List enrichr libraries#

bullkpy.tl.list_enrichr_libraries()[source]#

Return available Enrichr libraries as known by gseapy. Useful to discover exact names like ‘MSigDB_Hallmark_2020’.

Notes

Requires internet access (Enrichr).

List available Enrichr gene-set libraries.

This function queries Enrichr (via gseapy) and returns the exact names of all gene-set libraries currently available for enrichment analysis.

It is mainly intended as a discovery helper, so users know which library names can be passed to Enrichr-based workflows (e.g. GSEApy preranked analysis).

What it does#

•	Connects to the Enrichr API through gseapy
•	Fetches the list of registered gene-set libraries
•	Returns them as a Python list of strings

These names must be used exactly as returned when running Enrichr analyses.

Returns#

list[str]
List of Enrichr library identifiers.

Examples include: • “MSigDB_Hallmark_2020” • “KEGG_2021_Human” • “GO_Biological_Process_2023” • “Reactome_2022”

Requirements.#

•	Internet access
•	gseapy installed
•	Enrichr service available

If Enrichr is unreachable, a RuntimeError is raised.

Examples#

List all available Enrichr libraries

libs = bk.tl.list_enrichr_libraries()
print(libs[:10])

Check if a library exists before running GSEA

if "MSigDB_Hallmark_2020" in bk.tl.list_enrichr_libraries():
    print("Hallmark gene sets available")

Use with Enrichr-based GSEA

df_gsea = bk.tl.gsea_preranked(
    adata,
    res=de_res,
    gene_sets="MSigDB_Hallmark_2020",
)

Notes#

•	Library availability may change over time as Enrichr updates its database.
•	For reproducible analyses, it is recommended to record the library name and date.
•	This function does not download gene sets; it only lists metadata.