Usage

For the following examples, the example data can be found here: data.tar.gz . These examples are derived from webgestalt.org .

ORA Example

ora_test.py

import WebGestaltPy

res = WebGestaltPy.ora_from_files("kegg.gmt", "genelist.txt", "reference.txt")

Meta-analysis ORA Example

meta_ora_test.py

import WebGestaltPy

res = WebGestaltPy.meta_ora_from_files("kegg.gmt", ["genelist.txt", "second_genelist.txt"],
                      ["reference.txt", "reference.txt"])

GSEA Example

gsea_test.py

import WebGestaltPy

res = WebGestaltPy.gsea_from_files("kegg.gmt", "test.rnk")

Meta-analysis GSEA Example

meta_gsea_test.py

import WebGestaltPy

res = WebGestaltPy.meta_gsea_from_files("kegg.gmt", ["test.rnk", "second_test.rnk"])

NTA Example

nta_test.py

import WebGestaltPy
nta_method = webgestaltpy.NTAMethod.Prioritization
res = webgestaltpy.nta_from_files("data/hsapiens_network_CPTAC_Proteomics_OV_entrezgene.net", "data/net_genes.txt", nta_method, 5)