{"doi":"10.1093/bioadv/vbac028","title":"Pollock: fishing for cell states","abstract":"Motivation: The use of single-cell methods is expanding at an ever-increasing rate. While there are established algorithms that address cell classification, they are limited in terms of cross platform compatibility, reliance on the availability of a reference dataset and classification interpretability. Here, we introduce Pollock, a suite of algorithms for cell type identification that is compatible with popular single-cell methods and analysis platforms, provides a set of pretrained human cancer reference models, and reports interpretability scores that identify the genes that drive cell type classifications. Results: Pollock performs comparably to existing classification methods, while offering easily deployable pretrained classification models across a wide variety of tissue and data types. Additionally, it demonstrates utility in immune pan-cancer analysis. Availability and implementation: Source code and documentation are available at https://github.com/ding-lab/pollock. Pretrained models and datasets are available for download at https://zenodo.org/record/5895221. Supplementary information: online.","journal":"Bioinformatics Advances","year":2022,"id":293100,"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":2,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.9553,"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":51800,"name":"Daniel Cui Zhou","orcid":"0000-0002-7834-2778","position":1,"is_corresponding":false},{"id":1777,"name":"Michael C. Wendl","orcid":"0000-0002-5694-2668","position":2,"is_corresponding":false},{"id":18423,"name":"Matthew A. Wyczalkowski","orcid":"0000-0003-4197-551X","position":3,"is_corresponding":false},{"id":225686,"name":"Alla Y. Karpova","orcid":"0000-0003-0467-0215","position":4,"is_corresponding":false},{"id":51846,"name":"Liang-Bo Wang","orcid":"0000-0001-6977-9348","position":5,"is_corresponding":false},{"id":51772,"name":"Yize Li","orcid":"0000-0003-1074-281X","position":6,"is_corresponding":false},{"id":86837,"name":"Austin N. Southard-Smith","orcid":"0000-0003-0022-6897","position":7,"is_corresponding":false},{"id":14374,"name":"Reyka G. Jayasinghe","orcid":"0000-0003-2368-4890","position":8,"is_corresponding":false},{"id":634906,"name":"Lijun Yao","orcid":"0000-0001-6131-8491","position":9,"is_corresponding":false},{"id":81218,"name":"Ruiyang Liu","orcid":"0000-0002-8235-3998","position":10,"is_corresponding":false},{"id":31712,"name":"Yige Wu","orcid":"0000-0001-7727-901X","position":11,"is_corresponding":false},{"id":51764,"name":"Nadezhda V. Terekhanova","orcid":"0000-0001-8711-4649","position":12,"is_corresponding":false},{"id":616860,"name":"Houxiang Zhu","orcid":null,"position":13,"is_corresponding":false},{"id":651735,"name":"John M. Herndon","orcid":"0000-0002-8378-9654","position":14,"is_corresponding":false},{"id":977872,"name":"Sid Puram","orcid":null,"position":15,"is_corresponding":false},{"id":225140,"name":"Feng Chen","orcid":"0000-0002-5588-1082","position":16,"is_corresponding":false},{"id":235670,"name":"William E. Gillanders","orcid":"0000-0002-0465-3071","position":17,"is_corresponding":false},{"id":31720,"name":"Ryan C. Fields","orcid":"0000-0001-6176-8943","position":18,"is_corresponding":false},{"id":108228,"name":"Li Ding","orcid":"0000-0003-1517-2975","position":19,"is_corresponding":false},{"id":51856,"name":"Erik Storrs","orcid":"0000-0002-8041-0864","position":0,"is_corresponding":true}],"reference_count":42,"raw_metadata":null,"created_at":"2026-07-19T00:30:50.076284Z","pmid":"35603231","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":[]}