{"doi":"10.12688/f1000research.22969.2","title":"clustifyr: an R package for automated single-cell RNA sequencing cluster classification","abstract":"Assignment of cell types from single-cell RNA sequencing (scRNA-seq) data remains a time-consuming and error-prone process. Current packages for identity assignment use limited types of reference data and often have rigid data structure requirements. We developed the clustifyr R package to leverage several external data types, including gene expression profiles to assign likely cell types using data from scRNA-seq, bulk RNA-seq, microarray expression data, or signature gene lists. We benchmark various parameters of a correlation-based approach and implement gene list enrichment methods. clustifyr is a lightweight and effective cell-type assignment tool developed for compatibility with various scRNA-seq analysis workflows. clustifyr is publicly available at https://github.com/rnabioco/clustifyr.","journal":"F1000Research","year":2020,"id":52408,"datarank":3.502947763046331,"base_score":4.90527477843843,"endowment":4.90527477843843,"self_citation_contribution":0.7357912167657645,"citation_network_contribution":2.767156546280566,"self_endowment_contribution":0.7357912167657645,"citer_contribution":2.767156546280566,"corpus_percentile":null,"corpus_rank":null,"citation_count":134,"citer_count":100,"citers_with_citation_signal":93,"citers_with_endowment":93,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.9312,"is_data_producer":true,"deposit_databanks":{"figshare":["10.6084/m9.figshare.5435866.v8"]},"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2020-01-01","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":225904,"name":"Austin E. Gillen","orcid":"0000-0003-2928-6308","position":1,"is_corresponding":false},{"id":225905,"name":"Ryan M. Sheridan","orcid":"0000-0003-4012-3147","position":2,"is_corresponding":false},{"id":264536,"name":"Chengzhe Tian","orcid":"0000-0002-2269-1979","position":3,"is_corresponding":false},{"id":218535,"name":"Michelle Daya","orcid":"0000-0002-9057-6593","position":4,"is_corresponding":false},{"id":264537,"name":"Yue Hao","orcid":"0000-0002-5065-8906","position":5,"is_corresponding":false},{"id":87044,"name":"Jay R. Hesselberth","orcid":"0000-0002-6299-179X","position":6,"is_corresponding":false},{"id":225903,"name":"Kent Riemondy","orcid":"0000-0003-0750-1273","position":7,"is_corresponding":false},{"id":225902,"name":"Rui Fu","orcid":"0000-0001-8183-4549","position":0,"is_corresponding":true}],"reference_count":34,"raw_metadata":null,"created_at":"2026-07-18T20:42:26.843314Z","pmid":"32765839","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":[]}