{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,15]],"date-time":"2026-04-15T04:28:36Z","timestamp":1776227316196,"version":"3.50.1"},"reference-count":15,"publisher":"Oxford University Press (OUP)","issue":"10","license":[{"start":{"date-parts":[[2022,3,18]],"date-time":"2022-03-18T00:00:00Z","timestamp":1647561600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100005010","name":"Associazione Italiana per la Ricerca sul Cancro","doi-asserted-by":"crossref","award":["IG23573"],"award-info":[{"award-number":["IG23573"]}],"id":[{"id":"10.13039\/501100005010","id-type":"DOI","asserted-by":"crossref"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022,5,13]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>Hundreds of gene expression signatures have been developed during the last two decades. However, due to the multitude of development procedures and sometimes a lack of explanation for their implementation, it can become challenging to apply the original method on custom data. Moreover, at present, there is no unified and tidy interface to compute signature scores with different single sample enrichment methods. For these reasons, we developed hacksig, an R package intended as a unified framework to obtain single sample scores with a tidy output as well as a collection of manually curated gene signatures and methods from cancer transcriptomics literature.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>The hacksig R package is freely available on CRAN (https:\/\/CRAN.R-project.org\/package=hacksig) under the MIT license. The source code can be found on GitHub at https:\/\/github.com\/Acare\/hacksig.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Supplementary information<\/jats:title>\n                  <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btac161","type":"journal-article","created":{"date-parts":[[2022,3,16]],"date-time":"2022-03-16T12:31:27Z","timestamp":1647433887000},"page":"2940-2942","source":"Crossref","is-referenced-by-count":28,"title":["hacksig: a unified and tidy R framework to easily compute gene expression signature scores"],"prefix":"10.1093","volume":"38","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-6804-9984","authenticated-orcid":false,"given":"Andrea","family":"Carenzo","sequence":"first","affiliation":[{"name":"Molecular Mechanisms Unit, Department of Research, Fondazione IRCCS Istituto Nazionale dei Tumori , Milan 20133, Italy"}]},{"given":"Federico","family":"Pistore","sequence":"additional","affiliation":[{"name":"Head and Neck Cancer Medical Oncology 3 Department, Fondazione IRCCS Istituto Nazionale dei Tumori , Milan 20133, Italy"}]},{"given":"Mara S","family":"Serafini","sequence":"additional","affiliation":[{"name":"Molecular Mechanisms Unit, Department of Research, Fondazione IRCCS Istituto Nazionale dei Tumori , Milan 20133, Italy"}]},{"given":"Deborah","family":"Lenoci","sequence":"additional","affiliation":[{"name":"Molecular Mechanisms Unit, Department of Research, Fondazione IRCCS Istituto Nazionale dei Tumori , Milan 20133, Italy"}]},{"given":"Armando G","family":"Licata","sequence":"additional","affiliation":[{"name":"Molecular Mechanisms Unit, Department of Research, Fondazione IRCCS Istituto Nazionale dei Tumori , Milan 20133, Italy"}]},{"given":"Loris","family":"De Cecco","sequence":"additional","affiliation":[{"name":"Molecular Mechanisms Unit, Department of Research, Fondazione IRCCS Istituto Nazionale dei Tumori , Milan 20133, Italy"}]}],"member":"286","published-online":{"date-parts":[[2022,3,18]]},"reference":[{"key":"2023020109053655400_btac161-B1","doi-asserted-by":"crossref","first-page":"108","DOI":"10.1038\/nature08460","article-title":"Systematic RNA interference reveals that oncogenic KRAS-driven cancers require TBK1","volume":"462","author":"Barbie","year":"2009","journal-title":"Nature"},{"key":"2023020109053655400_btac161-B2","doi-asserted-by":"crossref","first-page":"208","DOI":"10.32614\/RJ-2021-048","article-title":"A unifying framework for parallel and distributed processing in R using futures","volume":"13","author":"Bengtsson","year":"2021","journal-title":"R J"},{"key":"2023020109053655400_btac161-B3","doi-asserted-by":"crossref","first-page":"2","DOI":"10.1038\/s41540-017-0038-8","article-title":"Classification of gene signatures for their information value and functional redundancy","volume":"4","author":"Cantini","year":"2018","journal-title":"NPJ Syst. Biol. Appl"},{"key":"2023020109053655400_btac161-B4","doi-asserted-by":"crossref","first-page":"248","DOI":"10.1016\/j.celrep.2016.12.019","article-title":"Pan-cancer immunogenomic analyses reveal genotype-immunophenotype relationships and predictors of response to checkpoint blockade","volume":"18","author":"Charoentong","year":"2017","journal-title":"Cell Rep"},{"key":"2023020109053655400_btac161-B5","doi-asserted-by":"crossref","first-page":"781","DOI":"10.1038\/nm.2174","article-title":"Validated prediction of clinical outcome in sarcomas and multiple types of cancer on the basis of a gene expression signature related to genome complexity","volume":"16","author":"Chibon","year":"2010","journal-title":"Nat. Med"},{"key":"2023020109053655400_btac161-B6","doi-asserted-by":"crossref","first-page":"1628","DOI":"10.1093\/annonc\/mdu173","article-title":"Comprehensive gene expression meta-analysis of head and neck squamous cell carcinoma microarray data defines a robust survival predictor","volume":"25","author":"De Cecco","year":"2014","journal-title":"Ann. Oncol"},{"key":"2023020109053655400_btac161-B7","doi-asserted-by":"crossref","DOI":"10.1186\/s12859-018-2435-4","article-title":"Single sample scoring of molecular phenotypes","volume":"19","author":"Foroutan","year":"2018","journal-title":"BMC Bioinformatics"},{"key":"2023020109053655400_btac161-B8","doi-asserted-by":"crossref","first-page":"7","DOI":"10.1186\/1471-2105-14-7","article-title":"GSVA: gene set variation analysis for microarray and RNA-seq data","volume":"14","author":"H\u00e4nzelmann","year":"2013","journal-title":"BMC Bioinformatics"},{"key":"2023020109053655400_btac161-B9","doi-asserted-by":"crossref","first-page":"115","DOI":"10.1038\/nmeth.3252","article-title":"Orchestrating high-throughput genomic analysis with bioconductor","volume":"12","author":"Huber","year":"2015","journal-title":"Nature Methods"},{"key":"2023020109053655400_btac161-B10","doi-asserted-by":"crossref","first-page":"e1000217","DOI":"10.1371\/journal.pcbi.1000217","article-title":"Inferring pathway activity toward precise disease classification","volume":"4","author":"Lee","year":"2008","journal-title":"PLoS Comput. Biol"},{"key":"2023020109053655400_btac161-B11","doi-asserted-by":"crossref","first-page":"5282","DOI":"10.1158\/0008-5472.CAN-20-0512","article-title":"A global and integrated analysis of CINSARC-associated genetic defects","volume":"80","author":"Lesluyes","year":"2020","journal-title":"Cancer Res"},{"key":"2023020109053655400_btac161-B12","doi-asserted-by":"crossref","first-page":"48","DOI":"10.1016\/j.cell.2014.12.033","article-title":"Molecular and genetic properties of tumors associated with local immune cytolytic activity","volume":"160","author":"Rooney","year":"2015","journal-title":"Cell"},{"key":"2023020109053655400_btac161-B14","doi-asserted-by":"crossref","first-page":"100806","DOI":"10.1016\/j.drup.2022.100806","article-title":"Microenvironment-driven intratumoral heterogeneity in head and neck cancers: clinical challenges and opportunities for precision medicine","volume":"60","author":"Van den Bossche","year":"2022","journal-title":"Drug Resist. Updat"},{"key":"2023020109053655400_btac161-B15","doi-asserted-by":"crossref","first-page":"1686","DOI":"10.21105\/joss.01686","article-title":"Welcome to the tidyverse","volume":"4","author":"Wickham","year":"2019","journal-title":"J. Open Source Softw"},{"key":"2023020109053655400_btac161-B16","doi-asserted-by":"crossref","first-page":"2612","DOI":"10.1038\/ncomms3612","article-title":"Inferring tumour purity and stromal and immune cell admixture from expression data","volume":"4","author":"Yoshihara","year":"2013","journal-title":"Nat. Commun"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/advance-article-pdf\/doi\/10.1093\/bioinformatics\/btac161\/43222776\/btac161.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/38\/10\/2940\/49009624\/btac161.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/38\/10\/2940\/49009624\/btac161.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,2,1]],"date-time":"2023-02-01T20:58:21Z","timestamp":1675285101000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/38\/10\/2940\/6550502"}},"subtitle":[],"editor":[{"given":"Can","family":"Alkan","sequence":"additional","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2022,3,18]]},"references-count":15,"journal-issue":{"issue":"10","published-print":{"date-parts":[[2022,5,13]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btac161","relation":{},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"value":"1367-4803","type":"print"},{"value":"1367-4811","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2022,5,15]]},"published":{"date-parts":[[2022,3,18]]}}}