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Introduction
Network Classes
State Spaces
Attractor Landscapes
Information Analysis
Sensitivity Analysis
Network Randomization
API Reference
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A
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B
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C
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D
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E
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F
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H
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I
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K
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L
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M
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N
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P
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R
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S
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T
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U
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V
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W
_
__contains__() (neet.StateSpace method)
__iter__() (neet.StateSpace method)
_unsafe_encode() (neet.StateSpace method)
_unsafe_update() (neet.Network method)
A
active_information() (neet.Information method)
attractor_lengths (neet.LandscapeMixin attribute)
attractors (neet.LandscapeMixin attribute)
average_difference_matrix() (neet.boolean.SensitivityMixin method)
average_sensitivity() (neet.boolean.SensitivityMixin method)
B
base (neet.UniformNetwork attribute)
(neet.UniformSpace attribute)
basin_entropy (neet.LandscapeMixin attribute)
basin_sizes (neet.LandscapeMixin attribute)
basins (neet.LandscapeMixin attribute)
BooleanNetwork (class in neet.boolean)
boundary (neet.boolean.ECA attribute)
(neet.boolean.RewiredECA attribute)
C
c_elegans (in module neet.boolean.examples)
canalizing_edges() (neet.boolean.SensitivityMixin method)
canalizing_nodes() (neet.boolean.SensitivityMixin method)
clear_landscape() (neet.LandscapeMixin method)
code (neet.boolean.ECA attribute)
(neet.boolean.RewiredECA attribute)
D
decode() (neet.StateSpace method)
difference_matrix() (neet.boolean.SensitivityMixin method)
distance() (neet.boolean.BooleanNetwork method)
draw_landscape_graph() (neet.LandscapeMixin method)
draw_network_graph() (neet.Network method)
E
ECA (class in neet.boolean)
encode() (neet.StateSpace method)
entropy_rate() (neet.Information method)
expound() (neet.LandscapeMixin method)
F
FormatError (class in neet.exceptions)
H
hamming_neighbors() (neet.boolean.BooleanNetwork method)
heights (neet.LandscapeMixin attribute)
hgf_signaling_in_keratinocytes (in module neet.boolean.examples)
I
il_6_signaling (in module neet.boolean.examples)
in_degrees (neet.LandscapeMixin attribute)
Information (class in neet)
is_canalizing() (neet.boolean.SensitivityMixin method)
is_dependent() (neet.boolean.LogicNetwork method)
K
k (neet.Information attribute)
L
lambdaQ() (neet.boolean.SensitivityMixin method)
landscape() (neet.LandscapeMixin method)
landscape_data (neet.LandscapeMixin attribute)
landscape_graph() (neet.LandscapeMixin method)
LandscapeData (class in neet)
LandscapeMixin (class in neet)
LogicNetwork (class in neet.boolean)
M
metadata (neet.Network attribute)
mouse_cortical_7B (in module neet.boolean.examples)
mouse_cortical_7C (in module neet.boolean.examples)
mutual_information() (neet.Information method)
myeloid (in module neet.boolean.examples)
N
names (neet.Network attribute)
neet (module)
neet.boolean (module)
neet.boolean.conv (module)
neet.boolean.eca (module)
neet.boolean.examples (module)
neet.boolean.logicnetwork (module)
neet.boolean.network (module)
neet.boolean.reca (module)
neet.boolean.sensitivity (module)
neet.boolean.wtnetwork (module)
neet.draw (module)
neet.exceptions (module)
neet.information (module)
neet.landscape (module)
neet.network (module)
neet.statespace (module)
negative_threshold() (neet.boolean.WTNetwork static method)
neighbors() (neet.Network method)
neighbors_in() (neet.Network method)
neighbors_out() (neet.Network method)
net (neet.Information attribute)
Network (class in neet)
network_graph() (neet.Network method)
P
p53_dmg (in module neet.boolean.examples)
p53_no_dmg (in module neet.boolean.examples)
positive_threshold() (neet.boolean.WTNetwork static method)
R
read() (neet.boolean.WTNetwork static method)
read_logic() (neet.boolean.LogicNetwork class method)
read_table() (neet.boolean.LogicNetwork class method)
recurrence_times (neet.LandscapeMixin attribute)
reduce_table() (neet.boolean.LogicNetwork method)
RewiredECA (class in neet.boolean)
S
s_cerevisiae (in module neet.boolean.examples)
s_pombe (in module neet.boolean.examples)
sensitivity() (neet.boolean.SensitivityMixin method)
SensitivityMixin (class in neet.boolean)
shape (neet.StateSpace attribute)
size (neet.StateSpace attribute)
split_threshold() (neet.boolean.WTNetwork static method)
StateSpace (class in neet)
subspace() (neet.boolean.BooleanNetwork method)
T
table (neet.boolean.LogicNetwork attribute)
theta (neet.boolean.WTNetwork attribute)
thresholds (neet.boolean.WTNetwork attribute)
timeseries() (neet.LandscapeMixin method)
timesteps (neet.Information attribute)
trajectory() (neet.LandscapeMixin method)
transfer_entropy() (neet.Information method)
transitions (neet.LandscapeMixin attribute)
U
UniformNetwork (class in neet)
UniformSpace (class in neet)
update() (neet.Network method)
V
view_pygraphviz() (in module neet.draw)
volume (neet.StateSpace attribute)
W
weights (neet.boolean.WTNetwork attribute)
wiring (neet.boolean.RewiredECA attribute)
wt_to_logic() (in module neet.boolean.conv)
WTNetwork (class in neet.boolean)
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