Welcome to BioplexPy’s documentation!
BioplexPy (/baɪˈoʊ plɛks paɪ/) package provides access to PPI data from Gygi lab. It fetches protein interaction data and offers a simple and intuitive API for Analysis.
Getting Started
The package can be installed through pypi or through github
pip install bioplexpy
or
pip install git+https://github.com/ccb-hms/BioPlexPy.git#egg=BioPlexPy
Examples of Functions and Analysis:
- Overview of Functionality
- Examples for how to use functions from bioplexpy
- [1] getBioPlex - function to retrieve interactions data
- [2] getGSE122425 - function to retrieve HEK293 RNAseq expression data
- [3] bioplex2graph - function to convert BioPlex PPIs into a graph data structure
- [4] getCorum - function to retrieve CORUM complex data
- [5] get_PPI_network_for_complex - that returns matching edges (PPI data) for a given CORUM complex as a sub-graph
- [6] get_DataFrame_from_PPI_network - that takes an AP-MS graph (NetworkX) and returns a dataframe of PPIs (Edges)
- [7] get_prop_edges_in_complex_identified - function that returns the proportion of interactions between proteins in a CORUM complex detected by AP-MS
- [8] permutation_test_for_CORUM_complex - function that runs permutation test to test whether number of edges for CORUM complex PPI network is enriched for interactions
- [9] display_PPI_network_for_complex - function to visualize PPI data for a given complex from CORUM
- [10] Functions to calculate and visualize physical interactions between chains of PDB structure and compare with PPI data