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, and for an in depth explanation of the general optimization approach see my MSci thesis.

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, which shows how to load and simulate datasets, run analysis methods and compute performance metrics on simulated data.