{"id":"https://openalex.org/W3024433232","doi":"https://doi.org/10.1093/bioinformatics/btaa296","title":"rScudo: an R package for classification of molecular profiles using rank-based signatures","display_name":"rScudo: an R package for classification of molecular profiles using rank-based signatures","publication_year":2020,"publication_date":"2020-05-06","ids":{"openalex":"https://openalex.org/W3024433232","doi":"https://doi.org/10.1093/bioinformatics/btaa296","mag":"3024433232","pmid":"https://pubmed.ncbi.nlm.nih.gov/32399554"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btaa296","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaa296","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"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":null,"license_id":null,"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":"green","oa_url":"https://hdl.handle.net/11572/266258","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5070464616","display_name":"Matteo Ciciani","orcid":"https://orcid.org/0000-0003-2045-5435"},"institutions":[],"countries":[],"is_corresponding":true,"raw_author_name":"Matteo Ciciani","raw_affiliation_strings":["CIBIO\u2013\u2013Centre for Integrative Biology"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"CIBIO\u2013\u2013Centre for Integrative Biology","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5011678234","display_name":"Thomas Cantore","orcid":"https://orcid.org/0000-0003-2538-4496"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Thomas Cantore","raw_affiliation_strings":["CIBIO\u2013\u2013Centre for Integrative Biology"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"CIBIO\u2013\u2013Centre for Integrative Biology","institution_ids":[]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5026481712","display_name":"Mario Lauria","orcid":"https://orcid.org/0000-0001-5983-7292"},"institutions":[{"id":"https://openalex.org/I193223587","display_name":"University of Trento","ror":"https://ror.org/05trd4x28","country_code":"IT","type":"education","lineage":["https://openalex.org/I193223587"]},{"id":"https://openalex.org/I2802934434","display_name":"The Microsoft Research - University of Trento Centre for Computational and Systems Biology","ror":"https://ror.org/04kcgyj43","country_code":"IT","type":"nonprofit","lineage":["https://openalex.org/I1290206253","https://openalex.org/I193223587","https://openalex.org/I2802934434","https://openalex.org/I4210164937"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Mario Lauria","raw_affiliation_strings":["Department of Mathematics , University of Trento, 38123 Povo, Trentino, Italy","The Microsoft Research\u2013University of Trento Centre for Computational and Systems Biology (COSBI) , 38068 Rovereto, Trentino, Italy"],"raw_orcid":"https://orcid.org/0000-0001-5983-7292","affiliations":[{"raw_affiliation_string":"Department of Mathematics , University of Trento, 38123 Povo, Trentino, Italy","institution_ids":["https://openalex.org/I193223587"]},{"raw_affiliation_string":"The Microsoft Research\u2013University of Trento Centre for Computational and Systems Biology (COSBI) , 38068 Rovereto, Trentino, Italy","institution_ids":["https://openalex.org/I2802934434","https://openalex.org/I193223587"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5070464616"],"corresponding_institution_ids":[],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.08184783,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"36","issue":"13","first_page":"4095","last_page":"4096"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.31459999084472656,"subfield":{"id":"https://openalex.org/subfields/1703","display_name":"Computational Theory and Mathematics"},"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/T10211","display_name":"Computational Drug Discovery Methods","score":0.31459999084472656,"subfield":{"id":"https://openalex.org/subfields/1703","display_name":"Computational Theory and Mathematics"},"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/T10885","display_name":"Gene expression and cancer classification","score":0.06440000236034393,"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/T12867","display_name":"Advanced Biosensing Techniques and Applications","score":0.04470000043511391,"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":0.9308725595474243},{"id":"https://openalex.org/keywords/signature","display_name":"Signature (topology)","score":0.7545871734619141},{"id":"https://openalex.org/keywords/r-package","display_name":"R package","score":0.7255187034606934},{"id":"https://openalex.org/keywords/rank","display_name":"Rank (graph theory)","score":0.7234077453613281},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7004273533821106},{"id":"https://openalex.org/keywords/suite","display_name":"Suite","score":0.6452345252037048},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.5759760737419128},{"id":"https://openalex.org/keywords/similarity","display_name":"Similarity (geometry)","score":0.5500060319900513},{"id":"https://openalex.org/keywords/novelty","display_name":"Novelty","score":0.4956556558609009},{"id":"https://openalex.org/keywords/sample","display_name":"Sample (material)","score":0.44411739706993103},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.2752510905265808},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.12840530276298523},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.11548048257827759},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.09822890162467957},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.07280263304710388}],"concepts":[{"id":"https://openalex.org/C2779694297","wikidata":"https://www.wikidata.org/wiki/Q2888953","display_name":"Bioconductor","level":3,"score":0.9308725595474243},{"id":"https://openalex.org/C2779696439","wikidata":"https://www.wikidata.org/wiki/Q7512811","display_name":"Signature (topology)","level":2,"score":0.7545871734619141},{"id":"https://openalex.org/C2984074130","wikidata":"https://www.wikidata.org/wiki/Q73539779","display_name":"R package","level":2,"score":0.7255187034606934},{"id":"https://openalex.org/C164226766","wikidata":"https://www.wikidata.org/wiki/Q7293202","display_name":"Rank (graph theory)","level":2,"score":0.7234077453613281},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7004273533821106},{"id":"https://openalex.org/C79581498","wikidata":"https://www.wikidata.org/wiki/Q1367530","display_name":"Suite","level":2,"score":0.6452345252037048},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.5759760737419128},{"id":"https://openalex.org/C103278499","wikidata":"https://www.wikidata.org/wiki/Q254465","display_name":"Similarity (geometry)","level":3,"score":0.5500060319900513},{"id":"https://openalex.org/C2778738651","wikidata":"https://www.wikidata.org/wiki/Q16546687","display_name":"Novelty","level":2,"score":0.4956556558609009},{"id":"https://openalex.org/C198531522","wikidata":"https://www.wikidata.org/wiki/Q485146","display_name":"Sample (material)","level":2,"score":0.44411739706993103},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.2752510905265808},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.12840530276298523},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.11548048257827759},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.09822890162467957},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.07280263304710388},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0},{"id":"https://openalex.org/C115961682","wikidata":"https://www.wikidata.org/wiki/Q860623","display_name":"Image (mathematics)","level":2,"score":0.0},{"id":"https://openalex.org/C114614502","wikidata":"https://www.wikidata.org/wiki/Q76592","display_name":"Combinatorics","level":1,"score":0.0},{"id":"https://openalex.org/C27206212","wikidata":"https://www.wikidata.org/wiki/Q34178","display_name":"Theology","level":1,"score":0.0},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0},{"id":"https://openalex.org/C43617362","wikidata":"https://www.wikidata.org/wiki/Q170050","display_name":"Chromatography","level":1,"score":0.0},{"id":"https://openalex.org/C95457728","wikidata":"https://www.wikidata.org/wiki/Q309","display_name":"History","level":0,"score":0.0},{"id":"https://openalex.org/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","level":0,"score":0.0},{"id":"https://openalex.org/C166957645","wikidata":"https://www.wikidata.org/wiki/Q23498","display_name":"Archaeology","level":1,"score":0.0},{"id":"https://openalex.org/C2524010","wikidata":"https://www.wikidata.org/wiki/Q8087","display_name":"Geometry","level":1,"score":0.0}],"mesh":[{"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}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btaa296","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaa296","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:32399554","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/32399554","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:iris.unitn.it:11572/266258","is_oa":true,"landing_page_url":"https://hdl.handle.net/11572/266258","pdf_url":null,"source":{"id":"https://openalex.org/S4306401913","display_name":"Institutional Research Information System (Universit\u00e0 degli Studi di Trento)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I193223587","host_organization_name":"University of Trento","host_organization_lineage":["https://openalex.org/I193223587"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"info:eu-repo/semantics/article"}],"best_oa_location":{"id":"pmh:oai:iris.unitn.it:11572/266258","is_oa":true,"landing_page_url":"https://hdl.handle.net/11572/266258","pdf_url":null,"source":{"id":"https://openalex.org/S4306401913","display_name":"Institutional Research Information System (Universit\u00e0 degli Studi di Trento)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I193223587","host_organization_name":"University of Trento","host_organization_lineage":["https://openalex.org/I193223587"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"info:eu-repo/semantics/article"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/17","score":0.5199999809265137,"display_name":"Partnerships for the goals"}],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":8,"referenced_works":["https://openalex.org/W1865654416","https://openalex.org/W2116437349","https://openalex.org/W2119025581","https://openalex.org/W2173079606","https://openalex.org/W2315378439","https://openalex.org/W2319256006","https://openalex.org/W2517637924","https://openalex.org/W2793008414"],"related_works":["https://openalex.org/W3044771955","https://openalex.org/W2982252354","https://openalex.org/W2728564446","https://openalex.org/W3045904767","https://openalex.org/W2161868542","https://openalex.org/W2140163842","https://openalex.org/W3156537409","https://openalex.org/W2747931568","https://openalex.org/W2921090651","https://openalex.org/W2133055377"],"abstract_inverted_index":{"SUMMARY:":[0],"The":[1,55,94,130],"classification":[2,34],"of":[3,8,16,35,48,51,57,116,136],"biological":[4],"samples":[5],"by":[6],"means":[7],"their":[9],"respective":[10],"molecular":[11,36,117],"profiles":[12,37,118],"is":[13,28,83,132],"a":[14,40],"topic":[15],"great":[17],"interest":[18],"for":[19,32,86,90],"its":[20,80,111],"potential":[21],"diagnostic,":[22],"prognostic":[23],"and":[24,89,119],"investigational":[25],"applications.":[26,93],"rScudo":[27,58,95],"an":[29],"R":[30],"package":[31,96,131],"the":[33,46,49,71,105,137],"based":[38],"on":[39],"radically":[41],"new":[42],"approach":[43,60],"consisting":[44],"in":[45,70],"analysis":[47],"similarity":[50],"rank-based":[52,106],"sample-specific":[53],"signatures.":[54],"validity":[56],"unconventional":[59],"has":[61,97],"been":[62,98],"validated":[63],"through":[64],"direct":[65,122],"comparison":[66,123],"with":[67,104,124],"current":[68],"methods":[69],"international":[72],"SBV":[73],"IMPROVER":[74],"Diagnostic":[75],"Signature":[76],"Challenge.":[77],"Due":[78],"to":[79,101,109,113,120],"novelty,":[81],"there":[82],"ample":[84],"room":[85],"conceptual":[87],"improvements":[88],"exploring":[91],"additional":[92],"specifically":[99],"designed":[100],"facilitate":[102],"experimenting":[103],"signature":[107],"approach,":[108],"test":[110],"application":[112],"different":[114],"types":[115],"simplify":[121],"existing":[125],"methods.":[126],"AVAILABILITY":[127],"AND":[128],"IMPLEMENTATION:":[129],"available":[133],"as":[134],"part":[135],"Bioconductor":[138],"suite":[139],"at":[140],"https://bioconductor.org/packages/rScudo.":[141]},"counts_by_year":[],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-10-10T00:00:00"}