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Node Classification - NoC

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.