DeepProg
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Tutorial: Simple DeepProg model
Tutorial: Ensemble of DeepProg model
Tutorial: Advanced usage of DeepProg model
Tutorial: use DeepProg from the docker image
Case study: Analyzing TCGA HCC dataset
Tutorial: Tuning DeepProg
License
simdeep package
DeepProg
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F
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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)
collect_cindex_for_full_dataset() (simdeep.simdeep_boosting.SimDeepBoosting method)
collect_cindex_for_test_dataset() (simdeep.simdeep_boosting.SimDeepBoosting method)
collect_cindex_for_test_fold() (simdeep.simdeep_boosting.SimDeepBoosting method)
collect_cindex_for_training_dataset() (simdeep.simdeep_boosting.SimDeepBoosting method)
collect_number_of_features_per_omic() (simdeep.simdeep_boosting.SimDeepBoosting method)
collect_pvalue_on_full_dataset() (simdeep.simdeep_boosting.SimDeepBoosting method)
collect_pvalue_on_test_dataset() (simdeep.simdeep_boosting.SimDeepBoosting method)
collect_pvalue_on_test_fold() (simdeep.simdeep_boosting.SimDeepBoosting method)
collect_pvalue_on_training_dataset() (simdeep.simdeep_boosting.SimDeepBoosting method)
compile_models() (simdeep.deepmodel_base.DeepBase method)
compute_c_indexes_for_full_dataset() (simdeep.simdeep_analysis.SimDeep method)
(simdeep.simdeep_boosting.SimDeepBoosting method)
compute_c_indexes_for_test_dataset() (simdeep.simdeep_analysis.SimDeep method)
(simdeep.simdeep_boosting.SimDeepBoosting method)
compute_c_indexes_for_test_fold_dataset() (simdeep.simdeep_analysis.SimDeep method)
compute_c_indexes_for_training_dataset() (simdeep.simdeep_analysis.SimDeep method)
compute_c_indexes_multiple_for_test_dataset() (simdeep.simdeep_analysis.SimDeep method)
(simdeep.simdeep_boosting.SimDeepBoosting method)
compute_c_indexes_multiple_for_test_fold_dataset() (simdeep.simdeep_analysis.SimDeep method)
compute_clusters_consistency_for_full_labels() (simdeep.simdeep_boosting.SimDeepBoosting method)
compute_clusters_consistency_for_test_labels() (simdeep.simdeep_boosting.SimDeepBoosting method)
compute_feature_scores() (simdeep.simdeep_analysis.SimDeep method)
compute_feature_scores_per_cluster() (simdeep.simdeep_analysis.SimDeep method)
(simdeep.simdeep_boosting.SimDeepBoosting method)
compute_pvalue_for_merged_test_fold() (simdeep.simdeep_boosting.SimDeepBoosting method)
compute_survival_feature_scores_per_cluster() (simdeep.simdeep_boosting.SimDeepBoosting method)
construct_autoencoders() (simdeep.deepmodel_base.DeepBase method)
construct_supervized_network() (simdeep.deepmodel_base.DeepBase method)
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)
create_autoencoders() (simdeep.deepmodel_base.DeepBase method)
D
DeepBase (class in simdeep.deepmodel_base)
E
embedding_predict() (simdeep.deepmodel_base.DeepBase method)
encoder_input_shape() (simdeep.deepmodel_base.DeepBase method)
encoder_predict() (simdeep.deepmodel_base.DeepBase method)
evalutate_cluster_performance() (simdeep.simdeep_analysis.SimDeep method)
(simdeep.simdeep_boosting.SimDeepBoosting method)
F
feature_selection_usage_type() (in module simdeep.simdeep_utils)
fit() (simdeep.simdeep_analysis.SimDeep method)
(simdeep.simdeep_boosting.SimDeepBoosting method)
(simdeep.survival_utils.CorrelationReducer method)
(simdeep.survival_utils.VarianceReducer method)
fit_alternative_embedding() (simdeep.deepmodel_base.DeepBase method)
fit_autoencoders() (simdeep.deepmodel_base.DeepBase method)
fit_classification_model() (simdeep.simdeep_analysis.SimDeep method)
fit_classification_test_model() (simdeep.simdeep_analysis.SimDeep method)
fit_on_pretrained_label_file() (simdeep.simdeep_analysis.SimDeep method)
(simdeep.simdeep_boosting.SimDeepBoosting 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_encoders() (simdeep.deepmodel_base.DeepBase method)
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)
(simdeep.simdeep_analysis.SimDeep method)
(simdeep.simdeep_boosting.SimDeepBoosting method)
load_survival() (simdeep.extract_data.LoadData method)
load_survival_file() (in module simdeep.survival_utils)
load_survival_test() (simdeep.extract_data.LoadData method)
load_test_dataset() (simdeep.deepmodel_base.DeepBase method)
load_training_dataset() (simdeep.deepmodel_base.DeepBase method)
LoadData (class in simdeep.extract_data)
look_for_prediction_nodes() (simdeep.simdeep_analysis.SimDeep method)
look_for_survival_nodes() (simdeep.simdeep_analysis.SimDeep method)
M
MadScaler (class in simdeep.survival_utils)
main() (in module simdeep.coxph_from_r)
(in module simdeep.deepmodel_base)
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.deepmodel_base
simdeep.extract_data
simdeep.plot_utils
simdeep.simdeep_analysis
simdeep.simdeep_boosting
simdeep.simdeep_multiple_dataset
simdeep.simdeep_utils
simdeep.survival_utils
N
normalize_training_array() (simdeep.extract_data.LoadData method)
P
partial_fit() (simdeep.simdeep_boosting.SimDeepBoosting method)
plot_kernel_for_test_sets() (simdeep.simdeep_analysis.SimDeep method)
plot_kernel_plots() (in module simdeep.plot_utils)
plot_supervised_kernel_for_test_sets() (simdeep.simdeep_analysis.SimDeep method)
(simdeep.simdeep_boosting.SimDeepBoosting method)
plot_supervised_predicted_labels_for_test_sets() (simdeep.simdeep_boosting.SimDeepBoosting method)
predict_labels() (simdeep.simdeep_analysis.SimDeep method)
predict_labels_on_full_dataset() (simdeep.simdeep_analysis.SimDeep method)
(simdeep.simdeep_boosting.SimDeepBoosting method)
predict_labels_on_test_dataset() (simdeep.simdeep_analysis.SimDeep method)
(simdeep.simdeep_boosting.SimDeepBoosting method)
predict_labels_on_test_fold() (simdeep.simdeep_analysis.SimDeep method)
predict_labels_using_external_labels() (simdeep.simdeep_analysis.SimDeep method)
predict_nodes_activities() (simdeep.simdeep_analysis.SimDeep method)
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_cv_models_classes() (simdeep.simdeep_boosting.SimDeepBoosting method)
save_encoders() (simdeep.deepmodel_base.DeepBase method)
save_matrix() (in module simdeep.survival_utils)
save_model() (in module simdeep.simdeep_utils)
save_models_classes() (simdeep.simdeep_boosting.SimDeepBoosting method)
save_ref_matrix() (simdeep.extract_data.LoadData method)
save_test_models_classes() (simdeep.simdeep_boosting.SimDeepBoosting method)
select_best_classif_params() (in module simdeep.survival_utils)
simdeep
module
SimDeep (class in simdeep.simdeep_analysis)
simdeep.config
module
simdeep.coxph_from_r
module
simdeep.deepmodel_base
module
simdeep.extract_data
module
simdeep.plot_utils
module
simdeep.simdeep_analysis
module
simdeep.simdeep_boosting
module
simdeep.simdeep_multiple_dataset
module
simdeep.simdeep_utils
module
simdeep.survival_utils
module
SimDeepBoosting (class in simdeep.simdeep_boosting)
SimDeepMultiple (class in simdeep.simdeep_multiple_dataset)
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)
W
write_feature_score_per_cluster() (simdeep.simdeep_analysis.SimDeep method)
(simdeep.simdeep_boosting.SimDeepBoosting method)
write_feature_scores() (simdeep.simdeep_analysis.SimDeep method)
write_logs() (simdeep.simdeep_boosting.SimDeepBoosting method)
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