Index

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) add_rfam_annotation() (openomics.database.sequence.RNAcentral 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) assign_transforms() (openomics.database.sequence.UniProt 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.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) (openomics.database.ontology.UniProtGOA attribute) (openomics.database.sequence.RNAcentral attribute) (openomics.database.sequence.UniProt attribute)

CopyNumberVariation (class in openomics)

D

Database (class in openomics.database.base) 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) 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_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_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_rename_dict() (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.RNAcentral method) (openomics.database.sequence.SequenceDatabase method) (openomics.database.sequence.UniProt method) get_species_list() (openomics.database.sequence.UniProt class method) GTEx (class in openomics.database.annotation)

H

HMDD (class in openomics.database.disease)

HumanPhenotypeOntology (class in openomics.database.ontology)

I

info() (openomics.database.ontology.GeneOntology method) IntAct (class in openomics.database.interaction)

Interactions (class in openomics.database.interaction) InterPro (class in openomics.database.ontology)

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_annotation() (openomics.database.ontology.InterPro method) 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.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.interaction.RNAInter method) (openomics.database.interaction.TarBase method) (openomics.database.ontology.GeneOntology method) (openomics.database.ontology.InterPro method) (openomics.database.sequence.GENCODE method) (openomics.database.sequence.MirBase method) (openomics.database.sequence.RNAcentral method) (openomics.database.sequence.UniProt 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.RNAInter method) (openomics.database.interaction.StarBase method) (openomics.database.interaction.STRING method) (openomics.database.interaction.TarBase method) (openomics.database.interaction.TargetScan method) (openomics.database.ontology.GeneOntology method) (openomics.database.ontology.InterPro method) (openomics.database.ontology.Ontology method) load_network_high_throughput() (openomics.database.interaction.LncRNA2Target method) load_network_low_throughput() (openomics.database.interaction.LncRNA2Target method) load_sequences() (openomics.database.sequence.RNAcentral method) (openomics.database.sequence.UniProt method) load_uniprot_parquet() (openomics.database.sequence.UniProt method) load_uniprot_xml() (openomics.database.sequence.UniProt 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

parse_interpro2go() (openomics.database.ontology.InterPro method) parse_ipr_treefile() (openomics.database.ontology.InterPro method) pathologic_stage_map (openomics.ClinicalData attribute) preprocess_table() (openomics.Expression method) print_sample_sizes() (openomics.MultiOmics method) (openomics.multiomics.MultiOmics 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

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.sequence) RNAInter (class in openomics.database.interaction)

S

samples (openomics.Expression 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) SPECIES_ID_NAME (openomics.database.sequence.UniProt attribute) SPECIES_ID_TAXONOMIC (openomics.database.sequence.UniProt attribute) StarBase (class in openomics.database.interaction) STRING (class in openomics.database.interaction)

T

TANRIC (class in openomics.database.annotation) TarBase (class in openomics.database.interaction)

TargetScan (class in openomics.database.interaction) traverse_predecessors() (in module openomics.database.ontology)

U

UniProt (class in openomics.database.sequence)

UniProtGOA (class in openomics.database.ontology)

W

write_taxonomy() (in module openomics.database.ontology)