API for ginnyintifa/PTMscape

Global functions
PTM_domain_mapping_enrichment Man page Source code
aaindex_feature_extraction Source code
assemble_window_score_cv Source code
assemble_window_score_target Source code
balanced_size_sampling Source code
balanced_size_sampling_after_combining_pos_neg Source code
build_candidate_df Source code
build_candidate_df_no_positive Source code
build_decoy_df Source code
build_pure_decoy_df Source code
build_purest_decoy_df Source code
calculate_MCC Source code
calculate_individual_ptm Source code
calculate_seq_pairs Source code
calculate_seq_pairs_negative Source code
calculate_tbt_negative_ptms Man page Source code
calculate_tbt_positive_ptms Man page Source code
calculate_tbt_single_ptm Source code
combine_all_features Source code
combine_all_features_no_spider Source code
combine_pos_neg Source code
construct_n_fold_cv_without_decoy Source code
create_gglogo_plot Source code
divide_candidate_to_train_test Source code
domain_subcellular_mapping Source code
extract_site_specific_features Source code
extract_site_specific_features_new Source code
generate_feature_t Man page Source code
generate_feature_wp Man page Source code
generate_training_test_data_t Man page Source code
generate_training_test_data_wp Man page Source code
get_3_roc Source code
get_all_candidate Source code
get_all_candidate_no_positive Source code
get_all_decoy Source code
get_all_pure_decoy Source code
get_all_purest_decoy Source code
get_average_weights_of_ten Source code
get_average_weights_of_two Source code
get_base_freq_matrix Source code
get_fasta_multi_lines_seq Source code
get_hist Source code
get_k_keep Source code
get_matrix_all Source code
get_non_redundant Source code
get_pca_plot Source code
get_pca_plot_two Source code
get_phosphoSVM_site Source code
get_plsda_pos_candi Source code
get_plsda_pos_candi_with_score_selection Source code
get_prot_mean_structure Source code
get_pssm_feature Source code
get_score_threshold Source code
get_slice_rest_subset_index Source code
get_spd33_combined Source code
get_structure_average Source code
get_structure_site_specific Source code
get_subset_train_test Source code
get_subset_train_test_no_shuffle Source code
get_subset_train_test_no_shuffle_windows Source code
get_train_test Source code
get_tsne_pos_candi Source code
get_wanted_proteins Source code
get_z_transform Source code
ggbiplot2 Source code
libsvm_formating Source code
libsvm_formating_single Source code
map_domain Source code
map_domain_old Source code
map_domain_subcellular Source code
map_subcellular_location Source code
plot_plsda_for_two_types Source code
plot_plsda_for_two_types_with_score_selection Source code
plot_weights Source code
predict_on_targeted_proteome Man page Source code
predict_on_whole_proteome Man page Source code
predict_with_liblinear Man page Source code
present_prediction_t Man page Source code
present_prediction_wp Man page Source code
process_n_fold_cross_validation Man page Source code
pssm_feature_extraction Source code
pssm_generation Source code
retrieve_domain_all_mod Source code
retrieve_for_each_mod Source code
scale_test Source code
scale_train Source code
scale_train_single Source code
scale_train_test Source code
scale_train_test_single Source code
select_equal_size_candidate_decoy Source code
spider_feature_joining_without_mean Source code
whichpart Source code
window_formation Source code
window_formation_no_positive Source code
ginnyintifa/PTMscape documentation built on Feb. 4, 2018, 1:19 p.m.