{"doi":"10.1101/2022.09.20.508796","title":"A unified framework of realistic in silico data generation and statistical model inference for single-cell and spatial omics","abstract":"Abstract In the single-cell and spatial omics field, computational challenges include method benchmarking, data interpretation, and in silico data generation. To address these challenges, we propose an all-in-one statistical simulator, scDesign3, to generate realistic single-cell and spatial omics data, including various cell states, experimental designs, and feature modalities, by learning interpretable parameters from real datasets. Furthermore, using a unified probabilistic model for single-cell and spatial omics data, scDesign3 can infer biologically meaningful parameters, assess the goodness-of-fit of inferred cell clusters, trajectories, and spatial locations, and generate in silico negative and positive controls for benchmarking computational tools.","journal":"bioRxiv (Cold Spring Harbor Laboratory)","year":2022,"id":298389,"datarank":0.29188652235829704,"base_score":1.9459101490553132,"endowment":1.9459101490553132,"self_citation_contribution":0.29188652235829704,"citation_network_contribution":0.0,"self_endowment_contribution":0.29188652235829704,"citer_contribution":0.0,"corpus_percentile":null,"corpus_rank":null,"citation_count":6,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.9045,"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":987363,"name":"Qingyang Wang","orcid":"0000-0002-1051-609X","position":1,"is_corresponding":false},{"id":987364,"name":"Guanao Yan","orcid":"0000-0002-6861-1882","position":2,"is_corresponding":false},{"id":987365,"name":"Tianyang Liu","orcid":"0000-0003-2598-8572","position":3,"is_corresponding":false},{"id":86014,"name":"Jingyi Jessica Li","orcid":"0000-0002-9288-5648","position":4,"is_corresponding":false},{"id":557612,"name":"Dongyuan Song","orcid":"0000-0003-1114-1215","position":0,"is_corresponding":true}],"reference_count":54,"raw_metadata":{"citation_network_status":"fetched"},"created_at":"2026-07-19T00:31:36.269611Z","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":[]}