{"id":"https://openalex.org/W4220668561","doi":"https://doi.org/10.1093/bioinformatics/btac161","title":"hacksig: a unified and tidy R framework to easily compute gene expression signature scores","display_name":"hacksig: a unified and tidy R framework to easily compute gene expression signature scores","publication_year":2022,"publication_date":"2022-03-16","ids":{"openalex":"https://openalex.org/W4220668561","doi":"https://doi.org/10.1093/bioinformatics/btac161","pmid":"https://pubmed.ncbi.nlm.nih.gov/35561166"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btac161","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btac161","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/38/10/2940/43705004/btac161.pdf","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/38/10/2940/43705004/btac161.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5016357939","display_name":"Andrea Carenzo","orcid":"https://orcid.org/0000-0001-6804-9984"},"institutions":[{"id":"https://openalex.org/I4210156707","display_name":"Fondazione IRCCS Istituto Nazionale dei Tumori","ror":"https://ror.org/05dwj7825","country_code":"IT","type":"healthcare","lineage":["https://openalex.org/I4210153126","https://openalex.org/I4210156707"]}],"countries":["IT"],"is_corresponding":true,"raw_author_name":"Andrea Carenzo","raw_affiliation_strings":["Molecular Mechanisms Unit, Department of Research, Fondazione IRCCS Istituto Nazionale dei Tumori , Milan 20133, Italy"],"affiliations":[{"raw_affiliation_string":"Molecular Mechanisms Unit, Department of Research, Fondazione IRCCS Istituto Nazionale dei Tumori , Milan 20133, Italy","institution_ids":["https://openalex.org/I4210156707"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5001137587","display_name":"Federico Pistore","orcid":"https://orcid.org/0000-0002-3254-9247"},"institutions":[{"id":"https://openalex.org/I4210156707","display_name":"Fondazione IRCCS Istituto Nazionale dei Tumori","ror":"https://ror.org/05dwj7825","country_code":"IT","type":"healthcare","lineage":["https://openalex.org/I4210153126","https://openalex.org/I4210156707"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Federico Pistore","raw_affiliation_strings":["Head and Neck Cancer Medical Oncology 3 Department, Fondazione IRCCS Istituto Nazionale dei Tumori , Milan 20133, Italy"],"affiliations":[{"raw_affiliation_string":"Head and Neck Cancer Medical Oncology 3 Department, Fondazione IRCCS Istituto Nazionale dei Tumori , Milan 20133, Italy","institution_ids":["https://openalex.org/I4210156707"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5035743173","display_name":"Mara Serena Serafini","orcid":"https://orcid.org/0000-0001-9192-9170"},"institutions":[{"id":"https://openalex.org/I4210156707","display_name":"Fondazione IRCCS Istituto Nazionale dei Tumori","ror":"https://ror.org/05dwj7825","country_code":"IT","type":"healthcare","lineage":["https://openalex.org/I4210153126","https://openalex.org/I4210156707"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Mara S Serafini","raw_affiliation_strings":["Molecular Mechanisms Unit, Department of Research, Fondazione IRCCS Istituto Nazionale dei Tumori , Milan 20133, Italy"],"affiliations":[{"raw_affiliation_string":"Molecular Mechanisms Unit, Department of Research, Fondazione IRCCS Istituto Nazionale dei Tumori , Milan 20133, Italy","institution_ids":["https://openalex.org/I4210156707"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5090525729","display_name":"Deborah Lenoci","orcid":"https://orcid.org/0000-0002-5958-8035"},"institutions":[{"id":"https://openalex.org/I4210156707","display_name":"Fondazione IRCCS Istituto Nazionale dei Tumori","ror":"https://ror.org/05dwj7825","country_code":"IT","type":"healthcare","lineage":["https://openalex.org/I4210153126","https://openalex.org/I4210156707"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Deborah Lenoci","raw_affiliation_strings":["Molecular Mechanisms Unit, Department of Research, Fondazione IRCCS Istituto Nazionale dei Tumori , Milan 20133, Italy"],"affiliations":[{"raw_affiliation_string":"Molecular Mechanisms Unit, Department of Research, Fondazione IRCCS Istituto Nazionale dei Tumori , Milan 20133, Italy","institution_ids":["https://openalex.org/I4210156707"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5088155517","display_name":"Armando G Licata","orcid":"https://orcid.org/0000-0001-5785-5163"},"institutions":[{"id":"https://openalex.org/I4210156707","display_name":"Fondazione IRCCS Istituto Nazionale dei Tumori","ror":"https://ror.org/05dwj7825","country_code":"IT","type":"healthcare","lineage":["https://openalex.org/I4210153126","https://openalex.org/I4210156707"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Armando G Licata","raw_affiliation_strings":["Molecular Mechanisms Unit, Department of Research, Fondazione IRCCS Istituto Nazionale dei Tumori , Milan 20133, Italy"],"affiliations":[{"raw_affiliation_string":"Molecular Mechanisms Unit, Department of Research, Fondazione IRCCS Istituto Nazionale dei Tumori , Milan 20133, Italy","institution_ids":["https://openalex.org/I4210156707"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5061225830","display_name":"Loris De Cecco","orcid":"https://orcid.org/0000-0002-7066-473X"},"institutions":[{"id":"https://openalex.org/I4210156707","display_name":"Fondazione IRCCS Istituto Nazionale dei Tumori","ror":"https://ror.org/05dwj7825","country_code":"IT","type":"healthcare","lineage":["https://openalex.org/I4210153126","https://openalex.org/I4210156707"]}],"countries":["IT"],"is_corresponding":true,"raw_author_name":"Loris De Cecco","raw_affiliation_strings":["Molecular Mechanisms Unit, Department of Research, Fondazione IRCCS Istituto Nazionale dei Tumori , Milan 20133, Italy"],"affiliations":[{"raw_affiliation_string":"Molecular Mechanisms Unit, Department of Research, Fondazione IRCCS Istituto Nazionale dei Tumori , Milan 20133, Italy","institution_ids":["https://openalex.org/I4210156707"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5016357939","https://openalex.org/A5061225830"],"corresponding_institution_ids":["https://openalex.org/I4210156707"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":2.2302,"has_fulltext":false,"cited_by_count":27,"citation_normalized_percentile":{"value":0.88541067,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":100},"biblio":{"volume":"38","issue":"10","first_page":"2940","last_page":"2942"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10885","display_name":"Gene expression and cancer classification","score":0.9995999932289124,"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":0.9995999932289124,"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":0.9991999864578247,"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/T11970","display_name":"Molecular Biology Techniques and Applications","score":0.9947999715805054,"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/signature","display_name":"Signature (topology)","score":0.8114656209945679},{"id":"https://openalex.org/keywords/expression","display_name":"Expression (computer science)","score":0.6042484045028687},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5159454941749573},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.5057580471038818},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5040063261985779},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.4354480504989624},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.3691496253013611},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.31404584646224976},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.3100103735923767},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.2913225591182709},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.15548938512802124},{"id":"https://openalex.org/keywords/geometry","display_name":"Geometry","score":0.06877356767654419}],"concepts":[{"id":"https://openalex.org/C2779696439","wikidata":"https://www.wikidata.org/wiki/Q7512811","display_name":"Signature (topology)","level":2,"score":0.8114656209945679},{"id":"https://openalex.org/C90559484","wikidata":"https://www.wikidata.org/wiki/Q778379","display_name":"Expression (computer science)","level":2,"score":0.6042484045028687},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5159454941749573},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.5057580471038818},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5040063261985779},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.4354480504989624},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.3691496253013611},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.31404584646224976},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.3100103735923767},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.2913225591182709},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.15548938512802124},{"id":"https://openalex.org/C2524010","wikidata":"https://www.wikidata.org/wiki/Q8087","display_name":"Geometry","level":1,"score":0.06877356767654419}],"mesh":[{"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":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"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":"D059467","descriptor_name":"Transcriptome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btac161","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btac161","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/38/10/2940/43705004/btac161.pdf","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:35561166","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/35561166","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics (Oxford, England)","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:9113261","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/9113261","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btac161","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btac161","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/38/10/2940/43705004/btac161.pdf","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/17","score":0.4699999988079071,"display_name":"Partnerships for the goals"}],"awards":[{"id":"https://openalex.org/G828445452","display_name":null,"funder_award_id":"IG23573","funder_id":"https://openalex.org/F4320323054","funder_display_name":"Associazione Italiana per la Ricerca sul Cancro"}],"funders":[{"id":"https://openalex.org/F4320323054","display_name":"Associazione Italiana per la Ricerca sul Cancro","ror":"https://ror.org/02g2x7380"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4220668561.pdf","grobid_xml":"https://content.openalex.org/works/W4220668561.grobid-xml"},"referenced_works_count":15,"referenced_works":["https://openalex.org/W1973094248","https://openalex.org/W1992045522","https://openalex.org/W2024781765","https://openalex.org/W2028433016","https://openalex.org/W2114291651","https://openalex.org/W2123879591","https://openalex.org/W2130430382","https://openalex.org/W2159707944","https://openalex.org/W2900032527","https://openalex.org/W2949273159","https://openalex.org/W2952223936","https://openalex.org/W2990427812","https://openalex.org/W3046858608","https://openalex.org/W3092038761","https://openalex.org/W4206951704"],"related_works":["https://openalex.org/W1671124163","https://openalex.org/W2168674042","https://openalex.org/W3030774134","https://openalex.org/W2104499293","https://openalex.org/W2535275505","https://openalex.org/W2392243736","https://openalex.org/W3032874291","https://openalex.org/W2005057264","https://openalex.org/W2363156284","https://openalex.org/W2415025170"],"abstract_inverted_index":{"Supplementary":[0],"data":[1],"are":[2],"available":[3],"at":[4],"Bioinformatics":[5],"online.":[6]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":15},{"year":2024,"cited_by_count":6},{"year":2023,"cited_by_count":4},{"year":2022,"cited_by_count":1}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
