netcoloc 0.1.7

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NetColoc

Description

Here we introduce NetColoc, a tool which evaluates the extent to which two gene sets are related in network space, i.e. the extent to which they are colocalized in a molecular interaction network, and interrogates the underlying biological pathways and processes using multiscale community detection.

This framework may be applied to any number of scenarios in which gene sets have been associated with a phenotype or condition, including rare and common variants within the same disease, genes associated with two comorbid diseases, genetically correlated GWAS phenotypes, GWAS across two different species, or gene expression changes after treatment with two different drugs, to name a few.

NetColoc relies on a dual network propagation approach to identify the region of network space which is significantly proximal to both input gene sets, and as such is highly effective for small to medium input gene sets.

Documentation

For a quick-start on NetColoc’s functionality, please see the example notebooks.

Usage Note: Please follow steps in example notebooks for correct usage of NetColoc. At this time, individual functionalities have not been tested for independent use.

Dependencies

NetColoc requires the following python packages:

Note

All of the following packages minus DDOT and cdapsutil will be automatically installed via pip install netcoloc

• click

• matplotlib

• ndex2

• networkx

• numpy

• seaborn

• tqdm

• mygene >= 3.2.2

• scipy >= 1.5.3

• statsmodels

• gprofiler-official >= 1.0.0

• ipywidgets

• ipycytoscape

• python3 branch of DDOT

  DDOT can be installed one of two ways:

  1. To install DDOT by downloading the zip file of the source tree:

     wget https://github.com/idekerlab/ddot/archive/refs/heads/python3.zip
     unzip python3.zip
     cd ddot-python3
     python setup.py bdist_wheel
     pip install dist/ddot*py3*whl

  2. To install DDOT by cloning the repo:

     git clone --branch python3 https://github.com/idekerlab/ddot.git
     cd ddot
     python setup.py bdist_wheel
     pip install dist/ddot*py3*whl

  Note

  Due to dependency issue DDOT, will not work with Python 3.10 or later

Additional requirements for full functionality of example notebook:

• cdapsutil >= 0.2.0a1

Installation

NetColoc is available on PyPI

pip install netcoloc

License

• Free software: MIT license

Citing NetColoc

Coming soon…

Credits

This package was created with Cookiecutter and the audreyr/cookiecutter-pypackage project template.

History

0.1.7 (2022-06-28)

• Removed unused network_localization.py module

0.1.6 (2022-06-16)

• ipycytoscape added as a dependency

• ipywidgets added as a dependency

• Added network_colocalization.sweep_input_pvals() to sweep p-values and scores

• Added network_colocalization.calculate_network_enrichment() to sweep over z-score thresholds

• netprop.get_individual_heats_matrix() can take a networkx Graph object and internally call netprop.get_normalized_adjancency_matrix(). Documentation updated in both methods to note that the resulting matrices can be saved via numpy.save() and retrieved via numpy.load()

• example_notebooks/ASD_CHD_NetColoc_analysis.ipynb now visualizes hierarchy using ipycytoscape

• example_notebooks/ASD_CHD_NetColoc_analysis.ipynb updated with a note about using numpy.save() and numpy.load() to save and retrieve result from netprop.get_individual_heats_matrix()

0.1.5 (2022-03-09)

• Fixed divide by zero error seen when calculating cosine distance by updating netprop.get_normalized_adjancency_matrix() to properly normalize an adjacency matrix that is asymetric (UD-1863)

0.1.4 (2021-08-31)

• If import of DDOT package fails, only a warning message will be displayed unless user invokes netcoloc.validation.load_MPO() in which case an ImportError is raised

• Fixed bug where z1_threshold parameter was being passed to z2_threshold parameter in netcoloc.network_cololcalization.calcualte_network_overlap method called by netcoloc.network_colocalization.calculate_network_overlap_subgraph method

0.1.3 (2021-08-18)

• Added dependency gprofiler-official to setup.py and requirements.txt because this is used by network_colocalization.py

0.1.2 (2021-08-17)

• Added new validation.py module containing mouse knockout database functionality

0.1.1 (2021-08-06)

• Fixed netcoloc imports in netprop_zcore.py

0.1.0 (2021-03-10)

• First release on PyPI.