keggtools

Library for KEGG pathway enrichment analysis.

Quick Start

You can install keggtools with pip:

pip install keggtools

For more details, see Installation.

Contact

If you found a bug, please use the Issue tracker.

Start

• Installation
  • Dependencies
  • Package Installation
  • Alternativ Installation Methods
• Vignette
  • Load preprocessed PMBC3K dataset
  • Plot UMAP with cluster annotations
  • Differential analysis results to pandas dataframe
  • Perform KEGGTOOLS enrichment analysis
  • Plot results of enrichment analysis
  • Plot pathway
  • Plot with KEGG prerendered image
• KEGG Markup Language
  • Schema
  • Data types
  • Elements
    • pathway
    • entry
    • graphics
    • component
    • relation
    • subtype
    • reaction
    • substrate
    • product
    • alt

API Documentation

• keggtools
  • Submodules
    • keggtools.analysis
      • Classes
      • Functions
      • Module Contents
    • keggtools.const
      • Attributes
      • Module Contents
    • keggtools.models
      • Classes
      • Module Contents
    • keggtools.render
      • Classes
      • Functions
      • Module Contents
    • keggtools.resolver
      • Classes
      • Functions
      • Module Contents
    • keggtools.storage
      • Classes
      • Module Contents
    • keggtools.utils
      • Classes
      • Functions
      • Module Contents
  • Attributes
  • Classes
  • Functions
  • Package Contents
    • AMINO_ACID_METABOLISM
    • BIOSYNTHESIS_OF_OTHER_SECONDARY_METABOLITES
    • CARBOHYDRATE_METABOLISM
    • CHEMICAL_STRUCTURE_TRANSFORMATION_MAPS
    • ColorGradient
      • ColorGradient.get_list()
      • ColorGradient.start
      • ColorGradient.steps
      • ColorGradient.stop
      • ColorGradient.to_css()
      • ColorGradient.to_hex()
    • Component
      • Component.id
    • ENERGY_METABOLISM
    • Enrichment
      • Enrichment.all_pathways
      • Enrichment.get_subset()
      • Enrichment.result
      • Enrichment.run_analysis()
      • Enrichment.to_csv()
      • Enrichment.to_dataframe()
      • Enrichment.to_json()
    • EnrichmentResult
      • EnrichmentResult.__str__()
      • EnrichmentResult.found_genes
      • EnrichmentResult.get_header()
      • EnrichmentResult.json_summary()
      • EnrichmentResult.organism
      • EnrichmentResult.pathway_genes
      • EnrichmentResult.pathway_genes_count
      • EnrichmentResult.pathway_id
      • EnrichmentResult.pathway_name
      • EnrichmentResult.pathway_title
      • EnrichmentResult.pvalue
      • EnrichmentResult.study_count
    • Entry
      • Entry.components
      • Entry.get_gene_id()
      • Entry.graphics
      • Entry.has_multiple_names()
      • Entry.id
      • Entry.link
      • Entry.name
      • Entry.reaction
      • Entry.type
    • GLOBAL_AND_OVERVIEW_MAPS
    • GLYCAN_BIOSYNTHESIS_AND_METABOLISM
    • Graphics
      • Graphics.bgcolor
      • Graphics.coords
      • Graphics.fgcolor
      • Graphics.height
      • Graphics.name
      • Graphics.type
      • Graphics.width
      • Graphics.x
      • Graphics.y
    • IMMUNE_SYSTEM_PATHWAYS
    • LIPID_METABOLISM
    • METABOLISM_OF_COFACTORS_AND_VITAMINS
    • METABOLISM_OF_OTHER_AMINO_ACIDS
    • METABOLISM_OF_TERPENOIDS_AND_POLYKETIDES
    • NUCLEOTIDE_METABOLISM
    • Pathway
      • Pathway.entries
      • Pathway.get_entry_by_id()
      • Pathway.get_genes()
      • Pathway.image
      • Pathway.link
      • Pathway.name
      • Pathway.number
      • Pathway.org
      • Pathway.reactions
      • Pathway.relations
      • Pathway.title
    • Relation
      • Relation.entry1
      • Relation.entry2
      • Relation.subtypes
      • Relation.type
    • Renderer
      • Renderer.cmap_downreg
      • Renderer.cmap_upreg
      • Renderer.get_gene_color()
      • Renderer.graph
      • Renderer.lower_color
      • Renderer.overlay
      • Renderer.pathway
      • Renderer.render()
      • Renderer.resolver
      • Renderer.to_binary()
      • Renderer.to_file()
      • Renderer.to_string()
      • Renderer.upper_color
    • Resolver
      • Resolver.check_organism()
      • Resolver.get_compounds()
      • Resolver.get_organism_list()
      • Resolver.get_pathway()
      • Resolver.get_pathway_list()
      • Resolver.storage
    • Storage
      • Storage.build_cache_path()
      • Storage.cachedir
      • Storage.check_cache_dir()
      • Storage.exist()
      • Storage.load()
      • Storage.load_dump()
      • Storage.save()
      • Storage.save_dump()
    • Subtype
      • Subtype.name
      • Subtype.value
    • XENOBIOTICS_BIODEGRADATION_AND_METABOLISM
    • __version__
    • msig_to_kegg_id()
    • plot_enrichment_result()
    • render_overlay_image()