Package: netcoloc
NetColocDescriptionHere 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.DocumentationFor a quick-start on NetColoc’s functionality, please see theexample 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.DependenciesNetColoc requires the following python packages:NoteAll of the following packages minusDDOTandcdapsutilwill be automatically installed viapip install netcolocclickmatplotlibndex2networkxnumpyseaborntqdmmygene >= 3.2.2scipy >= 1.5.3statsmodelsgprofiler-official >= 1.0.0ipywidgetsipycytoscapepython3 branch of DDOTDDOTcan be installed one of
two ways:To installDDOTby 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*whlTo installDDOTby 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*whlNoteDue to dependency issue DDOT, will not work with Python 3.10 or laterAdditional requirements for full functionality of example notebook:cdapsutil >= 0.2.0a1InstallationNetColoc is available onPyPIpip install netcolocLicenseFree software: MIT licenseCiting NetColocComing soon…CreditsThis package was created withCookiecutterand theaudreyr/cookiecutter-pypackageproject template.History0.1.7 (2022-06-28)Removed unusednetwork_localization.pymodule0.1.6 (2022-06-16)ipycytoscapeadded as a dependencyipywidgetsadded as a dependencyAddednetwork_colocalization.sweep_input_pvals()to sweep p-values and scoresAddednetwork_colocalization.calculate_network_enrichment()to sweep over z-score thresholdsnetprop.get_individual_heats_matrix()can take a networkxGraphobject and internally callnetprop.get_normalized_adjancency_matrix(). Documentation updated in both methods to note
that the resulting matrices can be saved vianumpy.save()and retrieved vianumpy.load()example_notebooks/ASD_CHD_NetColoc_analysis.ipynbnow visualizes hierarchy usingipycytoscapeexample_notebooks/ASD_CHD_NetColoc_analysis.ipynbupdated with a note about usingnumpy.save()andnumpy.load()to save and retrieve result fromnetprop.get_individual_heats_matrix()0.1.5 (2022-03-09)Fixed divide by zero error seen when calculating cosine distance by updatingnetprop.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 invokesnetcoloc.validation.load_MPO()in which case anImportErroris raisedFixed bug wherez1_thresholdparameter was being passed toz2_thresholdparameter innetcoloc.network_cololcalization.calcualte_network_overlapmethod called bynetcoloc.network_colocalization.calculate_network_overlap_subgraphmethod0.1.3 (2021-08-18)Added dependencygprofiler-officialtosetup.pyandrequirements.txtbecause this is used bynetwork_colocalization.py0.1.2 (2021-08-17)Added newvalidation.pymodule containing mouse knockout database
functionality0.1.1 (2021-08-06)Fixed netcoloc imports innetprop_zcore.py0.1.0 (2021-03-10)First release on PyPI.