score":0.4345674514770508},{"id":"https://openalex.org/C153209595","wikidata":"https://www.wikidata.org/wiki/Q501128","display_name":"Single-nucleotide polymorphism","level":4,"score":0.36143386363983154},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3502013087272644},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.21765825152397156},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.21577584743499756},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.17514950037002563},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.10384407639503479},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0},{"id":"https://openalex.org/C135763542","wikidata":"https://www.wikidata.org/wiki/Q106016","display_name":"Genotype","level":3,"score":0.0},{"id":"https://openalex.org/C138626823","wikidata":"https://www.wikidata.org/wiki/Q916504","display_name":"Chromosomal translocation","level":3,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","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":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020641","descriptor_name":"Polymorphism, Single Nucleotide","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020641","descriptor_name":"Polymorphism, Single Nucleotide","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020641","descriptor_name":"Polymorphism, Single Nucleotide","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D056915","descriptor_name":"DNA Copy Number Variations","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D056915","descriptor_name":"DNA Copy Number Variations","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D056915","descriptor_name":"DNA Copy Number Variations","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D058977","descriptor_name":"Molecular Sequence Annotation","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D058977","descriptor_name":"Molecular Sequence Annotation","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D058977","descriptor_name":"Molecular Sequence Annotation","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/bty546","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bty546","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/35/1/126/48962677/bioinformatics_35_1_126.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:30561549","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/30561549","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":"Journal Article"},{"id":"pmh:oai:europepmc.org:5888551","is_oa":false,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/6298054","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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/bty546","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bty546","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/35/1/126/48962677/bioinformatics_35_1_126.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":[{"id":"https://metadata.un.org/sdg/4","display_name":"Quality Education","score":0.4399999976158142}],"awards":[{"id":"https://openalex.org/G1459186046","display_name":null,"funder_award_id":"P30CA021765","funder_id":"https://openalex.org/F4320337351","funder_display_name":"National Cancer Institute"},{"id":"https://openalex.org/G169511485","display_name":null,"funder_award_id":"R35\u2010CA197695","funder_id":"https://openalex.org/F4320337351","funder_display_name":"National Cancer Institute"},{"id":"https://openalex.org/G1744533847","display_name":null,"funder_award_id":"GM 115279","funder_id":"https://openalex.org/F4320337351","funder_display_name":"National Cancer Institute"},{"id":"https://openalex.org/G2484864540","display_name":null,"funder_award_id":"GM 115279","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G2490302200","display_name":null,"funder_award_id":"P50 GM115279","funder_id":"https://openalex.org/F4320337351","funder_display_name":"National Cancer Institute"},{"id":"https://openalex.org/G2554726104","display_name":null,"funder_award_id":"P50 GM115279","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G2954099590","display_name":null,"funder_award_id":"CA021765","funder_id":"https://openalex.org/F4320310040","funder_display_name":"St. Jude Children's Research Hospital"},{"id":"https://openalex.org/G3271267690","display_name":null,"funder_award_id":"P50 GM115279","funder_id":"https://openalex.org/F4320313598","funder_display_name":"American Lebanese Syrian Associated Charities"},{"id":"https://openalex.org/G425884651","display_name":null,"funder_award_id":"P30 CA021765","funder_id":"https://openalex.org/F4320310040","funder_display_name":"St. Jude Children's Research Hospital"},{"id":"https://openalex.org/G4766096375","display_name":null,"funder_award_id":"CA021765","funder_id":"https://openalex.org/F4320337351","funder_display_name":"National Cancer Institute"},{"id":"https://openalex.org/G4869702982","display_name":null,"funder_award_id":"CA021765","funder_id":"https://openalex.org/F4320313598","funder_display_name":"American Lebanese Syrian Associated Charities"},{"id":"https://openalex.org/G6289520395","display_name":null,"funder_award_id":"CA197695","funder_id":"https://openalex.org/F4320337351","funder_display_name":"National Cancer Institute"}],"funders":[{"id":"https://openalex.org/F4320310040","display_name":"St. Jude Children's Research Hospital","ror":"https://ror.org/02r3e0967"},{"id":"https://openalex.org/F4320313598","display_name":"American Lebanese Syrian Associated Charities","ror":"https://ror.org/03rx10x31"},{"id":"https://openalex.org/F4320337351","display_name":"National Cancer Institute","ror":"https://ror.org/040gcmg81"},{"id":"https://openalex.org/F4320337354","display_name":"National Institute of General Medical Sciences","ror":"https://ror.org/04q48ey07"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2809708472.pdf","grobid_xml":"https://content.openalex.org/works/W2809708472.grobid-xml"},"referenced_works_count":12,"referenced_works":["https://openalex.org/W1984065010","https://openalex.org/W1986522151","https://openalex.org/W1988785484","https://openalex.org/W2040329520","https://openalex.org/W2104224322","https://openalex.org/W2115919763","https://openalex.org/W2144924266","https://openalex.org/W2146948473","https://openalex.org/W2149681218","https://openalex.org/W2158605807","https://openalex.org/W2159595235","https://openalex.org/W2224894504"],"related_works":["https://openalex.org/W2996064479","https://openalex.org/W2164371156","https://openalex.org/W3001862779","https://openalex.org/W3011291019","https://openalex.org/W1965724869","https://openalex.org/W2188551670","https://openalex.org/W2006736564","https://openalex.org/W4319734519","https://openalex.org/W2140968934","https://openalex.org/W2809708472"],"abstract_inverted_index":{"Motivation:":[0],"Single":[1],"nucleotide":[2],"polymorphism":[3],"(SNP)":[4],"array":[5],"is":[6,57,60,164],"the":[7,30,54,107,115,123,128,137,194],"most":[8],"widely":[9],"used":[10],"platform":[11],"to":[12,81,139,151,166,185],"assess":[13],"somatic":[14],"copy":[15],"number":[16],"variations":[17],"(CNVs)":[18],"in":[19],"cancer":[20,170],"studies.":[21],"Many":[22],"SNP":[23,55,91],"data-based":[24],"CNV":[25,51,143],"callers":[26],"are":[27,37,158,196,205],"available,":[28],"however,":[29],"false":[31],"positive":[32],"rates":[33],"from":[34,145,160,199],"automated":[35],"calling":[36],"commonly":[38,141],"high,":[39],"and":[40,83,99,110,150,172,190,193],"reported":[41,50,108,161],"breakpoints":[42],"can":[43,103,112,135,173],"be":[44,104,167,174],"inaccurate.":[45],"Manual":[46],"review":[47],"for":[48,62,169,177],"each":[49],"by":[52],"visualizing":[53],"data":[56,204],"important,":[58],"but":[59],"challenging":[61],"users":[63,111],"lacking":[64],"computational":[65],"experience.":[66],"To":[67],"address":[68],"this,":[69],"we":[70],"present":[71],"a":[72,146],"Shiny/R":[73],"application":[74],"ShinyCNV,":[75],"an":[76],"interactive":[77,129],"graphical":[78],"user":[79],"interface":[80],"view":[82],"annotate":[84],"CNVs.":[85,162],"Results:":[86],"With":[87],"this":[88],"application,":[89],"normalized":[90],"data,":[92],"which":[93],"includes":[94],"log":[95],"R":[96],"ratio":[97],"(LRR)":[98],"B":[100],"allele":[101],"frequency,":[102],"plotted":[105],"against":[106],"CNVs,":[109],"visually":[113,152],"check":[114,153],"reliability":[116],"of":[117,148],"CNVs":[118],"per":[119],"se":[120],"or":[121,181],"adjust":[122],"incorrectly":[124],"assigned":[125],"breakpoints.":[126],"Further,":[127],"LRR":[130],"spectrum":[131],"panel":[132],"within":[133],"ShinyCNV":[134,163,192],"facilitate":[136],"process":[138],"identify":[140],"affected":[142],"regions":[144],"group":[147],"samples,":[149],"if":[154],"important":[155],"focal":[156],"gains/losses":[157],"missing":[159],"designed":[165],"intuitive":[168],"researchers":[171],"easily":[175],"installed":[176],"either":[178],"personal":[179],"use":[180],"deployed":[182],"on":[183],"servers":[184],"provide":[186],"online":[187],"service.":[188],"Availability":[189],"implementation:":[191],"tutorial":[195],"freely":[197],"available":[198,206],"https://github.com/gzhmat/ShinyCNV.":[200],"Supplementary":[201,203],"information:":[202],"at":[207],"Bioinformatics":[208],"online.":[209]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2022,"cited_by_count":4},{"year":2020,"cited_by_count":2},{"year":2019,"cited_by_count":1},{"year":2018,"cited_by_count":1}],"updated_date":"2026-08-29T07:29:34.045763","created_date":"2025-10-10T00:00:00"}