diffupath 0.0.1

Installation

1. diffupath can be installed with the following commands:

$ python3 -m pip install git+https://github.com/multipaths/DiffuPath.git@master

2. or in editable mode with:

$ git clone https://github.com/multipaths/DiffuPath.git
$ cd diffupath
$ python3 -m pip install -e .

Requirements

diffupath requires the following libraries:

networkx (>=2.1)
pybel (0.13.2)
biokeen (0.0.14)
click (7.0)
tqdm (4.31.1)
numpy (1.16.3)
scipy (1.2.1)
scikit-learn (0.21.3)
pandas (0.24.2)
openpyxl (3.0.2)
plotly (4.5.3)
matplotlib (3.1.2)
matplotlib_venn (0.11.5)
bio2bel (0.2.1)
pathme
diffupy

Command Line Interface

The following commands can be used directly use from your terminal:

1. Download a database for network analysis.

The following command generates a BEL file representing the network of the given database.

$ python3 -m diffupath database network --database=<database-name>

To check the available databases, run the following command:

$ python3 -m diffupath database ls

2. Run a diffusion analysis

The following command will run a diffusion method on a given network with the given data

$ python3 -m diffupath diffusion run --network=<path-to-network-file> --input=<path-to-data-file> --method=<method>

Networks

You can choose networks to run diffusion methods in the following ways:

• Select a network representing an individual biological database

• Select multiple databases to generate a harmonized network

• Select from one of four predefined collections of biological databases representing a harmonized network

• Submit your own network from one of the accepted formats

Disclaimer

DiffuPath is a scientific software that has been developed in an academic capacity, and thus comes with no warranty or guarantee of maintenance, support, or back-up of data.

References