Analysis tools for epiGeEC
pip install epigeec-analysis==1.3.0
The epiGenomic Efficient Correlator Analysis tools are a suite to analyse correlation matrix from epiGenomic Efficient Correlator.
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
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