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Kasper Daniel Hansen 6.5k@kasper-daniel-hansen-2979
Last seen 10 weeks ago
The 'bumphunter' package has just been accepted to Bioconductor (we anticipate binary build being available in around 36 hours). Bump hunting is a general methodology we have successfully used to analyze various types of DNA methylation data. It is more formally described in . Variants of the code are already included in the charm package and the bsseq package; we anticipate both package to eventually depend on this new package. The package is meant to provide a backend for developers wishing to utilize (a variant) of the method on their own data. Usually, some adaptation needs to be done on any given data type and we envision various assay specific packages to use this backend (ie. it is not really meant for casual users). In addition, the package contain annotateNearest, a function we find very useful for further analysis of GenomicRanges::nearest. [ Now that bumphunter is available, we plan to release our version for the Illumina 450k platform in the minfi package "really soon". We just need to finish up the documentation, tidy up the user interface a bit, and move code from our internal repository into the public version of minfi. ] On behalf of the authors, Kasper D Hansen Nathan-McKusick Institute of Genetic Medicine Dept of Biostatistics Johns Hopkins University  Jaffe, A. E. et al. Bump hunting to identify differentially methylated regions in epigenetic epidemiology studies. International Journal of Epidemiology 41, 200?209 (2012).