{"id":"https://openalex.org/W4392472605","doi":"https://doi.org/10.1186/s12859-024-05721-w","title":"tRigon: an R package and Shiny App for integrative (path-)omics data analysis","display_name":"tRigon: an R package and Shiny App for integrative (path-)omics data analysis","publication_year":2024,"publication_date":"2024-03-05","ids":{"openalex":"https://openalex.org/W4392472605","doi":"https://doi.org/10.1186/s12859-024-05721-w","pmid":"https://pubmed.ncbi.nlm.nih.gov/38443821"},"language":"en","primary_location":{"id":"doi:10.1186/s12859-024-05721-w","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-024-05721-w","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-024-05721-w","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://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-024-05721-w","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5079377696","display_name":"David L. H\u00f6lscher","orcid":"https://orcid.org/0000-0001-8595-0694"},"institutions":[{"id":"https://openalex.org/I887968799","display_name":"RWTH Aachen University","ror":"https://ror.org/04xfq0f34","country_code":"DE","type":"education","lineage":["https://openalex.org/I887968799"]}],"countries":["DE"],"is_corresponding":true,"raw_author_name":"David L. H\u00f6lscher","raw_affiliation_strings":["Department of Nephrology and Immunology, RWTH Aachen University Clinic, Aachen, Germany","Institute of Pathology, RWTH Aachen University Clinic, Aachen, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Nephrology and Immunology, RWTH Aachen University Clinic, Aachen, Germany","institution_ids":["https://openalex.org/I887968799"]},{"raw_affiliation_string":"Institute of Pathology, RWTH Aachen University Clinic, Aachen, Germany","institution_ids":["https://openalex.org/I887968799"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5093528837","display_name":"Micha\u00ebl Goedertier","orcid":null},"institutions":[{"id":"https://openalex.org/I887968799","display_name":"RWTH Aachen University","ror":"https://ror.org/04xfq0f34","country_code":"DE","type":"education","lineage":["https://openalex.org/I887968799"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Michael Goedertier","raw_affiliation_strings":["Institute for Computational Genomics, RWTH Aachen University Clinic, Aachen, Germany","Institute of Pathology, RWTH Aachen University Clinic, Aachen, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute for Computational Genomics, RWTH Aachen University Clinic, Aachen, Germany","institution_ids":["https://openalex.org/I887968799"]},{"raw_affiliation_string":"Institute of Pathology, RWTH Aachen University Clinic, Aachen, Germany","institution_ids":["https://openalex.org/I887968799"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5068465621","display_name":"Barbara M. Klinkhammer","orcid":"https://orcid.org/0000-0002-1566-7129"},"institutions":[{"id":"https://openalex.org/I887968799","display_name":"RWTH Aachen University","ror":"https://ror.org/04xfq0f34","country_code":"DE","type":"education","lineage":["https://openalex.org/I887968799"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Barbara M. Klinkhammer","raw_affiliation_strings":["Institute of Pathology, RWTH Aachen University Clinic, Aachen, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute of Pathology, RWTH Aachen University Clinic, Aachen, Germany","institution_ids":["https://openalex.org/I887968799"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5054440690","display_name":"Patrick Droste","orcid":"https://orcid.org/0000-0001-9809-695X"},"institutions":[{"id":"https://openalex.org/I887968799","display_name":"RWTH Aachen University","ror":"https://ror.org/04xfq0f34","country_code":"DE","type":"education","lineage":["https://openalex.org/I887968799"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Patrick Droste","raw_affiliation_strings":["Department of Nephrology and Immunology, RWTH Aachen University Clinic, Aachen, Germany","Institute of Pathology, RWTH Aachen University Clinic, Aachen, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Nephrology and Immunology, RWTH Aachen University Clinic, Aachen, Germany","institution_ids":["https://openalex.org/I887968799"]},{"raw_affiliation_string":"Institute of Pathology, RWTH Aachen University Clinic, Aachen, Germany","institution_ids":["https://openalex.org/I887968799"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5057250270","display_name":"Ivan G. Costa","orcid":"https://orcid.org/0000-0003-2890-8697"},"institutions":[{"id":"https://openalex.org/I887968799","display_name":"RWTH Aachen University","ror":"https://ror.org/04xfq0f34","country_code":"DE","type":"education","lineage":["https://openalex.org/I887968799"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Ivan G. Costa","raw_affiliation_strings":["Institute for Computational Genomics, RWTH Aachen University Clinic, Aachen, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute for Computational Genomics, RWTH Aachen University Clinic, Aachen, Germany","institution_ids":["https://openalex.org/I887968799"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5049305761","display_name":"Peter Boor","orcid":"https://orcid.org/0000-0001-9921-4284"},"institutions":[{"id":"https://openalex.org/I887968799","display_name":"RWTH Aachen University","ror":"https://ror.org/04xfq0f34","country_code":"DE","type":"education","lineage":["https://openalex.org/I887968799"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Peter Boor","raw_affiliation_strings":["Department of Nephrology and Immunology, RWTH Aachen University Clinic, Aachen, Germany","Institute of Pathology, RWTH Aachen University Clinic, Aachen, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Nephrology and Immunology, RWTH Aachen University Clinic, Aachen, Germany","institution_ids":["https://openalex.org/I887968799"]},{"raw_affiliation_string":"Institute of Pathology, RWTH Aachen University Clinic, Aachen, Germany","institution_ids":["https://openalex.org/I887968799"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5082196815","display_name":"Roman D. B\u00fclow","orcid":"https://orcid.org/0000-0002-8527-7353"},"institutions":[{"id":"https://openalex.org/I887968799","display_name":"RWTH Aachen University","ror":"https://ror.org/04xfq0f34","country_code":"DE","type":"education","lineage":["https://openalex.org/I887968799"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Roman D. B\u00fclow","raw_affiliation_strings":["Institute of Pathology, RWTH Aachen University Clinic, Aachen, Germany. rbuelow@ukaachen.de","Institute of Pathology, RWTH Aachen University Clinic, Aachen, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute of Pathology, RWTH Aachen University Clinic, Aachen, Germany. rbuelow@ukaachen.de","institution_ids":["https://openalex.org/I887968799"]},{"raw_affiliation_string":"Institute of Pathology, RWTH Aachen University Clinic, Aachen, Germany","institution_ids":["https://openalex.org/I887968799"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":7,"corresponding_author_ids":["https://openalex.org/A5079377696"],"corresponding_institution_ids":["https://openalex.org/I887968799"],"apc_list":{"value":1690,"currency":"GBP","value_usd":2072},"apc_paid":{"value":1690,"currency":"GBP","value_usd":2072},"fwci":1.2588,"has_fulltext":true,"cited_by_count":4,"citation_normalized_percentile":{"value":0.81744593,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":99},"biblio":{"volume":"25","issue":"1","first_page":"98","last_page":"98"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10862","display_name":"AI in cancer detection","score":0.1688999980688095,"subfield":{"id":"https://openalex.org/subfields/1702","display_name":"Artificial Intelligence"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},"topics":[{"id":"https://openalex.org/T10862","display_name":"AI in cancer detection","score":0.1688999980688095,"subfield":{"id":"https://openalex.org/subfields/1702","display_name":"Artificial Intelligence"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T12859","display_name":"Cell Image Analysis Techniques","score":0.12349999696016312,"subfield":{"id":"https://openalex.org/subfields/1304","display_name":"Biophysics"},"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":0.09920000284910202,"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/computer-science","display_name":"Computer science","score":0.5694633722305298}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5694633722305298}],"mesh":[{"descriptor_ui":"D000078332","descriptor_name":"Data Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000078332","descriptor_name":"Data Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000078332","descriptor_name":"Data Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000078332","descriptor_name":"Data Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D063731","descriptor_name":"Mobile Applications","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D063731","descriptor_name":"Mobile Applications","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D063731","descriptor_name":"Mobile Applications","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D063731","descriptor_name":"Mobile Applications","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":4,"locations":[{"id":"doi:10.1186/s12859-024-05721-w","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-024-05721-w","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-024-05721-w","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:38443821","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/38443821","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":null},{"id":"pmh:oai:pubmedcentral.nih.gov:10916305","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/10916305","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC10916305/pdf/12859_2024_Article_5721.pdf","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"},{"id":"pmh:oai:doaj.org/article:b0d0aa69d8504016b2e20a8120906e4d","is_oa":false,"landing_page_url":"https://doaj.org/article/b0d0aa69d8504016b2e20a8120906e4d","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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics, Vol 25, Iss 1, Pp 1-11 (2024)","raw_type":"article"}],"best_oa_location":{"id":"doi:10.1186/s12859-024-05721-w","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-024-05721-w","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-024-05721-w","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":[{"id":"https://openalex.org/G1569319872","display_name":null,"funder_award_id":"ZMVI1-2520DAT111","funder_id":"https://openalex.org/F4320321721","funder_display_name":"Bundesministerium f\u00fcr Gesundheit"},{"id":"https://openalex.org/G1665756980","display_name":null,"funder_award_id":"454024652","funder_id":"https://openalex.org/F4320320879","funder_display_name":"Deutsche Forschungsgemeinschaft"},{"id":"https://openalex.org/G2449451988","display_name":null,"funder_award_id":"01GM1901A","funder_id":"https://openalex.org/F4320321114","funder_display_name":"Bundesministerium f\u00fcr Bildung und Forschung"},{"id":"https://openalex.org/G2669879858","display_name":null,"funder_award_id":"01VSF21048","funder_id":"https://openalex.org/F4320321114","funder_display_name":"Bundesministerium f\u00fcr Bildung und Forschung"},{"id":"https://openalex.org/G2820917408","display_name":null,"funder_award_id":"01VSF21048","funder_id":"https://openalex.org/F4320328691","funder_display_name":"Gemeinsame Bundesausschuss"},{"id":"https://openalex.org/G3703647185","display_name":null,"funder_award_id":"101001791","funder_id":"https://openalex.org/F4320334678","funder_display_name":"European Research Council"},{"id":"https://openalex.org/G5041476893","display_name":null,"funder_award_id":"01MK2002A","funder_id":"https://openalex.org/F4320323803","funder_display_name":"Bundesministerium f\u00fcr Wirtschaft und Energie"},{"id":"https://openalex.org/G7177034010","display_name":null,"funder_award_id":"STOP-FSGS-01GM1901A","funder_id":"https://openalex.org/F4320321114","funder_display_name":"Bundesministerium f\u00fcr Bildung und Forschung"},{"id":"https://openalex.org/G8315546971","display_name":null,"funder_award_id":"322900939","funder_id":"https://openalex.org/F4320320879","funder_display_name":"Deutsche Forschungsgemeinschaft"}],"funders":[{"id":"https://openalex.org/F4320320879","display_name":"Deutsche Forschungsgemeinschaft","ror":"https://ror.org/018mejw64"},{"id":"https://openalex.org/F4320321114","display_name":"Bundesministerium f\u00fcr Bildung und Forschung","ror":"https://ror.org/04pz7b180"},{"id":"https://openalex.org/F4320321721","display_name":"Bundesministerium f\u00fcr Gesundheit","ror":"https://ror.org/05vp4ka74"},{"id":"https://openalex.org/F4320323803","display_name":"Bundesministerium f\u00fcr Wirtschaft und Energie","ror":"https://ror.org/02vgg2808"},{"id":"https://openalex.org/F4320324232","display_name":"RWTH Aachen University","ror":"https://ror.org/04xfq0f34"},{"id":"https://openalex.org/F4320328691","display_name":"Gemeinsame Bundesausschuss","ror":"https://ror.org/008c2qm47"},{"id":"https://openalex.org/F4320334678","display_name":"European Research Council","ror":"https://ror.org/0472cxd90"}],"has_content":{"pdf":true,"grobid_xml":false},"content_urls":{"pdf":"https://content.openalex.org/works/W4392472605.pdf"},"referenced_works_count":31,"referenced_works":["https://openalex.org/W1551385575","https://openalex.org/W2154813452","https://openalex.org/W2765774350","https://openalex.org/W2914060790","https://openalex.org/W2922020904","https://openalex.org/W2943370629","https://openalex.org/W2964611302","https://openalex.org/W2964756323","https://openalex.org/W2980133212","https://openalex.org/W2999091210","https://openalex.org/W3008257790","https://openalex.org/W3044996171","https://openalex.org/W3080446999","https://openalex.org/W3095093830","https://openalex.org/W3099559583","https://openalex.org/W3131249490","https://openalex.org/W3132601888","https://openalex.org/W3134520547","https://openalex.org/W3154045578","https://openalex.org/W3160261825","https://openalex.org/W3212504472","https://openalex.org/W3213821111","https://openalex.org/W4205876996","https://openalex.org/W4224879967","https://openalex.org/W4225744402","https://openalex.org/W4285679076","https://openalex.org/W4296941367","https://openalex.org/W4318340562","https://openalex.org/W4362602099","https://openalex.org/W4385637627","https://openalex.org/W4389058230"],"related_works":["https://openalex.org/W4391375266","https://openalex.org/W2748952813","https://openalex.org/W2390279801","https://openalex.org/W2358668433","https://openalex.org/W2376932109","https://openalex.org/W2001405890","https://openalex.org/W2382290278","https://openalex.org/W4391913857","https://openalex.org/W2350741829","https://openalex.org/W2530322880"],"abstract_inverted_index":{"BACKGROUND:":[0],"Pathomics":[1],"facilitates":[2],"automated,":[3],"reproducible":[4,67],"and":[5,9,26,32,42,66,98,118,132,138,161],"precise":[6],"histopathology":[7],"analysis":[8,35,41],"morphological":[10],"phenotyping.":[11],"Similar":[12],"to":[13,154],"molecular":[14],"omics,":[15],"pathomics":[16,39,68,160],"datasets":[17,134,163],"are":[18],"high-dimensional,":[19],"but":[20],"also":[21],"face":[22],"large":[23,133],"outlier":[24],"variability":[25],"inherent":[27],"data":[28,34,40,58],"missingness,":[29],"making":[30],"quick":[31],"comprehensible":[33],"challenging.":[36],"To":[37],"facilitate":[38],"interpretation":[43],"as":[44,46],"well":[45],"support":[47],"a":[48,60,136,168],"broad":[49,143],"implementation":[50],"we":[51],"developed":[52],"tRigon":[53,71,92,148],"(Toolbox":[54],"foR":[55],"InteGrative":[56],"(path-)Omics":[57],"aNalysis),":[59],"Shiny":[61],"application":[62,100,114],"for":[63],"fast,":[64],"comprehensive":[65],"analysis.":[69],"RESULTS:":[70],"is":[72,115],"available":[73,85],"via":[74,108],"the":[75,105,109,113],"CRAN":[76],"repository":[77],"(":[78,88],"https://cran.r-project.org/web/packages/tRigon":[79],")":[80],"with":[81],"its":[82,99],"source":[83],"code":[84],"on":[86,164],"GitLab":[87],"https://git-ce.rwth-aachen.de/labooratory-ai/trigon":[89],").":[90],"The":[91],"package":[93],"can":[94,101,119],"be":[95,102,120],"installed":[96],"locally":[97],"executed":[103],"from":[104],"R":[106],"console":[107],"command":[110],"'tRigon::run_tRigon()'.":[111],"Alternatively,":[112],"hosted":[116],"online":[117],"accessed":[121],"at":[122],"https://labooratory.shinyapps.io/tRigon":[123],".":[124],"We":[125],"show":[126],"fast":[127],"computation":[128],"of":[129,145,159,170],"small,":[130],"medium":[131],"in":[135],"low-":[137],"high-performance":[139],"hardware":[140],"setting,":[141],"indicating":[142],"applicability":[144],"tRigon.":[146],"CONCLUSIONS:":[147],"allows":[149],"researchers":[150],"without":[151],"coding":[152],"abilities":[153],"perform":[155],"exploratory":[156],"feature":[157],"analyses":[158],"non-pathomics":[162],"their":[165],"own":[166],"using":[167],"variety":[169],"hardware.":[171]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":1}],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-10-10T00:00:00"}
