{"id":"https://openalex.org/W4391915536","doi":"https://doi.org/10.1093/bioinformatics/btae072","title":"SpatialDDLS: an R package to deconvolute spatial transcriptomics data using neural networks","display_name":"SpatialDDLS: an R package to deconvolute spatial transcriptomics data using neural networks","publication_year":2024,"publication_date":"2024-02-01","ids":{"openalex":"https://openalex.org/W4391915536","doi":"https://doi.org/10.1093/bioinformatics/btae072","pmid":"https://pubmed.ncbi.nlm.nih.gov/38366652"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btae072","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btae072","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/40/2/btae072/56731927/btae072.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/article-pdf/40/2/btae072/56731927/btae072.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5000652850","display_name":"Diego Ma\u00f1anes","orcid":"https://orcid.org/0000-0001-7247-6794"},"institutions":[{"id":"https://openalex.org/I2809107791","display_name":"Spanish National Centre for Cardiovascular Research","ror":"https://ror.org/02qs1a797","country_code":"ES","type":"facility","lineage":["https://openalex.org/I2809107791","https://openalex.org/I4210098440"]}],"countries":["ES"],"is_corresponding":true,"raw_author_name":"Diego Ma\u00f1anes","raw_affiliation_strings":["Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC) , 28029 Madrid, Spain"],"affiliations":[{"raw_affiliation_string":"Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC) , 28029 Madrid, Spain","institution_ids":["https://openalex.org/I2809107791"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5040751958","display_name":"In\u00e9s Rivero-Garc\u00eda","orcid":"https://orcid.org/0000-0002-9428-0992"},"institutions":[{"id":"https://openalex.org/I2809107791","display_name":"Spanish National Centre for Cardiovascular Research","ror":"https://ror.org/02qs1a797","country_code":"ES","type":"facility","lineage":["https://openalex.org/I2809107791","https://openalex.org/I4210098440"]},{"id":"https://openalex.org/I88060688","display_name":"Universidad Polit\u00e9cnica de Madrid","ror":"https://ror.org/03n6nwv02","country_code":"ES","type":"education","lineage":["https://openalex.org/I88060688"]}],"countries":["ES"],"is_corresponding":false,"raw_author_name":"In\u00e9s Rivero-Garc\u00eda","raw_affiliation_strings":["Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC) , 28029 Madrid, Spain","Departamento de Ingenier\u00eda Biom\u00e9dica, ETSI de Telecomunicaciones, Universidad Polit\u00e9cnica de Madrid , 28040 Madrid, Spain"],"affiliations":[{"raw_affiliation_string":"Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC) , 28029 Madrid, Spain","institution_ids":["https://openalex.org/I2809107791"]},{"raw_affiliation_string":"Departamento de Ingenier\u00eda Biom\u00e9dica, ETSI de Telecomunicaciones, Universidad Polit\u00e9cnica de Madrid , 28040 Madrid, Spain","institution_ids":["https://openalex.org/I88060688"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5092110388","display_name":"Carlos Rela\u00f1o\u2010Rup\u00e9rez","orcid":"https://orcid.org/0000-0002-1407-9245"},"institutions":[{"id":"https://openalex.org/I2809107791","display_name":"Spanish National Centre for Cardiovascular Research","ror":"https://ror.org/02qs1a797","country_code":"ES","type":"facility","lineage":["https://openalex.org/I2809107791","https://openalex.org/I4210098440"]}],"countries":["ES"],"is_corresponding":false,"raw_author_name":"Carlos Rela\u00f1o","raw_affiliation_strings":["Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC) , 28029 Madrid, Spain"],"affiliations":[{"raw_affiliation_string":"Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC) , 28029 Madrid, Spain","institution_ids":["https://openalex.org/I2809107791"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5025138239","display_name":"Miguel Torres","orcid":"https://orcid.org/0000-0003-0906-4767"},"institutions":[{"id":"https://openalex.org/I2809107791","display_name":"Spanish National Centre for Cardiovascular Research","ror":"https://ror.org/02qs1a797","country_code":"ES","type":"facility","lineage":["https://openalex.org/I2809107791","https://openalex.org/I4210098440"]}],"countries":["ES"],"is_corresponding":false,"raw_author_name":"Miguel Torres","raw_affiliation_strings":["Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC) , 28029 Madrid, Spain"],"affiliations":[{"raw_affiliation_string":"Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC) , 28029 Madrid, Spain","institution_ids":["https://openalex.org/I2809107791"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5047641235","display_name":"David Sancho","orcid":"https://orcid.org/0000-0003-2890-3984"},"institutions":[{"id":"https://openalex.org/I2809107791","display_name":"Spanish National Centre for Cardiovascular Research","ror":"https://ror.org/02qs1a797","country_code":"ES","type":"facility","lineage":["https://openalex.org/I2809107791","https://openalex.org/I4210098440"]}],"countries":["ES"],"is_corresponding":false,"raw_author_name":"David Sancho","raw_affiliation_strings":["Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC) , 28029 Madrid, Spain"],"affiliations":[{"raw_affiliation_string":"Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC) , 28029 Madrid, Spain","institution_ids":["https://openalex.org/I2809107791"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5008079031","display_name":"Daniel Jim\u00e9nez\u2010Carretero","orcid":"https://orcid.org/0000-0001-7858-1907"},"institutions":[{"id":"https://openalex.org/I2809107791","display_name":"Spanish National Centre for Cardiovascular Research","ror":"https://ror.org/02qs1a797","country_code":"ES","type":"facility","lineage":["https://openalex.org/I2809107791","https://openalex.org/I4210098440"]}],"countries":["ES"],"is_corresponding":false,"raw_author_name":"Daniel Jimenez-Carretero","raw_affiliation_strings":["Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC) , 28029 Madrid, Spain"],"affiliations":[{"raw_affiliation_string":"Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC) , 28029 Madrid, Spain","institution_ids":["https://openalex.org/I2809107791"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5001300536","display_name":"Carlos Torroja","orcid":"https://orcid.org/0000-0001-8914-3400"},"institutions":[{"id":"https://openalex.org/I2809107791","display_name":"Spanish National Centre for Cardiovascular Research","ror":"https://ror.org/02qs1a797","country_code":"ES","type":"facility","lineage":["https://openalex.org/I2809107791","https://openalex.org/I4210098440"]}],"countries":["ES"],"is_corresponding":false,"raw_author_name":"Carlos Torroja","raw_affiliation_strings":["Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC) , 28029 Madrid, Spain"],"affiliations":[{"raw_affiliation_string":"Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC) , 28029 Madrid, Spain","institution_ids":["https://openalex.org/I2809107791"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5014621950","display_name":"F\u00e1tima S\u00e1nchez\u2010Cabo","orcid":"https://orcid.org/0000-0003-1881-1664"},"institutions":[{"id":"https://openalex.org/I2809107791","display_name":"Spanish National Centre for Cardiovascular Research","ror":"https://ror.org/02qs1a797","country_code":"ES","type":"facility","lineage":["https://openalex.org/I2809107791","https://openalex.org/I4210098440"]}],"countries":["ES"],"is_corresponding":false,"raw_author_name":"F\u00e1tima S\u00e1nchez-Cabo","raw_affiliation_strings":["Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC) , 28029 Madrid, Spain"],"affiliations":[{"raw_affiliation_string":"Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC) , 28029 Madrid, Spain","institution_ids":["https://openalex.org/I2809107791"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":8,"corresponding_author_ids":["https://openalex.org/A5000652850"],"corresponding_institution_ids":["https://openalex.org/I2809107791"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":1.8564,"has_fulltext":true,"cited_by_count":8,"citation_normalized_percentile":{"value":0.845275,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":95,"max":100},"biblio":{"volume":"40","issue":"2","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":0.9994999766349792,"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":0.9994999766349792,"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":0.9854999780654907,"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/T11970","display_name":"Molecular Biology Techniques and Applications","score":0.9232000112533569,"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/r-package","display_name":"R package","score":0.691177248954773},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6372618675231934},{"id":"https://openalex.org/keywords/artificial-neural-network","display_name":"Artificial neural network","score":0.5862635374069214},{"id":"https://openalex.org/keywords/software-package","display_name":"Software package","score":0.4772926867008209},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.3935181796550751},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.38577163219451904},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.3569694757461548},{"id":"https://openalex.org/keywords/computational-science","display_name":"Computational science","score":0.16752710938453674},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.10211780667304993}],"concepts":[{"id":"https://openalex.org/C2984074130","wikidata":"https://www.wikidata.org/wiki/Q73539779","display_name":"R package","level":2,"score":0.691177248954773},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6372618675231934},{"id":"https://openalex.org/C50644808","wikidata":"https://www.wikidata.org/wiki/Q192776","display_name":"Artificial neural network","level":2,"score":0.5862635374069214},{"id":"https://openalex.org/C3020440742","wikidata":"https://www.wikidata.org/wiki/Q1176855","display_name":"Software package","level":3,"score":0.4772926867008209},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.3935181796550751},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.38577163219451904},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3569694757461548},{"id":"https://openalex.org/C459310","wikidata":"https://www.wikidata.org/wiki/Q117801","display_name":"Computational science","level":1,"score":0.16752710938453674},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.10211780667304993}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","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":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","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":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","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":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btae072","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btae072","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/40/2/btae072/56731927/btae072.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:38366652","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/38366652","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:10881086","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/10881086","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC10881086/pdf/btae072.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/btae072","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btae072","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/40/2/btae072/56731927/btae072.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/11","score":0.41999998688697815,"display_name":"Sustainable cities and communities"}],"awards":[],"funders":[{"id":"https://openalex.org/F4320322930","display_name":"Ministerio de Ciencia e Innovaci\u00f3n","ror":"https://ror.org/034900433"},{"id":"https://openalex.org/F4320334923","display_name":"Instituto de Salud Carlos III","ror":"https://ror.org/00ca2c886"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4391915536.pdf","grobid_xml":"https://content.openalex.org/works/W4391915536.grobid-xml"},"referenced_works_count":13,"referenced_works":["https://openalex.org/W1973094248","https://openalex.org/W2788357641","https://openalex.org/W2809368942","https://openalex.org/W2885927965","https://openalex.org/W2899224111","https://openalex.org/W2923300855","https://openalex.org/W3004618039","https://openalex.org/W3129476455","https://openalex.org/W4205817967","https://openalex.org/W4224218779","https://openalex.org/W4280533477","https://openalex.org/W4311404503","https://openalex.org/W4328048773"],"related_works":["https://openalex.org/W4389426664","https://openalex.org/W3008797681","https://openalex.org/W2566205467","https://openalex.org/W3012616639","https://openalex.org/W3126000805","https://openalex.org/W3198565742","https://openalex.org/W2010064959","https://openalex.org/W2157390150","https://openalex.org/W2119742499","https://openalex.org/W1985266044"],"abstract_inverted_index":{"The":[0],"R":[1,9],"package":[2,23],"SpatialDDLS":[3],"is":[4],"available":[5],"via":[6],"CRAN-The":[7],"Comprehensive":[8],"Archive":[10],"Network:":[11],"https://CRAN.R-project.org/package=SpatialDDLS.":[12],"A":[13],"detailed":[14],"manual":[15],"of":[16],"the":[17,22],"main":[18],"functionalities":[19],"implemented":[20],"in":[21],"can":[24],"be":[25],"found":[26],"at":[27],"https://diegommcc.github.io/SpatialDDLS.":[28]},"counts_by_year":[{"year":2026,"cited_by_count":3},{"year":2025,"cited_by_count":2},{"year":2024,"cited_by_count":3}],"updated_date":"2026-04-02T15:55:50.835912","created_date":"2025-10-10T00:00:00"}