dotools_py.tl.go_analysis

dotools_py.tl.go_analysis(df, gene_key, pval_key, log2fc_key, pval_cutoff=0.05, log2fc_cutoff=0.25, path=None, filename='', specie='Mouse', go_catgs=('GO_Molecular_Function_2023', 'GO_Cellular_Component_2023', 'GO_Biological_Process_2023'))

Run Gene Ontology using EnrichR API.

Perform gene ontology analysis base on the EnrichR interface.

Parameters:

df DataFrame

Dataframe with results of differential gene expression analysis.

gene_key str

Column with genes.

pval_key str

Column with pvals.

log2fc_key str

Column with log2 foldchanges.

pval_cutoff float (default: 0.05)

Cutoff for pvals.

log2fc_cutoff float (default: 0.25)

Cutoff for log2 foldchanges.

path str | PathLike[str] | Path (default: None)

Folder where output Excel files will be saved. A SubFolder called GSA_Tables will be created

filename str (default: '')

Suffix for the filename. Format GSA_CellType_Suffix.xlsx

specie Literal['Mouse', 'Human'] (default: 'Mouse')

Available Human, Mouse, Yeast, Fly, Fish, Worm.

go_catgs str | list (default: ('GO_Molecular_Function_2023', 'GO_Cellular_Component_2023', 'GO_Biological_Process_2023'))

Gene Ontology Classes to use

Return type:

None | DataFrame

Returns:

Return a DataFrame with Gene Ontology Analysis results. If a path is provided the results will be saved.