orbweaver

Orbweaver is a simple python API for performing gene co-expression network analysis. It's a pet project and it's currently still under development. Pull requests are welcome. However, this package is low priority, so I may not be extremely efficient at responding to contributors. Orbweaver relies heavily on the wonderful Networkx API. It is thus compatible with the wide range of network analysis tools available in Networkx. Other key dependencies are listed in the setup.py. A demonstration of the current Orbweaver workflow can be found in the notebooks/demo.ipynb Jupyter notebook.

Current features include:

1. Straightforward API for handling datasets, matrices, and network objects.

2. Multiple similarity metrics for comparing gene expression profiles.

3. Simple built-in visualizations for similarity matrices and networks.

4. Functions for re-weighting graphs and converting from weighted to unweighted.

5. Exporting of network objects in various formats.

Future features (in development) will include:

1. Simulation of networks and data with specified structure and co-expression relationships.

2. Improved network visualization.

3. Tools for handling uncertainty across replicate datasets.

4. Built-in approaches for data clustering.

5. Functions for calculating certain aspects of network topology.

Install

Clone this repository and install a development version using pip:

pip install -e .