{"id":"https://openalex.org/W4415489509","doi":"https://doi.org/10.1093/bioinformatics/btaf559","title":"ShortCake: an integrated platform for efficient and reproducible single-cell analysis","display_name":"ShortCake: an integrated platform for efficient and reproducible single-cell analysis","publication_year":2025,"publication_date":"2025-10-02","ids":{"openalex":"https://openalex.org/W4415489509","doi":"https://doi.org/10.1093/bioinformatics/btaf559","pmid":"https://pubmed.ncbi.nlm.nih.gov/41129381"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btaf559","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaf559","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/41/11/btaf559/64884065/btaf559.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","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":true,"oa_status":"gold","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/41/11/btaf559/64884065/btaf559.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5082449290","display_name":"Ryuichiro Nakato","orcid":"https://orcid.org/0000-0003-3019-5817"},"institutions":[{"id":"https://openalex.org/I4210098931","display_name":"Quantitative BioSciences","ror":"https://ror.org/010brsj79","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I4210098931"]},{"id":"https://openalex.org/I74801974","display_name":"The University of Tokyo","ror":"https://ror.org/057zh3y96","country_code":"JP","type":"education","lineage":["https://openalex.org/I74801974"]}],"countries":["JP","US"],"is_corresponding":true,"raw_author_name":"Ryuichiro Nakato","raw_affiliation_strings":["Laboratory of Computational Genomics, Institute for Quantitative Biosciences, The University of Tokyo , Tokyo 113-0032,","Laboratory of Computational Genomics, Institute for Quantitative Biosciences, The University of Tokyo, Tokyo, 113-0032, Japan"],"affiliations":[{"raw_affiliation_string":"Laboratory of Computational Genomics, Institute for Quantitative Biosciences, The University of Tokyo , Tokyo 113-0032,","institution_ids":["https://openalex.org/I4210098931"]},{"raw_affiliation_string":"Laboratory of Computational Genomics, Institute for Quantitative Biosciences, The University of Tokyo, Tokyo, 113-0032, Japan","institution_ids":["https://openalex.org/I74801974"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5040473614","display_name":"Lu\u00eds Augusto Eijy Nagai","orcid":"https://orcid.org/0000-0002-7672-8554"},"institutions":[{"id":"https://openalex.org/I4210098931","display_name":"Quantitative BioSciences","ror":"https://ror.org/010brsj79","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I4210098931"]},{"id":"https://openalex.org/I74801974","display_name":"The University of Tokyo","ror":"https://ror.org/057zh3y96","country_code":"JP","type":"education","lineage":["https://openalex.org/I74801974"]}],"countries":["JP","US"],"is_corresponding":false,"raw_author_name":"Luis Augusto Eijy Nagai","raw_affiliation_strings":["Laboratory of Computational Genomics, Institute for Quantitative Biosciences, The University of Tokyo , Tokyo 113-0032,","Laboratory of Computational Genomics, Institute for Quantitative Biosciences, The University of Tokyo, Tokyo, 113-0032, Japan"],"affiliations":[{"raw_affiliation_string":"Laboratory of Computational Genomics, Institute for Quantitative Biosciences, The University of Tokyo , Tokyo 113-0032,","institution_ids":["https://openalex.org/I4210098931"]},{"raw_affiliation_string":"Laboratory of Computational Genomics, Institute for Quantitative Biosciences, The University of Tokyo, Tokyo, 113-0032, Japan","institution_ids":["https://openalex.org/I74801974"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5082449290"],"corresponding_institution_ids":["https://openalex.org/I4210098931","https://openalex.org/I74801974"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":0.0,"has_fulltext":true,"cited_by_count":0,"citation_normalized_percentile":{"value":0.26398118,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"41","issue":"11","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/T12859","display_name":"Cell Image Analysis Techniques","score":0.9882000088691711,"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":0.9726999998092651,"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/source-code","display_name":"Source code","score":0.6978999972343445},{"id":"https://openalex.org/keywords/code","display_name":"Code (set theory)","score":0.5304999947547913},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.520799994468689},{"id":"https://openalex.org/keywords/image","display_name":"Image (mathematics)","score":0.4332999885082245},{"id":"https://openalex.org/keywords/open-source","display_name":"Open source","score":0.3652999997138977}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7659000158309937},{"id":"https://openalex.org/C43126263","wikidata":"https://www.wikidata.org/wiki/Q128751","display_name":"Source code","level":2,"score":0.6978999972343445},{"id":"https://openalex.org/C2776760102","wikidata":"https://www.wikidata.org/wiki/Q5139990","display_name":"Code (set theory)","level":3,"score":0.5304999947547913},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.520799994468689},{"id":"https://openalex.org/C115961682","wikidata":"https://www.wikidata.org/wiki/Q860623","display_name":"Image (mathematics)","level":2,"score":0.4332999885082245},{"id":"https://openalex.org/C3018397939","wikidata":"https://www.wikidata.org/wiki/Q3644502","display_name":"Open source","level":3,"score":0.3652999997138977},{"id":"https://openalex.org/C9417928","wikidata":"https://www.wikidata.org/wiki/Q1070689","display_name":"Image processing","level":3,"score":0.34310001134872437},{"id":"https://openalex.org/C149635348","wikidata":"https://www.wikidata.org/wiki/Q193040","display_name":"Embedded system","level":1,"score":0.3109999895095825},{"id":"https://openalex.org/C79403827","wikidata":"https://www.wikidata.org/wiki/Q3988","display_name":"Real-time computing","level":1,"score":0.3077999949455261},{"id":"https://openalex.org/C31972630","wikidata":"https://www.wikidata.org/wiki/Q844240","display_name":"Computer vision","level":1,"score":0.2865999937057495},{"id":"https://openalex.org/C9390403","wikidata":"https://www.wikidata.org/wiki/Q3966","display_name":"Computer hardware","level":1,"score":0.2791000008583069},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.272599995136261},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.25920000672340393},{"id":"https://openalex.org/C2983685735","wikidata":"https://www.wikidata.org/wiki/Q5227355","display_name":"Data source","level":2,"score":0.2574000060558319},{"id":"https://openalex.org/C26517878","wikidata":"https://www.wikidata.org/wiki/Q228039","display_name":"Key (lock)","level":2,"score":0.25450000166893005}],"mesh":[{"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":"D011381","descriptor_name":"Programming Languages","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011381","descriptor_name":"Programming Languages","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011381","descriptor_name":"Programming Languages","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011381","descriptor_name":"Programming Languages","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":"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":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"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":"D057188","descriptor_name":"Workflow","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D057188","descriptor_name":"Workflow","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D057188","descriptor_name":"Workflow","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D057188","descriptor_name":"Workflow","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":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":3,"locations":[{"id":"doi:10.1093/bioinformatics/btaf559","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaf559","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/41/11/btaf559/64884065/btaf559.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:41129381","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/41129381","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},{"id":"pmh:oai:europepmc.org:11427664","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/12619637","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btaf559","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaf559","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/41/11/btaf559/64884065/btaf559.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G4517769837","display_name":null,"funder_award_id":"JP23gm6310012h0004","funder_id":"https://openalex.org/F4320311405","funder_display_name":"Japan Agency for Medical Research and Development"}],"funders":[{"id":"https://openalex.org/F4320311405","display_name":"Japan Agency for Medical Research and Development","ror":"https://ror.org/004rtk039"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4415489509.pdf","grobid_xml":"https://content.openalex.org/works/W4415489509.grobid-xml"},"referenced_works_count":15,"referenced_works":["https://openalex.org/W2605897695","https://openalex.org/W2613409207","https://openalex.org/W2747877289","https://openalex.org/W2766437506","https://openalex.org/W2800392236","https://openalex.org/W2949177718","https://openalex.org/W2949829455","https://openalex.org/W2952582936","https://openalex.org/W3047141442","https://openalex.org/W4210587306","https://openalex.org/W4308484211","https://openalex.org/W4362737480","https://openalex.org/W4378212544","https://openalex.org/W4386563593","https://openalex.org/W4392121611"],"related_works":[],"abstract_inverted_index":{"The":[0,14],"ShortCake":[1],"image":[2],"is":[3,17],"available":[4,18],"on":[5,19],"DockerHub":[6],"(https://hub.docker.com/r/rnakato/shortcake)":[7],"and":[8,12],"Zenodo":[9],"(DOIs:":[10],"10.5281/zenodo.17116765":[11],"10.5281/zenodo.17118158).":[13],"source":[15],"code":[16],"GitHub":[20],"(https://github.com/rnakato/ShortCake).":[21]},"counts_by_year":[],"updated_date":"2026-04-09T08:11:56.329763","created_date":"2025-10-24T00:00:00"}