{"id":"https://openalex.org/W3022607788","doi":"https://doi.org/10.1093/bioinformatics/btaa283","title":"scDoc: correcting drop-out events in single-cell RNA-seq data","display_name":"scDoc: correcting drop-out events in single-cell RNA-seq data","publication_year":2020,"publication_date":"2020-04-24","ids":{"openalex":"https://openalex.org/W3022607788","doi":"https://doi.org/10.1093/bioinformatics/btaa283","mag":"3022607788","pmid":"https://pubmed.ncbi.nlm.nih.gov/32365169"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btaa283","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaa283","pdf_url":null,"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":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5112437973","display_name":"Di Ran","orcid":"https://orcid.org/0009-0003-3433-3495"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Di Ran","raw_affiliation_strings":["Division of Epidemiology and Biostatistics, Mel and Enid Zuckerman College of Public Health"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Division of Epidemiology and Biostatistics, Mel and Enid Zuckerman College of Public Health","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5046910090","display_name":"Shanshan Zhang","orcid":"https://orcid.org/0000-0002-6802-8769"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Shanshan Zhang","raw_affiliation_strings":["Graduate Interdisciplinary Program in Statistics and Data Science","School of Plant Sciences"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Graduate Interdisciplinary Program in Statistics and Data Science","institution_ids":[]},{"raw_affiliation_string":"School of Plant Sciences","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5006881858","display_name":"Nicholas Lytal","orcid":"https://orcid.org/0000-0003-2134-2715"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Nicholas Lytal","raw_affiliation_strings":["Graduate Interdisciplinary Program in Statistics and Data Science"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Graduate Interdisciplinary Program in Statistics and Data Science","institution_ids":[]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5042050677","display_name":"Lingling An","orcid":"https://orcid.org/0000-0001-8273-0776"},"institutions":[{"id":"https://openalex.org/I138006243","display_name":"University of Arizona","ror":"https://ror.org/03m2x1q45","country_code":"US","type":"education","lineage":["https://openalex.org/I138006243"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Lingling An","raw_affiliation_strings":["Department of Biosystems Engineering, University of Arizona , Tucson, AZ 85721, USA","Division of Epidemiology and Biostatistics, Mel and Enid Zuckerman College of Public Health","Graduate Interdisciplinary Program in Statistics and Data Science"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biosystems Engineering, University of Arizona , Tucson, AZ 85721, USA","institution_ids":["https://openalex.org/I138006243"]},{"raw_affiliation_string":"Division of Epidemiology and Biostatistics, Mel and Enid Zuckerman College of Public Health","institution_ids":[]},{"raw_affiliation_string":"Graduate Interdisciplinary Program in Statistics and Data Science","institution_ids":[]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5042050677"],"corresponding_institution_ids":["https://openalex.org/I138006243"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":1.667,"has_fulltext":false,"cited_by_count":27,"citation_normalized_percentile":{"value":0.84017941,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"36","issue":"15","first_page":"4233","last_page":"4239"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.9994999766349792,"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":0.9994999766349792,"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/T12859","display_name":"Cell Image Analysis Techniques","score":0.00019999999494757503,"subfield":{"id":"https://openalex.org/subfields/1304","display_name":"Biophysics"},"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/T11287","display_name":"Cancer Genomics and Diagnostics","score":0.0,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/imputation","display_name":"Imputation (statistics)","score":0.7133769989013672},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6335119009017944},{"id":"https://openalex.org/keywords/rna-seq","display_name":"RNA-Seq","score":0.5490251183509827},{"id":"https://openalex.org/keywords/rna","display_name":"RNA","score":0.4928162395954132},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.47467970848083496},{"id":"https://openalex.org/keywords/drop-out","display_name":"Drop out","score":0.4234536290168762},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.3727315068244934},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.31529340147972107},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.3027718663215637},{"id":"https://openalex.org/keywords/missing-data","display_name":"Missing data","score":0.23470237851142883},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.21801477670669556},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.1641441285610199},{"id":"https://openalex.org/keywords/transcriptome","display_name":"Transcriptome","score":0.11517688632011414},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.09391310811042786}],"concepts":[{"id":"https://openalex.org/C58041806","wikidata":"https://www.wikidata.org/wiki/Q1660484","display_name":"Imputation (statistics)","level":3,"score":0.7133769989013672},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6335119009017944},{"id":"https://openalex.org/C107397762","wikidata":"https://www.wikidata.org/wiki/Q2542347","display_name":"RNA-Seq","level":5,"score":0.5490251183509827},{"id":"https://openalex.org/C67705224","wikidata":"https://www.wikidata.org/wiki/Q11053","display_name":"RNA","level":3,"score":0.4928162395954132},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.47467970848083496},{"id":"https://openalex.org/C2984949393","wikidata":"https://www.wikidata.org/wiki/Q1260241","display_name":"Drop out","level":2,"score":0.4234536290168762},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3727315068244934},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.31529340147972107},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.3027718663215637},{"id":"https://openalex.org/C9357733","wikidata":"https://www.wikidata.org/wiki/Q6878417","display_name":"Missing data","level":2,"score":0.23470237851142883},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.21801477670669556},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.1641441285610199},{"id":"https://openalex.org/C162317418","wikidata":"https://www.wikidata.org/wiki/Q252857","display_name":"Transcriptome","level":4,"score":0.11517688632011414},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.09391310811042786},{"id":"https://openalex.org/C162324750","wikidata":"https://www.wikidata.org/wiki/Q8134","display_name":"Economics","level":0,"score":0.0},{"id":"https://openalex.org/C4249254","wikidata":"https://www.wikidata.org/wiki/Q3044431","display_name":"Demographic economics","level":1,"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":"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":"D020869","descriptor_name":"Gene Expression Profiling","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":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","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":true},{"descriptor_ui":"D059010","descriptor_name":"Single-Cell Analysis","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":true}],"locations_count":2,"locations":[{"id":"doi:10.1093/bioinformatics/btaa283","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaa283","pdf_url":null,"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:32365169","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/32365169","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}],"best_oa_location":null,"sustainable_development_goals":[{"score":0.5,"id":"https://metadata.un.org/sdg/4","display_name":"Quality Education"}],"awards":[{"id":"https://openalex.org/G6976995078","display_name":null,"funder_award_id":"ARZT-1360830-H22-138","funder_id":"https://openalex.org/F4320306114","funder_display_name":"U.S. Department of Agriculture"},{"id":"https://openalex.org/G7670369070","display_name":null,"funder_award_id":"ARZT-1361620-H22-149","funder_id":"https://openalex.org/F4320306114","funder_display_name":"U.S. Department of Agriculture"}],"funders":[{"id":"https://openalex.org/F4320306114","display_name":"U.S. Department of Agriculture","ror":"https://ror.org/01na82s61"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":49,"referenced_works":["https://openalex.org/W1536902151","https://openalex.org/W1552434751","https://openalex.org/W1967327758","https://openalex.org/W1979283544","https://openalex.org/W1984883254","https://openalex.org/W1988391018","https://openalex.org/W2010653277","https://openalex.org/W2023887100","https://openalex.org/W2030017878","https://openalex.org/W2049633694","https://openalex.org/W2060245619","https://openalex.org/W2068881679","https://openalex.org/W2069295116","https://openalex.org/W2071010503","https://openalex.org/W2086277161","https://openalex.org/W2110065044","https://openalex.org/W2114104545","https://openalex.org/W2125336256","https://openalex.org/W2152239989","https://openalex.org/W2152692691","https://openalex.org/W2165232124","https://openalex.org/W2190545194","https://openalex.org/W2281322842","https://openalex.org/W2316095770","https://openalex.org/W2338756998","https://openalex.org/W2343956310","https://openalex.org/W2345356016","https://openalex.org/W2516756255","https://openalex.org/W2559702793","https://openalex.org/W2605810679","https://openalex.org/W2611660641","https://openalex.org/W2739329039","https://openalex.org/W2751468300","https://openalex.org/W2753518299","https://openalex.org/W2783644856","https://openalex.org/W2788908087","https://openalex.org/W2792693509","https://openalex.org/W2801949492","https://openalex.org/W2899348912","https://openalex.org/W2916779758","https://openalex.org/W2944189019","https://openalex.org/W2949067670","https://openalex.org/W2951217100","https://openalex.org/W2951381561","https://openalex.org/W2952303649","https://openalex.org/W4231157025","https://openalex.org/W4235169531","https://openalex.org/W4235276207","https://openalex.org/W4244203357"],"related_works":["https://openalex.org/W4211215373","https://openalex.org/W3217094455","https://openalex.org/W2989589450","https://openalex.org/W3119637569","https://openalex.org/W2405773734","https://openalex.org/W4394426846","https://openalex.org/W2791189374","https://openalex.org/W3123325766","https://openalex.org/W4403319084","https://openalex.org/W3002447856"],"abstract_inverted_index":{"MOTIVATION:":[0],"Single-cell":[1],"RNA-sequencing":[2],"(scRNA-seq)":[3],"has":[4,105],"become":[5],"an":[6],"important":[7],"tool":[8],"to":[9,28,41,91,135],"unravel":[10],"cellular":[11],"heterogeneity,":[12],"discover":[13],"new":[14],"cell":[15,19,138],"(sub)types,":[16],"and":[17,120,141],"understand":[18],"development":[20],"at":[21,155,163],"single-cell":[22,60],"resolution.":[23],"However,":[24],"one":[25],"major":[26],"challenge":[27],"scRNA-seq":[29,101,122,146],"research":[30],"is":[31,39,82,98,153],"the":[32,47,73,83,112,129],"presence":[33],"of":[34,50,114],"'drop-out'":[35],"events,":[36],"which":[37,97],"usually":[38],"due":[40],"extremely":[42],"low":[43],"mRNA":[44],"input":[45],"or":[46],"stochastic":[48],"nature":[49],"gene":[51,75],"expression.":[52],"In":[53],"this":[54],"article,":[55],"we":[56],"present":[57],"a":[58],"novel":[59],"RNA-seq":[61],"drop-out":[62,67,89,102],"correction":[63],"(scDoc)":[64],"method,":[65],"imputing":[66],"events":[68],"by":[69],"borrowing":[70],"information":[71,90],"for":[72,93],"same":[74],"from":[76],"highly":[77],"similar":[78],"cells.":[79],"RESULTS:":[80],"scDoc":[81,115,127],"first":[84],"method":[85],"that":[86,126],"directly":[87],"involves":[88],"accounting":[92],"cell-to-cell":[94],"similarity":[95],"estimation,":[96],"crucial":[99],"in":[100,133,145],"imputation":[103,131],"but":[104],"not":[106],"been":[107],"appropriately":[108],"examined.":[109],"We":[110],"evaluated":[111],"performance":[113],"using":[116],"both":[117],"simulated":[118],"data":[119,136,160],"real":[121],"studies.":[123],"Results":[124],"show":[125],"outperforms":[128],"existing":[130],"methods":[132],"reference":[134],"visualization,":[137],"subpopulation":[139],"identification":[140],"differential":[142],"expression":[143],"detection":[144],"data.":[147],"AVAILABILITY":[148],"AND":[149],"IMPLEMENTATION:":[150],"R":[151],"code":[152],"available":[154,162],"https://github.com/anlingUA/scDoc.":[156],"SUPPLEMENTARY":[157],"INFORMATION:":[158],"Supplementary":[159],"are":[161],"Bioinformatics":[164],"online.":[165]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2025,"cited_by_count":6},{"year":2024,"cited_by_count":4},{"year":2023,"cited_by_count":4},{"year":2022,"cited_by_count":8},{"year":2021,"cited_by_count":2},{"year":2020,"cited_by_count":1}],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-10-10T00:00:00"}
