Prerequisites
ICoVeR is designed and implemented as a regular R package. This guide was tested with R v3.3.1 and RStudio v0.99.903. Newer versions should work, please report any problems at the LIST ICoVeR github page. Furthermore, a modern browser is required. We have had most convenient experience with Chrome, but recent versions of Firefox worked as well.
N.B. some users who have their default R library location stored on a network drive have reported issues with installing the application.
If this is the case the solution is to set another local folder as the location for storing installed libraries. This should only be done if there are issues in installing the ICoVeR project.
To set another location for installing packages , for example c:\R_libs
use the following command
.libPaths("c:/R_libs")
Download the most recent version of the project package from here
To run our interactive interface, some packages must be installed. To this end run the following commands in R or RStudio.
# Bioconductor is required for the preprocessing of the fasta files
source("http://bioconductor.org/biocLite.R")
library(BiocInstaller)
biocLite("Biostrings")
# OpenCPU is required to run the interactive binning tool
install.packages("opencpu")
# The packages FactoMiner and Hmisc should be preinstalled
install.packages("FactoMineR")
install.packages("Hmisc")
# devtools is required to install the interactive binning tool
install.packages("devtools")
To get started with the guide you will have to download our prepared package or clone the github repository. In the remainder of this guide we will assume that the package is extracted in your home directory: ~/ICoVeR/
.