{"doi":"10.1186/s13059-021-02452-6","title":"Sfaira accelerates data and model reuse in single cell genomics","abstract":"Single-cell RNA-seq datasets are often first analyzed independently without harnessing model fits from previous studies, and are then contextualized with public data sets, requiring time-consuming data wrangling. We address these issues with sfaira, a single-cell data zoo for public data sets paired with a model zoo for executable pre-trained models. The data zoo is designed to facilitate contribution of data sets using ontologies for metadata. We propose an adaption of cross-entropy loss for cell type classification tailored to datasets annotated at different levels of coarseness. We demonstrate the utility of sfaira by training models across anatomic data partitions on 8 million cells.","journal":"Genome Biology","year":2021,"id":7202,"datarank":0.4943755299006494,"base_score":3.295836866004329,"endowment":3.295836866004329,"self_citation_contribution":0.4943755299006494,"citation_network_contribution":0.0,"self_endowment_contribution":0.4943755299006494,"citer_contribution":0.0,"corpus_percentile":null,"corpus_rank":null,"citation_count":26,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.3218,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2021-08-25","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":12138,"name":"Leander Dony","orcid":"0000-0001-5697-6991","position":1,"is_corresponding":false},{"id":64915,"name":"Martin König","orcid":null,"position":2,"is_corresponding":false},{"id":64916,"name":"Abdul Moeed","orcid":null,"position":3,"is_corresponding":false},{"id":11447,"name":"Luke Zappia","orcid":"0000-0001-7744-8565","position":4,"is_corresponding":false},{"id":3563,"name":"Lukas Heumos","orcid":"0000-0002-8937-3457","position":5,"is_corresponding":false},{"id":34876,"name":"Sophie Tritschler","orcid":"0000-0003-0977-9957","position":6,"is_corresponding":false},{"id":19635,"name":"Olle G. Holmberg","orcid":"0000-0001-5558-7628","position":7,"is_corresponding":false},{"id":537,"name":"Meshal Ansari","orcid":"0000-0002-8819-7965","position":8,"is_corresponding":false},{"id":42,"name":"Fabian Joachim Theis","orcid":"0000-0002-2419-1943","position":9,"is_corresponding":false},{"id":3574,"name":"David S. Fischer","orcid":"0000-0002-1293-7656","position":0,"is_corresponding":true}],"reference_count":78,"raw_metadata":null,"created_at":"2026-03-01T18:20:47.508186Z","pmid":null,"pmcid":null,"fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":null,"license":null,"views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":null,"fair_a":null,"fair_i":null,"fair_r":null,"fair_zscore":null,"fair_rationale":null,"fair_model":null,"fair_agent_version":null,"fair_fulltext_source":null,"fair_has_llm":null,"fair_computed_at":null,"clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}