Difference between revisions of "IPS ROC-curves (analysis)"

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;Analysis title
 
;Analysis title
:[[File:Binding-regions-IPS-ROC-curves-icon.png]] IPS ROC-curves
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:[[File:Default-analysis-icon.png]] IPS ROC-curves
 
;Provider
 
;Provider
 
:[[Institute of Systems Biology]]
 
:[[Institute of Systems Biology]]
 
;Class
 
;Class
:{{Class|ru.biosoft.bsa.analysis.bindingRegions.IPSROCCurve}}
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:{{Class|biouml.plugins.bindingregions.analysis.IPSROCCurve}}
 
;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>2.1.1.1.4<nowiki>'</nowiki>)
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** '''Sequence collection''' – Specify path to folder containing sequences if <nowiki>'</nowiki>Custom<nowiki>'</nowiki> sequences source is selected
* '''Log transformation''' – Check to consider log-models
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* '''Input track''' – Select input track (it can be ChIP-seq track from GTRD; thus, it can be the result of MACS or SISSRs peak-finder)
* '''Output table''' – Table with charts will be created in this location
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* '''Minimal region length''' – Minimal length of sequence region
 +
* '''Is around summit''' – Is around summit
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* '''Matrix''' – Path to frequency matrix
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* '''Is IPS model?''' – Is IPS model? Otherwise multiplicative IPS model will be used
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* '''Path to output folder''' – Output folder will be created under this location when it doesn<nowiki>'</nowiki>t exist
  
 
[[Category:Analyses]]
 
[[Category:Analyses]]

Latest revision as of 19:00, 13 February 2017

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

[edit] Description

ROC-curves: influence of common score threshold on IPSSiteModel (or logIPSSiteModel) in merged binding regions

[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
  • Input track – Select input track (it can be ChIP-seq track from GTRD; thus, it can be the result of MACS or SISSRs peak-finder)
  • Minimal region length – Minimal length of sequence region
  • Is around summit – Is around summit
  • Matrix – Path to frequency matrix
  • Is IPS model? – Is IPS model? Otherwise multiplicative IPS model will be used
  • Path to output folder – Output folder will be created under this location when it doesn't exist
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