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shinyMethyl =========== |Package|BioC-release|BioC-devel |---|---|---| |[shinyMethyl](|[![Release OK](](|[![Devel OK](]( |[shinyMethylData](|[![Release OK](](|[![Devel OK](]( Authors: [Jean-Philippe Fortin]( and [Kasper Daniel Hansen]( Welcome to `shinyMethyl`, an interactive R application based on the `shiny` package for exploration of DNA methylation data from Illumina arrays (450k and EPIC arrays). `shinyMethyl` is part of the [Bioconductor project]( The `shinyMethyl` paper can be found [here]( Installation ------------ First, you will need to install at least the following packages from Bioconductor ```{r} if (!requireNamespace("BiocManager", quietly=TRUE)) install.packages("BiocManager") BiocManager::install("minfi") BiocManager::install("minfiData") ``` and from CRAN ```{r} install.packages("httpuv") install.packages("devtools") install.packages("matrixStats") install.packages("RColorBrewer") ``` To install the development version of shinyMethyl: ```{r} library(devtools) install_github("rstudio/shiny") install_github("jfortin1/shinyMethyl") install_github("jfortin1/shinyMethylData") ``` Vignette ------------ You can find the vignette for `shinyMethyl` at []( Quick example ------------ After installation, you can launch `shinyMethyl` with an example dataset from TCGA with the following code: ```{r} library(shinyMethyl) library(shinyMethylData) runShinyMethyl(summary.tcga.raw, summary.tcga.norm) ``` # Citation To cite package __shinyMethyl__ in publications use: Fortin J, Fertig EJ and Hansen KD (2014). “shinyMethyl: interactive quality control of Illumina 450k DNA methylation arrays in R.”, F1000Research A BibTeX entry for LaTeX users is @Article{shinymethyl, author = {Jean-Philippe Fortin and Elana J. Fertig and Kasper D. Hansen}, title = {{shinyMethyl: interactive quality control of Illumina 450k DNA methylation arrays in R}}, journal = {F1000Research}, year = {2014}, volume = {3}, pages = {175}, doi = {10.12688/f1000research.4680.2}, pubmed = {25285208} }