{"doi":"10.1101/2022.05.04.490536","title":"Modeling fragment counts improves single-cell ATAC-seq analysis","abstract":"Single-cell ATAC-sequencing (scATAC-seq) coverage in regulatory regions is typically binarized as an indicator of open chromatin. However, the implications of scATAC-seq data binarization have not systematically been assessed. Here, we show that the goodness-of-fit of existing models and their applications, including clustering, cell type identification, and batch integration, are improved by a quantitative treatment of the fragment counts. These results have immediate implications for scATAC-seq analysis.","journal":"bioRxiv (Cold Spring Harbor Laboratory)","year":2022,"id":4870,"datarank":0.6609435245735436,"base_score":2.70805020110221,"endowment":2.70805020110221,"self_citation_contribution":0.40620753016533157,"citation_network_contribution":0.25473599440821204,"self_endowment_contribution":0.40620753016533157,"citer_contribution":0.25473599440821204,"corpus_percentile":null,"corpus_rank":null,"citation_count":14,"citer_count":11,"citers_with_citation_signal":9,"citers_with_endowment":9,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.0502,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2022-05-04","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":3574,"name":"David S. Fischer","orcid":"0000-0002-1293-7656","position":1,"is_corresponding":false},{"id":50557,"name":"Vicente A. Yépez","orcid":"0000-0001-7916-3643","position":2,"is_corresponding":false},{"id":42,"name":"Fabian Joachim Theis","orcid":"0000-0002-2419-1943","position":3,"is_corresponding":false},{"id":28474,"name":"Julia-Stefanie Frick","orcid":"0000-0002-7662-7956","position":4,"is_corresponding":false},{"id":50556,"name":"Laura D. Martens","orcid":"0000-0001-6520-4029","position":0,"is_corresponding":true}],"reference_count":32,"raw_metadata":{"citation_network_status":"fetched"},"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":[]}