Index

C

c_index() (in module simdeep.coxph_from_r) c_index_from_python() (in module simdeep.coxph_from_r) c_index_from_r() (in module simdeep.coxph_from_r) c_index_multiple() (in module simdeep.coxph_from_r) c_index_multiple_from_python() (in module simdeep.coxph_from_r) c_index_multiple_from_r() (in module simdeep.coxph_from_r)

convert_metadata_frame_to_matrix() (in module simdeep.survival_utils) convert_to_rmatrix() (in module simdeep.coxph_from_r) CorrelationReducer (class in simdeep.survival_utils) coxph() (in module simdeep.coxph_from_r) coxph_from_python() (in module simdeep.coxph_from_r) coxph_from_r() (in module simdeep.coxph_from_r) create_a_cv_split() (simdeep.extract_data.LoadData method)

F

feature_selection_usage_type() (in module simdeep.simdeep_utils) fit() (simdeep.survival_utils.CorrelationReducer method) (simdeep.survival_utils.VarianceReducer method)

fit_transform() (simdeep.survival_utils.CorrelationReducer method) (simdeep.survival_utils.MadScaler method) (simdeep.survival_utils.RankNorm method) (simdeep.survival_utils.VarianceReducer method)

L

load_array() (simdeep.extract_data.LoadData method) load_data_from_tsv() (in module simdeep.survival_utils) load_entrezID_to_ensg() (in module simdeep.survival_utils) load_labels_file() (in module simdeep.simdeep_utils) load_matrix_full() (simdeep.extract_data.LoadData method) load_matrix_test() (simdeep.extract_data.LoadData method) load_matrix_test_fold() (simdeep.extract_data.LoadData method)

load_meta_data() (simdeep.extract_data.LoadData method) load_meta_data_test() (simdeep.extract_data.LoadData method) load_model() (in module simdeep.simdeep_utils) load_new_test_dataset() (simdeep.extract_data.LoadData method) load_survival() (simdeep.extract_data.LoadData method) load_survival_file() (in module simdeep.survival_utils) load_survival_test() (simdeep.extract_data.LoadData method) LoadData (class in simdeep.extract_data)

M

MadScaler (class in simdeep.survival_utils) main() (in module simdeep.coxph_from_r) make_color_dict() (in module simdeep.plot_utils) make_color_dict_from_r() (in module simdeep.plot_utils) make_color_list() (in module simdeep.plot_utils) metadata_usage_type() (in module simdeep.simdeep_utils) module simdeep simdeep.config simdeep.coxph_from_r simdeep.extract_data simdeep.plot_utils simdeep.simdeep_utils simdeep.survival_utils

N

normalize_training_array() (simdeep.extract_data.LoadData method)

P

plot_kernel_plots() (in module simdeep.plot_utils)

predict_with_coxph_glmnet() (in module simdeep.coxph_from_r)

R

RankCorrNorm (class in simdeep.survival_utils) RankNorm (class in simdeep.survival_utils)

reorder_matrix_array() (simdeep.extract_data.LoadData method) return_intersection_indexes() (in module simdeep.survival_utils)

S

sample_to_keep() (simdeep.survival_utils.SampleReducer method) SampleHTML (class in simdeep.plot_utils) SampleReducer (class in simdeep.survival_utils) save_matrix() (in module simdeep.survival_utils) save_model() (in module simdeep.simdeep_utils) save_ref_matrix() (simdeep.extract_data.LoadData method) select_best_classif_params() (in module simdeep.survival_utils) simdeep module simdeep.config module simdeep.coxph_from_r module simdeep.extract_data module

simdeep.plot_utils module simdeep.simdeep_utils module simdeep.survival_utils module subset_training_sets() (simdeep.extract_data.LoadData method) surv_mean() (in module simdeep.coxph_from_r) surv_mean_from_python() (in module simdeep.coxph_from_r) surv_mean_from_r() (in module simdeep.coxph_from_r) surv_median() (in module simdeep.coxph_from_r) surv_median_from_python() (in module simdeep.coxph_from_r) surv_median_from_r() (in module simdeep.coxph_from_r)

T

transform() (simdeep.survival_utils.CorrelationReducer method) (simdeep.survival_utils.VarianceReducer method)

transform_matrices() (simdeep.extract_data.LoadData method) translate_index() (in module simdeep.survival_utils)

V

VarianceReducer (class in simdeep.survival_utils)