View source for Site search result optimization (analysis)

;Analysis title
:[[File:TF-binding-site-search-Site-search-result-optimization-icon.png]] Site search result optimization
;Provider
:[[Institute of Systems Biology]]
;Class
:{{Class|ru.biosoft.bsa.analysis.OptimizeSiteSearchAnalysis}}
;Plugin
:[[Ru.biosoft.bsa (plugin)|ru.biosoft.bsa (Bio-sequences analyses plugin)]]

==== Description ====
Tune matrix weights to minimize p-values.

==== Parameters: ====

* '''Input yes track''' – Site search result for genes expressed in experiment
* '''Input no track''' – Site search result for background genes
* '''P-value cutoff''' – Matrix will be removed from result if p-value cannot be optimized to values lower than specified cutoff
* '''Optimization type''' – Whether to optimize only matrix cutoffs, promoter windows or both
* '''Output yes track''' – Filtered site search result for expressed genes
* '''Output no track''' – Filtered site search result for background genes
* '''Overrepresented matrices in summary''' – Remove underrepresented matrices from the output (not applicable if no-set is not specified)
* '''Output name''' – Output name
* '''Output profile''' – Output profile

[[Category:Analyses]]
[[Category:TF binding site search (analyses group)]]
[[Category:ISB analyses]]
[[Category:Autogenerated pages]]