{"id":"https://openalex.org/W3123418868","doi":"https://doi.org/10.1371/journal.pcbi.1008625","title":"mbkmeans: Fast clustering for single cell data using mini-batch k-means","display_name":"mbkmeans: Fast clustering for single cell data using mini-batch k-means","publication_year":2021,"publication_date":"2021-01-26","ids":{"openalex":"https://openalex.org/W3123418868","doi":"https://doi.org/10.1371/journal.pcbi.1008625","mag":"3123418868","pmid":"https://pubmed.ncbi.nlm.nih.gov/33497379"},"language":"en","primary_location":{"id":"doi:10.1371/journal.pcbi.1008625","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1008625","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1008625&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1008625&type=printable","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5028505800","display_name":"Stephanie C. Hicks","orcid":"https://orcid.org/0000-0002-7858-0231"},"institutions":[{"id":"https://openalex.org/I145311948","display_name":"Johns Hopkins University","ror":"https://ror.org/00za53h95","country_code":"US","type":"education","lineage":["https://openalex.org/I145311948"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Stephanie C. Hicks","raw_affiliation_strings":["Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA"],"affiliations":[{"raw_affiliation_string":"Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA","institution_ids":["https://openalex.org/I145311948"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101570871","display_name":"Ruoxi Liu","orcid":"https://orcid.org/0000-0003-1488-5789"},"institutions":[{"id":"https://openalex.org/I145311948","display_name":"Johns Hopkins University","ror":"https://ror.org/00za53h95","country_code":"US","type":"education","lineage":["https://openalex.org/I145311948"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Ruoxi Liu","raw_affiliation_strings":["Department of Applied Mathematics and Statistics, Johns Hopkins University, Baltimore, Maryland, USA"],"affiliations":[{"raw_affiliation_string":"Department of Applied Mathematics and Statistics, Johns Hopkins University, Baltimore, Maryland, USA","institution_ids":["https://openalex.org/I145311948"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5031101083","display_name":"Yuwei Ni","orcid":"https://orcid.org/0000-0003-3038-3682"},"institutions":[{"id":"https://openalex.org/I205783295","display_name":"Cornell University","ror":"https://ror.org/05bnh6r87","country_code":"US","type":"education","lineage":["https://openalex.org/I205783295"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Yuwei Ni","raw_affiliation_strings":["Department of Healthcare Policy and Research, Weill Cornell Medical College, New York, New York, USA"],"affiliations":[{"raw_affiliation_string":"Department of Healthcare Policy and Research, Weill Cornell Medical College, New York, New York, USA","institution_ids":["https://openalex.org/I205783295"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5044209711","display_name":"Elizabeth Purdom","orcid":"https://orcid.org/0000-0001-9455-7990"},"institutions":[{"id":"https://openalex.org/I95457486","display_name":"University of California, Berkeley","ror":"https://ror.org/01an7q238","country_code":"US","type":"education","lineage":["https://openalex.org/I95457486"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Elizabeth Purdom","raw_affiliation_strings":["Department of Statistics, University of California, Berkeley, Berkeley, California, USA"],"affiliations":[{"raw_affiliation_string":"Department of Statistics, University of California, Berkeley, Berkeley, California, USA","institution_ids":["https://openalex.org/I95457486"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5088632823","display_name":"Davide Risso","orcid":"https://orcid.org/0000-0001-8508-5012"},"institutions":[{"id":"https://openalex.org/I138689650","display_name":"University of Padua","ror":"https://ror.org/00240q980","country_code":"IT","type":"education","lineage":["https://openalex.org/I138689650"]}],"countries":["IT"],"is_corresponding":true,"raw_author_name":"Davide Risso","raw_affiliation_strings":["Department of Statistical Sciences, University of Padova, Padova, Italy"],"affiliations":[{"raw_affiliation_string":"Department of Statistical Sciences, University of Padova, Padova, Italy","institution_ids":["https://openalex.org/I138689650"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5088632823"],"corresponding_institution_ids":["https://openalex.org/I138689650"],"apc_list":{"value":2655,"currency":"USD","value_usd":2655},"apc_paid":{"value":2655,"currency":"USD","value_usd":2655},"fwci":4.6351,"has_fulltext":true,"cited_by_count":65,"citation_normalized_percentile":{"value":0.96154119,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":98,"max":100},"biblio":{"volume":"17","issue":"1","first_page":"e1008625","last_page":"e1008625"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11289","display_name":"Single-cell and spatial transcriptomics","score":1.0,"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":1.0,"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":0.9693999886512756,"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":0.9207000136375427,"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/bioconductor","display_name":"Bioconductor","score":0.9881911277770996},{"id":"https://openalex.org/keywords/cluster-analysis","display_name":"Cluster analysis","score":0.7696731090545654},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7684671878814697},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.6065508127212524},{"id":"https://openalex.org/keywords/r-package","display_name":"R package","score":0.591475784778595},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.5609564781188965},{"id":"https://openalex.org/keywords/software-package","display_name":"Software package","score":0.4246608018875122},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.1520756483078003},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.14789965748786926},{"id":"https://openalex.org/keywords/computational-science","display_name":"Computational science","score":0.11329910159111023},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.0862160325050354}],"concepts":[{"id":"https://openalex.org/C2779694297","wikidata":"https://www.wikidata.org/wiki/Q2888953","display_name":"Bioconductor","level":3,"score":0.9881911277770996},{"id":"https://openalex.org/C73555534","wikidata":"https://www.wikidata.org/wiki/Q622825","display_name":"Cluster analysis","level":2,"score":0.7696731090545654},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7684671878814697},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.6065508127212524},{"id":"https://openalex.org/C2984074130","wikidata":"https://www.wikidata.org/wiki/Q73539779","display_name":"R package","level":2,"score":0.591475784778595},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.5609564781188965},{"id":"https://openalex.org/C3020440742","wikidata":"https://www.wikidata.org/wiki/Q1176855","display_name":"Software package","level":3,"score":0.4246608018875122},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.1520756483078003},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.14789965748786926},{"id":"https://openalex.org/C459310","wikidata":"https://www.wikidata.org/wiki/Q117801","display_name":"Computational science","level":1,"score":0.11329910159111023},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.0862160325050354},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000069558","descriptor_name":"Unsupervised Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000069558","descriptor_name":"Unsupervised Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000069558","descriptor_name":"Unsupervised Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000069558","descriptor_name":"Unsupervised Machine Learning","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":"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":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001921","descriptor_name":"Brain","qualifier_ui":"Q000166","qualifier_name":"cytology","is_major_topic":false},{"descriptor_ui":"D001921","descriptor_name":"Brain","qualifier_ui":"Q000166","qualifier_name":"cytology","is_major_topic":false},{"descriptor_ui":"D001921","descriptor_name":"Brain","qualifier_ui":"Q000166","qualifier_name":"cytology","is_major_topic":false},{"descriptor_ui":"D001921","descriptor_name":"Brain","qualifier_ui":"Q000166","qualifier_name":"cytology","is_major_topic":false},{"descriptor_ui":"D001921","descriptor_name":"Brain","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D001921","descriptor_name":"Brain","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D001921","descriptor_name":"Brain","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D001921","descriptor_name":"Brain","qualifier_ui":"Q000378","qualifier_name":"metabolism","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":"D012984","descriptor_name":"Software","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":"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":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051379","descriptor_name":"Mice","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},{"descriptor_ui":"D059010","descriptor_name":"Single-Cell Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":6,"locations":[{"id":"doi:10.1371/journal.pcbi.1008625","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1008625","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1008625&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},{"id":"pmid:33497379","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/33497379","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":"PLoS computational biology","raw_type":null},{"id":"pmh:oai:RePEc:plo:pcbi00:1008625","is_oa":false,"landing_page_url":"https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1008625","pdf_url":null,"source":{"id":"https://openalex.org/S4306401271","display_name":"RePEc: Research Papers in Economics","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I77793887","host_organization_name":"Federal Reserve Bank of St. Louis","host_organization_lineage":["https://openalex.org/I77793887"],"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":"article"},{"id":"pmh:oai:doaj.org/article:3a3b17b7493c49b9b0d3f1a9a8775f88","is_oa":true,"landing_page_url":"https://doaj.org/article/3a3b17b7493c49b9b0d3f1a9a8775f88","pdf_url":null,"source":{"id":"https://openalex.org/S112646816","display_name":"SHILAP Revista de lepidopterolog\u00eda","issn_l":"0300-5267","issn":["0300-5267","2340-4078"],"is_oa":true,"is_in_doaj":true,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PLoS Computational Biology, Vol 17, Iss 1, p e1008625 (2021)","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:7864438","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/7864438","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PLoS Comput Biol","raw_type":"Text"},{"id":"pmh:oai:www.research.unipd.it:11577/3371062","is_oa":true,"landing_page_url":"https://hdl.handle.net/11577/3371062","pdf_url":null,"source":{"id":"https://openalex.org/S4306402547","display_name":"Padua Research Archive (University of Padova)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I138689650","host_organization_name":"University of Padua","host_organization_lineage":["https://openalex.org/I138689650"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"info:eu-repo/semantics/article"}],"best_oa_location":{"id":"doi:10.1371/journal.pcbi.1008625","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1008625","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1008625&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1901265509","display_name":null,"funder_award_id":"2019-002443","funder_id":"https://openalex.org/F4320315474","funder_display_name":"Chan Zuckerberg Initiative"},{"id":"https://openalex.org/G2195708039","display_name":null,"funder_award_id":"Programma per Giovani Ricercatori Rita Levi Montalcini","funder_id":"https://openalex.org/F4320321873","funder_display_name":"Ministero dell\u2019Istruzione, dell\u2019Universit\u00e0 e della Ricerca"},{"id":"https://openalex.org/G2490195592","display_name":null,"funder_award_id":"2018-183201","funder_id":"https://openalex.org/F4320306192","funder_display_name":"Silicon Valley Community Foundation"},{"id":"https://openalex.org/G3342043461","display_name":null,"funder_award_id":"R00HG009007","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G4251197725","display_name":null,"funder_award_id":"CZF2019-002443","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G4554797933","display_name":null,"funder_award_id":"CZF2019-002443","funder_id":"https://openalex.org/F4320306192","funder_display_name":"Silicon Valley Community Foundation"},{"id":"https://openalex.org/G4667119938","display_name":null,"funder_award_id":"U19MH11483","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G4760074400","display_name":null,"funder_award_id":"U19MH114830","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G5119885683","display_name":null,"funder_award_id":"CZF2019-00244","funder_id":"https://openalex.org/F4320315474","funder_display_name":"Chan Zuckerberg Initiative"},{"id":"https://openalex.org/G6218475188","display_name":null,"funder_award_id":"2019-002443","funder_id":"https://openalex.org/F4320306192","funder_display_name":"Silicon Valley Community Foundation"},{"id":"https://openalex.org/G8165731190","display_name":null,"funder_award_id":"CZF2019-002443","funder_id":"https://openalex.org/F4320315474","funder_display_name":"Chan Zuckerberg Initiative"}],"funders":[{"id":"https://openalex.org/F4320306192","display_name":"Silicon Valley Community Foundation","ror":"https://ror.org/001ader08"},{"id":"https://openalex.org/F4320315474","display_name":"Chan Zuckerberg Initiative","ror":"https://ror.org/02qenvm24"},{"id":"https://openalex.org/F4320321873","display_name":"Ministero dell\u2019Istruzione, dell\u2019Universit\u00e0 e della Ricerca","ror":"https://ror.org/0166hxq48"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W3123418868.pdf","grobid_xml":"https://content.openalex.org/works/W3123418868.grobid-xml"},"referenced_works_count":64,"referenced_works":["https://openalex.org/W223097185","https://openalex.org/W1907099735","https://openalex.org/W1973094248","https://openalex.org/W1977361006","https://openalex.org/W1977556410","https://openalex.org/W1979283544","https://openalex.org/W2046489888","https://openalex.org/W2073459066","https://openalex.org/W2101234009","https://openalex.org/W2116762767","https://openalex.org/W2127218421","https://openalex.org/W2131681506","https://openalex.org/W2142838865","https://openalex.org/W2150593711","https://openalex.org/W2159325249","https://openalex.org/W2173213060","https://openalex.org/W2272004637","https://openalex.org/W2343956310","https://openalex.org/W2507157276","https://openalex.org/W2553595002","https://openalex.org/W2559479590","https://openalex.org/W2588978745","https://openalex.org/W2598326928","https://openalex.org/W2739329039","https://openalex.org/W2781205255","https://openalex.org/W2794083495","https://openalex.org/W2800147381","https://openalex.org/W2800392236","https://openalex.org/W2802823096","https://openalex.org/W2884197618","https://openalex.org/W2885927965","https://openalex.org/W2896353945","https://openalex.org/W2897249806","https://openalex.org/W2899224111","https://openalex.org/W2907783748","https://openalex.org/W2908670724","https://openalex.org/W2915848182","https://openalex.org/W2916020270","https://openalex.org/W2923101443","https://openalex.org/W2948513373","https://openalex.org/W2950976066","https://openalex.org/W2951158909","https://openalex.org/W2951337536","https://openalex.org/W2951506174","https://openalex.org/W2963174546","https://openalex.org/W2963314742","https://openalex.org/W2967177832","https://openalex.org/W2972983657","https://openalex.org/W2989807288","https://openalex.org/W2993207812","https://openalex.org/W3032550492","https://openalex.org/W3089158795","https://openalex.org/W3090056044","https://openalex.org/W3099438925","https://openalex.org/W3099768174","https://openalex.org/W3106188259","https://openalex.org/W3123418868","https://openalex.org/W4233637541","https://openalex.org/W4289038146","https://openalex.org/W6600704223","https://openalex.org/W6644682428","https://openalex.org/W6675354045","https://openalex.org/W6943948790","https://openalex.org/W6963023718"],"related_works":["https://openalex.org/W2982252354","https://openalex.org/W2728564446","https://openalex.org/W3045904767","https://openalex.org/W2161868542","https://openalex.org/W3156537409","https://openalex.org/W2140163842","https://openalex.org/W2747931568","https://openalex.org/W2921090651","https://openalex.org/W2792883187","https://openalex.org/W2098339479"],"abstract_inverted_index":{"Single-cell":[0],"RNA-Sequencing":[1],"(scRNA-seq)":[2],"is":[3,179],"the":[4,16,21,34,65,91,99,112,127,139,142,159,165],"most":[5,22],"widely":[6,117],"used":[7,118],"high-throughput":[8],"technology":[9],"to":[10,53,67,80,129],"measure":[11],"genome-wide":[12],"gene":[13],"expression":[14],"at":[15,134,183],"single-cell":[17,120,173],"level.":[18],"One":[19],"of":[20,25,31,36,55,98,141,162,168],"common":[23,113],"analyses":[24],"scRNA-seq":[26,44],"data":[27,66,108,128],"detects":[28],"distinct":[29],"subpopulations":[30],"cells":[32],"through":[33],"use":[35],"unsupervised":[37],"clustering":[38,58,174],"algorithms.":[39],"However,":[40],"recent":[41],"advances":[42],"in":[43,47,181],"technologies":[45],"result":[46],"current":[48],"datasets":[49],"ranging":[50],"from":[51],"thousands":[52],"millions":[54],"cells.":[56,153],"Popular":[57],"algorithms,":[59],"such":[60,110],"as":[61,111],"k-means,":[62],"typically":[63],"require":[64,125],"be":[68,76,130],"loaded":[69,131],"entirely":[70],"into":[71,132],"memory":[72,133],"and":[73,157,170],"therefore":[74],"can":[75],"slow":[77],"or":[78],"impossible":[79],"run":[81],"with":[82,150],"large":[83,146],"datasets.":[84],"To":[85],"address":[86],"this":[87],"problem,":[88],"we":[89],"developed":[90],"mbkmeans":[92,143,163],"R/Bioconductor":[93],"package,":[94],"an":[95],"open-source":[96],"implementation":[97,167],"mini-batch":[100],"k-means":[101,169],"algorithm.":[102],"Our":[103,176],"package":[104,144,178],"allows":[105],"for":[106,119],"on-disk":[107],"representations,":[109],"HDF5":[114],"file":[115],"format":[116],"data,":[121],"that":[122],"do":[123],"not":[124],"all":[126],"one":[135,149],"time.":[136],"We":[137,154],"demonstrate":[138],"performance":[140,161],"using":[145],"datasets,":[147],"including":[148],"1.3":[151],"million":[152],"also":[155],"highlight":[156],"compare":[158],"computing":[160],"against":[164],"standard":[166],"other":[171],"popular":[172],"methods.":[175],"software":[177],"available":[180],"Bioconductor":[182],"https://bioconductor.org/packages/mbkmeans.":[184]},"counts_by_year":[{"year":2025,"cited_by_count":10},{"year":2024,"cited_by_count":19},{"year":2023,"cited_by_count":14},{"year":2022,"cited_by_count":14},{"year":2021,"cited_by_count":8}],"updated_date":"2026-04-10T15:06:20.359241","created_date":"2025-10-10T00:00:00"}