goscripts - Python script and package for Gene Ontology enrichment analysis

Welcome to goscripts’s documentation!

The full documentation for this project is available at: https://pmoris.github.io/goscripts/

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A ready to use python script to perform GO enrichment tests by inputting a list of uniprot_kb accession numbers, an ontology (.obo) file and a gene association (.gaf) file. No install required!

The goscripts package provides further functionality to parse and manipulate .obo and .gaf files; e.g.

• Parsing .obo gene ontology files in order to retrieve child/parent terms: goscripts.obo_tools
• Remapping gene ontology terms to a specified depth: goscripts.obo_tools
• Parse .gaf gene association files: goscripts.gaf_parser
• Performing an enrichment test using various multiple testing correction procedures (provided by statsmodels): goscripts.enrichment_stats

Contents:

• goscripts - Python script and package for Gene Ontology enrichment analysis
  • How to get started
    • Without installation
    • Installing the goscripts package
  • Using the GO enrichment test script
    • Input files
    • Details
  • Dependencies
• goscripts package
  • Submodules
    • goscripts.enrichment_stats module
    • goscripts.gaf_parser module
    • goscripts.genelist_importer module
    • goscripts.obo_tools module

Indices and tables

• Index
• Module Index
• Search Page