Difference between revisions of "Mixture of normal components (analysis)"

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* '''Minimal region length''' – Minimal length of sequence region
 
* '''Minimal region length''' – Minimal length of sequence region
 
* '''Input track''' – Select input track (it must contain ChIP-Seq peaks or merged binding regions depending on input parameter <nowiki>'</nowiki>Is ChIP-Seq peaks<nowiki>'</nowiki>
 
* '''Input track''' – Select input track (it must contain ChIP-Seq peaks or merged binding regions depending on input parameter <nowiki>'</nowiki>Is ChIP-Seq peaks<nowiki>'</nowiki>
* '''Matrix''' – Path to positional weight matrix
+
* '''Matrix''' – Path to frequency matrix
* '''Type of site model''' – Type of site model
+
* '''Type of site model''' – Select type of site model
* '''Number of mixture components''' – Number of mixture components
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* '''Number of mixture components''' – Define number of mixture components (it must be > 1
* '''P-value''' – P-value
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* '''P-value threshold''' – P-value threshold
* '''Max iterations''' – Maximal number of iterations for algorithm
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* '''Maximal number of iterations''' – Maximal number of iterations in algorithm
 
* '''Output table''' – Table with charts will be created in this location
 
* '''Output table''' – Table with charts will be created in this location
  

Latest revision as of 19:00, 13 February 2017

Analysis title
Default-analysis-icon.png Mixture of normal components
Provider
Institute of Systems Biology
Class
NormalComponentsMixture
Plugin
biouml.plugins.bindingregions (Binding-regions related analyses)

[edit] Description

Mixture of normal components for maximal IPS scores predicted in binding regions (singleTrack) of given tfClass (charts table is created)

[edit] Parameters:

  • Sequences collection – Select a source of nucleotide sequences
    • Sequences source – Select database to get sequences from or 'Custom' to specify sequences location manually
    • Sequence collection – Specify path to folder containing sequences if 'Custom' sequences source is selected
  • Is ChIP-Seq peaks – Is ChIP-Seq peaks (or merged binding regions)
  • TF class – TF class in Wingender classification (like '2.1.1.1.4')
  • Minimal region length – Minimal length of sequence region
  • Input track – Select input track (it must contain ChIP-Seq peaks or merged binding regions depending on input parameter 'Is ChIP-Seq peaks'
  • Matrix – Path to frequency matrix
  • Type of site model – Select type of site model
  • Number of mixture components – Define number of mixture components (it must be > 1
  • P-value threshold – P-value threshold
  • Maximal number of iterations – Maximal number of iterations in algorithm
  • Output table – Table with charts will be created in this location
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