{"id":"https://openalex.org/W4412366514","doi":"https://doi.org/10.1093/bioinformatics/btaf402","title":"SCassist: an AI based workflow assistant for single-cell analysis","display_name":"SCassist: an AI based workflow assistant for single-cell analysis","publication_year":2025,"publication_date":"2025-07-12","ids":{"openalex":"https://openalex.org/W4412366514","doi":"https://doi.org/10.1093/bioinformatics/btaf402","pmid":"https://pubmed.ncbi.nlm.nih.gov/40650988"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btaf402","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaf402","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btaf402/63735739/btaf402.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/advance-article-pdf/doi/10.1093/bioinformatics/btaf402/63735739/btaf402.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5022793691","display_name":"Vijayaraj Nagarajan","orcid":null},"institutions":[{"id":"https://openalex.org/I4210139686","display_name":"National Eye Institute","ror":"https://ror.org/03wkg3b53","country_code":"US","type":"facility","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1299303238","https://openalex.org/I4210139686"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Vijayaraj Nagarajan","raw_affiliation_strings":["Laboratory of Immunology, National Eye Institute, NIH , Bethesda, MD 20892,","Laboratory of Immunology, National Eye Institute, NIH, Bethesda, MD 20892, United States"],"raw_orcid":"https://orcid.org/0000-0003-2455-7172","affiliations":[{"raw_affiliation_string":"Laboratory of Immunology, National Eye Institute, NIH , Bethesda, MD 20892,","institution_ids":["https://openalex.org/I4210139686"]},{"raw_affiliation_string":"Laboratory of Immunology, National Eye Institute, NIH, Bethesda, MD 20892, United States","institution_ids":["https://openalex.org/I4210139686"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101596031","display_name":"Guangpu Shi","orcid":"https://orcid.org/0000-0002-0528-2030"},"institutions":[{"id":"https://openalex.org/I4210139686","display_name":"National Eye Institute","ror":"https://ror.org/03wkg3b53","country_code":"US","type":"facility","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1299303238","https://openalex.org/I4210139686"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Guangpu Shi","raw_affiliation_strings":["Laboratory of Immunology, National Eye Institute, NIH , Bethesda, MD 20892,","Laboratory of Immunology, National Eye Institute, NIH, Bethesda, MD 20892, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Laboratory of Immunology, National Eye Institute, NIH , Bethesda, MD 20892,","institution_ids":["https://openalex.org/I4210139686"]},{"raw_affiliation_string":"Laboratory of Immunology, National Eye Institute, NIH, Bethesda, MD 20892, United States","institution_ids":["https://openalex.org/I4210139686"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5117290454","display_name":"Samyuktha Arunkumar","orcid":null},"institutions":[{"id":"https://openalex.org/I4210139686","display_name":"National Eye Institute","ror":"https://ror.org/03wkg3b53","country_code":"US","type":"facility","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1299303238","https://openalex.org/I4210139686"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Samyuktha Arunkumar","raw_affiliation_strings":["Laboratory of Immunology, National Eye Institute, NIH , Bethesda, MD 20892,","Laboratory of Immunology, National Eye Institute, NIH, Bethesda, MD 20892, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Laboratory of Immunology, National Eye Institute, NIH , Bethesda, MD 20892,","institution_ids":["https://openalex.org/I4210139686"]},{"raw_affiliation_string":"Laboratory of Immunology, National Eye Institute, NIH, Bethesda, MD 20892, United States","institution_ids":["https://openalex.org/I4210139686"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100654044","display_name":"Chunhong Liu","orcid":"https://orcid.org/0000-0002-3666-2343"},"institutions":[{"id":"https://openalex.org/I4210139686","display_name":"National Eye Institute","ror":"https://ror.org/03wkg3b53","country_code":"US","type":"facility","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1299303238","https://openalex.org/I4210139686"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Chunhong Liu","raw_affiliation_strings":["Neuro-Immune Regulome Unit (Alumni), National Eye Institute, NIH , Bethesda, MD 20892,","Neuro-Immune Regulome Unit (Alumni), National Eye Institute, NIH, Bethesda, MD 20892, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Neuro-Immune Regulome Unit (Alumni), National Eye Institute, NIH , Bethesda, MD 20892,","institution_ids":["https://openalex.org/I4210139686"]},{"raw_affiliation_string":"Neuro-Immune Regulome Unit (Alumni), National Eye Institute, NIH, Bethesda, MD 20892, United States","institution_ids":["https://openalex.org/I4210139686"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5067919853","display_name":"Jaanam Gopalakrishnan","orcid":null},"institutions":[{"id":"https://openalex.org/I4210139686","display_name":"National Eye Institute","ror":"https://ror.org/03wkg3b53","country_code":"US","type":"facility","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1299303238","https://openalex.org/I4210139686"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jaanam Gopalakrishnan","raw_affiliation_strings":["Neuro-Immune Regulome Unit, National Eye Institute, NIH , Bethesda, MD 20892,","Neuro-Immune Regulome Unit, National Eye Institute, NIH, Bethesda, MD 20892, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Neuro-Immune Regulome Unit, National Eye Institute, NIH , Bethesda, MD 20892,","institution_ids":["https://openalex.org/I4210139686"]},{"raw_affiliation_string":"Neuro-Immune Regulome Unit, National Eye Institute, NIH, Bethesda, MD 20892, United States","institution_ids":["https://openalex.org/I4210139686"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5103176864","display_name":"Pulak Ranjan Nath","orcid":"https://orcid.org/0000-0001-9643-5217"},"institutions":[{"id":"https://openalex.org/I4210139686","display_name":"National Eye Institute","ror":"https://ror.org/03wkg3b53","country_code":"US","type":"facility","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1299303238","https://openalex.org/I4210139686"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Pulak R Nath","raw_affiliation_strings":["Laboratory of Immunology (Alumni), National Eye Institute, NIH , Bethesda, MD 20892,","Laboratory of Immunology (Alumni), National Eye Institute, NIH, Bethesda, MD 20892, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Laboratory of Immunology (Alumni), National Eye Institute, NIH , Bethesda, MD 20892,","institution_ids":["https://openalex.org/I4210139686"]},{"raw_affiliation_string":"Laboratory of Immunology (Alumni), National Eye Institute, NIH, Bethesda, MD 20892, United States","institution_ids":["https://openalex.org/I4210139686"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5075912207","display_name":"Jun\u2010Ho Jang","orcid":"https://orcid.org/0000-0003-1590-6414"},"institutions":[{"id":"https://openalex.org/I4210139686","display_name":"National Eye Institute","ror":"https://ror.org/03wkg3b53","country_code":"US","type":"facility","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1299303238","https://openalex.org/I4210139686"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Junseok Jang","raw_affiliation_strings":["Laboratory of Immunology, National Eye Institute, NIH , Bethesda, MD 20892,","Laboratory of Immunology, National Eye Institute, NIH, Bethesda, MD 20892, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Laboratory of Immunology, National Eye Institute, NIH , Bethesda, MD 20892,","institution_ids":["https://openalex.org/I4210139686"]},{"raw_affiliation_string":"Laboratory of Immunology, National Eye Institute, NIH, Bethesda, MD 20892, United States","institution_ids":["https://openalex.org/I4210139686"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5004732672","display_name":"Rachel R Caspi","orcid":"https://orcid.org/0000-0002-7140-7671"},"institutions":[{"id":"https://openalex.org/I4210139686","display_name":"National Eye Institute","ror":"https://ror.org/03wkg3b53","country_code":"US","type":"facility","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1299303238","https://openalex.org/I4210139686"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Rachel R Caspi","raw_affiliation_strings":["Laboratory of Immunology, National Eye Institute, NIH , Bethesda, MD 20892,","Laboratory of Immunology, National Eye Institute, NIH, Bethesda, MD 20892, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Laboratory of Immunology, National Eye Institute, NIH , Bethesda, MD 20892,","institution_ids":["https://openalex.org/I4210139686"]},{"raw_affiliation_string":"Laboratory of Immunology, National Eye Institute, NIH, Bethesda, MD 20892, United States","institution_ids":["https://openalex.org/I4210139686"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":[],"corresponding_institution_ids":["https://openalex.org/I4210139686"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":2.9231,"has_fulltext":true,"cited_by_count":7,"citation_normalized_percentile":{"value":0.91373983,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":91,"max":99},"biblio":{"volume":"41","issue":"8","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":0.9983000159263611,"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":0.9983000159263611,"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":0.0003000000142492354,"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":9.999999747378752e-05,"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/workflow","display_name":"Workflow","score":0.8716757297515869},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7980916500091553},{"id":"https://openalex.org/keywords/normalization","display_name":"Normalization (sociology)","score":0.7118880152702332},{"id":"https://openalex.org/keywords/cluster-analysis","display_name":"Cluster analysis","score":0.5306892395019531},{"id":"https://openalex.org/keywords/key","display_name":"Key (lock)","score":0.4791226387023926},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.40007415413856506},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.3950902223587036},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.24754926562309265},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.21651619672775269}],"concepts":[{"id":"https://openalex.org/C177212765","wikidata":"https://www.wikidata.org/wiki/Q627335","display_name":"Workflow","level":2,"score":0.8716757297515869},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7980916500091553},{"id":"https://openalex.org/C136886441","wikidata":"https://www.wikidata.org/wiki/Q926129","display_name":"Normalization (sociology)","level":2,"score":0.7118880152702332},{"id":"https://openalex.org/C73555534","wikidata":"https://www.wikidata.org/wiki/Q622825","display_name":"Cluster analysis","level":2,"score":0.5306892395019531},{"id":"https://openalex.org/C26517878","wikidata":"https://www.wikidata.org/wiki/Q228039","display_name":"Key (lock)","level":2,"score":0.4791226387023926},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.40007415413856506},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3950902223587036},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.24754926562309265},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.21651619672775269},{"id":"https://openalex.org/C38652104","wikidata":"https://www.wikidata.org/wiki/Q3510521","display_name":"Computer security","level":1,"score":0.0},{"id":"https://openalex.org/C144024400","wikidata":"https://www.wikidata.org/wiki/Q21201","display_name":"Sociology","level":0,"score":0.0},{"id":"https://openalex.org/C19165224","wikidata":"https://www.wikidata.org/wiki/Q23404","display_name":"Anthropology","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D001185","descriptor_name":"Artificial Intelligence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D001185","descriptor_name":"Artificial Intelligence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D001185","descriptor_name":"Artificial Intelligence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D001185","descriptor_name":"Artificial Intelligence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D001185","descriptor_name":"Artificial Intelligence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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":"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":"D012984","descriptor_name":"Software","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":true},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","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":"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},{"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/btaf402","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaf402","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btaf402/63735739/btaf402.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:40650988","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/40650988","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:pubmedcentral.nih.gov:12341677","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/12341677","pdf_url":null,"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":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btaf402","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaf402","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btaf402/63735739/btaf402.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/G1104209294","display_name":null,"funder_award_id":"EY000184","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G1872421171","display_name":null,"funder_award_id":"R01 EY032482","funder_id":"https://openalex.org/F4320337350","funder_display_name":"National Eye Institute"},{"id":"https://openalex.org/G2007519026","display_name":null,"funder_award_id":"EY032482","funder_id":"https://openalex.org/F4320337350","funder_display_name":"National Eye Institute"},{"id":"https://openalex.org/G2381539595","display_name":null,"funder_award_id":"EY032482","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G2902104123","display_name":null,"funder_award_id":"EY000184","funder_id":"https://openalex.org/F4320337350","funder_display_name":"National Eye Institute"},{"id":"https://openalex.org/G5219498744","display_name":null,"funder_award_id":"Z01 EY000184","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"}],"funders":[{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337350","display_name":"National Eye Institute","ror":"https://ror.org/03wkg3b53"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4412366514.pdf","grobid_xml":"https://content.openalex.org/works/W4412366514.grobid-xml"},"referenced_works_count":22,"referenced_works":["https://openalex.org/W2023741270","https://openalex.org/W2911489562","https://openalex.org/W2963341956","https://openalex.org/W3127238141","https://openalex.org/W4297243391","https://openalex.org/W4316096017","https://openalex.org/W4366526178","https://openalex.org/W4366563389","https://openalex.org/W4378838672","https://openalex.org/W4379958259","https://openalex.org/W4384561707","https://openalex.org/W4391835299","https://openalex.org/W4392168151","https://openalex.org/W4392953700","https://openalex.org/W4393153069","https://openalex.org/W4396213452","https://openalex.org/W4396544943","https://openalex.org/W4399387478","https://openalex.org/W4401173214","https://openalex.org/W4401455022","https://openalex.org/W4403174218","https://openalex.org/W6633724138"],"related_works":["https://openalex.org/W2591697403","https://openalex.org/W1981780420","https://openalex.org/W2944728705","https://openalex.org/W2182707996","https://openalex.org/W2904022177","https://openalex.org/W45233828","https://openalex.org/W2964988449","https://openalex.org/W2359348847","https://openalex.org/W3011538607","https://openalex.org/W4294432981"],"abstract_inverted_index":{"SUMMARY:":[0],"Single-cell":[1],"RNA":[2],"sequencing":[3],"(scRNA-seq)":[4],"data":[5,54],"analysis":[6,103],"often":[7],"involves":[8],"complex":[9],"iterative":[10],"workflow,":[11],"requiring":[12],"significant":[13],"expertise":[14],"and":[15,40,55,62,75,83,98],"time.":[16],"To":[17],"navigate":[18],"this":[19],"complexity,":[20],"we":[21],"have":[22],"developed":[23],"SCassist,":[24],"an":[25],"R":[26],"package":[27],"that":[28],"leverages":[29],"the":[30,33,118],"power":[31],"of":[32,72],"large":[34],"language":[35],"models":[36],"(LLM's)":[37],"to":[38,51,105],"guide":[39],"enhance":[41],"scRNA-seq":[42,102],"analysis.":[43,85],"SCassist":[44,86,114],"integrates":[45],"LLM's":[46,92],"into":[47],"key":[48],"workflow":[49],"steps,":[50],"analyze":[52],"user":[53],"provide":[56],"relevant":[57],"recommendations":[58],"for":[59],"filtering,":[60],"normalization":[61],"clustering":[63],"parameters.":[64],"It":[65],"also":[66],"provides":[67,87],"LLM":[68],"guided":[69],"insightful":[70],"interpretations":[71],"variable":[73],"features":[74],"principal":[76],"components,":[77],"along":[78,116],"with":[79,117],"cell":[80],"type":[81],"annotations":[82],"enrichment":[84],"intelligent":[88],"assistance":[89],"using":[90],"popular":[91],"like":[93],"Google's":[94],"Gemini,":[95],"OpenAI's":[96],"GPT":[97],"Meta's":[99],"Llama3,":[100],"making":[101],"accessible":[104],"researchers":[106],"at":[107,123],"all":[108],"levels.":[109],"AVAILABILITY":[110],"AND":[111],"IMPLEMENTATION:":[112],"The":[113],"package,":[115],"detailed":[119],"tutorials,":[120],"is":[121],"available":[122],"GitHub.":[124],"https://github.com/NIH-NEI/SCassist.":[125]},"counts_by_year":[{"year":2026,"cited_by_count":6},{"year":2025,"cited_by_count":1}],"updated_date":"2026-07-26T07:53:14.480251","created_date":"2025-10-10T00:00:00"}
