{"id":"https://openalex.org/W4415011403","doi":"https://doi.org/10.1177/15578666251383561","title":"<tt>mcRigor</tt> : A Statistical Software Package for Evaluating and Optimizing Metacell Partitioning in Single-Cell Data Analysis","display_name":"<tt>mcRigor</tt> : A Statistical Software Package for Evaluating and Optimizing Metacell Partitioning in Single-Cell Data Analysis","publication_year":2025,"publication_date":"2025-10-09","ids":{"openalex":"https://openalex.org/W4415011403","doi":"https://doi.org/10.1177/15578666251383561","pmid":"https://pubmed.ncbi.nlm.nih.gov/41066085"},"language":"en","primary_location":{"id":"doi:10.1177/15578666251383561","is_oa":false,"landing_page_url":"https://doi.org/10.1177/15578666251383561","pdf_url":null,"source":{"id":"https://openalex.org/S78571599","display_name":"Journal of Computational Biology","issn_l":"1066-5277","issn":["1066-5277","1557-8666"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320443","host_organization_name":"Mary Ann Liebert, Inc.","host_organization_lineage":["https://openalex.org/P4310320443"],"host_organization_lineage_names":["Mary Ann Liebert, Inc."],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Computational Biology","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC12872216/","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5100617211","display_name":"Pan Liu","orcid":"https://orcid.org/0009-0002-8459-2922"},"institutions":[{"id":"https://openalex.org/I161318765","display_name":"University of California, Los Angeles","ror":"https://ror.org/046rm7j60","country_code":"US","type":"education","lineage":["https://openalex.org/I161318765"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Pan Liu","raw_affiliation_strings":["Department of Statistics and Data Science, University of California, Los Angeles, California, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Statistics and Data Science, University of California, Los Angeles, California, USA","institution_ids":["https://openalex.org/I161318765"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5045434495","display_name":"Jingyi Jessica Li","orcid":"https://orcid.org/0000-0002-9288-5648"},"institutions":[{"id":"https://openalex.org/I161318765","display_name":"University of California, Los Angeles","ror":"https://ror.org/046rm7j60","country_code":"US","type":"education","lineage":["https://openalex.org/I161318765"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Jingyi Jessica Li","raw_affiliation_strings":["Department of Statistics and Data Science, University of California, Los Angeles, California, USA"],"raw_orcid":"https://orcid.org/0000-0002-9288-5648","affiliations":[{"raw_affiliation_string":"Department of Statistics and Data Science, University of California, Los Angeles, California, USA","institution_ids":["https://openalex.org/I161318765"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5045434495"],"corresponding_institution_ids":["https://openalex.org/I161318765"],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.2106981,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"33","issue":"1","first_page":"43","last_page":"47"},"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/T12859","display_name":"Cell Image Analysis Techniques","score":0.98089998960495,"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/T10621","display_name":"Gene Regulatory Network Analysis","score":0.9747999906539917,"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/preprocessor","display_name":"Preprocessor","score":0.6766999959945679},{"id":"https://openalex.org/keywords/r-package","display_name":"R package","score":0.6348999738693237},{"id":"https://openalex.org/keywords/hyperparameter","display_name":"Hyperparameter","score":0.600600004196167},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.5634999871253967},{"id":"https://openalex.org/keywords/software-package","display_name":"Software package","score":0.4440000057220459},{"id":"https://openalex.org/keywords/statistical-analysis","display_name":"Statistical analysis","score":0.4032999873161316},{"id":"https://openalex.org/keywords/installation","display_name":"Installation","score":0.3935000002384186},{"id":"https://openalex.org/keywords/data-pre-processing","display_name":"Data pre-processing","score":0.37380000948905945}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7935000061988831},{"id":"https://openalex.org/C34736171","wikidata":"https://www.wikidata.org/wiki/Q918333","display_name":"Preprocessor","level":2,"score":0.6766999959945679},{"id":"https://openalex.org/C2984074130","wikidata":"https://www.wikidata.org/wiki/Q73539779","display_name":"R package","level":2,"score":0.6348999738693237},{"id":"https://openalex.org/C8642999","wikidata":"https://www.wikidata.org/wiki/Q4171168","display_name":"Hyperparameter","level":2,"score":0.600600004196167},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.5666000247001648},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.5634999871253967},{"id":"https://openalex.org/C3020440742","wikidata":"https://www.wikidata.org/wiki/Q1176855","display_name":"Software package","level":3,"score":0.4440000057220459},{"id":"https://openalex.org/C2986587452","wikidata":"https://www.wikidata.org/wiki/Q938438","display_name":"Statistical analysis","level":2,"score":0.4032999873161316},{"id":"https://openalex.org/C146778888","wikidata":"https://www.wikidata.org/wiki/Q836862","display_name":"Installation","level":2,"score":0.3935000002384186},{"id":"https://openalex.org/C10551718","wikidata":"https://www.wikidata.org/wiki/Q5227332","display_name":"Data pre-processing","level":2,"score":0.37380000948905945},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.3158999979496002},{"id":"https://openalex.org/C2987757206","wikidata":"https://www.wikidata.org/wiki/Q494735","display_name":"Statistical software","level":2,"score":0.31209999322891235},{"id":"https://openalex.org/C134261354","wikidata":"https://www.wikidata.org/wiki/Q938438","display_name":"Statistical inference","level":2,"score":0.3111000061035156},{"id":"https://openalex.org/C137345334","wikidata":"https://www.wikidata.org/wiki/Q7303350","display_name":"Recursive partitioning","level":2,"score":0.29010000824928284},{"id":"https://openalex.org/C114289077","wikidata":"https://www.wikidata.org/wiki/Q3284399","display_name":"Statistical model","level":2,"score":0.288100004196167},{"id":"https://openalex.org/C107673813","wikidata":"https://www.wikidata.org/wiki/Q812534","display_name":"Bayesian probability","level":2,"score":0.2761000096797943},{"id":"https://openalex.org/C87007009","wikidata":"https://www.wikidata.org/wiki/Q210832","display_name":"Statistical hypothesis testing","level":2,"score":0.2671000063419342},{"id":"https://openalex.org/C189950617","wikidata":"https://www.wikidata.org/wiki/Q937228","display_name":"Property (philosophy)","level":2,"score":0.25529998540878296},{"id":"https://openalex.org/C1009929","wikidata":"https://www.wikidata.org/wiki/Q179550","display_name":"Software bug","level":3,"score":0.25119999051094055}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","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":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":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D059010","descriptor_name":"Single-Cell Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D059010","descriptor_name":"Single-Cell Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D059010","descriptor_name":"Single-Cell Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D059010","descriptor_name":"Single-Cell Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true}],"locations_count":4,"locations":[{"id":"doi:10.1177/15578666251383561","is_oa":false,"landing_page_url":"https://doi.org/10.1177/15578666251383561","pdf_url":null,"source":{"id":"https://openalex.org/S78571599","display_name":"Journal of Computational Biology","issn_l":"1066-5277","issn":["1066-5277","1557-8666"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320443","host_organization_name":"Mary Ann Liebert, Inc.","host_organization_lineage":["https://openalex.org/P4310320443"],"host_organization_lineage_names":["Mary Ann Liebert, Inc."],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Computational Biology","raw_type":"journal-article"},{"id":"pmid:41066085","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/41066085","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":"Journal of computational biology : a journal of computational molecular cell biology","raw_type":null},{"id":"pmh:oai:europepmc.org:11679776","is_oa":false,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/12872216","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"},{"id":"pmh:oai:pubmedcentral.nih.gov:12872216","is_oa":true,"landing_page_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC12872216/","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"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":"J Comput Biol","raw_type":"Text"}],"best_oa_location":{"id":"pmh:oai:pubmedcentral.nih.gov:12872216","is_oa":true,"landing_page_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC12872216/","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"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":"J Comput Biol","raw_type":"Text"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G2108729386","display_name":null,"funder_award_id":"R35GM140888","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":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":6,"referenced_works":["https://openalex.org/W2979981308","https://openalex.org/W4224290465","https://openalex.org/W4291201938","https://openalex.org/W4360999291","https://openalex.org/W4399128391","https://openalex.org/W4409739115"],"related_works":[],"abstract_inverted_index":{"Metacell":[0],"partitioning":[1,22,65],"is":[2],"a":[3,57],"common":[4],"preprocessing":[5],"step":[6],"in":[7,66],"single-cell":[8,67],"data":[9,68],"analysis,":[10],"used":[11],"to":[12,50,79],"reduce":[13],"sparsity":[14],"by":[15],"aggregating":[16],"similar":[17],"cells.":[18],"However,":[19],"existing":[20],"metacell":[21,35,64],"algorithms":[23],"may":[24],"inadvertently":[25],"group":[26],"heterogeneous":[27],"cells,":[28],"potentially":[29],"biasing":[30],"downstream":[31],"analyses.":[32],"The":[33,52],"resulting":[34],"partitions":[36],"can":[37],"vary":[38],"substantially":[39],"with":[40],"different":[41],"hyperparameter":[42],"settings,":[43],"leaving":[44],"users":[45],"uncertain":[46],"about":[47],"which":[48],"result":[49],"trust.":[51],"mcRigor":[53,78],"R":[54],"package":[55],"offers":[56],"statistical":[58],"method":[59],"for":[60,74],"evaluating":[61],"and":[62,76,83],"optimizing":[63],"analysis.":[69],"This":[70],"article":[71],"provides":[72],"instructions":[73],"installing":[75],"using":[77],"support":[80],"more":[81],"rigorous":[82],"interpretable":[84],"metacell-based":[85],"workflows.":[86]},"counts_by_year":[],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-10-10T00:00:00"}
