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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, but it can work on any platform with python and pip installed.

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

This tool suite provide multiple analysis program.

For more info on each parameter use the help flag

epigeec-analysis [tool] --help

Annotate matrix

Essentialy, this tool apply a hierachical cluster method on a correlation matrix to regroup datasets in clusters associated with their metadatas.

Hierarchical clustering

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

GNU General Public License v3

Project details


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