Difference between revisions of "Site search result optimization (analysis)"
From BioUML platform
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;Analysis title | ;Analysis title | ||
| − | :[[File: | + | :[[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 (plugin)|ru.biosoft.bsa (Bio-sequences analyses plugin)]] | :[[Ru.biosoft.bsa (plugin)|ru.biosoft.bsa (Bio-sequences analyses plugin)]] | ||
==== Description ==== | ==== Description ==== | ||
| − | Tune matrix weights to minimize p-values | + | Tune matrix weights to minimize p-values. |
==== Parameters: ==== | ==== Parameters: ==== | ||
| Line 19: | Line 21: | ||
* '''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: | + | [[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
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
