Difference between revisions of "Site search result optimization (analysis)"

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;Analysis title
 
;Analysis title
:[[File:BSA-Site-search-result-optimization-icon.png]] Site search result optimization
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:[[File:TF-binding-site-search-Site-search-result-optimization-icon.png]] Site search result optimization
 
;Provider
 
;Provider
 
:[[Institute of Systems Biology]]
 
:[[Institute of Systems Biology]]
 +
;Class
 +
:{{Class|ru.biosoft.bsa.analysis.OptimizeSiteSearchAnalysis}}
 
;Plugin
 
;Plugin
:ru.biosoft.bsa (Bio-sequences analyses plugin)
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:[[Ru.biosoft.bsa (plugin)|ru.biosoft.bsa (Bio-sequences analyses plugin)]]
  
 
==== Description ====
 
==== Description ====
Tune matrix weights to minimize p-values
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Tune matrix weights to minimize p-values.
  
 
==== Parameters: ====
 
==== Parameters: ====
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* '''Overrepresented matrices in summary''' – Remove underrepresented matrices from the output (not applicable if no-set is not specified)
 
* '''Overrepresented matrices in summary''' – Remove underrepresented matrices from the output (not applicable if no-set is not specified)
 
* '''Output name''' – Output name
 
* '''Output name''' – Output name
 +
* '''Output profile''' – Output profile
  
 
[[Category:Analyses]]
 
[[Category:Analyses]]
[[Category:BSA (analyses group)]]
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[[Category:TF binding site search (analyses group)]]
 
[[Category:ISB analyses]]
 
[[Category:ISB analyses]]
 
[[Category:Autogenerated pages]]
 
[[Category:Autogenerated pages]]

Latest revision as of 18:15, 9 December 2020

Analysis title
TF-binding-site-search-Site-search-result-optimization-icon.png Site search result optimization
Provider
Institute of Systems Biology
Class
OptimizeSiteSearchAnalysis
Plugin
ru.biosoft.bsa (Bio-sequences analyses plugin)

[edit] Description

Tune matrix weights to minimize p-values.

[edit] 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
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