Harissa API documentation

Main package

harissa

Harissa

Sub packages

harissa.model	harissa.model
harissa.inference	harissa.inference
harissa.simulation	harissa.simulation
harissa.utils	harissa.utils

Modules

harissa.model.base	Main class for network inference and simulation
harissa.model.cascade	Generate cascade networks
harissa.model.tree	Generate random trees
harissa.inference.kinetics	Inference of basal parameters
harissa.inference.network	Core functions for network inference using likelihood maximization
harissa.inference.network_fast	Core functions for network inference using likelihood maximization NB: This is the fast version using Numba
harissa.simulation.base	Store simulations
harissa.simulation.ode	Perform simulations using the ODE model
harissa.simulation.pdmp	Perform simulations using the PDMP model
harissa.simulation.pdmp_fast	Perform simulations using the PDMP model - Fast version using Numba NB: This module takes time to compile (~8s) but is much more efficient, which is typically suited for large numbers of genes and/or cells
harissa.utils.plot_network	Plot a gene regulatory network.
harissa.utils.processing	Data processing