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Table of Contents
Installation Instructions
SQUID
MAVE-NN
Example
Modeling Tutorials
API Reference
squid
Submodules
squid
Index
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Index
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A
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B
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C
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D
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F
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G
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H
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I
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M
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O
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P
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R
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S
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T
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__call__() (squid.mutagenizer.BaseMutagenesis method)
(squid.mutagenizer.CombinatorialMutagenesis method)
(squid.mutagenizer.RandomMutagenesis method)
(squid.mutagenizer.TwoHotMutagenesis method)
(squid.predictor.BasePredictor method)
(squid.predictor.BPNetPredictor method)
(squid.predictor.ProfilePredictor method)
(squid.predictor.ScalarPredictor method)
__enter__() (squid.impress.hidden_prints method)
__exit__() (squid.impress.hidden_prints method)
A
apply_mut_by_seq_index() (in module squid.mutagenizer)
arr2pd() (in module squid.utils)
B
BaseMutagenesis (class in squid.mutagenizer)
BasePredictor (class in squid.predictor)
BPNetPredictor (class in squid.predictor)
build() (squid.surrogate_zoo.SurrogateLinear method)
C
CombinatorialMutagenesis (class in squid.mutagenizer)
D
data_splits() (in module squid.surrogate_zoo)
dataframe() (squid.surrogate_zoo.SurrogateLasso method)
(squid.surrogate_zoo.SurrogateLIME method)
(squid.surrogate_zoo.SurrogateMAVENN method)
(squid.surrogate_zoo.SurrogateRidgeCV method)
delimit_range() (squid.mave.InSilicoMAVE method)
dinuc_shuffle() (in module squid.mave)
F
fix_gauge() (in module squid.utils)
G
generate() (squid.mave.InSilicoMAVE method)
get_info() (squid.surrogate_zoo.SurrogateMAVENN method)
get_logo() (squid.surrogate_zoo.SurrogateLasso method)
(squid.surrogate_zoo.SurrogateLIME method)
(squid.surrogate_zoo.SurrogateLinear method)
(squid.surrogate_zoo.SurrogateMAVENN method)
(squid.surrogate_zoo.SurrogateRidgeCV method)
get_params() (squid.surrogate_zoo.SurrogateBase method)
(squid.surrogate_zoo.SurrogateLasso method)
(squid.surrogate_zoo.SurrogateLIME method)
(squid.surrogate_zoo.SurrogateLinear method)
(squid.surrogate_zoo.SurrogateMAVENN method)
(squid.surrogate_zoo.SurrogateRidgeCV method)
H
hidden_prints (class in squid.impress)
I
InSilicoMAVE (class in squid.mave)
M
module
squid
squid.impress
squid.mave
squid.mutagenizer
squid.predictor
squid.surrogate_zoo
squid.utils
O
oh2seq() (in module squid.utils)
P
pad_seq() (squid.mave.InSilicoMAVE method)
pad_seq_random() (squid.mave.InSilicoMAVE method)
plot_additive_logo() (in module squid.impress)
plot_eig_vals() (in module squid.impress)
plot_eig_vecs() (in module squid.impress)
plot_pairwise_matrix() (in module squid.impress)
plot_performance() (in module squid.impress)
plot_y_hist() (in module squid.impress)
plot_y_vs_phi() (in module squid.impress)
plot_y_vs_yhat() (in module squid.impress)
predict_in_batches() (in module squid.predictor)
profile_pca() (in module squid.predictor)
profile_sum() (in module squid.predictor)
ProfilePredictor (class in squid.predictor)
R
random_shuffle() (in module squid.mave)
RandomMutagenesis (class in squid.mutagenizer)
S
save_dir (squid.predictor.BasePredictor attribute)
ScalarPredictor (class in squid.predictor)
seq2oh() (in module squid.utils)
seq2twohot() (in module squid.mutagenizer)
squid
module
squid.impress
module
squid.mave
module
squid.mutagenizer
module
squid.predictor
module
squid.surrogate_zoo
module
squid.utils
module
SurrogateBase (class in squid.surrogate_zoo)
SurrogateLasso (class in squid.surrogate_zoo)
SurrogateLIME (class in squid.surrogate_zoo)
SurrogateLinear (class in squid.surrogate_zoo)
SurrogateMAVENN (class in squid.surrogate_zoo)
SurrogateRidgeCV (class in squid.surrogate_zoo)
T
train() (squid.surrogate_zoo.SurrogateBase method)
(squid.surrogate_zoo.SurrogateLasso method)
(squid.surrogate_zoo.SurrogateLIME method)
(squid.surrogate_zoo.SurrogateLinear method)
(squid.surrogate_zoo.SurrogateMAVENN method)
(squid.surrogate_zoo.SurrogateRidgeCV method)
twohot2seq() (in module squid.mutagenizer)
TwoHotMutagenesis (class in squid.mutagenizer)
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