{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,8]],"date-time":"2025-10-08T15:56:33Z","timestamp":1759938993165},"reference-count":8,"publisher":"Oxford University Press (OUP)","issue":"17","license":[{"start":{"date-parts":[[2019,1,10]],"date-time":"2019-01-10T00:00:00Z","timestamp":1547078400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"name":"Richard and Helen DeVos foundation"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2019,9,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>The L1000 dataset from the NIH LINCS program holds the promise to deconvolute a wide range of biological questions in transcriptional space. However, using this large and decentralized dataset presents its own challenges. The slinky package was created to streamline the process of identifying samples of interest and their corresponding control samples, and loading their associated expression data and metadata. The package can integrate with workflows leveraging the BioConductor collection of tools by encapsulating the L1000 data as a SummarizedExperiment object.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>Slinky is freely available as an R package at http:\/\/bioconductor.org\/packages\/slinky<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btz002","type":"journal-article","created":{"date-parts":[[2019,1,4]],"date-time":"2019-01-04T20:11:19Z","timestamp":1546632679000},"page":"3176-3177","source":"Crossref","is-referenced-by-count":4,"title":["Streamlined analysis of LINCS L1000 data with the slinky package for R"],"prefix":"10.1093","volume":"35","author":[{"given":"Eric J","family":"Kort","sequence":"first","affiliation":[{"name":"Van Andel Research Institute, Grand Rapids DeVos Cardiovascular Research Program, Spectrum Health and , MI, USA"},{"name":"Michigan State University, East Lansing Department of Pediatrics and Human Development, , MI, USA"}]},{"given":"Stefan","family":"Jovinge","sequence":"additional","affiliation":[{"name":"Van Andel Research Institute, Grand Rapids DeVos Cardiovascular Research Program, Spectrum Health and , MI, USA"}]}],"member":"286","published-online":{"date-parts":[[2019,1,10]]},"reference":[{"key":"2023062711321880400_btz002-B1","doi-asserted-by":"crossref","first-page":"79","DOI":"10.1186\/1471-2105-15-79","article-title":"The characteristic direction: a geometrical approach to identify differentially expressed genes","volume":"15","author":"Clark","year":"2014","journal-title":"BMC Bioinformatics"},{"key":"2023062711321880400_btz002-B2","doi-asserted-by":"crossref","first-page":"96ra76","DOI":"10.1126\/scitranslmed.3002648","article-title":"Computational repositioning of the anticonvulsant topiramate for inflammatory bowel disease","volume":"3","author":"Dudley","year":"2011","journal-title":"Sci. Transl. Med"},{"key":"2023062711321880400_btz002-B3","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":"Nat. Methods"},{"key":"2023062711321880400_btz002-B4","doi-asserted-by":"crossref","first-page":"13","DOI":"10.1016\/j.cels.2017.11.001","article-title":"The library of integrated network-based cellular signatures NIH program: system-level cataloging of human cells response to perturbations","volume":"6","author":"Keenan","year":"2018","journal-title":"Cell Syst"},{"key":"2023062711321880400_btz002-B5","doi-asserted-by":"crossref","first-page":"144.","DOI":"10.1186\/1471-2105-6-144","article-title":"PAGE: parametric analysis of gene set enrichment","volume":"6","author":"Kim","year":"2005","journal-title":"BMC Bioinformatics"},{"key":"2023062711321880400_btz002-B6","doi-asserted-by":"crossref","first-page":"1929","DOI":"10.1126\/science.1132939","article-title":"The Connectivity Map: using gene-expression signatures to connect small molecules, genes, and disease","volume":"313","author":"Lamb","year":"2006","journal-title":"Science"},{"key":"2023062711321880400_btz002-B7","doi-asserted-by":"crossref","DOI":"10.1016\/j.cell.2017.10.049","article-title":"A next generation connectivity map: L 1000 platform and the first 1, 000, 000 profiles","volume":"171","author":"Subramanian","year":"2017","journal-title":"Cell"},{"key":"2023062711321880400_btz002-B8","doi-asserted-by":"crossref","first-page":"2150","DOI":"10.1093\/bioinformatics\/bty060","article-title":"L1000FWD: fireworks visualization of drug-induced transcriptomic signatures","volume":"34","author":"Wang","year":"2018","journal-title":"Bioinformatics"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/35\/17\/3176\/50720023\/bioinformatics_35_17_3176.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/35\/17\/3176\/50720023\/bioinformatics_35_17_3176.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,6,27]],"date-time":"2023-06-27T11:33:20Z","timestamp":1687865600000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/35\/17\/3176\/5284904"}},"subtitle":[],"editor":[{"given":"Janet","family":"Kelso","sequence":"additional","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2019,1,10]]},"references-count":8,"journal-issue":{"issue":"17","published-print":{"date-parts":[[2019,9,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btz002","relation":{},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"value":"1367-4803","type":"print"},{"value":"1367-4811","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2019,9,1]]},"published":{"date-parts":[[2019,1,10]]}}}