{"doi":"10.1016/j.crmeth.2021.100056","title":"Improved integration of single-cell transcriptome and surface protein expression by LinQ-View","abstract":"Multimodal advances in single-cell sequencing have enabled the simultaneous quantification of cell surface protein expression alongside unbiased transcriptional profiling. Here, we present LinQ-View, a toolkit designed for multimodal single-cell data visualization and analysis. LinQ-View integrates transcriptional and cell surface protein expression profiling data to reveal more accurate cell heterogeneity and proposes a quantitative metric for cluster purity assessment. Through comparison with existing multimodal methods on multiple public CITE-seq datasets, we demonstrate that LinQ-View efficiently generates accurate cell clusters, especially in CITE-seq data with routine numbers of surface protein features, by preventing variations in a single surface protein feature from affecting results. Finally, we utilized this method to integrate single-cell transcriptional and protein expression data from SARS-CoV-2-infected patients, revealing antigen-specific B cell subsets after infection. Our results suggest LinQ-View could be helpful for multimodal analysis and purity assessment of CITE-seq datasets that target specific cell populations (e.g., B cells).","journal":"Cell Reports Methods","year":2021,"id":191141,"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":13,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.9244,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2021-01-01","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":233143,"name":"Haley L. Dugan","orcid":"0000-0003-2238-0094","position":1,"is_corresponding":false},{"id":266562,"name":"Christopher T. Stamper","orcid":"0000-0002-5568-8880","position":2,"is_corresponding":false},{"id":266559,"name":"Linda Yu-Ling Lan","orcid":"0000-0003-1400-5307","position":3,"is_corresponding":false},{"id":553849,"name":"Nicholas Asby","orcid":"0000-0002-1675-7601","position":4,"is_corresponding":false},{"id":756106,"name":"Matthew Knight","orcid":"0009-0004-6756-1504","position":5,"is_corresponding":false},{"id":266560,"name":"Olivia Stovicek","orcid":"0000-0001-6413-855X","position":6,"is_corresponding":false},{"id":269129,"name":"Nai‐Ying Zheng","orcid":null,"position":7,"is_corresponding":false},{"id":553712,"name":"Maria Lucia L. Madariaga","orcid":"0000-0002-2950-7230","position":8,"is_corresponding":false},{"id":451388,"name":"Kumaran Shanmugarajah","orcid":"0009-0005-3056-352X","position":9,"is_corresponding":false},{"id":553709,"name":"Maud O. Jansen","orcid":"0000-0002-0659-4298","position":10,"is_corresponding":false},{"id":266563,"name":"Siriruk Changrob","orcid":"0000-0002-1826-4333","position":11,"is_corresponding":false},{"id":266564,"name":"Henry A. Utset","orcid":"0000-0003-0607-3086","position":12,"is_corresponding":false},{"id":105581,"name":"Carole Henry","orcid":"0000-0002-5696-527X","position":13,"is_corresponding":false},{"id":325679,"name":"Christopher A. Nelson","orcid":"0000-0001-8730-4768","position":14,"is_corresponding":false},{"id":226921,"name":"R. Jedrzejczak","orcid":"0000-0001-6375-7199","position":15,"is_corresponding":false},{"id":225534,"name":"Daved H. Fremont","orcid":"0000-0002-8544-2689","position":16,"is_corresponding":false},{"id":91662,"name":"A. Joachimiak","orcid":"0000-0003-2535-6209","position":17,"is_corresponding":false},{"id":103779,"name":"Florian Krammer","orcid":"0000-0003-4121-776X","position":18,"is_corresponding":false},{"id":497061,"name":"Jun Huang","orcid":"0000-0003-0271-4384","position":19,"is_corresponding":false},{"id":226352,"name":"Aly A. Khan","orcid":"0000-0003-3933-8538","position":20,"is_corresponding":false},{"id":233144,"name":"Patrick C. Wilson","orcid":"0000-0002-3537-1245","position":21,"is_corresponding":false},{"id":441791,"name":"Lei Li","orcid":"0000-0001-5478-5681","position":0,"is_corresponding":true}],"reference_count":42,"raw_metadata":null,"created_at":"2026-07-18T23:49:31.121780Z","pmid":"35475142","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":[]}