{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2023,10,10]],"date-time":"2023-10-10T05:06:59Z","timestamp":1696914419009},"reference-count":10,"publisher":"Oxford University Press (OUP)","issue":"19","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2016,10,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary: The computational speed of many gene set analysis methods can be slow due to the computationally demanding permutation step. This article introduces GSA-Lightning, a fast implementation of permutation-based gene set analysis. GSA-Lightning achieves significant speedup compared with existing methods, particularly when the number of gene sets and permutations are large.<\/jats:p>\n               <jats:p>Availability and implementation: The GSA-Lightning R package is available on Github at https:\/\/github.com\/billyhw\/GSALightning and on R Bioconductor. The package also contains a comprehensive user's guide with a step-by-step tutorial vignette.<\/jats:p>\n               <jats:p>Contact: \u00a0weidong.tian@fudan.edu.cn<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btw349","type":"journal-article","created":{"date-parts":[[2016,6,14]],"date-time":"2016-06-14T02:00:59Z","timestamp":1465869659000},"page":"3029-3031","source":"Crossref","is-referenced-by-count":3,"title":["GSA-Lightning: ultra-fast permutation-based gene set analysis"],"prefix":"10.1093","volume":"32","author":[{"given":"Billy Heung Wing","family":"Chang","sequence":"first","affiliation":[{"name":"1 State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, Department of Biostatistics and Computational Biology, School of Life Sciences, Fudan University, Shanghai 200436, People\u2019s Republic of China"},{"name":"2 Jockey Club School of Public Health and Primary Care, the Chinese University of Hong Kong, Shatin, Hong Kong SAR"}]},{"given":"Weidong","family":"Tian","sequence":"additional","affiliation":[{"name":"1 State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, Department of Biostatistics and Computational Biology, School of Life Sciences, Fudan University, Shanghai 200436, People\u2019s Republic of China"}]}],"member":"286","published-online":{"date-parts":[[2016,6,13]]},"reference":[{"key":"2023020113440479400_btw349-B1","doi-asserted-by":"crossref","first-page":"1943","DOI":"10.1093\/bioinformatics\/bti260","article-title":"Significance analysis of functional categories in gene expression studies: a structured permutation approach","volume":"21","author":"Barry","year":"2005","journal-title":"Bioinformatics"},{"key":"2023020113440479400_btw349-B2","doi-asserted-by":"crossref","first-page":"107","DOI":"10.1214\/07-AOAS101","article-title":"On testing the significance of sets of genes","volume":"1","author":"Efron","year":"2007","journal-title":"Ann. 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