A node classification tool for gene regulatory networks (GRNs).
Requirements:
- Linux, or unix like OS with support to conda package mananger and bash shell
- Weka 3.8.5
- Python 3
- Pandas
- Numpy
- scipy
- igraph
Installation:
Download NoC files with:
git clone https://github.com/ivanrwolf/NoC
Change directory to the NoC folder:
cd ./NoC
Download Weka version 3.8.5 (https://waikato.github.io/weka-wiki/downloading_weka/) and paste it in NoC folder. Alternatively you can edit NoC.sh and add the path to the "weka.jar" file manually.
In order to provide a easy setup please use conda or miniconda. Install instruction for conda https://docs.anaconda.com/anaconda/install/index.html.
With conda installed, you can install all dependecies with:
conda env create -f conda_NoC_environment.yml
Then, activate conda enviropnment:
conda activate NoC
Usage:
With conda environment activated you can simply run:
bash NoC.sh [input]
Positional arguments:
- input
Input file, currently only supports "ncol" format.
Example:
bash NoC.sh input_Scerevisiae_net.ncol
In order to exit from conda environment:
conda deactivate
If you use NoC please cite: Wolf, I.R., Simões, R.P. & Valente, G.T. Three topological features of regulatory networks control life-essential and specialized subsystems. Sci Rep 11, 24209 (2021). https://doi.org/10.1038/s41598-021-03625-w.