FunMappOne

A user-friendly graphical interface that allows to visualize and summarize the functional annotations of one or multiple molecular biology experiments at once.

Reference paper:

Scala, G., Serra, A., Marwah, V. S., Saarimäki, L. A., & Greco, D. (2019). FunMappOne: a tool to hierarchically organize and visually navigate functional gene annotations in multiple experiments. BMC bioinformatics, 20(1), 79.

More information at: https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-019-2639-2

Running the FunMappOne 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 FunMappOne docker image is available at https://hub.docker.com/r/grecolab/funmappone

Using FunMappOne source from GitHub

Linux system library dependencies

libv8-3.14-dev
libxml2-dev
libssl-dev

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("org.Hs.eg.db", "org.Mm.eg.db", "org.Rn.eg.db", "KEGG.db", "reactome.db", "GOSim")
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("ggplotify", "RColorBrewer", "reshape", "ggplot2", "shiny", "shinyjs", "tibble",
               "gProfileR","gprofiler2", "DT", "randomcoloR", "readxl", "cellranger", "devtools", "scales",
               "gtools", "shinycssloaders", "shinyBS", "tidyverse",
                "gridExtra", "gtable", "grid", "xlsx")
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 FunMappOne 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("FunMappOne", "Greco-Lab")

or from a local copy

  # Clone the git repository
  git clone https://github.com/Greco-Lab/FunMappOne FunMappOne
  # 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("./FunMappOne/")