https://github.com/menchelab/endotypy
package formulation of endotyping pipeline
https://github.com/menchelab/endotypy
Last synced: 8 months ago
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package formulation of endotyping pipeline
- Host: GitHub
- URL: https://github.com/menchelab/endotypy
- Owner: menchelab
- License: mit
- Created: 2025-06-11T12:32:42.000Z (about 1 year ago)
- Default Branch: main
- Last Pushed: 2025-09-11T11:39:33.000Z (9 months ago)
- Last Synced: 2025-09-29T23:39:14.521Z (9 months ago)
- Language: Jupyter Notebook
- Size: 8.48 MB
- Stars: 0
- Watchers: 0
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
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README
# EndotypY
A short description of your package.
## Installation
```sh
#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](https://menchelab.github.io/EndotypY/)
## Usage
#### import
```python
import EndotypY as edy
```
#### create endotyper object and read in network and seed genes
```python
endo = edy.Endotyper()
path_network =
path_seed =
endo.import_network(path_network)
endo.import_seeds(path_seed)
```
#### prepare RWR
```python
endo.prepare_rwr(r=0.8)
```
#### explore the seed clusters
```python
#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
```python
endo.extract_disease_module(seed_cluster_id = None, scaling=True, k=200)
```
#### explore the local neighborhood around all seeds
```python
endo.define_local_neighborhood(scaling=True, neighbor_percentage=1)
```
#### annotate the local neighborhoods with gene set enrichment
```python
endo.annotate_local_neighborhood(enrichr_lib='GO_Biological_Process_2023',
organism='Human',
sig_threshold=0.05)
```
#### find endotypes
```python
endo.define_endotypes()
```
#### visualise a single endotype
```python
endo.plot_endotype(iteration=1, cluster_id=2, node_size='betweenness', path_length=3)
```
#### visualize the network
```python
endo.visualize_network()
```
#### visualize all endotypes
```python
endo.plot_multiple_endotypes(node_size='degree', path_length=2)
```
