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

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(Automatic synchronization with BioUML)
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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)
+
* '''Sequences collection''' – Select a source of nucleotide sequences
* '''Matrix''' – Path to positional weight matrix
+
** '''Sequences source''' – Select database to get sequences from or <nowiki>'</nowiki>Custom<nowiki>'</nowiki> to specify sequences location manually
 +
** '''Sequence collection''' – Specify path to folder containing sequences if <nowiki>'</nowiki>Custom<nowiki>'</nowiki> sequences source is selected
 +
* '''Is ChIP-Seq peaks''' – Is ChIP-Seq peaks (or merged binding regions)
 
* '''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
 +
* '''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
 +
* '''Type of site model''' – Type of site model
 
* '''Number of mixture components''' – Number of mixture components
 
* '''Number of mixture components''' – Number of mixture components
 
* '''P-value''' – P-value
 
* '''P-value''' – P-value
 +
* '''Max iterations''' – Maximal number of iterations for algorithm
 
* '''Output table''' – Table with charts will be created in this location
 
* '''Output table''' – Table with charts will be created in this location
  

Revision as of 16:17, 11 December 2014

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)

Description

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

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 positional weight matrix
  • Type of site model – Type of site model
  • Number of mixture components – Number of mixture components
  • P-value – P-value
  • Max iterations – Maximal number of iterations for algorithm
  • Output table – Table with charts will be created in this location
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