{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,14]],"date-time":"2026-04-14T15:37:10Z","timestamp":1776181030725,"version":"3.50.1"},"reference-count":12,"publisher":"Oxford University Press (OUP)","issue":"11","license":[{"start":{"date-parts":[[2018,10,22]],"date-time":"2018-10-22T00:00:00Z","timestamp":1540166400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"name":"CDC\/NIOSH","award":["U01 OH011478-01"],"award-info":[{"award-number":["U01 OH011478-01"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2019,6,1]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:sec><jats:title>Motivation<\/jats:title><jats:p>An important downstream analysis following differential expression from RNA sequencing (RNA-Seq) or DNA methylation analysis is the gene set testing to relate significant genes or CpGs to known biological properties. However, the traditional gene set testing approaches result in biased P-values due to the difference in gene length. Existing methods accounting for length bias were primarily developed for RNA-Seq data. For DNA methylation data profiled using the Illumina arrays, separate methods adjusting for the number of CpGs instead of gene length are necessary.<\/jats:p><\/jats:sec><jats:sec><jats:title>Results<\/jats:title><jats:p>We developed methylGSA, a Bioconductor package for gene set testing in DNA methylation data. Our accompanying Shiny app provides an interactive way of accessing functions and visualizing the results in methylGSA package.<\/jats:p><\/jats:sec><jats:sec><jats:title>Availability and implementation<\/jats:title><jats:p>methylGSA is available at Bioconductor repository: https:\/\/bioconductor.org\/packages\/methylGSA and Shiny app is available at: http:\/\/www.ams.sunysb.edu\/%7epfkuan\/softwares.html#methylGSA.<\/jats:p><\/jats:sec><jats:sec><jats:title>Supplementary information<\/jats:title><jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p><\/jats:sec>","DOI":"10.1093\/bioinformatics\/bty892","type":"journal-article","created":{"date-parts":[[2018,10,19]],"date-time":"2018-10-19T11:13:02Z","timestamp":1539947582000},"page":"1958-1959","source":"Crossref","is-referenced-by-count":184,"title":["methylGSA: a Bioconductor package and Shiny app for DNA methylation data length bias adjustment in gene set testing"],"prefix":"10.1093","volume":"35","author":[{"given":"Xu","family":"Ren","sequence":"first","affiliation":[{"name":"Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, NY, USA"}]},{"given":"Pei Fen","family":"Kuan","sequence":"additional","affiliation":[{"name":"Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, NY, USA"}]}],"member":"286","published-online":{"date-parts":[[2018,10,22]]},"reference":[{"key":"2023012713230586300_bty892-B1","doi-asserted-by":"crossref","first-page":"289","DOI":"10.1111\/j.2517-6161.1995.tb02031.x","article-title":"Controlling the false discovery rate: a practical and powerful approach to multiple testing","volume":"57","author":"Benjamini","year":"1995","journal-title":"J. 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