{"id":"https://openalex.org/W4386623320","doi":"https://doi.org/10.1093/bioinformatics/btad550","title":"<i>MoleculeExperiment</i> enables consistent infrastructure for molecule-resolved spatial omics data in bioconductor","display_name":"<i>MoleculeExperiment</i> enables consistent infrastructure for molecule-resolved spatial omics data in bioconductor","publication_year":2023,"publication_date":"2023-09-01","ids":{"openalex":"https://openalex.org/W4386623320","doi":"https://doi.org/10.1093/bioinformatics/btad550","pmid":"https://pubmed.ncbi.nlm.nih.gov/37698995"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btad550","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btad550","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btad550/51529640/btad550.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"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":"gold","oa_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btad550/51529640/btad550.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5091971416","display_name":"B\u00e1rbara Zita Peters Couto","orcid":"https://orcid.org/0000-0001-7388-8897"},"institutions":[{"id":"https://openalex.org/I129604602","display_name":"The University of Sydney","ror":"https://ror.org/0384j8v12","country_code":"AU","type":"education","lineage":["https://openalex.org/I129604602"]}],"countries":["AU"],"is_corresponding":true,"raw_author_name":"B\u00e1rbara Zita Peters Couto","raw_affiliation_strings":["Charles Perkins Centre, The University of Sydney , Camperdown, NSW 2006, Australia","School of Mathematics and Statistics, The University of Sydney , Camperdown, NSW 2006, Australia","Sydney Precision Data Science Centre, The University of Sydney , Camperdown, NSW 2006, Australia"],"affiliations":[{"raw_affiliation_string":"Charles Perkins Centre, The University of Sydney , Camperdown, NSW 2006, Australia","institution_ids":["https://openalex.org/I129604602"]},{"raw_affiliation_string":"School of Mathematics and Statistics, The University of Sydney , Camperdown, NSW 2006, Australia","institution_ids":["https://openalex.org/I129604602"]},{"raw_affiliation_string":"Sydney Precision Data Science Centre, The University of Sydney , Camperdown, NSW 2006, Australia","institution_ids":["https://openalex.org/I129604602"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5102715801","display_name":"Nicholas Robertson","orcid":"https://orcid.org/0000-0003-4227-8652"},"institutions":[{"id":"https://openalex.org/I129604602","display_name":"The University of Sydney","ror":"https://ror.org/0384j8v12","country_code":"AU","type":"education","lineage":["https://openalex.org/I129604602"]}],"countries":["AU"],"is_corresponding":false,"raw_author_name":"Nicholas Robertson","raw_affiliation_strings":["Charles Perkins Centre, The University of Sydney , Camperdown, NSW 2006, Australia","School of Mathematics and Statistics, The University of Sydney , Camperdown, NSW 2006, Australia","Sydney Laboratory of Data Discovery for Health Limited (D24H), Science Park , Hong Kong SAR, China","Sydney Precision Data Science Centre, The University of Sydney , Camperdown, NSW 2006, Australia"],"affiliations":[{"raw_affiliation_string":"Charles Perkins Centre, The University of Sydney , Camperdown, NSW 2006, Australia","institution_ids":["https://openalex.org/I129604602"]},{"raw_affiliation_string":"School of Mathematics and Statistics, The University of Sydney , Camperdown, NSW 2006, Australia","institution_ids":["https://openalex.org/I129604602"]},{"raw_affiliation_string":"Sydney Laboratory of Data Discovery for Health Limited (D24H), Science Park , Hong Kong SAR, China","institution_ids":[]},{"raw_affiliation_string":"Sydney Precision Data Science Centre, The University of Sydney , Camperdown, NSW 2006, Australia","institution_ids":["https://openalex.org/I129604602"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5042620584","display_name":"Ellis Patrick","orcid":"https://orcid.org/0000-0002-5253-4747"},"institutions":[{"id":"https://openalex.org/I129604602","display_name":"The University of Sydney","ror":"https://ror.org/0384j8v12","country_code":"AU","type":"education","lineage":["https://openalex.org/I129604602"]},{"id":"https://openalex.org/I4210145422","display_name":"Westmead Institute for Medical Research","ror":"https://ror.org/04zj3ra44","country_code":"AU","type":"facility","lineage":["https://openalex.org/I4210145422"]}],"countries":["AU"],"is_corresponding":false,"raw_author_name":"Ellis Patrick","raw_affiliation_strings":["Centre for Cancer Research, The Westmead Institute for Medical Research, The University of Sydney , Westmead, NSW 2145, Australia","Charles Perkins Centre, The University of Sydney , Camperdown, NSW 2006, Australia","School of Mathematics and Statistics, The University of Sydney , Camperdown, NSW 2006, Australia","Sydney Laboratory of Data Discovery for Health Limited (D24H), Science Park , Hong Kong SAR, China","Sydney Precision Data Science Centre, The University of Sydney , Camperdown, NSW 2006, Australia"],"affiliations":[{"raw_affiliation_string":"Centre for Cancer Research, The Westmead Institute for Medical Research, The University of Sydney , Westmead, NSW 2145, Australia","institution_ids":["https://openalex.org/I4210145422","https://openalex.org/I129604602"]},{"raw_affiliation_string":"Charles Perkins Centre, The University of Sydney , Camperdown, NSW 2006, Australia","institution_ids":["https://openalex.org/I129604602"]},{"raw_affiliation_string":"School of Mathematics and Statistics, The University of Sydney , Camperdown, NSW 2006, Australia","institution_ids":["https://openalex.org/I129604602"]},{"raw_affiliation_string":"Sydney Laboratory of Data Discovery for Health Limited (D24H), Science Park , Hong Kong SAR, China","institution_ids":[]},{"raw_affiliation_string":"Sydney Precision Data Science Centre, The University of Sydney , Camperdown, NSW 2006, Australia","institution_ids":["https://openalex.org/I129604602"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5087355766","display_name":"Shila Ghazanfar","orcid":"https://orcid.org/0000-0001-7861-6997"},"institutions":[{"id":"https://openalex.org/I129604602","display_name":"The University of Sydney","ror":"https://ror.org/0384j8v12","country_code":"AU","type":"education","lineage":["https://openalex.org/I129604602"]}],"countries":["AU"],"is_corresponding":false,"raw_author_name":"Shila Ghazanfar","raw_affiliation_strings":["Charles Perkins Centre, The University of Sydney , Camperdown, NSW 2006, Australia","School of Mathematics and Statistics, The University of Sydney , Camperdown, NSW 2006, Australia","Sydney Precision Data Science Centre, The University of Sydney , Camperdown, NSW 2006, Australia"],"affiliations":[{"raw_affiliation_string":"Charles Perkins Centre, The University of Sydney , Camperdown, NSW 2006, Australia","institution_ids":["https://openalex.org/I129604602"]},{"raw_affiliation_string":"School of Mathematics and Statistics, The University of Sydney , Camperdown, NSW 2006, Australia","institution_ids":["https://openalex.org/I129604602"]},{"raw_affiliation_string":"Sydney Precision Data Science Centre, The University of Sydney , Camperdown, NSW 2006, Australia","institution_ids":["https://openalex.org/I129604602"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5091971416"],"corresponding_institution_ids":["https://openalex.org/I129604602"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":1.9917,"has_fulltext":true,"cited_by_count":13,"citation_normalized_percentile":{"value":0.86615366,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":100},"biblio":{"volume":"39","issue":"9","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11289","display_name":"Single-cell and spatial transcriptomics","score":1.0,"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":1.0,"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/T11313","display_name":"Immune cells in cancer","score":0.972000002861023,"subfield":{"id":"https://openalex.org/subfields/2403","display_name":"Immunology"},"field":{"id":"https://openalex.org/fields/24","display_name":"Immunology and Microbiology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10885","display_name":"Gene expression and cancer classification","score":0.9677000045776367,"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":0.9759290218353271},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6843855381011963},{"id":"https://openalex.org/keywords/plug-in","display_name":"Plug-in","score":0.5141327977180481},{"id":"https://openalex.org/keywords/context","display_name":"Context (archaeology)","score":0.47607511281967163},{"id":"https://openalex.org/keywords/source-code","display_name":"Source code","score":0.44752538204193115},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.42488428950309753},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.3506949543952942},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.33059170842170715},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.17127209901809692},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.10944771766662598}],"concepts":[{"id":"https://openalex.org/C2779694297","wikidata":"https://www.wikidata.org/wiki/Q2888953","display_name":"Bioconductor","level":3,"score":0.9759290218353271},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6843855381011963},{"id":"https://openalex.org/C4924752","wikidata":"https://www.wikidata.org/wiki/Q184148","display_name":"Plug-in","level":2,"score":0.5141327977180481},{"id":"https://openalex.org/C2779343474","wikidata":"https://www.wikidata.org/wiki/Q3109175","display_name":"Context (archaeology)","level":2,"score":0.47607511281967163},{"id":"https://openalex.org/C43126263","wikidata":"https://www.wikidata.org/wiki/Q128751","display_name":"Source code","level":2,"score":0.44752538204193115},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.42488428950309753},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.3506949543952942},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.33059170842170715},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.17127209901809692},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.10944771766662598},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0},{"id":"https://openalex.org/C151730666","wikidata":"https://www.wikidata.org/wiki/Q7205","display_name":"Paleontology","level":1,"score":0.0},{"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":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","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":true},{"descriptor_ui":"D023281","descriptor_name":"Genomics","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":true},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btad550","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btad550","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btad550/51529640/btad550.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"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:37698995","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/37698995","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:10504467","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/10504467","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC10504467/pdf/btad550.pdf","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btad550","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btad550","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btad550/51529640/btad550.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"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":0.6299999952316284}],"awards":[],"funders":[{"id":"https://openalex.org/F4320315885","display_name":"Australian Government","ror":"https://ror.org/0314h5y94"},{"id":"https://openalex.org/F4320320966","display_name":"University of Sydney","ror":"https://ror.org/0384j8v12"},{"id":"https://openalex.org/F4320321920","display_name":"Innovation and Technology Commission","ror":"https://ror.org/04vf9tr09"}],"has_content":{"pdf":true,"grobid_xml":false},"content_urls":{"pdf":"https://content.openalex.org/works/W4386623320.pdf"},"referenced_works_count":24,"referenced_works":["https://openalex.org/W1975389666","https://openalex.org/W2557069473","https://openalex.org/W2989807288","https://openalex.org/W3041345852","https://openalex.org/W3117538519","https://openalex.org/W4205541212","https://openalex.org/W4210583065","https://openalex.org/W4225476238","https://openalex.org/W4225678977","https://openalex.org/W4283075169","https://openalex.org/W4283704002","https://openalex.org/W4286005528","https://openalex.org/W4362663294","https://openalex.org/W4378212544","https://openalex.org/W4383710649","https://openalex.org/W4385174515","https://openalex.org/W4386034444","https://openalex.org/W4387494379","https://openalex.org/W4389670555","https://openalex.org/W4389938094","https://openalex.org/W4393004135","https://openalex.org/W6849910751","https://openalex.org/W6851060205","https://openalex.org/W6855012515"],"related_works":["https://openalex.org/W2135678793","https://openalex.org/W2109288169","https://openalex.org/W2157684052","https://openalex.org/W4223449272","https://openalex.org/W2978247079","https://openalex.org/W2166887457","https://openalex.org/W2148708580","https://openalex.org/W3037604406","https://openalex.org/W2140163842","https://openalex.org/W2982252354"],"abstract_inverted_index":{"The":[0,18],"MoleculeExperiment":[1,21],"package":[2],"is":[3,12],"publicly":[4],"available":[5,13],"on":[6,14],"Bioconductor":[7],"at":[8,25],"https://bioconductor.org/packages/release/bioc/html/MoleculeExperiment.html.":[9,26],"Source":[10],"code":[11],"Github":[15],"at:":[16],"https://github.com/SydneyBioX/MoleculeExperiment.":[17],"vignette":[19],"for":[20],"can":[22],"be":[23],"found":[24]},"counts_by_year":[{"year":2026,"cited_by_count":4},{"year":2025,"cited_by_count":4},{"year":2024,"cited_by_count":4},{"year":2023,"cited_by_count":1}],"updated_date":"2026-04-03T22:45:19.894376","created_date":"2023-09-13T00:00:00"}
