{"doi":"10.1101/2023.10.05.560733","title":"Characterizing cell-type spatial relationships across length scales in spatially resolved omics data","abstract":"Spatially resolved omics (SRO) technologies enable the identification of cell types while preserving their organization within tissues. Application of such technologies offers the opportunity to delineate cell-type spatial relationships, particularly across different length scales, and enhance our understanding of tissue organization and function. To quantify such multi-scale cell-type spatial relationships, we developed CRAWDAD, Cell-type Relationship Analysis Workflow Done Across Distances, as an open-source R package with source code and additional documentation at https://jef.works/CRAWDAD/. To demonstrate the utility of such multi-scale characterization, recapitulate expected cell-type spatial relationships, and evaluate against other cell-type spatial analyses, we applied CRAWDAD to various simulated and real SRO datasets of diverse tissues assayed by diverse SRO technologies. We further demonstrate how such multi-scale characterization enabled by CRAWDAD can be used to compare cell-type spatial relationships across multiple samples. Finally, we applied CRAWDAD to SRO datasets of the human spleen to identify consistent as well as patient and sample-specific cell-type spatial relationships. In general, we anticipate such multi-scale analysis of SRO data enabled by CRAWDAD will provide useful quantitative metrics to facilitate the identification, characterization, and comparison of cell-type spatial relationships across axes of interest.","journal":"bioRxiv (Cold Spring Harbor Laboratory)","year":2023,"id":397464,"datarank":0.16479184330021646,"base_score":1.0986122886681096,"endowment":1.0986122886681096,"self_citation_contribution":0.16479184330021646,"citation_network_contribution":0.0,"self_endowment_contribution":0.16479184330021646,"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":0.9043,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2023-01-01","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":806368,"name":"Brendan F. Miller","orcid":"0000-0002-9559-4045","position":1,"is_corresponding":false},{"id":356517,"name":"Maigan A. Brusko","orcid":"0000-0002-4331-2202","position":2,"is_corresponding":false},{"id":893071,"name":"Gohta Aihara","orcid":"0000-0002-2492-9610","position":3,"is_corresponding":false},{"id":25153,"name":"Lyla Atta","orcid":"0000-0002-6113-0082","position":4,"is_corresponding":false},{"id":1017840,"name":"Manjari Anant","orcid":"0000-0002-6600-3410","position":5,"is_corresponding":false},{"id":23929,"name":"Mark A. Atkinson","orcid":"0000-0001-8489-4782","position":6,"is_corresponding":false},{"id":356521,"name":"Todd M. Brusko","orcid":"0000-0003-2878-9296","position":7,"is_corresponding":false},{"id":477240,"name":"Clive Wasserfall","orcid":"0000-0002-3522-8932","position":8,"is_corresponding":false},{"id":25158,"name":"Jean Fan","orcid":"0000-0002-0212-5451","position":9,"is_corresponding":false},{"id":888439,"name":"Rafael dos Santos Peixoto","orcid":"0000-0002-7184-2868","position":0,"is_corresponding":true}],"reference_count":38,"raw_metadata":{"citation_network_status":"fetched"},"created_at":"2026-07-19T01:19:39.497368Z","pmid":"39314450","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":[]}