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OpenOmics 0.8.9 documentation
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OpenOmics 0.8.9 documentation

Using OpenOmics Python API

  • Installation
  • Getting started
  • Loading a multi-omics dataset
  • External annotation databases
  • Creating biological interaction networks
  • Preparing data for downstream analyses

API Reference

  • MultiOmics data
    • ClinicalData
    • CopyNumberVariation
    • DNAMethylation
    • Expression
    • LncRNA
    • MessengerRNA
    • MicroRNA
    • MultiOmics
    • Protein
    • SomaticMutation
  • Annotation interfaces
    • Database
    • Annotatable
  • Genomic databases
    • ProteinAtlas
    • GTEx
    • NONCODE
    • EnsemblGenes
    • EnsemblGeneSequences
    • EnsemblTranscriptSequences
    • EnsemblSNP
    • EnsemblSomaticVariation
    • TANRIC
  • Sequence databases
    • GENCODE
    • UniProt
    • MirBase
    • RNAcentral
  • Interaction databases
    • STRING
    • GeneMania
    • IntAct
    • BioGRID
    • MiRTarBase
    • LncBase
    • TargetScan
    • TarBase
    • LncReg
    • LncRNA2Target
    • lncRNome
    • NPInter
    • RNAInter
    • StarBase
  • Disease databases
    • DiseaseAssociation
    • MalaCards
    • DisGeNet
    • HMDD
    • LncRNADisease
  • Ontology databases
    • GeneOntology
    • UniProtGOA
    • InterPro
    • HumanPhenotypeOntology
  • Utilities

MISC

  • Frequently Asked Questions (FAQ)

Contributing and releases

  • Contributing
  • Release history
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Disease databases#

openomics.database.disease Module#

Classes#

DiseaseAssociation(path[, file_resources])

MalaCards([path, file_resources, col_rename])

Loads the MalaCards database from "http://zdzlab.einstein.yu.edu/1/hedd/" .

DisGeNet([path, file_resources, curated, ...])

Loads the database from .

HMDD([path, file_resources, col_rename])

Loads the HMDD database from "http://www.cuilab.cn/static/hmdd3" .

LncRNADisease([path, file_resources, ...])

Class Inheritance Diagram#

Inheritance diagram of openomics.database.disease.DiseaseAssociation, openomics.database.disease.MalaCards, openomics.database.disease.DisGeNet, openomics.database.disease.HMDD, openomics.database.disease.LncRNADisease
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  • Disease databases
    • openomics.database.disease Module
      • Classes
      • Class Inheritance Diagram