Install-instructions

Install instructions

You will receive a Github TOKEN in the provided email from the download form. You must use it to install Methyl-IT in your R session as you follow the folowing instructions. Please take care of the token EXPIRATION DATE, if you take over that date you will need to fill again the download form from this website.

Installation

Be sure that both the R and bioconductor packages are up to date. To get the latest version of Bioconductor by starting R and entering the commands:

if (!requireNamespace("BiocManager")) install.packages("BiocManager")

BiocManager::install()

CentOS 7

sudo yum -y install libcurl-devel.x86_64 openssl-devel.x86_64 libxml2-devel mariadb-devel.x86_64

Ubuntu

sudo apt install libmysqlclient-dev libcurl4-openssl-dev libssl-dev libxml2-dev git build-essential

Install R dependencies:

BiocManager::install(c("caret", "Epi", "e1071", "minpack.lm", "nls2", "caTools", "RCurl",'GenomicRanges','BiocParallel', 'biovizBase', 'genefilter', 'data.table', 'dplyr', 'GenomeInfoDb', 'randomForest', dependencies=TRUE))

Install MethylIT:

# Stable version (0.3.2.7)

After your request, you will receive an email with a "token" (a code text). In the R console, use the "BiocManager::install " command to install Methyl-IT as shown below:

BiocManager::install("epimethyl/MethylIT", auth_token = "PASTE THE TOKEN SENT BY EMAIL HERE")