{"id":"https://openalex.org/W3009765943","doi":"https://doi.org/10.1093/bioinformatics/btaa128","title":"V-SVA: an R Shiny application for detecting and annotating hidden sources of variation in single-cell RNA-seq data","display_name":"V-SVA: an R Shiny application for detecting and annotating hidden sources of variation in single-cell RNA-seq data","publication_year":2020,"publication_date":"2020-02-26","ids":{"openalex":"https://openalex.org/W3009765943","doi":"https://doi.org/10.1093/bioinformatics/btaa128","mag":"3009765943","pmid":"https://pubmed.ncbi.nlm.nih.gov/32119082"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btaa128","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaa128","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/36/11/3582/33329278/btaa128.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-nc","license_id":"https://openalex.org/licenses/cc-by-nc","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/36/11/3582/33329278/btaa128.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5080546686","display_name":"Nathan Lawlor","orcid":"https://orcid.org/0000-0003-3263-6057"},"institutions":[{"id":"https://openalex.org/I4210115256","display_name":"Jackson Laboratory","ror":"https://ror.org/021sy4w91","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I4210115256"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Nathan Lawlor","raw_affiliation_strings":["The Jackson Laboratory for Genomic Medicine , Farmington, CT 06032, USA"],"affiliations":[{"raw_affiliation_string":"The Jackson Laboratory for Genomic Medicine , Farmington, CT 06032, USA","institution_ids":["https://openalex.org/I4210115256"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5032360243","display_name":"Eladio J. M\u00e1rquez","orcid":"https://orcid.org/0000-0001-5548-5795"},"institutions":[{"id":"https://openalex.org/I4210115256","display_name":"Jackson Laboratory","ror":"https://ror.org/021sy4w91","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I4210115256"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Eladio J Marquez","raw_affiliation_strings":["The Jackson Laboratory for Genomic Medicine , Farmington, CT 06032, USA"],"affiliations":[{"raw_affiliation_string":"The Jackson Laboratory for Genomic Medicine , Farmington, CT 06032, USA","institution_ids":["https://openalex.org/I4210115256"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101839040","display_name":"Donghyung Lee","orcid":"https://orcid.org/0000-0002-5145-3806"},"institutions":[{"id":"https://openalex.org/I4210115256","display_name":"Jackson Laboratory","ror":"https://ror.org/021sy4w91","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I4210115256"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Donghyung Lee","raw_affiliation_strings":["The Jackson Laboratory for Genomic Medicine , Farmington, CT 06032, USA"],"affiliations":[{"raw_affiliation_string":"The Jackson Laboratory for Genomic Medicine , Farmington, CT 06032, USA","institution_ids":["https://openalex.org/I4210115256"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5081776556","display_name":"Duygu Ucar","orcid":"https://orcid.org/0000-0002-9772-3066"},"institutions":[{"id":"https://openalex.org/I75929689","display_name":"UConn Health","ror":"https://ror.org/02kzs4y22","country_code":"US","type":"funder","lineage":["https://openalex.org/I75929689"]},{"id":"https://openalex.org/I4210115256","display_name":"Jackson Laboratory","ror":"https://ror.org/021sy4w91","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I4210115256"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Duygu Ucar","raw_affiliation_strings":["Department of Genetics and Genome Sciences","Institute of Systems Genomics , University of Connecticut Health Center, Farmington, CT 06032, USA","The Jackson Laboratory for Genomic Medicine , Farmington, CT 06032, USA"],"affiliations":[{"raw_affiliation_string":"Department of Genetics and Genome Sciences","institution_ids":[]},{"raw_affiliation_string":"Institute of Systems Genomics , University of Connecticut Health Center, Farmington, CT 06032, USA","institution_ids":["https://openalex.org/I75929689"]},{"raw_affiliation_string":"The Jackson Laboratory for Genomic Medicine , Farmington, CT 06032, USA","institution_ids":["https://openalex.org/I4210115256"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5081776556","https://openalex.org/A5101839040"],"corresponding_institution_ids":["https://openalex.org/I4210115256","https://openalex.org/I75929689"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":0.8364,"has_fulltext":false,"cited_by_count":12,"citation_normalized_percentile":{"value":0.70761907,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":99},"biblio":{"volume":"36","issue":"11","first_page":"3582","last_page":"3584"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.9998999834060669,"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/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.9998999834060669,"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/T10885","display_name":"Gene expression and cancer classification","score":0.9825999736785889,"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/T11970","display_name":"Molecular Biology Techniques and Applications","score":0.9703999757766724,"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/variation","display_name":"Variation (astronomy)","score":0.713710367679596},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6696478128433228},{"id":"https://openalex.org/keywords/source-code","display_name":"Source code","score":0.6294852495193481},{"id":"https://openalex.org/keywords/annotation","display_name":"Annotation","score":0.6124187707901001},{"id":"https://openalex.org/keywords/identification","display_name":"Identification (biology)","score":0.5743623375892639},{"id":"https://openalex.org/keywords/variable","display_name":"Variable (mathematics)","score":0.4614180028438568},{"id":"https://openalex.org/keywords/visualization","display_name":"Visualization","score":0.4103667140007019},{"id":"https://openalex.org/keywords/code","display_name":"Code (set theory)","score":0.41022989153862},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.39158540964126587},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.22050076723098755},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.16723713278770447},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.1467222273349762}],"concepts":[{"id":"https://openalex.org/C2778334786","wikidata":"https://www.wikidata.org/wiki/Q1586270","display_name":"Variation (astronomy)","level":2,"score":0.713710367679596},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6696478128433228},{"id":"https://openalex.org/C43126263","wikidata":"https://www.wikidata.org/wiki/Q128751","display_name":"Source code","level":2,"score":0.6294852495193481},{"id":"https://openalex.org/C2776321320","wikidata":"https://www.wikidata.org/wiki/Q857525","display_name":"Annotation","level":2,"score":0.6124187707901001},{"id":"https://openalex.org/C116834253","wikidata":"https://www.wikidata.org/wiki/Q2039217","display_name":"Identification (biology)","level":2,"score":0.5743623375892639},{"id":"https://openalex.org/C182365436","wikidata":"https://www.wikidata.org/wiki/Q50701","display_name":"Variable (mathematics)","level":2,"score":0.4614180028438568},{"id":"https://openalex.org/C36464697","wikidata":"https://www.wikidata.org/wiki/Q451553","display_name":"Visualization","level":2,"score":0.4103667140007019},{"id":"https://openalex.org/C2776760102","wikidata":"https://www.wikidata.org/wiki/Q5139990","display_name":"Code (set theory)","level":3,"score":0.41022989153862},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.39158540964126587},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.22050076723098755},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.16723713278770447},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.1467222273349762},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.0},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.0},{"id":"https://openalex.org/C134306372","wikidata":"https://www.wikidata.org/wiki/Q7754","display_name":"Mathematical analysis","level":1,"score":0.0},{"id":"https://openalex.org/C59822182","wikidata":"https://www.wikidata.org/wiki/Q441","display_name":"Botany","level":1,"score":0.0},{"id":"https://openalex.org/C44870925","wikidata":"https://www.wikidata.org/wiki/Q37547","display_name":"Astrophysics","level":1,"score":0.0},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.0}],"mesh":[{"descriptor_ui":"D000081246","descriptor_name":"RNA-Seq","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000081246","descriptor_name":"RNA-Seq","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000081246","descriptor_name":"RNA-Seq","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000081246","descriptor_name":"RNA-Seq","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":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D059010","descriptor_name":"Single-Cell Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059010","descriptor_name":"Single-Cell Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059010","descriptor_name":"Single-Cell Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059010","descriptor_name":"Single-Cell Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":5,"locations":[{"id":"doi:10.1093/bioinformatics/btaa128","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaa128","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/36/11/3582/33329278/btaa128.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-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:32119082","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/32119082","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:mouseion.jax.org:stfb2020-1121","is_oa":true,"landing_page_url":"https://mouseion.jax.org/stfb2020/117","pdf_url":null,"source":{"id":"https://openalex.org/S4377196421","display_name":"The Mouseion at the JAXlibrary (Jackson Laboratory)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I4210115256","host_organization_name":"Jackson Laboratory","host_organization_lineage":["https://openalex.org/I4210115256"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Faculty Research 2020","raw_type":"text"},{"id":"pmh:oai:mouseion.jax.org:stfbaop-1224","is_oa":false,"landing_page_url":"https://mouseion.jax.org/stfbaop/227","pdf_url":null,"source":{"id":"https://openalex.org/S4377196421","display_name":"The Mouseion at the JAXlibrary (Jackson Laboratory)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I4210115256","host_organization_name":"Jackson Laboratory","host_organization_lineage":["https://openalex.org/I4210115256"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Faculty Research Ahead of Print","raw_type":"text"},{"id":"pmh:oai:pubmedcentral.nih.gov:7267827","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/7267827","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","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":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btaa128","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaa128","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/36/11/3582/33329278/btaa128.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-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1380022865","display_name":null,"funder_award_id":"GM124922","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"}],"funders":[{"id":"https://openalex.org/F4320337354","display_name":"National Institute of General Medical Sciences","ror":"https://ror.org/04q48ey07"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W3009765943.pdf","grobid_xml":"https://content.openalex.org/works/W3009765943.grobid-xml"},"referenced_works_count":11,"referenced_works":["https://openalex.org/W54517741","https://openalex.org/W645554778","https://openalex.org/W1875842236","https://openalex.org/W2035618305","https://openalex.org/W2076198632","https://openalex.org/W2127008679","https://openalex.org/W2137499573","https://openalex.org/W2169353806","https://openalex.org/W2774307122","https://openalex.org/W2783644856","https://openalex.org/W2900576466"],"related_works":["https://openalex.org/W2361861616","https://openalex.org/W2386430105","https://openalex.org/W2263699433","https://openalex.org/W2377979023","https://openalex.org/W2218034408","https://openalex.org/W2392921965","https://openalex.org/W2356521405","https://openalex.org/W2358755282","https://openalex.org/W2625833328","https://openalex.org/W2384358604"],"abstract_inverted_index":{"Supplementary":[0],"data":[1],"are":[2],"available":[3],"at":[4],"Bioinformatics":[5],"online.":[6]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":8},{"year":2022,"cited_by_count":2}],"updated_date":"2026-03-04T09:10:02.777135","created_date":"2025-10-10T00:00:00"}