Difference between revisions of "IPS prediction (analysis)"

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(Automatic synchronization with BioUML)
 
(Automatic synchronization with BioUML)
 
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;Analysis title
 
;Analysis title
:[[File:Binding-regions-IPS-prediction-icon.png]] IPS prediction
+
:[[File:Default-analysis-icon.png]] IPS prediction
 
;Provider
 
;Provider
 
:[[Institute of Systems Biology]]
 
:[[Institute of Systems Biology]]
 
;Class
 
;Class
:{{Class|ru.biosoft.bsa.analysis.bindingRegions.IPSPrediction}}
+
:{{Class|biouml.plugins.bindingregions.analysis.IPSPredictionAnalysis}}
 
;Plugin
 
;Plugin
:[[Ru.biosoft.bsa (plugin)|ru.biosoft.bsa (Bio-sequences analyses plugin)]]
+
:[[Biouml.plugins.bindingregions (plugin)|biouml.plugins.bindingregions (Binding-regions related analyses)]]
  
 
==== Description ====
 
==== Description ====
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** '''Sequence collection''' – Specify path to folder containing sequences if <nowiki>'</nowiki>Custom<nowiki>'</nowiki> sequences source is selected
 
** '''Sequence collection''' – Specify path to folder containing sequences if <nowiki>'</nowiki>Custom<nowiki>'</nowiki> sequences source is selected
 
* '''Folder containing ChIP-seq tracks''' – Folder containing ChIP-seq tracks
 
* '''Folder containing ChIP-seq tracks''' – Folder containing ChIP-seq tracks
* '''Matrix''' – Path to positional weight matrix
+
* '''Matrix''' – Path to frequency matrix
 
* '''Species''' – Select a taxonomical species
 
* '''Species''' – Select a taxonomical species
 
* '''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>)

Latest revision as of 19:00, 13 February 2017

Analysis title
Default-analysis-icon.png IPS prediction
Provider
Institute of Systems Biology
Class
IPSPredictionAnalysis
Plugin
biouml.plugins.bindingregions (Binding-regions related analyses)

[edit] Description

IPS-prediction and tag density

[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
  • Folder containing ChIP-seq tracks – Folder containing ChIP-seq tracks
  • Matrix – Path to frequency matrix
  • Species – Select a taxonomical species
  • TF class – TF class in Wingender classification (like '2.1.1.1.4')
  • Output table – Table with charts will be created in this location
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