celloracle.go_analysis module

The go_analysis module implements Gene Ontology analysis. This module use goatools internally.

celloracle.go_analysis.geneID2Symbol(IDs, species='mouse')

Convert Entrez gene id into gene symbol.

Parameters

  • IDs (array of str) – Entrez gene id.

  • species (str) – Select species. Either “mouse” or “human”.

Returns

Gene symbol

Return type

list of str

celloracle.go_analysis.geneSymbol2ID(symbols, species='mouse')

Convert gene symbol into Entrez gene id.

Parameters

  • symbols (array of str) – gene symbol

  • species (str) – Select species. Either “mouse” or “human”

Returns

Entrez gene id

Return type

list of str

celloracle.go_analysis.get_GO(gene_query, species='mouse')

Get Gene Ontologies (GOs).

Parameters

  • gene_query (array of str) – gene list.

  • species (str) – Select species. Either “mouse” or “human”

Returns

GO analysis results as dataframe.

Return type

pandas.dataframe