Analysis tools for epiGeEC
Project description
epiGeEC Analysis
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/.
Installation
Linux/x64 is the only OS currently supported
Dependencies
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
For more info on each parameter use the help flag
epigeec-analysis [tool] --help
Annotate a matrix
epigeec-analysis annotate --pdf output.pdf --tsv output.tsv epiGeEC_Correlate.mat epiGeEC_Datasets.json assay cell_type timepoint
Evaluate clusters
epigeec-analysis evaluate epiGeEC_Correlate.mat epiGeEC_Datasets.json -b assay cell_type timepoint -r assay cell_type timepoint > output.ari
License
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