EndotypY

A short description of your package.

Installation

#clone git repo and navigate to directory containing the setup.py file
pip install .

#or run this command in your jupyter notebook
!pip install git+https://github.com/menchelab/EndotypY.git

Documentation

View the full documentation here

Usage

import

import EndotypY as edy

create endotyper object and read in network and seed genes

endo = edy.Endotyper()

path_network = <path_to_network_file.tsv>
path_seed = <path_to_seed_file.txt>

endo.import_network(path_network)
endo.import_seeds(path_seed)

prepare RWR

endo.prepare_rwr(r=0.8)

explore the seed clusters

#k is the size of the neighborhoods to explore
endo.explore_seed_clusters(scaling=True, k=50)

extract a connected disease module based on seeds

endo.extract_disease_module(seed_cluster_id = None, scaling=True, k=200)

explore the local neighborhood around all seeds

endo.define_local_neighborhood(scaling=True, neighbor_percentage=1)

annotate the local neighborhoods with gene set enrichment

endo.annotate_local_neighborhood(enrichr_lib='GO_Biological_Process_2023',
                                 organism='Human',
                                 sig_threshold=0.05)

find endotypes

endo.define_endotypes()

visualise a single endotype

endo.plot_endotype(iteration=1, cluster_id=2, node_size='betweenness', path_length=3)

visualize the network

endo.visualize_network()

visualize all endotypes

endo.plot_multiple_endotypes(node_size='degree', path_length=2)