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Streamlined workflow for the quality control, normalization and bias-free analysis of Illumina methylation array data - The Leiden approach

Workflow

Check out our complete workflow: workflow

Installation

The DNAmArray-package can be installed in several ways which are described below. The package has been installed successfully for >= R-4.4.3 on different linux-builds.

The package depends on many other packages from BioConductor or cran. Usually these are installed automatically, otherwise, we refer to BioConductor or cran documentation for the installation of these packages.

Install using the devtools-package

First install devtools. Next use:

library(devtools)
install_github("molepi/DNAmArray") ##for master
install_github("molepi/DNAmArray", ref="R-4.4.3") ##for other branches

Sometimes install_github fails with CA cert error. Try running httr::set_config(httr::config( ssl_verifypeer = 0L)) before running install_github!

Install from source using git/R

Using git, e.g, use git clone and then build and install the package from source:

git clone git@git.lumc.nl:molepi/DNAmArray.git
R CMD build DNAmArray
R CMD INSTALL DNAmArray_x.y.z.tar.gz

Change _x.y.z. to the proper version you downloaded!