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GOATOOLS
GOATOOLS

User guide

  • Command-line guides
    • Gene Ontolog Enrichment Analyses (GOEA) from the command-line
    • Plot the GO hierarchy with goatools go_plot
    • Print all or part of the GO hierarchy
    • NCBI GeneID and Symbol
  • Tutorials
    • Do enrichment analyses using the Human Phenotype Ontology (HPO)
    • Loading the optional definition attribute
    • Calculating Annotation Coverage
    • Reading Annotations from a GO Association File (GAF)
    • Reading a Gene Product Association Data (GPAD) file
    • Annotations in NCBI’s gene2go file
    • How to download background genes from NCBI
    • Cell Cycle genes
    • How to traverse to GO children and descendants
    • Information Content for Custom GO Annotations (id2go format)
    • How to get Descendants Count and Information Content
    • How to get GO IDs up both the ‘is a’ and ‘part of’ relationships
    • Loading obsolete GO terms
    • Run a Gene Ontology Enrichment Analysis (GOEA)
    • Run a GOEA. Print study genes as either IDs symbols
    • Gene Ontology Enrichment Analysis (GOEA)
    • Group Significant GO terms by Frequently Seen Words
    • How to extract information from parent GO terms
    • How to traverse to GO parents and ancestors
    • Adding optional relationships changes the dcnt value
    • Relationships in the GO
    • Report counts of GO terms at various levels and depths
    • Computing basic semantic similarities between GO terms
    • Calculating Wang’s Semantic Similarity between two GO Terms
    • Notebook Images
    • GO parents

Reference

  • API reference
    • goatools package
      • goatools.anno package
        • goatools.anno.extensions package
          • goatools.anno.extensions.extension module
          • goatools.anno.extensions.extensions module
          • goatools.anno.extensions.factory module
        • goatools.anno.init package
          • goatools.anno.init.reader_gaf module
          • goatools.anno.init.reader_genetogo module
          • goatools.anno.init.reader_gpad module
          • goatools.anno.init.reader_idtogos module
          • goatools.anno.init.utils module
        • goatools.anno.annoreader_base module
        • goatools.anno.broad_gos module
        • goatools.anno.dnld_ebi_goa module
        • goatools.anno.eco2group module
        • goatools.anno.factory module
        • goatools.anno.gaf_reader module
        • goatools.anno.genetogo_reader module
        • goatools.anno.gpad_reader module
        • goatools.anno.idtogos_reader module
        • goatools.anno.opts module
        • goatools.anno.update_association module
      • goatools.cli package
        • goatools.cli.compare_gos module
        • goatools.cli.docopt_parse module
        • goatools.cli.fetch_associations module
        • goatools.cli.find_enrichment module
        • goatools.cli.gos_get module
        • goatools.cli.gosubdag_plot module
        • goatools.cli.grouped module
        • goatools.cli.main module
        • goatools.cli.map_to_slim module
        • goatools.cli.ncbi_gene_results_to_python module
        • goatools.cli.plot_go_term module
        • goatools.cli.prt_terms module
        • goatools.cli.wr_hierarchy module
        • goatools.cli.wr_sections module
      • goatools.godag package
        • goatools.godag.consts module
        • goatools.godag.go_tasks module
        • goatools.godag.obo_optional_attributes module
        • goatools.godag.obographs module
        • goatools.godag.prtfncs module
        • goatools.godag.prttime module
        • goatools.godag.relationship_combos module
        • goatools.godag.relationship_str module
        • goatools.godag.reldepth module
        • goatools.godag.typedef module
      • goatools.goea package
        • goatools.goea.algorithms package
          • goatools.goea.algorithms.base module
          • goatools.goea.algorithms.classic module
          • goatools.goea.algorithms.elim module
        • goatools.goea.go_enrichment_ns module
      • goatools.gosubdag package
        • goatools.gosubdag.plot package
          • goatools.gosubdag.plot.go2color module
          • goatools.gosubdag.plot.go_edge module
          • goatools.gosubdag.plot.go_name_shorten module
          • goatools.gosubdag.plot.go_node module
          • goatools.gosubdag.plot.goea_results module
          • goatools.gosubdag.plot.gosubdag_plot module
          • goatools.gosubdag.plot.plot module
        • goatools.gosubdag.rpt package
          • goatools.gosubdag.rpt.wr_xlsx module
          • goatools.gosubdag.rpt.write_hierarchy module
        • goatools.gosubdag.go_edges module
        • goatools.gosubdag.go_most_specific module
        • goatools.gosubdag.go_paths module
        • goatools.gosubdag.go_tasks module
        • goatools.gosubdag.godag_rcnt module
        • goatools.gosubdag.godag_rcnt_init module
        • goatools.gosubdag.gosubdag module
        • goatools.gosubdag.gosubdag_init module
        • goatools.gosubdag.utils module
      • goatools.grouper package
        • goatools.grouper.aart_geneproducts_all module
        • goatools.grouper.aart_geneproducts_one module
        • goatools.grouper.colors module
        • goatools.grouper.grprdflts module
        • goatools.grouper.grprobj module
        • goatools.grouper.grprobj_init module
        • goatools.grouper.grprplt module
        • goatools.grouper.hdrgos module
        • goatools.grouper.plotobj module
        • goatools.grouper.read_goids module
        • goatools.grouper.sorter module
        • goatools.grouper.sorter_gos module
        • goatools.grouper.sorter_nts module
        • goatools.grouper.tasks module
        • goatools.grouper.utils module
        • goatools.grouper.wr_sections module
        • goatools.grouper.wrxlsx module
      • goatools.parsers package
        • goatools.parsers.david_chart module
        • goatools.parsers.ncbi_gene_file_reader module
      • goatools.rpt package
        • goatools.rpt.goea_nt_xfrm module
        • goatools.rpt.nts_xfrm module
        • goatools.rpt.prtfmt module
        • goatools.rpt.rpt_lev_depth module
        • goatools.rpt.write_hierarchy_base module
      • goatools.semsim package
        • goatools.semsim.termwise package
          • goatools.semsim.termwise.dag_a module
          • goatools.semsim.termwise.wang module
      • goatools.associations module
      • goatools.base module
      • goatools.evidence_codes module
      • goatools.go_enrichment module
      • goatools.go_search module
      • goatools.godag_obosm module
      • goatools.godag_plot module
      • goatools.godag_small module
      • goatools.mapslim module
      • goatools.multiple_testing module
      • goatools.nt_utils module
      • goatools.obo_parser module
      • goatools.obo_tasks module
      • goatools.pvalcalc module
      • goatools.randseed module
      • goatools.ratio module
      • goatools.semantic module
      • goatools.statsdescribe module
      • goatools.utils module
      • goatools.version module
      • goatools.wr_tbl module
      • goatools.wr_tbl_class module
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goatools.semsim.termwise package¶

Submodules¶

  • goatools.semsim.termwise.dag_a module
    • DagA
      • DagA.get_sv()
      • DagA.get_svalues()
  • goatools.semsim.termwise.wang module
    • SsWang
      • SsWang.dflt_rel2scf
      • SsWang.get_sim()
      • SsWang.prt_cfg()

Module contents¶

Termwise semantic similarity

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goatools.semsim.termwise.dag_a module
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goatools.semsim package
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    • Submodules
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