{"doi":"10.1093/bioadv/vbaf091","title":"ReSort enhances reference-based cell type deconvolution for spatial transcriptomics through regional information integration","abstract":"Motivation: Spatial transcriptomics (ST) captures positional gene expression within tissues but lacks single-cell resolution. Reference-based cell type deconvolution methods were developed to understand cell type distributions for ST. However, batch/platform discrepancies between references and ST impact their accuracy. Results: We present Region-based Cell Sorting (ReSort), which utilizes ST's region-level data to lessen reliance on reference data and alleviate these technical issues. In simulation studies, ReSort enhances reference-based deconvolution methods. Applying ReSort to a mouse breast cancer model highlights macrophages M0 and M2 enrichment in the epithelial clone, revealing insights into epithelial-mesenchymal transition and immune infiltration. Availability and implementation: Source codes for ReSort are publicly available at (https://github.com/LiuzLab/RESORT), implemented in Python.","journal":"Bioinformatics Advances","year":2024,"id":474935,"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":0.9204,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2024-01-01","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":330786,"name":"Ling Wu","orcid":"0000-0002-5786-4315","position":1,"is_corresponding":false},{"id":1311854,"name":"Guantong Qi","orcid":null,"position":2,"is_corresponding":false},{"id":335327,"name":"Chaozhong Liu","orcid":"0000-0002-6960-1977","position":3,"is_corresponding":false},{"id":999124,"name":"Wanli Wang","orcid":"0000-0003-4134-1699","position":4,"is_corresponding":false},{"id":239995,"name":"Xiang H.-F. Zhang","orcid":"0000-0002-5674-8670","position":5,"is_corresponding":false},{"id":110460,"name":"Zhandong Liu","orcid":"0000-0002-7608-0831","position":6,"is_corresponding":false},{"id":562886,"name":"Linhua Wang","orcid":"0000-0002-6717-860X","position":0,"is_corresponding":true}],"reference_count":33,"raw_metadata":null,"created_at":"2026-07-19T02:06:13.042906Z","pmid":"40510374","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":[]}