Example

Still not understand how to use Phenolyzer? Not a big deal, try some exciting examples here!

Some pregenerated examples could be found below
(Caution: they might not be updated!)

Sample commands for Phenolyzer command line tools:

Help:

perl disease_annotation.pl --help
Prioritize 'sleep' genes:

perl disease_annotation.pl sleep -p -ph -logistic -out out/sleep/out
Use the terms in 'disease' file:

perl disease_annotation.pl disease -f -p -ph -logistic -out out/disease/out
Use the cnv.bed region:

perl disease_annotation.pl alzheimer -bedfile cnv.bed -p -ph -logistic -out out/alzheimer/out
Use the Mentha gene-gene interaction database as Addon

perl disease_annotation.pl alzheimer -p -ph -logistic -out out/alzheimer_addon/out -addon_gg DB_MENTHA_GENE_GENE_INTERACTION -addon_gg_weight 0.05