{"doi":"10.1101/174029","title":"Scanpy for analysis of large-scale single-cell gene expression data","abstract":"We present Scanpy, a scalable toolkit for analyzing single-cell gene expression data. It includes preprocessing, visualization, clustering, pseudotime and trajectory inference, differential expression testing and simulation of gene regulatory networks. The Python-based implementation efficiently deals with datasets of more than one million cells and enables easy interfacing of advanced machine learning packages. Code is available from https://github.com/theislab/scanpy .","journal":"bioRxiv (Cold Spring Harbor Laboratory)","year":2017,"id":1047,"datarank":1.3639163877606455,"base_score":3.091042453358316,"endowment":3.091042453358316,"self_citation_contribution":0.4636563680037475,"citation_network_contribution":0.900260019756898,"self_endowment_contribution":0.4636563680037475,"citer_contribution":0.900260019756898,"corpus_percentile":null,"corpus_rank":null,"citation_count":21,"citer_count":19,"citers_with_citation_signal":18,"citers_with_endowment":18,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.0646,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2017-08-09","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":3570,"name":"Philipp Angerer","orcid":"0000-0002-0369-2888","position":1,"is_corresponding":false},{"id":42,"name":"Fabian Joachim Theis","orcid":"0000-0002-2419-1943","position":2,"is_corresponding":false},{"id":3587,"name":"Francesca Finotello","orcid":"0000-0003-0712-4658","position":0,"is_corresponding":true}],"reference_count":50,"raw_metadata":{"citation_network_status":"fetched"},"created_at":"2026-03-01T18:20:47.508186Z","pmid":null,"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":[]}