Difference between revisions of "Matrix comparison (analysis)"

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==== Parameters: ====
 
==== Parameters: ====
  
* '''Input track''' – Select input ChIP-seq track (must be the result of MACS or SISSRs analysis)
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* '''Type of site model''' – Select type of site model that will be used for matrix derivation
* '''Sequences collection''' – Select a source of nucleotide sequences
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* '''Window size''' – Window size
** '''Sequences source''' – Select database to get sequences from or <nowiki>'</nowiki>Custom<nowiki>'</nowiki> to specify sequences location manually
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* '''Path to table with sequence sample''' – Select path to table with sequence sample
** '''Sequence collection''' – Specify path to folder containing sequences if <nowiki>'</nowiki>Custom<nowiki>'</nowiki> sequences source is selected
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* '''Name of table column with sequence sample''' – Select name of table column with sequence sample
* '''Is around summit''' – Is around summit
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* '''Are both strands?''' – Do analize both strands of sequences? (if <nowiki>'</nowiki>no<nowiki>'</nowiki>, then only strand (+) will be analyzed)
* '''Minimal region length''' – Minimal length of sequence region
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* '''% of best sites''' – Best sites percentage
 
* '''% of best sites''' – Best sites percentage
* '''Type of site model''' – Type of site model that will be used for matrix derivation
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* '''Are also all matrices''' – Would you like to consider also all matrices simultaneously?
* '''Matrices''' – Select matrices
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* '''Paths to matrices''' – Paths to matrices
* '''Are also all matrices''' – Would you like to consider also all matrices selected?
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* '''Path to output folder''' – Output folder will be created under this location when it doesn<nowiki>'</nowiki>t exist
* '''Path to output folder''' – Output folder will be created under this location
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[[Category:Analyses]]
 
[[Category:Analyses]]

Latest revision as of 19:00, 13 February 2017

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

[edit] Description

Comparison of matrices by given site model type

[edit] Parameters:

  • Type of site model – Select type of site model that will be used for matrix derivation
  • Window size – Window size
  • Path to table with sequence sample – Select path to table with sequence sample
  • Name of table column with sequence sample – Select name of table column with sequence sample
  • Are both strands? – Do analize both strands of sequences? (if 'no', then only strand (+) will be analyzed)
  • % of best sites – Best sites percentage
  • Are also all matrices – Would you like to consider also all matrices simultaneously?
  • Paths to matrices – Paths to matrices
  • Path to output folder – Output folder will be created under this location when it doesn't exist
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