{"id":"https://openalex.org/W4417221226","doi":"https://doi.org/10.3389/fbinf.2025.1684227","title":"Celline: a flexible tool for one-step retrieval and integrative analysis of public single-cell RNA sequencing data","display_name":"Celline: a flexible tool for one-step retrieval and integrative analysis of public single-cell RNA sequencing data","publication_year":2025,"publication_date":"2025-12-11","ids":{"openalex":"https://openalex.org/W4417221226","doi":"https://doi.org/10.3389/fbinf.2025.1684227","pmid":"https://pubmed.ncbi.nlm.nih.gov/41458999"},"language":"en","primary_location":{"id":"doi:10.3389/fbinf.2025.1684227","is_oa":true,"landing_page_url":"https://doi.org/10.3389/fbinf.2025.1684227","pdf_url":"https://public-pages-files-2025.frontiersin.org/journals/bioinformatics/articles/10.3389/fbinf.2025.1684227/pdf","source":{"id":"https://openalex.org/S4210219554","display_name":"Frontiers in Bioinformatics","issn_l":"2673-7647","issn":["2673-7647"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320527","host_organization_name":"Frontiers Media","host_organization_lineage":["https://openalex.org/P4310320527"],"host_organization_lineage_names":["Frontiers Media"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Frontiers in Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://public-pages-files-2025.frontiersin.org/journals/bioinformatics/articles/10.3389/fbinf.2025.1684227/pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5090597202","display_name":"Yuya Sato","orcid":"https://orcid.org/0000-0003-2959-9603"},"institutions":[{"id":"https://openalex.org/I150744194","display_name":"Waseda University","ror":"https://ror.org/00ntfnx83","country_code":"JP","type":"education","lineage":["https://openalex.org/I150744194"]}],"countries":["JP"],"is_corresponding":true,"raw_author_name":"Yuya Sato","raw_affiliation_strings":["Graduate School of Advanced Science and Engineering, Waseda University, Tokyo, Japan"],"affiliations":[{"raw_affiliation_string":"Graduate School of Advanced Science and Engineering, Waseda University, Tokyo, Japan","institution_ids":["https://openalex.org/I150744194"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5010067834","display_name":"Toru Asahi","orcid":"https://orcid.org/0000-0003-4925-8259"},"institutions":[{"id":"https://openalex.org/I150744194","display_name":"Waseda University","ror":"https://ror.org/00ntfnx83","country_code":"JP","type":"education","lineage":["https://openalex.org/I150744194"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Toru Asahi","raw_affiliation_strings":["Comprehensive Research Organization, Waseda University, Tokyo, Japan","Graduate School of Advanced Science and Engineering, Waseda University, Tokyo, Japan"],"affiliations":[{"raw_affiliation_string":"Comprehensive Research Organization, Waseda University, Tokyo, Japan","institution_ids":["https://openalex.org/I150744194"]},{"raw_affiliation_string":"Graduate School of Advanced Science and Engineering, Waseda University, Tokyo, Japan","institution_ids":["https://openalex.org/I150744194"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5091003598","display_name":"Kosuke Kataoka","orcid":"https://orcid.org/0000-0001-6023-7710"},"institutions":[{"id":"https://openalex.org/I150744194","display_name":"Waseda University","ror":"https://ror.org/00ntfnx83","country_code":"JP","type":"education","lineage":["https://openalex.org/I150744194"]},{"id":"https://openalex.org/I92614990","display_name":"Tokyo University of Agriculture and Technology","ror":"https://ror.org/00qg0kr10","country_code":"JP","type":"education","lineage":["https://openalex.org/I92614990"]}],"countries":["JP"],"is_corresponding":true,"raw_author_name":"Kosuke Kataoka","raw_affiliation_strings":["Comprehensive Research Organization, Waseda University, Tokyo, Japan","Institute of Engineering, Tokyo University of Agriculture and Technology, Tokyo, Japan"],"affiliations":[{"raw_affiliation_string":"Comprehensive Research Organization, Waseda University, Tokyo, Japan","institution_ids":["https://openalex.org/I150744194"]},{"raw_affiliation_string":"Institute of Engineering, Tokyo University of Agriculture and Technology, Tokyo, Japan","institution_ids":["https://openalex.org/I92614990"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5090597202","https://openalex.org/A5091003598"],"corresponding_institution_ids":["https://openalex.org/I150744194","https://openalex.org/I92614990"],"apc_list":{"value":1900,"currency":"USD","value_usd":1900},"apc_paid":{"value":1900,"currency":"USD","value_usd":1900},"fwci":0.0,"has_fulltext":true,"cited_by_count":0,"citation_normalized_percentile":{"value":0.34174292,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"5","issue":null,"first_page":"1684227","last_page":"1684227"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.9988999962806702,"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":0.9988999962806702,"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":0.00039999998989515007,"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/T10505","display_name":"Pluripotent Stem Cells Research","score":9.999999747378752e-05,"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/workflow","display_name":"Workflow","score":0.6955999732017517},{"id":"https://openalex.org/keywords/metadata","display_name":"Metadata","score":0.6177999973297119},{"id":"https://openalex.org/keywords/modular-design","display_name":"Modular design","score":0.6043999791145325},{"id":"https://openalex.org/keywords/python","display_name":"Python (programming language)","score":0.5184999704360962},{"id":"https://openalex.org/keywords/pipeline","display_name":"Pipeline (software)","score":0.5117999911308289},{"id":"https://openalex.org/keywords/data-curation","display_name":"Data curation","score":0.4108999967575073},{"id":"https://openalex.org/keywords/raw-data","display_name":"Raw data","score":0.40700000524520874},{"id":"https://openalex.org/keywords/quality","display_name":"Quality (philosophy)","score":0.34139999747276306}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7540000081062317},{"id":"https://openalex.org/C177212765","wikidata":"https://www.wikidata.org/wiki/Q627335","display_name":"Workflow","level":2,"score":0.6955999732017517},{"id":"https://openalex.org/C93518851","wikidata":"https://www.wikidata.org/wiki/Q180160","display_name":"Metadata","level":2,"score":0.6177999973297119},{"id":"https://openalex.org/C101468663","wikidata":"https://www.wikidata.org/wiki/Q1620158","display_name":"Modular design","level":2,"score":0.6043999791145325},{"id":"https://openalex.org/C519991488","wikidata":"https://www.wikidata.org/wiki/Q28865","display_name":"Python (programming language)","level":2,"score":0.5184999704360962},{"id":"https://openalex.org/C43521106","wikidata":"https://www.wikidata.org/wiki/Q2165493","display_name":"Pipeline (software)","level":2,"score":0.5117999911308289},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.426800012588501},{"id":"https://openalex.org/C91632574","wikidata":"https://www.wikidata.org/wiki/Q15088675","display_name":"Data curation","level":2,"score":0.4108999967575073},{"id":"https://openalex.org/C132964779","wikidata":"https://www.wikidata.org/wiki/Q2110223","display_name":"Raw data","level":2,"score":0.40700000524520874},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.40059998631477356},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.36640000343322754},{"id":"https://openalex.org/C115903868","wikidata":"https://www.wikidata.org/wiki/Q80993","display_name":"Software engineering","level":1,"score":0.34389999508857727},{"id":"https://openalex.org/C2779530757","wikidata":"https://www.wikidata.org/wiki/Q1207505","display_name":"Quality (philosophy)","level":2,"score":0.34139999747276306},{"id":"https://openalex.org/C133462117","wikidata":"https://www.wikidata.org/wiki/Q4929239","display_name":"Data collection","level":2,"score":0.33469998836517334},{"id":"https://openalex.org/C24756922","wikidata":"https://www.wikidata.org/wiki/Q1757694","display_name":"Data quality","level":3,"score":0.3310999870300293},{"id":"https://openalex.org/C97250363","wikidata":"https://www.wikidata.org/wiki/Q235557","display_name":"File format","level":2,"score":0.3147999942302704},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.2948000133037567},{"id":"https://openalex.org/C2777655017","wikidata":"https://www.wikidata.org/wiki/Q1501161","display_name":"Toolbox","level":2,"score":0.2921000123023987},{"id":"https://openalex.org/C72634772","wikidata":"https://www.wikidata.org/wiki/Q386824","display_name":"Data integration","level":2,"score":0.27810001373291016},{"id":"https://openalex.org/C171730128","wikidata":"https://www.wikidata.org/wiki/Q5227290","display_name":"Data file","level":2,"score":0.27630001306533813},{"id":"https://openalex.org/C2776207758","wikidata":"https://www.wikidata.org/wiki/Q5303302","display_name":"Downstream (manufacturing)","level":2,"score":0.26669999957084656},{"id":"https://openalex.org/C56288433","wikidata":"https://www.wikidata.org/wiki/Q58673","display_name":"Data manipulation language","level":2,"score":0.2533000111579895}],"mesh":[],"locations_count":4,"locations":[{"id":"doi:10.3389/fbinf.2025.1684227","is_oa":true,"landing_page_url":"https://doi.org/10.3389/fbinf.2025.1684227","pdf_url":"https://public-pages-files-2025.frontiersin.org/journals/bioinformatics/articles/10.3389/fbinf.2025.1684227/pdf","source":{"id":"https://openalex.org/S4210219554","display_name":"Frontiers in Bioinformatics","issn_l":"2673-7647","issn":["2673-7647"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320527","host_organization_name":"Frontiers Media","host_organization_lineage":["https://openalex.org/P4310320527"],"host_organization_lineage_names":["Frontiers Media"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Frontiers in Bioinformatics","raw_type":"journal-article"},{"id":"pmid:41458999","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/41458999","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":"Frontiers in bioinformatics","raw_type":null},{"id":"pmh:oai:doaj.org/article:6b87f0a9cbf34642a05437ab54c51308","is_oa":true,"landing_page_url":"https://doaj.org/article/6b87f0a9cbf34642a05437ab54c51308","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","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Frontiers in Bioinformatics, Vol 5 (2025)","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:12738925","is_oa":true,"landing_page_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC12738925/","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Front Bioinform","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.3389/fbinf.2025.1684227","is_oa":true,"landing_page_url":"https://doi.org/10.3389/fbinf.2025.1684227","pdf_url":"https://public-pages-files-2025.frontiersin.org/journals/bioinformatics/articles/10.3389/fbinf.2025.1684227/pdf","source":{"id":"https://openalex.org/S4210219554","display_name":"Frontiers in Bioinformatics","issn_l":"2673-7647","issn":["2673-7647"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320527","host_organization_name":"Frontiers Media","host_organization_lineage":["https://openalex.org/P4310320527"],"host_organization_lineage_names":["Frontiers Media"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Frontiers in Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G2845794101","display_name":"Uncovering transcription factors that directly induce pericytes from myofibroblasts for the treatment of fibrosis","funder_award_id":"24KJ2100","funder_id":"https://openalex.org/F4320334764","funder_display_name":"Japan Society for the Promotion of Science"},{"id":"https://openalex.org/G3236194794","display_name":null,"funder_award_id":"Grant-in-Aid","funder_id":"https://openalex.org/F4320334764","funder_display_name":"Japan Society for the Promotion of Science"},{"id":"https://openalex.org/G5396239172","display_name":null,"funder_award_id":"Grant-in-Aid for JSPS Fellows","funder_id":"https://openalex.org/F4320334764","funder_display_name":"Japan Society for the Promotion of Science"}],"funders":[{"id":"https://openalex.org/F4320334764","display_name":"Japan Society for the Promotion of Science","ror":"https://ror.org/00hhkn466"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4417221226.pdf","grobid_xml":"https://content.openalex.org/works/W4417221226.grobid-xml"},"referenced_works_count":22,"referenced_works":["https://openalex.org/W2817838603","https://openalex.org/W2901677030","https://openalex.org/W2905317377","https://openalex.org/W2949237386","https://openalex.org/W2951506174","https://openalex.org/W2951799803","https://openalex.org/W2984472267","https://openalex.org/W2995410603","https://openalex.org/W3118393359","https://openalex.org/W3159756629","https://openalex.org/W3175922295","https://openalex.org/W3211595762","https://openalex.org/W4322753855","https://openalex.org/W4367312557","https://openalex.org/W4380785637","https://openalex.org/W4388510403","https://openalex.org/W4388847162","https://openalex.org/W4408131648","https://openalex.org/W4409199080","https://openalex.org/W4410026608","https://openalex.org/W4410456482","https://openalex.org/W4411435191"],"related_works":[],"abstract_inverted_index":{"Single-cell":[0],"RNA":[1],"sequencing":[2],"(scRNA-seq)":[3],"has":[4],"generated":[5],"a":[6,63,72],"rapidly":[7],"expanding":[8],"collection":[9],"of":[10,47,218],"public":[11,86,195],"datasets":[12,151,201],"that":[13,66,161,172],"provide":[14],"insight":[15],"into":[16,125,198],"development,":[17],"disease,":[18],"and":[19,32,43,50,88,106,111,115,120,137,156,168,187,214],"therapy.":[20],"However,":[21],"researchers":[22],"lack":[23],"an":[24,68],"end-to-end":[25],"solution":[26],"for":[27,102,108,117,122],"seamlessly":[28],"retrieving,":[29],"preprocessing,":[30],"integrating,":[31],"analyzing":[33],"these":[34],"data":[35,83,135],"because":[36],"existing":[37],"tools":[38],"address":[39],"only":[40],"isolated":[41],"steps":[42],"require":[44],"manual":[45],"curation":[46],"accessions,":[48],"metadata,":[49,167],"technical":[51],"variability,":[52],"known":[53],"as":[54],"batch":[55,118],"effects.":[56],"In":[57],"this":[58],"study,":[59],"we":[60,143],"developed":[61],"Celline,":[62],"Python":[64],"package":[65],"executes":[67],"entire":[69],"workflow":[70],"using":[71,91],"single-line":[73],"commands":[74],"per":[75],"step.":[76],"Celline":[77,162,192],"automatically":[78],"gathers":[79],"raw":[80],"single-cell":[81,219],"RNA-seq":[82],"from":[84,152],"multiple":[85],"repositories":[87],"extracts":[89],"metadata":[90],"large":[92],"language":[93],"models.":[94],"It":[95],"then":[96],"wraps":[97],"established":[98],"tools,":[99],"including":[100],"Scrublet":[101],"doublet":[103],"removal,":[104],"Seurat":[105],"Scanpy":[107],"quality":[109,136,183],"control":[110],"cell-type":[112],"annotation,":[113],"Harmony":[114],"scVI":[116],"correction,":[119],"Slingshot":[121],"trajectory":[123,189],"inference,":[124],"one-line":[126],"commands,":[127],"enabling":[128],"seamless":[129],"integrative":[130],"analyses.":[131],"To":[132],"validate":[133],"Celline-acquired":[134],"the":[138,216],"integrated":[139],"framework's":[140],"practical":[141],"utility,":[142],"applied":[144],"it":[145],"to":[146],"2":[147],"mouse":[148],"brain":[149],"cortex":[150],"embryonic":[153],"days":[154],"14.5":[155],"18.":[157],"Technical":[158],"validation":[159],"demonstrated":[160],"successfully":[163],"retrieved":[164],"data,":[165],"standardized":[166],"enabled":[169],"standard":[170],"analyses":[171],"removed":[173],"low-quality":[174],"cells,":[175],"annotated":[176],"11":[177],"major":[178],"cell":[179],"types,":[180],"improved":[181],"integration":[182],"(scIB":[184],"score":[185],"+0.22),":[186],"completed":[188],"analysis.":[190],"Thus,":[191],"transforms":[193],"scattered":[194],"scRNA-seq":[196],"resources":[197],"unified,":[199],"analysis-ready":[200],"with":[202],"minimal":[203],"effort.":[204],"Its":[205],"modular":[206],"design":[207],"allows":[208],"pipeline":[209],"extension,":[210],"encourages":[211],"community-driven":[212],"advances,":[213],"accelerates":[215],"discovery":[217],"data.":[220]},"counts_by_year":[],"updated_date":"2026-04-21T08:09:41.155169","created_date":"2025-12-11T00:00:00"}
