eUTOPIA: solUTion for Omics data PreprocessIng and Analysis
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README.md

eUTOPIA

A solUTion for Omics data PreprocessIng and Analysis

Graphically accessible guided workflow for preprocessing and analysis of omics data. Supports Agilent 2-color, Agilent 1-color, Affymetrix, and Illumina methylation microarray platforms (Ongoing efforts to add support for RNA-Seq data). Discreetly separated steps in analysis designed in R Shiny, incorporates widely used microarray analysis practices and R packages. Reporting is and data interpretation is leveraged from dynamically generated plots.

Install Dependencies

  #Install impute dependency
  source("http://bioconductor.org/biocLite.R")
  biocLite("impute")

  #Install CRAN dependencies
  cran_pkgs <- c("bibtex", "RMySQL", "progress", "swamp", "infotheo", "gplots", "RColorBrewer",
  "shiny", "shinyjs", "shinyBS", "shinydashboard", "shinyFiles", "DT", "shinycssloaders",
  "ggplot2", "ggrepel", "WriteXLS", "rmarkdown", "VennDiagram", "grid", "futile.logger",
  "reshape2", "htmlTable", "devtools", "httr", "randomcoloR")
  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!!!")
    }
  }

  #Install latest version of rhandsontable from GitHub
  print("Installing rhandsontable from GitHub!")
  devtools::install_github("jrowen/rhandsontable")

  #Install latest version of UpSetR from GitHub
  print("Installing UpSetR from GitHub!")
  devtools::install_github("hms-dbmi/UpSetR")

  #Install Bioconductor dependencies
  source("http://bioconductor.org/biocLite.R")
  bioc_pkgs <- c("limma", "sva", "Biobase", "biomaRt", "affy", "affyQCReport",
  "arrayQualityMetrics", "made4", "vsn", "GEOquery", "minfi",
  "IlluminaHumanMethylation450kmanifest", "IlluminaHumanMethylation450kanno.ilmn12.hg19",
  "IlluminaHumanMethylationEPICmanifest", "IlluminaHumanMethylationEPICanno.ilm10b2.hg19",
  "affyio", "simpleaffy", "yaqcaffy", "GO.db", "shinyMethyl")
  bioc_pkgs.inst <- bioc_pkgs[!(bioc_pkgs %in% rownames(installed.packages()))]
  if(length(bioc_pkgs.inst)>0){
    source("http://bioconductor.org/biocLite.R")
    print(paste0("Missing ", length(bioc_pkgs.inst), " Bioconductor Packages:"))
    for(pkg in bioc_pkgs.inst){
      print(paste0("Installing Package:'", pkg, "'..."))
      biocLite(pkg, suppressUpdates=TRUE)
      print("Installed!!!")
    }
  }

  #Install latest version of GOSemSim from GitHub
  print("Installing GOSemSim from GitHub!")
  devtools::install_github("GuangchuangYu/GOSemSim")

How to run eUTOPIA from GitHub

  # Load 'shiny' library
  library(shiny)

  # Using runGitHub
  runGitHub("eUTOPIA", "Greco-Lab", subdir="eUTOPIA-app")

  # Using the archived file
  runUrl("https://github.com/Greco-Lab/eUTOPIA/archive/master.tar.gz", subdir="eUTOPIA-app")
  runUrl("https://github.com/Greco-Lab/eUTOPIA/archive/master.zip", subdir="eUTOPIA-app")

How to run locally

  # Clone the git repository
  git clone https://github.com/Greco-Lab/eUTOPIA eUTOPIA_clone

  # Start R session and run by using runApp()
  setwd("./eUTOPIA_clone")
  library(shiny)
  runApp("eUTOPIA-app/")