Analysis tools for epiGeEC
The epiGenomic Efficient Correlator (epiGeEC) Analysis is a suite of tools to process, annotate and analyse correlation matrices generated by epiGeEC. A galaxy implementation featuring these tools and including thousands of pre-computed public epigenomic datasets is availalble at http://epigeec.genap.ca/galaxy/.
Linux/x64 is the only OS currently supported, but it can work on any platform with python and pip installed.
You will need pip to install the python package, use the following command if not already installed
sudo apt-get install python-pip
Pip will attempt to install all dependencies but most likely will fail
See documentation on how to install pandas.
You might have more success with
sudo apt-get install python-pandas
Install epiGeEC Analysis
sudo pip install epigeec-analysis
How To Use
This tool suite provide multiple analysis program.
For more info on each parameter use the help flag
epigeec-analysis [tool] --help
Essentialy, this tool apply a hierachical cluster method on a correlation matrix to regroup datasets in clusters associated with their metadatas.
epigeec-analysis annotate --pdf output.pdf --tsv output.tsv epiGeEC_Correlate.mat epiGeEC_Datasets.json assay cell_type timepoint
epigeec-analysis evaluate epiGeEC_Correlate.mat epiGeEC_Datasets.json -b assay cell_type timepoint -r assay cell_type timepoint > output.ari
Download the file for your platform. If you're not sure which to choose, learn more about installing packages.
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