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src/o/r/Orange-Bioinformatics-2.5.25/docs/rst/reference/code/gsea2.py   Orange-Bioinformatics(Download)
data = data.translate([data.domain.attributes[0]], True)
 
matcher = gene.matcher([[gene.GMKEGG("dicty"), gene.GMDicty()]])
genesets =  geneset.collections((("KEGG",), "dicty"))
 

src/o/r/Orange-Bioinformatics-2.5.25/docs/rst/reference/code/genematch2.py   Orange-Bioinformatics(Download)
targets = Orange.bio.kegg.KEGGOrganism("9606").get_genes() #KEGG gene IDs
 
gmkegg = Orange.bio.gene.GMKEGG("9606")
gmgo = Orange.bio.gene.GMGO("9606")
gmkegggo = Orange.bio.gene.matcher([[gmkegg, gmgo]], direct=False) #joined matchers

src/o/r/Orange-Bioinformatics-2.5.25/docs/rst/reference/code/gsea_instances.py   Orange-Bioinformatics(Download)
data = gds.getdata(transpose=True) 
 
matcher = gene.matcher([gene.GMKEGG("Homo sapiens")])
genesets = geneset.collections((("KEGG",), "Homo sapiens"))
 

src/o/r/Orange-Bioinformatics-2.5.25/docs/rst/reference/code/gsea_genes.py   Orange-Bioinformatics(Download)
data = gds.getdata() 
 
matcher = gene.matcher([gene.GMKEGG("Homo sapiens")])
genesets = geneset.collections((("KEGG",), "Homo sapiens"))
 

src/o/r/Orange-Bioinformatics-2.5.25/docs/rst/reference/code/genematch_path.py   Orange-Bioinformatics(Download)
query = [ "Fndc4", "Itgb8", "Cdc34", "Olfr1403" ] 
 
gm = Orange.bio.gene.GMKEGG("mmu") #use KEGG aliases for gene matching
gm.set_targets(kegg_genes) #set KEGG gene aliases as targets