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.
Reference Paper:
Marwah, V. S., Scala, G., Kinaret, P. A. S., Serra, A., Alenius, H., Fortino, V., & Greco, D. (2019). eUTOPIA: solUTion for Omics data PreprocessIng and Analysis. Source code for biology and medicine, 14(1), 1.
More information at: https://link.springer.com/article/10.1186/s13029-019-0071-7
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 eUTOPIA docker image is available at https://hub.docker.com/r/grecolab/eutopia
Pandoc - https://pandoc.org/installing.html
Latex Compiling - http://www.tug.org/texlive/
Perl - https://www.perl.org/get.html
Cairo - https://cairographics.org/download/
#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 impute dependency
install.bioc("impute")
#Install CRAN dependencies
cran_pkgs <- c("bibtex", "RMySQL", "progress", "swamp", "infotheo", "gplots", "RColorBrewer",
"shiny", "shinyjs", "shinyBS", "shinydashboard", "shinyFiles", "DT", "shinycssloaders", "cowplot",
"ggplot2", "ggrepel", "WriteXLS", "rmarkdown", "VennDiagram", "grid", "futile.logger", "base2grob",
"reshape2", "htmlTable", "devtools", "httr", "randomcoloR", "doParallel", "foreach", "import","calibrate")
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
bioc_pkgs <- c("limma", "sva", "Biobase", "biomaRt", "affy", "affyPLM",
"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){
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 latest version of GOSemSim from GitHub
print("Installing GOSemSim from GitHub!")
devtools::install_github("GuangchuangYu/GOSemSim")
#Install Tex distribution
tinytex::install_tinytex()
# 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")
# 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/")
install.packages("usethis")
usethis::edit_r_environ() #Opens the R enviroenment file in an editor
#Specify the following line in the file, save and close
R_MAX_NUM_DLLS=256
#Restart R session and OS if required
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE92900
ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE92nnn/GSE92900/suppl/GSE92900_raw_data_files.tar.gz
https://github.com/Greco-Lab/eUTOPIA/blob/master/sample_data/Phenotype_File.tsv