Installation

To use ODAMNet you need python>=3.9.

From PyPI

ODAMNet is available in PyPI. You can easily install it using pip.

python3 -m pip install odamnet

From Conda - It’s ongoing

ODAMNet is also available in bioconda using conda.

conda install odamnet

From Github

  1. Clone the repository from GitHub

git clone https://github.com/MOohTus/ODAMNet.git

  1. Then, install it

python3 -m pip install -e ODAMNet/

Usage

Three different approaches are available:

  1. Overlap analysis

  2. Active Modules Identification (AMI, using DOMINO)

  3. Random Walk with Restart (RWR, using multiXrank)

To run one of these approaches:

odamnet [overlap | domino | multixrank] [ARGS]

To create a disconnected rare disease pathways network and its corresponding gene - rare disease pathways bipartite network (these networks may be used for the RWR approach):

odamnet networkCreation [ARGS]

To download biological networks directly from NDEx:

odamnet networkDownloading [ARGS]

To display help:

odamnet [-h] [--help]