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

From BioUML platform
Jump to: navigation, search
(Space after icon)
(Automatic synchronization with BioUML)
 
(6 intermediate revisions by one user not shown)
Line 2: Line 2:
 
:[[File:Molecular-networks-Cluster-by-shortest-path-icon.png]] Cluster by shortest path
 
:[[File:Molecular-networks-Cluster-by-shortest-path-icon.png]] Cluster by shortest path
 
;Provider
 
;Provider
:[[Institute of Systems Biology]]
+
:[[geneXplain GmbH]]
 +
;Class
 +
:{{Class|biouml.plugins.keynodes.ShortestPathClustering}}
 +
;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
+
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: ====
Line 15: Line 19:
 
* '''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.
Line 20: Line 25:
 
[[Category:Analyses]]
 
[[Category:Analyses]]
 
[[Category:Molecular networks (analyses group)]]
 
[[Category:Molecular networks (analyses group)]]
[[Category:ISB analyses]]
+
[[Category:GeneXplain analyses]]
 
[[Category:Autogenerated pages]]
 
[[Category:Autogenerated pages]]

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.
Personal tools
Namespaces

Variants
Actions
BioUML platform
Community
Modelling
Analysis & Workflows
Collaborative research
Development
Virtual biology
Wiki
Toolbox