Difference between revisions of "Create matrix by mixture of normal components (analysis)"

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(Automatic synchronization with BioUML)
(Automatic synchronization with BioUML)
 
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;Analysis title
 
;Analysis title
:[[File:Binding-regions-Create-matrix-by-mixture-of-normal-components-icon.png]] Create matrix by mixture of normal components
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:[[File:Default-analysis-icon.png]] Create matrix by mixture of normal components
 
;Provider
 
;Provider
 
:[[Institute of Systems Biology]]
 
:[[Institute of Systems Biology]]
 
;Class
 
;Class
:{{Class|ru.biosoft.bsa.analysis.bindingRegions.CreateMatrixByMixture}}
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:{{Class|biouml.plugins.bindingregions.analysis.CreateMatrixByMixture}}
 
;Plugin
 
;Plugin
:[[Ru.biosoft.bsa (plugin)|ru.biosoft.bsa (Bio-sequences analyses plugin)]]
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:[[Biouml.plugins.bindingregions (plugin)|biouml.plugins.bindingregions (Binding-regions related analyses)]]
  
 
==== Description ====
 
==== Description ====
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==== Parameters: ====
 
==== Parameters: ====
  
* '''Input track''' – Select input ChIP-seq track (must be the result of <nowiki>'</nowiki>Merge binding regions for cell-lines<nowiki>'</nowiki> analysis)
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* '''Input track''' – Select input track (it has to contain the merged binding regions; it can be the result of <nowiki>'</nowiki>Merge binding regions for cell-lines<nowiki>'</nowiki> analysis)
 
* '''TF class''' – TF class in Wingender classification (like <nowiki>'</nowiki>2.1.1.1.4<nowiki>'</nowiki>)
 
* '''TF class''' – TF class in Wingender classification (like <nowiki>'</nowiki>2.1.1.1.4<nowiki>'</nowiki>)
 
* '''Minimal region length''' – Minimal length of sequence region
 
* '''Minimal region length''' – Minimal length of sequence region
* '''P-value''' – P-value
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* '''P-value threshold''' – P-value threshold
* '''Max iterations''' – Number of iterations for algorithm
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* '''Maximal number of iterations''' – Maximal number of iterations in algorithm
 
* '''Number of matrices''' – How many matrices will be constructed
 
* '''Number of matrices''' – How many matrices will be constructed
 
* '''Initial matrix as consensus''' – Check this if you want to specify an initial matrix as consensus
 
* '''Initial matrix as consensus''' – Check this if you want to specify an initial matrix as consensus
* '''Consensus''' – Specify the consensus of initial matrix
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* '''Consensus''' – Specify the consensus
 
* '''Matrix path''' – Specify the path to the initial matrix
 
* '''Matrix path''' – Specify the path to the initial matrix
 
* '''Output matrix library''' – Matrix library to store the resulting matrices (will be created if not exists)
 
* '''Output matrix library''' – Matrix library to store the resulting matrices (will be created if not exists)
* '''Matrix name prefix''' – All matrices will be created with given prefix
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* '''Matrix name prefix''' – All matrices will be created with given name prefix
  
 
[[Category:Analyses]]
 
[[Category:Analyses]]

Latest revision as of 19:00, 13 February 2017

Analysis title
Default-analysis-icon.png Create matrix by mixture of normal components
Provider
Institute of Systems Biology
Class
CreateMatrixByMixture
Plugin
biouml.plugins.bindingregions (Binding-regions related analyses)

[edit] Description

Calculation of matrix by using mixture of normal components for maximal IPS scores

[edit] Parameters:

  • Input track – Select input track (it has to contain the merged binding regions; it can be the result of 'Merge binding regions for cell-lines' analysis)
  • TF class – TF class in Wingender classification (like '2.1.1.1.4')
  • Minimal region length – Minimal length of sequence region
  • P-value threshold – P-value threshold
  • Maximal number of iterations – Maximal number of iterations in algorithm
  • Number of matrices – How many matrices will be constructed
  • Initial matrix as consensus – Check this if you want to specify an initial matrix as consensus
  • Consensus – Specify the consensus
  • Matrix path – Specify the path to the initial matrix
  • Output matrix library – Matrix library to store the resulting matrices (will be created if not exists)
  • Matrix name prefix – All matrices will be created with given name prefix
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