{"doi":"10.1101/2022.02.07.479293","title":"iDESC: Identifying differential expression in single-cell RNA sequencing data with multiple subjects","abstract":"Abstract Single-cell RNA sequencing (scRNA-seq) enables assessment of transcriptome-wide changes at single-cell resolution. However, dominant subject effect in scRNA-seq datasets with multiple subjects severely confounds cell-type-specific differential expression (DE) analysis. We developed iDESC to separate subject effect from disease effect with consideration of dropouts to identify DE genes. iDESC was shown to have well-controlled type I error and high power compared to existing methods and obtained the best consistency between datasets and disease relevance in two scRNA-seq datasets from same disease, suggesting the importance of considering subject effect and dropouts in the DE analysis of scRNA-seq data with multiple subjects.","journal":"bioRxiv (Cold Spring Harbor Laboratory)","year":2022,"id":302660,"datarank":0.0,"base_score":0.0,"endowment":0.0,"self_citation_contribution":0.0,"citation_network_contribution":0.0,"self_endowment_contribution":0.0,"citer_contribution":0.0,"corpus_percentile":null,"corpus_rank":null,"citation_count":1,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.8667,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2022-01-01","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":994877,"name":"Ningya Wang","orcid":null,"position":1,"is_corresponding":false},{"id":34734,"name":"Taylor Adams","orcid":"0000-0003-4280-9070","position":2,"is_corresponding":false},{"id":34716,"name":"Jonas C. Schupp","orcid":"0000-0002-7714-8076","position":3,"is_corresponding":false},{"id":492533,"name":"Weimiao Wu","orcid":"0000-0001-6348-619X","position":4,"is_corresponding":false},{"id":268390,"name":"John E. McDonough","orcid":"0000-0003-2497-0258","position":5,"is_corresponding":false},{"id":348691,"name":"Geoffrey Chupp","orcid":"0000-0001-9968-6564","position":6,"is_corresponding":false},{"id":12162,"name":"Naftali Kaminski","orcid":"0000-0001-5917-4601","position":7,"is_corresponding":false},{"id":323455,"name":"Zuoheng Wang","orcid":"0000-0002-7251-3687","position":8,"is_corresponding":false},{"id":106132,"name":"Xiting Yan","orcid":"0000-0001-8688-9004","position":9,"is_corresponding":false},{"id":566861,"name":"Yunqing Liu","orcid":"0000-0003-3515-2314","position":0,"is_corresponding":true}],"reference_count":57,"raw_metadata":null,"created_at":"2026-07-19T00:32:16.279991Z","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":[]}