Index

_

__init__() (aaanalysis.AAclust method) (aaanalysis.AAclustPlot method) (aaanalysis.AAlogo method) (aaanalysis.AAlogoPlot method) (aaanalysis.CPP method) (aaanalysis.CPPPlot method) (aaanalysis.dPULearn method) (aaanalysis.SequenceFeature method) (aaanalysis.ShapModel method) (aaanalysis.TreeModel method)

A

aa_comparison() (aaanalysis.AAMutPlot method) aaanalysis.py module AAclust (class in aaanalysis) AAclustPlot (class in aaanalysis) AAlogo (class in aaanalysis)

AAlogoPlot (class in aaanalysis) AAMut (class in aaanalysis) AAMutPlot (class in aaanalysis) add_feat_impact() (aaanalysis.ShapModel method) add_feat_importance() (aaanalysis.TreeModel method) add_sample_mean_dif() (aaanalysis.ShapModel static method)

C

centers() (aaanalysis.AAclustPlot method) centers_ (aaanalysis.AAclust attribute) comp_auc_adjusted() (in module aaanalysis) comp_bic_score() (in module aaanalysis) comp_centers() (aaanalysis.AAclust static method) comp_correlation() (aaanalysis.AAclust static method) comp_coverage() (aaanalysis.AAclust static method)

comp_kld() (in module aaanalysis) comp_medoids() (aaanalysis.AAclust static method) comp_seq_sim (class in aaanalysis) compare_sets_negatives() (aaanalysis.dPULearn static method) correlation() (aaanalysis.AAclustPlot method) CPP (class in aaanalysis) CPPPlot (class in aaanalysis)

D

df_cat (aaanalysis.CPP attribute) df_parts (aaanalysis.CPP attribute) df_pu_ (aaanalysis.dPULearn attribute)

df_scales (aaanalysis.CPP attribute) display_df() (in module aaanalysis) dPULearn (class in aaanalysis) dPULearnPlot (class in aaanalysis)

E

encode_integer() (aaanalysis.SequencePreprocessor static method) encode_one_hot() (aaanalysis.SequencePreprocessor static method) eval() (aaanalysis.AAclust method) (aaanalysis.AAclustPlot static method) (aaanalysis.AAMut method) (aaanalysis.CPP method) (aaanalysis.CPPPlot static method) (aaanalysis.dPULearn static method) (aaanalysis.dPULearnPlot static method) (aaanalysis.ShapModel method) (aaanalysis.TreeModel method)

exp_value (aaanalysis.ShapModel attribute) extend_alphabet() (aaanalysis.NumericalFeature static method)

F

feat_importance (aaanalysis.TreeModel attribute) feat_importance_std (aaanalysis.TreeModel attribute) feature() (aaanalysis.CPPPlot method) feature_map() (aaanalysis.CPPPlot method) feature_matrix() (aaanalysis.SequenceFeature method) filter_correlation() (aaanalysis.NumericalFeature static method) filter_coverage() (aaanalysis.AAclust method)

filter_seq (class in aaanalysis) fit() (aaanalysis.AAclust method) (aaanalysis.AAMut method) (aaanalysis.dPULearn method) (aaanalysis.SeqMut method) (aaanalysis.ShapModel method) (aaanalysis.TreeModel method)

G

get_aa_window() (aaanalysis.SequencePreprocessor static method) get_conservation() (aaanalysis.AAlogo static method) get_df_feat() (aaanalysis.SequenceFeature method) get_df_logo() (aaanalysis.AAlogo method) get_df_logo_info() (aaanalysis.AAlogo method) get_df_parts() (aaanalysis.SequenceFeature method)

get_df_pos() (aaanalysis.SequenceFeature static method) get_feature_names() (aaanalysis.SequenceFeature static method) get_feature_positions() (aaanalysis.SequenceFeature static method) get_features() (aaanalysis.SequenceFeature method) get_sliding_aa_window() (aaanalysis.SequencePreprocessor static method) get_split_kws() (aaanalysis.SequenceFeature static method)

H

heatmap() (aaanalysis.CPPPlot method)

I

is_medoid_ (aaanalysis.AAclust attribute)

is_selected_ (aaanalysis.TreeModel attribute)

L

labels_ (aaanalysis.AAclust attribute) (aaanalysis.dPULearn attribute) labels_centers_ (aaanalysis.AAclust attribute) labels_medoids_ (aaanalysis.AAclust attribute)

list_models_ (aaanalysis.TreeModel attribute) load_dataset (class in aaanalysis) load_features (class in aaanalysis) load_scales (class in aaanalysis)

M

medoid_names_ (aaanalysis.AAclust attribute) medoids() (aaanalysis.AAclustPlot method) medoids_ (aaanalysis.AAclust attribute) model (aaanalysis.AAclust attribute)

module aaanalysis.py multi_logo() (aaanalysis.AAlogoPlot method) mutation_landscape() (aaanalysis.SeqMutPlot method)

N

n_clusters (aaanalysis.AAclust attribute)

name_clusters() (aaanalysis.AAclust static method) NumericalFeature (class in aaanalysis)

O

options (in module aaanalysis)

P

pca() (aaanalysis.dPULearnPlot static method) plot_gcfs() (in module aaanalysis) plot_get_cdict() (in module aaanalysis) plot_get_clist() (in module aaanalysis)

plot_get_cmap() (in module aaanalysis) plot_legend() (in module aaanalysis) plot_settings() (in module aaanalysis) predict_proba() (aaanalysis.TreeModel method) profile() (aaanalysis.CPPPlot method)

R

ranking() (aaanalysis.CPPPlot method) read_fasta (class in aaanalysis)

residue_mutation_impact() (aaanalysis.SeqMutPlot method) run() (aaanalysis.CPP method)

S

scale_ranking() (aaanalysis.AAMutPlot method) scan() (aaanalysis.SeqMut method) SeqMut (class in aaanalysis) SeqMutPlot (class in aaanalysis) SequenceFeature (class in aaanalysis)

SequencePreprocessor (class in aaanalysis) shap_values (aaanalysis.ShapModel attribute) ShapModel (class in aaanalysis) single_logo() (aaanalysis.AAlogoPlot method) split_kws (aaanalysis.CPP attribute) substitution_matrix() (aaanalysis.AAMutPlot method)

T

to_fasta (class in aaanalysis)

TreeModel (class in aaanalysis)

U

update_seq_size() (aaanalysis.CPPPlot method)