{"id":"https://openalex.org/W4220766413","doi":"https://doi.org/10.1186/s12859-022-04641-x","title":"classifieR a flexible interactive cloud-application for functional annotation of cancer transcriptomes","display_name":"classifieR a flexible interactive cloud-application for functional annotation of cancer transcriptomes","publication_year":2022,"publication_date":"2022-03-31","ids":{"openalex":"https://openalex.org/W4220766413","doi":"https://doi.org/10.1186/s12859-022-04641-x","pmid":"https://pubmed.ncbi.nlm.nih.gov/35361119"},"language":"en","primary_location":{"id":"doi:10.1186/s12859-022-04641-x","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-022-04641-x","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-022-04641-x","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/track/pdf/10.1186/s12859-022-04641-x","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5020254608","display_name":"Gerard P. Quinn","orcid":"https://orcid.org/0000-0001-8784-0157"},"institutions":[{"id":"https://openalex.org/I126231945","display_name":"Queen's University Belfast","ror":"https://ror.org/00hswnk62","country_code":"GB","type":"education","lineage":["https://openalex.org/I126231945"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Gerard P. Quinn","raw_affiliation_strings":["Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, 97 Lisburn Road, Belfast, BT9 7AE, Northern Ireland, UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, 97 Lisburn Road, Belfast, BT9 7AE, Northern Ireland, UK","institution_ids":["https://openalex.org/I126231945"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5112381734","display_name":"Tamas Sessler","orcid":null},"institutions":[{"id":"https://openalex.org/I126231945","display_name":"Queen's University Belfast","ror":"https://ror.org/00hswnk62","country_code":"GB","type":"education","lineage":["https://openalex.org/I126231945"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Tamas Sessler","raw_affiliation_strings":["Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, 97 Lisburn Road, Belfast, BT9 7AE, Northern Ireland, UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, 97 Lisburn Road, Belfast, BT9 7AE, Northern Ireland, UK","institution_ids":["https://openalex.org/I126231945"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5006911790","display_name":"Baharak Ahmaderaghi","orcid":"https://orcid.org/0000-0003-4166-6290"},"institutions":[{"id":"https://openalex.org/I126231945","display_name":"Queen's University Belfast","ror":"https://ror.org/00hswnk62","country_code":"GB","type":"education","lineage":["https://openalex.org/I126231945"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Baharak Ahmaderaghi","raw_affiliation_strings":["Electronics, Electrical Engineering and Computer Science, Queen's University Belfast, Belfast, UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Electronics, Electrical Engineering and Computer Science, Queen's University Belfast, Belfast, UK","institution_ids":["https://openalex.org/I126231945"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5050702589","display_name":"Shauna Lambe","orcid":"https://orcid.org/0000-0002-9671-2082"},"institutions":[{"id":"https://openalex.org/I126231945","display_name":"Queen's University Belfast","ror":"https://ror.org/00hswnk62","country_code":"GB","type":"education","lineage":["https://openalex.org/I126231945"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Shauna Lambe","raw_affiliation_strings":["Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, 97 Lisburn Road, Belfast, BT9 7AE, Northern Ireland, UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, 97 Lisburn Road, Belfast, BT9 7AE, Northern Ireland, UK","institution_ids":["https://openalex.org/I126231945"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5022602216","display_name":"Harper VanSteenhouse","orcid":"https://orcid.org/0000-0002-9401-5929"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Harper VanSteenhouse","raw_affiliation_strings":["BioClavis, Glasgow, UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"BioClavis, Glasgow, UK","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5002719979","display_name":"Mark Lawler","orcid":"https://orcid.org/0000-0002-3930-8470"},"institutions":[{"id":"https://openalex.org/I126231945","display_name":"Queen's University Belfast","ror":"https://ror.org/00hswnk62","country_code":"GB","type":"education","lineage":["https://openalex.org/I126231945"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Mark Lawler","raw_affiliation_strings":["Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, 97 Lisburn Road, Belfast, BT9 7AE, Northern Ireland, UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, 97 Lisburn Road, Belfast, BT9 7AE, Northern Ireland, UK","institution_ids":["https://openalex.org/I126231945"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5076845937","display_name":"Mark Wappett","orcid":null},"institutions":[{"id":"https://openalex.org/I126231945","display_name":"Queen's University Belfast","ror":"https://ror.org/00hswnk62","country_code":"GB","type":"education","lineage":["https://openalex.org/I126231945"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Mark Wappett","raw_affiliation_strings":["Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, 97 Lisburn Road, Belfast, BT9 7AE, Northern Ireland, UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, 97 Lisburn Road, Belfast, BT9 7AE, Northern Ireland, UK","institution_ids":["https://openalex.org/I126231945"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5002573031","display_name":"Bruce Seligmann","orcid":"https://orcid.org/0000-0002-1342-801X"},"institutions":[{"id":"https://openalex.org/I4210145439","display_name":"Biospyder (United States)","ror":"https://ror.org/05076r819","country_code":"US","type":"company","lineage":["https://openalex.org/I4210145439"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Bruce Seligmann","raw_affiliation_strings":["BioSpyder Technologies, Carlsbad, CA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"BioSpyder Technologies, Carlsbad, CA, USA","institution_ids":["https://openalex.org/I4210145439"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5078841356","display_name":"Daniel B. Longley","orcid":"https://orcid.org/0000-0003-2495-2033"},"institutions":[{"id":"https://openalex.org/I126231945","display_name":"Queen's University Belfast","ror":"https://ror.org/00hswnk62","country_code":"GB","type":"education","lineage":["https://openalex.org/I126231945"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Daniel B. Longley","raw_affiliation_strings":["Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, 97 Lisburn Road, Belfast, BT9 7AE, Northern Ireland, UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, 97 Lisburn Road, Belfast, BT9 7AE, Northern Ireland, UK","institution_ids":["https://openalex.org/I126231945"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5067775652","display_name":"Simon S. McDade","orcid":"https://orcid.org/0000-0002-3024-4773"},"institutions":[{"id":"https://openalex.org/I126231945","display_name":"Queen's University Belfast","ror":"https://ror.org/00hswnk62","country_code":"GB","type":"education","lineage":["https://openalex.org/I126231945"]}],"countries":["GB"],"is_corresponding":true,"raw_author_name":"Simon S. McDade","raw_affiliation_strings":["Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, 97 Lisburn Road, Belfast, BT9 7AE, Northern Ireland, UK. s.mcdade@qub.ac.uk","Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, 97 Lisburn Road, Belfast, BT9 7AE, Northern Ireland, UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, 97 Lisburn Road, Belfast, BT9 7AE, Northern Ireland, UK. s.mcdade@qub.ac.uk","institution_ids":["https://openalex.org/I126231945"]},{"raw_affiliation_string":"Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, 97 Lisburn Road, Belfast, BT9 7AE, Northern Ireland, UK","institution_ids":["https://openalex.org/I126231945"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5067775652"],"corresponding_institution_ids":["https://openalex.org/I126231945"],"apc_list":{"value":2790,"currency":"USD","value_usd":2790},"apc_paid":{"value":2790,"currency":"USD","value_usd":2790},"fwci":0.3917,"has_fulltext":true,"cited_by_count":6,"citation_normalized_percentile":{"value":0.52964335,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":94,"max":97},"biblio":{"volume":"23","issue":"1","first_page":"114","last_page":"114"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10885","display_name":"Gene expression and cancer classification","score":0.7098000049591064,"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/T10885","display_name":"Gene expression and cancer classification","score":0.7098000049591064,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.0966000035405159,"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/T10183","display_name":"Breast Cancer Treatment Studies","score":0.029200000688433647,"subfield":{"id":"https://openalex.org/subfields/1306","display_name":"Cancer Research"},"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/classifier","display_name":"Classifier (UML)","score":0.5735822916030884},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.4927239716053009},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.4763500988483429},{"id":"https://openalex.org/keywords/dna-microarray","display_name":"DNA microarray","score":0.43072837591171265},{"id":"https://openalex.org/keywords/transcriptome","display_name":"Transcriptome","score":0.4279817044734955},{"id":"https://openalex.org/keywords/subtyping","display_name":"Subtyping","score":0.4232422113418579},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.40911728143692017},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.35878098011016846},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.3346552848815918},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.32354143261909485},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.28841444849967957},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.21976238489151},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.19992098212242126}],"concepts":[{"id":"https://openalex.org/C95623464","wikidata":"https://www.wikidata.org/wiki/Q1096149","display_name":"Classifier (UML)","level":2,"score":0.5735822916030884},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4927239716053009},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4763500988483429},{"id":"https://openalex.org/C95371953","wikidata":"https://www.wikidata.org/wiki/Q591745","display_name":"DNA microarray","level":4,"score":0.43072837591171265},{"id":"https://openalex.org/C162317418","wikidata":"https://www.wikidata.org/wiki/Q252857","display_name":"Transcriptome","level":4,"score":0.4279817044734955},{"id":"https://openalex.org/C83852419","wikidata":"https://www.wikidata.org/wiki/Q2713292","display_name":"Subtyping","level":2,"score":0.4232422113418579},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.40911728143692017},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.35878098011016846},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3346552848815918},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.32354143261909485},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.28841444849967957},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.21976238489151},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.19992098212242126},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D001943","descriptor_name":"Breast Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D001943","descriptor_name":"Breast Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D001943","descriptor_name":"Breast Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D001943","descriptor_name":"Breast Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D001943","descriptor_name":"Breast Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D005260","descriptor_name":"Female","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005260","descriptor_name":"Female","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005260","descriptor_name":"Female","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005260","descriptor_name":"Female","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005260","descriptor_name":"Female","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":"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":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"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":"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":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","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":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","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":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},{"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":5,"locations":[{"id":"doi:10.1186/s12859-022-04641-x","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-022-04641-x","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-022-04641-x","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:35361119","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/35361119","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:pure.qub.ac.uk/portal:openaire/3aca1733-7e40-4b75-9422-a771b9bc12e9","is_oa":true,"landing_page_url":"https://pure.qub.ac.uk/en/publications/3aca1733-7e40-4b75-9422-a771b9bc12e9","pdf_url":null,"source":{"id":"https://openalex.org/S4306402319","display_name":"Research Portal (Queen's University Belfast)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I126231945","host_organization_name":"Queen's University Belfast","host_organization_lineage":["https://openalex.org/I126231945"],"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":"Quinn, G P, Sessler, T, Ahmaderaghi, B, Lambe, S, VanSteenhouse, H, Lawler, M, Wappett, M, Seligmann, B, Longley, D B & McDade, S S 2022, 'classifieR a flexible interactive cloud-application for functional annotation of cancer transcriptomes', BMC Bioinformatics, vol. 23, 114. https://doi.org/10.1186/s12859-022-04641-x","raw_type":"info:eu-repo/semantics/article"},{"id":"pmh:oai:doaj.org/article:c0829fc0ca034492a1c3d272aaaac828","is_oa":true,"landing_page_url":"https://doaj.org/article/c0829fc0ca034492a1c3d272aaaac828","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 23, Iss 1, Pp 1-9 (2022)","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:8974006","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/8974006","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/s12859-022-04641-x","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-022-04641-x","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-022-04641-x","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":[{"display_name":"Reduced inequalities","score":0.6200000047683716,"id":"https://metadata.un.org/sdg/10"}],"awards":[{"id":"https://openalex.org/G2281759492","display_name":null,"funder_award_id":"C11884/A24387","funder_id":"https://openalex.org/F4320319985","funder_display_name":"Cancer Research UK"},{"id":"https://openalex.org/G3275479868","display_name":null,"funder_award_id":"BB/T002824/1","funder_id":"https://openalex.org/F4320334629","funder_display_name":"Biotechnology and Biological Sciences Research Council"},{"id":"https://openalex.org/G4125273568","display_name":null,"funder_award_id":"C11884/A24367","funder_id":"https://openalex.org/F4320319985","funder_display_name":"Cancer Research UK"},{"id":"https://openalex.org/G5196472102","display_name":null,"funder_award_id":"C36697/A25176","funder_id":"https://openalex.org/F4320333939","funder_display_name":"Imperial Experimental Cancer Medicine Centre"},{"id":"https://openalex.org/G582926436","display_name":null,"funder_award_id":"MC_PC_19050","funder_id":"https://openalex.org/F4320334626","funder_display_name":"Medical Research Council"},{"id":"https://openalex.org/G8872917983","display_name":"Regulation of cell fate by a novel p53-inducible ligand-independent TRAIL-R2 complex","funder_award_id":"BB/T002824/1","funder_id":"https://openalex.org/F4320334629","funder_display_name":"Biotechnology and Biological Sciences Research Council"}],"funders":[{"id":"https://openalex.org/F4320319985","display_name":"Cancer Research UK","ror":"https://ror.org/054225q67"},{"id":"https://openalex.org/F4320333939","display_name":"Imperial Experimental Cancer Medicine Centre","ror":null},{"id":"https://openalex.org/F4320334626","display_name":"Medical Research Council","ror":"https://ror.org/03x94j517"},{"id":"https://openalex.org/F4320334629","display_name":"Biotechnology and Biological Sciences Research Council","ror":"https://ror.org/00cwqg982"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4220766413.pdf","grobid_xml":"https://content.openalex.org/works/W4220766413.grobid-xml"},"referenced_works_count":18,"referenced_works":["https://openalex.org/W1934094702","https://openalex.org/W2005895632","https://openalex.org/W2105882193","https://openalex.org/W2123879591","https://openalex.org/W2172358623","https://openalex.org/W2179438025","https://openalex.org/W2310046094","https://openalex.org/W2472255748","https://openalex.org/W2533508881","https://openalex.org/W2617865703","https://openalex.org/W2618505595","https://openalex.org/W2770459634","https://openalex.org/W2808042645","https://openalex.org/W2914981515","https://openalex.org/W2944727022","https://openalex.org/W2949097641","https://openalex.org/W2950796920","https://openalex.org/W2952001873"],"related_works":["https://openalex.org/W2396009657","https://openalex.org/W2799110842","https://openalex.org/W3032826521","https://openalex.org/W2391332606","https://openalex.org/W4229853287","https://openalex.org/W1462775415","https://openalex.org/W2008549446","https://openalex.org/W1535483699","https://openalex.org/W4399363637","https://openalex.org/W2333832190"],"abstract_inverted_index":{"BACKGROUND:":[0],"Transcriptionally":[1],"informed":[2],"predictions":[3,78,229],"are":[4,195,277],"increasingly":[5],"important":[6],"for":[7,272,287],"sub-typing":[8],"cancer":[9,47,164],"patients,":[10],"understanding":[11],"underlying":[12],"biology":[13],"and":[14,43,57,74,82,191,206,217,225,267,274,282],"to":[15,71,99,179,246],"inform":[16],"novel":[17],"treatment":[18],"strategies.":[19],"For":[20],"instance,":[21],"colorectal":[22,189],"cancers":[23],"(CRCs)":[24],"can":[25,250],"be":[26],"classified":[27],"into":[28,263],"four":[29],"CRC":[30],"consensus":[31],"molecular":[32,52,255],"subgroups":[33,53,201],"(CMS)":[34],"or":[35,132],"five":[36,50],"intrinsic":[37],"(CRIS)":[38],"sub-types":[39,203],"that":[40,152],"have":[41],"prognostic":[42],"predictive":[44],"value.":[45],"Breast":[46],"(BRCA)":[48],"has":[49],"PAM50":[51],"with":[54,197,230],"similar":[55],"value,":[56],"the":[58,104,172,175,183,254],"OncotypeDX":[59,208],"test":[60],"provides":[61,118,238],"transcriptomic":[62],"based":[63,149],"clinically":[64],"actionable":[65],"treatment-risk":[66],"stratification.":[67],"However,":[68],"assigning":[69],"samples":[70,166],"these":[72],"subtypes":[73],"other":[75],"transcriptionally":[76],"inferred":[77],"is":[79,88],"time":[80],"consuming":[81],"requires":[83],"significant":[84],"bioinformatics":[85],"experience.":[86],"There":[87],"no":[89],"\"universal\"":[90],"method":[91],"of":[92,108,134,159,174,185,212,257],"using":[93,103,215],"data":[94],"from":[95,163,188],"diverse":[96,168],"assay/sequencing":[97],"platforms":[98],"provide":[100],"subgroup":[101],"classification":[102],"established":[105],"classifier":[106],"sets":[107],"genes":[109],"(CMS,":[110],"CRIS,":[111],"PAM50,":[112],"OncotypeDX),":[113],"nor":[114],"one":[115],"which":[116,241],"in":[117,204,209],"additional":[119],"useful":[120],"functional":[121],"annotations":[122],"such":[123],"as":[124,269],"cellular":[125,213],"composition,":[126],"single-sample":[127,219],"Gene":[128,220],"Set":[129,221],"Enrichment":[130,222],"Analysis,":[131],"prediction":[133],"transcription":[135,226],"factor":[136,227],"activity.":[137],"RESULTS:":[138],"To":[139],"address":[140],"this":[141],"bottleneck,":[142],"we":[143],"developed":[144],"classifieR,":[145],"an":[146,261,288],"easy-to-use":[147],"R-Shiny":[148],"web":[150],"application":[151],"supports":[153],"flexible":[154],"rapid":[155],"single":[156],"sample":[157],"annotation":[158],"transcriptional":[160,186,200],"profiles":[161,187],"derived":[162],"patient":[165,264],"form":[167],"platforms.":[169],"We":[170],"demonstrate":[171],"utility":[173],"\"":[176],"classifieR\"":[177],"framework":[178,240],"applications":[180],"focused":[181],"on":[182,253,290],"analysis":[184,273],"(classifieRc)":[190],"breast":[192],"(classifieRb).":[193],"Samples":[194],"annotated":[196],"disease":[198],"relevant":[199],"(CMS/CRIS":[202],"classifieRc":[205],"PAM50/inferred":[207],"classifieRb),":[210],"estimation":[211],"composition":[214],"MCP-counter":[216],"xCell,":[218],"Analysis":[223,234],"(ssGSEA)":[224],"activity":[228],"Discriminant":[231],"Regulon":[232],"Expression":[233],"(DoRothEA).":[235],"CONCLUSIONS:":[236],"classifieR":[237],"a":[239,247,270],"enables":[242],"labs":[243],"without":[244],"access":[245],"dedicated":[248],"bioinformation":[249],"get":[251],"information":[252],"makeup":[256],"their":[258],"samples,":[259],"providing":[260],"insight":[262],"prognosis,":[265],"druggability":[266],"also":[268],"tool":[271],"discovery.":[275],"Applications":[276],"hosted":[278],"online":[279],"at":[280],"https://generatr.qub.ac.uk/app/classifieRc":[281],"https://generatr.qub.ac.uk/app/classifieRb":[283],"after":[284],"signing":[285],"up":[286],"account":[289],"https://generatr.qub.ac.uk":[291],".":[292]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2024,"cited_by_count":2},{"year":2023,"cited_by_count":3}],"updated_date":"2026-07-23T08:03:31.855105","created_date":"2025-10-10T00:00:00"}