gprofiler-official

import os from gprofiler import GProfiler # Initialize GProfiler object # user_agent is optional but good practice to identify your application. # Setting return_dataframe=True makes results easier to work with using pandas. gp = GProfiler( user_agent=os.environ.get('GPROFILER_USER_AGENT', 'MyAwesomeBioTool/1.0'), return_dataframe=True ) # Example: Functional enrichment analysis (g:GOSt) # Query a list of genes for Homo sapiens genes_query = ['NR1H4', 'TRIP12', 'UBC', 'FCRL3', 'PLXNA3', 'GDNF', 'VPS11'] print(f"Querying genes: {genes_query}") results = gp.profile(organism='hsapiens', query=genes_query) print("\nFunctional Enrichment Results (head):") if results is not None and not results.empty: print(results.head()) else: print("No enrichment results found or query failed.") # Example: Gene ID conversion (g:Convert) # Convert gene IDs from one namespace to another convert_query = ['NR1H4', 'TRIP12'] print(f"\nConverting gene IDs: {convert_query}") converted_genes = gp.convert( organism='hsapiens', query=convert_query, target_namespace='ENTREZGENE_ACC' ) print("\nGene ID Conversion Results (head):") if converted_genes is not None and not converted_genes.empty: print(converted_genes.head()) else: print("No conversion results found or query failed.")