{"doi":"10.1101/2025.09.15.676389","title":"SpaceSequest: A unified pipeline for spatial transcriptomics data analysis","abstract":"<jats:title>ABSTRACT</jats:title>\n                <jats:sec>\n                  <jats:title>Background</jats:title>\n                  <jats:p>Spatial transcriptomics has emerged as one of the most powerful tools for gaining biological insights, enabling researchers to uncover intricate relationships between gene expression patterns and tissue architecture. Recent advances in the field have resulted in a variety of new platforms, including Visium, Visium HD, and Xenium from 10x Genomics, as well as GeoMx and CosMx from NanoString Technologies, which has now been acquired by the Bruker Corporation. However, the existence of diverse spatial transcriptomics platforms and various data formats poses challenges in standardizing data analysis. Thus, there remains a critical gap in the availability of a comprehensive pipeline capable of conducting end-to-end analysis that is necessary to extract biological insights from multiple spatial transcriptomics platforms.</jats:p>\n                </jats:sec>\n                <jats:sec>\n                  <jats:title>Results</jats:title>\n                  <jats:p>Here, we present SpaceSequest, a tailored pipeline that utilizes cutting-edge computational methodologies to conduct a thorough analysis, enabling the extraction of crucial biological insights from five major spatial transcriptomics technologies. SpaceSequest performs (1) standardized quality control and general data processing, (2) key analyses customized for each spatial platform, (3) automated cell type annotation and deconvolution, and (4) high-quality figure and analysis result generation. In addition, SpaceSequest allows for smooth integration with cellxgene VIP and Quickomics for user-friendly data access and interactive visualization.</jats:p>\n                </jats:sec>\n                <jats:sec>\n                  <jats:title>Conclusions</jats:title>\n                  <jats:p>\n                    SpaceSequest is a unified and comprehensive pipeline designed for the analysis, visualization, and publication of spatial transcriptomics data from various platforms. The source code is available at\n                    <jats:ext-link xmlns:xlink=\"http://www.w3.org/1999/xlink\" ext-link-type=\"uri\" xlink:href=\"https://github.com/interactivereport/SpaceSequest\">https://github.com/interactivereport/SpaceSequest</jats:ext-link>\n                    . To facilitate seamless installation and usage, we have also created a detailed Bookdown tutorial that can be accessed through\n                    <jats:ext-link xmlns:xlink=\"http://www.w3.org/1999/xlink\" ext-link-type=\"uri\" xlink:href=\"https://interactivereport.github.io/SpaceSequest/tutorial/docs/index.html\">https://interactivereport.github.io/SpaceSequest/tutorial/docs/index.html</jats:ext-link>\n                    .\n                  </jats:p>\n                </jats:sec>","journal":null,"year":null,"id":653191,"datarank":0.10397207708399181,"base_score":0.6931471805599453,"endowment":0.6931471805599453,"self_citation_contribution":0.10397207708399181,"citation_network_contribution":0.0,"self_endowment_contribution":0.10397207708399181,"citer_contribution":0.0,"corpus_percentile":null,"corpus_rank":null,"citation_count":1,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":null,"is_data_producer":false,"deposit_databanks":null,"is_oa":false,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":null,"fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":1704278,"name":"Sarbottam Piya","orcid":"0000-0002-1070-8008","position":1,"is_corresponding":false},{"id":80476,"name":"Zhengyu Ouyang","orcid":null,"position":2,"is_corresponding":false},{"id":1011813,"name":"Yirui Chen","orcid":"0000-0003-1522-8908","position":3,"is_corresponding":false},{"id":877008,"name":"Jake Gagnon","orcid":null,"position":4,"is_corresponding":false},{"id":106812,"name":"Shaolong Cao","orcid":"0000-0002-4443-9424","position":5,"is_corresponding":false},{"id":1189115,"name":"Haotian Zhang","orcid":"0000-0002-2275-3412","position":6,"is_corresponding":false},{"id":273732,"name":"Baobao Song","orcid":"0000-0002-0062-2710","position":7,"is_corresponding":false},{"id":1135945,"name":"Jing Zhu","orcid":"0000-0001-5555-8560","position":8,"is_corresponding":false},{"id":994195,"name":"Khyati Chandratre","orcid":"0000-0003-3698-3670","position":9,"is_corresponding":false},{"id":430968,"name":"Houlin Yu","orcid":"0000-0002-5374-2783","position":10,"is_corresponding":false},{"id":320624,"name":"Wenxing Hu","orcid":"0000-0003-2477-6383","position":11,"is_corresponding":false},{"id":373134,"name":"Matthew Ryals","orcid":null,"position":12,"is_corresponding":false},{"id":620475,"name":"Fergal Casey","orcid":"0000-0002-6781-8670","position":13,"is_corresponding":false},{"id":1704287,"name":"Dann Huh","orcid":null,"position":14,"is_corresponding":false},{"id":135498,"name":"Baohong Zhang","orcid":"0000-0003-4735-4212","position":15,"is_corresponding":false},{"id":264115,"name":"Yu Sun","orcid":"0000-0003-0333-2898","position":0,"is_corresponding":false}],"reference_count":0,"raw_metadata":{"has_enrichment":true,"resolved":true,"title":"SpaceSequest: A unified pipeline for spatial transcriptomics data analysis","abstract":"<jats:title>ABSTRACT</jats:title>\n                <jats:sec>\n                  <jats:title>Background</jats:title>\n                  <jats:p>Spatial transcriptomics has emerged as one of the most powerful tools for gaining biological insights, enabling researchers to uncover intricate relationships between gene expression patterns and tissue architecture. Recent advances in the field have resulted in a variety of new platforms, including Visium, Visium HD, and Xenium from 10x Genomics, as well as GeoMx and CosMx from NanoString Technologies, which has now been acquired by the Bruker Corporation. However, the existence of diverse spatial transcriptomics platforms and various data formats poses challenges in standardizing data analysis. Thus, there remains a critical gap in the availability of a comprehensive pipeline capable of conducting end-to-end analysis that is necessary to extract biological insights from multiple spatial transcriptomics platforms.</jats:p>\n                </jats:sec>\n                <jats:sec>\n                  <jats:title>Results</jats:title>\n                  <jats:p>Here, we present SpaceSequest, a tailored pipeline that utilizes cutting-edge computational methodologies to conduct a thorough analysis, enabling the extraction of crucial biological insights from five major spatial transcriptomics technologies. SpaceSequest performs (1) standardized quality control and general data processing, (2) key analyses customized for each spatial platform, (3) automated cell type annotation and deconvolution, and (4) high-quality figure and analysis result generation. In addition, SpaceSequest allows for smooth integration with cellxgene VIP and Quickomics for user-friendly data access and interactive visualization.</jats:p>\n                </jats:sec>\n                <jats:sec>\n                  <jats:title>Conclusions</jats:title>\n                  <jats:p>\n                    SpaceSequest is a unified and comprehensive pipeline designed for the analysis, visualization, and publication of spatial transcriptomics data from various platforms. The source code is available at\n                    <jats:ext-link xmlns:xlink=\"http://www.w3.org/1999/xlink\" ext-link-type=\"uri\" xlink:href=\"https://github.com/interactivereport/SpaceSequest\">https://github.com/interactivereport/SpaceSequest</jats:ext-link>\n                    . To facilitate seamless installation and usage, we have also created a detailed Bookdown tutorial that can be accessed through\n                    <jats:ext-link xmlns:xlink=\"http://www.w3.org/1999/xlink\" ext-link-type=\"uri\" xlink:href=\"https://interactivereport.github.io/SpaceSequest/tutorial/docs/index.html\">https://interactivereport.github.io/SpaceSequest/tutorial/docs/index.html</jats:ext-link>\n                    .\n                  </jats:p>\n                </jats:sec>","is_dataset_classified":null,"base_score":0.6931471805599453,"endowment":0.6931471805599453,"datacite_reuse_total":0,"file_count":0,"downloads":0,"views":0,"has_version_chain":false,"is_dataset":false,"is_oa":false,"pmid":"19965766","pmcid":null,"openalex_id":"https://openalex.org/W4414430539","authors":[],"funders":[],"total_grants":0,"fwci":null,"citation_percentile":null,"influential_citations":0,"citation_trend":[{"year":2026,"count":1}],"oa_status":"green","license":"cc-by","oa_locations":[{"url":"https://doi.org/10.1101/2025.09.15.676389","host_type":"repository"},{"url":"https://doi.org/10.1101/2025.09.15.676389","host_type":"repository"},{"url":"https://syndication.highwire.org/content/doi/10.1101/2025.09.15.676389","host_type":"publisher"}],"fields_of_study":["Microbial Community Ecology and Physiology","Genomics and Phylogenetic Studies","Gene expression and cancer classification"],"mesh_terms":[],"keywords":["Pipeline (software)","Variety (cybernetics)","Field (mathematics)","Annotation","Spatial analysis","Data type","Source code","Biological data"],"sdg_mappings":[],"linked_datasets":[],"clinical_trials":[],"software_tools":[],"database_accessions":[],"source":"live","citation_network_status":"fetched"},"created_at":"2026-08-10T19:59:57.134629Z","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":[]}