https://github.com/willjgh/interaction-inference
Inference of interaction between genes using constrained optimization
https://github.com/willjgh/interaction-inference
biomathematics inference optimization package single-cell-genomics stochastic-simulation
Last synced: 6 months ago
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Inference of interaction between genes using constrained optimization
- Host: GitHub
- URL: https://github.com/willjgh/interaction-inference
- Owner: willjgh
- License: mit
- Created: 2024-12-23T13:19:33.000Z (over 1 year ago)
- Default Branch: main
- Last Pushed: 2025-08-30T23:13:45.000Z (9 months ago)
- Last Synced: 2025-08-31T01:09:00.276Z (9 months ago)
- Topics: biomathematics, inference, optimization, package, single-cell-genomics, stochastic-simulation
- Language: Python
- Homepage:
- Size: 288 KB
- Stars: 0
- Watchers: 1
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
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README
# interaction-inference
Python package implementing an optimization based inference method to detect interaction between pairs of genes from cellular observations, together with tools for simulation of synthetic datasets and visualizations of performance.
For current research on the method applied to interaction detection see the repository [here](https://github.com/willjgh/M5R), and for an in depth explanation of the general optimization approach see my [MSci thesis](https://github.com/willjgh/Year-4-Project/blob/master/Report/01844345_WH.pdf).
## Installation
Package is available on PyPi and installable through pip via
```
pip install interaction-inference
```
## Background and Examples
For a brief overiew of biological background and example usage of the package see the [example notebook](https://github.com/willjgh/interaction-inference/blob/main/examples/example_notebook.ipynb), which shows how to load and simulate datasets, run analysis methods and compute performance metrics on simulated data.