Index A | C | D | E | F | G | I | L | M | P | S | U A add_custom_annotation() (in module ptm_pose.annotate) add_ELM_interactions() (in module ptm_pose.annotate) add_ELM_matched_motifs() (in module ptm_pose.annotate) add_omnipath_data() (in module ptm_pose.annotate) annotate_ptms() (in module ptm_pose.annotate) annotation_enrichment() (in module ptm_pose.analyze.annotations) append_from_gmt() (in module ptm_pose.annotate) assess_filter_range() (in module ptm_pose.analyze.filter) C check_file() (in module ptm_pose.annotate) check_gmt_file() (in module ptm_pose.annotate) combine_enzyme_data() (in module ptm_pose.annotate) combine_interaction_data() (in module ptm_pose.annotate) combine_outputs() (in module ptm_pose.analyze.summarize) compare_flanking_sequences() (in module ptm_pose.analyze.flank_analysis) compare_inclusion_motifs() (in module ptm_pose.analyze.flank_analysis) compare_KL_for_sequence() (in module ptm_pose.analyze.enzyme) compare_to_nease() (ptm_pose.analyze.interactions.protein_interactions method) construct_annotation_dict_from_df() (in module ptm_pose.annotate) construct_annotation_dict_from_gmt() (in module ptm_pose.annotate) construct_combined_enzyme_gmt_df() (in module ptm_pose.annotate) construct_combined_interactions_gmt_df() (in module ptm_pose.annotate) construct_custom_gmt_file() (in module ptm_pose.annotate) construct_DEPOD_gmt_file() (in module ptm_pose.annotate) construct_gmt_df() (in module ptm_pose.annotate) construct_omnipath_gmt_file() (in module ptm_pose.annotate) construct_PhosphoSitePlus_gmt_files() (in module ptm_pose.annotate) construct_PTMcode_interprotein_gmt_file() (in module ptm_pose.annotate) construct_PTMInt_gmt_file() (in module ptm_pose.annotate) construct_PTMsigDB_gmt_files() (in module ptm_pose.annotate) construct_RegPhos_gmt_file() (in module ptm_pose.annotate) convert_PSP_label_to_UniProt() (in module ptm_pose.annotate) D download_translator() (in module ptm_pose.pose_config) draw_pie() (in module ptm_pose.analyze.annotations) E extract_ids_PTMcode() (in module ptm_pose.annotate) extract_interaction_details() (in module ptm_pose.annotate) extract_positions_from_DEPOD() (in module ptm_pose.annotate) F find_motifs() (in module ptm_pose.analyze.flank_analysis) find_ptms_in_region() (in module ptm_pose.project) findAlteredPositions() (in module ptm_pose.analyze.flank_analysis) G gene_set_enrichment() (in module ptm_pose.analyze.annotations) get_all_KL_scores() (in module ptm_pose.analyze.enzyme) get_available_annotations() (in module ptm_pose.analyze.annotations) get_available_gmt_annotations() (in module ptm_pose.annotate) get_background_annotation_counts() (in module ptm_pose.analyze.annotations) get_edge_colors() (in module ptm_pose.analyze.interactions) get_enrichment_inputs() (in module ptm_pose.analyze.annotations) get_flanking_changes() (in module ptm_pose.flanking_sequences) get_flanking_changes_from_rMATS() (in module ptm_pose.flanking_sequences) get_flanking_changes_from_splice_data() (in module ptm_pose.flanking_sequences) get_flanking_changes_from_splicegraph() (in module ptm_pose.flanking_sequences) get_interaction_network() (ptm_pose.analyze.interactions.protein_interactions method) get_interaction_stats() (in module ptm_pose.analyze.interactions) (ptm_pose.analyze.interactions.protein_interactions method) get_modification_class_data() (in module ptm_pose.analyze.summarize) get_modification_counts() (in module ptm_pose.analyze.summarize) get_protein_interaction_network() (ptm_pose.analyze.interactions.protein_interactions method) get_ptm_annotations() (in module ptm_pose.analyze.annotations) getSequenceIdentity() (in module ptm_pose.analyze.flank_analysis) I identify_change_to_specific_motif() (in module ptm_pose.analyze.flank_analysis) L load_gmt_file() (in module ptm_pose.annotate) M module ptm_pose.analyze.annotations ptm_pose.analyze.enzyme ptm_pose.analyze.filter ptm_pose.analyze.flank_analysis ptm_pose.analyze.interactions ptm_pose.analyze.summarize ptm_pose.annotate ptm_pose.flanking_sequences ptm_pose.pose_config ptm_pose.project P plot_alterations_matrix() (in module ptm_pose.analyze.flank_analysis) plot_annotation_counts() (in module ptm_pose.analyze.annotations) plot_available_annotations() (in module ptm_pose.analyze.annotations) plot_EnrichR_pies() (in module ptm_pose.analyze.annotations) plot_filter_impact() (in module ptm_pose.analyze.filter) plot_interaction_network() (in module ptm_pose.analyze.interactions) (ptm_pose.analyze.interactions.protein_interactions method) plot_location_of_altered_flanking_residues() (in module ptm_pose.analyze.flank_analysis) plot_modification_breakdown() (in module ptm_pose.analyze.summarize) plot_nease_comparison() (ptm_pose.analyze.interactions.protein_interactions method) plot_network_centrality() (in module ptm_pose.analyze.interactions) (ptm_pose.analyze.interactions.protein_interactions method) plot_sequence_differences() (in module ptm_pose.analyze.flank_analysis) process_database_annotations() (in module ptm_pose.annotate) project_ptms_onto_MATS() (in module ptm_pose.project) project_ptms_onto_splice_events() (in module ptm_pose.project) project_ptms_onto_SpliceSeq() (in module ptm_pose.project) protein_interactions (class in ptm_pose.analyze.interactions) ptm_pose.analyze.annotations module ptm_pose.analyze.enzyme module ptm_pose.analyze.filter module ptm_pose.analyze.flank_analysis module ptm_pose.analyze.interactions module ptm_pose.analyze.summarize module ptm_pose.annotate module ptm_pose.flanking_sequences module ptm_pose.pose_config module ptm_pose.project module S simplify_annotation() (in module ptm_pose.annotate) summarize_protein_network() (ptm_pose.analyze.interactions.protein_interactions method) U unify_interaction_data() (in module ptm_pose.annotate)