ebits: bioinformatics-related R modules

This repository is meant as a collection of bioinformatics-related R code that simplify workflows and can be shared with other people.

For details, see the README.md files and API documentation in the respective directories.

Requirements

This collection of tools requires modules, install using using devtools:

# install.packages('devtools')
devtools::install_github('klmr/modules')

The scripts also depend on a range of R packages. If using only a few modules, you may want to install only the packages you need. Otherwise you can list/install all of them by typing:

./dependencies.sh # list all packages
make deps # install all packages (warning: there's a lot)

Setup

cd your_local_directory
git clone https://github.com/EBI-predocs/ebits.git
cd ebits && git submodule --init --recursive

Additionally, you need load the modules package and tell R where to find the ebits module. In order to do this, set your import.path in your ~/.Rprofile:

library(modules) # can also load manually
options(import.path=c("/path/to/ebits",
                      "/path/to/other/module")

Usage

Modules can be imported and used as described in the modules documentation

mod = import('module') # imports the module
mod$func(x=5)          # calls the module function