{"doi":"10.1101/2025.09.03.674100","title":"DAESC+: High-performance, integrated software for single-cell allele-specific expression data","abstract":"Single-cell allele-specific expression (ASE) provides valuable insights into gene regulatory mechanisms. However, its utility is limited by the lack of dedicated computational tools. We present DAESC+, an end-to-end software package for the processing and analysis of single-cell ASE. The preprocessing module, DAESC-P, is a user-friendly bioinformatics pipeline to obtain ASE counts from multiplexed scRNA-seq data. The analysis module, DAESC-GPU, is a scalable tool for differential ASE analysis powered by graphics processing units (GPUs). We demonstrated that DAESC-P is more accurate than the existing SALSA pipeline. DAESC-GPU is dozens of times faster than our previous method (DAESC) and scalable to over a million cells. Applying DAESC+ to a subset of the OneK1K cohort, we identified 15 genes exhibiting differential regulatory patterns between naïve and central memory CD4+ T cells, and 2 genes between naïve and memory B cells.","journal":"bioRxiv (Cold Spring Harbor Laboratory)","year":2025,"id":574707,"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":0,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.9533,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2025-01-01","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":225485,"name":"Guanghao Qi","orcid":"0000-0002-8085-4748","position":1,"is_corresponding":false},{"id":1482396,"name":"Tengfei Cui","orcid":"0000-0001-7676-9041","position":0,"is_corresponding":true}],"reference_count":31,"raw_metadata":null,"created_at":"2026-07-19T02:57:44.572630Z","pmid":"40964337","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":[]}