Preprocessing, normalization and integration of the Illumina HumanMethylationEPIC array with minfi.
作者： Jean-Philippe Fortin , Timothy J Triche Jr , Kasper D Hansen
DOI: 10.1093/BIOINFORMATICS/BTW691
关键词:
摘要: … This increased resolution, coupled with greatly expanded coverage of regulatory elements, makes the EPIC array an attractive platform for large-scale profiling of DNA methylation. …
oup.com
elsevier.com
sci-hub.se 参考文章(15)
Jean-Philippe Fortin, Kasper D. Hansen, Reconstructing A/B compartments as revealed by Hi-C using long-range correlations in epigenetic data Genome Biology. ,vol. 16, pp. 180- 180 ,(2015) , 10.1186/S13059-015-0741-Y
Wolfgang Huber, Vincent J Carey, Robert Gentleman, Simon Anders, Marc Carlson, Benilton S Carvalho, Hector Corrada Bravo, Sean Davis, Laurent Gatto, Thomas Girke, Raphael Gottardo, Florian Hahne, Kasper D Hansen, Rafael A Irizarry, Michael Lawrence, Michael I Love, James MacDonald, Valerie Obenchain, Andrzej K Oleś, Hervé Pagès, Alejandro Reyes, Paul Shannon, Gordon K Smyth, Dan Tenenbaum, Levi Waldron, Martin Morgan, Orchestrating high-throughput genomic analysis with Bioconductor Nature Methods. ,vol. 12, pp. 115- 121 ,(2015) , 10.1038/NMETH.3252
Lovisa E. Reinius, Nathalie Acevedo, Maaike Joerink, Göran Pershagen, Sven-Erik Dahlén, Dario Greco, Cilla Söderhäll, Annika Scheynius, Juha Kere, Differential DNA Methylation in Purified Human Blood Cells: Implications for Cell Lineage and Studies on Disease Susceptibility PLOS ONE. ,vol. 7, ,(2012) , 10.1371/JOURNAL.PONE.0041361
Richard Shen, Marina Bibikova, Bret Barnes, Chan Tsan, Vincent Ho, Brandy Klotzle, Jennie M. Le, David Delano, Lu Zhang, Gary P. Schroth, Kevin L. Gunderson, Jian-Bing Fan, High density DNA methylation array with single CpG site resolution Genomics. ,vol. 98, pp. 288- 295 ,(2011) , 10.1016/J.YGENO.2011.07.007
Jean-Philippe Fortin, Elana Fertig, Kasper Hansen, shinyMethyl: interactive quality control of Illumina 450k DNA methylation arrays in R. F1000Research. ,vol. 3, pp. 175- 175 ,(2014) , 10.12688/F1000RESEARCH.4680.2
Timothy J Triche Jr, Daniel J Weisenberger, David Van Den Berg, Peter W Laird, Kimberly D Siegmund, Low-level processing of Illumina Infinium DNA Methylation BeadArrays Nucleic Acids Research. ,vol. 41, ,(2013) , 10.1093/NAR/GKT090
Martin J. Aryee, Andrew E. Jaffe, Hector Corrada-Bravo, Christine Ladd-Acosta, Andrew P. Feinberg, Kasper D. Hansen, Rafael A. Irizarry, Minfi: A flexible and comprehensive Bioconductor package for the analysis of Infinium DNA Methylation microarrays Bioinformatics. ,vol. 30, pp. 1363- 1369 ,(2014) , 10.1093/BIOINFORMATICS/BTU049
Jerry Guintivano, Martin J. Aryee, Zachary A. Kaminsky, A cell epigenotype specific model for the correction of brain cellular heterogeneity bias and its application to age, brain region and major depression Epigenetics. ,vol. 8, pp. 290- 302 ,(2013) , 10.4161/EPI.23924
Jovana Maksimovic, Lavinia Gordon, Alicia Oshlack, SWAN: Subset-quantile within array normalization for illumina infinium HumanMethylation450 BeadChips. Genome Biology. ,vol. 13, pp. 1- 12 ,(2012) , 10.1186/GB-2012-13-6-R44
Jean-Philippe Fortin, Aurélie Labbe, Mathieu Lemire, Brent W Zanke, Thomas J Hudson, Elana J Fertig, Celia MT Greenwood, Kasper D Hansen, Functional normalization of 450k methylation array data improves replication in large cancer studies Genome Biology. ,vol. 15, pp. 503- 503 ,(2014) , 10.1186/S13059-014-0503-2