Index A | C | D | E | F | G | M | P | S | T | U A add_annotation() (in module ptm_pose.annotate) add_custom_annotation() (in module ptm_pose.annotate) add_ELM_interactions() (in module ptm_pose.annotate) add_PSP_disease_association() (in module ptm_pose.annotate) add_PSP_kinase_substrate_data() (in module ptm_pose.annotate) add_PSP_regulatory_site_data() (in module ptm_pose.annotate) add_PTMInt_data() (in module ptm_pose.annotate) annotate_ptms() (in module ptm_pose.annotate) annotation_enrichment() (in module ptm_pose.analyze), [1] C check_file() (in module ptm_pose.annotate) combine_interaction_data() (in module ptm_pose.annotate) combine_KS_data() (in module ptm_pose.annotate) combine_outputs() (in module ptm_pose.analyze), [1] compare_inclusion_motifs() (in module ptm_pose.analyze), [1] convert_PSP_label_to_UniProt() (in module ptm_pose.annotate) D download_ptm_coordinates() (in module ptm_pose.pose_config) E edit_sequence_for_kinase_library() (in module ptm_pose.analyze), [1] extract_positions_from_DEPOD() (in module ptm_pose.annotate) extract_region_from_splicegraph() (in module ptm_pose.flanking_sequences) F find_motifs() (in module ptm_pose.analyze), [1] findAlteredPositions() (in module ptm_pose.analyze), [1] G gene_set_enrichment() (in module ptm_pose.analyze), [1] get_annotation_categories() (in module ptm_pose.analyze), [1] get_annotation_col() (in module ptm_pose.analyze), [1] get_enrichment_inputs() (in module ptm_pose.analyze), [1] get_flanking_changes() (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_flanking_sequence() (in module ptm_pose.flanking_sequences) get_modification_counts() (in module ptm_pose.analyze), [1] get_ptm_annotations() (in module ptm_pose.analyze), [1] get_ptm_locs_in_spliced_sequences() (in module ptm_pose.flanking_sequences) get_ptms_in_splicegraph_flank() (in module ptm_pose.flanking_sequences) get_spliceseq_event_regions() (in module ptm_pose.flanking_sequences) get_spliceseq_flank_loc() (in module ptm_pose.flanking_sequences) getSequenceIdentity() (in module ptm_pose.analyze), [1] M module ptm_pose.analyze, [1] ptm_pose.annotate ptm_pose.flanking_sequences ptm_pose.pose_config ptm_pose.project P project_ptms_onto_MATS() (in module ptm_pose.project) project_ptms_onto_splice_events() (in module ptm_pose.project) ptm_pose.analyze module, [1] 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.analyze), [1] T translate_flanking_sequence() (in module ptm_pose.flanking_sequences) U unify_interaction_data() (in module ptm_pose.annotate)