Index A | B | C | D | E | F | G | H | I | L | M | N | O | P | Q | R | S | T | V | W A add_biospecimen_data() (openomics.ClinicalData method) add_clinical_data() (openomics.MultiOmics method) (openomics.multiomics.MultiOmics method) add_drug_response_data() (openomics.ClinicalData method) add_omic() (openomics.MultiOmics method) (openomics.multiomics.MultiOmics method) add_predecessor_terms() (openomics.database.ontology.GeneOntology method) Annotatable (class in openomics.database.base) annotate_attributes() (openomics.database.base.Annotatable method) annotate_diseases() (openomics.database.base.Annotatable method) annotate_expressions() (openomics.database.base.Annotatable method) annotate_interactions() (openomics.database.base.Annotatable method) annotate_samples() (openomics.multiomics.MultiOmics method) annotate_sequences() (openomics.database.base.Annotatable method) B BioGRID (class in openomics.database.interaction) BioMartManager (class in openomics.database.annotation) build_clinical_samples() (openomics.ClinicalData method) build_samples() (openomics.MultiOmics method) (openomics.multiomics.MultiOmics method) C cache_dataset() (openomics.database.annotation.BioMartManager method) ClinicalData (class in openomics) close() (openomics.database.base.Database method) COLUMNS_RENAME_DICT (openomics.database.annotation.EnsemblGenes attribute) (openomics.database.annotation.GTEx attribute) (openomics.database.annotation.ProteinAtlas attribute) (openomics.database.annotation.RNAcentral attribute) (openomics.database.base.Database attribute) (openomics.database.disease.DisGeNet attribute) (openomics.database.disease.HMDD attribute) (openomics.database.disease.LncRNADisease attribute) (openomics.database.disease.MalaCards attribute) (openomics.database.interaction.STRING attribute) (openomics.database.ontology.GeneOntology attribute) CopyNumberVariation (class in openomics) D Database (class in openomics.database.base) DELIM (openomics.database.ontology.Ontology attribute) dfs_path() (in module openomics.database.ontology) DISEASE_ASSOCIATIONS_COL (openomics.database.base.Annotatable attribute) DiseaseAssociation (class in openomics.database.disease) DisGeNet (class in openomics.database.disease) DNAMethylation (class in openomics) drop_genes() (openomics.Expression method) drop_samples() (openomics.Expression method) E EnsemblGenes (class in openomics.database.annotation) EnsemblGeneSequences (class in openomics.database.annotation) EnsemblSNP (class in openomics.database.annotation) EnsemblSomaticVariation (class in openomics.database.annotation) EnsemblTranscriptSequences (class in openomics.database.annotation) Expression (class in openomics) F features (openomics.Expression attribute) filter_annotation() (openomics.database.ontology.Ontology method) filter_dfs_paths() (in module openomics.database.ontology) filter_network() (openomics.database.ontology.GeneOntology method) (openomics.database.ontology.Ontology method) filter_values() (openomics.database.interaction.Interactions method) flatten() (in module openomics.database.ontology) flatten_list() (in module openomics.database.ontology) G GENCODE (class in openomics.database.sequence) gene_index (openomics.Expression attribute) GeneMania (class in openomics.database.interaction) GeneOntology (class in openomics.database.ontology) get_adjacency_matrix() (openomics.database.ontology.Ontology method) get_aggregator() (openomics.database.sequence.SequenceDatabase static method) get_annotation_expressions() (openomics.database.base.Annotatable method) get_annotations() (openomics.database.base.Annotatable method) (openomics.database.base.Database method) get_child_nodes() (openomics.database.ontology.Ontology method) get_dfs_paths() (openomics.database.ontology.Ontology method) get_disease_assocs() (openomics.database.disease.DiseaseAssociation method) get_expressions() (openomics.database.annotation.ProteinAtlas method) (openomics.database.annotation.TANRIC method) (openomics.database.base.Database method) get_functional_annotations() (openomics.database.annotation.EnsemblGenes method) get_genes_list() (openomics.Expression method) get_interactions() (openomics.database.interaction.Interactions method) get_node_color() (openomics.database.ontology.Ontology static method) get_omics_list() (openomics.MultiOmics method) (openomics.multiomics.MultiOmics method) get_patient_barcodes() (openomics.ClinicalData method) get_pkg_data_filename() (in module openomics.utils) get_predecessor_terms() (openomics.database.ontology.GeneOntology method) get_rename_dict() (openomics.database.annotation.EnsemblGenes method) (openomics.database.base.Annotatable method) (openomics.database.interaction.LncBase method) (openomics.database.sequence.GENCODE method) get_root_nodes() (openomics.database.ontology.Ontology method) get_sample_attributes() (openomics.multiomics.MultiOmics method) get_sample_barcodes() (openomics.ClinicalData method) get_samples_list() (openomics.Expression method) get_sequences() (openomics.database.interaction.STRING method) (openomics.database.sequence.GENCODE method) (openomics.database.sequence.MirBase method) (openomics.database.sequence.SequenceDatabase method) GTEx (class in openomics.database.annotation) H HMDD (class in openomics.database.disease) HumanPhenotypeOntology (class in openomics.database.ontology) I info() (openomics.database.base.Database method) (openomics.database.interaction.Interactions method) (openomics.database.ontology.GeneOntology method) initialize_annotations() (openomics.database.base.Annotatable method) Interactions (class in openomics.database.interaction) L list_databases() (openomics.database.base.Database static method) LncBase (class in openomics.database.interaction) LncReg (class in openomics.database.interaction) lncRInter (class in openomics.database.interaction) LncRNA (class in openomics) LncRNA2Target (class in openomics.database.interaction) LncRNADisease (class in openomics.database.disease) lncRNome (class in openomics.database.interaction) load_data() (openomics.database.annotation.EnsemblGenes method) (openomics.MultiOmics method) (openomics.multiomics.MultiOmics method) load_dataframe() (openomics.database.annotation.GTEx method) (openomics.database.annotation.NONCODE method) (openomics.database.annotation.ProteinAtlas method) (openomics.database.annotation.RNAcentral method) (openomics.database.annotation.TANRIC method) (openomics.database.base.Database method) (openomics.database.disease.DisGeNet method) (openomics.database.disease.HMDD method) (openomics.database.disease.LncRNADisease method) (openomics.database.disease.MalaCards method) (openomics.database.interaction.lncRNome method) (openomics.database.ontology.GeneOntology method) (openomics.database.sequence.GENCODE method) (openomics.database.sequence.MirBase method) (openomics.Expression method) load_dataframe_glob() (openomics.Expression method) load_network() (openomics.database.interaction.BioGRID method) (openomics.database.interaction.GeneMania method) (openomics.database.interaction.Interactions method) (openomics.database.interaction.LncBase method) (openomics.database.interaction.LncReg method) (openomics.database.interaction.lncRInter method) (openomics.database.interaction.LncRNA2Target method) (openomics.database.interaction.lncRNome method) (openomics.database.interaction.MiRTarBase method) (openomics.database.interaction.NPInter method) (openomics.database.interaction.StarBase method) (openomics.database.interaction.STRING method) (openomics.database.interaction.TargetScan method) (openomics.database.ontology.GeneOntology method) (openomics.database.ontology.Ontology method) load_network_high_throughput() (openomics.database.interaction.LncRNA2Target method) load_network_low_throughput() (openomics.database.interaction.LncRNA2Target method) M MalaCards (class in openomics.database.disease) match_samples() (openomics.MultiOmics method) (openomics.multiomics.MultiOmics method) MessengerRNA (class in openomics) MicroRNA (class in openomics) MirBase (class in openomics.database.sequence) MiRTarBase (class in openomics.database.interaction) module openomics openomics.database.annotation openomics.database.base openomics.database.disease openomics.database.interaction openomics.database.ontology openomics.database.sequence openomics.utils MultiOmics (class in openomics) (class in openomics.multiomics) N name() (openomics.ClinicalData class method) (openomics.CopyNumberVariation class method) (openomics.database.base.Database class method) (openomics.database.interaction.Interactions class method) (openomics.DNAMethylation class method) (openomics.Expression class method) (openomics.LncRNA class method) (openomics.MessengerRNA class method) (openomics.MicroRNA class method) (openomics.Protein class method) (openomics.SomaticMutation class method) NONCODE (class in openomics.database.annotation) NPInter (class in openomics.database.interaction) O OMIM (class in openomics.database.disease) Ontology (class in openomics.database.ontology) openomics module openomics.database.annotation module openomics.database.base module openomics.database.disease module openomics.database.interaction module openomics.database.ontology module openomics.database.sequence module openomics.utils module P pathologic_stage_map (openomics.ClinicalData attribute) preprocess_table() (openomics.Expression method) print_sample_sizes() (openomics.MultiOmics method) (openomics.multiomics.MultiOmics method) process_HPRD_PPI_network() (openomics.Protein method) process_interactions_table() (openomics.database.interaction.TargetScan method) process_miR_family_info_table() (openomics.database.interaction.TargetScan method) Protein (class in openomics) ProteinAtlas (class in openomics.database.annotation) Q query_biomart() (openomics.database.annotation.BioMartManager method) R read_fasta() (openomics.database.sequence.GENCODE method) (openomics.database.sequence.MirBase method) (openomics.database.sequence.SequenceDatabase method) read_gtf() (in module openomics.utils) remove_duplicate_genes() (openomics.MultiOmics method) (openomics.multiomics.MultiOmics method) remove_predecessor_terms() (openomics.database.ontology.Ontology method) retrieve_dataset() (openomics.database.annotation.BioMartManager method) RNAcentral (class in openomics.database.annotation) S samples (openomics.Expression attribute) SEQUENCE_COL_NAME (openomics.database.base.Annotatable attribute) SequenceDatabase (class in openomics.database.sequence) set_backend() (in module openomics) set_cache_dir() (in module openomics) set_genes_index() (openomics.Expression method) set_index() (openomics.database.base.Annotatable method) SomaticMutation (class in openomics) StarBase (class in openomics.database.interaction) STRING (class in openomics.database.interaction) T TANRIC (class in openomics.database.annotation) TargetScan (class in openomics.database.interaction) traverse_predecessors() (in module openomics.database.ontology) V validate_file_resources() (openomics.database.base.Database method) W write_taxonomy() (in module openomics.database.ontology)