{"id":"https://openalex.org/W3169525669","doi":"https://doi.org/10.1093/bib/bbab204","title":"REBET: a method to determine the number of cell clusters based on batch effect removal","display_name":"REBET: a method to determine the number of cell clusters based on batch effect removal","publication_year":2021,"publication_date":"2021-05-10","ids":{"openalex":"https://openalex.org/W3169525669","doi":"https://doi.org/10.1093/bib/bbab204","mag":"3169525669","pmid":"https://pubmed.ncbi.nlm.nih.gov/34131702"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbab204","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bib/bbab204","pdf_url":null,"source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"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":"Briefings in 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/A5009458572","display_name":"Zhaoyu Fang","orcid":null},"institutions":[{"id":"https://openalex.org/I139660479","display_name":"Central South University","ror":"https://ror.org/00f1zfq44","country_code":"CN","type":"education","lineage":["https://openalex.org/I139660479"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Zhao-Yu Fang","raw_affiliation_strings":["School of Mathematics and Statistics, Central South University, Changsha, Hunan 410083, P.R. China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Mathematics and Statistics, Central South University, Changsha, Hunan 410083, P.R. China","institution_ids":["https://openalex.org/I139660479"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5054012280","display_name":"Cuixiang Lin","orcid":null},"institutions":[{"id":"https://openalex.org/I139660479","display_name":"Central South University","ror":"https://ror.org/00f1zfq44","country_code":"CN","type":"education","lineage":["https://openalex.org/I139660479"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Cui-Xiang Lin","raw_affiliation_strings":["Hunan Provincial Key Lab on Bioinformatics, Central South University, Changsha, Hunan 410083, P.R. China","School of Computer Science and Engineering, Central South University, Changsha, Hunan 410083, P.R. China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Hunan Provincial Key Lab on Bioinformatics, Central South University, Changsha, Hunan 410083, P.R. China","institution_ids":["https://openalex.org/I139660479"]},{"raw_affiliation_string":"School of Computer Science and Engineering, Central South University, Changsha, Hunan 410083, P.R. China","institution_ids":["https://openalex.org/I139660479"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5038763794","display_name":"Yunpei Xu","orcid":null},"institutions":[{"id":"https://openalex.org/I139660479","display_name":"Central South University","ror":"https://ror.org/00f1zfq44","country_code":"CN","type":"education","lineage":["https://openalex.org/I139660479"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yun-Pei Xu","raw_affiliation_strings":["Hunan Provincial Key Lab on Bioinformatics, Central South University, Changsha, Hunan 410083, P.R. China","School of Computer Science and Engineering, Central South University, Changsha, Hunan 410083, P.R. China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Hunan Provincial Key Lab on Bioinformatics, Central South University, Changsha, Hunan 410083, P.R. China","institution_ids":["https://openalex.org/I139660479"]},{"raw_affiliation_string":"School of Computer Science and Engineering, Central South University, Changsha, Hunan 410083, P.R. China","institution_ids":["https://openalex.org/I139660479"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101819060","display_name":"Hong\u2010Dong Li","orcid":null},"institutions":[{"id":"https://openalex.org/I139660479","display_name":"Central South University","ror":"https://ror.org/00f1zfq44","country_code":"CN","type":"education","lineage":["https://openalex.org/I139660479"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Hong-Dong Li","raw_affiliation_strings":["Hunan Provincial Key Lab on Bioinformatics, Central South University, Changsha, Hunan 410083, P.R. China","School of Computer Science and Engineering, Central South University, Changsha, Hunan 410083, P.R. China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Hunan Provincial Key Lab on Bioinformatics, Central South University, Changsha, Hunan 410083, P.R. China","institution_ids":["https://openalex.org/I139660479"]},{"raw_affiliation_string":"School of Computer Science and Engineering, Central South University, Changsha, Hunan 410083, P.R. China","institution_ids":["https://openalex.org/I139660479"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5100763748","display_name":"Qingsong Xu","orcid":"https://orcid.org/0000-0001-9100-0425"},"institutions":[{"id":"https://openalex.org/I139660479","display_name":"Central South University","ror":"https://ror.org/00f1zfq44","country_code":"CN","type":"education","lineage":["https://openalex.org/I139660479"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Qing-Song Xu","raw_affiliation_strings":["School of Mathematics and Statistics, Central South University, Changsha, Hunan 410083, P.R. China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Mathematics and Statistics, Central South University, Changsha, Hunan 410083, P.R. China","institution_ids":["https://openalex.org/I139660479"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5100763748","https://openalex.org/A5101819060"],"corresponding_institution_ids":["https://openalex.org/I139660479"],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":null,"fwci":0.2379,"has_fulltext":false,"cited_by_count":3,"citation_normalized_percentile":{"value":0.51242048,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":94},"biblio":{"volume":"22","issue":"6","first_page":null,"last_page":null},"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/T10621","display_name":"Gene Regulatory Network Analysis","score":0.9771000146865845,"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":0.9593999981880188,"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/range","display_name":"Range (aeronautics)","score":0.5930424928665161},{"id":"https://openalex.org/keywords/cluster","display_name":"Cluster (spacecraft)","score":0.4766983687877655},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.4739297032356262},{"id":"https://openalex.org/keywords/biological-system","display_name":"Biological system","score":0.4543641209602356},{"id":"https://openalex.org/keywords/batch-processing","display_name":"Batch processing","score":0.4449580907821655},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.4200800359249115},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.1458013653755188},{"id":"https://openalex.org/keywords/materials-science","display_name":"Materials science","score":0.11613881587982178}],"concepts":[{"id":"https://openalex.org/C204323151","wikidata":"https://www.wikidata.org/wiki/Q905424","display_name":"Range (aeronautics)","level":2,"score":0.5930424928665161},{"id":"https://openalex.org/C164866538","wikidata":"https://www.wikidata.org/wiki/Q367351","display_name":"Cluster (spacecraft)","level":2,"score":0.4766983687877655},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4739297032356262},{"id":"https://openalex.org/C186060115","wikidata":"https://www.wikidata.org/wiki/Q30336093","display_name":"Biological system","level":1,"score":0.4543641209602356},{"id":"https://openalex.org/C172658912","wikidata":"https://www.wikidata.org/wiki/Q661613","display_name":"Batch processing","level":2,"score":0.4449580907821655},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.4200800359249115},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.1458013653755188},{"id":"https://openalex.org/C192562407","wikidata":"https://www.wikidata.org/wiki/Q228736","display_name":"Materials science","level":0,"score":0.11613881587982178},{"id":"https://openalex.org/C159985019","wikidata":"https://www.wikidata.org/wiki/Q181790","display_name":"Composite material","level":1,"score":0.0},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000081246","descriptor_name":"RNA-Seq","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D000081246","descriptor_name":"RNA-Seq","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D000081246","descriptor_name":"RNA-Seq","qualifier_ui":"Q000379","qualifier_name":"methods","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":"D000465","descriptor_name":"Algorithms","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":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016000","descriptor_name":"Cluster Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016000","descriptor_name":"Cluster Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016000","descriptor_name":"Cluster Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059010","descriptor_name":"Single-Cell Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D059010","descriptor_name":"Single-Cell Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D059010","descriptor_name":"Single-Cell Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1093/bib/bbab204","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bib/bbab204","pdf_url":null,"source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"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":"Briefings in Bioinformatics","raw_type":"journal-article"},{"id":"pmid:34131702","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/34131702","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":"Briefings in bioinformatics","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G2601088333","display_name":"\u57fa\u4e8e\u5f02\u8d28\u5c5e\u6027\u7f51\u7edc\u8868\u5f81\u5b66\u4e60\u7684\u8bc6\u522b\u764c\u75c7\u9a71\u52a8\u57fa\u56e0\u7b97\u6cd5\u7814\u7a76","funder_award_id":"61972185","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G4066238608","display_name":null,"funder_award_id":"B18059","funder_id":"https://openalex.org/F4320327912","funder_display_name":"Higher Education Discipline Innovation Project"},{"id":"https://openalex.org/G8196091623","display_name":null,"funder_award_id":"U1909208","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"}],"funders":[{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"},{"id":"https://openalex.org/F4320327912","display_name":"Higher Education Discipline Innovation Project","ror":null}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":59,"referenced_works":["https://openalex.org/W1548779692","https://openalex.org/W1552434751","https://openalex.org/W1673310716","https://openalex.org/W1754857113","https://openalex.org/W1886306325","https://openalex.org/W1967489571","https://openalex.org/W1984689597","https://openalex.org/W1987219048","https://openalex.org/W1990517717","https://openalex.org/W2007439698","https://openalex.org/W2013444425","https://openalex.org/W2023461603","https://openalex.org/W2023887100","https://openalex.org/W2030017878","https://openalex.org/W2033072655","https://openalex.org/W2068881679","https://openalex.org/W2071949631","https://openalex.org/W2082774227","https://openalex.org/W2094247852","https://openalex.org/W2107665951","https://openalex.org/W2109890799","https://openalex.org/W2115462905","https://openalex.org/W2120205807","https://openalex.org/W2121690903","https://openalex.org/W2132914434","https://openalex.org/W2137499573","https://openalex.org/W2146512944","https://openalex.org/W2169353806","https://openalex.org/W2307567449","https://openalex.org/W2308998873","https://openalex.org/W2335920499","https://openalex.org/W2337733832","https://openalex.org/W2396681433","https://openalex.org/W2592285292","https://openalex.org/W2598326928","https://openalex.org/W2610509384","https://openalex.org/W2733002388","https://openalex.org/W2765654979","https://openalex.org/W2790370540","https://openalex.org/W2791624046","https://openalex.org/W2794480084","https://openalex.org/W2889213939","https://openalex.org/W2907783748","https://openalex.org/W2912149112","https://openalex.org/W2937917790","https://openalex.org/W2942256847","https://openalex.org/W2949067670","https://openalex.org/W2949177718","https://openalex.org/W2949329924","https://openalex.org/W2952303649","https://openalex.org/W2953251392","https://openalex.org/W2980183989","https://openalex.org/W3002417351","https://openalex.org/W3036429887","https://openalex.org/W3102347392","https://openalex.org/W4235169531","https://openalex.org/W6682541512","https://openalex.org/W6685380521","https://openalex.org/W6768818580"],"related_works":["https://openalex.org/W2107962325","https://openalex.org/W2248928492","https://openalex.org/W2008053682","https://openalex.org/W2949696262","https://openalex.org/W3194172383","https://openalex.org/W2171127997","https://openalex.org/W1964768744","https://openalex.org/W2464204116","https://openalex.org/W2085616392","https://openalex.org/W2375638766"],"abstract_inverted_index":{"In":[0,129],"single-cell":[1],"RNA-seq":[2],"(scRNA-seq)":[3],"data":[4,54,60],"analysis,":[5],"a":[6,111,180],"fundamental":[7],"problem":[8],"is":[9,29,157,194],"to":[10,36,190,196],"determine":[11],"the":[12,19,24,41,50,73,88,100,124,140,151,160,172,185,191,198,228],"number":[13,89,125,200,229],"of":[14,26,75,90,116,126,153,163,182,201,230],"cell":[15,45,81,91,127,231],"clusters":[16,82,92,103,146,232],"based":[17],"on":[18,209],"gene":[20],"expression":[21,42],"profiles.":[22],"However,":[23],"performance":[25],"current":[27],"methods":[28,208],"still":[30],"far":[31],"from":[32,63],"satisfactory,":[33],"presumably":[34],"due":[35],"their":[37],"limitations":[38],"in":[39,56],"capturing":[40],"variability":[43,52],"among":[44,102,143],"clusters.":[46,128,138,202],"Batch":[47],"effects":[48,69,142],"represent":[49],"undesired":[51],"between":[53],"measured":[55],"different":[57,64],"batches.":[58,84],"When":[59],"are":[61,133,147,176],"obtained":[62],"labs":[65],"or":[66,240],"protocols":[67],"batch":[68,76,105,117,141,154],"occur.":[70],"Motivated":[71],"by":[72],"practice":[74],"effect":[77,118,155],"removal,":[78],"we":[79],"considered":[80],"as":[83],"We":[85,109,203],"hypothesized":[86],"that":[87,188,221],"(i.e.":[93,104],"batches)":[94],"could":[95],"be":[96,197],"correctly":[97],"determined":[98,195],"if":[99],"variances":[101],"effects)":[106],"were":[107],"removed.":[108,149],"developed":[110],"new":[112],"method,":[113,131],"namely,":[114],"removal":[115,156],"and":[119,213,225,233],"testing":[120,179],"(REBET),":[121],"for":[122],"determining":[123],"this":[130],"cells":[132,173],"first":[134],"partitioned":[135],"into":[136],"k":[137,145,183,186],"Second,":[139],"these":[144],"then":[148],"Third,":[150],"quality":[152],"evaluated":[158],"with":[159,174,206],"average":[161],"range":[162,181],"normalized":[164],"mutual":[165],"information":[166],"(ARNMI),":[167],"which":[168],"measures":[169],"how":[170],"uniformly":[171],"batch-effects-removal":[175],"mixed.":[177],"By":[178],"values,":[184],"value":[187],"corresponds":[189],"lowest":[192],"ARNMI":[193],"optimal":[199],"compared":[204],"REBET":[205,222],"state-of-the-art":[207],"32":[210],"simulated":[211],"datasets":[212],"14":[214],"published":[215],"scRNA-seq":[216],"datasets.":[217],"The":[218],"results":[219],"show":[220],"can":[223],"accurately":[224],"robustly":[226],"estimate":[227],"outperform":[234],"existing":[235],"methods.":[236],"Contact:":[237],"H.D.L.":[238],"(hongdong@csu.edu.cn)":[239],"Q.S.X.":[241],"(qsxu@csu.edu.cn).":[242]},"counts_by_year":[{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":1}],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-10-10T00:00:00"}
