epigeec-analysis

Analysis tools for epiGeEC


License
GPL-3.0
Install
pip install epigeec-analysis==1.3.0

Documentation

epiGeEC Analysis


The epiGenomic Efficient Correlator Analysis tools are a suite to analyse correlation matrix from epiGenomic Efficient Correlator.

Installation


Linux/x64 is the only OS currently supported

Install epiGeEC Analysis

git clone git@bitbucket.org:labjacquespe/geec_analysis.git

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.

In geec_analysis path:

sudo pip install -r requirements.txt

You might have more success with

sudo apt-get install python-pandas

How To Use


For more info on each parameter use the help flag

python toolname.py --help

Annotate a matrix

python geec_annotate.py --pdf output.pdf --tsv output.tsv epiGeEC_Correlate.mat epiGeEC_Datasets.json assay cell_type timepoint

Evaluate clusters

python geec_ari.py epiGeEC_Correlate.mat epiGeEC_Datasets.json -b assay cell_type timepoint -r assay cell_type timepoint > output.ari

License


GNU General Public License v3