Difference between revisions of "Non-merged ChIP-Seq tracks summary (analysis)"

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;Analysis title
 
;Analysis title
:[[File:Binding-regions-Non-merged-ChIP-Seq-tracks-summary-icon.png]] Non-merged ChIP-Seq tracks summary
+
:[[File:Default-analysis-icon.png]] Non-merged ChIP-Seq tracks summary
 
;Provider
 
;Provider
 
:[[Institute of Systems Biology]]
 
:[[Institute of Systems Biology]]
 
;Class
 
;Class
:{{Class|ru.biosoft.bsa.analysis.bindingRegions.NonmergedChIPSeqSummary}}
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:{{Class|biouml.plugins.bindingregions.analysis.NonmergedChIPSeqSummary}}
 
;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: ====
  
* '''Sequences collection''' – Select a source of nucleotide sequences
 
** '''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
 
 
* '''Folder containing ChIP-seq tracks''' – Folder containing ChIP-seq tracks
 
* '''Folder containing ChIP-seq tracks''' – Folder containing ChIP-seq tracks
 
* '''Species''' – Select a taxonomical species
 
* '''Species''' – Select a taxonomical species
 
* '''Cell line synonyms table''' – Cell line synonyms table (must contain the <nowiki>'</nowiki>newNameOfCellLine<nowiki>'</nowiki> column)
 
* '''Cell line synonyms table''' – Cell line synonyms table (must contain the <nowiki>'</nowiki>newNameOfCellLine<nowiki>'</nowiki> column)
 
* '''TF names table''' – TF names table (TF class as a row name and TF title in <nowiki>'</nowiki>tfName<nowiki>'</nowiki> column)
 
* '''TF names table''' – TF names table (TF class as a row name and TF title in <nowiki>'</nowiki>tfName<nowiki>'</nowiki> column)
* '''Path to output folder''' – Output folder will be created under this location
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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 12:20, 25 August 2015

Analysis title
Default-analysis-icon.png Non-merged ChIP-Seq tracks summary
Provider
Institute of Systems Biology
Class
NonmergedChIPSeqSummary
Plugin
biouml.plugins.bindingregions (Binding-regions related analyses)

[edit] Description

Summary of non-merged ChIP-Seq tracks (creation of tables: 'summaryOfTracks', 'summaryOfCellLines', 'summaryOfTfClasses', 'countsOfTfClassesInCellLines')

[edit] Parameters:

  • Folder containing ChIP-seq tracks – Folder containing ChIP-seq tracks
  • Species – Select a taxonomical species
  • Cell line synonyms table – Cell line synonyms table (must contain the 'newNameOfCellLine' column)
  • TF names table – TF names table (TF class as a row name and TF title in 'tfName' column)
  • Path to output folder – Output folder will be created under this location when it doesn't exist
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