Difference between revisions of "Cluster by shortest path (analysis)"

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;Provider
 
;Provider
 
:[[geneXplain GmbH]]
 
:[[geneXplain GmbH]]
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;Class
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:{{Class|biouml.plugins.keynodes.ShortestPathClustering}}
 
;Plugin
 
;Plugin
 
:[[Biouml.plugins.keynodes (plugin)|biouml.plugins.keynodes (Master regulator node analysis plugin)]]
 
:[[Biouml.plugins.keynodes (plugin)|biouml.plugins.keynodes (Master regulator node analysis plugin)]]
  
 
==== Description ====
 
==== Description ====
This analysis allows you to make a cluster of genes/molecules upstream or downstream or both by taking reactions and all intermediate molecules from a specified search collection
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This analysis allows you to make a cluster of genes/molecules upstream or downstream or both by taking reactions and all intermediate molecules using shortest paths from a specified search collection.
  
 
==== Parameters: ====
 
==== Parameters: ====
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* '''Display intermediate molecules''' – Output the diagram with the direct reactions and all intermediate molecules
 
* '''Display intermediate molecules''' – Output the diagram with the direct reactions and all intermediate molecules
 
* '''Search collection''' – Collection containing reactions
 
* '''Search collection''' – Collection containing reactions
 +
* '''Custom search collection''' – Path to the custom search collection
 
* '''Species''' – Species to which analysis should be confined
 
* '''Species''' – Species to which analysis should be confined
 
* '''Output name''' – Output name.
 
* '''Output name''' – Output name.

Latest revision as of 18:15, 9 December 2020

Analysis title
Molecular-networks-Cluster-by-shortest-path-icon.png Cluster by shortest path
Provider
geneXplain GmbH
Class
ShortestPathClustering
Plugin
biouml.plugins.keynodes (Master regulator node analysis plugin)

[edit] Description

This analysis allows you to make a cluster of genes/molecules upstream or downstream or both by taking reactions and all intermediate molecules using shortest paths from a specified search collection.

[edit] Parameters:

  • Molecules collection – Input the collection of molecules/genes
  • Input size (expert) – Size of input list
  • Search direction – Direction to perform search in (either upstream, downstream reactions or both directions)
  • Max radius – Maximal search radius
  • Display intermediate molecules – Output the diagram with the direct reactions and all intermediate molecules
  • Search collection – Collection containing reactions
  • Custom search collection – Path to the custom search collection
  • Species – Species to which analysis should be confined
  • Output name – Output name.
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