{"id":"https://openalex.org/W4412347897","doi":"https://doi.org/10.1093/bioinformatics/btaf401","title":"shinyDSP: a Shiny application for interactive analysis and visualization of NanoString GeoMx Whole Transcriptome Atlas data","display_name":"shinyDSP: a Shiny application for interactive analysis and visualization of NanoString GeoMx Whole Transcriptome Atlas data","publication_year":2025,"publication_date":"2025-07-01","ids":{"openalex":"https://openalex.org/W4412347897","doi":"https://doi.org/10.1093/bioinformatics/btaf401","pmid":"https://pubmed.ncbi.nlm.nih.gov/40644626"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btaf401","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaf401","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btaf401/63730392/btaf401.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/btaf401/63730392/btaf401.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5010482887","display_name":"Seung J. Kim","orcid":"https://orcid.org/0000-0001-5263-0758"},"institutions":[{"id":"https://openalex.org/I4210117296","display_name":"Institute of Health Visiting","ror":"https://ror.org/01p894e02","country_code":"GB","type":"healthcare","lineage":["https://openalex.org/I4210117296"]},{"id":"https://openalex.org/I4210153355","display_name":"Interstitial Cystitis Association","ror":"https://ror.org/04hnnkw05","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I4210153355"]}],"countries":["GB","US"],"is_corresponding":true,"raw_author_name":"Seung J Kim","raw_affiliation_strings":["Interstitial Lung Disease Lab, London Health Sciences Research Institute , London, ON, N6A 5W9,","London Health Sciences Research Institute Interstitial Lung Disease Lab, , London, ON"],"affiliations":[{"raw_affiliation_string":"Interstitial Lung Disease Lab, London Health Sciences Research Institute , London, ON, N6A 5W9,","institution_ids":["https://openalex.org/I4210153355"]},{"raw_affiliation_string":"London Health Sciences Research Institute Interstitial Lung Disease Lab, , London, ON","institution_ids":["https://openalex.org/I4210117296"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Matthew J Cecchini","orcid":null},"institutions":[{"id":"https://openalex.org/I125749732","display_name":"Western University","ror":"https://ror.org/02grkyz14","country_code":"CA","type":"education","lineage":["https://openalex.org/I125749732"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Matthew J Cecchini","raw_affiliation_strings":["Department of Pathology and Laboratory Medicine, Schulich School of Medicine and Dentistry, Western University , London, ON, N6A 5C1,","Western University Department of Medicine, Schulich School of Medicine and Dentistry, , London, ON"],"affiliations":[{"raw_affiliation_string":"Department of Pathology and Laboratory Medicine, Schulich School of Medicine and Dentistry, Western University , London, ON, N6A 5C1,","institution_ids":["https://openalex.org/I125749732"]},{"raw_affiliation_string":"Western University Department of Medicine, Schulich School of Medicine and Dentistry, , London, ON","institution_ids":["https://openalex.org/I125749732"]}]},{"author_position":"last","author":{"id":null,"display_name":"Marco Mura","orcid":null},"institutions":[{"id":"https://openalex.org/I125749732","display_name":"Western University","ror":"https://ror.org/02grkyz14","country_code":"CA","type":"education","lineage":["https://openalex.org/I125749732"]},{"id":"https://openalex.org/I4210153355","display_name":"Interstitial Cystitis Association","ror":"https://ror.org/04hnnkw05","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I4210153355"]}],"countries":["CA","US"],"is_corresponding":false,"raw_author_name":"Marco Mura","raw_affiliation_strings":["Department of Medicine, Schulich School of Medicine and Dentistry, Western University , London, ON, N6A 5W9,","Interstitial Lung Disease Lab, London Health Sciences Research Institute , London, ON, N6A 5W9,"],"affiliations":[{"raw_affiliation_string":"Department of Medicine, Schulich School of Medicine and Dentistry, Western University , London, ON, N6A 5W9,","institution_ids":["https://openalex.org/I125749732"]},{"raw_affiliation_string":"Interstitial Lung Disease Lab, London Health Sciences Research Institute , London, ON, N6A 5W9,","institution_ids":["https://openalex.org/I4210153355"]}]}],"institutions":[],"countries_distinct_count":3,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5010482887"],"corresponding_institution_ids":["https://openalex.org/I4210117296","https://openalex.org/I4210153355"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":0.0,"has_fulltext":true,"cited_by_count":0,"citation_normalized_percentile":{"value":0.14816291,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"41","issue":"7","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11970","display_name":"Molecular Biology Techniques and Applications","score":0.998199999332428,"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/T11970","display_name":"Molecular Biology Techniques and Applications","score":0.998199999332428,"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/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.9896000027656555,"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":0.9557999968528748,"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":0.9410892128944397},{"id":"https://openalex.org/keywords/mit-license","display_name":"MIT License","score":0.765544056892395},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7553038001060486},{"id":"https://openalex.org/keywords/personalization","display_name":"Personalization","score":0.6373065710067749},{"id":"https://openalex.org/keywords/normalization","display_name":"Normalization (sociology)","score":0.6264485120773315},{"id":"https://openalex.org/keywords/visualization","display_name":"Visualization","score":0.5622732043266296},{"id":"https://openalex.org/keywords/profiling","display_name":"Profiling (computer programming)","score":0.5599220395088196},{"id":"https://openalex.org/keywords/open-source","display_name":"Open source","score":0.41817429661750793},{"id":"https://openalex.org/keywords/transcriptome","display_name":"Transcriptome","score":0.4166160821914673},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.40848666429519653},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.3528648614883423},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.3294193148612976},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.31507065892219543},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.15462613105773926},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.15233096480369568},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.09035012125968933},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.08744695782661438}],"concepts":[{"id":"https://openalex.org/C2779694297","wikidata":"https://www.wikidata.org/wiki/Q2888953","display_name":"Bioconductor","level":3,"score":0.9410892128944397},{"id":"https://openalex.org/C174183944","wikidata":"https://www.wikidata.org/wiki/Q334661","display_name":"MIT License","level":3,"score":0.765544056892395},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7553038001060486},{"id":"https://openalex.org/C183003079","wikidata":"https://www.wikidata.org/wiki/Q1000371","display_name":"Personalization","level":2,"score":0.6373065710067749},{"id":"https://openalex.org/C136886441","wikidata":"https://www.wikidata.org/wiki/Q926129","display_name":"Normalization (sociology)","level":2,"score":0.6264485120773315},{"id":"https://openalex.org/C36464697","wikidata":"https://www.wikidata.org/wiki/Q451553","display_name":"Visualization","level":2,"score":0.5622732043266296},{"id":"https://openalex.org/C187191949","wikidata":"https://www.wikidata.org/wiki/Q1138496","display_name":"Profiling (computer programming)","level":2,"score":0.5599220395088196},{"id":"https://openalex.org/C3018397939","wikidata":"https://www.wikidata.org/wiki/Q3644502","display_name":"Open source","level":3,"score":0.41817429661750793},{"id":"https://openalex.org/C162317418","wikidata":"https://www.wikidata.org/wiki/Q252857","display_name":"Transcriptome","level":4,"score":0.4166160821914673},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.40848666429519653},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.3528648614883423},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.3294193148612976},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.31507065892219543},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.15462613105773926},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.15233096480369568},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.09035012125968933},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.08744695782661438},{"id":"https://openalex.org/C144024400","wikidata":"https://www.wikidata.org/wiki/Q21201","display_name":"Sociology","level":0,"score":0.0},{"id":"https://openalex.org/C19165224","wikidata":"https://www.wikidata.org/wiki/Q23404","display_name":"Anthropology","level":1,"score":0.0},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","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":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":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051379","descriptor_name":"Mice","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}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btaf401","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaf401","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btaf401/63730392/btaf401.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:40644626","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/40644626","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:12311272","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/12311272","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btaf401","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaf401","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btaf401/63730392/btaf401.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":[{"score":0.5199999809265137,"display_name":"Industry, innovation and infrastructure","id":"https://metadata.un.org/sdg/9"}],"awards":[{"id":"https://openalex.org/G4679650479","display_name":null,"funder_award_id":"INN19-006","funder_id":"https://openalex.org/F4320312153","funder_display_name":"Academic Medical Organization of Southwestern Ontario"},{"id":"https://openalex.org/G5867779975","display_name":null,"funder_award_id":"23-02","funder_id":"https://openalex.org/F4320319981","funder_display_name":"Physicians' Services Incorporated Foundation"}],"funders":[{"id":"https://openalex.org/F4320312153","display_name":"Academic Medical Organization of Southwestern Ontario","ror":null},{"id":"https://openalex.org/F4320319981","display_name":"Physicians' Services Incorporated Foundation","ror":"https://ror.org/0385yzn06"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4412347897.pdf","grobid_xml":"https://content.openalex.org/works/W4412347897.grobid-xml"},"referenced_works_count":13,"referenced_works":["https://openalex.org/W2135061646","https://openalex.org/W2137526110","https://openalex.org/W2146512944","https://openalex.org/W2946046628","https://openalex.org/W2969514086","https://openalex.org/W3023701177","https://openalex.org/W3049216986","https://openalex.org/W4310167913","https://openalex.org/W4388615764","https://openalex.org/W4400982971","https://openalex.org/W6634743113","https://openalex.org/W6724262999","https://openalex.org/W6802152031"],"related_works":["https://openalex.org/W2489977678","https://openalex.org/W2151651283","https://openalex.org/W2098339479","https://openalex.org/W2152150816","https://openalex.org/W3117086625","https://openalex.org/W2792006949","https://openalex.org/W3118004748","https://openalex.org/W2164765928","https://openalex.org/W2170830174","https://openalex.org/W4391342995"],"abstract_inverted_index":{"The":[0],"release":[1],"and":[2,16],"development":[3],"versions":[4],"of":[5],"shinyDSP":[6],"are":[7],"available":[8],"on":[9],"Bioconductor":[10],"under":[11],"the":[12],"MIT":[13],"license":[14],"(https://www.bioconductor.org/packages/release/bioc/html/shinyDSP.html)":[15],"Github":[17],"(https://github.com/kimsjune/shinyDSP).":[18]},"counts_by_year":[],"updated_date":"2026-04-10T15:06:20.359241","created_date":"2025-10-10T00:00:00"}