Installation

Installation (via pip)

The simplest way to keep up-to-date with the cmonkey2 versions is to install it through pip.

pip install cmonkey2

MEME for motif finding

Note that in order to use MEME, you will need to have MEME installed and available in your $PATH. MEME is available here. cMonkey₂ is compatible with MEME versions 4.3.0, 4.8.x, 4.9.x and 4.10.x.

The cMonkey₂ distribution contains a MEME installation script which will download, configure, compile, and locally install the relevant MEME suite tools in the current working directory. MEME requires csh. Simply execute

sudo apt-get install csh   ## or tcsh
tools/install_meme.sh

Usage

Installing cmonkey2 makes the commands cmonkey2, cm2view, cm2plot and cm2export available. It is recommended that you create a project directory for your run containing your gene expression file and run it from there. cmonkey2 will create a cache and out directory in that directory by default.

cmonkey2 --organism <your organism> --ratios <your_ratios.tsv>