{"id":"https://openalex.org/W4417095315","doi":"https://doi.org/10.1186/s12859-025-06335-6","title":"GeDi: simplifying gene set distances for enhanced omics interpretation in R/Bioconductor","display_name":"GeDi: simplifying gene set distances for enhanced omics interpretation in R/Bioconductor","publication_year":2025,"publication_date":"2025-12-07","ids":{"openalex":"https://openalex.org/W4417095315","doi":"https://doi.org/10.1186/s12859-025-06335-6","pmid":"https://pubmed.ncbi.nlm.nih.gov/41354776"},"language":"en","primary_location":{"id":"doi:10.1186/s12859-025-06335-6","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-025-06335-6","pdf_url":null,"source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://doi.org/10.1186/s12859-025-06335-6","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5005408698","display_name":"Annekathrin Silvia Nedwed","orcid":"https://orcid.org/0000-0002-2475-4945"},"institutions":[{"id":"https://openalex.org/I197323543","display_name":"Johannes Gutenberg University Mainz","ror":"https://ror.org/023b0x485","country_code":"DE","type":"education","lineage":["https://openalex.org/I197323543"]},{"id":"https://openalex.org/I4210094062","display_name":"University Medical Center of the Johannes Gutenberg University Mainz","ror":"https://ror.org/00q1fsf04","country_code":"DE","type":"healthcare","lineage":["https://openalex.org/I4210094062"]}],"countries":["DE"],"is_corresponding":true,"raw_author_name":"Annekathrin Silvia Nedwed","raw_affiliation_strings":["Institute of Medical Biostatistics, Epidemiology and Informatics (IMBEI), University Medical Center of the Johannes Gutenberg University, Mainz, Germany. anedwed@uni-mainz.de","Institute of Medical Biostatistics, Epidemiology and Informatics (IMBEI), University Medical Center of the Johannes Gutenberg University, Mainz, Germany. annekathrin.nedwed@gmail.com"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute of Medical Biostatistics, Epidemiology and Informatics (IMBEI), University Medical Center of the Johannes Gutenberg University, Mainz, Germany. anedwed@uni-mainz.de","institution_ids":["https://openalex.org/I197323543","https://openalex.org/I4210094062"]},{"raw_affiliation_string":"Institute of Medical Biostatistics, Epidemiology and Informatics (IMBEI), University Medical Center of the Johannes Gutenberg University, Mainz, Germany. annekathrin.nedwed@gmail.com","institution_ids":["https://openalex.org/I197323543","https://openalex.org/I4210094062"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5039591070","display_name":"Arsenij Ustjanzew","orcid":"https://orcid.org/0000-0002-1014-4521"},"institutions":[{"id":"https://openalex.org/I197323543","display_name":"Johannes Gutenberg University Mainz","ror":"https://ror.org/023b0x485","country_code":"DE","type":"education","lineage":["https://openalex.org/I197323543"]},{"id":"https://openalex.org/I4210094062","display_name":"University Medical Center of the Johannes Gutenberg University Mainz","ror":"https://ror.org/00q1fsf04","country_code":"DE","type":"healthcare","lineage":["https://openalex.org/I4210094062"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Arsenij Ustjanzew","raw_affiliation_strings":["Institute of Medical Biostatistics, Epidemiology and Informatics (IMBEI), University Medical Center of the Johannes Gutenberg University, Mainz, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute of Medical Biostatistics, Epidemiology and Informatics (IMBEI), University Medical Center of the Johannes Gutenberg University, Mainz, Germany","institution_ids":["https://openalex.org/I197323543","https://openalex.org/I4210094062"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5094005270","display_name":"Najla Abassi","orcid":"https://orcid.org/0000-0001-8357-0938"},"institutions":[{"id":"https://openalex.org/I197323543","display_name":"Johannes Gutenberg University Mainz","ror":"https://ror.org/023b0x485","country_code":"DE","type":"education","lineage":["https://openalex.org/I197323543"]},{"id":"https://openalex.org/I4210094062","display_name":"University Medical Center of the Johannes Gutenberg University Mainz","ror":"https://ror.org/00q1fsf04","country_code":"DE","type":"healthcare","lineage":["https://openalex.org/I4210094062"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Najla Abassi","raw_affiliation_strings":["Institute of Medical Biostatistics, Epidemiology and Informatics (IMBEI), University Medical Center of the Johannes Gutenberg University, Mainz, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute of Medical Biostatistics, Epidemiology and Informatics (IMBEI), University Medical Center of the Johannes Gutenberg University, Mainz, Germany","institution_ids":["https://openalex.org/I197323543","https://openalex.org/I4210094062"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5102822506","display_name":"Leon Dammer","orcid":"https://orcid.org/0009-0008-4132-7639"},"institutions":[{"id":"https://openalex.org/I197323543","display_name":"Johannes Gutenberg University Mainz","ror":"https://ror.org/023b0x485","country_code":"DE","type":"education","lineage":["https://openalex.org/I197323543"]},{"id":"https://openalex.org/I4210094062","display_name":"University Medical Center of the Johannes Gutenberg University Mainz","ror":"https://ror.org/00q1fsf04","country_code":"DE","type":"healthcare","lineage":["https://openalex.org/I4210094062"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Leon Dammer","raw_affiliation_strings":["Institute of Medical Biostatistics, Epidemiology and Informatics (IMBEI), University Medical Center of the Johannes Gutenberg University, Mainz, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute of Medical Biostatistics, Epidemiology and Informatics (IMBEI), University Medical Center of the Johannes Gutenberg University, Mainz, Germany","institution_ids":["https://openalex.org/I197323543","https://openalex.org/I4210094062"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5001630716","display_name":"Alicia Schulze","orcid":"https://orcid.org/0000-0003-2527-0763"},"institutions":[{"id":"https://openalex.org/I197323543","display_name":"Johannes Gutenberg University Mainz","ror":"https://ror.org/023b0x485","country_code":"DE","type":"education","lineage":["https://openalex.org/I197323543"]},{"id":"https://openalex.org/I4210094062","display_name":"University Medical Center of the Johannes Gutenberg University Mainz","ror":"https://ror.org/00q1fsf04","country_code":"DE","type":"healthcare","lineage":["https://openalex.org/I4210094062"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Alicia Schulze","raw_affiliation_strings":["Institute of Medical Biostatistics, Epidemiology and Informatics (IMBEI), University Medical Center of the Johannes Gutenberg University, Mainz, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute of Medical Biostatistics, Epidemiology and Informatics (IMBEI), University Medical Center of the Johannes Gutenberg University, Mainz, Germany","institution_ids":["https://openalex.org/I197323543","https://openalex.org/I4210094062"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5064264142","display_name":"Sara Salome Helbich","orcid":"https://orcid.org/0000-0003-0479-5448"},"institutions":[{"id":"https://openalex.org/I197323543","display_name":"Johannes Gutenberg University Mainz","ror":"https://ror.org/023b0x485","country_code":"DE","type":"education","lineage":["https://openalex.org/I197323543"]},{"id":"https://openalex.org/I4210094062","display_name":"University Medical Center of the Johannes Gutenberg University Mainz","ror":"https://ror.org/00q1fsf04","country_code":"DE","type":"healthcare","lineage":["https://openalex.org/I4210094062"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Sara Salome Helbich","raw_affiliation_strings":["Institute of Immunology, University Medical Center Mainz, Mainz, Germany","Research Center for Immunotherapy (FZI), Mainz, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute of Immunology, University Medical Center Mainz, Mainz, Germany","institution_ids":["https://openalex.org/I197323543","https://openalex.org/I4210094062"]},{"raw_affiliation_string":"Research Center for Immunotherapy (FZI), Mainz, Germany","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5072787875","display_name":"Michael Delacher","orcid":"https://orcid.org/0000-0002-6716-9156"},"institutions":[{"id":"https://openalex.org/I197323543","display_name":"Johannes Gutenberg University Mainz","ror":"https://ror.org/023b0x485","country_code":"DE","type":"education","lineage":["https://openalex.org/I197323543"]},{"id":"https://openalex.org/I4210094062","display_name":"University Medical Center of the Johannes Gutenberg University Mainz","ror":"https://ror.org/00q1fsf04","country_code":"DE","type":"healthcare","lineage":["https://openalex.org/I4210094062"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Michael Delacher","raw_affiliation_strings":["Institute of Immunology, University Medical Center Mainz, Mainz, Germany","Research Center for Immunotherapy (FZI), Mainz, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute of Immunology, University Medical Center Mainz, Mainz, Germany","institution_ids":["https://openalex.org/I197323543","https://openalex.org/I4210094062"]},{"raw_affiliation_string":"Research Center for Immunotherapy (FZI), Mainz, Germany","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5030831306","display_name":"Konstantin Strauch","orcid":"https://orcid.org/0000-0002-1814-5860"},"institutions":[{"id":"https://openalex.org/I197323543","display_name":"Johannes Gutenberg University Mainz","ror":"https://ror.org/023b0x485","country_code":"DE","type":"education","lineage":["https://openalex.org/I197323543"]},{"id":"https://openalex.org/I4210094062","display_name":"University Medical Center of the Johannes Gutenberg University Mainz","ror":"https://ror.org/00q1fsf04","country_code":"DE","type":"healthcare","lineage":["https://openalex.org/I4210094062"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Konstantin Strauch","raw_affiliation_strings":["Institute of Medical Biostatistics, Epidemiology and Informatics (IMBEI), University Medical Center of the Johannes Gutenberg University, Mainz, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute of Medical Biostatistics, Epidemiology and Informatics (IMBEI), University Medical Center of the Johannes Gutenberg University, Mainz, Germany","institution_ids":["https://openalex.org/I197323543","https://openalex.org/I4210094062"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5087884887","display_name":"F\u00e9d\u00e9rico Marini","orcid":"https://orcid.org/0000-0003-3252-7758"},"institutions":[{"id":"https://openalex.org/I164387090","display_name":"University of Applied Sciences Mainz","ror":"https://ror.org/02re32a17","country_code":"DE","type":"education","lineage":["https://openalex.org/I164387090"]},{"id":"https://openalex.org/I197323543","display_name":"Johannes Gutenberg University Mainz","ror":"https://ror.org/023b0x485","country_code":"DE","type":"education","lineage":["https://openalex.org/I197323543"]},{"id":"https://openalex.org/I4210094062","display_name":"University Medical Center of the Johannes Gutenberg University Mainz","ror":"https://ror.org/00q1fsf04","country_code":"DE","type":"healthcare","lineage":["https://openalex.org/I4210094062"]}],"countries":["DE"],"is_corresponding":true,"raw_author_name":"Federico Marini","raw_affiliation_strings":["Center for Thrombosis and Hemostasis (CTH), Mainz, Germany. marinif@uni-mainz.de","Institute of Medical Biostatistics, Epidemiology and Informatics (IMBEI), University Medical Center of the Johannes Gutenberg University, Mainz, Germany. marinif@uni-mainz.de","Research Center for Immunotherapy (FZI), Mainz, Germany. marinif@uni-mainz.de"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Thrombosis and Hemostasis (CTH), Mainz, Germany. marinif@uni-mainz.de","institution_ids":["https://openalex.org/I197323543","https://openalex.org/I4210094062"]},{"raw_affiliation_string":"Institute of Medical Biostatistics, Epidemiology and Informatics (IMBEI), University Medical Center of the Johannes Gutenberg University, Mainz, Germany. marinif@uni-mainz.de","institution_ids":["https://openalex.org/I197323543","https://openalex.org/I4210094062"]},{"raw_affiliation_string":"Research Center for Immunotherapy (FZI), Mainz, Germany. marinif@uni-mainz.de","institution_ids":["https://openalex.org/I164387090"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5005408698","https://openalex.org/A5087884887"],"corresponding_institution_ids":["https://openalex.org/I164387090","https://openalex.org/I197323543","https://openalex.org/I4210094062"],"apc_list":{"value":2990,"currency":"USD","value_usd":2990},"apc_paid":{"value":2990,"currency":"USD","value_usd":2990},"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.21725635,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"27","issue":"1","first_page":"14","last_page":"14"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9829000234603882,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9829000234603882,"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":0.006500000134110451,"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":0.0035000001080334187,"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":0.7684000134468079},{"id":"https://openalex.org/keywords/context","display_name":"Context (archaeology)","score":0.6643999814987183},{"id":"https://openalex.org/keywords/cluster-analysis","display_name":"Cluster analysis","score":0.6590999960899353},{"id":"https://openalex.org/keywords/set","display_name":"Set (abstract data type)","score":0.5985000133514404},{"id":"https://openalex.org/keywords/biological-network","display_name":"Biological network","score":0.5133000016212463},{"id":"https://openalex.org/keywords/mit-license","display_name":"MIT License","score":0.5016999840736389},{"id":"https://openalex.org/keywords/interpretation","display_name":"Interpretation (philosophy)","score":0.4964999854564667},{"id":"https://openalex.org/keywords/redundancy","display_name":"Redundancy (engineering)","score":0.45980000495910645},{"id":"https://openalex.org/keywords/r-package","display_name":"R package","score":0.44519999623298645}],"concepts":[{"id":"https://openalex.org/C2779694297","wikidata":"https://www.wikidata.org/wiki/Q2888953","display_name":"Bioconductor","level":3,"score":0.7684000134468079},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7041000127792358},{"id":"https://openalex.org/C2779343474","wikidata":"https://www.wikidata.org/wiki/Q3109175","display_name":"Context (archaeology)","level":2,"score":0.6643999814987183},{"id":"https://openalex.org/C73555534","wikidata":"https://www.wikidata.org/wiki/Q622825","display_name":"Cluster analysis","level":2,"score":0.6590999960899353},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.5985000133514404},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.5450000166893005},{"id":"https://openalex.org/C28225019","wikidata":"https://www.wikidata.org/wiki/Q4915005","display_name":"Biological network","level":2,"score":0.5133000016212463},{"id":"https://openalex.org/C174183944","wikidata":"https://www.wikidata.org/wiki/Q334661","display_name":"MIT License","level":3,"score":0.5016999840736389},{"id":"https://openalex.org/C527412718","wikidata":"https://www.wikidata.org/wiki/Q855395","display_name":"Interpretation (philosophy)","level":2,"score":0.4964999854564667},{"id":"https://openalex.org/C152124472","wikidata":"https://www.wikidata.org/wiki/Q1204361","display_name":"Redundancy (engineering)","level":2,"score":0.45980000495910645},{"id":"https://openalex.org/C2984074130","wikidata":"https://www.wikidata.org/wiki/Q73539779","display_name":"R package","level":2,"score":0.44519999623298645},{"id":"https://openalex.org/C201797286","wikidata":"https://www.wikidata.org/wiki/Q4914986","display_name":"Biological data","level":2,"score":0.4219000041484833},{"id":"https://openalex.org/C67339327","wikidata":"https://www.wikidata.org/wiki/Q1502576","display_name":"Gene regulatory network","level":4,"score":0.4047999978065491},{"id":"https://openalex.org/C72634772","wikidata":"https://www.wikidata.org/wiki/Q386824","display_name":"Data integration","level":2,"score":0.3287999927997589},{"id":"https://openalex.org/C136197465","wikidata":"https://www.wikidata.org/wiki/Q1729295","display_name":"Variety (cybernetics)","level":2,"score":0.3165999948978424},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3165999948978424},{"id":"https://openalex.org/C2908923196","wikidata":"https://www.wikidata.org/wiki/Q5205742","display_name":"Gene Annotation","level":4,"score":0.31290000677108765},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.30880001187324524},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.30640000104904175},{"id":"https://openalex.org/C187191949","wikidata":"https://www.wikidata.org/wiki/Q1138496","display_name":"Profiling (computer programming)","level":2,"score":0.2992999851703644},{"id":"https://openalex.org/C168167062","wikidata":"https://www.wikidata.org/wiki/Q1117970","display_name":"Component (thermodynamics)","level":2,"score":0.2987000048160553},{"id":"https://openalex.org/C2780801425","wikidata":"https://www.wikidata.org/wiki/Q5164392","display_name":"Construct (python library)","level":2,"score":0.296999990940094},{"id":"https://openalex.org/C79581498","wikidata":"https://www.wikidata.org/wiki/Q1367530","display_name":"Suite","level":2,"score":0.2946999967098236},{"id":"https://openalex.org/C58489278","wikidata":"https://www.wikidata.org/wiki/Q1172284","display_name":"Data set","level":2,"score":0.2842999994754791},{"id":"https://openalex.org/C2781162219","wikidata":"https://www.wikidata.org/wiki/Q26250693","display_name":"Replicate","level":2,"score":0.2816999852657318},{"id":"https://openalex.org/C12590798","wikidata":"https://www.wikidata.org/wiki/Q3933199","display_name":"Replication (statistics)","level":2,"score":0.2808000147342682},{"id":"https://openalex.org/C32946077","wikidata":"https://www.wikidata.org/wiki/Q618079","display_name":"Network analysis","level":2,"score":0.2720000147819519},{"id":"https://openalex.org/C95371953","wikidata":"https://www.wikidata.org/wiki/Q591745","display_name":"DNA microarray","level":4,"score":0.27079999446868896},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.26840001344680786},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.26429998874664307},{"id":"https://openalex.org/C189206191","wikidata":"https://www.wikidata.org/wiki/Q222046","display_name":"Genomics","level":4,"score":0.25780001282691956},{"id":"https://openalex.org/C173801870","wikidata":"https://www.wikidata.org/wiki/Q201413","display_name":"Heuristic","level":2,"score":0.25429999828338623}],"mesh":[{"descriptor_ui":"D000098430","descriptor_name":"Clustering Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","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":"D019295","descriptor_name":"Computational Biology","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":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true}],"locations_count":4,"locations":[{"id":"doi:10.1186/s12859-025-06335-6","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-025-06335-6","pdf_url":null,"source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},{"id":"pmid:41354776","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/41354776","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":"BMC bioinformatics","raw_type":"Journal Article"},{"id":"pmh:oai:doaj.org/article:6f79f71100084ec9960090d2cbb29f1b","is_oa":true,"landing_page_url":"https://doaj.org/article/6f79f71100084ec9960090d2cbb29f1b","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics, Vol 27, Iss 1, Pp 1-13 (2025)","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:12809992","is_oa":true,"landing_page_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC12809992/","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"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":"BMC Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/s12859-025-06335-6","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-025-06335-6","pdf_url":null,"source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320336167","display_name":"Universit\u00e4tsmedizin der Johannes Gutenberg-Universit\u00e4t Mainz","ror":"https://ror.org/00q1fsf04"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":43,"referenced_works":["https://openalex.org/W1973094248","https://openalex.org/W2033403400","https://openalex.org/W2053154970","https://openalex.org/W2086320398","https://openalex.org/W2097553067","https://openalex.org/W2097795961","https://openalex.org/W2097948046","https://openalex.org/W2100761975","https://openalex.org/W2100980426","https://openalex.org/W2103017472","https://openalex.org/W2120024428","https://openalex.org/W2123402141","https://openalex.org/W2124166542","https://openalex.org/W2130410032","https://openalex.org/W2131681506","https://openalex.org/W2133465414","https://openalex.org/W2158217645","https://openalex.org/W2214074259","https://openalex.org/W2345356016","https://openalex.org/W2898389114","https://openalex.org/W2898598946","https://openalex.org/W2906480617","https://openalex.org/W2947925171","https://openalex.org/W2950595506","https://openalex.org/W2984996233","https://openalex.org/W2989807288","https://openalex.org/W3000221858","https://openalex.org/W3004747635","https://openalex.org/W3025060722","https://openalex.org/W3038655749","https://openalex.org/W3092495933","https://openalex.org/W3153543576","https://openalex.org/W4214879506","https://openalex.org/W4220684489","https://openalex.org/W4224792601","https://openalex.org/W4225463239","https://openalex.org/W4233698560","https://openalex.org/W4306353191","https://openalex.org/W4307425304","https://openalex.org/W4372332501","https://openalex.org/W4387521577","https://openalex.org/W4392168151","https://openalex.org/W4412006463"],"related_works":[],"abstract_inverted_index":{"BACKGROUND:":[0],"Functional":[1],"enrichment":[2,86,174],"analysis":[3,12],"is":[4,64,155,199,217],"a":[5,16,97,128,133,159,184,214],"standard":[6],"component":[7],"in":[8,202],"many":[9],"omics":[10],"data":[11],"workflows,":[13],"supported":[14],"by":[15,67,137,176],"variety":[17],"of":[18,41,84,99,119,127,173],"methods":[19,30],"and":[20,26,38,46,80,104,111,143,151,154,162,179,195,213],"algorithms.":[21],"However,":[22],"despite":[23],"their":[24,144],"utility":[25],"wide":[27],"application,":[28],"these":[29],"often":[31,65],"return":[32],"the":[33,82,117,125,203,207,220],"results":[34,175],"as":[35,157],"an":[36,74,163],"extensive":[37],"redundant":[39],"list":[40],"gene":[42,90,100],"sets,":[43],"impeding":[44],"interpretation":[45,83,172],"hypothesis":[47],"generation.":[48],"Moreover,":[49],"network":[50,180],"based":[51],"information":[52],"can":[53],"provide":[54],"additional":[55],"biological":[56,135,190],"context":[57,136],"through":[58,124],"functional":[59,85,139],"interaction":[60,121],"data,":[61,123],"yet":[62],"this":[63],"overlooked":[66],"existing":[68],"tools.":[69],"RESULTS:":[70],"We":[71],"developed":[72],"GeDi,":[73],"R/Bioconductor":[75],"package":[76,147],"designed":[77],"to":[78,108,183],"streamline":[79],"standardize":[81],"results.":[87],"GeDi":[88,114,168,198],"aggregates":[89],"sets":[91],"into":[92],"biologically":[93],"meaningful":[94],"clusters":[95],"using":[96],"suite":[98],"set":[101],"distance":[102,130],"metrics":[103],"clustering":[105,178],"algorithms,":[106],"aimed":[107],"reduce":[109],"redundancy":[110],"improve":[112],"clarity.":[113],"also":[115],"enables":[116],"integration":[118],"protein\u2013protein":[120],"(PPI)":[122],"implementation":[126],"weighted":[129],"metric,":[131],"providing":[132],"richer":[134],"capturing":[138],"connectivity":[140],"between":[141],"pathways":[142],"components.":[145],"The":[146],"offers":[148],"visualizations,":[149],"aggregation,":[150],"automated":[152],"reporting,":[153],"available":[156,201],"both":[158,193],"stand-alone":[160],"R-package":[161],"interactive":[164],"Shiny":[165,221],"application.":[166],"CONCLUSION:":[167],"facilitates":[169],"clearer,":[170],"faster":[171],"combining":[177],"context.":[181],"Application":[182],"public":[185],"RNA-seq":[186],"dataset":[187],"revealed":[188],"coherent":[189],"themes,":[191],"supporting":[192],"experimental":[194],"computational":[196],"research.":[197],"freely":[200],"Bioconductor":[204],"project":[205],"under":[206],"MIT":[208],"license":[209],"(":[210,223],"https://bioconductor.org/packages/GeDi":[211],"),":[212],"demo":[215],"instance":[216],"accessible":[218],"on":[219],"server":[222],"http://shiny.imbei.uni-mainz.de:3838/GeDi":[224],").":[225]},"counts_by_year":[],"updated_date":"2026-08-21T09:56:20.448147","created_date":"2025-12-07T00:00:00"}