Index

A

ApproxODE (class in harissa.simulation.ode)

B

binarize() (in module harissa.utils) (in module harissa.utils.processing)

build_pos() (in module harissa.utils) BurstyPDMP (class in harissa.simulation.pdmp) (class in harissa.simulation.pdmp_fast)

C

Cascade (class in harissa) (class in harissa.model) (class in harissa.model.base)

cascade() (in module harissa.model.cascade)

E

estim_gamma() (in module harissa.inference.kinetics)

estim_gamma_poisson() (in module harissa.inference.kinetics)

F

fit() (harissa.model.base.NetworkModel method) (harissa.model.NetworkModel method) (harissa.NetworkModel method)

flow() (harissa.simulation.pdmp.BurstyPDMP method) (in module harissa.simulation.pdmp_fast)

G

get_kinetics() (harissa.model.base.NetworkModel method) (harissa.model.NetworkModel method) (harissa.NetworkModel method) grad_p1() (in module harissa.inference.network) (in module harissa.inference.network_fast)

grad_penalization() (in module harissa.inference.network) (in module harissa.inference.network_fast) grad_theta() (in module harissa.inference.network) (in module harissa.inference.network_fast)

H

harissa module harissa.inference module harissa.inference.kinetics module harissa.inference.network module harissa.inference.network_fast module harissa.model module harissa.model.base module harissa.model.cascade module

harissa.model.tree module harissa.simulation module harissa.simulation.base module harissa.simulation.ode module harissa.simulation.pdmp module harissa.simulation.pdmp_fast module harissa.utils module harissa.utils.processing module

I

infer_kinetics() (in module harissa.inference) (in module harissa.inference.kinetics) infer_network() (in module harissa.inference.network) (in module harissa.inference.network_fast)

infer_proteins() (in module harissa.inference) (in module harissa.inference.network) (in module harissa.inference.network_fast)

K

kon() (harissa.simulation.ode.ApproxODE method) (harissa.simulation.pdmp.BurstyPDMP method) (in module harissa.simulation.pdmp_fast)

kon_bound() (harissa.simulation.pdmp.BurstyPDMP method) (in module harissa.simulation.pdmp_fast)

L

loop_erasure() (in module harissa.model.tree)

M

module harissa harissa.inference harissa.inference.kinetics harissa.inference.network harissa.inference.network_fast harissa.model harissa.model.base harissa.model.cascade harissa.model.tree harissa.simulation harissa.simulation.base harissa.simulation.ode harissa.simulation.pdmp harissa.simulation.pdmp_fast harissa.utils harissa.utils.processing

N

NetworkModel (class in harissa) (class in harissa.model) (class in harissa.model.base)

O

objective() (in module harissa.inference.network) (in module harissa.inference.network_fast)

P

p1() (in module harissa.inference.network) (in module harissa.inference.network_fast)

penalization() (in module harissa.inference.network) (in module harissa.inference.network_fast) plot_network() (in module harissa.utils), [1]

R

random_step() (in module harissa.model.tree)

random_tree() (in module harissa.model.tree)

S

simulate() (harissa.model.base.NetworkModel method) (harissa.model.NetworkModel method) (harissa.NetworkModel method) (in module harissa.simulation.pdmp_fast) simulate_ode() (harissa.model.base.NetworkModel method) (harissa.model.NetworkModel method) (harissa.NetworkModel method)

Simulation (class in harissa.simulation.base) simulation() (harissa.simulation.ode.ApproxODE method) (harissa.simulation.pdmp.BurstyPDMP method) (harissa.simulation.pdmp_fast.BurstyPDMP method) step() (harissa.simulation.pdmp.BurstyPDMP method) (in module harissa.simulation.pdmp_fast) step_ode() (harissa.simulation.ode.ApproxODE method)

T

transform() (in module harissa.inference.kinetics) Tree (class in harissa) (class in harissa.model) (class in harissa.model.base)

tree() (in module harissa.model.tree)