parrot
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Contents:
Getting Started with PARROT
parrot-train
parrot-optimize
parrot-predict
parrot-cvsplit
Basic Examples:
Advanced Examples:
Evaluating a Network with Cross-Validation:
Machine Learning Resources:
Module Documentation
parrot
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B
BayesianOptimizer (class in parrot.bayesian_optimization)
biophysics() (in module parrot.encode_sequence)
BRNN_MtM (class in parrot.brnn_architecture)
BRNN_MtO (class in parrot.brnn_architecture)
C
compute_cv_loss() (parrot.bayesian_optimization.BayesianOptimizer method)
confusion_matrix() (in module parrot.brnn_plot)
D
decode() (parrot.encode_sequence.UserEncoder method)
E
encode() (parrot.encode_sequence.UserEncoder method)
eval_cv_brnns() (parrot.bayesian_optimization.BayesianOptimizer method)
F
forward() (parrot.brnn_architecture.BRNN_MtM method)
(parrot.brnn_architecture.BRNN_MtO method)
I
initial_search() (parrot.bayesian_optimization.BayesianOptimizer method)
O
one_hot() (in module parrot.encode_sequence)
optimize() (parrot.bayesian_optimization.BayesianOptimizer method)
output_predictions_to_file() (in module parrot.brnn_plot)
P
parrot.bayesian_optimization (module)
parrot.brnn_architecture (module)
parrot.brnn_plot (module)
parrot.encode_sequence (module)
parrot.process_input_data (module)
parrot.py_predictor (module)
parrot.train_network (module)
parse_encode_file() (in module parrot.encode_sequence)
parse_file() (in module parrot.process_input_data)
plot_precision_recall_curve() (in module parrot.brnn_plot)
plot_roc_curve() (in module parrot.brnn_plot)
predict() (parrot.py_predictor.Predictor method)
Predictor (class in parrot.py_predictor)
R
read_split_file() (in module parrot.process_input_data)
read_tsv_raw() (in module parrot.process_input_data)
res_class_collate() (in module parrot.process_input_data)
res_confusion_matrix() (in module parrot.brnn_plot)
res_regress_collate() (in module parrot.process_input_data)
residue_regression_scatterplot() (in module parrot.brnn_plot)
rev_biophysics() (in module parrot.encode_sequence)
rev_one_hot() (in module parrot.encode_sequence)
S
seq_class_collate() (in module parrot.process_input_data)
seq_regress_collate() (in module parrot.process_input_data)
sequence_regression_scatterplot() (in module parrot.brnn_plot)
SequenceDataset (class in parrot.process_input_data)
split_data() (in module parrot.process_input_data)
split_data_cv() (in module parrot.process_input_data)
T
test_labeled_data() (in module parrot.train_network)
test_unlabeled_data() (in module parrot.train_network)
train() (in module parrot.train_network)
training_loss() (in module parrot.brnn_plot)
U
UserEncoder (class in parrot.encode_sequence)
V
vector_split() (in module parrot.process_input_data)
W
write_performance_metrics() (in module parrot.brnn_plot)
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