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

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;Analysis title
 
;Analysis title
:[[File:Binding-regions-Mixture-of-normal-components-icon.png]] Mixture of normal components
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:[[File:Default-analysis-icon.png]] Mixture of normal components
 
;Provider
 
;Provider
 
:[[Institute of Systems Biology]]
 
:[[Institute of Systems Biology]]
 
;Class
 
;Class
:{{Class|ru.biosoft.bsa.analysis.bindingRegions.NormalComponentsMixture}}
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:{{Class|biouml.plugins.bindingregions.analysis.NormalComponentsMixture}}
 
;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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* '''Sequences collection''' – Select a source of nucleotide sequences
* '''Matrix''' – Path to positional weight matrix
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** '''Sequences source''' – Select database to get sequences from or <nowiki>'</nowiki>Custom<nowiki>'</nowiki> to specify sequences location manually
* '''TF class''' – TF class in Wingender classification (like <nowiki>'</nowiki>1.1.2.1<nowiki>'</nowiki>)
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** '''Sequence collection''' – Specify path to folder containing sequences if <nowiki>'</nowiki>Custom<nowiki>'</nowiki> sequences source is selected
* '''Number of mixture components''' – Number of mixture components
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* '''Is ChIP-Seq peaks''' – Is ChIP-Seq peaks (or merged binding regions)
* '''P-value''' – P-value
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* '''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
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* '''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>
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* '''Matrix''' – Path to frequency matrix
 +
* '''Type of site model''' – Select type of site model
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* '''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
 
* '''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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