CpGmotifs

A user-friendly graphical interface that allows searching and visualising motifs linked to CpG sites from differential methylation analyses.

Running the CpGmotifs Docker image (suggested)

If you don't have docker installed on your system you can install it by following the instructions at https://www.docker.com/get-docker.

The CpGmotifs docker image is available at https://hub.docker.com/r/grecolab/cpgmotifs

Using CpGmotifs source from GitHub

Linux system library dependencies

     pandoc
     pandoc-citeproc
     libexpat1-dev
     libcairo2-dev
     libxt-dev
     libssl-dev
     libssh2-1-dev
     libssl1.0.0
     libcurl4-openssl-dev
     libxml2-dev
     ghostscript

PERL dependencies

  File::Which 
  HTML::PullParser 
  HTML::Template 
  HTML::TreeBuilder
  JSON XML::Simple
  XML::Parser::Expat

meme suite

   wget http://meme-suite.org/meme-software/5.0.5/meme-5.0.5.tar.gz
   tar -xvf meme-5.0.5.tar.gz && rm meme-5.0.5.tar.gz
   cd meme-5.0.5/
   ./configure --prefix=/meme --with-url=http://meme-suite.org/ --enable-build-libxml2 --enable-build-libxslt
   make
   make install

meme motifs database

  wget http://meme-suite.org/meme-software/Databases/motifs/motif_databases.12.18.tgz
  tar -xvf motif_databases.12.18.tgz

Install R dependencies

#Universal Bioconductor package installation function
  install.bioc <- function(pkg){
    vers <- getRversion()
    if (vers >= "3.6"){
      if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager")
      BiocManager::install(pkg)
    }else{
      if (!requireNamespace("BiocInstaller", quietly = TRUE)){
        source("https://bioconductor.org/biocLite.R")
        biocLite(pkg, suppressUpdates=TRUE)
      }else{
        BiocInstaller::biocLite(pkg, suppressUpdates=TRUE)
      }
    }
  }

#Install Bioconductor dependencies
bioc_pkgs <- c('minfi','BSgenome.Hsapiens.UCSC.hg19','IlluminaHumanMethylation450kanno.ilmn12.hg19', 'IlluminaHumanMethylationEPICanno.ilm10b2.hg19', 'Biostrings')
bioc_pkgs.inst <- bioc_pkgs[!(bioc_pkgs %in% rownames(installed.packages()))]
if(length(bioc_pkgs.inst)>0){
  print(paste0("Missing ", length(bioc_pkgs.inst), " Bioconductor Packages:"))
  for(pkg in bioc_pkgs.inst){
    print(paste0("Installing Package:'", pkg, "'..."))
    install.bioc(pkg)
    print("Installed!!!")
  }
}

#Install CRAN dependencies
cran_pkgs <- c('curl','RCurl','shiny', 'shinyjs', 'shinydashboard', 'readr', 'DT', 'tibble', 'gplots',
                              'dendextend', 'foreach', 'doParallel', 'XML', 'BiocManager')

cran_pkgs.inst <- cran_pkgs[!(cran_pkgs %in% rownames(installed.packages()))]
if(length(cran_pkgs.inst)>0){
  print(paste0("Missing ", length(cran_pkgs.inst), " CRAN Packages:"))
  for(pkg in cran_pkgs.inst){
    print(paste0("Installing Package:'", pkg, "'..."))
    install.packages(pkg, repo="http://cran.rstudio.org", dependencies=TRUE)
    print("Installed!!!")
  }
}

Run CpGmotifs From GitHub

# Load 'shiny' library
library(shiny)
library(shinyjs)
# run on the host port 8787 (or whaterver port you want to map on your system)
runGitHub("CpGmotifs", "Greco-Lab")

or from a local copy

  # Clone the git repository
  git clone https://github.com/Greco-Lab/CpGmotifs CpGmotifs
  # Start R session and run by using runApp()
  library(shiny)
  library(shinyjs)
  # run on the host port 8787 (or whaterver port you want to map on your system)
  runApp("./CpGmotifs/")