{"id":"https://openalex.org/W4225678977","doi":"https://doi.org/10.1093/bioinformatics/btac299","title":"SpatialExperiment: infrastructure for spatially-resolved\u00a0transcriptomics data in R using Bioconductor","display_name":"SpatialExperiment: infrastructure for spatially-resolved\u00a0transcriptomics data in R using Bioconductor","publication_year":2022,"publication_date":"2022-04-25","ids":{"openalex":"https://openalex.org/W4225678977","doi":"https://doi.org/10.1093/bioinformatics/btac299","pmid":"https://pubmed.ncbi.nlm.nih.gov/35482478"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btac299","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btac299","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/38/11/3128/43857926/btac299.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/38/11/3128/43857926/btac299.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5075149591","display_name":"Dario Righelli","orcid":"https://orcid.org/0000-0003-1504-3583"},"institutions":[{"id":"https://openalex.org/I138689650","display_name":"University of Padua","ror":"https://ror.org/00240q980","country_code":"IT","type":"education","lineage":["https://openalex.org/I138689650"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Dario Righelli","raw_affiliation_strings":["Department of Statistical Sciences, University of Padova, 35121 Padova, Italy"],"affiliations":[{"raw_affiliation_string":"Department of Statistical Sciences, University of Padova, 35121 Padova, Italy","institution_ids":["https://openalex.org/I138689650"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5066778646","display_name":"Lukas M. Weber","orcid":"https://orcid.org/0000-0002-3282-1730"},"institutions":[{"id":"https://openalex.org/I145311948","display_name":"Johns Hopkins University","ror":"https://ror.org/00za53h95","country_code":"US","type":"education","lineage":["https://openalex.org/I145311948"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Lukas M Weber","raw_affiliation_strings":["Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA"],"affiliations":[{"raw_affiliation_string":"Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA","institution_ids":["https://openalex.org/I145311948"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5025531524","display_name":"Helena L. Crowell","orcid":"https://orcid.org/0000-0002-4801-1767"},"institutions":[{"id":"https://openalex.org/I202697423","display_name":"University of Zurich","ror":"https://ror.org/02crff812","country_code":"CH","type":"education","lineage":["https://openalex.org/I202697423"]},{"id":"https://openalex.org/I12708293","display_name":"SIB Swiss Institute of Bioinformatics","ror":"https://ror.org/002n09z45","country_code":"CH","type":"funder","lineage":["https://openalex.org/I12708293"]}],"countries":["CH"],"is_corresponding":false,"raw_author_name":"Helena L Crowell","raw_affiliation_strings":["Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland","SIB Swiss Institute of Bioinformatics , Zurich, Switzerland"],"affiliations":[{"raw_affiliation_string":"Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland","institution_ids":["https://openalex.org/I202697423"]},{"raw_affiliation_string":"SIB Swiss Institute of Bioinformatics , Zurich, Switzerland","institution_ids":["https://openalex.org/I12708293"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5003078239","display_name":"Brenda Pardo","orcid":"https://orcid.org/0000-0001-8103-7136"},"institutions":[{"id":"https://openalex.org/I8961855","display_name":"Universidad Nacional Aut\u00f3noma de M\u00e9xico","ror":"https://ror.org/01tmp8f25","country_code":"MX","type":"education","lineage":["https://openalex.org/I8961855"]},{"id":"https://openalex.org/I4210151493","display_name":"Lieber Institute for Brain Development","ror":"https://ror.org/04q36wn27","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I4210151493"]}],"countries":["MX","US"],"is_corresponding":false,"raw_author_name":"Brenda Pardo","raw_affiliation_strings":["Escuela Nacional de Estudios Superiores Unidad Juriquilla, Universidad Nacional Aut\u00f3noma de M\u00e9xico, Queretaro 76230, Mexico","Lieber Institute for Brain Development, Baltimore, MD 21205, USA"],"affiliations":[{"raw_affiliation_string":"Escuela Nacional de Estudios Superiores Unidad Juriquilla, Universidad Nacional Aut\u00f3noma de M\u00e9xico, Queretaro 76230, Mexico","institution_ids":["https://openalex.org/I8961855"]},{"raw_affiliation_string":"Lieber Institute for Brain Development, Baltimore, MD 21205, USA","institution_ids":["https://openalex.org/I4210151493"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5075979341","display_name":"Leonardo Collado\u2010Torres","orcid":"https://orcid.org/0000-0003-2140-308X"},"institutions":[{"id":"https://openalex.org/I4210151493","display_name":"Lieber Institute for Brain Development","ror":"https://ror.org/04q36wn27","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I4210151493"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Leonardo Collado-Torres","raw_affiliation_strings":["Lieber Institute for Brain Development, Baltimore, MD 21205, USA"],"affiliations":[{"raw_affiliation_string":"Lieber Institute for Brain Development, Baltimore, MD 21205, USA","institution_ids":["https://openalex.org/I4210151493"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5087355766","display_name":"Shila Ghazanfar","orcid":"https://orcid.org/0000-0001-7861-6997"},"institutions":[{"id":"https://openalex.org/I2801316944","display_name":"Cancer Research UK","ror":"https://ror.org/054225q67","country_code":"GB","type":"funder","lineage":["https://openalex.org/I2801316944"]},{"id":"https://openalex.org/I241749","display_name":"University of Cambridge","ror":"https://ror.org/013meh722","country_code":"GB","type":"education","lineage":["https://openalex.org/I241749"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Shila Ghazanfar","raw_affiliation_strings":["Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, United Kingdom"],"affiliations":[{"raw_affiliation_string":"Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, United Kingdom","institution_ids":["https://openalex.org/I2801316944","https://openalex.org/I241749"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5072824003","display_name":"Aaron T. L. Lun","orcid":"https://orcid.org/0000-0002-3564-4813"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Aaron T L Lun","raw_affiliation_strings":["Genentech, South San Francisco, CA 94080, USA"],"affiliations":[{"raw_affiliation_string":"Genentech, South San Francisco, CA 94080, USA","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5028505800","display_name":"Stephanie C. Hicks","orcid":"https://orcid.org/0000-0002-7858-0231"},"institutions":[{"id":"https://openalex.org/I145311948","display_name":"Johns Hopkins University","ror":"https://ror.org/00za53h95","country_code":"US","type":"education","lineage":["https://openalex.org/I145311948"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Stephanie C Hicks","raw_affiliation_strings":["Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA"],"affiliations":[{"raw_affiliation_string":"Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA","institution_ids":["https://openalex.org/I145311948"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5088632823","display_name":"Davide Risso","orcid":"https://orcid.org/0000-0001-8508-5012"},"institutions":[{"id":"https://openalex.org/I138689650","display_name":"University of Padua","ror":"https://ror.org/00240q980","country_code":"IT","type":"education","lineage":["https://openalex.org/I138689650"]}],"countries":["IT"],"is_corresponding":true,"raw_author_name":"Davide Risso","raw_affiliation_strings":["Department of Statistical Sciences, University of Padova, 35121 Padova, Italy"],"affiliations":[{"raw_affiliation_string":"Department of Statistical Sciences, University of Padova, 35121 Padova, Italy","institution_ids":["https://openalex.org/I138689650"]}]}],"institutions":[],"countries_distinct_count":5,"institutions_distinct_count":9,"corresponding_author_ids":["https://openalex.org/A5028505800","https://openalex.org/A5088632823"],"corresponding_institution_ids":["https://openalex.org/I138689650","https://openalex.org/I145311948"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":10.8081,"has_fulltext":false,"cited_by_count":135,"citation_normalized_percentile":{"value":0.99163491,"is_in_top_1_percent":true,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":89,"max":100},"biblio":{"volume":"38","issue":"11","first_page":"3128","last_page":"3131"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.9997000098228455,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.9997000098228455,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10885","display_name":"Gene expression and cancer classification","score":0.9887999892234802,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10621","display_name":"Gene Regulatory Network Analysis","score":0.9377999901771545,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/bioconductor","display_name":"Bioconductor","score":0.9474380016326904},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6075726747512817},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.4785345494747162},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.3862196207046509},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.18125414848327637},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.13033729791641235},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.06471934914588928}],"concepts":[{"id":"https://openalex.org/C2779694297","wikidata":"https://www.wikidata.org/wiki/Q2888953","display_name":"Bioconductor","level":3,"score":0.9474380016326904},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6075726747512817},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.4785345494747162},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3862196207046509},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.18125414848327637},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.13033729791641235},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.06471934914588928},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0}],"mesh":[{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":4,"locations":[{"id":"doi:10.1093/bioinformatics/btac299","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btac299","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/38/11/3128/43857926/btac299.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:35482478","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/35482478","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics (Oxford, England)","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:9154247","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/9154247","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"Text"},{"id":"pmh:oai:www.research.unipd.it:11577/3444098","is_oa":true,"landing_page_url":"https://hdl.handle.net/11577/3444098","pdf_url":null,"source":{"id":"https://openalex.org/S4306402547","display_name":"Padua Research Archive (University of Padova)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I138689650","host_organization_name":"University of Padua","host_organization_lineage":["https://openalex.org/I138689650"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"info:eu-repo/semantics/article"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btac299","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btac299","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/38/11/3128/43857926/btac299.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/9","display_name":"Industry, innovation and infrastructure","score":0.6600000262260437}],"awards":[{"id":"https://openalex.org/G7145945914","display_name":null,"funder_award_id":"U01MH122849","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"}],"funders":[{"id":"https://openalex.org/F4320306192","display_name":"Silicon Valley Community Foundation","ror":"https://ror.org/001ader08"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4225678977.pdf","grobid_xml":"https://content.openalex.org/works/W4225678977.grobid-xml"},"referenced_works_count":35,"referenced_works":["https://openalex.org/W1973094248","https://openalex.org/W2042789810","https://openalex.org/W2126537932","https://openalex.org/W2471536144","https://openalex.org/W2516455020","https://openalex.org/W2520858613","https://openalex.org/W2533012945","https://openalex.org/W2540833380","https://openalex.org/W2804233742","https://openalex.org/W2807856729","https://openalex.org/W2808465642","https://openalex.org/W2809368942","https://openalex.org/W2915848182","https://openalex.org/W2923300855","https://openalex.org/W2951158909","https://openalex.org/W2952076809","https://openalex.org/W2952383043","https://openalex.org/W2972445800","https://openalex.org/W2989807288","https://openalex.org/W3036371598","https://openalex.org/W3037329734","https://openalex.org/W3112563877","https://openalex.org/W3126958162","https://openalex.org/W3129476455","https://openalex.org/W3134482219","https://openalex.org/W3164692211","https://openalex.org/W3176766013","https://openalex.org/W3196495189","https://openalex.org/W4210583065","https://openalex.org/W4244166529","https://openalex.org/W4281716652","https://openalex.org/W4386156610","https://openalex.org/W6728888212","https://openalex.org/W6777499545","https://openalex.org/W6800409366"],"related_works":["https://openalex.org/W4391375266","https://openalex.org/W2899084033","https://openalex.org/W2748952813","https://openalex.org/W2135678793","https://openalex.org/W2011682793","https://openalex.org/W2109288169","https://openalex.org/W2157684052","https://openalex.org/W2978247079","https://openalex.org/W2140163842","https://openalex.org/W2148708580"],"abstract_inverted_index":{"Supplementary":[0],"data":[1],"are":[2],"available":[3],"at":[4],"Bioinformatics":[5],"online.":[6]},"counts_by_year":[{"year":2026,"cited_by_count":8},{"year":2025,"cited_by_count":43},{"year":2024,"cited_by_count":32},{"year":2023,"cited_by_count":45},{"year":2022,"cited_by_count":4},{"year":2021,"cited_by_count":2},{"year":2012,"cited_by_count":1}],"updated_date":"2025-11-23T05:10:03.516525","created_date":"2025-10-10T00:00:00"}